Matthew Pipkin

Matthew Pipkin, Ph.D.

Associate Professor

Department: SR-IM-PIPKIN LAB
Business Phone: (561) 228-2182
Business Email: m.pipkin@ufl.edu

About Matthew Pipkin

Additional Positions:
Associate Professor, Cancer Biology
2014 – 2017 · Scripps Research
Associate Professor (Joint Appointment), Immunology and Microbial Science (IMS)
2014 – 2017 · Scripps Research
Assistant Professor, Cancer Biology
2012 – 2014 · Scripps Research
Assistant Professor (Joint Appointment), Immunology and Microbial Science (IMS)
2012 – 2014 · Scripps Research

Research Profile

The overall focus of the Pipkin lab is to elucidate how chromatin structure and transcription controls the gene expression programs that establish and maintain the differentiated states of T cells. The lab specifically studies how naïve CD8 T cells differentiate into effector and memory cytotoxic T lymphocytes (CTL). CTL are killer lymphocytes that hold outstanding promise for controlling viral infections and cancer therapeutically, as they can be employed in adoptive immunotherapy and are the target of successful vaccination. The Pipkin lab has developed novel approaches to map the fundamental repeating structures of chromatin (nucleosomes) at unprecedented resolution, novel reporter genes to track cells in vivo that induce expression of Prf1, an essential gene that is required for the anti-tumor killing activity of CTL, and the only systems to conduct genome-scale pooled RNAi screens in T cells, in vivo, during the course of actual viral infections. Using these tools and approaches, the Pipkin lab is clarifying how transcription factors govern the specific organization of nucleosomes that enforces CTL differentiation, identifying the chromatin regulatory factors that maintain the differentiated state epigenetically, and demonstrating how these processes mediate durable immunity.

Open Researcher and Contributor ID (ORCID)

