2022 Nano-Bio Report

Directors’ Letter

Hello and welcome to the Institute for NanoBioTechnology’s annual report! A little over a year ago, Dean Schlesinger appointed us as the new team to lead INBT. As longtime colleagues and collaborators, we are excited to build on the Institute’s legacy of scientific excellence. In the last year, we’ve augmented our research portfolio, expanded education and outreach initiatives, and initiated translational initiatives to bring the benefits of the Institute’s creations to the wider world. We are excited to share these updates in the latest edition of the report.

Research excellence has always been the INBT’s core. Working with our faculty, we’ve expanded into new areas. We launched a new research pillar in genome engineering, recruiting Bloomberg Distinguished Professor Jeff Coller and biomedical engineer Reza Kalhor to spearhead the efforts. Our 2022 symposium kicked off this new pillar with keynote addresses from genome sciences luminary, George Church and gene therapy pioneer, Steven Altschuler.

Under David Lee and Sulaiman Jenkins’s leadership, we continued to expand our education programs, ensuring that our students can access bioengineering frontiers in academic and industry labs. We are particularly proud of the student diversity in these programs. Last year, more than half of the students in our NSF Research Experience for Undergraduates program and Co-Op Master’s program identified as women, and nearly half were from historically underrepresented backgrounds. After two years of construction, the INBT office and lab renovations were completed in late fall. The renovations also created state-of-art open wet-lab space for INBT researchers Jude Phillip and Sangmoo Jeong, and a new conference room and a huddle space to encourage the collaboration that is INBT’s hallmark.

The INBT’s success comes from a desire to push science and engineering to improve people’s lives. This motivation is seen in the staff who expertly guide administrative and operational functions to the students and faculty conducting research. We are proud of our teams, thank them for all they do, and look forward to what we will accomplish together in 2023. Thank you for being part of the enterprise!

Hai-Quan Mao Director

Sashank Reddy Associate Director

Faculty News

New faculty

Jeffery Coller specializes in mRNA translation and degradation pathways. He is interested in the signals that end mRNA translation and begin mRNA degradation. Coller is a Bloomberg Distinguished Professor of RNA Biology and Therapeutics, professor of molecular biology and genetics, and an INBT core researcher.

Jochen Mueller combines additive manufacturing, functional materials, and computational design to create programmable matter. He is an assistant professor of civil and systems engineering and INBT associate researcher.

Ashley Kiemen uses artificial intelligence and 3D computer modeling to view cells at the single cell level to better understand how cancer tumors form. Kiemen is an assistant professor of pathology and INBT associate researcher.

Xiaobo Mao is exploring the role of prion-like proteins in the pathogenesis of neurodegeneration, including protein misfolding strains and structures, pathology spread, neurotoxicity, and neuroinflammation. Mao is an associate professor of neurology at the Institute for Cell Engineering at the Johns Hopkins School of Medicine and an INBT affiliate researcher.

Dingchang Lin develops biomolecules, materials, and electronic devices for probing and modulation in biological systems. These tools will grow new possibilities in basic science and provide translatable solutions for clinical applications. He is an assistant professor of materials science and engineering and INBT associate researcher.

Appointments

Rebecca Schulman, associate professor in the Department of Chemical and Biomolecular Engineering and an INBT associate researcher, has been appointed as the Kent Gordon Croft Investment Management Faculty Scholar. This endowed faculty scholarship was established in 2015 by alumnus L. Gordon Croft ’56 in honor of his son, Kent Gordon Croft.

Awards

Sangmoo Jeong and Dingchang Lin both received the National Institutes of Health’s Maximizing Investigators Research Award. The five-year grant supports early-stage investigators to pursue basic research that could deepen our understanding of biological processes. Jeong is an assistant professor of chemical and bimolecular engineering and an INBT core researcher. Lin is an assistant professor of materials science and engineering and an INBT associate researcher.

Yun Chen received a Defense Advanced Research Projects Agency (DARPA) Young Faculty Award for her project on, “Fibrosis, Inflammation, Revascularization, and Migration (FIRM) Modulation for Muscle Regeneration.” It will help her study how biophysical and biochemical factors are coordinated to achieve homeostasis, or to facilitate disease, across molecular, cellular, and tissue levels. Chen is an assistant professor in the Department of Mechanical Engineering and an INBT associate researcher.

Jamie Spangler is the recipient of a National Science Foundation Early CAREER Award and a Maryland Outstanding Young Engineer Award. Spangler’s research focuses on redesigning naturally occurring proteins and engineering molecules to overcome the shortcomings of existing medications and therapeutics. She is the William R. Brody Faculty Scholar, assistant professor of biomedical engineering, and an INBT affiliate researcher.

Research team Jude Phillip, Sean Sun, and Jeremy Walston received a Catalyst Award in the Healthy Longevity Global Competition from the National Academy of Sciences to help develop standard measurements for frailty and resilience. Phillip is an assistant professor of biomedical engineering and an INBT core researcher. Sun is a professor of mechanical engineering and an INBT core research. Walston is the Raymond and Anna Lublin Professor of Geriatric Medicine and Gerontology at the Johns Hopkins School of Medicine and an INBT associate researcher.

Jennifer Elisseeff was elected to the American Academy of Arts and Sciences. Her research focuses on the immune system as a therapeutic target for regenerative medicine, and biomaterials development. Elisseeff is a professor of biomedical engineering, the Morton Goldberg Professor of Ophthalmology at the School of Medicine, director of the Johns Hopkins Translational Tissue Engineering Center, and an INBT associate researcher.

