Author: The Wistar Institute

Tian is a molecular systems biologist whose research is focused on understanding how gene expression is regulated at the RNA level. His lab was among the first to discover the widespread nature of alternative polyadenylation (APA) using bioinformatic and genomic approaches. They have also revealed multiple molecular mechanisms that regulate APA, cellular consequences of APA isoform regulation in diverse biological systems. His recent interests are APA regulation in cancers.

Tian received his B.S. degree in biochemistry from East China University of Science and Technology and his Ph.D. degree in molecular biology from Rutgers Biomedical and Health Sciences (formerly UMDNJ). He was a postdoctoral fellow in bioinformatics and genomics at Johnson & Johnson Pharmaceutical Research & Development in La Jolla, California. In 2003, he established his research group at Rutgers New Jersey Medical School, where he rose through the ranks and became a tenured professor in 2014. Tian joined The Wistar Institute in 2020.

The Tian Laboratory

Expression of the genetic code, from DNA to protein, can be regulated at different stages, much of which takes place after RNA is made. The Tian lab studies RNA biology using a variety of approaches including functional genomics, computational biology, and molecular and cellular biology. They have contributed important knowledge on the mechanisms and consequences of alternative polyadenylation (APA) in development and disease.

Cleavage and polyadenylation (CPA) is responsible for the 3′ end maturation of almost all protein-coding and long non-coding RNAs in eukaryotic cells. The CPA site, commonly known as polyA site or PAS, also plays a key role in termination of transcription. Over 70-80% of human genes harbor multiple PASs, resulting in expression of mRNA isoforms with different 3′ termini, a phenomenon known as alternative cleavage and polyadenylation (APA). APA isoforms can differ in coding sequences and/or 3’ untranslated regions (3’UTRs). The Tian lab has been using a battery of sequencing tools, based on short-read and long-read sequencing technologies, to comprehensively map PASs across species and understand APA site evolution. They are also using single cell RNA sequencing methods to examine cell type specificity of APA isoform expression under physiological and pathology conditions. Moreover, using these technologies, the Tian lab is addressing how PAS choice is coupled with other events of mRNA biogenesis and processing, such as transcription, splicing and base modifications.  

While most PASs in human genes are located in the last exon, a sizable fraction (~20%) of genes display APA in regions upstream of the last exon. PAS usage upstream of the last exon, which has been named intronic polyadenylation, premature cleavage and polyadenylation or alternative terminal, leads to early transcriptional termination (ETT). While some ETT transcripts encode distinct proteins, the majority of them are unstable in the cell, making ETT a powerful mechanism to effectively inhibit gene expression. As such, regulation of ETT, often involving modulation of splicing and CPA activities as well as transcriptional elongation rate, can have substantial impacts on the gene expression program.  The Tian lab is developing tools to regulate genes through ETT. In addition, they are studying how perturbation of ETT impacts neoantigen expression in cancer cells with the goal of enhancing cancer immunotherapies.

The 3’UTRs of protein-coding transcripts play regulatory roles in mRNA metabolism, including mRNA decay, translation and subcellular localization. Sequence and structural motifs embedded in 3’UTRs contribute to 3’UTR functions through interactions with their cognate RNA binding proteins (RBPs) and microRNAs (miRNAs). The Tian lab recently reported widespread translation-independent endoplasmic reticulum association (TiERA) of mRNAs, in which 3’UTRs play an important role in modulating mRNA interactions with the endomembrane system in the cell. The Tian lab is studying how TiERA could impact cell signaling through localized mRNA translation. In addition, the Tian lab recently reported widespread transcript shortening in secretory cell differentiation. The phenomenon, named secretion-coupled APA (SCAP), was observed in multiple professional secretory cells. They are studying how SCAP perturbation in B cells can alter their differentiation into antibody-producing plasma cells, which are critical for humoral immunity. They are also pursuing novel therapeutics to modulate immune cells and cancer cells that display unique mRNA 3’UTR isoform biogenesis and metabolism.

Small molecule inhibitors of CPA (CPAi) have recently been found to be effective anti-cancer therapeutics.  The Tian lab has revealed multiple mechanisms by which CPAi can impact the transcriptome in a cell, including APA isoform changes and transcriptional readthrough. In addition, they found that cancer cells with a high CPA activity and a high proliferation rate are particularly vulnerable to CPAi, due to replication-transcript conflicts.  They are now developing novel, more potent CPAi compounds through medicinal chemistry and antisense oligonucleotides (ASOs) that are amenable to distinct therapeutic deliveries. In addition, they are studying cancer cell signatures that determine the effectiveness of CPAi in multiple cancer types.

