Current Investigators

Matthew E. Pipkin, Ph.D.


The Pipkin lab is interested in understanding how systemic and tissue-specific T cell mediated immunity to infections and cancer develops, and how transcription controls HIV latency. We specifically focus on CD4 and CD8 T cells, and how transcription factors (TFs) and chromatin regulatory factors (CRFs) govern transcriptional programs that establish gene expression which defines distinct effector and memory T cell states, functions and tissue-adaptations. The laboratory developed one of the first first-ever pooled RNA interference (RNAi) mediated approaches in T cells to conduct pooled in vivo phenotypic screens to elucidate genes that control T cell mediated immunity during viral infection. We have applied these and other tools to define the roles of individual factors among entire gene families in CD4 and CD8 T cells as they participate in various immune-mediated processes in vivo, and how chromatin regulation establishes and maintains HIV latency in CD4 T cells. We are coupling these perturbation approaches with single cell sequencing methods, dynamic cell barcoding using CRISPR-Cas mediated homing guide RNAs, and advanced computational strategies to elucidate the single cell trajectories and lineage-coupled transcriptional histories that establish and maintain memory T cell ontogeny.

MIST Research

The gut is a major immunological organ where host-microbe interactions shape both local and systemic immune tolerance. However, current views of intestinal immune regulation ignore fundamental differences in the function and metabolite composition of the two distinct organs that comprise the gut—the small and large intestine (or SI and LI). This impedes a more detailed understanding of immune regulatory mechanisms along the intestinal tract, and limits efforts to develop safer, more targeted treatments for the two major forms of human inflammatory bowel diseases (IBDs), ulcerative colitis and small bowel Crohn's disease. We hypothesize that mucosal CD4 T cells use different sets of ligand-regulated nuclear receptors (NRs) in the SI and LI to control key regulatory functions, including IL-10 expression, to local concentration gradients of bile- and microbe-derived metabolites. On one hand, we have discovered that Foxp3– effector (Teff) subsets in the SI—including Th1 and Th17 cells— utilize the nuclear xenobiotic receptor, constitutive androstane receptor (CAR/Nr1i3), to direct a 'hepatocyte-like' transcriptional response to contend with high local bile acid (BA) concentrations, which are far greater in SI than in LI (millimolar vs micromolar) due to 'enterohepatic' circulation—where primary BAs synthesized in the liver, stored in the gallbladder, and secreted into the duodenum are actively reabsorbed by specialized enterocytes in the ileum for portal recirculation to the liver. Because BAs are lipophilic, they can be toxic and pro-inflammatory, and several nuclear receptors—including CAR—have evolved to suppress BA toxicity. These studies suggest that enterohepatic circulation establishes a unique SI microenvironment that is distinct from that in the LI and requires unique transcriptional machinery to protect T cells in the SI. Conversely, the LI harbors 103-107 times more bacteria than SI, and ~1000-fold lower BA concentrations. Accordingly, microbes and their metabolites— short chain fatty acids (SCFAs; e.g., butyrate), secondary BAs (produced via microbial metabolism of residual primary BAs)—are central to immune regulation in the LI. SCFAs inhibit histone deacetylase enzymes (HDACs) and stabilize Foxp3 gene expression in peripherally-induced T regulatory cells (iTregs), whereas secondary Bas appear to promote regulatory functions of RORgt+ Tregs in the LI through another NR, vitamin D receptor (VDR). Thus, while antigens from the enteric flora prime both pro- and anti-inflammatory T cell responses throughout the gut, marked concentration gradients of bile- and bacteria-derived metabolites in the SI vs. LI are sensed by different NRs to execute compartmentalized T cell regulatory functions. In testing this hypothesis, we will apply cutting-edge genomics and computational approaches to comprehensively map the contributions of each of the 49 mouse NRs to specialized regulatory functions in the SI and LI in vivo, using IL-10 expression as the primary screening target. We will also interrogate the regulation and molecular functions of two key NRs, CAR/Nr1i3 and VDR/Nr1i1, in SI type 1 regulatory (Tr1) and LI iTreg cells, respectively. These studies will advance understanding of lymphocyte specialization in the gut, and inform new approaches to treat IBDs.

