Current Rotation Opportunities

Rotation Projects 2024-2025

Welcome to the University of Pittsburgh School of Medicine Interdisciplinary Biomedical Graduate Program. Rotation opportunities available in the Cell Biology and Molecular Physiology (CBMP) Graduate Program are listed below. Faculty are drawn from both basic science and clinical departments. Research in the CBMP program is focused on normal cellular biology and function, as well as disfunction in renal, liver, lung, eye and heart disease, cancer, diabetes, ageing, and inherited disorders of developmental and reproductive functions. If you are interested in a rotation opportunity, speak to faculty at orientation or contact them by email. 

Molecular Genetics of Aging - Arjumand Ghazi

We study the biology of aging using molecular genetic and genomic approaches in the model system, C. elegans. In particular, we focus on genes that link lifespan to healthspan, immune health and reproduction. The rotation projects will expand on our recent studies on:

1. Alternative Splicing of endocannabinoid-producing genes during pathogen response and aging: This project focuses on our discovery that a pro-longevity protein, TCER-1 (homolog of human transcription elongation and splicing factor, TCERG1), represses immunity, depending on the status of the animal’s fertility (Amrit et al., Nature Communications, 2019). We have recently discovered that TCER-1 represses immunity by regulating the alternative splicing of lipases responsible for endocannabinoid production. The rotation project will address the role of this alternative splicing event in healthspan.
2. Mechanisms by which germline dysfunction accelerates somatic aging: Our lab recently demonstrated that dysfunction of germline health, by disrupting meiosis, reduced lifespan, accelerated loss of protein homeostasis and healthspan and premature aging in C. elegans, through a potentially conserved molecular signature (Loose et al., Aging Cell, 2022). The rotation project will detail the decline in different aspects of somatic proteostasis in progeric meiosis mutants. 

Contact Dr. Ghazi.

Lipid signaling in healthy cells and cancer - Gerry Hammond

Cancers are caused by mutations that drive uncontrolled growth and proliferation ofcells, and eventually unbridled migration. A common class of mutations is found in more than half of all cancer cases: those that activate a central lipid signalingpathway – the PI 3-kinase or PI3K pathway. The lipid products of this pathway activate downstream cellular programs promoting proliferation, survival and migration – all hallmarks of tumors.

So it seems like a good idea to stop this pathway with PI3K inhibitors, and big pharma has many compounds approved or in late-stage clinical development.The huge caveat is that PI3K is crucial for other processes in the body – such as activation of the immune system, and the cellular response to insulin. So, PI3K blockers are not well tolerated. We need a more nuanced approach.

We are studying the lipid products of PI3K. Whilst the pathway is famous, it is less well known that the pathway actually produces two signaling lipids – a major and minor lipid. We developed a biosensor for the latter (the rainbow colored image, above). We have also used gene editing to tag the enzymes involvedso we can track their activity in intact cells. While no one really understood what this lipid is doing, we can now study it in real time.

The aim of the project is to test the hypothesis that this minor lipid actually drives long term proliferative signaling intumors, whilst the major lipid is responsible for more acute effects of insulin or activation of the immune system. We therefore believe that down-regulating the minor lipid will selectively attenuate signaling in tumors, whilst sparing normalimmunological and metabolic pathways elsewhere in the body. As an added bonus, this may actually improve insulin sensitivity and reduce the accumulation of tauopathy (as seen in Alzheimer’s disease).

The project will involve training in live cell imaging, molecular genetics and gene editing in cell culture models.

Learn more at: hammondlab.com

Contact Dr. Hammond.

Cardiomyocyte Adhesion and Cytoskeletal Organization at the Intercalated Disc - Adam Kwiatkowski

A long-term objective of the Kwiatkowski Lab is to gain a deep, mechanistic understanding of cardiomyocyte adhesion and cytoskeletal organization at the intercalated disc. Our approach is to define mechanisms of cell-cell adhesion, and downstream regulation of actin and intermediate filament organization, by the cadherin/catenin family of adhesion proteins. This is an important biomedical problem because mutations in cell adhesion and cytoskeletal proteins at the intercalated disc are linked to cardiomyopathies.

