Jason Brenchley, Ph.D.

Barrier Immunity Section

Established in 2008

NIH Main Campus, Bethesda, MD

Jason Brenchley, Ph.D. (He/Him/His)

Senior Investigator, Barrier Immunity Section

Contact: For contact information, search the NIH Enterprise Directory.

Specialty(s): Pathology, Medical Microbiology

Photo of Jason Brenchley, Ph.D.

Major Areas of Research

  • Immunopathogenesis in nonhuman primate models of HIV
  • Microbial translocation and immune activation
  • Mucosal immunology and mechanisms of microbial translocation

Program Description

Our work aims to understand better the mechanisms that underlie HIV disease progression. The immune system, particularly its T-cell arm, plays a central role in HIV pathogenesis. Our long-term goal is to use the knowledge gained through these studies to develop novel therapeutic approaches. We use multiple nonhuman primate models with differing disease progression courses, and we study T-cell immunology in HIV-infected individuals or SIV-infected nonhuman primates in order to elucidate mechanisms of disease progression. The main areas of research are summarized below.

Mechanisms underlying lack of disease progression in natural hosts of SIV

Several species of African nonhuman primates are naturally infected with SIV but do not develop AIDS. We have identified a putative mechanism underlying the lack of disease progression in SIVagm-infected African green monkeys. These animals are capable of down-regulating the CD4 receptor for SIV as naïve CD4 T cells enter the memory pool in vivo. Indeed, adult African green monkeys (whether SIVagm-infected or not) have very low frequencies of CD4 T cells but a high frequency of memory T cells that express the alpha chain of CD8 without expression of CD4. Many of these CD8aa+ T cells were originally CD4 T cells and maintain effector functions typically restricted to CD4 T cells (see below). Down-regulation of CD4 renders these memory CD8aa+ T cells resistant to SIV infection in vivo. Hence, these animals are able to maintain immunological function by cells that are not susceptible to infection by SIVagm in vivo. We are currently studying the molecular mechanisms responsible for down-regulation of CD4 by African green monkeys. We are using next generation sequencing approaches to understand the transcriptional regulation of CD4 expression. By comparing the transcriptomes of T cells in AGMs induced to down-regulate CD4 in vitro with those of closely-related Patas monkeys (also natural hosts) and CD4+ T cells of rhesus macaques, we have identified a gene set unique to CD4-downregulated T cells (Figure below). We are currently investigating the particular gene pathways enriched in this dataset. One of these pathways involves genes regulating DNA methylation, a process that, when occurring near gene regulatory regions, can be associated with gene silencing. We are presently exploring a model whereby natural hosts differentially regulate the DNA methylation machinery to allow silencing of the CD4 gene. In future work, we will determine the degree to which the CD4 gene locus is methylated in CD4-CD8aa+ T cells and ectopically overexpress DNA de-methylating enzymes to probe whether CD4 can become re-expressed in these cells.

Imagre showing  the comparative assessment of genes uniquely differentially expressed in AGM T cells induced to down-regulate CD4 in vitro.

Comparative assessment of genes uniquely differentially expressed in AGM T cells induced to down-regulate CD4 in vitro.

Credit: NIAID

Microbial translocation and disease progression

Chronic activation of the immune system is a hallmark of progressive HIV infection of humans and SIV infection of Asian macaque monkeys. Immune activation can be quantified, and the degree of immune activation is the best predictor of disease progression. We have shown that one cause of immune activation during the chronic phase of infection is translocation of microbial products from the lumen of the gastrointestinal (GI) tract into peripheral circulation. Moreover, our recent data suggests that the epithelial barrier (green, below) of the GI tract is damaged during chronic infection, and this damage allows microbial products, which we can identify by immunohistochemistry and confocal microscopy using monoclonal antibodies specific for bacterial antigens (red, below) to translocate directly into the lamina propria (see below).

Confocal microscopy of cytokeratin (green) and E coli (red) in the colon of a chronically SIV-infected rhesus. 

Confocal microscopy of cytokeratin (green) and E coli (red) in the colon of a chronically SIV-infected rhesus. 

