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Current Rotation Opportunities - MGDB

Faculty email Research interest/projects
Katherine Aird, PhD The lab focuses on bidirectional control of metabolism and the cell cycle with interests in cancer, senescence, and aging. We use cell culture models, in vivo cancer/aging models, CRISPR screens, high throughput data, and metabolomics to mechanistically explore these concepts and translate our findings by identifying targetable pathways. Current rotation projects include nutrient exchange between senescent cells and cancer/immune cells and metabolic changes driven by tumor suppressors/oncogenes. Other projects that fall under the umbrella of metabolism with be considered. Projects are tailored to the unique interests of each lab member.
Rannar Airik, PhD The lab studies the role of DNA damage in the development of chronic kidney disease. We work with DNA repair deficient transgenic mouse models that are orthologous to human chronic kidney disease and patient derived cells. Our current focus is to investigate the role of DNA damage in kidney tubular metabolic reprogramming and mitochondrial dysfunction.
Michael Butterworth, PhD The research focus of the lab is the (sex-specific) role of microRNAs in renal sodium handling. We use KO and gain-of-function mouse models with primary and engineered cell lines to investigate the hormonal regulation of microRNAs in the kidney. Findings are linked to in vivo physiologic regulation of sodium transport and blood pressure. These studies aim to uncover novel pathways to account for sex-specific differences in hypertension. See more
Yuan Chang, MD and Patrick S. Moore, MD, MPH Our lab (jointly co-directed with Dr. Yuan Chang) seeks to identify new human cancer viruses and to understand how these viruses initiate cell transformation and tumorigenesis.  To this end, we discovered the viruses causing Kaposi sarcoma (Kaposi sarcoma herpesvirus, KSHV) and Merkel cell carcinoma (Merkel cell polyomavirus, MCV) using molecular techniques.  Our laboratory is currently seeking to new proteomic methods that may help inform us on the presence of undiscovered viruses in cancers thought to have an infectious etiology. See more
Susana da Silva, PhD The research in our lab is centered on a small but highly specialized area of the retina named fovea. The fovea is a high acuity area responsible for our ability to read, drive and recognize faces. We are very interested in deciphering the molecular underpinnings of fovea development and subsequently establish new experimental models of human foveal diseases. Our lab uses a multidisciplinary research program based on multiple model systems, such as chick embryos and human retinal organoids, combining classical embryological manipulations and state of the art genomic, molecular (multiomics) and human iPSCs 3D culture techniques.
Wei Du, MD, PhD Our lab studies the underlying mechanisms by which the normal and abnormal hematopoiesis are regulated. We use DDR deficient mouse model, human xenograft model to identify potential therapeutic targets for leukemia treatment. We are also interested in understanding hematopoietic stem cell (HSC) and Bone marrow niche interaction. Potential projects include: 1) Define the molecular and functional collaboration between a major cell signaling (FA) pathway and immunometabolic regulation in HSCs; 2) Target stem cell-niche interaction for improved therapy for patients with bone marrow failure and leukemia; 3) Study a novel interplay between DDR and immune responses in FA leukemogenesis; 4) Study on the systemic immune effects of persistent DNA damage using mouse and human models of DNA repair deficiency and aging; 5) Molecular mechanism and therapeutic potential of synthetic lethal targeting our newly identified PRMT5-CtIP-FANCD2 complex in homologous recombination repair-competent cancers; and 6) Mechanistic and functional elucidation of the role of a novel paracrine Wnt5a-Prox1 signaling axis in regulating HSC regeneration under conditions of injury and aging.
