2016 Van Andel Research Institute Scientific Report

Van Andel Research Institute SCIENTIFIC REPORT 2016

333 Bostwick Avenue, N.E., Grand Rapids, Michigan 49503 Phone 616.234.5000 Fax 616.234.5001 www.vai.org

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The Van Andel Institute and its affiliated organizations (collectively the “Institute�) support and comply with applicable laws prohibiting discrimination based on race, color, national origin, religion, gender, age, disability, pregnancy, height, weight, marital status, U.S. military veteran status, genetic information, or other personal characteristics covered by applicable law. The Institute also makes reasonable accommodations required by law. The Institute’s policy in this regard covers all aspects of the employment relationship, including recruiting, hiring, training, and promotion, and, if applicable, the student relationship.

Published June 2016.

Cover design by Nicole Ethen.

Copyright 2016 by Van Andel Institute; all rights reserved.

Van Andel Institute, 333 Bostwick Avenue, N.E. Grand Rapids, Michigan 49503, U.S.A.

Printed by Wolverine Printing Company, Grand Rapids, Michigan

VAN ANDEL RESEARCH INSTITUTE is proud to announce that its Chief Scientific Officer, Peter Jones, Ph.D., D.Sc., was elected a member of the National Academy of Sciences in May 2016. He joins VARI’s founding Director, George Vande Woude, Ph.D., who has been a member since 1993.

Dr. Jones has been a long-standing leader in the field of epigenomics. His accomplishments include • publication of the first study to prove how epigenetics regulates cellular differentiation • development of DNA methylation inhibitors (DNMTi’s) as drugs • discovery that epigenetics plays a fundamental role in aging • elucidation of the biological processes for cellular self-control • identification of ways to manipulate endogenous retroviruses at the root of some cancers • co-founding the Stand Up To Cancer (SU2C) Epigenetics Dream Team and the Van Andel Research Institute–Stand Up To Cancer Epigenetics Dream Team with Stephen Baylin, M.D.

We congratulate Peter on this well-deserved recognition.

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Van Andel Research Institute | Scientific Report

Director's Introduction

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Laboratory Reports Center for Cancer and Cell Biology

TABLE OF CONTENTS

Arthur S. Alberts, Ph.D.

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Patrick J. Grohar, M.D., Ph.D.

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Brian B. Haab, Ph.D.

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Yuanzheng (Ajian) He, Ph.D.

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Xiaohong Li, Ph.D.

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Jeffrey P. MacKeigan, Ph.D.

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Karsten Melcher, Ph.D.

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Lorenzo F. Sempere, Ph.D.

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Matthew Steensma, M.D.

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George F. Vande Woude, Ph.D.

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Bart O. Williams, Ph.D.

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Ning Wu, Ph.D.

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H. Eric Xu, Ph.D.

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Tao Yang, Ph.D.

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Center for Epigenetics Stephen B. Baylin, M.D.

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Peter A. Jones, Ph.D., D.Sc.

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Stefan Jovinge, M.D., Ph.D.

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Peter W. Laird, Ph.D.

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Gerd Pfeifer, Ph.D

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Scott Rothbart, Ph.D.

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Hui Shen, Ph.D.

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Piroska E. Szabรณ, Ph.D.

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Steven J. Triezenberg, Ph.D.

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Laboratory Reports

continued

Center for Neurodegenerative Science Lena Brundin, M.D., Ph.D.

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Patrik Brundin, M.D., Ph.D.

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Gerhard A. Coetzee, Ph.D.

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Viviane Labrie, Ph.D.

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Jiyan Ma, Ph.D.

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Darren Moore, Ph.D.

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Jeremy M. Van Raamsdonk, Ph.D.

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Core Technologies and Services

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Van Andel Research Institute | Scientific Report

Bryn Eagleson, B.S., RLATG Vivarium and Transgenics Core

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Scott D. Jewell, Ph.D. Pathology and Biorepository Core

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Heather Schumacher, B.S., MT(ASCP) Flow Cytometry Core

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Mary E. Winn, Ph.D. Bioinformatics and Biostatistics Core

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Confocal Microscopy and Quantitative Imaging Core

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Small-Animal Imaging Facility

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Awards for Scientific Achievement Jay Van Andel Award for Outstanding Achievement in Parkinson’s Disease Research Han-Mo Koo Memorial Award

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Educational and Training Programs Van Andel Institute Graduate School Postdoctoral Fellowship Program Internship Programs VARI and Jay Van Andel Seminar Series

75 76 77 79

Organization Boards Office of the Chief Scientific Officer Administrative Organization VAI Organizational Structure

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PETER A. JONES, Ph.D., D.SC. CHIEF SCIENTIFIC OFFICER VAN ANDEL RESEARCH INSTITUTE

Van Andel Research Institute | Scientific Report

VAN ANDEL RESEARCH INSTITUTE had strong growth and progress in the past year.

Most recently, in February 2016, Eric Xu was selected by The Protein Society for its prestigious Hans Neurath Award, which is presented to "individuals who have made a recent contribution of exceptional merit to basic protein research". The basis for this award was the July 2015 article in Nature titled “Crystal structure of rhodopsin bound to arrestin determined by femtosecond X-ray laser”. This project involved many international collaborators and an intense effort by VARI's Xu and Melcher labs, and it produced a major advance in the field of G protein–coupled receptors. We congratulate Eric on this well-deserved honor. We at VARI are pleased at this recognition and proud to be his colleagues and collaborators.

Beyond that award-winning paper, our faculty had excellent publications success in 2015.

Three articles were selected as Notable Advances of 2015 by Nature Medicine: one on heart cell regeneration coauthored by Stefan Jovinge published in Cell, and two others in Cell on the DNA methyltransferase inhibitor 5-azacitidine, which stimulates an immune-like inflammatory response in hindering tumor growth, coauthored by Peter Jones and by Stephen Baylin.

Peter Laird and Hui Shen were coauthors on a series of papers published in Cell and the New England Journal of Medicine coming out of work by the Cancer Genome Atlas Network.

Scott Jewell coauthored several papers in Science resulting from his deep involvement in the Genotype-Tissue Expression (GTEx) project. And, Karsten Melcher and Eric Xu were coauthors of a second Nature paper on signaling by the plant hormone jasmonate.

We look forward to continuing this strong record of publication in the best scientific journals.

FACULTY In 2015 the Center for Epigenetics welcomed Scott Rothbart, who will focus on understanding how histone post-translational modifications and DNA methylation work together to orchestrate the dynamic functions associated with chromatin. The Center was also joined part-time

by Stephen Baylin, who is co-leader of the VARI-SU2C Epigenetics Dream Team. He will continue his primary appointment at Johns Hopkins and the Sidney Kimmel Comprehensive Cancer Center.

Joining the Center for Neurodegenerative Science in 2015 was Gerhard Coetzee. Dr. Coetzee will use his expertise with GWAS to uncover the roles of genetic risk variants in Parkinson’s disease. Early in 2016, Dr. Jeffrey Kordower, of Rush University Medical Center, began a part-time appointment at VARI and will continue his collaboration with Patrik Brundin. Also in early 2016, Viviane Labrie arrived at VARI, and she will pursue her studies of the role of epigenetics in Parkinson’s disease and Alzheimer’s disease.

Patrick Grohar joined the Center for Cancer and Cell Biology in July 2015. His research and clinical work is on Ewing sarcoma, a type of tumor that can occur in bone or soft tissue.

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EVENTS AND AWARDS

FUNDING

Research!America, the nation’s largest nonprofit public education and advocacy alliance, which works to make health research a higher national priority, named David Van Andel and George Vande Woude its 2015 Advocacy Award winners. The annual Research!America Advocacy Awards program was established in 1996 to honor outstanding advocates for medical, health, and scientific research.

Congratulations to both for a well-deserved recognition of their years-long efforts.

Scott Jewell received a major multiyear grant from the NIH's National Cancer Institute to support operations of the VARI biorepository in serving as the Biospecimen Core Resource for the NCI's Clinical Proteomic Tumor Analysis Consortium. VARI also received part of a collaborative NSF grant that will provide us with advanced networking hardware to improve data storage and sharing.

Dr. Matt Steensma was one of two recipients of the inaugural Francis S. Collins Scholars Award in Neurofibromatosis Clinical and Translational Research.

The award was presented by Dr. Collins at VARI's NF1 Mini-Symposium in April 2015.

In May, Eric S. Lander, founding director of the Broad Institute of MIT and Harvard University, was honored with the Han-Mo Koo Award. He delivered both a scientific seminar and a lay lecture in accepting the award for his outstanding scientific achievements in genomics and the Human Genome Project.

The Jay Van Andel Award for Outstanding Achievement in Parkinson’s Disease Research was presented at the September Grand Challenges in Parkinson's Disease symposium held at VARI. The awardees were Maria Grazia Spillantini, FMedSci, FRS, of the University of Cambridge, and Robert Nussbaum, M.D., of the University of California, San Francisco. In 1997, the two made related discoveries that linked Parkinson's disease to the α-synuclein gene and its protein, which have since been the focus of major research efforts.

Also in 2015, VARI hosted the Michigan C. elegans meeting (April); a joint USA/Netherlands biomedical symposium, followed by a visit to VARI by His Majesty King Willem-Alexander and Her Majesty Queen Máxima of the Netherlands (June); the Origins of Cancer Symposium "Beyond the Genome: The Role of Posttranslational Modifications in Cancer" (July); and the International Society for Tryptophan Research Conference (September).

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Other 2015 funding awards to our researchers included the following: • An NCI R01 award to Jeffrey MacKeigan for "Computational Model of Autophagy-Mediated Survival in Chemoresistant Lung Cancer".

• An R01 award to Darren Moore for "Novel Mechanisms of LRRK2-Dependent Neurodegeneration in Parkinson's Disease". He also signed a new agreement with a pharmaceutical firm.

• A Michigan Economic Development Corporation award to Peter Jones to support two new epigenetics faculty members and their research.

• An NCI K99/R00 grant to Scott Rothbart for "Mechanisms Regulating DNA Methylation Maintenance in Chromatin".

• An R21 award to Bart Williams for "Generation and Initial Characterization of Osteocalcin-Deficient Rats".

• A Cure Parkinson's Trust award to Patrik Brundin for "Preclinical Evaluation of Deuterium-Reinforced Polyunsaturated Fatty Acids as a Therapeutic Intervention for Parkinson's Disease".

We continue working in all areas toward even more success in future years.

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CENTER FOR CANCER AND CELL BIOLOGY

Bart O. Williams, Ph.D. Director

The Center’s scientists study the basic mechanisms and molecular biology of cancer and other diseases, with the goal of developing better diagnostics and therapies.

A depiction of arrestin binding by a phosphorylated and active rhodopsin.

The cell membrane lipids are shown as off-white, rhodopsin is blue, arrestin is red, and phosphorus molecules are orange. The phosphorylated C-terminal tail of rhodopsin binds to the N-domain (left) of the arrestin molecule. In the main contact region between the two molecules (central), arrestin accommodates the ICL2 helix of rhodopsin. In this fully activated state, the tip of arrestin’s C-domain contacts the membrane (right).

(Model by Parker de Waal of the Xu lab)

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ARTHUR S. ALBERTS, PH.D. Dr. Alberts earned his degrees in biochemistry and cell biology (B.A., 1987) and in physiology and pharmacology (Ph.D., 1993) from the University of California, San Diego. He joined VARI in January 2000, and he was promoted to Professor in 2009.

STAFF SARAH VANOEVEREN, B.S., B.S.

STUDENT ANDREW HOWARD, B.A.

VISITING SCIENTIST

RESEARCH INTERESTS Our lab seeks to gain a full understanding of how cells spatially and temporally organize the biochemical circuits that govern responses to injury, infection, and age. Our goal is to use this information to guide the development of pharmacological agents that block the acquisition of cancer traits. In 2015, we focused our translational research on targeted therapies that reinforce and/or repair blood cell structure and function and otherwise impair the ability of cancer cells to metastasize.

JULIE TURNER, PH.D.

RECENT PUBLICATIONS Vargas, Pablo, Paolo Maiuri, Marine Bretou, Pablo J. Sáez, Paolo Pierobon, Mathieu Maurin, Mélanie Chabaud, Danielle Lanakar, Dorian Obino, et al. 2016. Innate control of actin nucleation determines two distinct migration behaviours in dendritic cells.

Nature Cell Biology 18(1): 43–53.

Arden, Jessica D., Kari I. Lavik, Kaitlin A. Rubinic, Nicolas Chiaia, Sadik A. Khuder, Marthe J. Howard, Andrea L. Nestor-Kalinoski, Arthur S. Alberts, and Kathryn M. Eisenmann. 2015. Small molecule agonists of mammalian Diaphanous-related (mDia) formins reveal an effective glioblastoma anti-invasion strategy. Molecular Biology of the Cell 26(21): 3704–3718.

Ercan-Sencicek, A. Gulhan, Samira Jambi, Daniel Franjic, Sayoko Nishimura, Mingfeng Li, Paul El-Fishawy, Thomas M. Morgan, Stephan J. Sanders, Kaya Bilguvar, Mohnish Suri, et al. 2015. Homozygous loss of DIAPH1 is a novel cause of microcephaly in humans. European Journal of Human Genetics 23(2): 165–172.

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Van Andel Research Institute | Scientific Report

PATRICK J. GROHAR, M.D., PH.D. Dr. Grohar earned his Ph.D. in chemistry and his M.D. from Wayne State University. He joined VARI in 2015 as an Associate Professor, and he has clinical and research responsibilities at Spectrum Health and Michigan State University, respectively.

STAFF MATT EASTON SUSAN GOOSEN, B.S., M.B.A. MATT HARLOW, M.S. DIANA LEWIS, A.S.

RESEARCH INTERESTS Our laboratory studies pediatric sarcomas, and our goal is to develop novel, molecularly targeted therapies and to translate those therapies into the clinic. Most pediatric sarcomas are characterized by oncogenic transcription factors formed by chromosomal translocations. In many cases, the tumors depend on the continued expression and activity of those transcription factors for cell survival, but few therapies that directly target specific factors have achieved clinical efficacy. Therefore, we are developing new approaches to target those transcription factors.

To date, we have focused on targeting the EWS-FLI1 transcription factor in Ewing sarcoma. EWS-FLI1 is an oncogenic transcription factor formed by the t(11;22)(q24;12) chromosomal translocation that leads to the fusion of the EWSR1 and FLI1 genes. The result is a dysregulated transcription factor that alters the expression of over 500 genes and drives tumorigenesis and progression. Several independent studies have shown that silencing of EWS-FLI1 is incompatible with Ewing sarcoma cell survival. By directly targeting EWS-FLI1, we hope to eliminate its activity as the dominant oncogene in this tumor and thus improve patient survival.

Trabectedin (ET-743; ecteinascidin 743; Yondelis) is a natural product originally isolated from the sea squirt, Ectenascidia turbinata. We became interested in this compound because early clinical studies suggested that translocation-positive sarcomas were sensitive to it. We subsequently demonstrated that trabectedin blocks EWS-FLI1 activity at the promoter, mRNA, and protein levels of expression. In addition, we demonstrated on a genome-wide scale that it reverses the expression of the gene signature of EWSFLI1. However, the compound failed in a phase II study on Ewing sarcoma.

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Subsequently, our work has focused on characterizing the mechanism of EWS-FLI1 suppression with the goals of understanding the failure in the phase II study, identifying second-generation trabectedin analogs, and developing new mechanism-based combination therapies. We have developed a novel combination therapy of trabectedin plus irinotecan that is synergistic. We have shown that this combination markedly improves the suppression of EWS-FLI1 and substantially increases the DNA damage in Ewing sarcoma cells. We translated this therapy into the clinic in Europe and found it was active in a patient in Italy and in a series of patients in Germany (manuscript in preparation). Since the drug is now approved in the United States, we are writing a phase II protocol for this combination therapy for the Children’s Oncology Group, which will open nationwide for patients with relapsed Ewing sarcoma.

Over the past year, we have characterized the mechanism of EWS-FLI1 suppression by trabectedin, and we have shown that mechanism is not effective at the serum concentrations achieved in the failed phase II study, explaining the lack of activity. More importantly, we have identified a second-generation compound with an improved pharmacokinetic profile that will make successful EWS-FLI1 suppression more likely, and we are working to translate this compound to the clinic.

We have also extensively studied mithramycin, which reverses EWS-FLI1 activity and blocks the expression of key downstream targets. In a phase I/II trial at the National Cancer Institute, we found that mithramycin did not achieve serum levels high enough to block EWS-FLI1 activity. Over the past year, our work has identified two compounds with an improved clinical profile, one that is more potent and another that is less toxic than the parent compound. Both compounds reverse EWS-FLI1 activity and are extremely active in xenograft models of Ewing sarcoma. Work continues to understand the mechanism of EWS-FLI1 suppression for this class of compounds.

We are also taking a broader look at transcription as a Ewing sarcoma drug target, using an siRNA screening platform. We have identified a therapeutic vulnerability based on alternative mRNA splicing, and we are developing companion biomarkers that will accompany our trials and aid in the clinical translation of our EWS-FLI1-directed therapies. We have also identified a commonly employed positron emission tomography (PET) radiotracer that reflects EWS-FLI1 activity in Ewing sarcoma cells, which will allow more precise dosing of our therapies and the direct correlation of EWS-FLI1 activity to PET activity. Finally, we are beginning to expand our studies to other pediatric tumors characterized by oncogenic fusion transcription factors.

RECENT PUBLICATIONS Caropreso, Vittorio, Emad Darvishi, Thomas J. Turbyville, Ranjala Ratnayake, Patrick J. Grohar, James B. MacMahon, and Girma Woldenmichael. In press. Englerin A inhibits EWS-FLI1 DNA binding in Ewing’s sarcoma cells. Journal of Biological Chemistry.

Osgood, Christy L., Nichole Maloney, Christopher G. Kidd, Susan Kitchen-Goosen, Laura Segars, Meti Gebregiorgis, Girma M. Woldemichael, Min He, Savita Sankar, et al. In press. Identification of mithramycin analogs with improved targeting of the EWSFLI1 transcription factor. Clinical Cancer Research.

Kovar, Heinrich, James Amatruda, Erika Brunet, Stefan Burdach, Florencia Cidre-Aranaz, Enrique de Alava, Uta Dirksen, Wietske van der Ent, Patrick Grohar, et al. 2016. The second European interdisciplinary Ewing sarcoma research summit — a joint effort to deconstructing the multiple layers of a complex disease. Oncotarget 7(8): 8613–8624.

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Van Andel Research Institute | Scientific Report

BRIAN B. HAAB, PH.D. Dr. Haab obtained his Ph.D. in chemistry from the University of California at Berkeley in 1998. He joined VARI as a Special Program Investigator in 2000, became a Scientific Investigator in 2004, and is now a Professor.

STAFF STEPHANIE GRANT, M.P.A. KATIE PARTYKA, B.S. BRYAN REATINI, B.S. SUDHIR SINGH, PH.D.

RESEARCH INTERESTS The promise of molecular biomarkers: improving patient outcomes through better detection and subtyping.

JESSICA SINHA, M.S. HUIYUAN TANG, PH.D.

STUDENTS DANIEL BARNETT, B.A., B.S. LELAND DUNWOODIE ELLIOT ENSINK PETER HSUEH, B.S. JOEY KRETOWICZ GARIMA VORHA, B.SC., M.B.A.

Tests to detect and diagnose pancreatic cancer The successful treatment of pancreatic cancer critically depends on achieving an accurate and early diagnosis, but this can be frustratingly difficult. Conventional methods of evaluating patients—assessing scans, visual inspection of cells from a biopsy, and weighing behavioral, health, and demographic data—do not have the detail necessary to distinguish between benign and malignant disease or between cancers with vastly different behaviors. Sometimes a physician can see a mass or other unusual feature in the pancreas but is unsure what it is. Is it benign or cancerous? And if it is cancer, what is the best course of treatment?