Our primary focus is the adherens junction core, the cadherin/catenin complex, which links the actin networks of adjoining cells. Adhesive homeostasis requires the cadherin/ catenin complex to be resilient andresponsive to mechanical load. Yet how the cadherin/catenin complex is regulated by mechanical load remains unclear.

The Kwiatkowski Lab takes an interdisciplinary approach to biomedical research. We combine protein biochemistry, cell biology, proteomics, bioengineering, and light and electron microscopy to study cell adhesion at the molecular and cellular levels. Potential rotation projects using cultured primary cardiomyocytes and combining advanced live cell fluorescence microscopy with biochemistry include:

1) determining how ligand recruitment to the cadherin/catenin complex promotes cadherin organization and intercalateddisc assembly; and 2) defining how external mechanical cues are sensed and transduced through adhesion complexes to regulate cardiomyocyte organization.

For more information on the Kwiatkowski lab, see: www.kwiatkowskilab.com 

Contact Dr. Kwiatkowski.

Neurobiology of cancer and pain - Jami Saloman

The Saloman lab is interested in several areas of research including: 1) peripheral nervous system function; 2) neuralregulation of tumorigenesis, anti-tumor immunity and cancer pain; 3) autonomic-sensory circuit regulation of pancreas, including normal function, disease and pain; and 4) diagnostic, predictive, and therapeutic biomarkers for pancreatitis and pancreatitis pain. The Saloman lab is currenty using in vitro and in vivo modeling including mouse, rat,monkey and humans. Our lab has several ongoing projects which a rotation student could get involved in includinganatomical studies, cell-cell crosstalk in the context of inflammation and cancer, and neuroimmune studies. Below are examples of specific independent experiments that are potential projects for a rotation student.

1. We have data implicating Neuropilin-1 (NRP1) that is expressed on sensory neurons in the regulation of both pain and tumorigenesis. Our data suggests that neuronal NRP1 is involved in neuron-T cell interactions. This rotation project will be focused on co-culturing sensory neurons and T cells using time lapse imaging to quantify physical interactions betweencell types. Furthermore, utilization of NRP1-deficient neurons will enable you test the hypothesis that nueronal NRP1 mediates physical interactions between sensory neurons and T cells.

2.    We have several biomarker projects ongoing in diMerent contexts of pancreatitis pain patients. In addition to having the opportunity to work with human data, we are interested in reverse translating our observations into preclinical studies that emphasize mechanism and therapy. By performing proteomic and immunoassays we have identified the IL-6signal transducer (GP130) as a potential biomarker for pain in patients with chronic pancreatitis. This rotation project would be to induce a rodent model of chronic pancreatitis and assess expression of GP130.

3.    In both mouse(left) and human(right), innervation of the lymph node increases during tumorigenesis. This project is designed to characterize the type of nerve, timecourse, and potential mechanisms driving increased innervation.

4.    PDL1 is an inhibitory checkpoint protein that can be expressed on neurons and regulate neuronal activity (Meerschaert et al., 2023). PDL1 is also the known ligand for PD1 and binding PD1 on T cells can drive immunesuppression and promote tumor growth. This project is designed to further investigate the impact of neuronal PDL1 on tumorigenesis, anti-tumor immunity, and nociception.

For more information on the Saloman lab, see: https://www.salomanlab.pitt.edu

Contact Dr. Saloman.