Herlyn studies the normal and malignant tissue environment to develop rational approaches to cancer therapy, with a focus on melanoma, the most aggressive form of skin cancer.

Born and educated in Germany, Herlyn received his D.V.M. at the University of Veterinary Medicine, Hanover in 1970 and went on to receive a D.Sc. in medical microbiology at the University of Munich in 1976. He came to The Wistar Institute as an associate scientist in 1976, where he worked in the emerging field of monoclonal antibodies, a technology that formed the basis of a portion of today’s new targeted therapeutics. In 1981, Herlyn became an assistant professor and established a laboratory that is, today, one of the best-known research groups on the study of melanoma biology.

The Herlyn Laboratory

The Herlyn laboratory at The Wistar Institute focuses on the biology that underlies melanoma. His efforts have pioneered the use of the three-dimensional “artificial skin” cultures to study the behavior of both tumor and normal cells that sustain tumor growth, a system known as the tumor microenvironment. The Herlyn Laboratory has transformed the scientific understanding of stem cells as they relate to cancer, and their work on the networks of signaling pathways in melanoma has formed the basis of numerous therapies now in clinical trials or recently approved.

Due to the high demand for our cell lines, the Herlyn lab is pleased to collaborate with Rockland Immunochemicals Inc. for distribution.

Please contact Rockland customer service directly about acquiring our melanoma cell lines.

For help selecting lines, see the mutational chart below or search using Rockland’s website. For any questions, concerns, help, or other issues, please email Min Xiao at Wistar or contact customer service at Rockland.

View Cell Lines

Cell authentication has received considerable attention recently as more and more reports of cell line cross contaminations and misidentifications have come to light. As such, in 2008, we implemented and routinely perform Short tandem repeat (STR) profiling using AmpFlSTR® Identifiler® PCR Amplification Kit (Catalog Number 4322288) by Life Technologies which uses loci consistent with all major worldwide STR standards. PCR amplification and STR allele separation and sizing is performed by the Wistar Genomics Facility. Profile interpretation is performed in the Herlyn lab by interrogating the resulting DNA fingerprint to our internal database which includes over 1000 fingerprints, primarily Wistar Melanoma but also commonly used cell lines such as HeLa and 293T cells. The STR profile is provided here as a reference comparison to your results.

For additional inquiries, please email Min Xiao.

Download STR Profiles

The laboratory has generated more than 500 patient-derived xenografts (PDX), which have been extensively characterized. A selection of the PDX is available through Envigo.

For inquiries regarding any of the following techniques or resources, please email Jessica Kohn to be put in touch with the appropriate lab representative.

Cell Culture Techniques

Stem Cells

The Herlyn Laboratory seeks to further define the various signaling pathways that work in cancer cells in order to discover new opportunities to inhibit cancer growth through targeted therapeutics. Since therapy is increasingly guided by the genetic aberrations in tumors, Herlyn and his colleagues are developing combinations of compounds that take into account the genetic signature of tumors, with the specific goal of individualized cancer therapy. Currently, the Herlyn Laboratory collaborates with pharmaceutical companies as well as academic chemists and structural biologists to select and further develop compounds for tumor inhibition. Tumor heterogeneity, i.e., the differences between cells within one tumor, among different tumor lesions of the same patient, or between patients even if the tumors are of similar genetic signatures, provides major challenges for future therapy. The laboratory is developing biological signatures of melanoma cells that take into account the various forms of heterogeneity.

Another major effort of the Herlyn Laboratory is the study of therapy resistance and tumor dormancy. Tumor cells can become dormant in primary tumors or at any time after metastatic dissemination and can persist in the dormant state for many years, allowing tumors to resist treatment. Herlyn’s working hypothesis is that defined tumor subpopulations are central to dormancy and drug resistance due to their slow turnover and their non-responsiveness to growth signals. His efforts seek to define how tumor cells escape dormancy for growth, invasion, and metastasis, and how to best develop strategies for therapy.