Our research builds on the concept that molecular-level information will provide details about a condition that are not observable by conventional methods. Molecular biomarkers could provide such information and enable physicians to make accurate diagnoses and develop optimal treatment plans. We are making progress toward this goal for pancreatic cancer. For example, in recent publications in Molecular and Cellular Proteomics and the Journal of Proteome Research, we disclosed carbohydrate-based biomarkers in the blood serum that improve upon the widely used blood test called CA19-9. By using a panel of three or more independent biomarkers, we detected a greater percentage of cancers than we could with any individual biomarker. We are seeking to substantiate those findings and to evaluate their clinical value using serum samples from several clinical sites.

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Other research is aimed at further improving the biomarker tests. The results so far suggest that each individual biomarker arises from a distinct subpopulation of cancer patients and from a characteristic cell type. This finding is important because the biomarkers may reveal differences between subgroups of tumors—a possibility we are exploring in the research described below. For the purpose of improving our blood tests, determining the characteristics of the cells that produce each biomarker, as well as of the cells that do not produce any of our biomarkers, will help to optimize a blood test to accurately identify cancers across the entire spectrum of patients.

The ultimate goal is to get the new tests established in clinical laboratories in order to benefit patients. To that end, we are working with industry partners to transfer our biomarker assays to the clinical laboratory setting and to begin analyzing patient samples received consecutively from clinical sites. If we have good results, we hope to initiate clinical trials for the diagnosis of pancreatic cancer and, eventually, for evaluations of surveillance among people at elevated risk for pancreatic cancer.

Better treatment through subtyping Pancreatic cancer characteristics, such as the cell types within the tumor, the amount of metastasis, the responses to treatments, and overall outcomes, vary greatly among patients. So far, identifying the underlying causes of such differences and predicting the behavior of individual tumors have not been possible. If we could determine what drives the differences between the tumors or identify molecules

that help predict the behavior of each tumor, we could establish better treatment plans for each patient or determine the drugs that work best against each subtype.

Our research is revealing major groupings of tumors based on the carbohydrates on the surface of, and in the secretions from, cancer cells. The carbohydrates are related to the CA19-9 antigen and have distinct biological functions. In current research we want to determine the molecular nature of the subgroups of cells and whether the subgroups have different levels of aggressiveness or different responses to particular drugs. We are using new approaches for measuring carbohydrates and proteins in tumor tissue, and we are employing powerful new software—introduced in our recent publication in Analytical Chemistry—to examine the cell types that produce each carbohydrate-based biomarker. We are using that information to evaluate whether certain types of cells predict clinical behavior. As advances and new options in treatments become available, this type of research is increasingly important for guiding clinical decisions. We are working closely with our physician collaborators to evaluate on a case-by-case basis the value of the molecular information and to guide our research toward improving the tests. Ultimately, physicians could use the molecular tests on material from biopsies, surgical resections, or blood samples.

RECENT PUBLICATIONS Ensink, Elliot, Jessica Sinha, Arkadeep Sinha, Huiyuan Tang, Heather M. Calderone, Galen Hostetter, Jordan Winter, David Cherba, Randall E. Brand, et al. 2015. Segment and fit thresholding: a new method for image analysis applied to microarray and immunofluorescence data. Analytical Chemistry 87(19): 9715–9721.

Singh, Sudhir, Kuntal Pal, Jessica Yadav, Huiyuan Tang, Katie Partyka, Doron Kletter, Peter Hsueh, Elliot Ensink, Birendra KC, et al. 2015. Upregulation of glycans containing 3' fucose in a subset of pancreatic cancers uncovered using fusion-tagged lectins.

Journal of Proteome Research 14(6): 2594–2605.

Tang, Huiyuan, Sudhir Singh, Katie Partyka, Doron Kletter, Peter Hsueh, Jessica Yadav, Elliot Ensink, Marshall Bern, Galen Hostetter, et al. 2015. Glycan motif profiling reveals plasma sialyl-Lewis X elevations in pancreatic cancers that are negative for CA19-9. Molecular & Cellular Proteomics 14(5): 1323–1333.

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Van Andel Research Institute | Scientific Report

YUANZHENG (AJIAN) HE, PH.D. Dr. He earned his Ph.D. from the Chinese Academy of Sciences’ Shanghai Institute of Biochemistry in 2000. In 2008, he was recruited to Van Andel Research Institute, where he is currently a Research Assistant Professor.

RESEARCH INTERESTS Ligand binding is the key event that triggers intracellular signal transduction cascades, and it is also a major focus of drug discovery. My research involves the structural basis of ligand/receptor interactions and related drug discovery, focusing on steroid hormone receptors, specifically, the glucocorticoid receptor and the G protein–coupled receptors (GPCRs). My overall goal is to explore structural insights into receptor signaling and use them to design precision drugs that specifically deliver the desired treatment effect, but not unwanted side effects, to patients. Over the past year, we have made the following progress.

• We have developed “dissociated glucocorticoid” molecules based on our finding that the dissociation of transrepression from transactivation can be achieved by interfering with the dimerization interface of the glucocorticoid receptor.

• We have developed an exceptionally potent glucocorticoid for asthma treatment based on our uncovering of the structural key to glucocorticoid potency. Our primary compound outperforms the current leading drug in a mouse asthma model and promises a better side-effects profile.

• We have determined the structure of arrestin-bound rhodopsin, which provides a basis for understanding GPCR-mediated arrestin-biased signaling.

RECENT PUBLICATIONS Kang, Yanyong, Xiang Gao, X. Edward Zhou, Yuanzheng He, Karsten Melcher, and H. Eric Xu. 2016. A structural snapshot of the rhodopsin–arrestin complex. FEBS Journal 283(5): 816–821.

He, Yuanzheng, Jingjing Shi, Wei Yi, Xin Ren, Xiang Gao, Jianshuang Li, Nanyan Wu, Kevin Weaver, Qian Xie, et al. 2015.

Discovery of a highly potent glucocorticoid for asthma treatment. Cell Discovery 1: 15035.

Zhi, Xiaoyong, X. Edward Zhou, Yuanzheng He, Kelvin Searose-Xu, Chun-Li Zhang, Chih-Cheng Tasi, Karsten Melcher, and H. Eric Xu. 2015. Structural basis for corepressor assembly by the orphan nuclear receptor TLX. Genes and Development 29(4): 440–450.

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XIAOHONG LI, PH.D. Dr. Li received her Ph.D. from the Institute of Zoology, Chinese Academy of Sciences, in Beijing in 2001. She joined VARI as an Assistant Professor in September 2012.

STAFF PAUL G. DAFT, PH.D. SOURIK GANGULY, PH.D. DIANA LEWIS, A.S. NEIL (XIANGQI) MENG, PH.D. ALEXANDRA VANDER ARK, M.S. JIE WANG, M.D. QI ZENG, M.D.

STUDENTS AUSTIN M. MEADOWS GHADA Y.T. MOHSEN ERICA WOODFORD

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RESEARCH INTERESTS Our laboratory is committed to understanding tumor dormancy and cancer bone metastases, specifically of breast, lung, and prostate cancers. Our long-term goal is to create a dormancy-permissive bone microenvironment so that cancer cells can be kept dormant or be killed while they are in that state.

Project 1. Cell-specific roles of transforming growth factor (TGF)-β in bone metastases.

Most people who die of cancer have metastases somewhere in their body, but metastases of certain cancers, particularly of the breast, lung, or prostate, are more likely to be found in bone. Cancer cells in bone induce either osteolytic (bone resorption) or osteoblastic (abnormal bone formation) lesions, which can cause fractures, spinal cord compression, hypercalcemia, and extreme bone pain. Current treatments for bone-metastasis patients can reduce symptoms such as pain but do not increase survival. Better understanding of the mechanism of bone metastasis is needed in order to develop early diagnostic tests and targeted therapeutic strategies. The local events of bone lesion development are determined by the interactions of cancer cells with bone cells such as osteoblasts (mesenchymal lineage) and osteoclasts (myeloid lineage), and such events are regulated by growth factors and cytokines of the bone matrix. The cytokine TGF-β plays crucial roles in both cancerous and healthy bone, and its effects are highly context-dependent, spatially and temporally. We aim to delineate the cell-specific role of TGF-β in bone metastasis and identify downstream mediators that can be targeted by new therapies.

Van Andel Research Institute | Scientific Report

Our studies have produced the following results.

• Basic fibroblast growth factor (bFGF), mediated

by TGF-β signaling in cells of the myeloid lineage, promotes breast cancer bone metastasis. By blocking bFGF, we can reduce such bone lesion development. In bone metastatic tissues from breast cancer patients, TGF-β and bFGF signaling are likely to be activated in osteoclasts and cancer cells but inactivated in osteoblasts.

• TGF-β signaling in myeloid lineage cells promotes bone metastasis, but in cells of the mesenchymal lineage, the same signaling inhibits bone metastasis. We have found that bFGF is the functional mediator for TGF-β signaling effects only in cells of the myeloid lineage.

Project 2. TGF-β signaling in the bone microenvironment affects tumor dormancy.

Up to 70% of cancer patients have tumor cells in the bone marrow at the time of initial diagnosis. It is not known how cancer cells in bone remain dormant and later reactivate. Understanding tumor dormancy is important in trying to prevent the metastatic recurrences that kill patients. Studies have shown that external cues from the bone microenvironment can determine tumor cell dormancy. We aim to create a dormancy-permissive bone microenvironment and determine the mechanism by which it supports cancer cell dormancy. We have established a system in which loss of TGF-β signaling in myeloid lineage cells may promote the dormancy of prostate cancer or NSCLC in the bone marrow. We are now studying the underlying mechanism.

• The cell-specific roles of TGF-β signaling are more complex for bone metastasis of non-small-cell lung cancer (NSCLC). The effects are dependent on the types of bone lesions that are produced by different NSCLC tumors.

RECENT PUBLICATIONS Meng, X., A. Vander Ark, P. Lee, G. Hostetter, N.A. Bhowmick, L.M. Matrisian, B.O. Williams, C.K. Miranti, and X. Li. 2016.

Myeloid-specific TGF-β signaling in bone promotes basic-FGF and breast cancer bone metastasis. Oncogene 35(18): 2370-2378.

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JEFFREY P. MACKEIGAN, PH.D. Dr. MacKeigan received his Ph.D. in microbiology and immunology at the University of North Carolina Lineberger Comprehensive Cancer Center in 2002. Dr. MacKeigan joined VARI in 2006 as an Assistant Professor and was promoted to Associate Professor in 2010.

STAFF STEPHANIE CELANO, M.S. LUCUS CHAN, PH.D. KRISTIN DITTENHAFER-REED, PH.D. NICOLE DOPPEL, B.S. MATT KORTUS, M.S. KATIE MARTIN, PH.D. JOSH SCHIPPER, PH.D. KELLIE SISSON, B.S.

STUDENTS

RESEARCH INTERESTS The MacKeigan lab focuses on two hallmarks of cancer: the deregulation of cellular energetics and resistance to cell death. These hallmarks are regulated by mTOR signaling and contribute significantly to drug resistance in cancer. We seek a systems-level understanding of the network that encompasses the cell metabolism and autophagy signaling pathways. While our research focuses on human cancers, we also apply our tumor biology expertise and pathway knowledge to study tuberous sclerosis complex. Our laboratory uses cutting-edge tools and collaborates with multidisciplinary experts for robust experimental design and comprehensive data analysis. All of our research projects have one common goal: to identify novel therapeutic targets.

ADITI BAGCHI, M.D. ANNALISE BOWEN DANIELLE BURGENSKE, PH.D. LELAND DUNWOODIE NATE MERRILL, B.S. NANDA KUMAR SASI, B.S. ABIGAIL SOLITRO, B.S. MEGAN VANBAREN

ADJUNCT FACULTY BRIAN LANE, M.D., PH.D.

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Autophagy and resistance to cell death The process of autophagy functions to generate energy, clear damaged organelles, and delay or prevent cell death during times of cellular stress. Chemotherapeutic agents trigger autophagy, which allows cancer cells to adapt and withstand treatment.

Therefore, a better understanding of autophagy is crucial for developing new and improved treatment strategies against cancer.

In partnership with Los Alamos National Laboratory, our lab has used predictive computational modeling and cell-based measurements to accurately model the autophagic process. We are pleased to report that we have received a collaborative National Cancer Institute R01 award to validate and extend this model. The current efforts to enhance our model will help us predict the therapeutic benefit of inhibiting autophagy in cancer. We are also working with industry partners to determine the effects of candidate drugs on autophagic flux, and we have identified novel genes that are required for drug-induced autophagy. Lastly, our group conducts optimized kinase and phosphatase assays for in vitro evaluation of compounds identified in silico.

Our research suggests that kinase inhibitors modulate autophagy and may be more selective and effective than current lysosomotropic agents.

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Cancer metabolism and dysregulated cellular energetics Aggressive cancers are well known for their altered metabolic profiles and ability to withstand cytotoxic therapies. Thus, defining the relationship between dysregulated metabolism and evasion of apoptosis represents a critical need in the cancer field.

Our research has shown that increased glycolysis in cancer cells leads to significant enrichment of the mitochondrial lipid cardiolipin, which serves many important functions in maintaining mitochondrial health. Most intriguing is its role in preventing the release of cytochrome c, a key event in the initiation of apoptosis. Our results suggest that the altered metabolic program of cancer cells may inherently support the evasion of apoptosis through cardiolipin production.

We are investigating whether increased cardiolipin allows cancer cells to avoid death and resist chemotherapy. We have partnered with experts in glioblastoma multiforme and lipid mass spectrometry to uncover the mechanisms that may underlie cardiolipin’s ability to promote cell survival. A more complete understanding of the synthesis of cardiolipin and how changes in its concentration regulate cytochrome c release will contribute toward new mitochondria-targeted therapeutics for chemoresistant cancers.

Pathway of Hope Tuberous sclerosis complex (TSC) is a genetic disease resulting from mutations in the TSC1 and TSC2 genes.

These mutations inactivate the genes’ tumor-suppressive function, driving tumor cell growth and causing noncancerous tumors in vital organs such as the brain, skin, eyes, lung, and heart. These tumors can cause a host of health issues, including epilepsy and autism.

Using chemical screening techniques, we are identifying approved, targeted compounds as possible therapies for TSC. Our lab is also characterizing the genomic landscape of TSC tumors using next-generation sequencing. We have gained a comprehensive understanding of TSC tumor biology, and we are seeking other cellular changes that can be targeted by therapies. TSC tumors are not always associated with second-hit somatic mutations to TSC1 or TSC2, suggesting that their pathogenesis may involve other genetic events, which we are working to uncover. We are also developing preclinical models of TSC for future validation studies of our drug candidates and genomic findings. Lastly, we have partnered with physician-scientists expert in TSC to determine whether precision medicine approaches can inform treatment strategies for TSC and predict patient outcomes.

RECENT PUBLICATIONS Solitro, Abigail R., and Jeffrey P. MacKeigan. 2016. Leaving the lysosome behind: novel developments in autophagy inhibition.

Future Medicinal Chemistry 8(1): 73–86.

MacKeigan, Jeffrey P., and Darcy A. Krueger. 2015. Differentiating the mTOR inhibitors everolimus and sirolimus in the treatment of tuberous sclerosis complex. Neuro-Oncology 17(12): 1550–1559.

Szymańska, Paulina, Katie R. Martin, Jeffrey P. MacKeigan, William S. Hlavacek, and Tomasz Lipniacki. 2015. Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. PLoS One 10(3): e0116550.

Wang, Tong, Megan L. Goodall, Paul Gonzales, Mario Sepulveda, Katie R. Martin, Stephen Gately, and Jeffrey P. MacKeigan.

2015. Synthesis of improved lysomotropic autophagy inhibitors. Journal of Medicinal Chemistry 58(7): 3025–3035.

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KARSTEN MELCHER, PH.D. Dr. Melcher earned his Master’s degree in biology and his Ph.D. degree in biochemistry from the Eberhard Karls Universität in Tübingen, Germany. He was recruited to VARI in 2007, and in 2013 he was promoted to Associate Professor.

STAFF STEPHANIE GRANT, M.P.A. XIN GU, M.S. JIYUAN KE, PH.D. AMANDA KOVACH, B.S. EDWARD ZHOU, PH.D.

STUDENT CHRISTIAN CAVACECE

RESEARCH INTERESTS Our laboratory studies the structure and function of proteins that have central roles in cellular signaling. To do so, we employ X-ray crystallography in combination with biochemical and cellular methods to identify structural mechanisms of signaling at high resolution.

In addition to their fundamental physiological roles, most signaling proteins are also important targets of therapeutic drugs. Determination of the three-dimensional structures of protein–drug complexes at atomic resolution allows a detailed understanding of how a drug binds its target and modifies its activity. This knowledge allows the rational design of new and better drugs against diseases such as cancer, diabetes, and neurological disorders.

Three areas of focus in the lab are the adenosine monophosphate (AMP)–activated protein kinase (AMPK); the receptors and key signaling proteins for a plant hormone, abscisic acid (ABA); and the folate receptors.

AMP-activated protein kinase (AMPK) Cells use ATP to drive cellular processes such as muscle contraction, cell growth, and neuronal excitation. AMPK is a three-subunit protein kinase that functions as an energy sensor and regulator of homeostasis in human cells. Its kinase activity, triggered by energy stress (i.e., a drop in the ratio of ATP to AMP/ADP), activates ATP-generating pathways and reduces energy-consuming metabolic pathways and cell proliferation.

To adjust energy balance, AMPK regulates • almost all cellular metabolic processes (activation of ATP-generating pathways such as glucose and fatty acid uptake and catabolism, and inhibition of energy-consuming pathways such as the synthesis of glycogen, fatty acids, cholesterol, proteins, and ribosomal RNA);

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• whole-body energy balance (appetite regulation in the hypothalamus via leptin, adiponectin, ghrelin, and cannabinoids); and • many nonmetabolic processes (cell growth and proliferation, mitochondrial homeostasis, autophagy, aging, neuronal activity, and cell polarity).

Because of its central roles in the uptake and metabolism of glucose and fatty acids, AMPK is an important pharmacological target for treating diabetes and obesity.

Moreover, AMPK activation restrains the growth and metabolism of tumor cells and has thus become an exciting new target for cancer therapy. In this project we strive to determine the structural mechanisms of AMPK regulation by direct binding of AMP, ADP, ATP, drugs, and glycogen, in order to provide a structural framework for the rational design of new therapeutic AMPK modulators.

Abscisic acid Abscisic acid (ABA) is an ancient signaling molecule found in plants, fungi, and metazoans ranging from sponges to humans. In plants, ABA is an essential hormone and is also the central regulator protecting plants against abiotic stresses such as drought, cold, and high salinity. These stresses—most prominently, the scarcity of fresh water—are major limiting factors in crop production and therefore major contributors to malnutrition. Malnutrition affects an estimated one billion people and contributes to more than 50% of human disease worldwide, including cancer and infectious diseases.

We have determined the structure of ABA receptors in their free state and while bound to ABA. Using computational receptor-docking experiments, we have identified and verified synthetic small-molecule receptor activators as new chemical scaffolds toward the development of new, environmentally friendly, and affordable compounds that will protect plants against abiotic stresses. We have also identified the structural mechanism of the core ABA signaling pathway, which will allow modulation of this pathway through genetic engineering of crop plants.

Folate receptors Folic acid and its derivatives are one-carbon donors required for the synthesis of DNA. Rapidly dividing cells such as cancer cells require rapid DNA synthesis and are therefore selectively dependent on high folate levels.

This vulnerability has been therapeutically exploited since the 1940s, when toxic folate analogs (antifolates) were used as the first chemotherapeutic agents. However, current antifolates have severe side effects such as immunosuppression, nausea, and hair loss, because they also kill nonmalignant proliferative cells.

