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Gastroenterology and Hepatology

Research Labs

The Division of Gastroenterology and Hepatology in the Department of Medicine at the Johns Hopkins University School of Medicine has a long history of laboratory and clinical research, teaching and service activities. Our mission is to advance the understanding, diagnosis, treatment and prevention of gastrointestinal and liver disease. 

Focused areas of expertise and investigation include early detection of pancreatic cancer, epithelial biology and physiology, endoscopic device development and innovation, third space endoscopy techniques and outcomes, biomarker development for the early detection of GI diseases, inflammatory bowel disease genetics and clinical outcomes, alcohol-associated liver disease clinical and basic research, physiology and homeostasis of metals in the digestive organs, liver transplant-related clinical research, and many others. 

The division is known for seminal innovations that convey a steadfast commitment to alleviating the suffering caused by diseases and conditions of the digestive tract and liver. Faculty in the division have active research funding totaling more than $11.5 million annually.

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Basic and Translational Research Labs

GI Biomarkers Laboratory

The GI Biomarkers Laboratory studies gastrointestinal cancer and pre-cancer biogenesis and biomarkers. The lab is led by Dr. Stephen Meltzer, who is known for his research in the molecular pathobiology of gastrointestinal malignancy and premalignancy. Research in the lab has led to several groundbreaking genomic, epigenomic and bioinformatic studies of esophageal and colonic neoplasms, shifting the gastrointestinal research paradaigm toward genome-wide approaches.

Principal Investigator

Stephen J. Meltzer, MD

Department

Medicine

Oncology

Research Areas

Janet Staab Lab

The Janet Staab Lab performs basic and translational studies to understand bacterial and fungal/host interactions utilizing human intestinal organoids and colon cancer cell lines.

Principal Investigator

Janet Frances Staab, PhD

Department

Medicine

Jennifer Foulke-Abel Lab

The Jennifer Foulke-Abel Lab engages in basic and translational research focused on how intestinal epithelia interface with their environment. Our work is powered by human adult stem cell-derived intestinal organoids, which capture the unique genetic and phenotypic traits of an individual and enable a personalized approach to understanding epithelial pathophysiology. One project in the lab centers on dissecting the factors involved in mucosal recognition of pathogenic bacteria with the goal to optimize vaccine engineering. A second area of interest is characterizing the altered intestinal stem cell programming associated with dietary nutrient absorption and hormone secretion in obesity to tailor weight-loss therapies.

Principal Investigator

Jennifer Foulke-Abel, PhD

Department

Medicine

Research Areas

James Hamilton Lab

The James Hamilton laboratory performs pre-clinical experiments and basic studies investigating liver inflammation, fibrosis, and nuclear receptor signaling. In close collaboration with Dr Svetlana Lutsenko in Physiology, their team performs detailed studies of hepatocyte and non-parenchymal cell isolation, culture, biology and genetic manipulation. Working with models of Wilson disease, a disorder of copper overload, they discovered that hepatic nuclear receptor mediated control of lipid metabolism is a preferential and early target of copper toxicity. Furthermore, targeting nuclear receptors with pharmacologic agonists prevents and reverses liver inflammation and fibrosis.

Research Areas

Amy Kim Lab

The Amy Kim lab performs basic, translational, and clinical research on liver lesions and hepatocellular carcinoma (HCC). She uses state of the art techniques such artificial intelligence enhanced interpretation of pathology and imaging, as well as detection of circulating tumor cells for early detection and prediction of recurrence of HCC after resection and liver transplantation.

Principal Investigator

Amy Kim, MD

Department

Medicine

Oncology

Research Areas

Ashish Nimgoankar Lab

The Ashish Nimgoankar Lab is interested in translational technology development and image-guided therapies. Dr. Nimgoankar and his collaborative team of biomedical engineers specializes in developing innovative ideas and translating these into commercial products.

