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 symdrome, 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 research focuses on developing epigenetic biomarkers for gastrointestinal diseases, with an emphasis on differential diagnosis of irritable bowel syndrome. Dr. Joshi has published in peer-reviewed journals such as Nature and Gastroenterology and serves as a review editor for several journals as well as a guest editor for Frontiers in Physiology. She has received multiple honors, including Early Career Investigator recognition at Digestive Disease Week in 2018 and 2022, and is a co-inventor on two U.S. patents related to DNA methylation-based biomarkers for gastrointestinal disorders filed in 2019 and 2023.