Acute kidney injury - Sunder Sims-Lucas

 Acute kidney injury (AKI) occurs in nearly 1 of 5 hospitalized patients and is associated with increased morbidity and mortality across all ages. Many AKI patients will recover kidney function post-injury but then progress to chronic kidney disease (CKD). The mechanisms are poorly understood and there are currently no effective therapies to prevent, limit, or reverse the tissue damage. There is a critical need to identify mechanisms involved in the pathogenesis of AKI. Our long-term goal is to elucidate these mechanisms and leverage them for new therapies to limit AKI and prevent the transition to CKD. We have three major projects that are currently be investigated:

1.    Sirtuin 5 mediated protection against AKI.
2.    Role of succinylation in kidney injury
3.    Diacarboxylic acids as a therapeutic for AKI and the progression to CKD.

Contact Dr. Sims-Lucas.

Exploring mitochondrial stress signaling pathways - Shiori Sekine

 Mitochondria are multifunctional organelles that undertake multiple tasks, from ATP generation to cellular signaling. We are exploring the tiny, but sophisticated molecular machineries within mitochondria that support our lives. In particular, our recent research has extensively focused on the molecular mechanisms by which mitochondria monitor and handle small biomolecules to maintain the intracellular homeostasis of these. For example, we recently identified a novel iron-responsive mitochondrial protein and demonstrated its critical role in erythroid cells, one of the iron-demanding cell lineages (Sekine Y, Houson R et al., Mol. Cell., 2023). More recently, we are exploring novel roles of ER-Mitochondria contact sites in intracellular heme homeostasis. Heme is synthesized in mitochondria and subsequently delivered to othercellular compartments. However, the underlying molecular mechanismsof intracellular heme trafficking are poorly understood. We are now attempting to tackle this fundamental question using a variety of conventional and newly developed molecular and cell biological experimental techniques. Of note, our recent interactome analysis suggested several intriguing interactions that may occur between mitochondria and the ER depending on the availability of intracellular heme. During the rotation program, we will investigate these newly identified interacting partners at mitochondria-ER contact sites and explore their role in intracellular heme trafficking and beyond.
 

For more information on the Shiori Sekine lab, please visit: https://www.shiorilab.net

Contact Dr. Sekine.
 

Organelle functions in metabolic stress - Yusuke Sekine

 The Y. Sekine lab is working on the molecular mechanisms and organelle stress responses that allow a cell to adapt to metabolic alterations. Currently, we are focusing on the metabolite acetyl-CoA, which plays a central role in the biosynthesis of various biomaterials, as well as in protein acetylation. We have developed an experimental system to manipulate acetyl-CoA levels in cells and are investigating acetyl-CoA fluctuation-dependent functional alterations in organelles (including nucleoli, ER, mitochondria and lysosomes) and the subsequent activation of organelle-associated stress signaling pathways. A long-term goal is to understand the sensing mechanisms for various metabolite fluctuations in cells and to reveal their relevance to human aging and age-related diseases.

Potential rotation projects using state-of-the-art molecular and cellular biological approaches include: 1) investigating the role of the nucleolar stress response and class IIa HDACs in the novel type of transcriptional response under acetyl-CoA-limited conditions; and 2) investigating the contribution of the nucleolar stress response in pathogenesis of Alzheimer’s diseases and other neurodegenerative disorders.
https://aging.pitt.edu/labs/sekine-y-lab/

Contact Dr. Sekine.

Wnk signaling from biomolecular condensates - Arohan Subramanya

Our laboratory studies a kinase signaling pathway that forms biomolecular condensates – membraneless droplet-like assemblies that form via a process called phase separation. During cell shrinkage caused by hyperosmotic stress, water exits the cell, resulting in the crowding of cytoplasmic contents. In a recent paper (Boyd-Shiwarski et al, Cell 2022), we showed that WNK kinases sense this crowding, forming phase separated condensates that activate a phosphorylation-dependent cell volume recovery signal. While the ancient and ubiquitous version of this cascade regulates fluid volume in cells throughout the body, kidney tubules uniquely leverage the crowding-induced signal to control salt and water reabsorption, blood pressure, and potassium balance. Thus, WNK kinases provide one of the first clear examples of a signaling pathway that forms biomolecular condensates to control cell and whole animal physiology.

