All rights reserved. Contents are the property of the authors and/or journals cited. Cover Image from “Distinct Epigenetic Landscapes Underlie the Pathobiology of Pancreatic Cancer Subtypes�
Gwen Lomberk, PhD Associate Professor Department of Surgery Department of Pharmacology & Toxicology Chief, Division of Research Director of Basic Research Department of Surgery Medical College of Wisconsin
I joined MCW in June 2017 after 20 years at the Mayo Clinic in Rochester, MN. I am happy to be part of the MCW family serving as the Chief for the Division of Research and Director of Basic Research in the Department of Surgery. My research program is focused on the epigenetic landscapes that characterize subtypes of pancreatic cancer (PDAC) and refining the utility of epigenetic inhibitors for treatment and re-sensitization to conventional therapies. My lab team is strongly committed to pancreatic cancer research and is interested in further discovering molecular interactions and complex dynamics involved in epigenetic mechanisms triggered in response to cellular signals within the context of normal cell biology and pathophysiology to ultimately apply this knowledge to develop better therapeutic strategies in cancer.
“Distinct Epigenetic Landscapes Underlie the Pathobiology of Pancreatic Cancer Subtypes� Lomberk G, Blum Y, Nicolle R, et al. Nature Communications. 2018;9(1):1978. Using RNA-Seq, DNA methylation analysis and complementary ChIP-Seq studies on multiple histone modifications with markers for promoters, enhancers, super-enhancers, euchromatic, and heterochromatic regions, we performed the first comprehensive multi-parametric epigenomic profiling of human PDAC grown as patient-derived xenografts. We find that epigenomic profiles more accurately classify human PDAC subtypes than genomics and predict relative aggressiveness and survival. Interestingly, upon inactivation of a super-enhancer pathway associated with one subtype, we provide evidence for the existence of plasticity between subtypes. In addition, we have gained a detailed knowledge on new markers, which can serve for both diagnosis and prognosis. We are excited with these results since they represent a unique effort to better understand epigenomic landscapes, which promote human PDAC downstream of KRAS as well as other oncogenes and tumor suppressors. Epigenetic Model for Establishment of the Tumor Cell Phenotype
Michael Zimmermann, PhD Assistant Professor Clinical & Translational Sciences Institute
Director, Bioinformatics R&D Lab Genomic Sciences & Precision Medicine Center Medical College of Wisconsin
My research focuses on interpreting data so that we can act on resulting knowledge. For example, as we gather genomic sequencing data we need methods to interpret the functional impact of variants. That impact can be at a molecular, cellular, or physiologic level, and the interplay between these resolutions is critical. Therefore, my research starts from molecular modeling to see in 3D and over time how biomolecules achieve function and how genomic variants alter function. Observations and simulations at this high-resolution inform cellular and physiologic models, so that we can predict how cells or systems will respond to those alterations. The long-term goal is to make each person’s data relevant to their life – that we can learn from their data and tailor general knowledge to the individual, enabling Precision Medicine.
“The Impact of Pharmacokinetic Gene Profiles Across Human Cancers” Zimmermann MT, Therneau TM, Kocher JA. BMC Cancer. 2018;18(1):577. The right drug to the right patient at the right time is one of the ideals of Precision Medicine and remains one of the most compelling promises of the post-genomic age. Patient-level pharmacokinetics is well studied, but how the tumor genome changes that picture is not. We developed a simple rule-based approach to classify therapies administered to each patient from The Cancer Genome Atlas PanCancer dataset as effective or ineffective, accounting for each tumor’s gene expression profile. Our model identified ~5% of patients received a therapy with somatic contraindication. Controlling for multiple clinical characteristics, these patients had poorer long-term outcomes compared to those who did not have somatic contraindications. Our approach demonstrates that somatic PK should be integrated into tumor genomics data interpretation and prospective design of personalized therapeutic strategies. Fig. 2 Clinical decision making is augmented by interpreted tumor genomics. a The clinical decision making cycle of therapy selection is multifaceted and can be informed by properly interpreted tumor genomics profiling. Developing high-confidence and mechanism-based algorithms for properly interpreting genomic information remains a clinical challenge. b We considered a set of rules based on tumor genomics features for interpreting somatic PK gene expression. From these rules, we developed a simple Therapy Efficacy model for interpreting if an administered therapy may be ineffective due to somatic PK gene expression
Fig. 1 Human tumors may up- or down-regulate PK genes
Each gene was scored relative to a composite-normal reference to generate conservative estimates of aberrant somatic gene expression. RSEM normalized gene expression data were used. The expression score of each gene in each tumor sample is the signed Z-score relative to normal tissue samples. Example probability density distributions of gene expression for two genes are shown: (Top) drug importer SLC16A2 and (Bottom) drug exporter ABCC5.