Ebrahimkhani, MD Laboratory for Synthetic Biology and Regenerative Medicine led by Dr. Ebrahimkhani combines synthetic biology, systems biology and stem cell engineering to advance regenerative medicine, develop new therapies while also study human development. See more
Farzad Esni, PhD Pancreatic Development and Regeneration
Diabetes and pancreatic cancer are two major diseases linked to the pancreas. Type-1 diabetes is a syndrome defined by high blood glucose levels caused by reduction in number of insulin producing beta cells. A cure for diabetes will be achieved through replacement of beta cells. Pancreatic cancer is an almost uniformly fatal disease. Understanding the biology of pancreatic cancer and particularly, its precursor lesions, are prerequisites for the development of more sensitive early detection biomarkers and more potent therapeutic and chemopreventive strategies. See more
Shou-Jiang Gao, PhD The main research area in Dr. Gao’s laboratory has been on viral oncogenesis with current focus on Kaposi’s sarcoma-associate herpesvirus (KSHV) and AIDS-related malignancies. See more
Erin Kershaw, MD Our mission is to forward the understanding and treatment of obesity and related metabolic disorders (i.e. insulin resistance, glucose intolerance, diabetes, dyslipidemia, cardiovascular disease). A major focus includes disorders of “fat” (i.e. adipose tissue, lipids). We use a multidisciplinary approach that combines basic and translational research with clinical expertise. Our goal is to develop better strategies for prevention and treatment of obesity and its complications. See more
Bernhard Kuhn, MD While much is understood about the mechanisms of the human heart, when it is examined on the cellular and molecular level, many mysteries remain. Notably, these specialized contractile cells, called cardiomyocytes, are exceptional in that they lack the ability to replicate and proliferate, processes that are necessary to repair tissue damage and restore normal function. Our innovative work has already provided insight into the growth mechanisms of these cells. The Kühn Lab’s long-term goal is to regenerate human hearts. This involves developing therapies that can help the heart muscle, the myocardium, to heal itself – to recover from a heart attack, or to help it restore a congenital heart defect to normal cardiac function without requiring surgery.  See more
Adrienne Lee, PhD/ Steffi Oesterreich, PhD The Lee-Oesterreich team uses state-of-the-art technology to understand treatment resistance and progression in breast cancer. Focus areas are endocrine resistance, lobular breast cancer, metastases and precision medicine. For details, please see
Nara Lee, PhD Research in the Lee lab focusses on elucidating the molecular mechanism of how noncoding RNAs expressed by Epstein-Barr virus facilitate viral replication. To this end, we apply techniques entailing next-generation sequencing to examine RNA-RNA, RNA-protein, and RNA-chromatin interactions. 
Guang Li, PhD The Li lab has three research areas. 1) Heart development. We are studying the temporal and spatial molecular signatures of the developing hearts using single cell multiomics and spatial omics. 2) Heart organoid and spheroid: We are developing methods to generate a four-chambered hearts in dish using human iPSC and primary cells. 3) Heart regeneration. Multiple heart injury models including cell ablation, cryoinjury, and LAD models are used to study the heart regeneration process in embryonic and neonatal mice.
Nathan Lord, PhD Developing embryos must orchestrate the fates and movements of their cells with precision. However, precise control is no easy feat; genetic mutations, unexpected environmental perturbations and noisy signaling all threaten to scramble communication. Despite these challenges, development is remarkably robust. How do developing systems ensure precise pattern formation? How are mistakes corrected when they occur? Can we learn to engineer synthetic systems to have the reliability of developing embryos? Answers to these questions must span multiple scales, from signaling responses in individual cells to collective cell movement and morphogenesis. Our lab will tackle these questions with a combination of optogenetic manipulation, quantitative microscopy, computational modeling and classical embryology. Over the long run, we hope to learn the mechanistic principles that enable embryos to avoid and correct errors in development.
Opresko, Patricia, PhD Our lab studies DNA damage and repair at telomeres and roles for telomere damage in human diseases, aging and cancer. We are focused on three main areas: 1) how oxidative and genotoxic stress accelerates telomere shortening and loss, 2) defining the cellular pathways that preserve telomeres in the face of DNA damage and 3) determining the consequences of telomere damage on telomere function, cellular function and organisms health. Please visit
Kyle Orwig, PhD The lab develops and tests stem cell and tissue transplant technologies as well as gene therapy approaches for treating the most challenging infertility diagnoses (no eggs, no sperm).