Principal Investigator

Ashish Nimgaonkar, MBBS MSc

Department

Medicine

Biomedical Engineering

Research Areas

Cynthia Sears Laboratory

Work in the Cynthia Sears Laboratory focuses on the bacterial contributions to the development of human colon cancer and the impact of the microbiome on other cancers and the therapy of cancer. The current work involves mouse and human studies to define how enterotoxigenic Bacteroides fragilis, pks+ Escherichia coli, Fusobacterium nucleatum, biofilms and the colonic microbiota induce chronic colonic inflammation and colon cancer. Prospective human studies of the microbiome and biofilms in screening colonoscopy are in progress as are studies to determine if and how the microbiome impacts the response of individuals with cancer to immunotherapy and other cancer therapies.

Principal Investigator

Cynthia Louise Sears, MD

Department

Medicine

Oncology

Research Areas

Michael Goggins Lab

The Michael Goggins Lab performs basic, translational, and clinical research on pancreatic cancer.

Principal Investigator

Michael G. Goggins, MD

Department

Medicine

Oncology

Pathology

Research Areas

Florin Selaru Lab

Dr. Florin Selaru is the director of the Johns Hopkins Inflammatory Bowel disease Center and the research interests in the Selaru Lab comprise the molecular changes associated with the transition from inflammatory states in the GI tract (colon, stomach, biliary tree) to frank cancers. In addition, our current research funded by the AGA, FAMRI and the Broad Foundation works to further the understanding of cancer development and progression in the gastrointestinal tract. Additional areas of investigation include collaboration with biomedical engineers to develop novel compounds for the treatment of IBD associated fistulizing disease, as well as new techniques for administering medications directly to inflamed GI tissues.

Principal Investigator

Florin Selaru, MD

Department

Medicine

Oncology

Biomedical Engineering

Research Areas

Joanna Melia Lab

The Melia lab performs basic, translational, and clinical research on inflammatory bowel disease. Specifically, Dr Melia's basic science and translational research program is concentrated on novel roles of manganese (Mn) homeostasis in Crohn's disease and the interaction with aberrant N-glycosylation with current support from NIDDK and NICHD, including support as a co-investigator in the Center for Metals in Nutrition and Development.

Principal Investigator

Joanna Miller Peloquin Melia, MD

Department

Medicine

Research Areas

Ken Hui Lab

The Hui lab performs basic, translational and clinical research on genetics and genomics of neurogastroenterological disorders. Ongoing projects include evaluation of sensory mechanisms in the pathophysiology of nausea using single-cell sequencing analysis of the vagal nodose ganglion cells and real world clinical data in order to understand mechanisms of this debilitating and poorly understood condition.

Principal Investigator

Ken Hui, MD PhD

Department

Medicine

Research Areas

Laboratory for Endoscopy Advancement and Device Development

The principal goal of LEADD is to catalyze the development and dissemination of innovative techniques in advanced gastrointestinal endoscopy at Johns Hopkins Medical Institutions, by providing the resources and expertise to conceptualize, design, build, and test new endoscopic devices. LEADD resources will also provide resources for endoscopy education for trainees and faculty. Additional Faculty: Anthony Kalloo, M.D.; Mouen Khashab, M.D., Saowanee Ngamruengphong, M.D. 

Principal Investigator

Venkata Akshintala, MBBS PhD

Department

Medicine

Liudmila Cebotaru Lab

Dr. Cebotaru is the Director of Johns Hopkins Center for Gene Therapy research in Gastroenterology and research in the Cebotaru Lab studies cystic fibrosis transmembrane conductance regulator (CFTR) mutants as well as the pathophysiology of polycystic liver and kidney disease (PKD). They also investigate corrector molecules to get a better understanding of their mechanism of action. A major focus of her research is on developing more efficient gene therapy vectors with the ultimate goals of developing a gene therapy for cystic fibrosis and PKD.