Thao (Vicky) Nguyen has been elected a Fellow of the American Society of Mechanical Engineers, a designation recognizing exceptional engineering achievements and contributions to the profession. Nguyen is the Marlin U. Zimmerman, Jr. Faculty Scholar and professor in the Department of Mechanical Engineering, and INBT associate researcher.

Investigating the Secret Life of Tumors

By Amy Weldon

Johns Hopkins University joined forces with Yale University to establish the Johns Hopkins Center for 3D Multiscale Cancer Imaging, which will be a hub for interdisciplinary research with a goal of unlocking the mysteries surrounding tumorigenesis (the formation of tumors) through the integration of cutting-edge molecular and cellular analysis.

“Our multidisciplinary team of clinicians, computational biologists, and bioengineers is developing computer algorithms combined with advanced molecular tools to identify and map in three dimensions the key types of cells responsible for the spread of cancer,” said center co-founder Denis Wirtz, INBT core researcher, professor of chemical and biomolecular engineering, and vice provost for research at Johns Hopkins.

Researchers will use CODA, a cutting-edge computational research platform co-developed by Ashley Kiemen and Pei-Hsun Wu, an associate research professor in chemical and biomolecular engineering and the INBT, that turns tissue slides into a 3D model— a process that creates hundreds of images of ultrathin tissue sections and aligns them with extremely high accuracy, allowing researchers and clinicians to manipulate and examine them in ways never before possible.

“Our CODA system will allow us to produce 3D models by assembling sections of tissue samples so small we can see the anatomy of each cell and so large we can assess extremely large volumes of tumors,” said Laura Wood, associate professor of pathology and oncology at Johns Hopkins Medicine, director of gastrointestinal and liver pathology, INBT associate researcher, and center co-founder. “We believe this will give us a revolutionary ability to see, for example, the precise location where cancer cells enter the bloodstream to initiate metastasis.”

CODA not only performs the slide assembly process in a matter of minutes, but also creates an algorithm that automatically assigns characteristics to every tissue on each slide. As a result, a comprehensive 3D model of large pieces of tissue is created, giving researchers an unprecedented view and understanding of human tissue—including tumors.

CODA generated image of a mouse lung using CODA. Each color represents a different tissue.

Increasing EnantiomerSelective Production

By Gina Wadas

For some product manufacturers, one of the most important and costliest steps is the chemical-separation process. This is because large resource quantities are needed at the start of the process to yield the desired quantity, and by the end there is a lot of waste. Some manufacturers try to improve this process by manipulating the chemical reaction, which is no easy task. Johns Hopkins researchers may have found an efficient way of controlling those chemical reactions by creating enantiomers using a short DNA sequence catalyst.

Some molecules exist in pairs called enantiomers. Enantiomers are structurally the same, but are mirror images of each other, like a pair of hands. Enantiomers exhibit similar chemical and physical properties, making their separation challenging, but interact differently with substances that have chiral properties. For example, enantiomers can have different effects when used in drugs. This makes them desirable as researchers and manufactures can choose the enantiomer with the desirable effects they want. However, producing more of the desired enantiomer is challenging.

Efie Kokkoli, INBT core researcher and professor of chemical and biomolecular engineering, and Michael Tsapatsis, INBT core researcher, professor of chemical and biomolecular engineering, and Bloomberg Distinguished Professor, created their catalyst, an artificial metalloenzyme, by using

eight base-pairs of DNA with just two active nucleotide pairs of guanine and cytosine in the middle of the double stranded DNA sequence. This is a huge feat considering the field initially started with thousands of base pairs and was reduced to 20-30 before Kokkoli and Tsapatsis created the eight base-pair catalyst.

Another important part of this research is that they modified their design to accommodate reactions that occur in a mixture of solvents. Previous research in the field only accommodated for reactions in water.

“We demonstrated that if you take the short sequence with only two active nucleotide pairs and turn it into an amphiphile, that the reaction will work in a mixture of water and organic solvent,” said Kokkoli.

The new catalyst can be applied to selectively synthesize enantiomers that can be added in pharmaceuticals, perfumes, and food.

Kidney Cells Don’t Filter Blood, They Pump It

By Gina Wadas

Kidneys are a network of tubes that process roughly 190 quarts of blood daily. Lining these tubes are epithelial cells that transport blood through the kidneys. How these immobile cells generate mechanical forces needed to do their job is not fully understood. To unlock the secrets of this fluid transport process, Sean Sun created a device that measures mechanical forces generated by healthy and diseased kidney cells.

Sun, INBT core researcher and professor in the Mechanical Engineering Department, and his team, recreated the kidney microenvironment using their micro-fluidic kidney pump, or MFKP. The device has two microchannels separated by kidney epithelial cells. As the cells pass fluid between the channels, it records fluid pressures generated in real time.

The researchers noticed that the cells behave like mechanical fluid pumps and actively generate a fluid pressure gradient. The fluid pumping behavior is similar to a water pump in a house. Most people believe that kidneys behave like a conventional filter, which needs external pressure to move fluid. However, Sun and his team showed that cells can generate the pressure themselves—an insight with important implications for understanding kidney physiological function.

“Everyone hears that kidneys filter blood, but conceptually that is incorrect. What we showed is that kidney cells are pumps, not filters, and they are generating forces,” Sun said.

Collaborating with the Baltimore PKD Research and Clinical Core Center at the University of Maryland, Sun’s team used the device to examine cell mechanical behaviors in patients with autosomal dominant polycystic kidney disease, or ADPKD. ADPKD is a common inherited and aggressive disorder in which the kidney develops fluid-filled cysts. The device showed that ADPKD cells pump fluid in the opposite direction of healthy epithelial cells. This altered pumping behavior changes the kidney tube’s pressure profile, resulting in changes to their shape.