This discovery has opened several avenues of investigation that could be potential rotation projects. These include (1) determining the mechanism by which WNK kinases activate signaling within condensates to drive cell volume rescue, (2) elucidating signatures within the kinase that function as crowding-induced phase separation drivers, (3) identifying novel signaling partners that reside within WNK droplets, (4) testing the relevance of phase
separation in physiology using established mouse models of kidney-specific WNK condensate hyperactivation and dysfunction, and (5) testing how recently identified small molecule inhibitors of the WNK signaling pathway influence its stress-induced phase behavior.

Learn more at http://www.subramanyalab.org.

Contact Dr. Subramanya

Cytoskeleton-driven  motility in invasive parasites- Stella Sun

 The Sun Lab is interested to attain an in-depth, molecular and mechanistic understanding of how cytoskeleton-driven cell motility operates in highly invasive human parasites responsible for significant infectious diseases. Our research focuses on flagellate eukaryotic parasites,
specifically Trypanosoma brucei (T. brucei), lead to the lethal disease Trypanosomiasis. The swimming ability of these parasites is facilitated by a sensory organelle called the flagellum, which serves as an organelle ruler for cell size. This single flagellum connect to the cell body through membrane- membrane junctions, affecting the parasite’s size, deformability, and swimming behavior.

Our goal is to utilize a genetically engineered miniature T. brucei cell system called zoid and a cutting edge cryo-EM strategy spanning multiple scale to unravel the intricate process by which the intraflagellar transport (IFT) mechanism for flagellum assembly and maintains. Additionally, we seek to elucidate how extracellular vesicles (EVs), a process vital for cell-cell communication, can be coupled with flagellum membrane remodeling. By establishing this imaging platform, the researchers aim to contribute to the broader cryo-electron microscopy community’s knowledge and applications in cell biology studies, particularly those related to infectious diseases.

Potential rotation projects include:
1)    Unraveling the gating mechanism of IFT within the flagellum base.
2)    Exploring the assembly and function of EVs in cell-cell communication.
3)    Investigating the role of the essential organelle biogenesis such as close mitosis.

For more information on the Sun lab, see: https://sunlab.structbio.pitt.edu

Contact Dr. Sun

Cellular principles of aging and age-related disease - Jay Tan

The Tan lab studies molecular and biochemical mechanisms of cellular quality control in aging and age-related disease. We search for essential, unifying molecular principles behind complex stress responses using unbiased approaches, and dissect the underlying mechanisms using multidisciplinary methods including molecular biology, biochemistry, cell biology, genetics, proteomics, bioinformatics, and so on. We are actively working on two broad directions. (1) Lysosomal quality control mechanisms in response to cellular stress stimuli: Lysosomes are known as the longevity-promoting organelles, the dysfunction of which is commonly found in aging and age-related diseases including all kinds of dementia. We are searching for universal mechanisms underlying lysosomal quality control in response to diverse age-related cellular stresses, with the goal of discovering new strategies to promote longevity through lysosomal rejuvenation. Our recent discoveries in this direction include an essential rapid lysosomal repair pathway (the PITT pathway). (2) Innate immune signaling in aging and neurodegeneration. Abnormal exposure of DNA fragments in the cytosol is a common condition during microbial infection, cell damage, organismal aging, cellular senescence, and degenerative diseases. Such DNA exposure triggers the cGAS/STING DNA-sensing innate immune pathway to protect cells from infection but causes pathological consequences in other contexts. Our research focuses on elucidating the molecular mechanisms that underlie the detrimental functions of this pathway, including examining its interactions with lysosomes. Our goal is to develop targeted interventions that can inhibit its pathogenic effects while preserving its antimicrobial activity. Our recent progress in this direction includes a conserved ion channel function of STING that mediates noncanonical autophagy and cell death.