The Herlyn lab is differentiating multi-potent stem cells from the human dermis and reprogrammed stem cells into melanocytes to test the hypothesis that melanocyte stem cells are more prone to transformation than fully differentiated cells, and that neighboring cells and matrix in the microenvironment play critical roles in differentiation and transformation. The lab has developed a complex, three-dimensional model that mimics human skin, and are using it to reconstruct each step in the melanoma development and progression cascade. Genes associated with melanoma are overexpressed or silenced with shRNA constructs in lentiviral vectors and the lab increasingly uses cDNA and sh (short hairpin) RNA libraries for our experiments. Ultraviolet light irradiation is mimicking the DNA damaging effect of sunlight. Skin reconstructs can also be grafted onto immunodeficienct mice for long-term observation. Besides isolating melanocytes and keratinocytes from skin, we have begun to differentiate them from ‘induced pluripotent stem’ (iPS). This source also allows the lab to generate an intact human inflammatory and immune system in vivo, including from melanoma patients where we have cell lines or patient-derived xenografts (PDX). Studies on interactions among tumor cells, fibroblasts and endothelial cells are also done in 3-D models, in which cells are embedded into collagen to mimic the tumor microenvironment. Growing cells in organ-like models induces major changes in gene expression similar to those in animals and patients, making such models superbly suited for studies of cell-cell signaling, matrix formation, and drug resistance.

The Herlyn lab is defining signal transduction pathways that are constitutively activated in melanoma and squamous cell cancer cells through autocrine and paracrine growth factors and genetic alterations. With shRNA and CRISPR/Cas9 in lentiviral vectors, the lab is identifying genes in tumor cells, stromal fibroblasts, and endothelial cells that are potential targets for therapy. In melanoma, the MAPK and PI3K pathways are primary targets for therapy, but other pathways are also explored for inhibition by small molecule compounds. Since therapy is increasingly guided by genetic aberrations in tumors, the lab is developing combinations of compounds that take into account the genetic abnormalities of tumors, with the long-term goal of individualized cancer therapy. In recent years, the lab has actively collaborated with pharmaceutical companies to obtain compounds in early stages of preclinical and clinical development. Increasingly, the lab is collaborating with academic chemists and structural biologists to select and further develop compounds for tumor inhibition.

Tumor cells can become dormant in primary tumors or at any time after metastatic dissemination and can persist in the dormant state for many years, allowing them to resist treatment. The working hypothesis of the Herlyn lab is that tumor-maintenance cells (tumor stem cells) are central to dormancy due to their non-proliferation or very slow turnover and their non-responsiveness to growth signals. The lab is delineating tumor dormancy in melanoma and characterizing subpopulations of cells with a major focus on slow-proliferating cells that have high proliferation potential hypothesizing that these cells are critical for dormancy and therapy resistance. The lab will then define how tumor cells escape dormancy for growth, invasion, and metastasis, and developing strategies for therapy. Using the lab’s unique 3-D melanoma, Herlyn and his lab determine how microenvironmental cues from the matrix or other cells such as B cells, macrophages, and endothelial cells drive gene activation, leading to a signaling cascade for proliferation and invasion. These studies will lead to in-depth investigations of tumor heterogeneity and the dynamic regulation of genes that define subpopulations with specialized biologic functions. The long-term goal is to develop strategies for two therapies, one for eliminating the bulk of the tumor, the other for small subpopulations that escape all major therapeutic strategies. Such combinations should achieve elimination of all tumor cells, which is required in melanoma because single tumor cells are capable of tumor induction in immunodeficient animals.

Multipotent stem cells with neural crest-like properties have been identified by our lab and others in the dermis of human skin. The stem cells display self-renewal capacity and differentiate into neural crest derivatives including epidermal pigment-producing melanocytes. Neural crest-like stem cells (NCLSC) share many properties with aggressive melanoma cells, such as high migratory capabilities and expression of neural crest markers. However, little is known about which intrinsic or extrinsic signals determine proliferation or differentiation of stem cells. In our studies we have focused on major developmental pathways. Notch signaling is highly activated in stem cells, similar to cells within melanoma spheres. Inhibition of Notch signaling reduces proliferation of stem cells, induces cell death, and down-regulates non-canonical Wnt5a, suggesting that the Notch pathway contributes to maintenance and motility of the stem cells. In 3-D skin reconstructs, canonical Wnt signaling promotes differentiation of stem cells into melanocytes. This differentiation is triggered by the endogenous Notch inhibitor Numb, which is upregulated in the stem cells by Wnt7a derived from UV-irradiated keratinocytes. These studies reveal a crosstalk between the two conserved developmental pathways in human skin and highlight the role of the skin microenvironment in driving the generation of stem cells, and possibly tumor-initiating cells. They also provide a rationale for identifying novel targets for therapy among those groups of genes that are intimately involved in melanocyte development and highly expressed in melanoma while being largely absent in normal melanocytes.

