Icahn School of Medicine at Mount Sinai
IBD Genetics Research Center

Judy Cho, MD

Principal Investigator, IBDGC Data Coordinating Center

My major research efforts currently are: a) defining mechanisms of stromal/epithelial-immune cell cross talk in IBD; b) defining components of treatment refractory (specifically, non-response to pro-inflammatory cytokine blockade) IBD at the cellular and tissue level; c) predicting differences in clinical outcomes of interest across IBD clinical subtypes and populations; d) exploring the role of rare, IBD-associated variants of high effects; e) organizing large datasets for NIDDK IBDGC and IIBDGC; and f) developing select treatment targets based on IBD genetic and single cell expression findings. Since 2015, I have served as Director of the Personalized Medicine Institute at Mount Sinai. I am extremely excited by the explosion of data and new data tools that are accelerating collaborative efforts to benefit patients through genetic and genomic studies; I am eager to continue applying new data-approaches to benefit the NIDDK IBDGC.

Co-investigators

  • Miriam Merad, MD/PhD (Technology & immunology)
  • Ephraim Kenigsberg, PhD (single cell analysis)
  • Ke Hao, PhD (genetic analysis)
  • Bruce Sands, MD (Lead clinician)
  • Yuval Itan, PhD
  • Kyle Gettler, PhD

Lead Clinicians

  • Ryan Ungaro, MD, MS
  • Adam Steinlauf
  • Asher Kornbluth
  • Peter Legnani
  • James Marion
  • Adam Greenstein (surgeon)
  • Sergei Khaitov (surgeon)
  • Jean-Fred Colombel
  • Bachir Taouli (radiology)
  • Pathology (Noam Harpaz)

Lab and Project Management

  • Ksenija Sabic (Lab Manager)
  • Nai-Yun Hsu PhD (Senior staff scientist)

Clinical Coordinators

  • Colleen Chasteau
  • Ujunwa Korie, MD, MS

Specific Aims

Aim 1: To function as a multi-disciplinary genetics research center (GRC) in Consortium-wide projects. To recruit populations prioritized by the NIDDK IBDGC, including non-European cohorts. To ascertain and participate in intestine-focused, cross-Consortium studies. To pilot novel clinical research approaches, to scale select approaches across the NIDDK IBDGC. To deepen longitudinal phenotype data for recruited patients.

Aim 2: To define intestinal single-cell expression features with anti-TNF non-response and response in ileal resection and inception Crohn’s cohorts. To identify key measurements for large cohort, longitudinal analyses.

Administrative Supplement

Aim 1: Optimize cell isolation protocols and surface marker selection for CITE-Seq studies.

Aim 2: To apply optimized CITE-Seq protocols to Crohn’s disease resection tissues: comparing classic lineage to GWAS-prioritized surface protein expression

Aim 3: Improve imputation of single cell-based insights onto larger datasets: developing new expression quantitative traits and defining pathophysiologic heterogeneity

Ancillary liaisons

  • Yuval Itan (Mount Sinai), R01DK123530 Identifying population-specific IBD-associated mutations, genes and pathways
  • Ophir Klein (UCSF), R21DK127206, Using human organoids to model IBD pathogenesis

Additional resources at Mount Sinai

  • BioMe cohort: Dr. Cho manages the School’s blood-based biobank containing over 60K patients, for whom 30K have attained whole exome sequence data
  • MSCCR (Mount Sinai Crohn’s and Colitis Registry): under the leadership of Dr. Sands, the MSCCR cohort contains over 1500 IBD patients for whom RNASeq are attained, with whole exome sequencing and chip data pending (ongoing at the Broad Institute, for full NIH-sharing)
  • Radiology de-identification: The Imaging Institute at Mount Sinai has the capacity to de-identify all personal health identifiers from DICOM-attained radiology images.

Major interests

  • Ileal resection cohorts: primary interests are in integrating bulk RNASeq with single cell and genetic data. We have shared de-identified radiology images with the Cedars-Sinai GRC, valuable for longitucinal studies
  • Ulcerative colitis and enteroid-based studies: Dr. Hsu is studying the impact of loss-of-function mutations in reactive oxygen-generating enzymes (e.g NOX1) at the single cell level
  • Multi-omic single cell analyses and data integration. We have previously published on integration of single cell data with bulk RNASeq; we are actively exploring to what extent emerging multi-omic datasets provide insight into blood-to-tissue IBD physiology. Piloting new technologies with paraffin-tissues
 

Co-Investigators

Dr. Bruce Sands, MD, MS

Professor of Medicine

Bruce Sands, MD, MS is the Dr. Burrill B. Crohn Professor of Medicine. Dr. Sands is an expert in the management of inflammatory bowel diseases (IBD) and has earned an international reputation for his care of patients with complex and refractory disease.  He joined Mount Sinai in 2010 as Chief of the Dr. Henry D. Janowitz Division of Gastroenterology.  Prior to joining Mount Sinai, Dr. Sands was Medical Co-Director of the Crohn’s & Colitis Center at Massachusetts General Hospital in Boston, where he also served as the hospital’s Acting Chief of the Gastrointestinal Unit as well as Associate Professor of Medicine at Harvard Medical School.

Miriam Merad, MD, PhD

Professor of Oncological Science, Medicine and Immunology

Miriam Merad, M.D.; Ph.D. is the Mount Sinai Endowed professor in Cancer Immunology and the Director of the Precision Immunology Institute at Mount Sinai School of Medicine in New York. Dr. Merad also co-leads, the Cancer Immunology program at The Mount Sinai Tisch Cancer Institute and is the Director of the Mount Sinai Human Immune Monitoring Center (HIMC).

Ke Hao, PhD

Associate Professor, Genetics and Genomics Sciences

Dr. Hao is currently an associate professor of the Department of Genetics and Genomic Sciences and a member of Icahn Institute of Data Science and Genomic Technology. Dr. Hao received his ScD degree and postdoc training at Harvard University and has extensive expertise in statistical genetics, computational biology and environmental health. Over the past decade, Dr. Hao has contributed significantly in these areas.   He systematically collected large datasets of human tissue samples, and generated molecular trait quantitative loci (xQTLs), including adipose, blood vessel wall, skeleton muscle, lung, liver, brain, placenta, intestine, whole blood, monocyte, macrophage, etc.  Further he integrated the xQTLs with large GWAS data to identify genetic basis of human diseases and discover the mechanism: genetic variants → molecular/cellular alternation → disease.

Ephraim Kenigsberg, PhD

Assistant Professor, Genetics and Genomics Science

Dr. Ephraim Kenigsberg is an Assistant Professor for the Department of Genetics and Genomic Sciences and the Icahn Institute for Data Science and Genomic Technology.