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Oncology

Michael Bouvet, MD
As a surgical oncologist with a practice that focuses on endocrine and GI malignancies, I have integrated my research interests into my clinical practice. Our laboratory has developed near infrared fluorophore-conjugated antibodies and other tumor specific imaging probes for fluorescence-guided surgery of gastrointestinal cancers. Fluorescence-guided surgery allows the surgeon to obtain more complete resections by more accurately visualizing tumor margins and metastases in the operating room. This field is currently accelerating at a rapid pace with the advent of fluorescence laparoscopy and fluorescence-guided robotic surgery that is now available for clinical use. http://invivoimage.com/about-us/

Joseph Califano, MD
I am a physician-scientist who has translated multiple discoveries from the laboratory into the clinic, including detection of HPV-related and other head and neck cancers. Our laboratory focuses on leveraging computational genomic strategies in combination with molecular techniques to define novel molecular networks in head and neck and other cancers. Practical applications from these projects include defining novel clinical therapeutics based on discovery of novel molecular networks, as well as development of clinical molecular detection and screening tests. The laboratory has published over 300 articles related to both the clinical and basic scientific aspects of cancer, and includes a broad range of postdoctoral, predoctoral, and MD members.

Yuan Chen, PhD
The long-term objective of our laboratory is to identify novel mechanisms for developing treatments for cancer and other recalcitrant human diseases. For two decades, our research focus has been on ubiquitin-like (Ubl) modifications, the regulation of which influences major oncogenic pathways and anti-tumor immunity. Our research program is transdisciplinary, involving collaborations with other academic laboratories, clinicians and industry. Lab website

Theresa Guo, MD
Our research seeks to understand post-transcriptional changes, including alternative splicing events, which are prevalent in head and neck cancer. We use computational biology methods to achieve a deeper understanding of these post-transcriptional genomic alterations, which are not readily apparent through sequencing alone. Splicing and post-transcriptional alterations represent understudied gaps in genomic knowledge. Thus, we seek to understand changes that occur between DNA mutations and ultimately expressed protein phenotypes in tumors. By harnessing computational tools, we can come closer to translating this genomic knowledge towards the delivery of precision cancer care of our head and neck cancer patients.

Andrew Lowy, MD
Our laboratory-based research is primarily focused on the identification of novel drug targets and the testing of therapies to treat pancreatic and appendiceal cancer. We use a wide variety of systems, including 2D and 3D cell cultures (organoids), organotypic slice cultures, orthotopic cell derived models, patient derived xenografts and genetically engineered mouse models. We have been at the forefront of the field in model development in the pancreatic cancer space, and have most recently applied our expertise to develop new models of appendiceal cancer. We have a large number of collaborations both within and outside UC San Diego, including partnerships with pharma and biotech. From a clinical perspective, I similarly am engaged in the study of pancreatic cancer as chair of the NCI Pancreatic Cancer Task Force, which oversees clinical trial development within the NCCN cooperative groups. Within our division, we also study peritoneal surface malignancies using clinical data to improve patient outcomes.

Quyen Nguyen, MD PhD
Our laboratory has helped pioneer fluorescence guided surgery and co-holds several patents with Nobel Laureate Roger Tsien, PhD pertaining to our invention of peptides, imaging systems and methods to support fluorescence-guided cancer tumor resections and fluorescent labeling of nerves on the surgical bed. Based on this work, we founded Alume Biosciences, a biotechnology startup with the goal of translating nerve agents developed in the lab to aid physicians in visualizing nerves in the operating room.

Mark Onaitis, MD
Our laboratory uses transgenic mouse models and human tissue samples to investigate the origin and progression of lung cancer. In mouse models, oncogenes are inducibly activated and/or tumor suppressors are inducibly knocked out in specific epithelial cell subsets within the airways and alveoli. Tumor growth and metastasis are assayed. In human tissues, lentiviral CRISPR technology allows confirmation of similar phenotypes. Tumors from mice and humans are also used to assess therapeutic efficacy of potential drugs and small molecules using high-throughput screening approaches. Funding sources include the NCI, DOD, and VA.