Rotation projects include, but not limited to:
a.    Biochemical screening of lysosomal stress response pathways using established approaches in the lab.
b.    Cell biological screens of membrane contacts in cellular stress response using established tools.
c.     Examine the impact of the PITT pathway on the aggregate clearance activity of microglia.

More information can be found at: JayTanLab.org

Contact Dr. Tan

alpha-synuclein function in synapses and Parkinson's Disease - Karina Vargas

Our research focuses on the study of alpha-synuclein function in synapses and how its malfunction contributes to neurodegeneration in Parkinson’s disease. Alpha-synuclein participates in clathrin mediated synaptic vesicle endocytosis, affecting several key proteins in this pathway. We are interested in deciphering how alpha-synuclein affects AP2 and clathrin, the two main proteins driving clathrin mediated endocytosis and contribute to neurodegeneration. We use mouse and lamprey giant synapse models and a variety of techniques including expansion microscopy, biochemistry, electron microscopy, etc.

Current rotation projects include:
1.    Alpha-synuclein pathogenic effect on clathrin mediated synaptic vesicle endocytosis.
2.    AP2 associated kinase (AAK1) and alpha-synuclein interplay in the regulation of synaptic vesicle endocytosis.
3.    Synaptic effects of alpha-synuclein mutants in the nano-localization of synaptic proteins.

Contact Dr. Vargas

mRNA translation regulation in cellular stress - Deepika Vasudevan

 Lab overview: There are two active lines of investigation in my lab that are mutually independent, but thematically converge on understanding the role of stress response signaling in disease and development. The first set of projects focuses on uncovering new mechanisms of mRNA translation regulation during cellular stress, and the second on the role of stress response signaling in tissue function and dysfunction. The lab uses a potent combination of Drosophila (fruit fly) model and cultured cells to comprehensively map the physiological relevance and molecular mechanisms of stress response signaling.

Rotation/thesis project: From a pathobiological standpoint, cells across a tissue do not die simultaneously when challenged with a stressor; instead, there is a gradual attrition of cell viability and tissue function with different cells succumbing to the stress at different time points. Despite extensive documentation of such heterogenous stress resistance, what renders surviving cells resistant to stress-induced death remains unknown. The overarching goal of this project is to determine the basis of stress tolerance and establish the physiological relevance of heterogenous stress response activation.

While there are many modalities of cellular stress and many tissue types to select from, this project will focus on ER stress response activation in metabolic tissues. Specifically, the Drosophila fat tissue (a.k.a. the ‘fat body’) presents an excellent discovery platform for this research problem for multiple reasons including ease of isolation and availability of genetic tools for manipulation+visualization of stress. The included figure shows an example of heterogenous stress response activation, where even neighboring cells show vastly different levels of a transgenic ER stress reporter.

The ER stress response pathways famously restrict mRNA translation leading us to hypothesize that tolerance to ER stress in a given cell is intricately linked to regulated and selective protein synthesis. The project will use live imaging, flow cytometry, and Drosophila genetics to test this hypothesis.

www.flystresslab.com

Contact Dr. Vasudevan

G Protein-Coupled Receptor (GPCR) Signaling and Function - Jean-Pierre Viladarga, Ph.D. 

The Vilardaga lab in the Department of Pharmacology and Chemical Biology is actively seeking highly motivated students to join our team. Students in the lab will have the unique opportunity to engage in multidisciplinary research projects focused on uncovering the structural, molecular, and cellular mechanisms of signal transduction mediated by G-protein coupled receptors. This important family of receptors represents the largest group of cell surface receptors for hormones, neurotransmitters, and clinical drugs.