They also tested Tolvaptan on ADPKD cells using MFKP. Tolvaptan is an FDA-approved drug that helps delay ADPKD progression. The team showed that ADPKD cells responded to Tolvaptan by lowering the fluid pumping flux and pressure gradients, which means the cyst should develop more slowly. This finding demonstrates that the device has the potential to screen new treatments for ADPKD and other kidney diseases.

Monitoring Drug Resistance in Elusive Cancer Cells

By Catherine Graham

Found in a patient’s blood, circulating tumor cells, or CTCs, have powerful potential to indicate how well a cancer treatment is working and guide treatment decisions. However, CTC technologies are not widely implemented in clinics, in part because CTCs are rare, and separating them from the billion normal cells in blood is challenging.

A new microfluidic system developed by Soojung Claire Hur, INBT associate researcher and the Clare Boothe Luce Assistant Professor in the Mechanical Engineering Department, could make it easier to collect and test drug-resistant CTCs from blood samples called “liquid biopsies,” which are faster, less invasive, and safer than traditional tissue biopsies. Because they can be taken frequently, liquid biopsies help clinicians evaluate patients at different phases of their cancer treatment.

Hur previously developed a technique to isolate CTCs, which recognizes and traps the rare tumor cells. In this study, the researchers adapted those techniques to investigate cells’ real-time drug response. First, the team ran blood samples spiked with a drug-resistant lung cancer cell line through the previously mentioned purification process. Then they used their new device as an electroporator, creating holes in the cancer cell membranes with jolts of electricity before injecting them with two cancer drugs.

They found that combining the right drugs could overcome resistance and restore therapeutic response in the tumor cells, said Hyun Woo Sung, a PhD candidate in Hur’s lab and lead author of the study.

According to Sung, the system’s key innovation is its single-cell imaging pipeline, which identifies discrete differences within the cell population. This approach determined whether every cell they collect and electroporate is permeable for drug delivery, and whether the cell is alive after the jolt.

The single-cell analysis is also promising in that it addresses the rare nature of CTCs in blood samples. Conventional analysis techniques require a certain number of cells present to successfully process the sample. In contrast, Hur’s system offers an alternative to analyzing smaller cell populations, such as CTCs.

The researchers believe the system will someday give clinicians information about whether individual patients will respond to a specific drug.

Materials That Behave Like Organisms

by Gina Wadas

Our bodies’ genes work together to regulate how our cells behave. For example, if you skin your knee, your genes use a chemical messaging system to direct cells to heal the abrasion. If scientists could create artificial genes that could carry out the same functions but operate inside materials rather than organisms, a wide variety of new diagnostic, self-healing materials would be possible.

A team led by Johns Hopkins engineer Rebecca Schulman is laying the foundation for that work by engineering synthetic chemical systems that can emulate the complex behaviors of natural gene networks.

“Cells use genes to decide how to move, grow, and act. The ability to make simple ‘genes’ that could make decisions on their own could lead to better diagnostics or therapeutics, or even provide ways to build new types of soft material robots that are controlled by chemistry instead of electronics,” said Schulman, INBT associate researcher and associate professor of chemical and biomolecular engineering.

The human body has 25,000 genes, and they use many chemical interactions to regulate cells. Luckily, researchers don’t

need to recreate every biological step to create synthetic gene analogs capable of carrying out the same functions. To improve and better predict the behavior of gene analogs, Schulman and her team created a molecular tool kit which includes genelets (very small genes whose functions can vary, depending on instructions), and simplified mathematical models.

The team’s simplified genelet system uses DNA, RNA, a polymerase enzyme that transcribes DNA to make RNA copies, and an RNase enzyme that degrades RNA. Using just these simple elements, Schulman team’s system can adapt and reset as the environment changes, just like natural genes in the body do. Through screening and other chemical modifications to prevent unwanted reactions, the team created a library of about 15 genelets with universal standard performance.

They hope this toolkit will inspire new applications in other research groups and they developed a software package available on GitHub. Users can quickly simulate any network and produce the DNA sequences to test in the lab.

New Tissue Model to Study Lyme Disease

by Gina Wadas

An estimated 476,000 Americans are infected each year with Lyme disease, a condition causing a range of symptoms that include fever, rash, and joint pain, as well as effects on the central nervous system and heart. Though it’s common knowledge that Borrelia burgdorferi (B. burgdorferi)—the bacteria that causes the disease—enters the body through the bite of an infected deer tick, until now, how the bacteria migrates from that bite into a person’s bloodstream is not clearly understood.

Johns Hopkins engineers may have found the answer. Using a custom designed three-dimensional tissue-engineered model, they learned that B. burgdorferi uses tenacious trial-and-error movements to find and slip through tiny openings called junctions in the lining of blood vessels near the original bite site. This allows them to hitch a ride on the bloodstream throughout the body, potentially infecting other tissue and organs.

“Our observations showed that if the bacteria did not find one of these junctions on the first try, they continued searching until one was found,” said team leader Peter Searson, core researcher at the Institute for NanoBioTechnology and professor of materials science and engineering.

The team injected its three-dimensional model, which simulates a human blood vessel and its surrounding dermal tissue, with the bacteria, simulating a tick bite, and used a high-resolution optical imaging technique to observe its movements. The team observed that though the tissue at the original site of the bite was an obstacle for the spiral-shaped bacteria to traverse, little effort was needed for them to penetrate the junctions and enter the bloodstream.

Lyme disease is prevalent in North America, Europe, and Asia, and though antibiotic treatments are effective, some patients experience symptoms that can persist for months, and—in some cases—years. The Hopkins team says that understanding how B. burgdorferi spreads throughout the body could help inform treatments to prevent bacteria from the initial bite entering other tissues and organs.