Edward Prochownik, MD, PhD The Myc oncoprotein is a member of a simple transcription factor network that regulates cancer growth, metabolism and survival. It cross-talks with the related Mlx Network, which supervises similar functions. It has not been possible to determine the normal roles for these Networks in mice as Myc knockout (KO) is embryonic lethal. By delaying KO of Myc and/or Mlx until after birth, we have now been able to show that they exerts profound but distinct defects on metabolism and aging. Specifically, Myc KO mice show evidence of premature aging but are highly resistant to the development of spontaneous tumors. This is the first evidence that aging and cancer susceptibility can be genetically separated and identifies the Extended Myc Network as being a key player in this causative link.
Donghun Shin, PhD dhuns@pitt.eduong The Shin lab uses zebrafish as a model organism to understand the cellular and molecular mechanisms of liver regeneration, focusing on the plasticity of two main cell types in the liver, hepatocytes and biliary epithelial cells (BECs). Depending on the severity and type of liver injury, hepatocytes convert to BECs; BECs convert to hepatocytes. A better understanding of these phenomena will contribute to better strategies to augment innate liver regeneration in patients with severe liver diseases as therapeutics. Please visit the lab website  
Michael Tsang, PhD 1) Modeling human congenital heart disease in zebrafish  2) Understanding the molecular mechanism of heart regeneration 3) Modeling RASopathy using genetic code expansion. 
Bennett Van Houten, PhD Work in our laboratory is focused on two major research interests: 1)  analyzing DNA repair proteins at the single molecule level in real-time using purified proteins, nuclear extracts and in live cells, and 2) creating site-specific singlet oxygen damage in cellular compartments including the nucleus and mitochondria to examine mitochondria-nuclear cross-talk. See more
Xiaosong Wang, MD, PhD The research project for this rotation will interface the “dark side” of cancer genetics with cancer immunology. Specifically, we will investigate a cryptic class of adjacent gene rearrangements in more aggressive and therapy-resistant forms of breast cancer and/or other solid tumors, and examine their function in cancer progression and/or immunotherapy resistance at individual level or at system level. The student may choose to systematically characterize the function of adjacent gene rearrangements in immunotherapy resistance using clinical trial datasets, experimentally validate newly discovered genetic targets, characterize their molecular basis, elucidate their clinical significance using patient samples, confirm their role in tumor progression, immune disfunction, or therapy resistance, pinpoint their mechanistic basis, and explore potential clinical applications.
Xiangyun Wei, PhD Topic 1: Orientational cell adhesions for tissue morphogenesis Topic 2: Transcriptional regulation of polarity genes See more
Bokai Zhu, PhD We are a multidisciplinary lab that use quantatitive system biology approach to study stress response, proteostasis, biorhythms in the regulation of metabolism and aging, with both basic research and disease implication. Some of the key words related to our research are: xbp1, ultradian and circadian rhythm, epigenetics, proteostasis, transcription, phase separation, stress response. fatty liver, aging and senescence. Please visit and follow me @LabZhu on twitter.  
Li Gang, PhD Post-GWAS functional studies to understand the mechanism of Atherosclerosis and Alzheimer's disease for drug development.
Shou-Jiang (SJ) Gao, PhD The Gao lab is part of the Cancer Virology Program (CVP) in the UPMC Hillman Cancer Center. The lab primarily studies the mechanism of infection and oncogenesis of cancer viruses. The student will be exposed to molecular virology, cancer biology, cancer metabolism, epigenetics, epitranscriptomics, interactions of cancer cells with tumor microenvironment and immune cells, inflammation, microbiome and cancer therapy. The lab closely collaborates with computational biologists, particularly Dr Yufei Huang, who is also in CVP, allowing the development of novel systems approaches for dissecting complex biological questions, including the recent development of novel analytic tools for spatially-resolved single cell transcriptomics. Recent works have identified novel tumor suppressive functions of an arginine sensor CASTOR1, which regulates both tumor and immune cells. Ongoing works are examining the functions of CASTOR1 in other types of cancer including lung cancer and HPV-associated head and neck squamous cell carcinoma, and innate and adaptive immunity in models of colitis and colon cancer.
Bokai Zhu Zhu lab is working on multi-disciplinary research encompassing proteostasis, biorhythms, aging, senescence, epigenetics, stress response, phase separation, and metabolism in both basic research as well translational research in neurodegeneration, metaboic syndromes, and eye diseases. We combine computation, bioinformatics, cell biology, time-lapse imaging, next generation sequencing, and classical molecular and biochemsitry and utilize a wide range models, including C.elegans, mice, mammalian cell lines and also human sujects. Whether you are into basic research or translation research, this is the lab you should join. 