The Herlyn laboratory has a long history of collaborations with members of the Penn/Wistar campus, particularly those who have had an interest in melanoma. Additionally, the lab has partnered with several outreach organizations around the world to support melanoma research. Learn more about these collaborations.

The Herlyn laboratory is supported by a variety of grants to study melanoma.

Learn more about grants supporting this research.

The Herlyn laboratory can provide access to several additional resources. To request a copy of a research paper published by the Herlyn laboratory, or for additional lab resources, contact:

Jessica Kohn
215-495-6883
The Wistar Institute
3601 Spruce Street
Philadelphia, PA 19104

Sarma studies the mechanisms of RNA-mediated epigenetic gene regulation to understand how the loss of chromatin modifier-RNA interactions impacts cellular function.

Sarma completed her graduate studies with a Ph.D. in biochemistry from Rutgers University. She conducted her postdoctoral training at the Massachusetts General Hospital-Harvard Medical School, and joined The Wistar Institute in 2016 as an Assistant Professor.

The Sarma Laboratory

The Sarma laboratory is interested in the mechanisms of epigenetic gene regulation, or how the dynamic modifications of the architecture of chromatin, the complex of DNA and proteins within the nucleus of our cells, impacts gene expression and cellular function. The lab investigates consequences of epigenetic alterations in neuronal cancers and neurodegenerative diseases using a combination of biochemistry, cell and molecular biology with genome wide approaches to gain mechanistic insight into how chromatin architecture is modified in disease. The goal is to identify new pathways and interactions that can be targeted to correct these epigenetic perturbations.

We are interested in understanding the molecular mechanisms of RNA mediated epigenetic gene regulation. Aberrations in epigenetic gene silencing can be a causal mechanism of numerous human disease and developmental syndromes. We use a combination of biochemical, cell biological and functional genomics approaches in embryonic stem cell, neural stem cell, and cancer cell models to elucidate the molecular mechanisms and functional implications of RNA containing chromatin structures in gene regulation and in genome organization.

We are fascinated by triplex nucleic acid structures known as R-loops, that are comprised of a DNA:RNA hybrid and displaced ssDNA. R-loops are formed during transcription when the mRNA invades dsDNA (forming the DNA:RNA hybrid) and exposes a ssDNA that can then adopt a G quadruplex (G4) structure (see figure below). Transcription from G rich repetitive regions results in the formation of G4 DNA that impedes the reannealing of DNA strands, promotes DNA:RNA hybridization, and stabilizes R-loops. In addition to known regulatory roles, R-loops are closely linked to increased DNA damage and genome instability. Stable aberrant R-loops have also been discovered in several neurological disorders, neurodegenerative diseases, and cancers. Discovering the genome-wide locations of R-loops is challenging because of the requirement for large sample size and inefficient enrichment using the monoclonal antibody that recognizes the RNA:DNA hybrid within R-loops. We have developed a new antibody independent approach, called MapR, to identify native R-loops genome-wide. Some questions that we are interested in exploring are:

• Where do R-loops form in specific disease states?
• How do unscheduled R-loops contribute to neurodegenerative diseases and cancers?
• What are the protein factors that function in R-loop resolution and stabilization?
• How can R-loops impact gene regulation and genome organization in disease states?
• Do long non-coding RNAs localize to chromatin through R-loop formation?

Price’s research focus is on how DNA viruses co-opt and manipulate cellular RNA processing pathways.

Growing up on the west coast, Price obtained his Bachelor’s of Science degree in Genetics and Cell Biology at Washington State University. Moving to the east coast, he obtained a Ph.D. in Molecular Genetics and Microbiology from Duke University in 2016. To pursue postdoctoral research, Price moved to Philadelphia, where he was associated with the University of Pennsylvania and the Children’s Hospital of Philadelphia. In 2023 he joined the Wistar Institute as an Assistant Professor in the Gene Expression and Regulation Program, which became the Genome Regulation and Cell Signaling Program in 2024.

The Price Laboratory

The Price Lab studies how DNA viruses take over and subvert host cell biology, shining light on the fundamental processes they must steal from their host to replicate. While viruses have evolved to be masters of molecular mimicry, any viral process that deviates from standard cell biology allows a host cell to sense infection. DNA viruses obligately use cellular RNA processing machinery to make viral transcripts, yet are constrained by a hard limit on maximum genome size. This means that viruses often express tens to hundreds of messages from coding space the size of a single cellular gene. By pushing cellular machinery to the absolute limit, these pathogens have adopted a high risk, high reward strategy for maximizing gene expression that can inadvertently activate the innate immune system.