Researchers observed the behaviors of Borrelia burgdorferi, the bacteria that causes Lyme Disease, in their three-dimensional tissue model.

Research Experience for Undergraduates Summer Program

For 13 years, the Research for Undergraduate Experience (REU) program has been a staple of the Institute for Nanobiotechnology. It aspires to provide students from underrepresented communities with valuable opportunities to conduct cutting-edge research in nanobiotechnology. Since 2008, these recruitment efforts have resulted in a very diverse pool of participants, 92.7% of whom are members of underrepresented groups and 54.8% of whom have been women.

This year’s cohort saw a total of nine students, eight of whom were women, from various states across the country including Minnesota, Kansas, Oregon, California, Virginia, Rhode Island, and New York. They spent the first few weeks getting acquainted with the PIs and mentors of their respective labs, and they worked collectively to design research projects that were aligned with the students’ research interests in drug/gene delivery, biophysics and bioengineering, cancer, and neuroscience.

In the early weeks, the students attended various professional development workshops offered by Gina Wadas, INBT’s communications associate, on topics that ranged from digital identity to making effective presentations. They were also encouraged to attend the annual INBT symposium, where they had the opportunity to engage with current Hopkins students as they presented their research findings during virtual lectures and the

poster competition in Mudd Hall. The cohort was truly amazed at the scope and novelty of the different topics that were presented, and they gained valuable insight into gene engineering, genome tagging and genome structure.

During a hot summer, it was certainly not all research and no play; the students’ study time was punctuated with a number of fun, cohort-building activities through which they learned more about each other and Baltimore City. They went to the National Aquarium, the Maryland Zoo, and even attended an Orioles baseball game!

As the program wound down, cohort members put their research skills and experiences on display when they presented at the C.A.R.E.S. symposium (Three of the students received prizes for the quality of their research presentations!) and at the in-house REU INBT symposium during the final week. Although the program ended in mid-August, the cohort members walked away armed with deeper research insight and enriched by a rewarding summer experience in Baltimore.

Highlights of the Nano-Bio Symposium: Engineering Genes

and Genomes

Engineering Genes and Genomes was the focus of the Institute’s 15th Nano-Bio Symposium on Friday, June 10. This event went hybrid, which included virtual lectures and an in-person poster competition and reception. The symposium is the INBT’s signature event that showcases and celebrates the latest discoveries from our multidisciplinary research teams and partners.

The event featured 10 speakers from across Johns Hopkins schools of Medicine and Engineering, Spark Therapeutics, Harvard University, and MIT to discuss topics about genome structure and how to manipulate gene products. These included nanoscale system developments to deliver gene therapies in tissue and cell specific ways, RNA regulatory dynamics that govern how genotype manifests as phenotype, and genomic tagging to reveal lineage relationships in development and disease. The goal is to bring these advances to patients through safe, efficient, and equitable means.

“Today’s symposium focuses on engineering genes and genomics: an area where we are contributing to astonishing prog-

ress, and one that has important implications for biological understanding and the potential to deliver wholly new approaches to diagnostics and therapeutics,” said T.E. Schlesinger, the Benjamin T. Rome Dean at the Whiting School of Engineering.

The in-person poster competition and reception returned after a two-year hiatus due to COVID-19. It featured over 30 posters, had more than 100 attendees, and five poster winners. The two undergraduate poster awards are sponsored by Tom and Lois Fekete and the three graduate awards are sponsored by the INBT. Tom Fekete is the former INBT director of corporate partnerships and retired in 2018 after 10 years at the INBT. He was also in attendance to present the undergraduate awards and serve as a poster judge for the graduate students.

Virtual registrants came from around the United States and worldwide. By extending its reach outside the Baltimore area, INBT furthers its goal of bringing together people in academia, industry, and more to share knowledge, ideas, and foster new collaborations.

Supporting Communities Beyond the Office and Workbench

The INBT’s collaborative atmosphere extends beyond the workbench as many staff, students, and faculty participate in charitable events and activities to support people and communities in need. While the INBT has engaged in many programs, our community has participated in the following Johns Hopkins community engagement programs consistently in the past five years.

Vernon Rice Memorial Turkey Program

Named for the late Hopkins employee who started the program, the program collects monetary donations to purchase baskets with a fresh turkey and vegetables from a local farm for families in need for the Thanksgiving and December holidays.

Adopt-a-Family and Adopt-a-Senior Program

Johns Hopkins partners with local nonprofit and service agencies to connect employees who wish to bring a little extra cheer to a families and senior citizens in need during the December holiday season by providing gifts, clothing, and gift cards.

Adopt-a-Student Uniform and Supplies Drive

Since 2011, the program has assisted students in elementary, middle, and high school at Baltimore City Public Schools in purchasing new school uniforms. In 2021, the program was expanded to purchase essential school supplies.

To date, the INBT community has procured:

Turkey dinners for 73 families

Gifts, clothing, and gift cards for 17 senior citizens, adults, and children

Uniforms and school supplies for 11 students

INBT Leaps Into New Mission and Vision

By David Lee

It has been said that INBT is an exceptionally diverse, multidisciplinary team of faculty, researchers, and student experts uncovering new knowledge and creating innovative technologies at the interface of nanoscience, engineering, biology, and medicine, and that INBT aims to revolutionize research by fostering a collaborative environment among engineers, scientists, and clinicians to pioneer new ways to solve some of the most complex challenges in health care and the environment. When I joined INBT in November 2021, as the new director of corporate partnerships, I soon discovered that these aims and values have guided the institute to where it is today: a stalwart among the excellence prevalent throughout Johns Hopkins.