Current Grant Support

1P01 AI145815-01A1 M.E. Pipkin, PI 08/01/2020 – 07/31/2025
Transcription factor regulation of CD4 and CD8 T cell effector and memory differentiation and function

1R33 AI140439-01NIH S. Valente, PI; M.E. Pipkin 08/01/2021 – 07/31/2023
Identification and characterization of chromatin regulators of HIV-1 latency

1R01NS117926-01A1 J. Kissil, PI/Pipkin Co-I 08/31/2020 – 09/01/2025
Elucidating the epigenetic landscape of neurofibromatosis and development of therapeutic targets

U01 AI163063-01 M. Sundrud; M.E. Pipkin; C. Weaver 07/01/2021-06/30/2026
Nuclear Receptor Networks in Mucosal Immune Regulation


Matthew E. Pipkin, Ph.D.

Diao H, Chen R, Tsuda SM, Wang D, Frederick MA, Kim J, Karunadharma P, Martinez GJ, Getzler AJ, Toma C, Milner JJ, Venables TC, Martin DM, Goldrath AW, Crotty S, Pipkin ME. Single-cell lineage trajectories and chromatin regulators that initialize antiviral CD8 T cell ontogeny. In revision. Available via bioRxiv:

Milner JJ, Toma C, Quon S, Omilusik K, Scharping NE, Dey A, Reina-Campos M, Nguyen H, Getzler AJ, Diao H, Yu B, Delpoux A, Yoshida TM, Li D, Qi J, Vincek A, Hedrick SM, Egawa T, Zhou MM, Crotty S, Ozato K, Pipkin ME, Goldrath AW. Bromodomain protein BRD4 directs and sustains CD8 T cell differentiation during infection. J Exp Med. 2021 Aug 2;218(8):e20202512. doi: 10.1084/jem.20202512. PMID: 34037670

Tsuda S, Pipkin ME. Transcriptional Control of Cell Fate Determination in Antigen-Experienced CD8 T Cells. Cold Spring Harb Perspect Biol. 2021 Jun 14:a037945. doi: 10.1101/cshperspect.a037945. PMID: 34127445

Xu T, Schutte A, Jimenez L, Gonçalves ANA, Keller A, Pipkin ME, Nakaya HI, Pereira RM, Martinez GJ. Kdm6b Regulates the Generation of Effector CD8 + T Cells by Inducing Chromatin Accessibility in Effector-Associated Genes. J Immunol. 2021 May 1;206(9):2170-2183. doi: 10.4049/jimmunol.2001459. Epub 2021 Apr 16. PMID: 33863789.

Chen ML, Huang X, Wang H, Hegner C, Liu Y, Shang J, Eliason A, Diao H, Park H, Frey B, Wang G, Mosure SA, Solt SA, Kojetin DJ, Rodriguez-Palacios A, Schady DA, Weaver CT, Pipkin ME, Moore DD*, and Sundrud MS*. CAR directs T cell adaptation to bile acids in the small intestine. Nature, 2021 April 7. doi: 10.1038/s41586-021-03421-6. PMID: 33828301.

Pipkin ME. Runx proteins and transcriptional mechanisms that govern memory CD8 T cell development. Immunol Rev. 2021 Mar;300(1):100-124. doi: 10.1111/imr.12954. PMID: 33682165

Mori L, Jenike K, Yeh YHJ , Lacombe B, Li C, Getzler A, Mediouni S, Cameron M, Pipkin ME, Ho YC, Ramirez BC, Valente S. The XPB Subunit of the TFIIH Complex Plays a Critical Role in HIV-1 Transcription and XPB Inhibition by Spironolactone Prevents HIV-1 Reactivation from Latency. J Virol. 2020 Nov 25;95(4):e01247-20. doi: 10.1128/JVI.01247-20

Choi J, Diao H, Faliti CE, Truong J, Rossi M, Bélanger S, Yu B, Goldrath AW, Pipkin ME, Crotty S. Bcl-6 is the nexus transcription factor of T follicular helper cells via repressor-of-repressor circuits. Nat Immunol. 2020 Jul;21(7):777-789. doi: 10.1038/s41590-020-0706-5. PubMed PMID: 32572238.

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Current Investigators