Cells can take up folates in two main ways: by a ubiquitous, high-capacity, low-affinity uptake system known as RFC (reduced folate carrier) and by folate receptors. The latter are cysteine-rich cell surface glycoproteins that allow high-affinity uptake of folates by endocytosis but do not take up the current antifolate drugs. While folate receptors are expressed at very low levels in most tissues, they are “hijacked” and expressed at high levels in numerous cancers. This selective expression has been therapeutically and diagnostically exploited by administering antibodies against folate receptor α, folate-based imaging agents, and folate-conjugated drugs and toxins. We expect that antifolates that can be taken up by folate receptors but not by the RFC would have greatly reduced side effects.

We have determined the structure of folate receptor α in complex with folic acid. The structure, validated by systematic mutations of pocket residues and quantitative folic acid binding assays, has provided a detailed map of the extensive interactions between folic acid and FRα. It provides a structural framework for the design of new antifolates that are selectively taken up by folate receptors.

Our short-term goal is to determine the structures of novel, preclinical chemotherapeutic antifolates, bound to folate receptors and bound to the folate-metabolizing enzymes they inhibit, as a step toward designing antifolates that selectively target cancer cells.

RECENT PUBLICATIONS Kang, Yanyong, X. Edward Zhou, Xiang Gao, Yuanzheng He, Wei Liu, Andrii Ishchenko, Anton Barty, Thomas A. White, Oleksandr Yefanov, et al. 2015. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523(7562): 561–567.

Ke, Jiyuan, Honglei Ma, Xin Gu, Adam Thelen, Joseph S. Brunzelle, Jiayang Li, H. Eric Xu, and Karsten Melcher. 2015. Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors. Science Advances 1: 21500107.

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LORENZO F. SEMPERE, PH.D. Dr. Sempere obtained his B.S. in biochemistry at Universidad Miguel Hernández, Elche, Spain, and earned his Ph.D. at Dartmouth under Victor Ambros. He joined VARI in January 2014 as an Assistant Professor.

STAFF HEATHER CALDERONE, PH.D. STEPHANIE GRANT, M.P.A. JENNI WESTERHUIS, M.S.ED., M.S.

STUDENTS SHAYNA DONOGHUE DANIELA GOMEZ, B.S. ALYSSA SHEPARD

RESEARCH INTERESTS Our laboratory pursues complementary lines of translational research to explain the etiological role of microRNAs and to unravel microRNA regulatory networks during carcinogenesis. We mainly investigate these questions in clinical samples and preclinical models of breast cancer and pancreatic cancer. MicroRNAs can regulate and modulate the expression of hundreds of target genes, some of which are components of the same signaling pathways or biological processes. Thus, functional modulation of a single microRNA can affect multiple target mRNAs (i.e., one drug, multiple hits), unlike therapies based on small interfering RNAs, antibodies, or smallmolecule inhibitors.

The laboratory has active projects in the areas of cancer biology and tumor microenvironment, with a translational focus on molecular and cellular heterogeneity and its clinical implications for improving diagnostic applications and therapeutic strategies. Our knowledge of microRNAs is integrated into collaborative efforts with VARI researchers and cores, as well as into new technologies being developed for microRNA studies. Recent work includes the following.

We use innovative multiplexed immunohistochemical/in situ hybridization assays to implement diagnostic applications of microRNA biomarkers. Because tissue samples are the direct connection between cancer research and cancer medicine, detailed molecular/cellular characterization of tumors provides the opportunity to translate scientific knowledge into useful clinical information.

• Clinically validate tumor compartment–specific expression of the microRNA miR-21 as a prognostic marker for breast cancer. There is a focused interest in stromal expression of miR-21 in triple-negative breast cancer, for which prognostic markers and effective targeted therapies are lacking.

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• Develop integrative diagnostics for pancreatic cancer and precursor lesions using information from studies of cancer-associated microRNAs and protein glycosylation. Integrating the data from both microRNAs and protein markers should enhance diagnostic power and interpretation.

• Implement new technological platforms for high-content, tissue-based marker analysis.

Our goal is a fully automated pipeline from tissue stain to image analysis that we can use to characterize tumor features and to study tumor compartment–specific events, such as molecular changes in cancer cells, paracrine signaling by tumor-associated fibroblasts, and anti-tumor immune cell responses.

Molecular biology and cellular biology studies help to identify microRNA targets and regulatory networks.

• Develop methods for isolating microRNA/target mRNA interactions in in vitro and in vivo systems.

• In preclinical models and clinical specimens, identify tumor compartment–specific target networks that are regulated by microRNAs. • Evaluate tumor compartment–specific delivery of synthetic modulators of microRNA activity in preclinical cancer models and patient-derived cells.

Genetic engineering of models lets us assess the role of microRNAs within tumor microenvironment compartments.

• In animal models of breast and pancreatic cancers, evaluate the miR-21 activity required in cancer cell and tumor stroma compartments to support aggressive and metastatic features.

• In preclinical models of pancreatic cancer, replenish miR-155 immunostimulatory activity in combination with immune checkpoint regulators to boost anti-tumor immunity.

RECENT PUBLICATIONS Andrew, Angeline S., Carmen J. Marsit, Alan R. Schned, John D. Seigne, Karl T. Kelsey, Jason H. Moore, Laurent Perreard, Margaret R. Karagas, and Lorenzo F. Sempere. 2015. Expression of tumor suppressive microRNA-34a is associated with a reduced risk of bladder cancer recurrence. International Journal of Cancer 137(5): 1158–1166.

Ensink, Elliot, Jessica Sinha, Arkadeep Sinha, Huiyuan Tang, Heather M. Calderone, Galen Hostetter, Jordan Winter, David Cherba, Randall E. Brand, et al. 2015. Segment and fit thresholding: a new method for image analysis applied to microarray and immunofluorescence data. Analytical Chemistry 87(19): 9715–9721.

Graveel, Carrie R., Heather M. Calderone, Jennifer J. Westerhuis, Mary E. Winn, and Lorenzo F. Sempere. 2015. Critical analysis of the potential for microRNA biomarkers in breast cancer management. Breast Cancer: Targets and Therapy 7: 59–79.

Machiela, Emily, Anthony Popkie, and Lorenzo F. Sempere. 2015. Individual noncoding RNA variations: their role in shaping and maintaining the epigenetic landscape. In Personalized Epigenetics, Trygve Tollefsbol, ed. Waltham, Massachusetts: Academic Press, pp. 84–122.

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Prostate epithelial cells expressing a Pten mutant (C124S) were differentiated for 18 days under suboptimal conditions.

Androgen receptor (red) in the luminal cells and integrin Îą6 (green) in the basal cells were visualized by immunostaining and fluorescence microscopy. Image by Mclane Watson.

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MATTHEW STEENSMA, M.D. Dr. Steensma received his B.A. from Hope College and his M.D. from Wayne State University School of Medicine in Detroit. Dr. Steensma is a practicing surgeon in the Spectrum Health Medical Group, and he joined VARI as an Assistant Professor in 2010.

STAFF CURT ESSENBURG, B.S., LATG PATRICK DISCHINGER, B.S. DIANA LEWIS, A.S. MARIE MOONEY, M.S. MATT PRIDGEON, M.D.

RESEARCH INTERESTS Our laboratory conducts research into new treatment strategies for sarcomas.

Specifically, we are interested in determining the mechanisms underlying tumor formation in sporadic bone and soft tissue sarcomas and in neurofibromatosis type 1, a hereditary disorder caused by mutations in the neurofibromin 1 (NF1) gene.

Neurofibromin is considered a tumor suppressor that suppresses Ras activity by promoting Ras GTP hydrolysis to GDP. People with mutations in the neurofibromin 1 gene develop benign tumors called neurofibromas and have an elevated risk of malignancies ranging from solid tumors to leukemia, including sarcomas. The disease affects 1 in 3000 people in the United States, of whom 8–13% will ultimately develop a neurofibromatosis-related sarcoma in their lifetime. These aggressive tumors typically arise from benign neurofibromas, but the process of benign-to-malignant transformation is not well understood, and treatment options are limited, leading to poor five-year survival rates.

Our current sarcoma-related research efforts include the development of genetically engineered mouse models of neurofibromatosis type 1 tumor progression; the identification of targetable patterns of intratumoral and intertumoral heterogeneity through next-generation sequencing; genotype–phenotype correlations in neurofibromatosis type 1 and related diseases; and mechanisms of chemotherapy resistance in bone and soft-tissue sarcomas.

RECENT PUBLICATIONS Foley, Jessica M., Donald J. Scholten, Noel R. Monks, David Cherba, David J. Monsma, Paula Davidson, Dawna Dylewski, Karl Dykema, Mary E. Winn, and Matthew R. Steensma. 2015. Anoikis-resistant subpopulations of human osteosarcoma display significant chemoresistance and are sensitive to targeted epigenetic therapies predicted by expression profiling. Journal of Translational Medicine 13: 110.

Lane, Brian R., Jeffrey Bissonnette, Tracy Waldherr, Deborah Ritz-Holland, Dave Chesla, Sandra L. Cottingham, Sheryl Alberta, Cong Liu, Amanda Bartenbaker Thompson, et al. 2015. Development of a center for personalized cancer care at a regional cancer center. Journal of Molecular Diagnostics 17(6): 695–704.

Peacock, Jacqueline D., Karl J. Dykema, Helga V. Toriello, Marie R. Mooney, Donald J. Scholten II, Mary E. Winn, Andrew Borgman, Nicholas S. Duesbery, Judith A. Hiemenga, et al. 2015. Oculoectodermal syndrome is a mosaic RASopathy associated with KRAS alterations. American Journal of Medical Genetics A 167(7): 1429–1435.

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GEORGE F. VANDE WOUDE, PH.D. Dr. Vande Woude received his M.S. and Ph.D. degrees from Rutgers University. He joined the National Cancer Institute in 1972, becoming the director of the ABL–Basic Research Program in 1983, and then director of the Division of Basic Sciences in 1998. In 1999, he became the founding Director of VARI. In 2009, he stepped down as Director while retaining his laboratory as a Distinguished Scientific Fellow and Professor. He is a member of the National Academy of Sciences (1993) and a Fellow of the American Association for the Advancement of Science (2013).

STAFF CHONGFENG GAO, PH.D. LIANG KANG, B.S. KAY KOO DAFNA KAUFMAN, M.S. BEN STAAL, M.S.

RESEARCH INTERESTS ADJUNCT FACULTY BRIAN CAO, M.D. HENRY B. SKINNER, PH.D.

MET is overexpressed in many types of human cancer, and its expression correlates with aggressive disease and poor prognosis (visit http://www.vai.org/met/). Since discovering the MET receptor tyrosine kinase and its ligand, hepatocyte growth factor (HGF/SF), in the mid 1980s, our lab has focused on investigating the paramount role these molecules play in malignant progression and metastasis. As part of our ongoing effort, we focus on the mechanisms responsible for tumor progression under the hypothesis that phenotypic switching and chromosome instability can drive tumor progression. In addition, we continue to develop and characterize novel research models to be used in preclinical evaluation of new inhibitors that target MET in a variety of human cancers.

Tumor phenotypic switching: mechanism and therapeutic implications In human carcinomas, the acquisition by cells of an invasive phenotype, a process termed the epithelial-to-mesenchymal transition (E-MT), requires a breakdown of intercellular junctions with neighboring cells. Upon arriving at secondary sites, a few of the mesenchymal cells revert to an epithelial phenotype via a mesenchymal-to-epithelial transition (M-ET). We have implicated genetic instability in cell type determination and we have developed methods to isolate phenotypic variants from epithelial or mesenchymal subclones of carcinoma cell lines. We have explored the signal pathway underlying E-MT/M-ET phenotypic switching by gene expression analysis, spectral karyotyping (SKY), and fluorescent in situ hybridization (FISH). We found that changes in chromosome content are associated with phenotypic switching. We have further shown that these changes dictate the expression of specific genes, which in E-MT events are mesenchymal related and in M-ET events are epithelial related. Our results suggest that chromosome instability can provide the diversity of gene expression needed for tumor cells to switch phenotype.

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In vivo research models: model development and preclinical treatment evaluation Anti-cancer therapy based on blocking the HGF–Met signaling pathway has emerged as an important goal of pharmaceutical research. One of the limitations of studying the altered Met–HGF/SF signaling of human cancers grafted in mouse models has been that the murine HGF/SF protein has a low affinity for human MET. To overcome this, our lab developed a transgenic human HGF-SCID mouse model (hHGFtg-SCID), which generates a human-compatible HGF/SF protein and thus allows for the propagation of human tumors. This model has proven to be a valuable tool for in vivo testing of MET-dependent cancers and is used to evaluate treatment strategies aimed at targeting this pathway.

RECENT PUBLICATIONS Johnson, Jennifer, Maria Libera Ascierto, Sandeep Mittal, David Newsome, Liang Kang, Michael Briggs, Kirk Tanner, Francesco M. Marincola, Michael E. Berens, George F. Vande Woude, et al. 2015. Genomic profiling of a hepatocyte growth factor– dependent signature for MET-targeted therapy in glioblastoma. Journal of Translational Medicine 13: 306.

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BART O. WILLIAMS, PH.D. Dr. Williams received his Ph.D. in biology from Massachusetts Institute of Technology in 1996, where he trained with Tyler Jacks. Following his postdoctoral study with Harold Varmus, Dr. Williams joined VARI as a Scientific Investigator in July 1999. He is now a Professor and the Director of the Center for Cancer and Cell Biology.

STAFF CASSIE DIEGEL, B.S.

RESEARCH INTERESTS

NICOLE ETHEN, B.S. DIANA LEWIS, A.S. MITCH MCDONALD, B.S. ALEX ZHONG, PH.D.

STUDENTS CHERYL CHRISTIE, B.S. CASEY DROSCHA, B.S. JOHAN LEE JON LENSING KEVIN MAUPIN, B.A., B.S. AGNI NAIDU, B.S.

Our laboratory is interested in understanding how alterations in the Wnt signaling pathway cause human disease. Wnt signaling is a process, conserved throughout evolution, that functions in the differentiation of most tissues. Given its central role in growth and differentiation, it is not surprising that alterations in the Wnt pathway are among the most common events associated with human cancer. In addition, other human diseases including osteoporosis, cardiovascular disease, and diabetes have been linked to altered regulation of this pathway. A specific focus of our work is characterizing the role of Wnt signaling in bone formation. Our interest is not only in normal bone development but also in understanding whether aberrant Wnt signaling plays a role in the metastasis of some common cancers (for example, prostate, breast, lung, and renal tumors) to the bone. The long-term goal of this work is to provide insights useful in developing strategies to lessen the morbidity and mortality associated with skeletal metastasis.

Wnt signaling in normal bone development Mutations in Lrp5, a Wnt receptor, have been causally linked to alterations in human bone development. We have characterized a mouse strain deficient in Lrp5 and have shown that it recapitulates the low-bone-density phenotype seen in human patients who have that deficiency. We have further shown that mice carrying mutations in both Lrp5 and the related Lrp6 protein have even more-severe defects in bone density. To test whether Lrp5 deficiency causes changes in bone density due to aberrant signaling through β-catenin, we created OC-Cre;β-cateninflox/flox mice, which carry an osteoblastspecific deletion of β-catenin. We are addressing how other genetic alterations linked to Wnt/β-catenin signaling affect bone development and osteoblast function. We have generated mice with conditional alleles of Lrp6 and Lrp5 that can be inactivated via Cre-mediated recombination and have used them to show that both Lrp5 and Lrp6 function within osteoblasts to regulate normal bone development and homeostasis. We have also created mice lacking the ability to secrete Wnts from osteoblasts and shown that these mice have extremely low bone mass, establishing that the mature osteoblast is an important source of Wnts.

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We are also examining the effects on normal bone development and homeostasis of chemical inhibitors of the enzyme porcupine, which is required for the secretion and activity of all Wnts. Given that such inhibitors are currently in human clinical trials for treatment of several tumor types, their side effects related to the lowering of bone mass must be evaluated.

Wnt signaling in mammary development and cancer We are addressing the relative roles of Lrp5 and Lrp6 in Wnt1-induced mammary carcinogenesis. We have focused our initial efforts on Lrp5-deficient mice, because they are viable and fertile. A deficiency in Lrp5 dramatically inhibits the development of mammary tumors, and a germline deficiency in Lrp5 or Lrp6 results in delayed mammary development. We are also focusing on the mechanisms that underlie the role that Lrp6 plays in mammary development.

We are particularly interested in the pathways that may regulate the proliferation of normal mammary progenitor cells, as well as of tumor-initiating cells.

Wnt signaling in prostate development and cancer Two hallmarks of advanced prostate cancer are the development of skeletal osteoblastic metastasis and the ability of the tumor cells to become independent of androgen for survival. We have created mice with a prostate-specific deletion of the Apc gene as a disease model. These mice develop fully penetrant prostate hyperplasia by four months of age, and these tumors progress to frank carcinomas by seven months. We have found that these tumors initially regress under androgen ablation but show signs of androgen-independent growth some months later.

Genetically engineered mouse models of bone disease We have also focused on developing mouse models of osteoarthritis and of fracture repair. In addition, we are interested in identifying novel genes that play key roles in skeletal development and maintenance of bone mass. For example, current work is focused on the role of galectin-3, a member of the lectin family, in this context.

RECENT PUBLICATIONS Schumacher, Cassie A., Danese M. Joiner, Kennen D. Less, Melissa Oosterhouse Drewry, and Bart O. Williams. 2016.

Characterization of genetically engineered mouse models carrying Col2a1-cre-induced deletions of Lrp5 and/or Lrp6.

Bone Research 4: 15042.

Williams, Bart O. 2016. Genetically engineered mouse models to evaluate the role of Wnt secretion in bone development in homeostasis. American Journal of Medical Genetics C 172(1): 24–26.

Valkenburg, Kenneth C., Galen Hostetter, and Bart O. Williams. 2015. Concurrent hepsin overexpression and adenomatous polyposis coli deletion causes invasive prostate carcinoma in mice. The Prostate 75(14): 1579–1585.

Zhong, Zhendong, A., Juraj Zahatnansky, John Snider, Emily Van Wieren, Cassandra R. Diegel, and Bart O. Williams. 2015.

Wntless spatially regulates bone development through β-catenin-dependent and independent mechanisms. Developmental Dynamics 244(10): 1347–1355.

Zhong, Zhendong A., Anderson Peck, Shihong Li, Jeff VanOss, John Snider, Casey J. Droscha, TingTung A. Chang, and Bart O. Williams. 2015. 99mTc-Methylene diphosphonate uptake at injury site correlates with osteoblast differentiation and mineralization during bone healing in mice. Bone Research 3: 15013.

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NING WU, PH.D. Dr. Wu received her Ph.D. from the Department of Biochemistry of the University of Toronto in 2002. She joined VARI in 2013 as an Assistant Professor.

STAFF HOLLY DYKSTRA, B.S. ALTHEA WALDHART, B.S.

STUDENT MATT HOLLOWELL

RESEARCH INTERESTS Our laboratory studies the interface between cellular metabolism and signal transduction. The generation of two daughter cells depends on the proper uptake and use of nutrients that are often limited in the tumor environment. The distribution of these nutrients is controlled not only by the intrinsic catalytic rate and allosteric regulation of the enzymes, but also by post-translational modifications of these enzymes by signaling molecules. At the same time, signaling molecules must respond to cellular nutrient status and other cues such as environmental stresses and growth factors. Our laboratory focuses on key metabolic steps in glucose and lipid catabolism and aims to understand the mutual interactions between metabolites and signaling during cell replication.

Fundamentally, cancer is a disease of uncontrolled cell growth. Relative to normal cells, tumor cells have aberrant metabolic addictions that differ depending on the cell’s tissue of origin and genetic mutations. By understanding the energy requirements and regulatory pathways of tumor cells, more-effective treatments can be developed. Our projects include unraveling the molecular mechanisms that regulate glucose uptake in cancers, investigating the effect of glucose on mitochondrial activity, and exploring the role of glucose as the link between metabolic syndrome and cancer incidence.