Our goal is to discover how viruses balance the ability to produce diverse RNAs from limited coding capacity while preventing the deleterious formation of non-self RNAs. In doing so, we aim to uncover therapeutic vulnerabilities in the transcriptional programs enacted by diverse viruses. Beyond virology, our research will reveal how transcriptional processes affect innate immunity and inflammation, with broad implications for the progression of autoimmune diseases and cancers where RNA biogenesis has become dysregulated.

Research Assistant

Viruses with limited genome size maximize coding capacity via regulated expression of genes on both DNA strands. It is thought that convergent transcription of DNA virus genomes leads to the production of dsRNA, and this postulate is supported by the fact that these viruses encode inhibitors of dsRNA sensing pathways. However, there is little primary evidence of dsRNA accumulating during DNA virus infection. In my prior work I utilized monoclonal antibodies directed against dsRNA to examine cells infected by adenovirus, yet I was unable to detect dsRNA. However, infection with adenovirus mutant viruses that exhibit inefficient splicing of viral transcripts leads to robust dsRNA production in the nucleus. The presence of nuclear dsRNA during mutant adenovirus infection is accompanied by activation of cytoplasmic sensors PKR and RNase L, yet there is no known nuclear sensor of dsRNA. Assessing the role of nuclear dsRNA sensing is becoming increasingly important as it is more appreciated that hyperactivity of cellular antiviral sensors can lead to autoimmune disease. Specific questions include:

• How Is nuclear dsRNA sensed by the innate immune system?
• How does nuclear recognition of dsRNA communicate with existing components of the immune system?
• How do nuclear dsRNA-binding proteins interact with viral dsRNA?

Unprocessed adenoviral RNAs are likely to form dsRNA if they are synthesized in close proximity to antisense transcripts. Viruses that can regulate sense and antisense transcription in spatially distinct nuclear compartments would allow for localized processing that would preclude dsRNA formation. It was previously shown that viral DNA replication takes place inside biophysical viral replication centers, and that RNA synthesis occurs in a shell surrounding these regions. However, how this spatial segregation occurs is unknown. Specific questions include:

• How are viral genomes spatially organized?
• How do DNA viruses spatially regulate RNA transcription?
• Does transcription of viral genomes lead to viral mutation or genome instability?

Herpesvirus lytic transcripts are often intron-less and bypass many canonical processing steps on the path to expression. Viral RNA-binding proteins, whose functions are only recently being fully understood, often mediate these processes. In contrast, latent phase infection encodes complex transcripts with extensive alternative splicing reliant on cellular factors for expression. Furthermore, herpesvirus latency transcripts are prime targets for uncovering novel roles for non-coding RNAs, as they are often expressed in the absence of viral proteins. Projects will be available in the lab to study both the RNA-protein and RNA-RNA interactions of these transcripts using advanced proteomic and sequencing technologies.

Nishikura studies the process of RNA editing and has made pioneering strides in the understanding of how our cells utilize RNA to control gene expression and protein synthesis and how the malfunction of this process can lead to disease. She discovered and characterized a family of enzymes called ADAR, which are responsible for editing the RNA transcribed from DNA.

Nishikura received a bachelor’s and master’s degree in biochemistry from Kanazawa University, Japan, and obtained her Ph.D. in medical science from Osaka University, Japan, performing much of her thesis work at the Medical Research Council Laboratory of Molecular Biology (LMB) in Cambridge, England. She returned to LMB for her first postdoctoral fellowship before obtaining a second fellowship at Stanford University. Nishikura first joined The Wistar Institute in 1982 and became a full professor in 1995.

The Nishikura Laboratory

The Nishikura laboratory explores the phenomenon of RNA editing, which regulates expression of certain gene products by changing the sequence context of mRNAs. One type of RNA editing involves the conversion of adenosine residues into inosine specifically in double-stranded RNA (dsRNA). This A-to-I RNA editing is catalyzed by members of the ADAR (adenosine deaminases acting on RNA) gene family, discovered in the lab.

Postdoctoral Fellow

The research focus of the laboratory is to better understand the functions of ADAR as well as cellular processes regulated by A-to-I RNA editing and to identify possible new therapies based on these processes.

View Previous Projects and Past Accomplishments by the Nishikura lab.