And I hit the ground running. Not because I was forced to, but because I was driven by the unique opportunity at that point in time. Much like the rest of the world, INBT was in a state of transition with new leadership readying to steer the institute through the next 15 years. Equipped with my experiences in law, multinational corporations, academia, and startups, I recognized all the signs that pointed to the fact that INBT—firmly planted in its bedrock of excellence— was poised to take the next leap.

As much of the world struggled to make sense of the new modalities of life, INBT’s new leadership endeavored to prepare for the next 15 years by renewing our vision and mission. Driven by INBT’s history of excellence and passion—and after many days and nights of thoughtful and deliberate exercises in exposition—the renewed vision and mission were drafted.

At INBT, we are inspired to “Discover, Design, and Deliver” the nanoscale principles of living systems by building the preeminent translational research hub at Johns Hopkins University to turn bioengineering excellence into transformative solutions.

INBT will achieve these goals by strengthening and expanding our high-caliber research portfolio, attracting leading faculty in high-impact pillars from Johns Hopkins and beyond, and applying best practices from translation -

al leaders to create a unique model for our institution.

The “Discover-Design-Deliver” model was extracted from INBT’s successes in oncology research and applied to strengthen the two relatively new and growing sensing and aging research pillars. Two new pillars—genome engineering and cell programming—have since been identified based on the analysis of frontiers of bioengineering with a focus on critical impact in human health and local strengths in engineering and biomedical sciences. By the 20th anniversary of INBT in 2026, we envision building the premier translational research hub at Hopkins, with fully established top-notch research programs in all five pillar areas.

To bolster the “Deliver” part of the vision and strengthen the translational research culture on campus, we have planned to create programmatic support and incentives for high-value translation. The programmatic support will take the form of a dedicated team of business-minded professionals with expertise in IP, portfolio, and project management who will be strategically embedded into targeted INBT research. In collaboration with the WSE Office of Research and Translation, this support team will empower INBT researchers to refine their translational efforts to strengthen and smooth out the path to

JHTV—our key partner in translation. We are also planning to establish an institute initiative grant to encourage high reward/risk research projects. Our goal is to elevate the historical excellence of INBT’s translational research to the next level by not only streamlining the process but also de-risking certain translational research projects that will generate transformative value but comes with a proportionally higher risk.

Throughout 2022, society continued to boldly persevere and rebuild much of what was deconstructed by the pandemic. In a fateful parallel of sorts, INBT underwent a literal renovation during this time when we were physically dispersed. However, we focused on becoming more intentional about renewing and rebuilding our community despite the new obstacles. A fantastic example is the biweekly faculty seminar series in which INBT faculty members come together to freely discuss their research and build rapport with one another. Through these gatherings, the seeds of collaboration were planted on fertile soil of renewed vision and mission. INBT’s history of excellence stands as proof that our dynamic aim will lead to the translation of science and engineering research to create maximum value and impact for not only WSE or JHU, but also our community and mankind.

Interested in the INBT’s translational activities?

Find

licensing and partnership opportunities, start-up companies, research, and more on our website.

Tevard Biosciences Licenses Technology as Foundation for Third Therapeutic Platform

Jeffrey Coller,

Bloomberg Distinguished Professor in the Department of Molecular Biology and Genetics at the Johns Hopkins School of Medicine, is one of INBT’s newest core researchers and will lead INBT’s new research pillar in genome engineering. His groundbreaking work on RNA biology and therapeutics has led to

platform that addresses diseases in which a genetic mutation causes a reduction in or loss of an important protein. Coller’s research addresses a condition known as haploinsufficiency. People with haploinsufficiency have a gene mutation that causes one gene to be inactive or deleted while the other copy remains normal. However,

transformative impacts in the field, and his research is part of the foundation of the biotech startup Tevard Biosciences, where Coller is a scientific co-founder. The company develops RNA therapeutics to address the effects of Dravet syndrome, a genetic seizure disease with symptoms starting within the first year of life and can range from mild to severe, and other genetic diseases.

Tevard Biosciences signed a licensing agreement with Johns Hopkins to use Coller’s mRNA amplifier technology, which will be the foundation for Tevard’s third

the remaining copy cannot sufficiently produce the important protein to healthy levels. Coller’s technology will amplify the normal gene so the body can produce the needed protein to a healthy level.

Coller’s amplifier technology will join Tevard Biosciences’ other RNA therapeutic platforms that use transfer RNA, or tRNA. Transfer RNA, or tRNA, are small RNA molecules that are crucial to building proteins. Tevard Biosciences’ tRNA platforms include suppressor tRNAs and ehancer tRNAs.

People with haploinsufficiency have a gene mutation that causes one gene to be inactive or deleted while the other copy remains normal.…Coller’s technology will amplify the normal gene so the body can produce the needed protein to a healthy level.

Jeffrey Gray Receives Microsoft Acceleration Award

Jeffrey Gray, INBT associate researcher and professor of chemical and biomolecular engineering, has received a Microsoft Innovation Acceleration Award to support Ably Bio, deep-learning platform for the rapid development of next-generation antibody therapeutics. The company’s software can predict antibody structure from an amino acid sequence. Ably Bio was founded by Gray, Jeffrey Ruffolo, a molecular biophysics PhD candidate who works in Gray’s laboratory, and Tim Aikin, a graduate student in molecular biology and genetics.

The award is an extension of a collaboration established in 2020 between Johns Hopkins Technology Ventures (JHTV) and Microsoft to help startups launch, scale and commercialize. More than a dozen have joined the Microsoft for Startups program in the last two years and received access to technology including Azure, Microsoft 365, and GitHub enterprise programs, as well as Microsoft commercialization support. JHTV also has facilitated almost 100 office hour sessions for Johns Hopkins innovators and the team from Microsoft.

