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John P. Lynch, MD, PhD

John P. Lynch, MD, PhD Physician

Associate Professor of Medicine

Dr. Lynch is a Penn Medicine employed physician.

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Clinical Specialties


  • Gastroenterology

Programs & Centers:

Board Certification:

  • Gastroenterology, 2000

Clinical Expertise:

  • Endoscopy

Description of Clinical Expertise


Practice Locations and Appointments

Insurance Accepted

  • Aetna US Healthcare
  • Cigna
  • Cigna HealthSpring
  • Devon Health Services (Americare)
  • Gateway Health Plan
  • Geisinger Health Plan
  • HealthAmerica / HealthAssurance, a Coventry Plan
  • HealthPartners
  • HealthPartners Medicare
  • HealthSmart
  • Highmark Blue Shield
  • Horizon Blue Cross Blue Shield of New Jersey
  • Humana / Choicecare
  • Independence Blue Cross (Keystone East)
  • Intergroup
  • Keystone First
  • Multiplan
  • NJ Medicaid
  • NJ Qualcare
  • Oxford Health Plan
  • PA Medicaid
  • PA Medicare
  • Preferred Health Care/LGH
  • Rail Road Medicare / Palmetto GBA
  • Remedy Partners at Penn Medicine
  • Tricare
  • United Healthcare
  • UnitedHealthcare Community Plan
  • US Family Health Plan

Education and Training

Medical School: University of Connecticut
Residency: Hospital of the University of Pennsylvania
Fellowship: Hospital of the University of Pennsylvania


AGA Gastroenterology Research Group, International American Association for Cancer Research , International American College of Gastroenterology , National American Gastroenterological Association (AGA), International American Gastroenterology Association , International American Society for Cell Biology, International Cancer Research UK , International Cancer Research UK, International Cancer Research UK; Science Funding Committee, International Cancer Research UK; Science Funding Committee, International Environmental Protection Agency Grant Review "Organotypic Culture Models for Predictive Toxicology Center", National Gastroenterology Research Group of the American Gastroenterological Association., International GI Oncology Section, American Gastroenterological Association, International Health Research Board Ireland, International International Society of GI Cancers, International Italian Association for Cancer Research (AIRC), Milano, Italy, International Medical Research Council UK, International National Science Foundation-International Fellows Research Program , National NCI Special Emphasis Panel-Loan Repayment Program, National New York Academy of Science, International NIDDK Special Emphasis Panel (ZRG1 DKUS C) June 2011, National NIDDK Special Emphasis Panel (ZRG1 DKUS C) Oct 2011, National NIDDK Special Emphasis Panel ZDK1 GRB-8 (M3) 1, National NIH (NCI) Early Detection Research Laboratories and Centers--Clinical Epidemiology and Validation Center at the University of Michigan, National NIH Center for Molecular Studies in Digestive and Liver Diseases at the University of Pennsylvania, Local NIH Intestinal Stem Cell Consortium (ISCC). Cosponsored by the NIDDK and NIAID , National NIH NIDDK DDK-C Grant Review Subcommittee, National NIH Small Business, National NIH Small Business: Digestive Sciences review panel; NIDDK July 2012, National NIH Special Emphasis Panel (NCI) "Cancer Prevention Research Small Grant Program", National NIH Special Emphasis Panel/Scientific Review Group 2012/10 ZRG1 DKUS-C (04) June 2012, National NIH Special Emphasis Panel/Scientific Review Group 2014/08 ZCA1 PCRB-B, National NIH/NCI Early Detection Research Network Biomarker Development Lab review committee, National NIH/NCI Early Detection Research Network Biomarker Development Lab review committee, National NIH/NCI Special Emphasis Panel(SEP), National NIH/NIDDK Native American Research Centers for Health (NARCH)Study Section, National Projects in Knowledge, University of Pennsylvania Office of Continuing Medical Education, National Research Awards Committee of the American Gastroenterological Association., International Special Emphasis Panel ZCA1 PCRB-B Clinical Research -Loan Repayment Program , National Stars and Stripes Competitive Pilot Projects Committee, Department of Veterans Affairs, National UK Medical Research Council (MRC) Cancer Unit, Cambridge, Quinquennial Review, International University of Michigan Geriatrics Center, Pilot Grant Program, National US Department of Defense (DoD) Congressionally Directed Medical Research Programs (CDMRP, , National World Organization for Specialized Studies on Diseases of the Esophagus (OESO), International

Hospital Affiliation

Dr. Lynch is a Penn Medicine employed physician.