Murphy studies the genetics of the p53 tumor suppressor protein. Her laboratory focuses on genetic variants of p53 that exist in populations of African-descent (P47S and Y107H) and Ashkenazi Jewish descent (G334R). Her work seeks to understand the impact of these genetic variants of p53 on cancer risk and the efficacy of cancer therapy. She also seeks to identify personalized medicine approaches for tumors with these variants. Therefore, her work has direct relevance for improving the cancer prognosis and therapy of African and Ashkenazi Jewish Americans. Murphy also studies the cancer-survival protein HSP70. Her lab employs a novel series of HSP70 inhibitors for melanoma and colorectal cancer therapy.

Murphy obtained a B.S. degree in biochemistry at Rutgers University, followed by a doctorate in molecular biology at the University of Pennsylvania School of Medicine. In 1994, she began postdoctoral research at Princeton University in the laboratory of Arnold J. Levine, Ph.D., the co-discoverer of p53. In 1998, Murphy became an Assistant Professor at Fox Chase Cancer Center, where she was promoted to Associate Professor in 2003, and Full Professor in 2011. She joined The Wistar Institute in 2011 and became Program Leader of the Molecular and Cellular Oncogenesis Program in 2012. Murphy is an adjunct professor at Drexel University College of Medicine and The Perelman School of Medicine at the University of Pennsylvania.

The Murphy Laboratory

The Murphy laboratory focuses on two cancer-critical proteins involved in tumor cell survival and death: HSP70 and p53. p53 is the most frequently mutated gene in human cancer and is widely regarded as the most important anti-cancer defense protein in the body. The lab studies genetic variants of the p53 gene that exist in different ethnic groups. This work seeks to understand the impact of these genetic variants on the increased cancer burden experienced by these groups. Work in the Murphy lab also aims to identify novel cancer therapies that are more effective on tumors that contain genetic variants of p53 that exist in African Americans and Ashkenazi Jewish populations to improve personalized medicine.

The HSP70 protein is highly expressed in the majority of human tumors but is largely undetectable in normal cells, making it an ideal cancer target. The Murphy lab uses a series of novel HSP70 inhibitors they have created for the therapy of human tumors, with focus on colorectal cancer and melanoma. They also seek to understand why tumors that express high levels of HSP70 are more aggressive and are associated with poorer prognosis.

p53 is the most important gene in human cancer. Up to 60 percent of human tumors contain mutations in p53, making it the most frequently mutated gene in human cancer. In addition, germline mutations in p53 cause a syndrome called Li Fraumeni disease where people affected develop multiple tumors of the brain, breast, bone, and adrenal cortex before their second decade of life. Therefore, alterations that reduce p53 function have tremendous potential to increase cancer risk.

Unlike other tumor suppressor genes and oncogenes, p53 is unique because it possesses a number of coding region variants that differ in different ethnic populations. Our work has identified two coding region variants in p53 that exist in individuals of African descent. We find that these variants show impaired tumor suppressor function and may contribute to the increased cancer risk and reduced efficacy of cancer therapy, currently experienced by African Americans. Most recently, we have identified chemotherapeutic drugs that preferentially eradicate tumors that contain these African-centric variants of p53. A major goal in the laboratory is to improve the treatment of cancers from individuals of African descent.

HSP70 is a cancer-critical chaperone protein that allows tumor cells to survive under conditions of stress and aneuploidy by preventing proteotoxic stress. We identified a novel series of inhibitors for HSP70 that are potent and effective anti-cancer agents. More recently, we discovered that a significant fraction of HSP70 in tumors is localized to mitochondria. We modified our inhibitor to target mitochondrial HSP70, and found that this compound, which we call AP-4-139B, can effectively target melanoma tumors in mice, and can inhibit melanoma metastasis, with no evidence for toxicity to normal tissues. We also find that this compound extends the response of melanoma to current therapies like BRAF and MEK inhibitors. Our studies in this area seek to position our HSP70 inhibitors for eventual use in humans. These studies are done in collaboration with the Salvino laboratory at Wistar.

Lieberman studies how certain viruses establish a long-term latent infection that can lead to cancer or autoimmune disorders.

Lieberman joined The Wistar Institute in 1995 as an assistant professor. He earned his bachelor’s degree in chemistry from Cornell University and a doctorate in pharmacology/virology from The Johns Hopkins University School of Medicine, which was followed by a postdoctoral fellowship at the University of California, Los Angeles.