Andrea K. Morrison, MD, MS Assistant Professor Department of Pediatrics Medical College of Wisconsin
I am a Pediatric Emergency Medicine physician and health literacy researcher and advocate. I am interested in clear health communication with patients and caregivers. My vision is to transform healthcare communication to help children and families understand and make decisions about their health. My research work has focused on the effects of parent health literacy and the decision to seek emergency care for children. I have published work regarding health literacy and ED utilization, health literacy measurement in parents, and health literacy and clinical care in the ED. I am involved in health literacy clinical efforts at Children’s Hospital of Wisconsin including development of educational materials for caregivers and patients and serve as the Co-Director of the Children’s Hospital of Wisconsin Health Literacy Task Force.
“Parents’ Pain Medication Underdosing is Associated with More Emergency Department Visits in Sickle Cell Disease” Morrison AK, Myrvik MP, Brousseau DC, et al. Pediatric Blood & Cancer. 2018;65(4):e26906. This quantitative study of parents in the emergency department and clinic measured pain medication knowledge and pain treatment skills in relationship to health literacy and ED use. Using multiple methods including a pain medication knowledge recall and pain medication skills task, we found a 50% to 200% higher rate of ED visits for pain in children with SCD whose parents underdosed pain medication. We also found that health literacy was associated with underdose errors. This study expands the knowledge base regarding sickle cell disease home pain management, ED utilization, and health literacy. It also further describes how parent health literacy may affect parents’ medication knowledge and skills in relation to sickle cell disease pain management. Future studies will expand upon how parents detect pain and determine the severity of pain and why parents underdose pain medications. Figure 2. Model for Health Literacy Skills and ED Use for Pain
Table 2. Opioid Pain Medication Review and ED Utilization Variables Medications Not Recalled Name Not Recalled Underdose errors Dosage Frequency Overdose errors Dosage Frequency +
Mean (Standard Deviation (SD)) of Percent Recall or Adjusted Incidence Rate Ratio (aIRR) (95% Confidence Interval-(CI)) Percent of Parents Making Error ED Visits for Pain+ 12.4 (29.7) 1.3 (1.2-1.3)* 16.5 (34.2) 0.99 (0.99-1.01) 17% 31%
2.0 (1.3-3.0)* 1.7 (1.2-2.6)*
17% 1%
1.2 (0.7-1.9) n/a
ED visits include treat and release ED visits and ED visits resulting in hospitalization; * P<0.05
Paul Bergl, MD Assistant Professor Division of Pulmonary, Critical Care, & Sleep Medicine Department of Medicine Medical College of Wisconsin
I am an assistant professor and clinician-educator in the Division of Pulmonary and Critical Care. Clinically, I practice critical care and inpatient medicine. My primary research interests lie in medical education. I am particularly interested in understanding how hospital workflows and clinical teaching practices affect trainees’ development in diagnostic reasoning and psychomotor skills. I have ongoing research projects related to ICU rounding practices, diagnostic reasoning and diagnostic errors, and improving trainees’ airway management skills in the critical care setting.