Hospital Privileges:

  • Hospital of the University of Pennsylvania: Has privileges to treat patients in the hospital.
  • Penn Medicine Radnor: Has privileges to perform procedures.
  • Penn Presbyterian Medical Center: Has privileges to treat patients in the hospital.


Description of Research Expertise:

Research Interests

1. Mechanisms of intestinal metaplasia of the esophagus (Barrett’s esophagus) and stomach, with a focus on developing novel cell culture and animal models for this disorder.
2. Role of myeloid derived suppressor cells in the pathogenesis of barrett’s esophagus and esophageal adenocarcinoma.
3. autophagy in the pathogenesis of Barrett’s esophagus, progression to neoplasia, and resistance to therapies.
4. Modeling the effects of Cox-2 activity on oxidative stress and DNA damage in the esophagus.
5. Identification of cells and factors contributing to the intestinal stem cell niche, and their response to injury and disease conditions.
6. Live-cell imaging studies of intestinal stem cell and crypt niche cell interactions, crypt fissioning, mitosis, and early events in neoplastic transformation by confocal microscopy.

Description of Research

Barrett’s Esophagus Focus:
Esophageal adenocarcinoma (EAC) has been the fastest rising malignancy in the U.S.. Several conditions increase the risk for the development of EAC, including obesity, smoking, diet, acid reflux, and, most significantly, Barrett's esophagus (BE). BE occurs at the gastroesophageal (GE) junction and is the replacement of normal squamous esophageal mucosa with an intestinalized columnar epithelium. It typically arises in response to chronic acid exposure and is associated with acid reflux. Importantly, the histologic precursor lesions and molecular mechanisms underpinning BE pathogenesis remain poorly understood. One reason is the paucity of experimental models for BE. Our research has focused on this problem, and the development of innovative, genetically based and physiologically relevant human cell based 3D organotypic cultures and transgenic mouse models for BE is an important objective of my lab. We are broadly pursuing several strategies including exploring the role proinflammatory cytokines (IL-1beta), eicosanoids (Cox-2), myeloid derived suppressor cells, and autophagy in BE pathogenesis and progression to neoplasia.

Intestinal Stem Cell Focus:
Stem cells are defined by the capacity for long-term self-renewal and multilineage differentiation. Until relatively recently, our understanding of stem cell biology, as well as their role in many human disease processes from aging to cancer, has been rather limited. Moreover, interest in harnessing the stem cell’s capacity for self-renewal to promote organ and tissue regeneration cuts across many medical disciplines. Genetic studies have identified several robust markers for stem cell populations in the intestine. These advances now make it possible to isolate stem cell populations for more advanced molecular investigations and ex vivo culture. We are presently developing human multi-cell based 3D culture systems in which we can model inflammatory conditions of the gut as a method of studying physiologically the effects of immune cells, inflammatory microenvironment, oxidative stress and mitochondrial dysfunction on stem cell biology and stem cell DNA damage. Recently we have also begin using live cell confocal microscopy to investigate how the intestinal stem cell niche is established, the relationship between niche and stem cells, how intestinal crypts fission, how stem cells undergo mitosis, and early events in neoplastic transformation.

Rotation students invited to discuss projects

Lab personnel:
Mary Ann Crissey--Research Specialist and Lab Manager
Jianping Kong PhD--Senior research Investigator
James Bortner PhD--Post Doctoral FellowDoctoral Fellow
Kira Hartman PhD--Post Doctoral FellowDoctoral Fellow
Fang Wang PhD--Post Doctoral Fellow

Recent Publications:

1. Stairs, D. B., Nakagawa, H., Klein-Szanto, A., Mitchell, S., Silberg, D., Tobias, J.W., Lynch, J. P., Rustgi, A. K.; “Cdx1 and c-myc foster the initiation of transdifferentiation of the normal esophageal squamous epithelium toward Barrett's Esophagus” PloS ONE 2008;3(10):e3534; PMCID: PMC2568822.