Lieberman Chairs the Program in Gene Expression and Regulation at the Ellen and Ronald Caplan Cancer Center at The Wistar Institute. In 2010, Lieberman became the first director of The Wistar Institute Center for Chemical Biology and Translational Medicine. Using the advanced screening technologies of Wistar’s Molecular Screening Facility, the Center enables scientists to identify and characterize new molecules and compounds that hold the most promise for developing into therapeutic drugs for cancer and other diseases.

The Lieberman Laboratory

Research in the Lieberman laboratory centers on understanding how the cancer-associated viruses persist in a latent state and increase the risk of cancer and autoimmune disorders. EBV and KSHV establish latent infections that are associated with several human malignancies, including Burkitt’s lymphoma, nasopharyngeal carcinoma, Hodgkin’s disease, and post-transplant lymphoproliferative disorder for EBV, and Kaposi’s Sarcoma for KSHV. EBV has also been implicated in multiple sclerosis and other autoimmune disorders.

Lieberman and his team found that oncogenic viruses can interact with cellular proteins that regulate telomeres—the repetitive DNA sequences found at the ends of chromosomes. Telomeres protect chromosomes from loss of genetic information, and a similar process is thought to preserve the virus during latency. The Lieberman laboratory worked out several biochemical pathways that control the stability, replication, and gene expression patterns of the latent virus. New research also focuses on the epigenetic controls of latent viruses and human telomeres, and how interactions between viruses and telomeres may induce a malignant transformation of the infected cell.

Research in the Lieberman laboratory centers on understanding how the cancer-associated viruses, like Epstein-Barr virus (EBV) and Kaposi’s Sarcoma Associated Herpesvirus (KSHV), persist in a latent state and increases the risk of cancer cell evolution. EBV and KSHV establish latent infections that are associated with several human malignancies, including Burkitt’s lymphoma, nasopharyngeal carcinoma, Hodgkin’s disease, and post-transplant lymphoproliferative disorder for EBV, and Kaposi’s Sarcoma for KSHV.

The researchers have recently found that viral DNA replication and maintenance is regulated by interactions with cellular telomere binding proteins. Telomeres are the repetitive DNA sequences found at the ends of chromosomes. Telomeres protect chromosomes from loss of genetic information, and a similar process is thought to preserve the virus during latency. The Lieberman research team has worked out several biochemical pathways that control the stability, replication, and gene expression patterns of the latent virus. They have found that changes in viral chromatin structure alters the cancer-risk associated with latent infection.

The Lieberman lab continues to study EBV and KSHV genome maintenance proteins, EBNA1 and LANA, respectively. These proteins bind to the viral OriP, but they also bind to the cellular chromosome at unknown sites. The Lieberman lab has identified the cellular chromosome binding sites for both EBNA1 and LANA in latently infected B-lymphocytes. LANA was found to bind to host genes involved in gamma-interferon signaling and LANA may antagonize STAT1/STAT3 binding to host genes important for MHC peptide presentation and processing. EBNA1 may promote higher order structures, including interchromosome linkages that may promote translocations similar to those observed in Burkitt’s lymphoma.

The role of chromosome architecture and higher-ordered structure is also important for genome maintenance. The Lieberman lab has studied the role of chromatin architecture proteins CTCF and cohesins in regulating viral genome structure and gene expression during latent infection. They have shown that CTCF and cohesins mediate long-distance interactions that are important for control of gene expression and maintenance of a stable latent infection. Loss of genome architecture leads to a change in gene expression and a transition from a circular to linear viral genome.

Maintenance of telomere structures that maintain the ends of linear chromosomes is also important for human genome stability. The Lieberman lab is studying the chromatin structure of telomeres and the expression of a telomere repeat-containing non-coding RNA, termed TERRA. They have shown that TERRA is overexpressed in highly proliferating cells in human and mouse cancers. The TERRA form nuclear aggregates in cancer cells in mouse models of medulloblastoma, and TERRA RNA levels were highly over-expressed in human ovarian cancer biopsies. The regulation and function of TERRA expression, and its role in regulating telomere length and stability are the focus of future research.

The Lieberman laboratory is also pursuing the development of small molecule inhibitors of the EBV encoded origin binding protein EBNA1. The laboratory is collaborating with structural biologists and medicinal chemists to advance hits into lead compounds for testing in animal models of EBV lymphomagenesis. These small molecules will be considered for further development as inhibitors of EBV-associated malignancies.

Liang’s research explores basic mechanisms underlying fundamental cellular processes in inflammation, infection, and cancer, broadly focusing on autophagy, organelle homeostasis, genomic stability, membrane trafficking, and virus-host interaction.