Contact Dr. Vilardaga

Proteins uptake up by the kidney proximal tubule - Ora Weisz

 The Weisz lab uses imaging, biochemical, genomic, and modeling approaches in highly differentiated cell cultures and in animal models to study how proteins are taken up by the kidney proximal tubule (PT). PT cells have a highly developed apical endocytic pathway that is essential for maintaining the function of this nephron segment. Defects in endocytic pathway function result in protein excretion in the urine, and can also impact cell metabolism and transcription. Current projects in the lab are focused on identifying how the apical endocytic pathway is regulated in these uniquely specialized cells, understanding the crosstalk between endocytosis, cellular metabolism, and transcription in normal and disease states, creating integrated mathematical models for protein recovery in cells and along the entire PT, and discovering the mechanisms that cause genetic proteinuric disease. We welcome and support diverse and creative individuals who enjoy thinking outside the box and working in a collaborative interdisciplinary environment.

Contact Dr. Weisz

Ubiquilins  and Alzheimer’s Disease and Related Dementias - Matt Wohlever 

A hallmark of Alzheimer’s Disease and Related Dementias (ADRDs) is defects in proteostasis. Ubiquilins are a family of proteins that serve as a major hub in the proteostasis network and are also intimately linked with ADRDs. For example, single point mutations in Ubiquilins lead to Amyotrophic Lateral Sclerosis (ALS). Despite the clear medical relevance, the underlying mechanisms of Ubiquilin function are not understood at the molecular, subcellular, and neuronal levels, which presents a significant barrier to developing targeted therapeutics to treat ADRDs. Paradoxically, while Ubiquilins are traditionally thought to shuttle proteins to the proteasome for degradation, there are many reports in the literature of Ubiquilins stabilizing client proteins, including many ADRD proteins. It is unclear how this triage decision is made and executed.

We have recently discovered that Ubiquilins directly bind to ADRD proteins via the Sti1 domain and recruit E3 ligases to promote the formation of biomolecular condensates that protect substrates from degradation (Fig 1). This contrasts with the existing model, which posits that Ubiquilins interact with ubiquitinated proteins via the UBA domain and then shuttles these proteins to the proteasome for degradation. The new paradigm of Ubiquilins as molecular chaperones that stabilize ADRD proteins via the formation of condensates will fundamentally shift our approach for developing therapeutic interventions in Alzheimer’s Disease and Related Dementias.
https://wohleverlab.wordpress.com/lab-members/matt-wohlever/

Contact Dr. Wohlever

Unlocking the secretes of proteostasis: does the 12h oscillator hold the key for treatment of neurodegeneration - Bokai Zhu

 Proteostasis, the cellular mechanism that governs the synthesis, folding, and degradation of proteins, is crucial for maintaining proteome integrity, especially under proteotoxic stress. A decline in protein quality control is closely linked to aging and neurodegenerative diseases. Traditionally, proteostasis was believed to be constant under basal conditions.
However, using novel mathematical tools, our lab has uncovered a surprising 12-hour rhythm in global proteostasis dynamics in normal cells, operating under physiological conditions. This 12-hour rhythm is regulated by a cell-autonomous mammalian 12-hour ultradian oscillator, independent of the 24-hour circadian clock and the cell cycle. Our lab is interested in studying the gene regulatory network, chromatin and epigenetic landscape, biological function, and evolutionary origin of the 12-hour oscillator. We are further pursuing a new direction following our recent discovery of the critical role of nuclear speckle liquid-liquid phase separation in controlling proteostasis. We are actively studying how nuclear speckle sense proteostasis stress and preemptively elicit stress response. Lastly, we are developing innovative strategies for rejuvenating nuclear speckles to combat protein misfolding diseases, such as tauopathy in neurodegeneration.

Potential rotation projects:
1)    Developing 12h-clock reporter system using CRISPR-CAS9 based imaging approaches
2)    Identifying non-cell autonomous regulators of 12h clock and protein quality control using innovative proximity- labeling biochemical approaches
3)    Identify epigenetic regulators of mammalian 12h clock and UPR.
4)    12h clock in senescence and aging.
5)    12h clock in humans.
6)    Nuclear speckle rejuvenation in combating proteinopathies.

Bokai website link: www.bzhulab.com

Contact Dr. Zhu