Research Project

The CSBC U01 Research Project @ UPenn/Wistar Institute


Research Program Title

A plasticity and reprogramming paradigm for therapy resistance at the single cell level

List of Collaborating Institutions

University of Pennsylvania
Wistar Institute

Lab Websites

Project Description

Targeted therapies in melanoma have shown enormous promise in the sense that they can show dramatic reductions in tumor burden, with melanoma being a particularly stark example. However, this promise has failed to be fully realized because of the emergence of resistant tumor cells, which repopulate the tumor and are subsequently difficult or impossible to treat effectively. Typically, scientists have thought of therapy resistance as having genetic origins, with rare mutant tumor cells surviving therapy because of a mutation that causes resistance. Recent work from our labs using advanced single cell analysis, however, suggest that, at the point of attack, there may be other, complementary, non-genetic mechanisms that could also govern exactly why some rare cells are able to evade the effects of the therapy. Subsequently, the targeted therapy itself can reprogram these rare cells into a stably resistant population. This more nuanced “plasticity and reprogramming” view of resistance at the single cell level has opened the possibility of a far richer set of targets that can be exploited for forestalling therapy resistance; however, the current set of tools and models, both experimental and computational, for identifying these targets are underdeveloped and the origin of these biological processes remain mysterious. Here, we propose to develop and apply new concepts and methods in experimental and computational single cell biology to tackle the problem of non-genetic therapy resistance, translating our basic science results towards the clinic through the use of sophisticated in vivo models of melanoma. Our goal is to identify and validate the pathways that govern cellular plasticity in melanoma, develop computational tools to identify the gene networks that drive the formation of cellular plasticity, and ultimately test these interactions in in vivo mouse models. In conjunction, we developing tools for also specifically targeting the reprogramming phase of resistance, ultimately using all these data collectively to inform models of dosing regiments that we can test in in vivo systems. Collectively, our results may help shape treatment of melanoma to avoid the problem of resistance.


Arjun Raj

Arjun went to UC Berkeley, where he majored in math and physics, earned his PhD in math from the Courant Institute at NYU, and did his postdoctoral training at MIT before joining the faculty in Penn Bioengineering in 2010, where he is currently an associate professor. His research focus is on the developed experimental techniques for making highly quantitative measurements in single cells and models for linking those measurements to cellular function. His ultimate goal is to achieve a quantitative understanding of the molecular underpinnings of cellular behavior.

Ravi Radhakrishnan

Ravi Radhakrishnan is a trained Chemical and Biological Engineer who obtained his Bachelor’s Degree from the Indian Institute of Technology in Madras, India, and his Doctoral Degree from Cornell University in Ithaca NY. After Postdoctoral training at the Massachusetts Institute of Technology and at the New York University, he joined the faculty of the University of Pennsylvania, where currently holds the title of Professor of Bioengineering and Professor of Chemical and Biomolecular Engineering. He is also a member of the graduate groups of Genomics and Computational Biology and Biochemistry and Molecular Biology. He is a founding member and the Interim Director of the Penn Institute of Computational Sciences and a member of the Penn Physical Sciences in Oncology Center. Radhakrishnan directs a computational research laboratory with research interests at the interface of biophysics, chemical physics and biomedical engineering. The goal of his computational molecular systems biology laboratory is to provide quantitative and mechanistic molecular and cellular level characterization of complex systems and formulate quantitatively accurate and predictive models in physiology and pathology for systems pharmacology and insilico oncology applications. His lab specializes in several computational algorithms ranging from techniques to treat electronic structure, molecular dynamics, Monte Carlo simulations, and hydrodynamics of complex fluids, in conjunction with the theoretical formalisms of statistical mechanics, and applications of high performance computing in parallel architectures.

Junwei Shi

While whole exome sequencing of HCC cancer genome revealed many oncogene mutations, none of these genetic alterations lead to directly actionable therapeutic opportunities. A challenge in the HCC research community is to reveal non-oncogene dependencies that could be exploited with targeted therapeutics. A major objective of the lab is to annotate and dissect these non-oncogene vulnerabilities in HCC. To approach this, we will use our recently developed domain-focused CRISPR genetic knockout screening technology. This method directs the CRISPR-mediated mutagenesis to gene sequences encoding critical protein domains, which generates larger fraction of functional null alleles thus increases the severity in a phenotypic genetic screening. In contrast to RNA interference-based methods or prior CRISPR-based screening approaches, this new method is not only more efficient than other screening approaches, but also has the potential to evaluate protein domain function directly from genetic screening, and may allow high-throughput identification of protein domains that are suitable drug targets in cancer. Coupling with functional genomics screening, biochemical, and pre-clinical mouse models of HCC approaches, we will investigate the aberrant transcription signaling networks of HCC and explore them as potential therapeutic opportunities in HCC. Since genetic screenings are only as successful as the underlying technology, a major focus of the lab is to further optimize and expand our screening toolbox. Projects are underway to engineer different Cas proteins for multiplex genetic screening using a variety of methods, including structure-guided rational design and directed evolution. Our ultimate goal is to uncover complex genetic interactions in HCC that are therapeutically tractable.

Abhyudai Singh

Abhyudai Singh earned his bachelor’s degree in mechanical engineering from the Indian Institute of Technology in Kanpur, India. He received master’s degrees in both mechanical and electrical & computer engineering from Michigan State University, and a master’s degree in ecology, evolution and marine biology from University of California Santa Barbara (UCSB). After earning his doctoral degree in electrical & computer engineering in 2008, also from UCSB, he completed postdoctoral work in UC San Diego’s Department of Chemistry and Biochemistry. Since 2017, he is an Associate Professor in the Departments of Electrical & Computer Engineering, Biomedical Engineering and Mathematical Sciences at the University of Delaware. His research interests are in Systems Biology, with a particular focus on modeling, analysis and control of biomolecular systems at the single-cell level.

Ashani T. Weeraratna

Dr. Weeraratna is the Ira Brind Professor and Co-Program Leader, Immunology, Microenvironment & Metastasis Program Member at the Wistar Institute. Born in Sri Lanka and raised in Southern Africa, Weeraratna first came to the United States in 1988 to study biology at St. Mary’s College of Maryland. She earned a Ph.D. in Molecular and Cellular Oncology at the Department of Pharmacology of George Washington University Medical Center. From 1998 to 2000, she was a post-doctoral fellow at The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins Oncology Center, before joining the National Human Genome Research Institute as a staff scientist. In 2003, she moved to the National Institute on Aging, where she started her own research program. Weeraratna joined The Wistar Institute in 2011.Her primary research focus is on melanoma and how changes in the tumor cell’s microenvironment, which include changes in normal cells, blood vessels, and secreted molecules might initiate the disease’s spread to other parts of the body and also make it resistant to treatment. She is specifically interested in how age-related changes drive the progression of cancer.Through speaking engagements and social media, Dr. Weeraratna diligently promotes skin safety, from urging proper sunscreen use to regular mole checks, as well as the dangers of indoor tanning. She is also a fierce champion of and a mentor for women in science and girls pursuing a science, technology, engineering, and math (STEM) education.