“Teaching Physical Examination to Medical Students on Inpatient Medicine Teams: A Prospective, Mixed-Methods Descriptive Study” Bergl PA, Taylor AC, Klumb J, Quirk K, Muntz MD, Fletcher KE. Journal of Hospital Medicine. 2018;13(6):399-402. In this study, we observed how inpatient teaching teams incorporate teaching physical examination into their daily workflows. Most importantly, we quantified how often students were being observed performing their own examination and then receiving feedback –both components for gaining competence in any psychomotor skillset. Overall, we found that students were infrequently exposed to physical examination instruction on the clerkship (see Figure). When senior clinician conducted a physical examination on daily rounds, only 15% of the time did they directly observe the students performing any component of the examination. Through a qualitative analysis of field notes and daily reflections, we also identified numerous factors that seemed to influence the frequency of physical examination instruction, such as the timing of rounds and clinical workload. Table 1. Clinical and Teaching Activities on Attending Rounds
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“Diagnosis and Management of Pediatric Sinusitis: A Survey of Primary Care, Otolaryngology and Urgent Care Providers” Newton L, Kotowski A, Grinker M, Chun R. International Journal of Pediatric Otolaryngology. 2018;108:163-167. Purpose: To assess pediatric PCP, otolaryngology and urgent care providers' perception of their adherence to the 2013 AAP guidelines for the diagnosis and management of ARS in children. Methods: A questionnaire was designed and emailed to 138 providers. Results: Diagnosis: The following diagnostic criteria are utilized: persistent nasal congestion/cough lasting >10 days (95%), worsening of URI symptoms at days 5-7 (70%), severe onset and purulent nasal discharge for 3 consecutive days (45%). Management: Typically used antibiotics: amoxicillin (72%), Augmentin (98%), Cefdinir (73%), azithromycin (15%). Typical length of antibiotic therapy for all providers is 10 days (70%) and 14 days (17%). Recommendations for adjuvant therapies varied between groups. Conclusions: This project demonstrates that providers' diagnosis of ARS is consistent with the AAP guidelines while variation in clinical management exists.
Laurie Newton, DNP, RN, CPNP Pediatric Nurse Practitioner Department of Otolaryngology Children’s Hospital of Wisconsin
Chao Yang 4th Year Graduate Student Department of Microbiology & Immunology: Malarkannan/Thakar Lab
“mTORC1 and mTORC2 Differentially Promote Natural Killer Cell Development” Yang C, Tsaih SW, Lemke A, Flister MJ, Thakar MS, Malarkannan S. eLife. 2018;7:e35619. Natural killer (NK) cells are innate lymphoid cells that are essential for innate and adaptive immunity. The signaling events govern the development of NK cells have not been fully appreciated. In this work, we uncovered the independent roles of mTORC1 and mTORC2 in regulating this process. mTORC1 is required for the early NK cell development, while mTORC2 governs the terminal maturation. Loss of mTORC1 renders substantial alteration of the gene expression profile including transcription factors governing early NK cell development. Deficiency of mTORC2 causes reduced expression of T-bet due to impaired mTORC2-AktS473-FoxO1 signaling, potentially responsible for the terminal maturation defects.
“Antiproliferative and Apoptotic Effect of LY2090314, a GSK-3 Inhibitor, in Neuroblastoma In Vitro” Kunnimalaiyaan S, Schwartz VK, Jackson IA, Clark Gamblin T, Kunnimalaiyaan M. BMC Cancer. 2018;18(1):560. Glycogen synthase kinase-3 (GSK-3) is considered an oncogene and is highly expressed in Neuroblastoma (NB). Recently, LY2090314 has been shown to be a potent, selective inhibitor of GSK-3 and well tolerated in clinic but it’s effect in NB is not known. In this study, we show that LY2090314 significantly reduces GSK-3 activity, inhibits cellular proliferation and associated with induction of apoptosis in three genetically different human NB cell lines. Importantly, LY2090314 required lower concentration compared to Tideglusib, another GSK-3 inhibitor, that reduces NB growth. These results provide rationale for further preclinical analysis using LY2090314 in NB.
Selvi Kunnimalaiyaan, MS Research Technologist II Division of Surgical Oncology Department of Surgery
Peng Zhang, MD, PhD Postdoctoral Research Fellow Liang Wang Lab Department of Pathology
“High-Throughput Screening of Prostate Cancer Risk Loci by Single Nucleotide Polymorphisms Sequencing” Zhang P, Xia JH, Zhu J, et al. Nature Communications. 2018;9(1):2022. There has been a significant challenge for functional characterization of disease-causing genetic variants for common diseases. To address this challenge, Dr. Zhang et al. developed a high-throughput DNA sequencing technology to identify potential functional genetic variants. By applying this single nucleotide polymorphisms sequencing (SNPs-seq) technology to prostate cancer, he successfully identified over a hundred of genetic variants showing allele-dependent protein binding at prostate cancer susceptibility loci. He took advantage of gene-editing technology and confirmed functional variants at two prostate cancer susceptibility genes, RGS17 and ASCL2. Knowledge from this study will facilitate translational studies for better preventive strategies of prostate cancer.