Credit: NIAID

Recent studies have shown that damage that occurs within the GI tract of chronically HIV-infected humans and SIV-infected Asian macaques is not reversed after administration of antiretroviral (ARV) medications. Indeed, CD4 T cells reconstitute very poorly for even decades after administration of ARVs. Moreover, residual immune activation persists after administration of ARVs, and this residual inflammation is associated with increased mortality of ARV-treated, HIV-infected individuals. Therefore, we have initiated studies aimed at improving CD4 T-cell reconstitution in ARV-treated, SIV-infected Asian macaques. We have previously shown that therapeutic interventions with probiotic organisms improves immunological recovery. Our current work aims to understand how the composition of the GI tract microbiome might influence aspects of HIV disease progression. These approaches aim to specifically alter the composition of the microbiome with particular antibiotic regimens. Our work has demonstrated that vancomycin treatment results in the reduction of short-chained fatty acid-producing bacteria of the Firmicute phylum (red-shaded boxes in A) with increases in the inflammatory Proteobacteria phylum (blue-shaded boxes in A). These microbiome alterations result decreased integrity of the GI tract epithelium (B - immunohistochemical image showing decreased epithelial integrity with brown claudin staining), but this does not accelerate the natural course of untreated SIV-infection in Asian macaques (C).

Images of vancomycin treatment results. Full description provided in the image caption.

A: Vancomycin treatment results in the reduction of short-chained fatty acid-producing bacteria of the Firmicute phylum (red-shaded boxes) with increases in the inflammatory Proteobacteria phylum (blue-shaded boxes). B: Immunohistochemical image showing decreased epithelial integrity with brown claudin staining. C: Natural course of untreated SIV-infection in Asian macaques.

Credit: NIAID



M.S., 1999, Idaho State University

Ph.D., 2003, University of Texas Southwestern Medical Center at Dallas

Dr. Brenchley received a master’s degree from Idaho State University in 1999 and received a Ph.D. from the University of Texas Southwestern Medical Center at Dallas in 2003. He joined NIH as a research fellow, studying immunopathogenesis and mucosal immunology in HIV-infected individuals. Since 2008, he has become an investigator in the Laboratory of Molecular Microbiology and has been a senior investigator since 2013.

Selected Publications

Ortiz AM, Flynn JK, DiNapoli SR, Vujkovic-Cvijin I, Starke CE, Lai SH, Long ME, Sortino O, Vinton CL, Mudd JC, Johnston L, Busman-Sahay K, Belkaid Y, Estes JD, Brenchley JM. Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques. Nat Med. 2018 Sep;24(9):1313-1316.

Klase Z, Ortiz A, Deleage C, Mudd JC, Quiñones M, Schwartzman E, Klatt NR, Canary L, Estes JD, Brenchley JM. Dysbiotic bacteria translocate in progressive SIV infection. Mucosal Immunol. 2015 Sep;8(5):1009-20.

Calantone N, Wu F, Klase Z, Deleage C, Perkins M, Matsuda K, Thompson EA, Ortiz AM, Vinton CL, Ourmanov I, Loré K, Douek DC, Estes JD, Hirsch VM, Brenchley JM. Tissue myeloid cells in SIV-infected primates acquire viral DNA through phagocytosis of infected T cells. Immunity. 2014 Sep 18;41(3):493-502.

Klatt NR, Canary LA, Sun X, Vinton CL, Funderburg NT, Morcock DR, Quiñones M, Deming CB, Perkins M, Hazuda DJ, Miller MD, Lederman MM, Segre JA, Lifson JD, Haddad EK, Estes JD, Brenchley JM. Probiotic/prebiotic supplementation of antiretrovirals improves gastrointestinal immunity in SIV-infected macaques. J Clin Invest. 2013 Feb;123(2):903-7.

Estes JD, Harris LD, Klatt NR, Tabb B, Pittaluga S, Paiardini M, Barclay GR, Smedley J, Pung R, Oliveira KM, Hirsch VM, Silvestri G, Douek DC, Miller CJ, Haase AT, Lifson J, Brenchley JM. Damaged intestinal epithelial integrity linked to microbial translocation in pathogenic simian immunodeficiency virus infections. PLoS Pathog. 2010 Aug 19;6(8):e1001052.

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Research Group

The focus of the BIS is to understand the mechanisms that underly viral diseases. The work focuses, predominantly, on understanding the differential disease outcomes between natural hosts of immunodeficiency lentiviral infections and progressive infections. Our studies rely heavily on cellular and molecular immunological analyses in tissues.

Barrier Immunity section 2022: Back row (left to right): Jason Brenchley, Senior Investigator, Andrew Rahmberg, Postdoctoral fellow, Jacob Flynn, Graduate student. Middle row (left to right): Alex Ortiz O’sick, Staff Scientist, Kelsie Brooks, Postdoctoral fellow, Jen Simpson, Postdoctoral fellow. Front row (left to right): Fabiola Castello Casta, postbaccalaureate fellow, Debra Yee, biologist.
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