Digestive Diseases Research

Joshi Laboratory

Swapna Joshi, PhD

Dr. Joshi’s research interests include bioinformatic analysis and integration of genomic, epigenetic, and microbial data to identify diagnostic biomarkers and mechanisms of gastrointestinal (GI) diseases, including irritable bowel syndrome (IBS).  

Key investigators

  • Swapna Joshi, PhD
  • Lin Chang, MD

Funding

UCLA Innovation Fund 2018
Drs. Swapna Joshi and Lin Chang were awarded UCLA innovation grant to develop DNA methylation-based biomarkers for diagnosis of irritable bowel syndrome (IBS) and differential diagnosis of IBS from GI conditions that mimic IBS.

NIH R21 2016
This project is aimed at studying epigenetic alterations in PBMCs and colonic mucosa of IBS patients compared to healthy controls.

Current research projects

  • Epigenetic analysis of colonic mucosa in IBS patients compared to healthy controls
  • Colonic mucosal microbiota in IBS compared to healthy controls
  • Sex differences in DNA methylation profiles of IBS patients compared to healthy controls
  • MicroRNA expression in colonic mucosa of IBS compared to healthy controls
  • DNA methylation-based biomarkers for IBS diagnosis

Future directions

  • Study molecular mechanisms of IBS compared to healthy controls by integrating colonic mucosal DNA methylation, gene expression and microbial profiles
  • Develop DNA methylation-based biomarkers for diagnosis of GI disorders

Key publications (selected) - Full list on PubMed

  1. Irwin S, van Daelen M, Almaraz I, Park R, Nelson B, Mahurkar-Joshi S, Rieder F, Shih DQ, Ho W, Limketkai BN, Koon HW. Fidaxomicin Reduces Collagen Expression in Intestinal Fibroblasts Via Platelet-Derived Growth Factor Receptor Beta and Glycogen Synthase Kinase-3 Beta Inhibition. Gastroenterology. May 18, 2025
  2. Lee AH, Mahurkar-Joshi S, Naliboff B, Tillisch K, Mayer E, Chang L. Role of sex, anxiety, and resilience in the association between adverse childhood experiences and irritable bowel syndrome. Clinical Gastroenterology and Hepatology. January 2025
  3. Larauche M, Mahurkar-Joshi S, Biraud M, Ju T, Mayer EA, Chang L. Sex-dependent alterations of colonic epithelial permeability: Relevance to irritable bowel syndrome. Front Physiol. Gastrointestinal Sciences. 2025 Volume 16, doi: 10.3389/fphys.2025.1509935
  4. Mahurkar-Joshi S, Thompson M, Villarruel E, Lewis JD, Lin LD, Farid M, Nayeb-Hashemi H, Storage T, Weiss GA, Limketkai BN, Sauk JS, Mayer EA, Chang L. Genome-wide DNA methylation identifies potential disease-specific biomarkers and pathophysiologic mechanisms in irritable bowel syndrome, inflammatory bowel disease, and celiac disease. Neurogastroenterology & Motility. 13 December 2024
  5. Mahurkar-Joshi S, Rankin CR, Videlock EJ, Soroosh A, Verma A, Khandadash A, Iliopoulos D, Pothoulakis C, Mayer EA, Chang L. The colonic mucosal MicroRNAs, MicroRNA-219a-5p, and MicroRNA-338-3p are downregulated in irritable bowel syndrome and are associated with barrier function and MAPK signaling. Gastroenterology. 2021 Jun;160(7):2409-2422.e19. doi: 10.1053/j.gastro.2021.02.040. Epub 2021 Feb 20. PubMed PMID: 33617890; PubMed Central PMCID: PMC8169529
  6. Mahurkar-Joshi S, Chang L. Epigenetic mechanisms in irritable bowel syndrome. Front Psychiatry. 2020;11:805. doi: 10.3389/fpsyt.2020.00805. eCollection 2020. Review. PubMed PMID: 32922317; PubMed Central PMCID: PMC7456856
  7. Videlock EJ, Mahurkar-Joshi S, Hoffman JM, Iliopoulos D, Pothoulakis C, Mayer EA, Chang L. Sigmoid colon mucosal gene expression supports alterations of neuronal signaling in irritable bowel syndrome with constipation. Am J Physiol Gastrointest Liver Physiol. 2018 Jul 1;315(1):G140-G157. doi: 10.1152/ajpgi.00288.2017. Epub 2018 Mar 22. PubMed PMID: 29565640; PubMed Central PMCID: PMC6109711
  8. Mahurkar S, Polytarchou C, Iliopoulos D, Pothoulakis C, Mayer EA, Chang L. Genome-wide DNA methylation profiling of peripheral blood mononuclear cells in irritable bowel syndrome. Neurogastroenterol Motil. 2016 Mar;28(3):410-22. doi: 10.1111/nmo.12741. Epub 2015 Dec 16. PubMed PMID: 26670691; PubMed Central PMCID: PMC4760882

About Dr. Joshi

Dr. Joshi co-leads the Integrative Biostatistics and Bioinformatics Core at the Goodman-Luskin Microbiome Center. Her translational research focuses on developing epigenetic biomarkers for gastrointestinal diseases, with a specialized emphasis on the differential diagnosis of irritable bowel syndrome (IBS). Dr. Joshi has published in top-tier, peer-reviewed journals, including Nature and Gastroenterology. In addition to her research, she is deeply involved in the scientific community, serving as a review editor for several prominent journals and as an Associate Editor for Scientific Reports published by Springer Nature. Dr. Joshi’s research was acknowledged with the Early Career Investigator recognition at the Digestive Disease Week conference in 2018 and 2022. She is also a co-inventor on two U.S. patents (filed in 2019 and 2023) pioneering the use of DNA methylation-based biomarkers for gastrointestinal disorders.