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H. ERIC XU, PH.D. Dr. Xu went to Duke University and the University of Texas Southwestern Medical Center, earning his Ph.D. in molecular biology and biochemistry. He joined VARI in July 2002 and is now a Professor.

Dr. Xu is also the Primary Investigator and Distinguished Director of the VARI–SIMM Research Center in Shanghai, China.

STAFF XIANG GAO, PH.D. STEPHANIE GRANT, M.P.A. YUANZHENG (AJIAN) HE, PH.D. YANYONG KANG, PH.D. KUNTAL PAL, PH.D. KELLY POWELL, B.S. XIAOYIN (EDWARD) ZHOU, PH.D.

RESEARCH INTERESTS Hormone signaling is essential to eukaryotic life. Our research focuses on the signaling mechanisms of physiologically important hormones, striving to answer fundamental questions that have a broad impact on human health and disease. We are studying two families of proteins, the nuclear hormone receptors and the G protein–coupled receptors, because these proteins have fundamental roles in biology and are important drug targets for treating major human diseases.

STUDENTS ERIC LI HONGLEI MA, B.S.

PARKER DE WAAL, B.S. TINGHAI XU, B.S. YAN YAN, B.S. YANTING YIN, B.S. FENG ZHANG, B.S. VISITING SCIENTISTS DAVID BENSON, PH.D. SOK KEAN KHOO, PH.D.

Nuclear hormone receptors The nuclear hormone receptors form a large family comprising ligand-regulated and DNA-binding transcription factors, which include receptors for the classic steroid hormones such as estrogen, androgens, and glucocorticoids, as well as receptors for peroxisome proliferator activators, vitamin D, vitamin A, and thyroid hormones. These receptors are among the most successful targets in the history of drug discovery: every receptor has one or more synthetic ligands being used as medicines. In the last five years, we have developed the following projects centering on the structural biology of nuclear receptors.

ROSS REYNOLDS, PH.D.

Peroxisome proliferator–activated receptors The peroxisome proliferator–activated receptors (PPARα, β, and γ) are the key regulators of glucose and fatty acid homeostasis and, as such, are important therapeutic targets for treating cardiovascular disease, diabetes, and cancer. Millions of patients with type II diabetes have benefited from treatment with the novel PPARγ ligands rosiglitazone and pioglitazone. To understand the molecular basis of ligand-mediated signaling by PPARs, we have determined crystal structures of each PPAR’s ligand-binding domain (LBD) bound to many diverse ligands, including fatty acids, the lipid-lowering drugs called fibrates, and the new generation of anti-diabetic drugs, the glitazones. These structures have provided a framework for understanding the mechanisms of agonists

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and antagonists and the recruitment of co-activators and co-repressors in gene activation and repression. They also increase our understanding of the potency, selectivity, and binding mode of ligands and provide crucial insights for designing the next generation of PPAR medicines. We have discovered several natural ligands of PPARγ. Our plan is to test their physiological roles in glucose and insulin regulation and to develop them into therapeutics for diabetes and dislipidemia.

The human glucocorticoid receptor The human glucocorticoid receptor (GR), the prototypical steroid hormone receptor, affects a wide spectrum of human physiology including immune/inflammatory responses, metabolic homeostasis, and control of blood pressure. GR is a well-established target for drugs, and those drugs have an annual market of over $10 billion.

However, the clinical use of GR ligands is limited by undesirable side effects partly resulting from receptor cross-reactivity or low potency. The discovery of potent, more-selective GR ligands— “dissociated glucocorticoids” that have the potential to separate the good effects from the bad—remains a major goal of pharmaceutical research.

We have determined a number of GR crystal structures bound to unique ligands and have found an unexpected regulatory mechanism: degradation by lysosomes. We also are studying the molecular and structural mechanisms of the dissociated glucocorticoids identified by our research.

Structural genomics of receptor LBDs The ligand-binding domain of a nuclear receptor contains key structural elements that mediate ligand-dependent regulation of the receptors and, as such, it has been the

focus of intense structural studies. Crystal structures for most of the 48 human nuclear receptors have been determined and have illustrated the details of ligand binding, the conformational changes induced by agonists and antagonists, the basis of dimerization, and the mechanism of co-activator and co-repressor binding.

The structures also have provided many surprises about the identity of ligands and their implications for receptor signaling pathways. There are only a few “orphan” nuclear receptors for which the LBD structure remains unsolved.

In the past few years, we have determined the crystal structures of the LBDs of CAR, SHP, SF-1, COUP-TFII, and LRH-1, and our structures have helped to identify new ligands and signaling mechanisms for these orphan receptors.

G protein–coupled receptors (GPCRs) The GPCRs form the largest family of receptors in the human genome and account for over 40% of drug targets, but their structures remain a challenge because they are seven-transmembrane receptors. There are only a few crystal structures for class A GPCRs, and many important questions regarding GPCR ligand binding and activation remain unanswered. From our standpoint, GPCRs are similar to nuclear hormone receptors with respect to regulation by protein-ligand and protein–protein interactions. We focus on class B GPCRs, which includes receptors for parathyroid hormone (PTH), corticotropinreleasing factor (CRF), glucagon, and glucagon-like peptide-1. We have determined crystal structures of the ligand-binding domain of the PTH receptor and the CRF receptor, and we are developing hormone analogs for treating osteoporosis, depression, and diabetes. We are developing a mammalian overexpression system and plan to use it to express full-length GPCRs for crystallization and structural studies.

RECENT PUBLICATIONS He, Yuanzheng, Jingjing Shi, Wei Yi, Xin Ren, Xiang Gao, Jianshuang Li, Nanyan Wu, Kevin Weaver, Qian Xie, et al. 2015.

Discovery of a highly potent glucocorticoid for asthma treatment. Cell Discovery 1: 15035.

Kang, Yanyong, X. Edward Zhou, Xiang Gao, Yuanzheng He, Wei Liu, Andrii Ishchenko, Anton Barty, Thomas A. White, Oleksandr Yefanov, et al. 2015. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523(7562): 561–567.

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TAO YANG, PH.D. Dr. Yang received his Ph.D. in biochemistry at the Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, in 2001. He joined VARI as an Assistant Professor in February 2013.

STAFF DIANA LEWIS, A.S. JIANSHUANG LI, B.S. JIE LI, PH.D. HUADIE LIU, M.S. DI LU, M.S. KEVIN WEAVER, B.S.

RESEARCH INTERESTS The skeletal system develops from mesenchymal cells and is the major reservoir of mesenchymal stem cells (MSCs) in adult life. MSCs play pivotal roles in skeletal tissue growth, homeostasis, and repair, while dysregulations in MSC renewal, linage specification, and pool maintenance are common causes of skeletal disorders. Our long-term interest is to investigate the signals and cellular processes orchestrating the activities of MSCs and MSC-derived cells during skeletal development and homeostasis and how those processes are involved in skeletal aging and disorders. Our current projects in skeletal development and disease include a study of the sumoylation pathway and a study of LRP1 signaling. As part of these projects, we have established in vivo and in vitro genetic models to study the molecular mechanisms underlying osteoarthritis and osteoporosis.

RECENT PUBLICATIONS Chen, Shan, Monica Grover, Tarek Sibai, Jennifer Black, Nahid Rianon, Abbhirami Rajagopal, Elda Munivez, Terry Bertin, Brian Dawson, et al. 2015. Losartan increases bone mass and accelerates chondrocyte hypertrophy in developing skeleton.

Molecular Genetics and Metabolism 115(1): 53–60.

He, Yuanzheng, Jingjing Shi, Wei Yi, Xin Ren, Xiang Gao, Jianshuang Li, Nanyan Wu, Kevin Weaver, Qian Xie, et al. 2015.

Discovery of a highly potent glucocorticoid for asthma treatment. Cell Discovery 1: 15035.

Lu, Linchao, Karine Harutyunyan, Weidong Jin, Jianhong Wu, Tao Yang, Yuqing Chen, Kyu Sang Jeoeng, Yangjin Bae, Jianning Tao, et al. 2015. RECQL4 regulates p53 function in vivo during skeletogenesis. Journal of Bone and Mineral Research 30(6): 1077–1089.

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CENTER FOR EPIGENETICS

Peter A. Jones, Ph.D., D.Sc. Director

The Center’s researchers study epigenetics and epigenomics in health and disease, with the ultimate goal of developing novel therapies to treat cancer and neurodegenerative diseases. The Center collaborates extensively with other VARI research groups and with external partners to maximize its efforts to develop therapies that target epigenetic mechanisms.

Methyl (red) and acetyl (light blue) groups as epigenetic marks on nucleosomes and DNA. Illustration by Nicole Ethen.

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STEPHEN B. BAYLIN, M.D. Dr. Baylin joined VARI as a Professor in the Center for Epigenetics in January 2015 and is co-leader of the VARI-SU2C Epigenetics Dream Team. He devotes a portion of his time to VARI. His primary appointment is with Johns Hopkins University as the Virginia and D.K. Ludwig Professor of Oncology and Medicine and co-head of Cancer Biology at the Sidney Kimmel Comprehensive Cancer Center.

RESEARCH INTERESTS The Van Andel Research Institute–Stand Up To Cancer (VARI-SU2C) Epigenetics Dream Team is a multi-institutional effort to develop new epigenetic therapies against cancer and to move promising therapies to clinical trials. As co-leader, Dr. Baylin oversees the team’s research, which leverages the combined expertise of its members.

Epigenetics is the study of how the packaging and modification of DNA influences the genes that are active or kept silent in a particular cell, and it holds untold potential for treating cancer and other diseases. Through a detailed understanding of how normal epigenetic processes work, scientists can identify erroneous epigenetic modifications that may contribute to the development and progression of cancer. Epigenetic therapies, which work by correcting these errors, have the potential to directly treat cancer and to sensitize patients to traditional treatments such as chemotherapy and radiation and to promising new immunotherapy approaches.

The VARI-SU2C Epigenetics Dream Team is headquartered at VARI in Grand Rapids, Michigan, and it includes members from Johns Hopkins University, Memorial Sloan Kettering Cancer Center, Fox Chase Cancer Center/Temple University, University of Southern California, and Rigshospitalet/University of Copenhagen. The American Association for Cancer Research (AACR), as SU2C’s scientific partner, reviews projects and provides objective scientific oversight.

RECENT PUBLICATIONS Chaiappinelli, Katherine B., Pamela L. Strissel, Alexis Desrichard, Huili Li, Christine Henke, Benjamin Akman, Alexander Hein, Neal S. Rote, Leslie M. Cope, et al. 2015. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. Cell 162(5): 961–973.

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PETER A. JONES, PH.D., D.SC. Dr. Jones received his Ph.D. from the University of London. He joined the University of Southern California in 1977 and served as director of the USC Norris Comprehensive Cancer Center between 1993 and 2011. Dr. Jones joined VARI in 2014 as its Chief Scientific Officer and Director of the Center for Epigenetics.

STAFF MINMIN LIU, PH.D. HITOSHI OTANI, PH.D. ROCHELE TIEDEMANN, PH.D. WANDING ZHOU, PH.D.

ADJUNCT FACULTY RONALD CHANDLER, JR., PH.D. FEYRUZ RASSOOL, PH.D.

RESEARCH INTERESTS Epigenetics may be defined as mitotically heritable changes in gene expression that are not caused by changes in the DNA sequence itself. Epigenetic processes establish the differentiated state of cells and govern how genes are used to allow organs and cells to function correctly and inherit their properties through cell division. In the case of diseases such as cancer, these processes can go wrong, changing the behavior of cells to adverse effect. However, many of these changes are potentially reversible by treatment with drugs. Because epigenetic processes are at the root of biology, they have implications for all of human development and disease.

Our laboratory studies the mechanisms by which epigenetic processes become misregulated in cancer and contribute to the disease phenotype. We focus on the role of DNA methylation in controlling the expression of genes during normal development and in cancer. Our work has shifted to a holistic approach in which we are interested in the interactions between processes such as DNA methylation, histone modification, and nucleosomal positioning in the epigenome, and we want to determine how mutations in the genes which modify the epigenome contribute to the cancer phenotype. We have had a long-term interest in the mechanism of action of DNA methylation inhibitors, both in the lab and in the clinic. We are working with several major institutions to bring epigenetic therapies to the forefront of cancer medicine.

RECENT PUBLICATIONS Lay, Fides D., Yaping Liu, Theresa K. Kelly, Heather Witt, Peggy J. Farnham, Peter A. Jones, and Benjamin P. Berman. 2015.

The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Research 25(4): 467–477.

Roulois, David, Helen Loo Yau, Rajat Singhania, Yadong Wang, Amavaz Danesh, Shu Yi Shen, Han Han, Gangning Liang, Peter A. Jones, et al. 2015. DNA-demethylating agents target colorectal cancer cells by inducing viral mimicry by endogenous transcripts. Cell 162(5): 961–973.

Statham, Aaron L., Phillippa C. Taberlay, Theresa K. Kelly, Peter A. Jones, and Susan J. Clark. 2015. Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines. Genomics Data 3: 94–96.

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STEFAN JOVINGE, M.D., PH.D. Dr. Jovinge received his M.D. (1991) and his Ph.D. (1997) at Karolinska Institute in Stockholm. Since December 2013 he has been the Medical Director of Research at the Frederik Meijer Heart and Vascular Institute and a Professor at VARI. He also directs the DeVos Cardiovascular Research Program, is a Professor at the MSU College of Human Medicine, and is a Consulting Professor at Stanford University.

STAFF PAULA DAVIDSON, M.S. DAWNA DYLEWSKI, B.S. ELLEN ELLIS EMILY EUGSTER, M.A. JENS FORSBERG, PH.D. LISA KEFENE, M.A., MB(ASCP), RLAT ERIC KORT, M.D. BRITTANY MERRIFIELD, B.S. HSIAO-YUN YEH (CHRISTY) MILLIRON, PH.D. JORDAN PRAHL, B.S. LAURA TARNAWSKI, M.S. MATTHEW WEILAND, M.S. LAURA WINKLER, PH.D.

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RESEARCH INTERESTS The DeVos Cardiovascular Research Program is a joint effort between VARI and Spectrum Health. The basic science lab is the Jovinge laboratory at VARI, and a corresponding clinical research unit resides within the Fred Meijer Heart and Vascular Institute.

Cardiovascular diseases are among the major causes of death and disability worldwide.

While the incidence of ischemic heart diseases has started to decline, congestive heart failure is still rising. Medical treatment for the latter is supportive, and the only available therapy is heart transplantation.

To regenerate myocardium after disease or damage is one of the major challenges in medicine. Our group is working on true heart muscle regeneration along two axes: external and internal (cardiac) cell sources. The most robust external source for generating heart muscle cells has been stem cells, either from an embryonic stem cell (ESC) system or from reprogrammed pluripotent stem cells (iPSCs). The main drawback to the stem cell approach is that their differentiation will generate a multitude of different cell types at different stages of development. A mixed cell population of undifferentiated cells always has the potential to create tumors. Also, the use of ESCs creates a need for lifelong immunosuppressive treatment. iPSCs, however, could be generated from the patient’s own peripheral blood cells, a technique established by our group in Grand Rapids. To be able to use these sources, we have developed strategies based on establishing surface marker expression—similar to those for bone-marrow cells—to help select homogenous, safe populations to transplant.

Van Andel Research Institute | Scientific Report

The second axis we focus on is endogenous generation within the heart. Although adult human heart muscle cells are to a small extent generated after birth, the internal source of such cells and their cell cycle regulation are unknown. Some data indicate that cardiac progenitors could be involved, and other data suggest that differentiated heart muscle cells might be the source. We and our collaborators have rejected the view that adult heart muscle cells are not capable of undergoing a complete cell division.

With the use of 14C dating, the adult heart has been shown to have a regenerative capacity. This has opened a completely new field of induced local generation of heart muscle cells, which is now being explored.

The final phase of patient studies will involve the administration of cells or compounds to stimulate endogenous regeneration. To prepare cells for transplantation into humans, an accredited Good Manufacturing Practice facility will be established in collaboration with Stanford University, and the first safety studies (Phase II) will be followed by studies evaluating the best route for delivering the treatment and the best timing.

In the final stage, randomized prospective clinical trials will be launched.

Our program’s eventual aims are clinical concept studies of heart muscle cell regeneration in patients, either by cell transplantation or stimulation of endogenous sources. The program’s clinical side involves a multistep process to prepare for these studies. Patients with the most severe heart disease, i.e., those needing mechanical support, are being studied to optimize treatments that will be used in later safety studies. We have already derived mortality prediction algorithms for patients on bedside heart-lung machines.

RECENT PUBLICATIONS Bergmann, Olaf, Sofia Zdunek, Anastasia Felker, Mehran Salehpour, Kanar Alkass, Samuel Bernard, Staffan L. Sjostrom, Mirosława Szewcykowska, Teresa Jackowska, et al. 2015. Dynamics of cell generation and turnover in the human heart.

Cell 161(7): 1566–1575.

Raulf, Alexandra, Hannes Horder, Laura Tarnawski, Caroline Geisen, Annika Ottersbach, Wilhelm Röll, Stefan Jovinge, Bernd K. Fleischmann, and Michael Hesse. 2015. Transgenic systems for unequivocal identification of cardiac myocyte nuclei and analysis of cardiomyocyte cell cycle status. Basic Research in Cardiology 110(3): 33.

Tarnawski, Laura, Xiaojie Xian, Gustavo Monnerat, Iain C. Macauley, Daniela Malan, Andrew Borgman, Sean M. Wu, Bernd K. Fleischmann, and Stefan Jovinge. 2015. Integrin based isolation enables purification of murine lineage committed cardiomyocytes. PLoS One 10(8): e0135880.

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PETER W. LAIRD, PH.D. Dr. Laird earned his Ph.D. in 1988 from the University of Amsterdam with Piet Borst. Dr. Laird was a faculty member at the University of Southern California from 1996 to 2014, where he was Skirball-Kenis Professor of Cancer Research and directed the USC Epigenome Center. He joined VARI as a Professor in September 2014.

STAFF KELLY FOY, B.S. TOSHINORI HINOUE, PH.D. KWANGHO LEE, PH.D. ZHOUWEI ZHANG, M.S. WANDING ZHOU, PH.D.

STUDENT NICOLE VANDER SCHAAF, B.S.

RESEARCH INTERESTS Our goal is to develop a detailed understanding of the molecular basis of human disease, with a particular emphasis on the role of epigenetics in cancer. Cancer is often considered to have a primarily genetic basis, with contributions from germline variations in risk and somatically acquired mutations, rearrangements, and copy number alterations. However, it is clear that nongenetic mechanisms can exert a powerful influence on cellular phenotype, as evidenced by the marked diversity of cell types within our bodies, which virtually all contain an identical genetic code. This differential gene expression is controlled by tissue-specific transcription factors and variations in chromatin packaging and modification, which can provide stable phenotypic states governed by epigenetic, not genetic, mechanisms. It seems intrinsically likely that an opportunistic disease such as cancer would take advantage of such a potent mediator of cellular phenotype. Our laboratory is dedicated to understanding how epigenetic mechanisms contribute to the origins of cancer and how to translate this knowledge into more-effective cancer prevention, detection, treatment, and monitoring.

We use a multidisciplinary approach in our research, relying on mechanistic studies in model organisms and cell cultures, clinical and translational collaborations, genome-scale and bioinformatic analyses, and epidemiological studies to advance our understanding of cancer epigenetics. In recent years, we participated in the generation and analysis of high-dimensional epigenetic data sets, including the production of all epigenomic data for The Cancer Genome Atlas (TCGA) and the application of next-generation sequencing technology to single-base-pair-resolution, whole-genome DNA methylation analysis. We are leveraging this epigenomic data for translational applications and hypothesis testing in animal models. A major focus of our laboratory is to develop mouse models for investigating epigenetic mechanisms and drivers of cancer and to develop novel strategies for single-cell epigenomic analysis.

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RECENT PUBLICATIONS Cancer Genome Atlas Research Network. 2016. Comprehensive molecular characterization of papillary renal-cell carcinoma.