0000-0002-9688-0190

Publications

2022
The Transcription Factor YY-1 Is an Essential Regulator of T Follicular Helper Cell Differentiation
The Journal of Immunology. 209(8):1566-1573 [DOI] 10.4049/jimmunol.2101176.
2022
Transcriptional Control of Cell Fate Determination in Antigen-Experienced CD8 T Cells.
Cold Spring Harbor perspectives in biology. 14(2) [DOI] 10.1101/cshperspect.a037945. [PMID] 34127445.
2021
Bromodomain protein BRD4 directs and sustains CD8 T cell differentiation during infection
Journal of Experimental Medicine. 218(8) [DOI] 10.1084/jem.20202512. [PMID] 34037670.
2021
CAR directs T cell adaptation to bile acids in the small intestine.
Nature. 593(7857):147-151 [DOI] 10.1038/s41586-021-03421-6. [PMID] 33828301.
2021
Kdm6b Regulates the Generation of Effector CD8+ T Cells by Inducing Chromatin Accessibility in Effector-Associated Genes.
Journal of immunology (Baltimore, Md. : 1950). 206(9):2170-2183 [DOI] 10.4049/jimmunol.2001459. [PMID] 33863789.
2021
Runx proteins and transcriptional mechanisms that govern memory CD8 T cell development
Immunological Reviews. 300(1):100-124 [DOI] 10.1111/imr.12954.
2020
Bcl-6 is the nexus transcription factor of T follicular helper cells via repressor-of-repressor circuits.
Nature immunology. 21(7):777-789 [DOI] 10.1038/s41590-020-0706-5. [PMID] 32572238.
2020
Physiological expression and function of the MDR1 transporter in cytotoxic T lymphocytes.
The Journal of experimental medicine. 217(5) [DOI] 10.1084/jem.20191388. [PMID] 32302378.
2020
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.
Journal of virology. 95(4) [DOI] 10.1128/JVI.01247-20. [PMID] 33239456.
2020
YAP-Mediated Recruitment of YY1 and EZH2 Represses Transcription of Key Cell-Cycle Regulators.
Cancer research. 80(12):2512-2522 [DOI] 10.1158/0008-5472.CAN-19-2415. [PMID] 32409309.
2019
Stability and flexibility in chromatin structure and transcription underlies memory CD8 T-cell differentiation
F1000Research. 8 [DOI] 10.12688/f1000research.18211.1. [PMID] 31448086.
2018
The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation.
Immunity. 48(4):659-674.e6 [DOI] 10.1016/j.immuni.2018.03.028. [PMID] 29669249.
2017
Cbx3/HP1γ deficiency confers enhanced tumor-killing capacity on CD8+ T cells.
Scientific reports. 7 [DOI] 10.1038/srep42888. [PMID] 28220815.
2017
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation.
Nature immunology. 18(5):573-582 [DOI] 10.1038/ni.3706. [PMID] 28288100.
2017
Erratum: Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation.
Nature immunology. 18(6) [DOI] 10.1038/ni0617-705b. [PMID] 28518161.
2017
Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours.
Nature. 552(7684):253-257 [DOI] 10.1038/nature24993. [PMID] 29211713.
2015
In vivo RNAi screens: concepts and applications.
Trends in immunology. 36(5):315-22 [DOI] 10.1016/j.it.2015.03.007. [PMID] 25937561.
2015
The transcription factor NFAT promotes exhaustion of activated CD8⁺ T cells.
Immunity. 42(2):265-278 [DOI] 10.1016/j.immuni.2015.01.006. [PMID] 25680272.
2014
In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation.
Immunity. 41(2):325-38 [DOI] 10.1016/j.immuni.2014.08.002. [PMID] 25148027.
2013
MicroRNA-directed program of cytotoxic CD8+ T-cell differentiation.
Proceedings of the National Academy of Sciences of the United States of America. 110(46):18608-13 [DOI] 10.1073/pnas.1317191110. [PMID] 24163352.
2011
Memories in the snow: immune memory, persistent infection and chronic disease.
EMBO reports. 12(7):617-9 [DOI] 10.1038/embor.2011.122. [PMID] 21701505.
2010
The transcriptional control of the perforin locus.
Immunological reviews. 235(1):55-72 [DOI] 10.1111/j.0105-2896.2010.00905.x. [PMID] 20536555.
2009
Runx3 and T-box proteins cooperate to establish the transcriptional program of effector CTLs.
The Journal of experimental medicine. 206(1):51-9 [DOI] 10.1084/jem.20081242. [PMID] 19139168.
2009
SnapShot: effector and memory T cell differentiation.
Cell. 138(3):606.e1-2 [DOI] 10.1016/j.cell.2009.07.020. [PMID] 19665979.
2007
Chromosome transfer activates and delineates a locus control region for perforin.
Immunity. 26(1):29-41 [PMID] 17222571.
2006
A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes.
Nucleic acids research. 34(4) [PMID] 16510851.
2003
DNA methylation and chromatin structure regulate T cell perforin gene expression.
Journal of immunology (Baltimore, Md. : 1950). 170(10):5124-32 [PMID] 12734359.
Polycomb Repressive Complex 1 subunit Cbx4 positively regulates effector responses in CD8 T cells
. [DOI] 10.1101/2022.10.03.510675.

Grants

Apr 2022 ACTIVE
Nuclear Receptor Networks in Mucosal Immune Regulation
Role: Principal Investigator
Funding: NATL INST OF HLTH NIAID
Apr 2022 ACTIVE
Elucidating the epigenetic landscape of neurofibromatosis and development of therapeutic targets
Role: Principal Investigator
Funding: H LEE MOFFITT CANCER CTR & RES INST via NATL INST OF HLTH NINDS
Apr 2022 ACTIVE
Transcription factor regulation of CD4 and CD8 T cell effector and memory differentiation and function
Role: Principal Investigator
Funding: NATL INST OF HLTH NIAID
Apr 2022 ACTIVE
Identification and characterization of chromatin regulators of HIV-1 latency
Role: Co-Investigator
Funding: NATL INST OF HLTH NIAID

Education

Ph.D. in Microbiology and Immunology
2005 · University of Miami, School of Medicine
Bachelor's of Science in Microbiology and Immunology
1998 · University of Miami

Contact Details

Phones:
Business:
(561) 228-2182
Emails:
Business:
m.pipkin@ufl.edu
Addresses:
Business Mailing:
Location C243
130 SCRIPPS WAY BLDG, 2C2
JUPITER FL 33458