“This application process was a great illustration of just how many industries can be supported by innovation in the digital space, as well as the breadth of innovation occurring at Johns Hopkins,” says Mark VanderZyl, who manages the relationship between JHTV and Microsoft. “We’re thankful to have such a great partner in Microsoft and look forward to seeing how this year’s awardees and all of the teams working with Microsoft continue to advance.”

Jeff Gray (left), Jeff Ruffolo (middle), and Tim Aikin (right).

Molecular Detection Platform Provides New Insights into Gene Medicine Manufacturing

By Gina Wadas

An important component of the vaccines protecting people against SARS-CoV-2 virus and its variants are lipid nanoparticles, or LNPs. These circular particles carry therapeutic mRNA payloads, the snippets of genetic material that trigger our immune systems to defend against COVID-19. Even with their success, certain characteristics about the particles, such as payload distribution, are unknown. Researchers and the Food and Drug Administration want more insights about these characteristics to improve metrics reporting in pharmaceutical manufacturing.

A new molecular detection platform developed by two Whiting School of Engineering professors is answering the FDA’s call. Hai-Quan Mao and Tza-Huei (Jeff) Wang want to address how many mRNA molecules an LNP can carry and whether the mRNA is uniformly packed inside the particle to help researchers design more efficient and effective treatments and vaccines.

“Our platform processes molecules at the single nanoparticle level, but unlike the current imaging methods for mRNA LNPs, our approach is based on fluorescent spectroscopy and gives us the ability to see through the particles,” said Wang, a professor in the departments of Mechanical Engineering and Biomedical Engineering at the Whiting School, and a

core researcher at the Institute for NanoBioTechnology.

The ability to peer inside the nanoparticles allows the researchers to differentiate between and measure empty LNPs that do not contain mRNA, LNPs with mRNA, and free-floating mRNA in a sample.

Their platform, called cylindrical illumination confocal spectroscopy, or CICS, works by tagging mRNA and LNP components with fluorescent signals of up to three colors and passing the sample through a detection plane. The detection plane reads the fluorescent signals and measures their intensity before comparing the strength of the intensities with that of a single mRNA molecule. The data analysis with an algorithm called deconvolution tells the team both how many mRNA copies are inside the LNP—if any—and their distribution in the sample. The team’s platform overcomes contrast limitations and increases the sample analysis throughput, that are seen in cryo-transmission electron microscopy, the current gold standard for imaging mRNA LNPs.

Tests conducted using this sensing platform revealed that from a benchmark solution of mRNA LNP used in academic research studies, over 50% of the LNPs are not loaded with mRNA molecules, and of the mRNA-filled LNPs, most of them

contained two to three mRNA molecules per particle.

“Being able to quantitatively resolve payload characteristics of mRNA LNPs at the single particle level has never been done before. We are intrigued by the substantial presence of empty LNPs, and by altering formulation conditions, a single nanoparticle can load as few as one to as many as ten mRNA molecules.” said Mao, professor in the departments of Materials Science and Engineering and Biomedical Engineering at the Whiting School and director of the Institute for NanoBioTechnology.

“There are a lot of groups doing LNP research,” Wang said. “However, when they discover a formula that might work well, it has been hard to associate those discoveries back to the composition and payload distribution of the nanoparticles. With this platform we can provide a more comprehensive understanding on what is happening at the single particle level.”

More research is needed to learn how many mRNA molecules per LNP capsule is optimal for the most effective treatment. However, the empty LNPs revealed by the new platform show there is a need to improve methods for packaging the mRNA inside the LNPs.

Mao and Wang say that their platform shows that it has the potential to not only be used at all stages of LNP-related research and development, but also in the development of other drug delivery systems and quality control measures at the manufacturing stage. The team has filed a patent application covering the technique and is working with collaborators to use the platform to analyze other types of therapeutic cargos in diverse nanoparticle systems for treating different diseases.

“The FDA has recently addressed the need for better quality metrics in nanoparticle design in the pharmaceutical industry,” said Michael J. Mitchell, a leading scientist in the field of LNP research and Skirkanich Assistant Professor of Innovation in the Department of Bioengineering at the University of Pennsylvania. “This will become increasingly more important as mRNA LNP technology expands beyond vaccines into new therapeutics that are administered into the bloodstream, which have very stringent requirements. The new detection platform developed by Drs. Mao and Wang’s team is a potentially important step forward in addressing needs at the research and regulatory phase, and can potentially aid in the development of mRNA LNP technology beyond vaccines.”

Siebel Scholar Recipients

Siebel scholarships are prestigious awards that honor about 100 of the top graduate students nationwide in business, bioengineering, computer science, and energy science programs. The selection is based on their outstanding academic performance and leadership, and each recipient receives a $35,000 award toward their final year of studies. The 2022 recipients include two students from the Institute for NanoBioTechnology.

Zachary Schneiderman (far left in photo) began his career at the National Institutes of Health, where he established the first nonaffinity-based purification process for an HIV trimer vaccine and co-led a high-throughput development team. He then pursued his PhD with Efie Kokkoli, INBT core researcher and professor in the Chemical and Biomolecular Engineering Department where he works at the forefront of both DNA and lipid nanotechnology, focusing on targeted drug and

gene therapy delivery for the treatment of cancer using DNA nanotubes, liposomes, and lipid nanoparticles.