New England Journal of Medicine 374(2): 135–145.

Ceccarelli, Michele, Floris P. Barthel, Tathiane M. Malta, Thais S. Sabedot, Sofie R. Salama, Bradley A. Murray, Olena Morozova, Yulia Newton, Arnie Radenbaugh, et al. 2016. Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell 164(3): 550–563.

Levine, A. Joan, Amanda I. Phipps, John A. Baron, Daniel D. Buchanan, Dennis J. Ahnen, Stacey Cohen, Noralane M. Lindor, Polly A. Newcomb, Christophe Rosty, et al. 2016. Clinicopathological risk factor distributions for MLH1 promoter region methylation in CIMP positive tumors. Cancer Epidemiology, Biomarkers and Prevention 25(1): 68–75.

Ryland, Katherine E., Allegra G. Hawkins, Daniel J. Weisenberger, Vasu Punj, Scott C. Borinstein, Peter W. Laird, Jeffrey R. Martens, and Elizabeth R. Lawlor. 2016. Promoter methylation analysis reveals that SCNA5 ion channel silencing supports Ewing sarcoma cell proliferation. Molecular Cancer Research 14(1): 26–34.

Cancer Genome Atlas Research Network. 2015. The molecular taxonomy of primary prostate cancer. Cell 163(4): 1011–1025.

Ciriello, Giovanni, Michael L. Gatza, Andrew H. Beck, Matthew D. Wilkerson, Suhn K Rhie, Alessandro Pastore, Hailei Zhang, Michael McLellan, Christina Yau, et al. 2015. Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163(2): 506–519.

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GERD PFEIFER, PH.D. Dr. Pfeifer earned his M.S. in pharmacology in 1981 and his Ph.D. in biochemistry in 1984 from Goethe University in Frankfurt, Germany.

He most recently held the Lester M. and Irene C. Finkelstein Chair in Biology at the City of Hope in Duarte, California, before joining VARI in 2014 as a Professor.

STAFF ZHIJUN HUANG, PH.D. SEUNG-GI JIN, PH.D. JENNIFER JOHNSON, M.S. JIYOUNG YU, PH.D.

RESEARCH OVERVIEW The laboratory studies epigenetic mechanisms of disease, with a focus on DNA methylation and the role of 5-hydroxymethylcytosine in cancer and other diseases.

Specifically, the lab studies hypermethylation in cancer genes with the intent of determining the mechanisms and significance of CpG island methylation. The work centers on the hypothesis that CpG island hypermethylation in tumors is driven by one or a combination of the following: carcinogenic agents, inflammation, imbalances in methylation and demethylation pathways, oncogene activation leading to epigenetic changes, and dysfunction of the Polycomb repression complex.

The removal of methyl groups from DNA has recently been recognized as an important pathway in cancer and possibly in other diseases. Our lab studies mechanisms of 5-methylcytosine oxidation.

DNA methylation in cancer To effectively study genome-wide DNA methylation patterns, we previously developed the methylated CpG island recovery assay (MIRA), which is used in combination with sequencing to identify commonly methylated genes in human cancers and normal tissues. We investigate mechanisms of cancer-associated DNA hypermethylation using DNA-methylation and chromatin-component mapping in normal and malignant cells, as well as bioinformatics approaches and functional studies.

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Tet3 and related proteins We have identified three different isoforms of the Tet3 5-methylcytosine oxidase and characterized them using biochemical, functional, and genetic approaches. We observed that one isoform of Tet3 specifically binds to 5-carboxylcytosine, thus establishing an anchoring mechanism of Tet3 to its reaction product, which may aid in localized 5-methylcytosine oxidation and removal. We also study several Tet-associated proteins, trying to understand their biological roles.

5-methylcytosine oxidation and neurodegeneration Using ChIP sequencing, we mapped one of the isoforms of Tet3 in neuronal cell populations. Tet3 has a rather limited genomic distribution and is targeted to the transcription start sites of defined sets of genes, many of which function within the lysosome and autophagy pathways. We know these pathways are defective in neurodegenerative diseases. We are exploring the mechanistic consequences of 5-methylcytosine oxidation in this disease group, with the long-term goal of determining whether neurodegeneration has an epigenetic origin.

RECENT PUBLICATIONS Jin, Seung-Gi, Zhi-Min Zhang, Thomas L. Dunwell, Matthew R. Harter, Xiwei Wu, Jennifer Johnson, Zheng Li, Jiancheng Liu, Piroska E. Szabó, et al. 2016. Tet3 reads 5-carboxylcytosine through its CXXC domain and is a potential guardian against neurodegeneration. Cell Reports 14(3): 493–505.

Jung, Marc, Seung-Gi Jin, Xiaoying Zhang, Wenying Xiong, Grigoriy Gogoshin, Andrei S. Rodin, and Gerd P. Pfeifer. 2015.

Longitudinal epigentic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging. Nucleic Acids Research 43(15): e100.

Jung, Marc, Swati Kadam, Wenying Xiong, Tibor A. Rauch, Seung-Gi Jin, and Gerd P. Pfeifer. 2015. MIRA-seq for DNA methylation analysis of CpG islands. Epigenomics 7(5): 695–706.

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SCOTT ROTHBART, PH.D. Dr. Rothbart earned a Ph.D. in pharmacology and toxicology from Virginia Commonwealth University in 2010. He joined VARI in April 2015 as an Assistant Professor.

STAFF EVAN CORNETT, PH.D. BRADLEY DICKSON, PH.D. ROCHELLE TIEDEMANN, PH.D. STUDENT ROBERT VAUGHAN, B.S.

RESEARCH INTERESTS Two major epigenetic marks regulating the structure and function of eukaryotic chromatin are the methylation of DNA and post-translational modifications (PTMs) of histone proteins. Breakthroughs in our understanding of chromatin function have been made through the identification of protein machineries that incorporate (write), remove (erase), and bind (read) these epigenetic marks. Chromatin modification and remodeling shape cellular identity, and it is becoming increasingly apparent that deregulation of epigenetic signaling contributes to, and may cause, the initiation and progression of cancer and other human diseases. Unlike genetic abnormalities, chromatin modifications are reversible, making the writers, erasers, and readers of these marks attractive therapeutic targets. The goal of our research is to define the molecular details of chromatin accessibility, interaction, and function. We are particularly interested in understanding how DNA and histone modifications work together as a language or code that is read and interpreted by specialized proteins to orchestrate the dynamic functions of chromatin. We hope our studies will lead to a better understanding of the etiology of disease and will contribute to the discovery of effective therapeutic approaches that target the epigenetic machinery.

Mechanics of chromatin interaction It appears that many chromatin-associated factors have multiple known (or predicted) chromatin regulatory domains, both within a single protein and within the subunits of complexes. There is a diverse and exciting potential here, a previously underappreciated layer of complexity and specificity to chromatin recognition and regulation. Our studies are using expertise in biochemistry, computational and molecular biophysics, and cell biology to define the molecular underpinnings of multivalency and allostery in chromatin interaction and function.

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Mechanisms regulating the inheritance of DNA methylation

Application of microarray technology to the study of histone PTMs.

The faithful inheritance of DNA methylation patterns is essential for normal mammalian development and long-term transcriptional silencing. We recently discovered that the E3 ubiquitin ligase UHRF1 is a key regulator of this process through its interaction with a histone signature of transcriptionally silent heterochromatin. Current studies are focused on defining the molecular interconnections between UHRF1, DNMTs, and chromatin, and on elucidating the role of UHRF1 deregulation in tumor initiation and progression.

We recently developed a histone peptide microarray platform that has greatly improved our understanding of histone PTM function in development and disease, as well as during the fundamental processes of transcription, chromatin organization, and DNA repair. We are developing several new microarray-based platforms to enable high-throughput discovery of histone PTM function. Two areas of focus are to expand the utility of our current histone peptide array in defining the influence of the “histone code” on writers and erasers of these marks and to develop a multiplex array assay for comparative profiling of histone PTM patterns in stages of differentiation and disease.

RECENT PUBLICATIONS Rothbart, Scott B., Bradley M. Dickson, Jesse R. Raab, Adrian T. Grzybowski, Krzysztof Krajewski, Angela H. Guo, Erin K. Shanle, Steven Z. Josefowicz, Stephen M. Fuchs, et al. 2015. An interactive database for the assessment of histone antibody specificity.

Molecular Cell 59(3): 502–511.

Simon, Jeremy M., Joel S. Parker, Feng Liu, Scott B. Rothbart, Slimane Ait-Si-Ali, Brian D. Strahl, Jian Jin, Ian J. Davis, Amber L. Moseley, and Samantha G. Pattenden. 2015. A role for widely interspaced zinc finger (WIZ) in retention of the G9a methyltransferase on chromatin. Journal of Biological Chemistry 290(43): 26088–26102.

Zhang, Zhi-Min, Scott B. Rothbart, David F. Allison, Qian Cai, Joseph S. Harrison, Lin Li, Yinsheng Wang, Brian D. Strahl, Gang Greg Wang, and Jikui Song. 2015. An allosteric interaction links USP7 to deubiquitination and chromatin targeting of UHRF1.

Cell Reports 12(9): 1400–1406.

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Mapping of the mammalian 5-methylcytosine oxidase Tet3.

Top left: Ribbon representation of the mTet3 CXXC domain (light blue) bound to CcaCG DNA (tan). The zinc ions in the CXXC domain and the carboxylates in DNA are shown as green and red spheres, respectively. Top right: Electrostatic surface representation, with positive charge shown as blue and negative charge as red.

Bottom: ChiP-seq data shows that Tet3FL peaks center on transcription start sites (horizontal arrows) for four lysosome-related genes.

The peaks from neuronal progenitors (NPC) and mouse brain cells correspond to the locations of low 5-methylcytosine content in the DNA sequence of NPCs and mouse embryonic stem cells (Stadler et al., 2011). Figure from the Pfeifer laboratory.

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HUI SHEN, PH.D. Dr. Shen earned her Ph.D. at the University of Southern California in genetic, molecular, and cellular biology. She joined VARI in September 2014 as an Assistant Professor.

STAFF HUIHUI FAN, PH.D. WANDING ZHOU, PH.D.

RESEARCH INTERESTS The laboratory focuses on the epigenome and its interaction with the genome in various diseases, with a specific emphasis on female cancers and cross-cancer comparisons.

We use bioinformatics as a tool to understand the etiology, cell of origin, and epigenetic mechanisms of various diseases and to devise better approaches for cancer prevention, detection, therapy, and monitoring. We have extensive experience with genome-scale DNA methylation profiles in primary human samples, and we have made major contributions to epigenetic analysis within The Cancer Genome Atlas (TCGA).

DNA methylation is ideally suited for deconstructing heterogeneity among cell types within a tissue sample. In cancer research, this approach can be used for cancercell clonal evolution studies or for quantifying normal cell infiltration and stromal composition. The latter can provide insights into the tumor microenvironment, and in noncancer studies it can be a useful tool for accurately estimating cell populations and providing insights into lineage structures and population shifts in disease. In addition, we are interested in translational applications of epigenomic technology. To this end, we bring markers emerging from our bioinformatics analysis into clinical assay development, marker panel assembly, and optimization, with the ultimate goal of clinical testing and validation.

RECENT PUBLICATIONS Cancer Genome Atlas Research Network. 2016. Comprehensive molecular characterization of papillary renal-cell carcinoma.

New England Journal of Medicine 374(2): 135–145.

Ciriello, Giovanni, Michael L. Gatza, Andrew H. Beck, Matthew D. Wilkerson, Suhn K Rhie, Alessandro Pastore, Hailei Zhang, Michael McLellan, Christina Yau, et al. 2015. Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163(2): 506–519.

Yao, Lijing, Hui Shen, Peter W. Laird, Peggy J. Farnham, and Benjamin P. Berman. 2015. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biology 16: 105.

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PIROSKA E. SZABร , PH.D. Dr. Szabรณ earned an M.Sc. in biology and a Ph.D. in molecular biology from Jรณzsef Attila University, Szeged, Hungary. She joined VARI in 2014 as an Associate Professor.

STAFF FUJUNG CHANG, M.S. JI LIAO, PH.D. TIE-BO ZENG, PH.D.

STUDENT NICK PIERCE

RESEARCH INTERESTS Our laboratory studies the molecular mechanisms responsible for resetting the mammalian epigenome between generations, globally and specifically in the context of genomic imprinting. We focus on how genomic imprints are established at differentially methylated regions (DMRs) in germ cells and how they are maintained in the zygote and in the soma. Our main hypothesis is that cytosine 5-hydroxymethylation, chromatin composition, and noncoding RNAs are essential components of the imprint cycle, being involved at the DNA methylation imprint-maintenance phase in the zygote and in the soma, as well as at the imprint-erasure and -establishment phases in the germline.

Epigenetic mechanisms that maintain imprinting in the zygote and in the soma In somatic cells, the parental DMR alleles are differentially marked by covalent histone modifications, including H3K79 methylation. To test whether these methylation marks maintain imprinting in the soma, we will measure allele-specific gene expression, chromatin composition, and DNA methylation in embryos and placentas having targeted inactivation of histone methyltransferase genes (for example, of Dot1L). We and others have shown that oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) plays a role in global demethylation in the paternal pronucleus of the zygote.

H3K9 dimethylation protects some paternal methylation imprints from TET3-mediated oxidation in the zygote, but it is not known whether maternal imprints are similarly protected. In addition, 5hmC may be important in the maintenance of hypomethylation of one DMR allele after fertilization and in the soma, because it is not recognized by the maintenance methyltransferase. In agreement with this hypothesis, we have detected allele-specific 5hmC marks at some imprinted DMRs in somatic cells. We will follow up with genetic experiments to determine the exact role of 5hmC and H3K9 methylation at the phase of imprint maintenance in the zygote and in the soma.

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The role of transcription and chromatin in imprint establishment in the germline To understand how imprint establishment at specific loci is related to global epigenetic remodeling events, we recently mapped dynamic changes in DNA CpG methylation, transcription, and chromatin in fetal male germ cells. We found broad, low-level transcription across paternal DMRs prior to DNA de novo methylation in prospermatogonia.

We are testing genetically whether such transcription is required for paternal imprint establishment. Active chromatin marks such as H3K4 methylation diminish at paternal DMRs prior to establishment of the DNA methylation imprint. We are generating conditional mutant mice and prospermatogonia-specific inducible Cre-deletor mice to test whether removing H3K4 methylation is essential for paternal imprint establishment. Maternal DMRs are occupied by H3K4 methylation peaks in prospermatogonia. We are testing genetically whether this mark is sufficient to protect maternal DMRs from de novo DNA methylation.

RECENT PUBLICATIONS Jin, Seung-Gi, Zhi-Min Zhang, Thomas L. Dunwell, Matthew R. Harter, Xiwei Wu, Jennifer Johnson, Zheng Li, Jiancheng Liu, Piroska E. Szabó, et al. 2016. Tet3 reads 5-carboxylcytosine through its CXXC domain and is a potential guardian against neurodegeneration. Cell Reports 14(3): 493–505.

Iqbal, Khursheed, Diana A. Tran, Arthur X. Li, Charles Warden, Angela Y. Bai, Purnima Singh, Xiwei Wu, Gerd P. Pfeifer, and Piroska E. Szabó. 2015. Deleterious effects of endocrine disruptors are corrected in the mammalian germline by epigenome reprogramming. Genome Biology 16: 59.

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STEVEN J. TRIEZENBERG, PH.D. Dr. Triezenberg earned his Ph.D. at the University of Michigan. He was a faculty member at Michigan State University for more than 18 years before joining VAI in 2006 as the founding Dean of Van Andel Institute Graduate School and as a VARI Professor.

RESEARCH INTERESTS

STAFF GLEN ALBERTS, B.S. CAROLYN BOTTING, M.S. KRISTIE VANDERHOOF, B.S.

STUDENT NIKKI THELLMAN, D.V.M.

Our research explores the mechanisms that control how genes are expressed inside cells. Some genes must be expressed more or less constantly throughout the life of any eukaryotic cell; others must be turned on (or off) in particular cells at specific times or in response to specific signals or events. Regulation of gene expression helps determine how a given cell will function. Our laboratory explores the mechanisms that regulate the first step in that flow, the process of transcription. We use infection by herpes simplex virus as an experimental context for exploring the mechanisms of transcriptional activation in human cells.

Transcriptional activation during herpes simplex virus infection Herpes simplex virus type 1 (HSV-1) causes the common cold sore or fever blister. The initial lytic or productive infection by HSV-1 results in the obvious symptoms in the skin and mucosa, typically in or around the mouth. Like all viruses, HSV-1 relies on the molecular machinery of the infected cell to express viral genes so that the infection can proceed and new copies of the virus can be made. This process is triggered by a viral protein known as VP16, which stimulates the initial expression of viral genes in the infected cell. Much of our work over the years has explored how VP16 activates these genes during lytic infection.

After the initial infection resolves, HSV-1 finds its way into nerve cells, where the virus can remain in a latent mode for long periods of time—essentially for the entire life of the host. Occasionally, some triggering event (such as emotional stress or damage to the nerve from a sunburn or a root canal operation) will cause the latent virus to reactivate, producing new viruses in the nerve cell and sending them back to the skin to cause a recurrence of the cold sore. We are investigating the role that VP16 might play during such reactivation.

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Chromatin-modifying coactivators in reactivating latent HSV The strands of DNA in which the human genome is encoded are much longer than the diameter of a typical human cell.

To help fit the DNA into the cell, cellular DNA is typically packaged as chromatin, in which the DNA is wrapped around “spools” of histone proteins and then further arranged into higher-order structures. When genes need to be expressed, they are partially unpackaged by the action of chromatin-modifying coactivator proteins, which either chemically change the histone proteins or physically slide the histones along the DNA. Transcriptional activator proteins such as VP16 can recruit these chromatin-modifying coactivator proteins to specific genes. We have shown that this process is not very important during lytic infection, because viral DNA in either the viral particle or the infected cell is not effectively packaged into chromatin. However, in the latent state, few viral genes are expressed because the viral DNA is packaged much like the silent genes of the host cell. Our present hypothesis is that the coactivators recruited by VP16 are required to open up chromatin as an early step in reactivating the viral genes from latency. We are currently testing this hypothesis in quiescent infections of cultured human nerve cells.

Regulating the regulatory proteins: posttranslational modification of VP16 The activity of a given protein is not only dependent on being expressed at the right time, but also on chemical modifications of that protein. Proteins can be posttranslationally modified by adding chemical groups, including phosphates, sugars, methyl or acetyl groups, lipids, or small proteins such as ubiquitin. Each of these modifications can affect how the protein folds, how it interacts with other proteins, and how stable it remains in the cell.

We know that VP16 can be phosphorylated, and we have already identified several sites within the VP16 protein where this happens. We are now testing whether these or other modifications affect how VP16 functions, either as a transcriptional activator protein or as a structural protein of the HSV-1 virion. In some experiments, we make mutations that either prevent phosphorylation or that introduce an amino acid that mimics phosphorylation, and then we test the effects of these mutations on VP16 functions. In other experiments, we inhibit the enzymes, such as kinases, that apply the modifications. We expect that this work will lead to new ideas about ways to selectively inhibit the modification of VP16 using small-molecule drugs and thereby prevent or shorten infection.

Other cellular regulators of HSV infections When HSV makes use of cellular proteins to promote its infection, infected cells take defensive measures to inhibit the virus. We would like to find ways to block the cellular proteins that support the virus or boost the cellular proteins that inhibit it. Because some of the cellular proteins that normally repair damaged DNA in the host cell become active upon HSV infection, we predicted that the DNA damage response might be important for the growth of the virus, but our experimental results don’t support that hypothesis.

We have also found that a number of protein kinases from the host cell help with early steps in the infection process.

Some of those seem to be involved in the entry of the virus into the cell; we are now testing whether chemical inhibitors of those kinases might be useful treatments for cold sores.

