Identification of a core gene-regulatory trajectory to terminal T cell dysfunction in human tumors and discovery of potential target genes involved in this process

Diseases such as cancer are often associated with suppression of the immune sys- tem. Thereby, cytotoxic CD8+ T cells, originally meant to kill the cancerous cells, tend to become dysfunctional, as they are struggling with long term exposure to antigens and the immunosuppressive tumor microenvironment. As a consequence, tumor-specific CD8+ T cells often fail to fully eliminate cancer cells. Much research has been conducted on T cell exhaustion in the context of chronic viral infection. However, it remains unknown, whether gene-regulation patterns causing terminal T cell exhaustion in cancer are specific to cancer type or tumor microenvironment or, whether they are governed by a universal exhaustion program. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a great tool to identify cell states based on their open chromatin landscape. Therefore, we used this method to investigate chromatin states of CD8+ tumor-infiltrating lymphocytes, isolated from HCC (Hepatocellular Carcinoma), RCC (Renal Cell Carcinoma), and HNSCC (Head and Neck Squamous Cell Carcinoma) patients, on the single cell level. This approach enables unbiased identification of discrete TIL (tumor-infiltrating lymphocytes) subpopulations as well as key transcription factors and gene-regulatory elements that determine different cell states. Bioinformatic analysis verified terminal exhausted TIL populations in every cancer type except HNSCC and revealed candidate determinants of exhaustion common to RCC and HCC, as well as to BCC (Basal Cell Carcinoma, integrated data from a published study). Further, we sought to determine the role of these candidates using CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) knock-out in expanded TILs from melanoma patients. We anticipate that our findings will improve understanding gene-regulatory mechanisms leading to terminal T cell dysfunction in different human cancer types and help to identify factors, which could improve immunotherapies such as CAR T-cell therapy

Genome‐wide cooperation of EMT transcription factor ZEB 1 with YAP and AP ‐1 in breast cancer

Invasion, metastasis and therapy resistance are the major cause of cancer-associated deaths, and theEMT-inducing transcription factorZEB1 is a crucial stimulator of these processes. While work onZEB1 has mainly focused on its role as a transcriptional repressor, it can also act as a transcriptional activator. To further understand these two modes of action, we performed a genome-wideZEB1 binding study in triple-negative breast cancer cells. We identifiedZEB1 as a novel interactor of theAP-1 factorsFOSL1 andJUNand show that, together with the Hippo pathway effectorYAP, they form a transactivation complex, predominantly activating tumour-promoting genes, thereby synergising with its function as a repressor of epithelial genes. High expression ofZEB1,YAP,FOSL1 andJUNmarks the aggressive claudin-low subtype of breast cancer, indicating the translational relevance of our findings. Thus, our results link critical tumour-promoting transcription factors:ZEB1,AP-1 and Hippo pathway factors. Disturbing their molecular interaction may provide a promising treatment option for aggressive cancer types

Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF

Specialized regulatory T (Treg) cells accumulate and perform homeostatic and regenerative functions in nonlymphoid tissues. Whether common precursors for nonlymphoid-tissue Treg cells exist and how they differentiate remain elusive. Using transcription factor nuclear factor, interleukin 3 regulated (Nfil3) reporter mice and single-cell RNA-sequencing (scRNA-seq), we identified two precursor stages of interleukin 33 (IL-33) receptor ST2-expressing non lymphoid tissue Treg cells, which resided in the spleen and lymph nodes. Global chromatin profiling of nonlymphoid tissue Treg cells and the two precursor stages revealed a stepwise acquisition of chromatin accessibility and reprogramming toward the nonlymphoid-tissue Treg cell phenotype. Mechanistically, we identified and validated the transcription factor Batf as the driver of the molecular tissue program in the precursors. Understanding this tissue development program will help to harness regenerative properties of tissue Treg cells for therapy

Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells.

Murine regulatory T (Treg) cells in tissues promote tissue homeostasis and regeneration. We sought to identify features that characterize human Treg cells with these functions in healthy tissues. Single-cell chromatin accessibility profiles of murine and human tissue Treg cells defined a conserved, microbiota-independent tissue-repair Treg signature with a prevailing footprint of the transcription factor BATF. This signature, combined with gene expression profiling and TCR fate mapping, identified a population of tissue-like Treg cells in human peripheral blood that expressed BATF, chemokine receptor CCR8 and HLA-DR. Human BATF+CCR8+ Treg cells from normal skin and adipose tissue shared features with nonlymphoid T follicular helper-like (Tfh-like) cells, and induction of a Tfh-like differentiation program in naive human Treg cells partially recapitulated tissue Treg regenerative characteristics, including wound healing potential. Human BATF+CCR8+ Treg cells from healthy tissue share features with tumor-resident Treg cells, highlighting the importance of understanding the context-specific functions of these cells