Rutherford (Weg) Ongkeko, MD, PhD
The overarching goal of our laboratory is to elucidate the molecular mechanisms in the pathogenesis and progression of various solid tumors. We utilize a plethora of disciplines and tools including multi-omics to study individual genes and pathways. We focus on investigating the roles of various cancer etiologies including smoking, electronic cigarettes, alcohol, viruses, and other pathogens. Our lab also studies cancer immunology and the role of the microbiome in cancer development. We utilize computational biology, machine learning, and deep learning to analyze big data. All of these components have the ultimate goal of understanding the molecular biology of tumors in order to diagnose cancers early, identify biomarkers, and to discover therapeutic targets that will provide better outcomes for cancer patients.

Partha Ray, PhD
We employ aptamers for the discovery and detection of novel biomarkers, and as a platform for targeted drug delivery into cancer cells. Aptamers are single-stranded synthetic oligonucleotide ligands that bind to their protein targets with high affinity and specificity analogous to monoclonal antibodies. However, as compared to antibodies, aptamers are less expensive, can be selected against any target, are thermodynamically stable, and are amenable to a variety of chemical modifications for developing tumor imaging and point-of-care devices to detect and monitor cancer biomarkers. We are developing these novel technologies in collaboration with oncologists and bioengineers at the Moores Cancer Center.

Jason Sicklick, MD
Our laboratory studies the biology and treatment of Gastrointestinal Stromal Tumor (GIST), the most common sarcoma. We are currently focused on investigating mechanisms of GIST tumorigenesis, disease persistence and drug resistance. Our major research programs include: (1) investigating the biology of putative GIST cancer stem cells; (2) modeling and studying SDH-deficient GIST, a rare and hereditary subtype that affects adolescents and young adults; (3) studying the tumor microenvironment of GIST, including cancer-associated fibroblasts; and (4) understanding the genomic landscape of GIST and other cancers, which can be used to guide personalized-precision medicine approaches in the clinic.

Rebekah White, MD
Our research is focused on the development of novel therapeutic strategies for pancreatic cancer. In particular, we are interested in understanding how local tumor ablation can induce systemic immune responses that will kill metastatic cells. We are particularly interested in a non-thermal method of ablation known as irreversible electroporation (IRE) that is currently in clinical use for selected patients with locally advanced pancreatic cancer. We utilize a variety of mouse models and immunologic assays to study the effects of IRE in combination with various types of immunotherapy. We are also using IRE to deliver nucleic acid therapeutics that can modify the expression of genes that may improve immune responses.

Otolaryngology/Head and Neck

Rick Friedman, MD, PhD
Our laboratory is dedicated to discovering genes, pathways, and therapeutics for the treatment of common forms of hearing loss. We do this through genome-wide association studies in both mice and humans. This has led to the discovery of several genes and pathways involved in noise-induced hearing loss (NIHL), age-related hearing loss (ARHL), and balance function. ARHL and NIHL are the two most common sensory deficits in the world, both leading to troubling tinnitus, social isolation and withdrawal, and potentially early dementia. We also collaborate with colleagues at the Salk Institute and the Sanford Burnham Prebys Medical Discovery Institute. Together, our laboratory is committed to making a difference in these disease entities.

Jacqueline Greene, MD
We conduct research at the interface of nerve regeneration, neuroscience and bioengineering. Our interests include biomaterials and bioelectronics, tissue engineering, and neural regeneration, as well as both clinical and translational research in facial paralysis and facial reanimation surgery. We have developed a nanofiber-based neural conduit for facial reanimation that was featured on the cover of Tissue Engineering and Regenerative Medicine (2018), and we are currently working on a 3D-printed nerve scaffold for peripheral nerve repair. I also have a productive collaboration with the Coleman lab (Bioengineering) to develop a noninvasive high-resolution electrode array to monitor recovery from facial paralysis.

Allen Ryan, PhD
We are involved in a variety of aspects of otologic research. This includes a major focus on auditory neuroscience as it applies to preventing hearing loss and restoring hearing. A second major interest is otitis media, and how the natural protective and recovery responses of the middle ear can be enhanced to prevent ear infections or speed their resolution. We also work to develop new means to deliver drugs to the middle and inner ears. As Director of Research for Otolaryngology/Head and Neck Surgery, I also supports the research efforts of other members of the Division and is Principal Investigator of the Division's NIH T32 training grant, which provides one year of dedicated research time for each of our residents.