Wang Xiaosong, MD,PhD Apply a multiple disciplinary approach inclusive of bioinformatics, genetics, molecular and cell biology, and translational studies to detect driving genetic aberrations and qualify appropriate cancer targets on the basis of next generation sequencing and genome profiling technologies. Characterize driving genetic aberrations, therapeutic targets, and predictive biomarkers for the development of new cancer precision medicine. Develop novel bioinformatics tools and models to predict therapeutic responses of cancer targeted therapies and immunotherapies, as well as to facilitate clinically important decisions. For more information, please visit our website:
Yael Nechemia-Arbely We study mechanisms of epigenetic assembly, maintenance and propagation of human centromeres that are essential for faithful chromosome segregation during mitosis. Chromosome missegregation can lead to aneuploidy which is a hallmark of many human tumors. We use cutting edge genomic approaches (ChIP-sequencing, CUT&RUN, long-read Oxford nanopore sequencing, Repli-seq, and Hi-C combined with molecular biology and microscopy to determine how centromeres are structured and how they are epigenetically maintained and propagated across the cell cycle. Please check our lab website here: 
Possible Rotation Projects include: 
- Optimizing DiMelo-seq for various applications 
- Examining the relationship of CENP-A/C/T centromere proteins at human centromeres using next generation genome wide approaches 
- Chromosome elimination using CRISPR/Cas9 
- Optimizing single molecule approaches to detect histone PTMs
Mo Ebrahimkhani, MD please visit
Yvette Yien Our lab is interested in the interplay between iron metabolism and development.  Using an innovative multidisciplinary approach using multiple model systems (mouse, zebrafish, yeast and cell biology), we are identifying tissue specific roles of mitochondrial homeostasis proteins that couple iron metabolism with the specific needs of cells, with an eye towards identifying pathological and therapeutic mechanisms of iron dysregulation in specific tissues.  Secondly, we are working to interrogate the mechanisms by which iron functions within developmental signalling pathways and cell fate.  Lastly, we are actively attempting to identify hematopoietic and iron metabolism adaptations in the pregnant female's bone marrow (using mouse models) as they progress through pregnancy. 
Edward Prochownik, MD, PhD My laboratory has a long-standing interest in the oncogenic Myc transcription factor and its role not only in cancer but in normal growth and development as well. We have recently been able to overcome the long-known embryonal lethality of Myc KO mice by inactivating the gene soon after birth thereby allowing us to determine how Myc impacts normal growth and development. By following the mice over their entire life span, we have shown that they develop a marked premature aging phenotype. Surprisingly however, they live longer than control mice due to the fact that they are unable to develop tumors due to their lack of Myc. RNAseq analysis indicates that many Myc target genes are altered in aging humans, thereby indicating that the MycKO mouse represents an excellent model of human aging. Current efforts are aimed at understanding the molecular, biochemical and metabolic basis for these unexpected phenotypes. A second project concerns the use of a mouse model for the most common pediatric liver cancer, hepatoblastoma (HB). Using a variety of molecular and bio-informatics-based tools we have identified a group of 22 genes that are invariably dysregulated in mouse and human HBs, irrespective of cause, stage, growth rate or histologic subtype. They are also highly predictive of survival in human HB. We are currently over-expressing these genes using Sleeping Beauty vector-mediated over-expression or Crispr-mediated knockdown in vivo to determine whether we can alter the natural history of HBs, thus potentially identifying novel means of therapeutic intervention.
Aditi Gurkar, PhD Our lab is interested in understanding what drives age-related diseases and aging. The goal is to define interventions that can improve health and quality of life. Our lab uses C. elegans, mice, induced pluripotent stem cells (iPSc) and patient samples to understand the basic biology of aging. Potential projects include:
1. Role of lipid metabolism and epigenetics in aging.
2. Understanding the role of DNA damage-induced cellular senescence in cardiovascular disease.
3. Integration -omic and causal inference to translate ‘aging’ from bedside to bench.
Techniques commonly used in the lab vary from cell culture, molecular biology, immunofluorescence, single cell RNA-seq and data integration (metabolomics, lipidomics, RNA-seq), phenotyping mice including frailty and skeletal muscle integrity.