Justin Lowenthal (far right in photo) began the MD-PhD program at Johns Hopkins after graduating summa cum laude from Yale in 2011, where he was awarded the Alpheus Henry Snow Prize, the top honor awarded to an undergraduate. After completing a prestigious Fellowship in Bioethics at the National Institutes of Health Clinical Center and his first two years of medical training, he embarked on collaborative PhD research with Sharon Gerecht, former INBT director and core researcher. His work focused on probing the effects of oxygen on early cardiac development and on modeling the genetic heart disease arrhythmogenic cardiomyopathy, combining stem cell differentiation, three-dimensional platforms, and developmental biology techniques.

Alumni Achievements

Kelly Karl

PhD (’22) Molecular Biophysics, Mentor: Kalina Hristova, PhD

Kelly Karl is a research scientist in the Scientific Leaders Program at GSK. Her primary job responsibility is to increase throughput of antigen screening for vaccines. “INBT was a great experience. There was so much support from the faculty and staff and the science was great too! I’m so glad that I got to work under my advisor at this excellent school,” said Karl.

Elmer Zapata-Mercado

PhD (’22) Biophysics, Mentor: Kalina Hristova, PhD

Elmer Zapata-Mercado is a Biophysical Society-sponsored legislative fellow for U.S. Senator Chris Coons (D-Delaware). Zapata-Mercado’s work involves helping to build the health and education portfolio. Specifically, he is focusing on diversity, equity, and inclusion in STEM, how to help HBCUs so they can become R1/R2 universities, and implementation of drug price reductions.

Ashley Kiemen

PhD (’21) Chemical and Biomolecular Engineering, Mentor: Denis Wirtz

Ashley Kiemen is an assistant professor in the computational division of the Johns Hopkins Department of Pathology. Her main research focus is understanding microanatomical invasion patterns of pancreatic cancer using 3D reconstruction technology of serial histological sections.

David Stern

PhD (‘22) Chemical and Biomolecular Engineering, Mentor: Honggang Cui, PhD

David Stern is a research scientist at Gilead Sciences. He leads formulation and process development activities for preclinical and clinical projects to develop solid oral dosage forms and parenteral drug products and takes pharmaceutical drug candidates from research stage through commercial manufacturing.

Master’s Co-Op Hosts Largest Cohort in Program’s History

By Sulaiman Jenkins and David Lee

For seven years, the Institute for NanoBioTechnology has been home to the Master’s Industry Cooperative (Co-Op) Education Program, an initiative designed to provide students with an alternative curriculum where they earn valuable industry experience at various companies. Applicants from three departments (Chemical and Biomolecular Engineering, Material Science and Engineering, and Mechanical Engineering) embark on a six-month professional journey where they gain insight related to their research interests and develop a variety of technical and non-technical skills, all while earning credit toward their degrees. This year has seen the largest cohort in the program’s history with a total of 15 students, and its gender distribution of near 50% women/50% men reflect our efforts to increase representation in every cohort.

Through many hardships, the pandemic years have highlighted the value of resiliency and flexibility in all spectra of society. This narrative could even be found in the past few Co-Op cohorts. Despite the myriad diffi-

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culties, INBT was able to welcome a diverse and growing group of students and companies—all thanks to its solid foundation built by the founders of the program. Through a lens of flexibility and resiliency, the daunting obstacles became opportunities and challenges to overcome. INBT responded deftly by collaborating with the many internal and external stakeholders to create novel solutions and flexible arrangements that provide maximum value for the students.

David Lee, the director of corporate partnerships, and Sulaiman Jenkins, the director of academic programs, have spent the past few months preparing for the newest cohort by way of interviewing them, laying out the expectations of the Co-Op program, and gauging their employment interests. A number of students have already secured offers at various biotech, pharmaceutical and even defense companies; historically, a significant number of Co-Op participants go on to receive full-time employment offers after they finish the program.

57 Participants

47% Women Participants

Master’s Co-Op Program at a Glance

Looking ahead, both Lee and Jenkins are eager to explore ways to make the Co-Op program even more impactful. They aim to achieve this through strategically identifying short- and long-term action items and executing the plans with an eye towards greater collaboration and growth. The more immediate action items include: 1) increasing the number of new companies that will participate, 2) designing a robust professional development program to enhance students’ professionalism and competitiveness in the workplace, and 3) developing various cohort-building activities that

Yitong Chen

Mechanical Engineer II at BD

January–June 2022

enable participants to share their respective experiences and insight with each other. Lee and Jenkins believe that the program has the potential to expand into a schoolwide collaborative educational platform that will both amplify the value proposition of the Whiting School of Engineering and maximize educational opportunities for students.

Over the years, the Master’s Co-Op program has provided students with meaningful industry experience, and with Lee and Jenkins at the helm, the program is poised to go to even greater heights!

“The best part of my experience was the amount of responsibility the team gave me from day one. They treated me like one of their own and did not hesitate in allowing me to jump in immediately and contribute to the project.”

Co-Op Participant at BD

Citizen Scientists in Bloom

By Gina Wadas

Armed with low-cost but powerful paper microscopes, Johns Hopkins alum Ikbal Choudhury and his team are bringing science education and environmental conservation to teachers and young students in low-resource and low-income communities in the United States, India, and Bangladesh. Through their non-profit Open Field Collective, the team trains teachers in microscopy and spectroscopy techniques to help communities monitor local environmental health.

“Our goal is both to educate and inspire students and ordinary citizens in scientific exploration by giving them the tools they need to monitor the health of the environments in which they live,” says Choudhury, who received his PhD in mechanical engineering from Johns Hopkins in the spring.

With funding from the American Society of Cell Biology, National Geographic, and Awesome Foundation, the team developed an algal bloom monitoring program. The program relies on paper microscopes sold by Foldscope Instruments, which cost about $2, and basic spectroscope equipment. For many of the program participants, the program provides their first view of the microscopic world.