Other kinases seem to affect viral infection at later stages, but we don’t yet know why. We are studying each of these potential participants to find out what roles they play in virus infection and whether drugs that block these kinases might be useful in treating viral infection in humans.

RECENT PUBLICATIONS Botting, Carolyn, Xu Lu, and Steven J. Triezenberg. 2016. H2AX phosphorylation and DNA damage kinase activity are dispensable for herpes simplex virus replication. Virology Journal 13: 15.

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CENTER FOR NEURODENERATIVE SCIENCE

Patrik Brundin, M.D., Ph.D. Director

The Center’s laboratories focus on the development of novel treatments that slow or stop the progression of neurodegenerative disease, in particular Parkinson’s disease. The work revolves around three main goals: disease modification, biomarker discovery, and brain repair.

Neurons from the brain of a mouse model of Parkinson's disease.

The neurons are stained green, cell nuclei are stained blue with DAPI, and pathological inclusions of α-synuclein are stained red. (Image by Nolwen Rey of the Patrik Brundin lab.)

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LENA BRUNDIN, M.D., PH.D. Dr. Brundin earned her Ph.D. in neurobiology and her M.D. from Lund University, Sweden. In 2012, she arrived at VARI as an Associate Professor and she now holds a full-time appointment.

STAFF AUDREY ANDERSON, B.S. ELENA BRYLEVA, PH.D. STAN KRZYZANOWSKI, B.A. KEERTHI RAJAMANI, PH.D. ANALISE SAURO, B.S. DAN TUINSTRA, B.A.

STUDENTS JAMIE GRIT, B.S. SARAH KEATON, M.S.

RESEARCH INTERESTS Our laboratory works with the hypothesis that inflammation in the brain causes psychiatric symptoms such as depression and thoughts of suicide. This hypothesis stems from the fact that people with infections such as the flu often develop behavioral symptoms known as sickness behavior. We have shown that individuals who attempt suicide have high levels of inflammation and toxic products of inflammation in both the blood and the cerebrospinal fluid. The higher the degree of inflammation, the more depressed and suicidal is the affected patient. Therefore, we think that the biological mechanisms of sickness behavior and the disease traditionally known as psychiatric depression are similar, involving activation of the inflammatory response in the brain and subsequent effects on nerve cells. In a recent clinical study, we showed that when depression is successfully treated, it is associated with a significant decrease of inflammation products in the blood.

The laboratory is conducting clinical studies on patients in the Grand Rapids area and translational experiments in the laboratory at VARI, trying to detail what inflammatory mechanisms are responsible for the effects on emotion and behavior.

Such mechanisms could be the foundation of novel treatments directed at depression and suicidal behavior. The medications used today are based on principles identified about 50 years ago in the monoamine hypothesis of depression. Unfortunately, these medications help only about 50% of affected patients. If anti-inflammatory agents could be used to treat depressive and suicidal symptoms, it would be a huge step toward helping patients suffering from so-called treatment-resistant depression.

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In recent years, we have identified some infections and genetic variants associated with a higher risk for suicidal behavior and depression. Intriguingly, we found that infection with the parasite Toxoplasma gondii is associated with a sevenfold risk of attempted suicide. Some 10-20% of all Americans are infected with this parasite, which was previously considered harmless to everyone except pregnant women and immunocompromised individuals.

After initial infection by ingesting undercooked meat or contaminated soil, the parasite enters the brain and resides in nerve cells. The parasite may be the cause of subtle behavioral changes in the infected hosts, perhaps due to low-grade chronic brain inflammation. Toxoplasma infection may be treatable using current medications, but it still needs to be proved in clinical trials that such treatment has a beneficial effect on depressive and suicidal behavior.

Our laboratory is currently conducting two clinical studies in Grand Rapids. The first is a collaborative study of perinatal depression (depression during and after pregnancy) together with Pine Rest Christian Mental Health, Spectrum Health, and Michigan State University.

This multi-institutional NIH-sponsored effort, led by Dr. Brundin, investigates the possible role of inflammation of the placenta in the development of depression in pregnant women. The goals of the study are to understand the cause of depression during pregnancy, something that is currently

unknown, and to find biomarkers in the blood to identify women who are at risk for depression during and after pregnancy. If we know which women are at risk, they can be closely monitored during pregnancy for symptoms and receive prompt support and help. Finally, if we uncover the trigger of depression in pregnancy, we will be optimally positioned for developing novel therapies to target the cause of the disease.

The second clinical study is called the Heart Failure and Inflammation in Depression (HFIND) study. With Spectrum Health, we will look at the co-morbidity of cardiovascular disease and depression. We predict that patients suffering from heart failure who have a high level of inflammatory products in their blood will also suffer from depression. Our hypothesis is that if we treat the inflammation, the patient’s mood and cardiovascular status will both improve, giving a doubly beneficial effect.

RECENT PUBLICATIONS Ventorp, Filip, Cecillie Bay-Richter, Analise Sauro, Janelidze Shorena, Viktor Sjödahl Matsson, Jack Lipton, Ulrika Nordström, Åsa Westrin, and Lena Brundin. 2016. The CD44 ligand hyaluronic acid is elevated in the cerebrospinal fluid of suicide attempters and is associated with increased blood–brain barrier permeability. Journal of Affective Disorders 193: 349–354.

Bay-Richter, Cecillie, Shorena Janelidze, Analise Sauro, Richard Bucala, Jack Lipton, Tomas Deierborg, and Lena Brundin. 2015.

Behavioural and neurobiological consequences of macrophage migration inhibitory factor gene deletion in mice. Journal of Neuroinflammation 12: 163.

Bay-Richter, Cecillie, Klas R. Linderholm, Chai K. Lim, Martin Samuelsson, Lil Träskman-Bendz, Gilles J. Guillemin, Sophie Erhardt, and Lena Brundin. 2015. A role for inflammatory metabolites as modulators of the glutamate N-methyl-D-aspartate receptor in depression and suicidality. Brain, Behavior, and Immunity 43: 110–117.

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PATRIK BRUNDIN, M.D., PH.D. Dr. Brundin earned both his M.D. and Ph.D. at Lund University in Sweden. He was a professor of neuroscience at Lund before becoming a Professor and Associate Research Director of VARI in 2012.

STAFF KIM COUSINEAU, MPA SONIA GEORGE, PH.D. NOLAN REY, PH.D. EMILY SCHULTZ, B.S. JENNIFER STEINER, PH.D. TREVOR TYSON, PH.D.

ADJUNCT FACULTY WILLIAM BAER, M.D., PHARM.D.

RESEARCH INTERESTS The mission of the laboratory is to understand why Parkinson’s disease (PD) develops and to use cellular and animal PD models to discover new treatments that slow or stop disease progression. To achieve this goal, the laboratory has several ongoing, externally funded projects that study the pathogenic processes of PD. Misfolded variants of the protein α-synuclein (α-syn) are the main constituent of the protein aggregates that make up intraneuronal Lewy bodies, the major neuropathological hallmark of PD. Mutations in the gene encoding α-syn underlie rare forms of inherited PD, and these mutations trigger α-syn aggregation in neurons.

Furthermore, genetic changes that increase the amount of α-syn in neurons also result in α-syn aggregation and cause neurodegenerative disease. The molecular mechanisms that cause cell death when α-syn aggregates are poorly understood. Our team was one of the first to propose and demonstrate that intercellular propagation of abnormal α-syn protein might drive the progression of symptoms by involving more brain regions. Several of our projects aim to identify the mechanisms underlying α-syn transmission and to clarify the role of this process in PD development.

One project uses C. elegans to examine α-syn transfer and assembly into small aggregates. We have created a genetically modified worm in which α-syn coupled to a truncated fluorescent reporter protein is expressed in one set of neurons, while α-syn coupled to the remaining part of the fluorescent reporter is expressed in different neurons that are anatomically connected to the first set. When α-syn transfers from one neuron to a neighboring one, it can assemble with the α-syn protein already present, allowing the reporter protein to reconstitute and fluoresce. We are continuing to modify these worms to study the genetic pathways that control intercellular transfer and assembly of α-syn.

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We also use mouse models to evaluate α-syn transmission between brain regions. In one model, mice are first engineered to express large amounts of human α-syn protein in the nigrostriatal pathway. Immature neurons lacking human α-syn (graft) are transplanted into the striatum. After several weeks, human α-syn can be found in the transplanted neurons, which could only occur by transmission from the host brain to the grafted neurons.

We are currently defining how inflammation contributes to α-syn spread in this model. We hypothesize that microglia remove extracellular α-syn that is available for transfer from cell to cell, and that the activation of microglia (as occurs in PD) will influence the efficacy of clearance of α-syn from the extracellular space.

We have developed another mouse model based on injections of misfolded α-syn into the olfactory bulb. The loss of olfaction is an early change in PD, and the olfactory bulb has been proposed to be a starting point of Lewy body pathology, possibly due to an environmental insult. In our model, α-syn aggregate pathology gradually spreads along olfactory pathways, causing progressive olfactory deficits.

Given that α-syn transmission between cells is thought to drive PD progression, interfering with this process might slow the worsening of symptoms. We have partnered with GISMO Therapeutics Inc. and obtained funding from the Michael J. Fox Foundation to evaluate the ability of heparan sulfate proteoglycan (HSPG) inhibitors to prevent transfer of α-syn between cells in cell culture and in mouse models.

Genetic factors other than α-syn also influence PD risk. Recent genetic studies have identified the enzyme aminocarboxy-muconate semialdehyde decarboxylase (ACMSD) as a modifier of PD risk. This enzyme is a key regulator of the kynurenine pathway, which regulates neuroinflammation. The Michael J. Fox Foundation funds a joint project with Dr. Lena Brundin in which we are exploring whether overexpression of ACMSD in a rat model of PD can reduce neuroinflammation and be neuroprotective.

We are also exploring whether modulation of the mitochondrial pyruvate carrier (MPC) can protect neurons from death. We use the compound MSDC-0160, which is an MPC modulator originally developed as an anti-diabetic agent. Thanks to funding from the Cure Parkinson’s Trust UK, the Campbell Foundation, and the Spica family, we have shown that MSDC-0160 is a powerful protectant against neurodegeneration in several toxin and genetic models of PD. The compound influences the capacity of the neurons to carry out the autophagy process (a cell stress response that is altered in PD), promoting their survival, and it also inhibits neuroinflammation. Given the favorable safety profile of MSDC-0160, the drug is already under consideration for PD clinical trials, demonstrating its high potential for clinical translation.

RECENT PUBLICATIONS Brundin, Patrik, Graham Atkin, and Jennifer T. Lamberts. 2015. Basic science breaks through: new therapeutic advances in Parkinson’s disease. Movement Disorders 30(11): 1521–1527.

Nordström, Ulrika, Geneviève Beauvais, Anamitra Ghosh, Baby Chakrapani Pulikkaparambil Sasidharan, Martin Lundblad, Julia Fuchs, Rajiv L. Joshi, Jack W. Lipton, Andrew Roholt, et al. 2015. Progressive nigrostriatal terminal dysfunction and degeneration in the engrailed1 heterozygous mouse model of Parkinson’s disease. Neurobiology of Disease 73: 70–82.

Reyes, Juan F., Tomas T. Olsson, Jennifer T. Lamberts, Michael J. Devine, Tilo Kunath, and Patrik Brundin. 2015. A cell culture model for monitoring α-synuclein cell-to-cell transfer. Neurobiology of Disease 77: 266–275.

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GERHARD A. COETZEE, PH.D. Dr. Coetzee earned his Ph.D. in medical biochemistry from the University of Stellenbosch, South Africa, in 1977. He was a professor in the Departments of Urology, Microbiology, and Preventive Medicine at the Keck School of Medicine at USC before joining VARI as a Professor in November 2015.

STAFF ALIX BOOMS, B.S. KIM COUSINEAU, MPA STEVE PIERCE, PH.D. TREVOR TYSON, PH.D. J.C. VANDERSCHANS, B.S.

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RESEARCH INTERESTS Our laboratory focuses on applying genome-wide association studies (GWAS) to uncovering the roles of genetic risk variants in Parkinson’s disease. GWAS of complex phenotypes have become more powerful as the sample sizes of cases and controls have increased and meta-analyses have been employed. Additionally, as next-generation sequencing techniques have become more feasible and increasingly affordable, more single nucleotide polymorphisms (SNPs) with lower minor allele frequencies have been identified. Thus, association signals at any given locus have become increasingly complex, in large part due to the many candidate risk SNPs correlated with each other due to linkage disequilibrium (LD). Consequently, it is virtually impossible to assign functionality, let alone causality, to any given SNP at a risk locus. This dispiriting situation is only made more daunting by the unexpected finding that for many complex diseases, more than 80% of the risk SNPs are located in noncoding DNA. To address these issues, we and others have used chromatin biofeatures to inform potential functionality on the original discovery SNPs (known to the field as “index SNPs”) and their many surrogate SNPs—the former revealed by GWAS and the latter defined by the r2 of the population-specific LD.

Van Andel Research Institute | Scientific Report

VIVIANE LABRIE, PH.D. Dr. Labrie received her Ph.D. in genetics and neuroscience from the University of Toronto. She was an assistant professor at University of Toronto before joining VARI in early 2016.

STAFF AUDREY ANDERSON, B.S. JENNIFER JAKUBOWSKI, M.S.

RESEARCH INTERESTS Our goal is to gain an in-depth understanding of the primary molecular causes of Alzheimer’s disease and Parkinson’s disease in order to help develop new treatments.

Specifically, we study epigenetic involvement in these neurodegenerative illnesses.

Epigenetic marks act like a layer over the top of the DNA sequence code, controlling gene activities without changing the DNA sequence. Epigenetic marks are partially stable: i.e., they have the capacity to change in response to environmental signals and over time. This dynamic aspect is highly relevant, because advanced age is the best-known risk factor for both Alzheimer’s and Parkinson’s disease. It takes years before symptoms arise in patients, and after disease onset, the pathological features and symptoms worsen with time. We propose that aberrant epigenetic changes, accumulating with age at key genomic regions, contribute to the etiology of these diseases.

We perform genome-wide searches for epigenetic abnormalities in genomic regulatory elements such as enhancers, which affect the complex spatial and temporal expression of genes. Under the influence of regulatory elements, genes can be highly expressed in certain tissues or cell types and weakly or not at all in others. By activating or repressing regulatory elements, epigenetic marks can modify the abundance, timing, and cell-specific patterns of gene expression, which is central to healthy brain function.

By applying epigenomic and next generation sequencing–based techniques in human samples, we aim to identify epigenetically misregulated regulatory elements in Alzheimer’s and Parkinson’s disease. We also examine the interaction between DNA sequence factors (SNPs) and epigenetic marks to determine whether certain disease risk variants help coordinate epigenetic misregulation at regulatory elements.

Once the regulatory elements that bear epigenetic disturbances are identified, functional studies help to understand how these elements contribute to disease susceptibility. We look for changes in 3D chromatin conformation and in gene transcripts to identify the genes and pathways affected. We also use genome editing techniques (CRISPR-Cas9) in cell lines and mice to determine the extent to which epigenetically disrupted regulatory elements contribute to disease pathology and symptoms. Through this research we can uncover new genomic regions causally involved in Alzheimer’s and Parkinson’s disease.

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Double calcein-labeled bone cross section from a six-month-old female Hrpt2 cKO mouse.

Bones were labeled ten days apart to measure the bone formation rate. The large cortical pits outlined in green stain are due to mature osteoblasts and osteocytes lacking the Hrpt2 gene, which is required for proper regulation of transcription. Image by Casey Droscha of the Williams lab.

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JIYAN MA, PH.D. Dr. Ma earned his Ph.D. in biochemistry and molecular biology from the University of Illinois at Chicago. He was at Ohio State University from 2002 until he joined VARI in November 2013 as a Professor.

STAFF ROMANY ABSKHARON, PH.D. AUDREY ANDERSON, B.S. KATELYN BECKER, M.S. AMANDINE ROUX, PH.D. JUXIN RUAN, PH.D. FEI WANG, PH.D. XINHE WANG, PH.D.

RESEARCH INTERESTS Protein aggregation is a key pathological feature of a large group of late-onset neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases. Our overall goals are to elucidate the molecular events leading to protein misfolding in the aging central nervous system; to understand the relationship between misfolded protein aggregates and neurodegeneration; and, to develop approaches to prevent, stop, or reverse protein aggregation and neurodegeneration in these devastating diseases.

We study protein aggregates in prion diseases (transmissible spongiform encephalopathies). These are true infectious diseases that can spread from individual to individual and cause outbreaks. We have established an in vitro system to reconstitute prion infectivity with bacterially expressed prion protein plus defined cofactors. We use this system to dissect the essential components and the structural features of an infectious prion and to uncover the molecular mechanisms responsible for the prion strain and species barrier.

Recently, the concept of prions has expanded to Parkinson’s and Alzheimer’s diseases. α-Synuclein has been suggested to spread the disease pathology in a prionlike manner from a sick cell to healthy ones. We want to understand the similarities and differences between prions and amyloidogenic proteins. We are investigating cellular factors that affect α-synuclein aggregation and the connections between various α-synuclein aggregated forms, their prion-like spread, and dopaminergic neuron degeneration.

RECENT PUBLICATIONS Yu, Guohua, Ajun Deng, Wanbin Tang, Junzhi Ma, Chonggang Yuan, and Jiyan Ma. In press. Hydroxytyrosol induces phase II detoxifying enzyme expression and effectively protects dopaminergic cells against dopamine- and 6-hydroxydopamine induced cytotoxicity. Neurochemistry International.

Yu, Guohua, Huiyan Liu, Wei Zhou, Xuewei Zhu, Chao Yu, Na Wang, Yi Zhang, Ji Ma, Yulan Zhao, et al. 2015. In vivo protein targets for increased quinoprotein adduct formation in aged substantia nigra. Experimental Neurology 271: 13–24.

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DARREN J. MOORE, PH.D. Dr. Moore earned a Ph.D. in molecular neuroscience from the University of Cambridge, U.K., in 2001 in the laboratory of Piers Emson. He was at Johns Hopkins (2002–2008) and at the Swiss Federal Institute of Technology (EPFL) in Lausanne (2008–2014) before joining the VARI faculty as an Associate Professor in early 2014.

STAFF AUDREY ANDERSON, B.S. XI CHEN, PH.D. LINDSEY CUNNINGHAM, B.S. SHARIFUL ISLAM, PH.D. JEN KORDICH, M.S. NATE LEVINE, B.S. AN PHU TRAN NGUYEN, PH.D. ERIN WESTON, B.A. LESLIE WYMAN, B.S.

RESEARCH INTERESTS Our laboratory studies the molecular pathogenesis of Parkinson’s disease, with the long-term goal of developing novel, targeted, disease-modifying therapies and neuroprotective strategies. Although most cases of PD are sporadic, 5–10% of cases are inherited, with causative mutations identified in at least 12 genes. We focus on the cell biology and pathophysiology of several proteins that cause inherited PD, including the dominantly inherited leucine-rich repeat kinase 2 (LRRK2; a multi-domain protein with GTPase and kinase activity) and vacuolar protein sorting 35 ortholog (VPS35; a component of the retromer complex), as well as the recessive proteins parkin (a RINGtype E3 ubiquitin ligase) and ATP13A2 (a lysosomal P5B-type ATPase). We seek to explain the normal biological function of these proteins in the mammalian brain and the molecular mechanism(s) through which disease-associated variants produce neuronal dysfunction and eventual neurodegeneration in inherited forms of Parkinson’s.

We employ a multidisciplinary approach that combines molecular, cellular, and biochemical techniques in experimental model systems such as human cell lines, primary neuronal cultures, Saccharomyces cerevisiae, and human brain tissue. We also have developed several unique rodent-based models (transgenic, knock-out, knock-in) for mechanistic studies of these proteins.

