# 4DN Interrogation of T Cell Exhaustion in Cancer

> **NIH NIH U01** · STANFORD UNIVERSITY · 2020 · $523,564

## Abstract

PROJECT ABSTRACT/SUMMARY
Immunotherapies that enhance the ability of T cells to recognize and kill tumor cells have been transformational
in the treatment of human cancer, but immunotherapy is not effective in all patients or cancers, and therefore
studies interrogating the molecular basis for durable T cell responses to cancer are needed. A critical barrier for
the sustained activation of tumor-infiltrating T cells is the development of T cell ‘exhaustion,’ which leads to the
stable expression of inhibitory surface receptors, poor response to tumor antigens, and low cell proliferation and
persistence of T cells in vivo. However, to date, it has been difficult to study the gene regulatory mechanisms
that control the development of T cell exhaustion in humans, due to a lack of sensitive genomic tools to study
primary immune cells from patients. We recently developed a suite of high-throughput epigenomic technologies
that enable the measurement of three-dimensional (3D) genome conformation and single-cell chromatin
accessibility in primary T cells from human tumors. In the proposed research, we aim to utilize these methods to
identify changes in 4D nucleome (4DN) organization and accessibility that underlie the development of human
T cell exhaustion. In Aim 1, we will define 3D genome interactions that occur in human T cell exhaustion in
patients with advanced skin cancer. Exhaustion-associated genome conformation will be compared across
several cancer types to identify a consensus exhaustion profile, and these findings will be integrated with
chromatin accessibility and gene expression data to identify transcriptional effects of 3D changes. In Aim 2, we
will determine the dynamics and reversibility of regulatory 3D interactions in exhaustion using a novel chimeric
antigen-receptor (CAR)-T cell model. In Aim 3, we will perturb these interactions using CRISPR/Cas9 genome
editing in primary T cells, coupled with single-cell epigenomic read-outs, to engineer improved, durable, next-
generation immunotherapies. If successful, these findings will have a direct impact on the future design of
immunotherapy strategies, which will have a significant impact on the clinical care of cancer patients. Finally, we
will facilitate the dissemination of these findings by freely distributing protocols and data and releasing custom
software tools, and we will use these studies as a collaborative launch point in the 4DN network. We anticipate
that these results will lead to novel insights into the molecular regulation of T cell exhaustion and serve as an
effective research program for Dr. Satpathy to establish his independent laboratory at the interface of
immunology and genome science.

## Key facts

- **NIH application ID:** 10117957
- **Project number:** 1U01CA260852-01
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Ansuman Satpathy
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $523,564
- **Award type:** 1
- **Project period:** 2020-09-15 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10117957

## Citation

> US National Institutes of Health, RePORTER application 10117957, 4DN Interrogation of T Cell Exhaustion in Cancer (1U01CA260852-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10117957. Licensed CC0.

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