2. Huo, X., Zhang, H.Y., Zhang, X., Lynch, J.P., Strauch, E.D., Wang, J.Y., Hormi-Carver, K., Spechler, S.J., Souza, R.F.; “Differences in CDX-2 Expression after Exposure to Acid and Bile Salts in Esophageal Squamous Cell Lines from GERD Patients with and without Barrett’s Esophagus.” Gastroenterology 2010 Jul;139(1):194-203.e1 PMCID: PMC2902607

3. Funakoshi, S., Kong, J., Crissey, M.S., Dang, D., Dang, L., Lynch, J.P; “Cdx2 induces E-cadherin function by promoting E-cadherin localization to the cell surface” Am J Gastrointest Liver Physiol. (Editorial Highlight) 2010 Nov;299(5):G1054-67. PMCID: PMC2993167

4. Verzi, M.P., Hatzis, P., Philips, J., Sulahian, R., Schuijers, J., Freed, E., Brown, M.A., Lynch, J.P., Dang, D.T., Clevers, H., Liu, X.S., Shivdasani, R.A.; “TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-elements” Proc Natl Acad Sci USA 2010 Aug 24;107(34):15157-62. PMCID: PMC2930576

5. Stairs, D.B., Kong, J., Lynch, J.P.; “Cdx genes, inflammation, and the pathogenesis of intestinal metaplasias” in “Molecular Biology of Digestive Organs.” Editor: Klaus Kaestner. Series Progress in Molecular Biology and Translational Science. 2010;96:231-70. PMID:21075347

6. Crissey, M.S., Guo, R.J., Funakoshi, S., Liu, J., Kong, J., Lynch, J.P.: "Cdx2 Levels Modulate Intestinal Epithelium Maturity and Paneth Cell Development". Gastroenterology 140(2): 517-528, 2011 Notes: Editor's pick for the February 2011 issue. PMCID: PMC3031739

7. Kong, J., Crissey, M.S., Funakoshi, S., Kreindler, J.L., and Lynch, J.P.: "Ectopic Cdx2 expression in murine esophagus models early events in Barrett's esophagus. " PloS ONE 6(4): e18280, April 2011. PMCID: PMC3071814

8. Kong, J., Crissey, M.S., Stairs, D.B., Sepulveda, A.R., and Lynch, J.P.: Cox2 and β-catenin/TCF signaling intestinalize human esophageal keratinocytes when cultured under organotypic conditions. Neoplasia 2011 Sep;13(9):792-805. PMCID: PMC3182272

9. Kong, J., Crissey, M.S., Sepulveda, A.R., and Lynch, J.P.: Math1/Atoh1 contributes to intestinalization of esophageal keratinocytes by inducing the expression of Muc2 and Keratin-20. Digestive Diseases and Sciences 57(4): 845-857; 2012 PMCID: PMC3407817 [Available on 2013/4/1]

10. McAfee, Q.; Zhang, Z.; Samanta, A.; Levi, S.; Ma, X., Piao, S.; Lynch, J.P.; Uhera, T.; Sepulveda, A.R.; Davis, L.; Winkler, J.D.; Amaravadi, R.K.: A novel autophagy inhibitor with single agent antitumor activity reproduces the phenotype of a genetic autophagy deficiency Proceedings of the National Academy of Science 2012 PMCID: PMC3361415

11. Stelzner, M., Helmrath, M., Dunn, J.C.Y., Henning, S.J., Houchen, C.W., Kuo, C., Lynch, J.P., Li, L., Magness, S.T., Martin, M.G., Wong, M., Yu, J. for the NIH Intestinal Stem Cell Consortium: A Nomenclature for Intestinal In Vitro Cultures. American J. Phys, Gastrointestinal and Liver April 2012 2012 Jun;302(12):G1359-63 PMCID: PMC3378093