Rannar Airik, PhD Our lab focuses on identifying the genetic and molecular mechanisms of chronic kidney disease (including renal ciliopathies), to develop therapies against this condition. In our work we use transgenic mouse models, patient derived cells and various biochemical/proteomics assays to dissect the disease mechanisms. Current projects include: 1. Dissecting the role of DNA damage in chronic kidney disease. 2. Investigating the mechanisms that drive acute kidney injury to chronic kidney disease transition. 3. Use of senolytic therapy to counter chronic kidney disease.
Patricia Opresko, PhD Our lab focuses on telomeres at chromosome ends, which profoundly influence genome stability, life span and human health. When chromosomes lose their telomere caps the cells can no longer divide, impairing regeneration and driving degenerative diseases during aging. Loss of telomeric caps in pre-cancerous cells causes genetic alterations that hasten cancer progression. Telomeres shorten with age, but genetic and environmental factors including oxidative stress and inflammation can damage telomeres and accelerate shortening and dysfunction. Our lab is investigating how these factors increase telomere loss, how damaged telomeres affect health, and how telomere damage may be prevented or repaired.  We use cellular and biochemical approaches and a chemoptogenetic tool that selectively damages telomeres in living cells and model organisms.  Ultimately, we hope to develop new strategies that preserve telomeres in healthy cells and delay aging-related diseases including cancer, or that conversely deplete telomeres in cancer cells to stop their proliferation.
Arjumand Ghazi, PhD Ghazi Lab: Molecular Genetics of Aging 
Susana da Silva Our lab studies development of retinal specializations evolved for high acuity, aka, fovea. Our lab utilizes multiple model systems, including chick embryos and 3D retinal organoids differentiated from human iPSCs. We combine classical embryological techniques with state of the art genomic tools, such as single cell multiome sequencing, CRISPR/Cas9 gene editing. Our ultimate goal is to reveal the molecular and cellular mechanisms regulating fovea formation in order to develop better therapeutic strategies for diseases affecting the fovea, such as in age-related macular degeneration. 
Andrey Parkhitko The Parkhitko lab is interested in how metabolism is reprogrammed with aging and how age-dependent metabolic changes can be targeted to extend health- and lifespan. We use both Drosophila and mice to search for new metabolic pathways connected to the aging process, explore how these metabolic pathways regulate aging, test whether targeting these pathways late in life would extend healthspan, and create new tools to manipulate/study these pathways
Timothy Burns, MD, PhD My research and clinical interests revolve around the development of targeted therapies for KRAS-mutant NSCLC as well as novel strategies to overcome resistance to targeted therapies for EGFR-mutant and MET-altered NSCLC. My three main research themes are 1) novel pre-clinical target validation and drug development (TWIST1 in oncogene driven NSCLC and TKI resistance); and 2) elucidating mechanisms of resistance for targeted inhibitors to develop rationale therapeutic combinations that can be tested in the clinic (Hsp90, ERK1/2 inhibitors and 4th generation EGFR TKIs) and 3) development of targeted therapy approaches for the treatment of brain metastases. The first line of research in my laboratory focuses on the role of the EMT transcription factor TWIST1 in oncogene-driven NSCLC. We have demonstrated the TWIST1 is essential for lung tumorigenesis for KRAS mutant, EGFR mutant and MET mutant/amplified NSCLC and TWIST1 overexpression leads to resistance to EGFR and MET TKIs. We are examining the mechanism(s) through which this occurs and developing therapeutic combinations to overcome this resistance. Importantly, we have developed a novel TWIST1 inhibitor which serves a tool compound for our therapeutic studies and serves as the basis for our current drug screening efforts to develop a clinical TWIST1 inhibitor. The second line of research in my lab focuses on studying the mechanisms of resistance to targeted agents currently in phase 1 and 2 trials to develop rationale therapeutic combinations in the clinic. This is typified by our previous work with Hsp90 inhibitors and ongoing work on ERK inhibitors and a novel 4th generation EGFR TKI. Finally, my lab is interested in lung cancer brain metastases, and we are exploring whether targeting the HGF-MET-TWIST1 pathway can be an effective strategy for preventing or treating lung brain metastases. In additional to these preclinical studies, we are using both radiogenomic and cell free DNA approaches to predict molecular phenotypes of brain metastases to identify patients with brain metastases that can benefit from MET targeted therapy in the clinic.