Carol Yan, MD
Our research focuses on olfactory dysfunction as it's related to sinonasal disease, viral infections, and aging. We were the first group to describe that COVID-19 infections are associated with loss of smell. We are now studying the cellular and molecular mechanisms involved in post-infectious smell loss using animal models and human nasal tissue. We are also interested in studying the genetics of age-related smell loss, with its widespread presence in our aging population and its association with neurodegenerative diseases. Our translational research is paired with our clinical research, which investigates patient outcomes of olfactory dysfunction using validated smell testing in our Rhinology clinic. We are also conducting novel therapeutic clinical trials in patients with prolonged smell loss. We welcome any opportunity to collaborate with other researchers, clinicians, and students on these projects.

Inflammation and Acute Injury

Stephen Bickler, MD
Our research interests include surgical epidemiology, global surgery, and all aspects of pediatric surgery. Over the past Five years, our research has included epidemiological modeling studies using large datasets to estimate the burden of surgical diseases for the Lancet Commission on Global Surgery and the 3rd Edition Disease Control Priorities (World Bank). We are also interested in the biological changes that occur with the transition from a rural to an urban environment in sub-Saharan Africa and their relation to the origins of noncommunicable diseases. Recent studies have focused on how urbanization impacts the expression of nuclear genes encoding mitochondrial proteins.

Todd Costantini, MD
Our research is focused on how uniquely human genes define variability in the human injury and inflammation response. Our lab aims to understand the contribution of the uniquely human gene CHRFAM7A in the biology of human inflammation after injury with a focus on monocyte/macrophage proliferation and mobilization to sites of tissue injury. These studies focus on the ability of CHRFAM7A to modulate the host inflammatory response through dominant negative inhibition of cholinergic anti-inflammatory signaling that is controlled by the alpha-7 nicotinic acetylcholine receptor (α7nAchR). As CHRFAM7A expression is variable between individuals, this work seeks to explain human variability in the response to injury and infection. Lab Website

Antonio DeMaio, PhD
Our laboratory investigates the molecular and genetic basis for the intersection between stress and inflammation. We use genetic approaches to identify key players that regulate the response to injury and the potential use of hyperbaric oxygen as therapeutic intervention. In addition, we are studying the contribution of stress proteins and phospholipids within extracellular vesicles or exosomes in modulating cellular functions during infection. We are also assessing the potential role of heat shock proteins in reducing cytotoxicity during Alzheimer's Disease. Finally, we are exploring mechanisms of heat shock proteins' interaction with lipid membranes and their possible participation in the biogenesis of cellular membranes during evolution. In addition, Dr. DeMaio is highly engaged in motivating, mentoring and training students from disadvantaged backgrounds.

Brian Elicieri, PhD
Our laboratory uses state-of-the-art analytical and genetic technologies for the investigation of immune cells that mediate the resolution of the inflammation response. The neural regulation of immune cells is a mechanism that bridges inputs from the brain with the inflammation response ¾ a resolution mechanism that is dysfunctional in the cancer and following severe injury. With similarities to the neuronal synapse, the exosome regulation of immune cells is a mechanism that releases inflammatory factors from epithelial cells and macrophages into the circulation that act upon distal immune cells.

Jessica Weaver, MD, PhD
Our primary research focus is on the role of the gut-brain axis in traumatic brain injury (TBI). Inflammation from the intestine that occurs during TBI may feed back to the brain and worsen the initial injury. We utilize mouse models of TBI to study this interaction with the hope of developing treatments that will target this response in order to identify ways to improve outcomes in our brain-injured patients.

Chronic Injury & Repair

Marek Dobke, MD, PhD
My research is a hybrid of translational projects, linked with clinical practice and a vision of future directions in the field of cosmetic medicine and surgery. Two leading laboratory projects, namely, "Tissue repair, extracellular vesicular biogenesis, and the control of immune responses" - NIH R01 and "Microvascular tissue as a platform technology to modify healing tissue microenvironment and precipitate angiogenesis reversing senescence," focus on defining the mechanisms regulating immune response in wound healing via the adoptive transfer of extracellular vesicles and changing signaling pathways. We also investigate skin and gut microbiota's effect on aesthetic skin characteristics. Among clinical projects, we investigate the effects of microbes on skin aging and metabolism of cosmeceuticals aims to develop personalized cosmetic skin care and anti-aging procedures.