The team then teaches participants how to apply those microscopy and spectroscopy techniques to identify algal species collected from local water sources. Algae are environmental indicator species—the presence, or absence, of certain species helps people analyze local water and environmental health. Participants upload their findings to a database on Open Field

Collective’s website, which can be used to monitor environmental health long term. The idea for the programs took seed in 2020 during the COVID-19 pandemic when Choudhury was a PhD candidate working with the Johns Hopkins Institute for NanoBioTechnology. Unable to perform his experiments because of widespread shutdowns, he used his free time to connect with like-minded people on social media who wanted to organize science programs that engage people of all ages.

The algal bloom monitoring program has a special significance for Choudhury, as he was involved in a similar project when he was 13 years old. His home country of India had a national initiative to engage more children in science topics. Children took field trips with scientists and conducted their own experiments. Choudhury’s project involved identifying microbes present in drinking water he collected from wells, ponds, and rivers in and around his hometown of Silchar. As he identified species, he was amazed by the diversity of life in a seemingly insignificant pond and found the experience to be a catalyst for his interest in science discovery.

The team had originally tried teaching students in virtual camps, but they soon realized that students’ instructional needs varied across the United States and internationally, and they needed teachers as anchor points to implement strategies that worked best with their students. They now train fifth- to ninth-grade teachers in small cohorts over the course of a few short weeks.

“The teachers are the ones really helping us every step of the way and they are finding ways to incorporate the materials into their curriculum,” says Ankita Jha, Open Field Collective co-founder and a postdoctoral researcher at the National Institutes of Health.

The team has trained more than 150 teachers and reached 600 students. They have print materials available to people in remote areas or in areas with limited access to digital communications. Their training content appears in different languages, too. The team also noticed that the program has instilled in participants a sense of responsibility and accountability to their local environment.

The team is currently recruiting a new cohort in Nepal and several local governments in India have become involved to help expand the program. While the algal bloom monitoring program has become

the organization’s flagship program, the team wishes to develop more pilot projects in different fields and communities, such as astronomy.

“We don’t want to restrict ourselves to just spectroscopy and microscopy. We are identifying more researchers and teachers who want to get involved with us to make science education more accessible and equal,” Choudhury says.

The other Open Field Collective co-founders include Sayak Bhattacharya, a scientist at Johnson & Johnson; Ankit Dwivedi, bioinformatics analyst at the University of Maryland School of Medicine; and Kanika Khanna, postdoctoral researcher at University of California, Berkeley.

INBT Welcomes New Director of Academic Programs

by Sulaiman Jenkins

I’m pleased to assume the role as INBT’s new director of academic programs as of March 2022. I have been overwhelmed with the help and support I’ve received from faculty and staff alike, especially during my onboarding, and I was immediately struck by the INBT’s congenial environment. Having such qualities and features in an organization is a recipe for success, so it is no surprise to see the level of innovation and achievement that the institute enjoys on a regular basis.

Although I’ve found myself immersed in a scientific environment, my background is in language and applied linguistics. After obtaining my master’s degree in language teaching from NYU in 2004, I traveled to the Middle East, where I spent 17 years as an English professor and program administrator. I became adept at finetuning aspects of their academic programs and identifying key areas of growth and developing strategic plans to enhance the academic output of thousands of students. As a former student, professor, and administrator, I have enjoyed gaining a comprehensive overview of educational programs and developing impactful initiatives that take into account the needs of all stakeholders. In joining the INBT, my goal is to use that knowledge and experience as I assume responsibility for administrating the Research Experience for Undergraduate (REU), Master’s Co-Op, and Nanotechnology for Cancer Research (T32) programs.

This past summer, I got my feet wet running the REU program. In working diligently with Denis Wirtz and Efie Kokkoli (the PIs of the program) and Ada Simari, INBT’s senior academic director, we built a robust summer schedule for the newest cohort. They learned important technologies in various research labs, developed their digital identities and other professional skills through Gina Wadas’, INBT’s communications associate, insightful professional development seminars, participated in the CARES Symposium, and attended INBT’s annual Nano-Bio Symposium.

Currently, I’m working with Wirtz on the Nanotechnology for Cancer Research (T32) program, which got underway in September 2022. Among the goals of the program are for Ph.D and postdoc par-

ticipants to develop technologies that introduce new modalities for molecular imaging, develop new high-throughput diagnostic tools, and engineer novel drug/ antibody/siRNA viral and non-viral delivery systems to treat human cancers. We are also coordinating with the Sidney Kimmel Comprehensive Cancer Center to help afford opportunities for the participants to take full advantage of the research and clinical resources available.

I’m also pleased to work alongside David Lee, the director of corporate partnerships, as we co-manage the Master’s Co-Op program. Since our October deadline, we have been meeting with students to ascertain their career and academic goals and then placing them in companies that are most aligned with their interests. As the one responsible for the academic management of the Co-Op experience, I endeavor to develop a roadmap that will help equip students with the professional knowledge

necessary to thrive as they continue to gain valuable industry experience.

Beyond the excitement I have for being an integral part of the academic direction of the INBT, I am equally excited to work with Hai-Quan Mao and Sashank Reddy, two visionaries who have recently taken the helm as the director and associate director of the institute. Their openness and commitment to innovation will enable me to develop educational initiatives that increase the INBT’s recognizability among students, and it will enable me to explore new ways to enhance students’ academic and research experiences.

Suffice it to say, I am ecstatic to work with such amazing people at the forefront of innovation doing incredible things, incredibly grateful to work with such stellar and helpful colleagues, and truly happy to be a part of the INBT and Hopkins family. Let’s get it!

Sulaiman Jenkins with Adrian Johnston, chemical and biomolecular PhD candidate.