Research Areas

Mahya Faghih Lab

Dr. Faghih is a member of the Johns Hopkins Pancreas Center and is a translational pain researcher who is leading mechanistic studies and clinical trials in chronic pancreatitis-associated pain. One particular aspect of her research is the use of the “Scrambler” device in the treatment of pain from chronic pancreatitis.

Principal Investigator

Mahya Faghih, MD

Department

Medicine

Shaoyong Yu Lab

The Yu Lab does basic and translational research on sensory physiology and disorders of the gastrointestinal tract. Recently funded work by the NIH/NIDDK includes specific research into the pathophysiology of how mast cells and bile salt reflux effect motility of the esophagus.

Principal Investigator

Shaoyong Yu, MD

Department

Medicine

Neuroscience

Research Areas

Svetlana Lutsenko Laboratory

The research in the Svetlana Lutsenko Laboratory is focused on the molecular mechanisms that regulate copper concentration in normal and diseased human cells. To understand the molecular mechanisms of copper homeostasis in normal and diseased human cells, we utilize a multidisciplinary approach involving biochemical and biophysical studies of molecules involved in copper transport, cell biological studies of copper signaling, and analysis of copper-induced pathologies using Wilson's disease gene knock-out mice.
Lab Website

Research Areas

Varsha Singh

The Singh Lab does basic and translational research on intestinal ion transport, cellular physiology, and membrane trafficking in diabetic disorders and cystic fibrosis. Her work is currently focused on characterizing the role of early endosomal-PX domain binding protein Sorting Nexin-17 in intestinal fluid homeostasis and epithelial cell physiology.

Department

Medicine

Research Areas

Zachariah Foda Lab

The Foda lab conducts basic, translational, and clinical research on the early detection, prevention, and interception of gastrointestinal cancers. In collaboration with the other member of the Johns Hopkins Cancer Genomics Lab (https://cancergenomicslab.com/), the group develops and applies whole-genome sequencing-based liquid biopsy methods for the early detection and monitoring of gastrointestinal cancers. These approaches are tested and validated in large multi-national cohorts through international collaborations. Dr. Foda directs the Johns Hopkins Hereditary Colorectal Cancer Registry, which facilitates clinical research related to Familial Adenomatous Polyposis, Lynch syndrome, and other hereditary polyposis conditions.

Principal Investigator

Zachariah H. Foda, MD PhD

Department

Medicine

Oncology

Johns Hopkins Center for Gastrointestinal Epithelial Disorders

The Johns Hopkins Center for Epithelial Disorders focuses on research into the physiology and pathophysiology of epithelial cells of the gastrointestinal (GI) tract, liver, pancreas and kidney. Specifically, the center’s research seeks to:

  • Understand the mechanisms regulating the activity of transport proteins (including channels) of epithelial cells
  • Characterize the mechanisms by which polarity of epithelial cells are maintained
  • Investigate the mechanisms controlling transcription of epithelial-specific genes
  • Understand the pathophysiological basis of GI and renal diseases that involve the preceding three components
  • The center also provides a framework for training fellows in gastroenterology and hepatology to become independent investigators.

New translational research directions in the center utilize human intestinal organoids to model epithelial dysfunction and develop therapeutic strategies for chronic GI diseases:

  • Cystic Fibrosis (CF): Patient-derived organoids are used to study residual secretory capacity and identify new therapeutic approaches for CF-related constipation, beyond current laxative-based care.
  • Type 1 Diabetes (T1D): Organoid models help uncover epithelial mechanisms driving diabetic enteropathy and guide strategies to restore intestinal fluid balance in affected patients.
  • Ulcerative Colitis (UC): Colonoid and immune cell co-culture models are used to investigate mucus barrier dysfunction and support the development of therapies targeting epithelial–immune interactions.
  • Epithelial Homeostasis: Studies focus on epithelial polarity and signaling pathways such as endosomal trafficking and metabolic regulation, with implications for multiple GI diseases.
  • Ion Transport and Diarrheal Diseases: Ongoing studies explore the regulation of sodium and chloride transporters in the intestinal epithelium and their role in fluid balance, with the goal of
    identifying new therapeutic targets for diarrheal disorders.
  • Obesity: Patient-derived organoids have been used to identify dysregulated nutrient absorption and altered chromatin accessibility in obesity, suggesting a stem cell-imprinted epigenetic origin for weight loss resistance that is the focus of current studies.
  • Metabolic-associated steatotic liver disease (MASLD): Studies evaluate intestine-liver crosstalk via extracellular vesicles released by intestinal organoid monolayers (containing microRNAs and other cargo) that may communicate with hepatocytes via portal circulation to propagate development of obesity-associated MASLD.