Tatianna Kisseleva, MD, PhD
The major interest of our laboratory is the identification of new targets for anti-fibrotic therapy in the liver. We have shown that hepatic stellate cells (HSCs) are the major source of myofibroblasts in response to toxic liver injury, and described the mechanism of their epigenetic regulation during development and regression of liver fibrosis (Liu, Gastroenterology, 2020). We also investigate the contribution of activated Portal Fibroblasts (aPFs) to cholestatic liver fibrosis, and identified specific markers which distinguish aPFs from other myofibroblasts in the liver (Koyama, JCI, 2017). Our most recent work is focused on the role of IL-17 signaling in progression of fibrosis and hepatocellular carcinoma (HCC) (Ma, J Hepatol., 2020; Xu, JCI insight, 2019).

Patricia Thistlethwaite, MD, PhD
Our research is focused on understanding the molecular mechanism responsible for pulmonary arterial hypertension (PAH). We study the role of the NOTCH3 signaling pathway in vascular smooth muscle cell proliferation in this disease. Our group has shown that NOTCH3 signaling is pulmonary arterial smooth muscle cells is required for the development of human PAH, that knockout mice that lack the NOTCH3 do not develop PAH, and that mice with transgenic expression of HES-5, a downstream effector of NOTCH3 signaling spontaneously develop PAH. We are currently studying targeted antibody therapy to block this pathway for treatment of PAH in rodents and swine, with the goal of bringing this translational therapy to the clinic to treat patients. We are also developing a serum biomarker based on a portion of the NOTCH3 receptor to non-invasively to diagnosis PAH in patients.

Transplantation & Hepatobiliary Surgery

Aleah Brubaker, MD, PHD
Dr. Brubaker graduated cum laude with a combined Doctor of Medicine and Doctor of Philosophy from Loyola University Chicago. She completed her general surgery residency at Stanford University in the Stanford Accelerated Surgeon Scientist program and is a board-certified general surgeon by the American College of Surgeons. Dr. Brubaker remained at Stanford for her 2-year fellowship in pediatric and adult abdominal transplantation. At UC San Diego, Dr. Brubaker will be an active participant in all clinical activities in the division’s surgical service including liver and kidney transplants, living donor kidney nephrectomies, deceased donor organ procurements and general surgery. She will also help start and develop the pediatric liver transplant program at Rady Children’s Hospital. Academically, Dr. Brubaker will pursue a research program geared toward evaluating the microbiome in the setting of liver and kidney transplantation. She has a specific interest in the urinary microbiome of kidney transplant recipients and relationship to recurrent urinary tract infections, BK nephropathy, and rejection.

Cardiovascular and Thoracic Surgery

Mark Kearns, MD, FRCSC
Dr. Kearns studies various aspects of cardiac transplantation, with a particular focus on hearts from the donation after circulatory death (DCD) protocol, relying upon laboratory models to approximate the complex physiologic alterations associated with the clinical DCD protocol. Hearts exposed to varying levels of warm ischemic injury can be characterized prior to and following reperfusion using either in situ or ex situ perfusion techniques. Our group uses multiple modalities to assess such hearts, in an aim to identify thresholds of cardiac non-viability for transplantation. These include myocardial performance in volume-loaded states, histochemical markers, and transcription-based molecular predictors of myocardial injury severity. We are also interested in ischemic conditioning of donor hearts. We previously investigated an immune-based cardiac preconditioning strategy, which utilized molecular mimics of bacterial DNA to leverage innate immune signalling, conferring increased cardiac tolerance to episodes of ischemic injury associated with the DCD protocol.

Dr. Kearns’ current research interests remain closely associated with clinical and translational aspects of cardiac transplantation, in-situ and ex-situ machine perfusion of DCD hearts, and strategies aimed at addressing the imbalance of donor organ scarcity and the growing demand of end stage heart failure patients.






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