12. Hamilton, K. E., Crissey, M.S., Lynch, J.P., Rustgi, A.K.: Culturing adult stem cells from mouse small intestinal crypts Cold Spring Harbor Laboratory Press. (2014)

13. Magness ST, Puthoff BJ, Crissey MA, Dunn J, Henning SJ, Houchen C, Kaddis JS, Kuo CJ, Li L, Lynch J, Martin MG, May R, Niland JC, Olack B, Qian D, Stelzner M, Swain JR, Wang F, Wang J, Wang X, Yan K, Yu J, Wong MH. “A multi-center study to standardize reporting and analyses of fluorescence-activated cell sorted murine intestinal epithelial cells.” American Journal of Physiology: Gastrointestinal and Liver Physiology.
2013. Oct;305(8):G542-51 PMCID:3798732

14. Hartman KG, Bortner JD, Falk GW, Yu J, Martín MG, Rustgi AK, Lynch JP. “Modeling inflammation and oxidative stress in gastrointestinal disease development using novel organotypic culture systems.” Stem Cell Res Ther. 2013;4 Suppl 1:S5. PMCID: PMC3983655

15. Hartman KG, Bortner JD, Falk GW, Ginsberg GG, Jhala N, Yu J, Martín MG, Rustgi AK, Lynch JP. “Modeling human gastrointestinal inflammatory diseases using microphysiological culture systems.” Exp Biol Med. 2014 Apr 29. PMCID pending NIHMSID # 603683

16. Vega ME, Giroux V, Natsuizaka M, Liu JM, Klein- Szanto AJ, Stairs DB, Nakagawa H, Wang KK, Wang TC, Lynch JP, Rustgi AK. “Inhibition of Notch signaling enhances transdifferentiation of the esophageal squamous epithelium towards a Barrett’s-like metaplasia via KLF4” Accepted for publication in Cell Cycle June 2014 PMCID pending

Selected Publications:

Xiao F, Crissey MS, Lynch JP, Silberg DG, Suh ER: Intestinal Metaplasia with a High-Salt Diet Induces Epithelial Proliferation and Alters Cell Composition in the Gastric Mucosa of Mice. Cancer Biol Ther 6 (4): 669-75,2005.

Lynch JP, and Rustgi AK: Mechanisms of GI Malignancies Physiology of the Gastrointestinal Tract, Johnson LR, Barret KE, Gishan FK, Merchant JL, Said HM. : 477-498,2006.

Ezaki T, Guo RJ, Reynolds A, Lynch JP: The Homeodomain Transcription Factors Cdx1 and Cdx2 Induce E-cadherin Adhesion Activity by Reducing beta- and p120-catenin Tyrosine Phosphorylation. Am J Physiol Gastrointest Liver Physiol 293 : G54-G65,2007.

Hegde SR, Sun W, and Lynch JP: Systemic and Targeted Therapy for Advanced Colon Cancer Expert Review in Gastroenterology and Hepatology 2 (1): 135-149,2008.

Kong J, Isariyawonse BK, Ezaki T, Nakagawa H, Silberg DG, and Lynch JP: Induction of Intestinalization in Human Esophageal Keratinocytes is a Multi-step Process Carcinogenesis 30 (1): 122-130,2009.

Stairs DB, Nakagawa H, Klein-Szanto A, Mitchell S, Silberg DG, Tobias JW, Lynch JP, Rustgi AK: Cdx1 and c-myc foster the initiation of transdifferentiation of the normal esophageal squamous epithelium toward Barrett's Esophagus PloS ONE 3 (10): e3534,2008.

Sepulveda AR, and Lynch JP: Chronic Inflammation and Genetic Instability in Gastrointestinal Cancers Cancer Genome and Tumor Microenvironment, Springer : P.351-398,2010.

View all publications

Academic Contact Info

421 Curie Boulevard
912 Biomedical Research Building II/III

Philadelphia, PA 19104
Phone: (215) 898-0155
Fax: (215) 573-2024
Patient appointments: 800-789-7366 (PENN)

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