Principal Investigators: Jennifer Foulke-Abel, PhD and Varsh Singh, PhD
Emeritus Principal Investigator: Mark Donowitz, MD
Additional Faculty: Anthony Guerrerio, MD, PhD (Pediatrics); Janet Staab, PhD; Florin Selaru, MD; Joanna Melia, MD; David Muniz-Pedrogo, MD; Amy Kim, MD; Gerri Keane, M.B.B.Ch, Nicholas Zachos, PhD (Vanderbilt).
Department: Medicine 

Clinical Research Programs

Core Laboratories of the GI Division

James J. Potter Gastroenterology and Hepatology Translational Enhancement Core and Biorepository

This core laboratory supported by the GI division provides assistance with biospecimen collection, processing, and storage. It provides access to over 100,000 biospecimens with annotated clinical data that can be used for translational research. The lab uses state of the art barcoding for ease of specimen retrieval and has 8, -80C freezers, 1 ultra-low temperature freezer (-196 C), several -20C freezers, and 24hour monitoring.

GI Animal Research laboratory

This is a fully equipped lab allowing large as well as small animal surgery and endoscopy. The animal lab has 1 surgery rooms, and is fully equipped with endoscopic equipment, including upper endoscopes (Pentax and Olympus),colonoscopes (Pentax)and therapeutic scopes (Pentax). In addition, the animal lab has anesthesia machines and ventilators as well as a C arm for radiologic studies.

Ross 9 Gastroenterology Microscopy Core

The Ross imaging core dedicated to providing state-of-art microscopy technology to the members of the Johns Hopkins GI division and the general Hopkins scientific community.

Current scopes include: Olympus FV3000RS confocal, Olympus IX83 widefield inverted "FISHscope,” Keyence BZ-X710 (fluorescence/LED + cubes), and a Zeiss AxioObserver inverted epifluorescence microscope with Olympus camera.

Clinical and Translational Research Unit (CTRU) in Gastroenterology & Hepatology

The Clinical and Translational Research Unit (CTRU) promotes and enhances innovative, clinically- relevant, high-quality clinical and translational research in the Division of Gastroenterology and Hepatology and provides extensive resources and skilled personnel to support all research activities including protocol design, regulatory support, budget development, study conduct, patient recruitment, data management, and biostatistical consultations.

Research staff members in the CTRU include research coordinators, post-doctoral fellows and other support personnel. Each coordinator manages between 1-4 studies from research registries to multi-center IND/IDE randomized controlled clinical trials with recruitment across multiple campuses (JHH – East Baltimore, JH Bayview Medical Center, JH ASC and Clinic at Green Spring Station and White Marsh, JH GI at Knoll North in Howard County, MD and Sibley Memorial Hospital in Washington DC). Dedicated research exam rooms are available at some locations. Lab spaces in the Ross Building and Bond Street Annex are equipped with centrifuge, microscope, freezers, tissue culture and fume hoods and other common lab instruments and supplies. Storage facilities are located in the Blalock building with restricted access for study kits and documents.

The CTRU works collaboratively with the GI Biorepository which follows best practices for sample collection, processing, tracking and storage using the OpenSpecimen Lab Information Management System. All freezers and LN2 tanks are equipped with 24/7 continuous remote temperature monitoring systems to ensure sample integrity.