Liang obtained her M.D. degree from Qingdao University School of Medicine, China, and her Ph.D. degree in genetics from State University of New York (SUNY) at Stony Brook. She received postdoctoral training in tumor virology at Harvard Medical School in the Department of Microbiology and Molecular Genetics. She established her laboratory in 2009 in the Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine in Los Angeles, where she was promoted to tenured associate professor in 2015. Liang joined The Wistar Institute as a professor in 2020.

The Liang Laboratory

Autophagy (literally “self-eating”) is the natural, regulated mechanism cells use to digest and remove unwanted components. This process influences diverse aspects of cell homeostasis and constitutes a barrier against malignant transformation.

The Liang lab identified a novel autophagy pathway controlled by the tumor suppressor gene UVRAG (UV-radiation Resistance-Associated Gene) that also plays a direct role in DNA repair and chromosomal stability. The group studies autophagy and related pathways in leukemia, colorectal cancer, melanoma pathogenesis and therapy resistance, and in viral persistency.

Zhang studies the role of immune cells called macrophages in tumor growth and metastasis in the abdominal cavity.

Zhang received his B.S. in microbiology and immunology from Shandong University, China, and a Ph.D. in biochemistry and molecular biology from the University of Oklahoma Health Sciences Center. He completed his postdoctoral training in the Department of Pathology and Immunology of Washington University School of Medicine and joined The Wistar Institute in 2021 as an assistant professor.

The Zhang Laboratory

Macrophages are currently considered as highly heterogenous and plastic with different developmental origins and microenvironmental signatures.

The Zhang lab focuses on understanding how macrophages regulate tumor growth and metastasis in the peritoneal space. We use single-cell sequencing, ATAC sequencing, large-scale imaging, multiphoton intravital imaging, novel genetic mouse models, and patient samples to understand how different subsets of macrophages function differently in mice and in humans. Our long-term goal is to develop novel macrophage-based immunotherapies to treat peritoneal cancers.

Part of my lab focuses on the role of myeloid cells, including neutrophils and macrophages, in cancer progression, particularly metastatic ovarian cancer. The goal is to find novel myeloid cell-based immunotherapies to treat or cure metastases in combination with immune checkpoint therapies or conventional chemotherapy or radiotherapy. Currently, we focus on treating metastatic ovarian cancer by activating myeloid cells using clinically relevant syngeneic mouse models and humanized mouse models.

The other part of my lab focuses on understanding how macrophage heterogeneity forms in the steady state and in disease conditions. We are currently investigating the microenvironmental factors that regulate macrophage subsets in the peritoneal cavity, lung, and liver.

The major techniques in the lab include genetic mouse models, flow cytometry, ELISA, multiple types of fluorescence imaging (including multiphoton intravital imaging), single-cell RNA sequencing, spatial transcriptomics, proteomics, metabolomics, and bioinformatics.

There are currently three directions in the lab:

1. Understanding myeloid activation therapy in metastatic ovarian cancer.

2. Investigating the role of myeloid cells in chemoresistance in metastatic ovarian cancer.

3. Defining the microenvironmental factors that control macrophage heterogeneity.

Figure 1. Intraperitoneal metastasis of ovarian cancer. (A) Immune cell populations represented in the peritoneal fluid; macrophages represent the largest population followed by T cells, dendritic cells, mast cells, NK cells, and B cells. (B) Ovarian cancer cells metastasize via detaching from the primary tumor to form multicellular spheroids containing various stromal cells in the peritoneal fluid and seed in pro-tumor secondary sites including the peritoneum (C) and omentum (D). EGF, epidermal growth factor; TGF, transforming growth factor; MIP, macrophage inflammatory protein; MMT, mesothelial-to-mesenchymal transition; SDF, stromal cell-derived factor; hepatocyte growth factor (HGF); PAI, plasminogen activator inhibitor; CCR, C-C motif chemokine receptor; CCL, C-C motif chemokine ligand; NO, nitric oxide; MMP, matrix metalloproteinase; CAF, cancer associated fibroblasts; ASC, adipose-derived stromal cells.

Figure 2. Murine resident peritoneal macrophages and their supporting environment at steady state. Both embryonically-derived and monocyte-derived resident macrophages are present in murine peritoneal cavity at steady state. These resident macrophages from different origins are regulated differently in the tissue-specific niche. LPM, large peritoneal macrophage; SPM, small peritoneal macrophage; CSF1, colony stimulating factor 1; WT1, Wilms tumor 1.