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Some of our current projects focus on • the contribution of enzymatic activity and protein aggregation to neurodegeneration in novel, adenoviral-based, LRRK2 rodent models of PD; • neuroprotective effects of pharmacological kinase inhibition in LRRK2 rodent models; • genome-wide identification of genetic modifiers of LRRK2 toxicity in S. cerevisiae; • identification of novel GTPase effector proteins and kinase substrates for LRRK2; • the role of ArfGAP1 in mediating LRRK2-induced neurotoxic pathways; and • the development of novel rodent models of VPS35-linked PD and the pathological interactions of VPS35 with α-synuclein and LRRK2.

RECENT PUBLICATIONS Daniel, Guillaume, and Darren J. Moore. 2015. Modeling LRRK2 pathobiology in Parkinson’s disease: from yeast to rodents.

In Behavioral Neurobiology of Huntington’s Disease and Parkinson’s Disease, Hoa Huu Phuc Nguyen and M. Angela Cenci, eds.

Current Topics in Behavioral Neurosciences series, Vol. 22. Berlin: Springer Verlag, pp. 331–368.

Daniel, Guillaume, Alessandra Musso, Elpida Tsika, Aris Fiser, Liliane Glauser, Olga Pletnikova, Bernard L. Schneider, and Darren J. Moore. 2015. α-Synuclein-induced dopaminergic neurodegeneration in a rat model of Parkinson’s disease occurs independent of ATP13A2 (PARK9). Neurobiology of Disease 73: 229–243.

Tsika, Elpida, An Phu Tran Nguyen, Julien Dusonchet, Philippe Colin, Bernard L. Schneider, and Darren J. Moore. 2015.

Adenoviral-mediated expression of G2019S LRRK2 induces striatal pathology in a kinase-dependent manner in a rat model of Parkinson’s disease. Neurobiology of Disease 77: 49–61.

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JEREMY VAN RAAMSDONK, PH.D. Dr. Van Raamsdonk completed a Ph.D. in medical genetics at the University of British Columbia in 2005. He joined VARI as an Assistant Professor in 2012.

STAFF AUDREY ANDERSON, B.S. DYLAN DUES, B.S. MEGAN SENCHUK, PH.D.

STUDENTS JASON COOPER, B.S. EMILY MACHIELA, B.S.

RESEARCH INTERESTS As the average human life span continues to increase, the likelihood of an individual developing a neurodegenerative disease also increases. Thus, there is a need to understand the aging process and its role in the development of age-onset disorders such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease. Our research is focused on gaining insight into the aging process and the pathogenesis of such diseases. Beyond benefit to the individual, this work has potential benefits for society by decreasing health care costs and helping to maintain productivity and independence to a later age.

The free radical theory of aging (FRTA) proposes that aging results from the accumulation of oxidative damage caused by reactive oxygen species (ROS) generated during normal metabolism. However, recent work in the worm Caenorhabditis elegans has indicated that the relationship between ROS and life span is more complex.

Superoxide dismutase (SOD) is an enzyme that decreases the levels of ROS, but the deletion of SOD genes (individually or in combination) does not decrease life span. In fact, quintuple-mutant worms lacking all five sod genes live as long as wild-type worms despite a markedly increased sensitivity to oxidative stress. Thus, it appears that while oxidative damage increases with age, it does not cause aging, and the result with the quintuple mutants suggests a balance between the pro-survival signaling and the toxic effects of superoxide.

Recent evidence suggests that increased levels of superoxide can act as a pro-survival signal that leads to increased longevity. This is demonstrated by life-span increases following the deletion of the mitochondrial gene sod-2 and the treatment of wild-type worms with the superoxide generator paraquat. Thus, one of the main goals of this work is to uncover the mechanism by which superoxide-mediated pro-survival signaling leads to increased longevity. Using a combination of genetic mutants and RNA interference, we explore how increases in superoxide trigger the signal, how the signal is transmitted, and which of the changes the signal introduces lead to increased life span.

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The role of aging in Parkinson’s disease The greatest risk factor for developing Parkinson’s disease (PD) is advanced age. Even individuals with the inherited forms of PD live decades without exhibiting symptoms or neuronal loss, despite the fact that the disease-causing mutation is already present at birth. This suggests that changes taking place during normal aging make cells more susceptible to the mutations implicated in PD. This conclusion is supported by the fact that the onset of the disease in animal models is proportional to the life span of the organism and is not related to chronological time.

Moreover, several changes known to take place during the aging process have been shown to affect functions involved in the pathogenesis of PD.

crosses to generate double mutants and will use RNA interference via feeding to specifically knock down genes of interest. The health of the resulting worms will be compared with that of control worms to determine whether the aging gene affects the disease-like abnormalities. By examining the role of aging in PD, this project will provide new insight into the mechanism underlying the disease.

This knowledge will provide novel therapeutic targets that may lead to an effective treatment.

This work will be conducted using C. elegans PD models, because these worms have orthologs to almost all of the genes implicated in PD, including PARK2 (pdr-1), PINK-1 (pink-1), LRRK-2 (lrk-1), DJ-1 (djr-1.1,-1.2), UCHL-1 (ubh-1), ATP13A2 (catp-6), VPS-35 (vps-35), and GBA (gba-1-4).

Several worm models of PD have been developed, including chemical models such as 6-OHDA and MPTP transgenic worms expressing α-synuclein; transgenic worms expressing mutant LRRK2; and deletion mutants of pdr-1, pink-1, djr-1.1, and catp-6. These models exhibit a number of PD-related phenotypes, including aggregation of α-synuclein, decreased mobility, decreased adaption to food (a response mediated by dopamine neurons), and, importantly, degeneration of dopaminergic neurons. The main goals of this work will be 1) to determine whether genes that extend life span are beneficial in the treatment of worm models of PD and 2) to determine whether processes that show decreased function with age specifically exacerbate PD-like features. We will use genetic

RECENT PUBLICATIONS Cooper, Jason F., Dylan J. Dues, Katie K. Spielbauer, Emily Machiela, Megan M. Senchuk, and Jeremy M. Van Raamsdonk. 2015.

Delaying aging is neuroprotective in Parkinson’s disease: a genetic analysis in C. elegans models. npj Parkinson’s Disease 1: 15022.

Schaar, Claire E., Dylan J. Dues, Katie K. Spielbauer, Emily Machiela, Jason F. Cooper, Megan Senchuk, Siegfried Hekimi, and Jeremy M. Van Raamsdonk. 2015. Mitochondrial and cytoplasmic ROS have opposing effects on life span. PLoS Genetics 11(2): e1004972.

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CORE TECHNOLOGIES AND SERVICES

Scott D. Jewell, Ph.D. Director

Staining of mouse bone to visualize bone marrow (red cells), solid bone with embedded osteocytes (brown areas) and region of actively growing new bone (blue-green). Image by Alexis Bergsma.

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VIVARIUM AND TRANSGENICS CORE

BRYN EAGLESON, M.S., LATG Ms. Eagleson earned an M.S. degree in laboratory animal science from Drexel University’s College of Medicine. She worked for many years at the National Cancer Institute’s Frederick Cancer Research and Development Center in Maryland before joining VARI as the Director of Vivarium and Transgenics in 1999.

STAFF MEGAN BRIGGS, B.S. THOMAS DINGMAN NICHOLAS GETZ, B.S. NAOMI GRABER AUDRA GUIKEMA, B.S. TRISTAN KEMPSTON, B.S. MICHAEL KUBIK TINA MERINGA, A.A. DAVID MONSMA, PH.D. JANELLE POST, B.ED. MALISTA POWERS MATHEW RACKHAM LISA RAMSEY, A.S., LVT ADAM RAPP, B.S. APRIL STAFFORD, B.S. YANLI SU, A.M.A.T.

SERVICES The goal of the VARI Vivarium and Transgenics core is to develop, provide, and maintain high-quality mouse modeling services. The vivarium is a state-of-the-art facility that includes a high-level containment barrier. Van Andel Research Institute is an AAALACaccredited institution, most recently reaccredited in September 2013. All procedures are conducted according to the Guide for the Care and Use of Laboratory Animals.

The staff provides rederivation, surgery, dissection, necropsy, breeding, weaning, tail biopsies, sperm and embryo cryopreservation, animal data management, project management, and health-status monitoring. Transgenic mouse models are produced on request for project-specific needs. The creation of gene-targeted mice using the CRISPR/Cas9 systems has recently been implemented. We also provide therapeutic testing and preclinical model development services. Projects include pharmacological testing, target validation testing, patient-derived xenograft (PDX) development, orthotopic engraftment model development, and subcutaneous xenograft/allograft model development.

AURORA THOMS WILLIAM WEAVER, B.S.

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PATHOLOGY AND BIOREPOSITORY CORE

SCOTT D. JEWELL, PH.D. Dr. Jewell earned his Master’s and Ph.D. degrees in experimental pathology and immunology from The Ohio State University. He served there as director of the Human Tissue Resource Network in the Department of Pathology. He joined VARI in 2010 as a Professor, as well as Director of the Program for Technologies and Cores and of the Program for Biospecimen Science.

STAFF BREE BERGHUIS, B.S. ALEX BLANSKI, B.S. ERIC COLLINS, B.S. MELISSA DEHOLLANDER, M.B.A., B.S. BRIANNE DOCTER, M.S. KRISTIN FEENSTRA, B.S. PHIL HARBACH, M.S. MEGHAN HODGES, B.S. GALEN HOSTETTER, M.D. ERIC HUDSON, B.S. CARRIE JOYNT, B.S., HT JULIE KOEMAN, B.S., CG(ASCP)CM ROB MONTROY, B.S. LORI MOON, M.B.A. CHELSEA PETERSON, B.S. DANIEL ROHRER, M.B.A., B.S. LISA TURNER, B.S., HT, QIHC(ASCP) DANA VALLEY, B.A., CPIA ANTHONY WATKINS, A.S.

SERVICES The Pathology and Biorepository Core integrates anatomic pathology expertise with biorepository and biospecimen science in order to assist in VARI’s research. We build upon historical strengths in standard histology, microscopy, and biobanking, and we use novel technologies to test and apply best practices in biospecimen science. The pathology discipline provides complementary emphasis on high-quality biospecimens and interpretable results with which to validate experimental models and extend them to clinical samples, thereby advancing our common translational mission.

Dr. Jewell, with his expertise in experimental pathology, immunology, and biobanking, and Dr. Hostetter, who is board-certified in anatomic pathology, together provide a wide range of expertise to the VARI laboratories. Currently, they are studying the effects of preanalytical variables in tissue collection and transport on the integrity of downstream analytes. The assessment of tumor suppressors and immunomodulators in tumor tissues and the application of genomic and epigenomic assays for biospecimens are among the services provided by the core. The VARI biorepository is nationally and internationally recognized, serving as the NCI Comprehensive Biospecimen Resource for the Cancer Human Biobank (caHUB). In 2015, it was designated as the Biorepository Core Resource for the NCI Clinical Proteomic and Tumor Analysis Consortium (CPTAC) and as the biorepository for the Tuberous Sclerosis Alliance.

In addition, we are moving into our sixth year of providing biorepository services for the Multiple Myeloma Research Foundation’s CoMMpass Study. The biorepository is serving the VARI/SU2C consortium for epigenetics clinical trials biobanking, collaborating with Drs. Jones and Baylin. Dr. Jewell serves as a committee member for the College of American Pathologist (CAP) Biorepository Accreditation Program (BAP).

The VARI biorepository has been a CAP BAP-accredited biorepository since 2012 and was reaccredited in 2015.

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Pathology Core services

Biorepository Core services

• Histology and diagnostic tissue services, including morphology, immunohistochemistry, in situ hybridization, and multiplex fluorescent IHC assays

• Biobanking services for VARI investigators, the National Cancer Institute, the Multiple Myeloma Research Foundation, and the Tuberous Sclerosis Alliance

• Pathology review and annotation of clinical samples from VARI’s prospective and retrospective tissue collections

• Biospecimen kit construction, shipping, and tracking

• Design and construction of tissue microarrays • Digital imaging and spectral microscopy coupled with image analysis tools

• Clinical trials biobanking coordination • Quality management program

• Cell fractionation and biospecimen processing • Laser capture microdissection • Cytogenetics • Ion Torrent genomic technology

RECENT PUBLICATIONS The GTEx Consortium. 2015. The Genotype-Tissue Expression (GTEx) analysis: multitissue gene regulation in humans. Science 348(6235): 648–660.

Melé, Marta, Pedro G. Ferreira, Ferran Reverter, David S. DeLuca, Jean Monlong, Michael Sammeth, Taylor R. Young, Jakob M Goldmann, et al. 2015. The human transcriptome across tissues and individuals. Science 348(6235): 660–665.

Rivas, Manuel A,. Matti Pirinen, Donald F. Conrad, Monkol Lek, Emily K. Tsang, Konrad J. Karczewski, Julian B. Maller, Kimberly R. Kukurba, et al. 2015. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348(6235): 666-669.

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FLOW CYTOMETRY CORE

HEATHER SCHUMACHER, B.S., MT (ASCP) Heather Schumacher has a B.S. in medical technology from Ferris State University and is certified by the American Society of Clinical Pathologists as a generalist (MT). She has over 12 years of experience in hematology/flow cytometry and is proficient on three major vendor platforms, including eight different flow cytometers.

She joined VARI as the Flow Cytometry Core manager in 2012.

SERVICES The core provides comprehensive flow cytometry analysis and sorting services in support of VARI research. Additional services include assistance with protocol development and training in data analysis. Flow cytometry services are provided using a Beckman Coulter MoFlo Astrios and Beckman Coulter CytoFLEX S. Other equipment for blood analysis includes a VetScan instrument, a VetScan HMII, and a Shandon Cytospin 3.

CORE TECHNOLOGIES AND SERVICES

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BIOINFORMATICS AND BIOSTATISTICS CORE

MARY E. WINN, PH.D. Dr. Winn earned her Ph.D. from the University of California, San Diego.

She became VARI’s Bioinformatics and Biostatistics Core manager in 2013.

STAFF MEGAN BOWMAN, PH.D. BENJAMIN JOHNSON, PH.D. ZACHARY MADAJ, M.S.

STUDENTS MICHELE GORT MARGARET KLEIN ZACHARY WEBER NICOLE ZOLMAN

SERVICES Established in April 2013, the Bioinformatics and Biostatistics Core serves the analytical needs of VARI by providing efficient, high-quality computational and statistical support for VARI research labs wrestling with the analysis and interpretation of data.

The broader mission of the BBC is to strengthen and maintain bioinformatics and biostatistics techniques across all VARI laboratories. The BBC maintains sequencing pipelines for processing and analyzing genomic data sets; provides access to a variety of proprietary and open-source resources; supports the design, planning, conduct, analysis, and reporting of research; and more.

We provide statistical consulting; experimental design (including research proposal development, sample size determination, and randomization procedures); analysis, interpretation, and presentation of small and large data sets; manuscript preparation and data deposition; genomic variant detection and annotation; transcript/isoform differential expression; and DNA copy number determination. We also perform systems-level analysis such as gene-set or network-based analysis. We support the greater educational mission of the Institute, helping students and staff develop an analytic approach and skills in experimental design through seminars, lectures, and workshops.

The BBC maintains external collaborations with various academic and industrial partners, including Michigan State University and Henry Ford Health Systems.

RECENT PUBLICATIONS Osgood, Christy L., Nichole Maloney, Christopher G. Kidd, Susan Kitchen-Goosen, Laura Segars, Meti Gebregiorgis, Girma M. Woldemichael, Min He, Savita Sankar, et al. In press. Identification of mithramycin analogs with improved targeting of the EWSFLI1 transcription factor. Clinical Cancer Research.

Sameni, Mansoureh, Elizabeth A. Tovar, Curt Essenburg, Anita Chalasanik, Erik S. Linklater, Andrew Borgman, David M. Cherba, Arulselvi Anbalagan, Mary E. Winn, et al. 2016. Cabozantinib (XL184) inhibits growth and invasion of preclinical TNBC models.

Clinical Cancer Research 22(4): 923–934.

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CONFOCAL MICROSCOPY AND QUANTITATIVE IMAGING CORE

STAFF KRISTIN FEENSTRA, B.S. ERIC HUDSON, B.S. JEFFREY KORDOWER, PH.D. ANDERSON PECK, M.S.E.

SERVICES Established in October 2013, the core provides optical imaging services for Van Andel Research Institute and collaborating institutions, as well as the expertise and analytical tools to use them effectively. Our services include live-cell imaging and biosensor studies of cell signaling in cancer and brain tissue; the measurement of gene expression, protein transport, and protein-protein interactions; and 3D reconstruction of large fluorescent structures in tissue blocks. Training in these techniques and in the management of the data obtained is provided. We have two scanning confocal microscopes, a Nikon A1-RSi with coded stage and a Zeiss 510 META-MP instrument. The core has collaborations with academic partners at nearby universities, including Michigan State University and Western Michigan University.

The core allows users of all experience levels to perform quantitative research at or exceeding the professional standards of their field. We have implemented a comprehensive solution for the collection, management, and processing of all imaging data for researchers at VARI. A suite of commercial and open-source image analysis programs on a powerful Z620 workstation is available. Options include deconvolution and complex 3D visualization (Huygens Professional), neuron tracing (IMARIS Suite), high-throughput phenotype quantitation, machine learning (CellProfiler and CPAnalyst), sophisticated mathematical analysis options (MATLAB), and image manipulation or figure preparation software such as Fiji/Image J, Photoshop, and GIMP. The core has also added a PerkinElmer Vectra, a multi-modal, automated imaging system for scanning tissue sections and acquiring multispectral images. IT supports workflows including whole-slide scanning, annotation, and review through a simple, intuitive interface.

It includes an operator-centric system for performing whole-slide scans and acquiring multispectral images in regions of interest. Regions for image acquisition can be selected using inForm Tissue Finder software for fully automated operation.

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SMALL-ANIMAL IMAGING FACILITY

STAFF ANDERSON PECK, M.S.E.

SERVICES The Small-Animal Imaging Facility focuses on the development of preclinical imaging technologies that offer anatomic and functional information to biomedical investigators. We also aim to develop imaging technologies capable of monitoring organ/tissue activity at the molecular level in order to advance clinical applications such as early detection and staging of cancer. By combining new tracers, imaging analysis, and genomic information, we are assisting investigators in non-invasive imaging technologies for translational research. Our technologies include digital X-ray, high-resolution microCT, microSPECT/CT, microPET/CT, micro-ultrasound, optical imaging, radiochemistry, and custom tracers. Our comprehensive facility management system was designed to provide real-time analysis capabilities for imaging studies. This system allows researchers to group mice based on results from previous time points, enhancing the study’s overall quality and making effective use of resources.

We have developed 1) an automated system to quantify tail residual activity for correction of standard uptake value–related calculations in PET and SPECT imaging; 2) a QA/QC protocol to evaluate whether an optical imager with certain characteristics is adequate for Cherenkov luminescence imaging acquisition; 3) an in vivo, non-invasive, high-resolution imaging method for Kupffer cell migration in response to early liver metastasis; and 4) a method to reduce respiratory artifacts in microCT imaging by using a high-frequency oscillatory ventilation system.

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AWARDS FOR SCIENTIFIC ACHIEVEMENT

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JAY VAN ANDEL AWARD FOR OUTSTANDING ACHIEVEMENT IN PARKINSON’S DISEASE RESEARCH

This award was established to honor distinguished researchers in the field of Parkinson’s disease and is named after Van Andel Institute founder Jay Van Andel, who passed away in 2004 after a long struggle with the disease. Awardees are selected on the basis of their scientific achievements and renown as a leader in Parkinson’s research or in research on closely related neurodegenerative disorders.