“Assessment of Outer Retinal Remodeling in the Hibernating 13-Lined Ground Squirrel” Sajdak BS, Bell BA, Lewis TR, et al. Investigative Ophthalmology and Visual Science. 2018;59(6):2538-2547. Cone photoreceptor degeneration is the main cause of vision loss in retinal disorders such as age-related macular degeneration and retinitis pigmentosa. Our lab uses the 13-lined ground squirrel because its retina is >85% cones that undergo drastic and reversible remodeling during annual hibernation. In this work, we examined (in vivo and ex vivo) the retina in the 13-lined ground squirrel during its summer (euthermic) and winter (torpid) physiological states. We found significant changes in cone structure and their primary blood supply layer (the choroid). These data provide the first in vivo comparison of a mammalian retina in euthermia and torpor.
Benjamin S. Sajdak Graduate Assistant, PhD Candidate Department of Cell Biology, Neurobiology and Anatomy
Deepali Rathore, PhD Postdoctoral Research Fellow Center for Biomedical Mass Spectrometry Research
“The Role of Mass Spectrometry in the Characterization of Biologic Protein Products” Rathore D, Faustino A, Schiel J, Pang E, Boyne M, Rogstad S. Expert Review of Proteomics. 2018;15(5):431-449.
Biotechnology products (Biologics) is a multibillion dollar industry and will continue to dominate the global pharmaceutical market in the coming decades. Mass spectrometry (MS) is a powerful biophysical tool for the in-depth characterization of these products throughout their development lifecycle. In addition to intact mass analysis, peptide mapping, and PTM identification, emerging applications of MS such as higher order structure analysis allow isoform differentiation, epitope mapping and the study of conformational dynamics, demonstrating its utility in comparability, biosimilarity and quality control practices. Advancements in mass accuracy, resolution and ionization methods is likely to increase the use of MS-based methods in biopharmaceutical development.
“Heterogeneous Stock Rats: A Model to Study the Genetics of Despair-Like Behavior in Adolescence” Holl K, He H, Wedemeyer M, et al. Genes, Brain, and Behavior. 2018;17(2):139-148.
Very few genes have been identified for major depression or antidepressant response. The Wistar Kyoto (WKY) rat is a model for depression, is antidepressant resistant, and is one of the eight founders of the Heterogenous Stock (HS) strain of rats. We performed forced swim tests on adolescent HS rats treated with and without an antidepressant drug, Fluoxetine. We demonstrated heritability of despair-like behavior and show that HS rats exhibit differences in gene expression levels of genes associated with major depressive disorder in humans. The overlap between human and HS genes suggest these studies may translate to depression in humans.
Katie Holl, BS Research Associate II Department of Medicine
Cristina Maranto, PhD Postdoctoral Fellow Nevalainen Lab Department of Pathology
Vindhya Udhane, PhD Postdoctoral Fellow Nevalainen Lab Department of Pathology
“STAT5A/B Blockade Sensitizes Prostate Cancer to Radiation through Inhibition of RAD51 and DNA Repair.” Maranto C, Udhane V, Hoang DT, et al. Clinical Cancer Research. 2018;24(8):1917-1931. Radiation therapy is a key treatment option for both organ-confined and locally advanced prostate cancer. We investigated whether Stat5a/b participates in regulation of double strand DNA break repair in prostate cancer, and whether Stat5 inhibition may provide a novel strategy to sensitize prostate cancer to radiation therapy. This work introduces a novel concept of a pivotal role of Jak2-Stat5a/b signaling for Rad51 expression and homologous-recombination DNA repair in prostate cancer. Inhibition of Jak2-Stat5a/b signaling sensitizes prostate cancer to radiation and, therefore, may provide an adjuvant therapy for radiation to reduce radiation-induced damage to the neighboring tissues.