Miguel Brieño-Enriquez During early embryonic development, and particularly during the initial steps of organogenesis, cell, tissues, and organs are separated by wide intracellular spaces filled by extracellular matrix (ECM). The extracellular matrix (ECM) plays pivotal roles in cell self-renewal, fate, death and signaling to regulate diverse function including migration, proliferation, and differentiation. The organization of the ECM has been considered as favorable for the translocation of embryonic cells from one place to another until they reach their final destinations. The complexity of ECM biology derives in part from the heterogeneity of its components. One of ECM components is hyaluronan (HA), a ubiquitously expressed glycosaminoglycan. HA can be detected in the organism in its high-molecular-weight (HMW) form, HMW-HA binds water and promotes hydration and has anti-inflammatory properties. In contrast, low-molecular-weight (LMW) HA tends to have pro-inflammatory properties. HMW-HA has been shown as a critical element during the phases of separation, migration, and colonization of the gonads by precursors of the gametes, the primordial germ cells (PGCs).  Previous studies, performed in mouse gonadal somatic cells showed HA as the major class of glycosaminoglycan. These studies also showed that the levels of HA in the fetal ovary decreased with gestational age from higher levels at embryonic day e11.5, coinciding with a high primordial germ cell mitotic rate, the lowest occurring at e13.5 during the activation of the meiotic pathway. However, little is known about how HA regulates the number of PGCs, their differentiation, meiotic entry and establishment and maintenance of ovarian reserve. In the proposed research, we will test the overarching hypothesis that the stromal microenvironment of the fetal ovary, including an HA-rich matrix, regulates the establishment and maintenance of the ovarian reserve and reproductive longevity. To test this hypothesis, we will use the naked mole-rat (Heterocephalus glaber, NMR), mouse and human as a model. The NMR is a unique rodent species which lives up to four decades and maintains reproductive function throughout its entire lifespan. This extreme longevity is attributable in part to a) the production of large amounts of very-high-molecular-weight hyaluronan (vHMW-HA). vHMW-HA is produced in NMRs by a uniquely modified version of the hyaluronan synthase 2 gene (nmrHas2); and b) NMR ovary retains a population of germ cells far into postnatal life that bear markers of pluripotency as well as PGC identity and can divide in vivo, allowing the NMRs to establish and maintain an exceptionally large ovarian reserve relative to their small body size. To evaluate the role of vHMW-HA we will use transgenic mice that express the nmrHas2 in the different compartments/cells of mouse ovary using cell-specific Cre alleles. Evaluation of the conserved effect of high molecular hyaluronan in ovarian development we will evaluate the localization of HA in human ovaries, the total levels, and the gene expression. Taking this all together, this project will show the regulatory role of HA in the stromal microenvironment of the fetal ovary, and its functions in the establishment and maintenance of the ovarian.
Bennett Van Houten, PhD Dr. Van Houten’s laboratory is doing cutting-edge research in two fundamental areas of biology, namely, how cells maintain genome integrity and generate energy. More specifically, his group studies the structure and function of DNA repair enzymes at the single molecule level, and the role of mitochondria in cancer and neurodegenerative diseases. Dr. Van Houten’s laboratory is currently supported by a NIEHS Revolutionizing Innovative Visionary Environmental health Research (RIVER) Award R35 ES031638 which uses state-of-the-art single molecule approaches, including atomic force microscopy and real-time fluorescence microscopy to follow  fluorescently tagged-DNA repair molecules as they interrogate DNA for structural alternations in real time. The long-term goal of this project is to watch multiple protein machines do work on DNA at the single molecule level in purified systems, nuclear cell extracts and in living cells.

[updated: 8/29/2023]