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JoAnne Flynn, PhD

Dr. JoAnne Flynn


Fax: 412-383-7229
5058 Biomedical Science Tower 3
3501 Fifth Avenue


PhD in Microbiology and Immunology, University of California, Berkeley

BS in Biochemistry, University of California, Davis

Academic Affiliation(s)

Professor, Department of Microbiology and Molecular Genetics

Professor, Department of Immunology

Associate Professor, Department of Pediatrics

Member, Center for Vaccine Research

Member, Molecular Virology and Microbiology Graduate Program

Member, Immunology Graduate Program


My primary interest is in the interaction of pathogens with the host, with special emphasis on the immune mechanisms that protect against or exacerbate disease. Our focus is on Mycobacterium tuberculosis, the organism responsible for tuberculosis, which causes 2 million deaths per year worldwide. We are investigating the immune responses required for protection against tuberculosis, and the effect of these immune responses on both the host and the bacterium. We specifically study cytokine production, macrophage activation, and T cell subsets (CD4+ and CD8+ T cells) that are important in tuberculosis. Finally, we have a strong interest in the immune mechanisms responsible for maintaining a latent M. tuberculosis infection, and how deficiencies in the immune response can result in reactivation of disease. Our work is done in two model systems: mice and non-human primates. We have vaccine studies, drugs studies, and basic immunologic and pathogenesis studies ongoing. We also participate in projects involving mathematical modeling of the immune response to M. tuberculosis, and our plan is to incorporate nuclear imaging of live animals into our research.

Lab Personnel

Charles A. Scanga, Research Assistant Professor

Amy Fraser, Lab Manager

Chelsea Chedrick, Research Specialist

Daniel Fillmore, Research Technician 

Postdoctoral Associates: Joshua Mattila, Hannah Gideon

Senior Research Specialists: Melanie O'Malley, Jamie Tomko, Paul Johnston, Carolyn Mooney Bigbee, Catherine Thomas Cochran, Mark A. Rodgers

Graduate Students: Robert DiFazio, Anthony Cadena, Eileen Wong

Student Workers: Xueqi Fang, Yuan Yipu


Phuah J. Y, Mattila J. T, Lin P. L, and Flynn J. L. Activated B cells in the granulomas of nonhuman primates infected with Mycobacterium tuberculosis. Am J Pathol. 181: 508-514. |  View Abstract

Lin P. L, Rutledge T, Green A. M, Bigbee M, Fuhrman C, Klein E, and Flynn J. L. CD4 T Cell Depletion Exacerbates Acute Mycobacterium tuberculosis While Reactivation of Latent Infection Is Dependent on Severity of Tissue Depletion in Cynomolgus Macaques. AIDS Res Hum Retroviruses. [Epub ahead of print] |  View Abstract

Lin P. L, Dietrich J, Tan E, Abalos R. M, Burgos J, Bigbee C, Bigbee M, Milk L, Gideon H. P, Rodgers M, Cochran C, Guinn K. M, Sherman D. R, Klein E, Janssen C, Flynn J. L, Andersen P. The multistage vaccine H56 boosts the effects of BCG to protect cynomolgus macaques against active tuberculosis and reactivation of latent Mycobacterium tuberculosis infection. J Clin Invest. 122: 303-314. |  View Abstract

Lin P. L, Dartois V, Johnston P. J, Janssen C, Via L, Goodwin M. B, Klein E, Barry C. E., 3rd, and Flynn, J. L. Metronidazole prevents reactivation of latent Mycobacterium tuberculosis infection in macaques. Proc Natl Acad Sci USA. 109: 14188-14193. |  View Abstract

Mattila J. T, Diedrich C. R, Lin P. L, Phuah J, and Flynn J. L. Simian immunodeficiency virus-induced changes in T cell cytokine responses in cynomolgus macaques with latent Mycobacterium tuberculosis infection are associated with timing of reactivation. J Immunol. 186: 3527-3537. |  View Abstract

Ford C. B, Lin P. L, Chase M. R, Shah R. R, Iartchouk O, Galagan J, Mohaideen N, Ioerger T. R, Sacchettini J. C, Lipsitch M, Flynn J. L, and Fortune S. M. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet. 43: 482-486. |  View Abstract