2015 Award Recipients

Robert Nussbaum, M.D., FACP, FACMG Maria Grazia Spillantini, Ph.D., FMedSci, FRS Dr. Nussbaum was the senior author on a 1997 Science paper that first linked a mutation in the gene that codes for α-synuclein to an inherited form of Parkinson’s disease. Later that year, Dr. Spillantini and her colleagues published a paper in Nature that identified α-synuclein as the main component of Lewy bodies in all forms of Parkinson’s, not just inherited cases. These discoveries were groundbreaking, opening a new, crucial area of research into the role of this protein in Parkinson’s disease. Dr. Nussbaum holds the Holly Smith Distinguished Professorship in Science and Medicine and is Chief of the Division of Genomic Medicine at the University of California, San Francisco. Dr. Spillantini is a Professor of molecular neurology at the University of Cambridge’s Department of Clinical Neuroscience.

Drs. Spillanti and Nussbaum at the award ceremony.

Andrew John Lees, M.D., FRCP, FMedSci 2014 Alim-Louis Benabid, M.D., Ph.D. 2013 Andrew Singleton, Ph.D. 2012

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Prior Recipients

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HAN-MO KOO MEMORIAL AWARD

Dr. Han-Mo Koo joined the Van Andel Research Institute in 1999 as one of its founding investigators. He established important projects to identify genetic targets for anticancer drugs against melanoma and pancreatic cancer, and he worked tirelessly to contribute to the Institute's mission to improve health and enhance lives. In May 2004, Dr. Koo passed away following a six-month battle with cancer. To honor his memory and scientific contributions, the Han-Mo Koo Memorial Award and Lecture was established in 2010. Awardees are selected based upon their scientific achievements and their contributions to human health and research that align with the scientific legacy of Han-Mo Koo.

2015 Award Recipient

Eric S. Lander, Ph.D. Dr. Eric Lander is founding director of the Broad Institute, Professor of biology at Massachusetts Institute of Technology, and Professor of systems biology at Harvard Medical School.

As one of the principal leaders of the Human Genome Project, Lander and his colleagues created many of the key tools for the study of human genomics and have applied these tools in pioneering new ways to understand cancer, diabetes, and inflammatory diseases. In 2009, President Obama appointed him to co-chair the President’s Council of Advisors on Science and Technology. He is a member of the U.S. National Academy of Sciences, among many other honors. Dr. Lander earned his B.A. in mathematics from Princeton University and his Ph.D. in mathematics from Oxford University as a Rhodes Scholar.

Dr. Lander delivering his Dr. Han-Mo Koo Award address.

Prior Recipients

Frank P. McCormick, Ph.D., F.R.S 2013 Phillip A. Sharp, Ph.D. 2012

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EDUCATIONAL AND TRAINING PROGRAMS

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VAN ANDEL INSTITUTE GRADUATE SCHOOL

Steven J. Triezenberg, Ph.D. President and Dean

Van Andel Institute Graduate School develops future leaders in biomedical research through an intense, problem-focused Ph.D. degree in cellular, molecular, and genetic biology. VAIGS has created an innovative curriculum that guides doctoral students to think and act like research leaders through problem-based learning. In doing so, students develop key skills of finding and evaluating scientific knowledge and of designing experimental approaches to newly arising questions. We also foster the development of leadership skills and professional behavior, and we seek to integrate graduate students into the professional networks and culture of science. VAIGS currently has 23 students and seeks to admit five to six students each year. VAIGS alumni have gone on to postdoctoral positions at leading biomedical research institutions throughout the United States. VAIGS is accredited by the Higher Learning Commission (www.hlcommission.org; 1-800-621-7440).

Julie Davis Turner, Ph.D., Associate Dean Kathy Bentley, B.S. Patty Farrell-Cole, Ph.D. Michelle Love, M.A. Christy Mayo, M.A. Nancy Schaperkotter, A.M., LCSW, CEAP Kristie Vanderhoof, B.A.

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POSTDOCTORAL FELLOWSHIP PROGRAM Van Andel Research Institute provides postdoctoral training opportunities to advance the knowledge and research experience of new Ph.D.s while at the same time supporting our research endeavors. Each fellow is assigned to a scientific investigator who oversees the progress and direction of research. Fellows who worked in VARI laboratories in late 2015 and in 2016 are listed below.

Romany Abskharon

Xiangqi (Neil) Meng

Laura Tarnawski

Xi Chen

An Phu Tran Nguyen

Rochelle Tiedemann

Evan Cornett

Hitoshi Otani

Elizabeth Tovar

Paul Daft

Kuntal Pal

Laura Winkler

Kristin Dittenhafer-Reed

Keerthi Thirtamara Rajamani

Jiyoung Yu

Sourik Ganguly

Nolwen Rey

Tie-Bo Zeng

Shariful Islam

Amandine Roux

Wanding Zhou

Yanyong Kang

Juxin Ruan

Virje University, Egypt VARI mentor: Jiyan Ma

University of Liverpool, UK VARI mentor: Darren Moore

University of Central Florida, Orlando VARI mentor: Scott Rothbart

University of Alabama, Tuscaloosa VARI mentor: Xiaohong Li

University of Wisconsin, Madison VARI mentor: Jeff MacKeigan

University of Kentucky, Lexington VARI mentor: Cindy Miranti/Xiaohong Li

Max Plank Institute for Heart and Lung Research, Germany VARI mentor: Darren Moore

Institute of Biophysics, Chinese Academy of Sciences VARI mentor: Eric Xu

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Sun Yat-sen University, China VARI mentor: Xiaohong Li

Universität Tübingen, Germany VARI mentor: Darren Moore

Tokyo Medical and Dental University VARI mentor: Peter Jones

National University of Singapore VARI mentor: Eric Xu

The Ohio State University, Columbus VARI mentor: Lena Brundin

University of Lyon, France VARI mentor: Patrik Brundin

University of Pierre and Marie Currie, France VARI mentor: Jiyan Ma

Shanghai Institute for Biological Sciences, Chinese Academy of Sciences VARI mentor: Jiyan Ma

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Lund University, Sweden VARI mentor: Stefan Jovinge

Georgia Reagents University, Augusta VARI mentor: Peter Jones/Scott Rothbart

Wayne State University, Detroit, Michigan VARI mentor: Carrie Graveel

University of Wisconsin, Madison VARI mentor: Stefan Jovinge

Seoul National University, South Korea VARI mentor: Gerd Pfeifer

Harbin Institute of Technology, China VARI mentor: Prioska Szabó

Rice University, Houston, Texas VARI mentor: Peter Jones/Peter Laird/ Hui Shen

INTERNSHIP PROGRAMS The Summer Internship Programs are designed to provide undergraduate college students opportunities to be mentored by professionals in their chosen research field, to become familiar with the use of state-of-the-art scientific equipment and technology, and to learn valuable interpersonal and presentation skills. The goal of these programs is to expose aspiring researchers and clinicians to exciting advances in biomedical sciences that will help define their career paths. Internships last 10 weeks, with two cohorts per summer.

Since 2001, hundreds of VARI internships have been generously supported through the Frederik and Lena Meijer Summer Internship Program.

Meijer interns are noted in the listing below by an asterisk (*).

Van Andel Education Institute also partners with United Negro College Fund (UNCF) to match students interested in biomedical research careers with summer research internships at VARI.

2015 UNDERGRADUATE INTERNS Amherst College, Amherst, Massachusetts Michael Bessey (Williams)

Aquinas College, Grand Rapids, Michigan

Hannah Jablonski (D, C, and M) Caitlin Rietsema (D, C, and M)

Calvin College, Grand Rapids, Michigan

Amy Bohner (Graduate School) Rachel Buikema (Willliams) Michael DeMeester (Laird) Matthew Hollowell (Wu) John Lensing (Williams) Megan VanBaren (MacKeigan)

Central Michigan University, Mount Pleasant Alyssa Shepard (Sempere)

Clemson University, Clemson, South Carolina Leland Dunwoodie (Haab)

Dillard University, New Orleans, Louisiana

Latisha Franklin, (Duesbery)

Ferris State University, Big Rapids, Michigan

Shayna Donoghue (Sempere) Luke Gillespie (Facilities)

Grand Valley State University, Allendale, Michigan Daniela Gomez (Sempere) Margaret Klein (Winn) Austin Meadows (Li) Madison Schmidtmann (Glassware/media) Megan Thompson (Duesbery)

Hope College, Holland, Michigan

Zachary DeBruine (Melcher) Claire Schaar (Van Raamsdonk) Philip Versluis (Rothbart)

Kalamazoo College, Kalamazoo, Michigan

Reid Blanchett (Triezenberg)

Michigan State University, East Lansing

William Hanrahan (MacKeigan) Joseph Kretowicz (Haab) Jack Pfeiffer (Yang)

Purdue University, Lafayette, Indiana Eric Li (Xu)

University of Michigan, Ann Arbor

Christian Cavacece (Melcher) John Cooper (Ma) Kellie Spahr (Miranti)

University of Pennsylvania, Phildelphia

Elizabeth Goodspeed (P. Brundin)

Washington University in St. Louis, Missouri Saranya Sundaram (Moore)

Wayne State University, Detroit, Michigan Ethan Cutler (Library)

Western Michigan University, Kalamazoo Nathan Morgan (Logistics)

Wheaton College, Wheaton, Illinois

Devon Jeltema (Jewell)

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2015 Summer Interns Kneeling, left to right: Cavacece, Versluis, Gillespie, Morgan, Meadows, Dunwoodie, Shepard, Cutler. Standing, left to right: Lensing, DeBruin, Hanrahan, DeMeester, Bohner, Kretowicz, Goodspeed, Li, Sundaram, Klein, Pfeiffer, Rietsema, Schmidtmann, Blanchett, Spahr, Cooper, Buikema, Schaar, VanBaren, Jeltema, Bessey, Donoghue, Thompson, Hollowell, Franklin

Academy of Modern Engineering The Academy of Modern Engineering (AME) is one of four specialized programs within Innovation Central High School administered by Grand Rapids Public Schools. It provides selected high school students who plan to major in science or engineering the opportunity to work in a research laboratory. Since 2000, VARI has mentored 55 students in this program and its predecessor, GRAPCEP.

The 2015 AME interns, Vanessa Baraza and Yesenia Barnel.

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VARI AND JAY VAN ANDEL SEMINAR SERIES January 2015 Tiago Fleming Outeiro, University Medical Center, Göttingen, Germany “From the baker to the bedside: unraveling the molecular basis of neurodegeneration” February Steven Finkbeiner, Gladstone Institute of Neurological Disease, University of California, San Francisco “Unraveling mechanisms of neurodegeneration with genomics, single-cell analysis, and human iPSCs models” March Nora M. Navone, M.D. Anderson Cancer Center, Houston, Texas “Prostate cancer cell–stromal cell crosstalk via FGFR1 mediates antitumor activity of dovitinib in bone metastases” Jie Shen, Harvard Medical School, Boston, Massachusetts “Insights into Alzheimer's and Parkinson's diseases from genetic approaches”

April Robert Stroud, University of California, San Francisco “Wiggle wiggle, not a trickle: how do transmembrane transporters work”

September Chuan He, University of Chicago “Reversible RNA and DNA methylation in gene expression regulation”

Gerry Coetzee, USC Norris Comprehensive Cancer Center, Los Angeles “Unlocking the secrets of enhancer biology with GWAS”

October Yifan Cheng, Howard Hughes Medical Institute, University of California, San Francisco “Structures of TRP ion channels by single particle cryo-EM: from blob-ology to atomic structures”

May Michael F. Clarke, Stanford Institute, Stanford, California “Degenerative diseases and cancer: the yin and yang of stem cells” Matthew J. Farrer, University of British Columbia, Vancouver “Parkinson's disease: pathology, ontology, and etiology” June Douglas R. Spitz, University of Iowa, Iowa City “Metabolic oxidative stress in cancer biology and therapy: from the bench to the bedside” August Amy Manning-Bog, Sangamo BioSciences, Inc., Richmond, California “Unsuspected pathogenetic interactions in parkinsonism”

Anne C. Ferguson-Smith, University of Cambridge, England “Parental origin effects and the epigenetic control of genome function” November Li-Huei Tsai, Picower Institute for Learning and Memory, Cambridge, Massachusetts “Epigenetic mechanisms of neuronal gene expression and memory” December Yang Shi, Harvard Medical School, Boston Children’s Hospital “Histone methylation regulation, recognition, and link to human disease” Ali Shilatifard, Northwestern University, Evanston, Illinois “Enhancer malfunction in cancer” 79

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ORGANIZATION

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David L. Van Andel Chairman and CEO, Van Andel Institute

VARI Board of Trustees

Board of Scientific Advisors

The Board of Scientific Advisors advises the CEO and the Board of Trustees, providing recommendations and suggestions regarding the overall goals and scientific direction of VARI. The members are

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David L. Van Andel, Chairman and CEO Tom R. DeMeester, M.D. James B. Fahner, M.D. Michelle Le Beau, Ph.D. George F. Vande Woude, Ph.D. Ralph Weichselbaum, M.D. Max Wicha, M.D.

Van Andel Research Institute | Scientific Report

Michael S. Brown, M.D., Chairman Richard Axel, M.D. Joseph L. Goldstein, M.D. Tony Hunter, Ph.D. Phillip A. Sharp, Ph.D.

Office of the Chief Scientific Officer Van Andel Research Institute

Peter A. Jones, Ph.D., D.Sc. Chief Scientific Officer

Patrick Brundin, M.D., Ph.D. Associate Director

Staff

External Scientific Advisory Board

Aubrie Bruinsma, B.A., Events and Meetings Coordinator David Cabrera, M.S., Chief of Staff Kayla Habermehl, B.A., B.S., Science Communications Speciaist Jennifer Holtrop, B.S., Scientific Administrator Chelsea John, B.S., Research Department Administrator David Nadziejka, M.S., Science Editor Aaron Patrick, B.S., Research Operations Supervisor Bonnie Petersen, Executive Assistant Beth Resau, B.A., M.B.A., Events and Meetings SupervisorDaniel Rogers, B.S., CCRC, CIP, Clinical Research Administrator Ann Schoen, Senior Executive Assistant

Tony Hunter, Ph.D. Marie-Francoise Chesselet, M.D., Ph.D. Howard J. Federoff, M.D., Ph.D. Theresa Guise, M.D. Kristian Helin, Ph.D. Rudolf Jaenisch, Ph.D. Max S. Wicha, M.D.

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ADMINISTRATIVE ORGANIZATION The departments listed below provide administrative support to both the Van Andel Research Institute and the Van Andel Education Institute.

Executive

Facilities

David Van Andel, Chairman and CEO Christy Goss, Senior Executive Assistant

Samuel Pinto, Director Tim Bachinski Amber Baldwin Maria Bercerra-Mota Schuyler Black Rob Cairns Marilouise Carlson Jeff Cooling Deb Dale Jason Dawes Katherine Delacruz Lupe Delgado Ken DeYoung Art Dorsey Michelle Fraizer Kristi Gentry Hodilia Jimenez Matthew Jump Hannah Kaiserlian Todd Katerburg Tracy Lewis

Operations Jana Hall, Ph.D., M.B.A., Chief Operations Officer Ann Schoen, Senior Executive Assistant

Legal David Whitescarver, Vice President and Chief Legal Officer

Business Development and Extramural Administration Thomas DeKoning Robert Garces, Ph.D.

Emily Koster Andrea Poma, M.P.A.

Compliance Gwenn Oki, Director Jessica Austin Ryan Burgos Angie Jason

Laura Kersjies Dave Lutkenhoff

Finance

Communications and Marketing Beth Hinshaw Hall, Director Frank Brenner Rachel Harden

David Jackiewicz

Development Patrick Placzkowski, Director Hannah Acosta Kim Bosko Aubrie Bruinsma Sarah Murphy Lamb

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Lewis Lipsey Merriebelle Martinez Dave Marvin Samanthat Meekie Joan Morrison Anjayala Newland Jamison Pate Karen Pittman Amber Ritsema Tyler Rosel-Pieper Jose Santos Amber Smith Ebony Taylor Amber TenBrink Rich Ulrich Jeff Vadeboncouer Pete Van Conant Erik Varga Jeff Wilbourn LeeAnn Winger

Teresa Marchetti Ashley Owens Megan Schroeder Angie Stumpo

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Timothy Myers, Vice President and Chief Financial Officer Katie Helder, VAI/VAEI Finance Director Rich Herrick, VARI Finance Director Kathryn Bishop Mark Denhof Sandi Dulmes Nate Gras Tess Kittridge Angie Lawrence Jessica Parker Leah Postema Susan Raymond Cindy Turner

Human Resources

Security

Linda Zarzecki, Vice President Ryan DeCaire Pamela Murray Deirdre Griffin John Shereda Eric Miller

Kevin Denhof, CPP, Director Jonathan Fey Adam Garvey Katee McCarthy

Information Technology

Sponsored Research

Bryon Campbell, Ph.D., Chief Information Officer David Drolett, Manager Jason Kotecki  Candy Wilkerson, Manager Ben Lewitt Bill Baillod Deb Marshall Terry Ballard Randy Mathieu Tom Barney Matt McFarlane Phil Bott Bruce Racalla James Clinthorne Thad Roelofs Dan DeVries Michael Stolsky Sean Haak Lisa VanDyk Kenneth Hoekman

David Ross, Director Marilyn Becker Kathy Koehler Sara O’Neal

Brian Nix Andriana Vincent

Michele Quick Heather Wells Barbara Wygant

Contract Support Caralee Lane, Librarian (Grand Valley State University)

Innovation and Collaboration Jerry Callahan, Ph.D., M.B.A., I&C Officer Norma Torres

Investments Office Kathy Vogelsang, Chief Investment Officer Ted Heilman Turner Novak Austin Way Karla Mysels

Materials Management Richard M. Disbrow, C.P.M., Director Matt Donahue Cheryl Poole Tracey Farney Bob Sadowski Heather Frazee Kyle Sloan Chris Kutschinski Kim Stringham John Waldon Emily McPherson Shannon Moore

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VAN ANDEL INSTITUTE Van Andel Institute Board of Trustees David Van Andel, Chairman John C. Kennedy Mark Meijer

Board of Scientific Advisors Michael S. Brown, M.D., Chairman Richard Axel, M.D. Joseph L. Goldstein, M.D. Tony Hunter, Ph.D. Phillip A. Sharp, Ph.D.

Van Andel Research Institute Board of Trustees

Chief Executive Officer David Van Andel

Van Andel Education Institute Board of Trustees David Van Andel, Chairman James E. Bultman, Ed.D. Donald W. Maine Juan R. Olivarez, Ph.D. Gordon L. Van Harn, Ph.D.

David Van Andel, Chairman Tom R. DeMeester, M.D. James B. Fahner, M.D. Michelle Le Beau, Ph.D. George F. Vande Woude, Ph.D. Ralph Weichselbaum, M.D. Max Wicha, M.D.

Van Andel Research Institute Chief Scientific Officer Peter A. Jones, Ph.D., D.Sc.

Chief Operations Officer Jana Hall, Ph.D., M.B.A.

VP Business Development Jerry Callahan, Ph.D.

VP Human Resources Linda Zarzecki

Communications and Marketing Beth Hinshaw Hall

Facilities

Samuel Pinto

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VP and Chief Financial Officer Timothy Myers

Vice President and Chief Legal Officer David Whitescarver

Development

Patrick Placzkowski

Security

Kevin Denhof

The Van Andel Institute and its affiliated organizations (collectively the “Institute�) support and comply with applicable laws prohibiting discrimination based on race, color, national origin, religion, gender, age, disability, pregnancy, height, weight, marital status, U.S. military veteran status, genetic information, or other personal characteristics covered by applicable law. The Institute also makes reasonable accommodations required by law. The Institute’s policy in this regard covers all aspects of the employment relationship, including recruiting, hiring, training, and promotion, and, if applicable, the student relationship.

Published June 2016.

Cover design by Nicole Ethen.

Copyright 2016 by Van Andel Institute; all rights reserved.

Van Andel Institute, 333 Bostwick Avenue, N.E. Grand Rapids, Michigan 49503, U.S.A.

Van Andel Research Institute SCIENTIFIC REPORT 2016

333 Bostwick Avenue, N.E., Grand Rapids, Michigan 49503 Phone 616.234.5000 Fax 616.234.5001 www.vai.org

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