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Signals from the Tumor Microenvironment Drive Distinct Epigenetic Features in Terminally Exhausted CD8+ T Cells

Ford, Brinley Rhodes (2023) Signals from the Tumor Microenvironment Drive Distinct Epigenetic Features in Terminally Exhausted CD8+ T Cells. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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Immunotherapy has had major clinical successes, but response rates remain low due in part to increased dysfunctional exhausted CD8+ T cells in the tumor, characterized by decreased cytokine expression and increased expression of co-inhibitory receptors, such as PD-1 and Tim-3. CD8+ T cell differentiation in the tumor is a progressive process, whereby progenitor (PD1lo/mid) cells with some functional capacity differentiate further to terminally exhausted cells (PD1hiTim-3+), which have limited-to-no function. To understand the mechanisms promoting this progression, we used CUT&RUN, a low-input ChIP-seq alternative, to profile four histone modifications in progenitor and terminally exhausted CD8+ T cells in a murine model of melanoma. Unexpectedly, we identified two chromatin features unique to terminally exhausted cells, both of which have limited transcriptional potential at genes associated with stemness and function. First, we found a set of genes characterized by terminal exhaustion-specific active histone modifications without corresponding increases in gene expression. These chromatin regions are enriched for AP-1 transcription factor motifs, despite low expression of most AP-1 family members in terminally exhausted cells. Inducing expression of AP-1 factors using a 4-1BB agonist restored expression of these “anticorrelated” genes, which include genes involved in T cell activation and inflammation. Second, we found a substantial increase in the number of genes with bivalent promoters, defined by the presence of both activating (H3K4me3) and repressive (H3K27me3) marks, as well as decreased gene expression. Bivalent promoters in terminally exhausted T cells were hypermethylated in response to tumor hypoxia, and decreasing tumor hypoxia was sufficient to recover expression of these genes. Furthermore, overexpressing Kdm6b, an oxygen-insensitive histone demethylase for H3K27 was sufficient to recover tumor-infiltrating T cell function without reversing the differentiation state of terminal exhaustion. However, hypoxia alone was not sufficient to lower Kdm6b expression and drive increased bivalency in vitro. This study has described a unique decoupling of gene transcription from active histone modifications, clarifying how exhaustion is promoted and maintained in the tumor through epigenetic alterations. Modulating the activity of chromatin modifiers, such as Kdm6b, can increase the effector function of terminally exhausted cells, suggesting new avenues for immunotherapeutic approaches that specifically target terminally exhausted T cells, rather than their progenitors.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Ford, Brinley Rhodesbrf56@pitt.edubrf560000-0001-8777-5244
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Thesis AdvisorPoholek,
Committee ChairDelgoffe,
Committee MemberKane,
Committee MemberMcGeachy,
Committee MemberSingh,
Date: 17 November 2023
Date Type: Publication
Defense Date: 7 July 2023
Approval Date: 17 November 2023
Submission Date: 19 July 2023
Access Restriction: 2 year -- Restrict access to University of Pittsburgh for a period of 2 years.
Number of Pages: 160
Institution: University of Pittsburgh
Schools and Programs: School of Medicine > Microbiology and Immunology
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: Epigenetic
Related URLs:
Date Deposited: 17 Nov 2023 19:11
Last Modified: 17 Nov 2023 19:11


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