ABSTRACT
Regulatory T (Treg) cells are a barrier for tumor immunity and a target for immunotherapy. Using single-cell transcriptomics, we found that CD4+ T cells infiltrating primary and metastatic colorectal cancer and non-small-cell lung cancer are highly enriched for two subsets of comparable size and suppressor function comprising forkhead box protein P3+ Treg and eomesodermin homolog (EOMES)+ type 1 regulatory T (Tr1)-like cells also expressing granzyme K and chitinase-3-like protein 2. EOMES+ Tr1-like cells, but not Treg cells, were clonally related to effector T cells and were clonally expanded in primary and metastatic tumors, which is consistent with their proliferation and differentiation in situ. Using chitinase-3-like protein 2 as a subset signature, we found that the EOMES+ Tr1-like subset correlates with disease progression but is also associated with response to programmed cell death protein 1-targeted immunotherapy. Collectively, these findings highlight the heterogeneity of Treg cells that accumulate in primary tumors and metastases and identify a new prospective target for cancer immunotherapy.
Subject(s)
Carcinoma, Non-Small-Cell Lung/immunology , Clonal Hematopoiesis/immunology , Colorectal Neoplasms/immunology , Lung Neoplasms/immunology , T-Lymphocytes, Regulatory/immunology , Adult , Aged , Aged, 80 and over , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/secondary , Carcinoma, Non-Small-Cell Lung/therapy , Cell Differentiation/genetics , Cell Differentiation/immunology , Cell Proliferation/genetics , Chemotherapy, Adjuvant/methods , Chitinases/metabolism , Colectomy , Colon/pathology , Colon/surgery , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Colorectal Neoplasms/therapy , Datasets as Topic , Disease Progression , Drug Resistance, Neoplasm/immunology , Female , Flow Cytometry , Forkhead Transcription Factors/metabolism , Gene Expression Regulation, Neoplastic/immunology , Granzymes/metabolism , Humans , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Kaplan-Meier Estimate , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Lung Neoplasms/therapy , Male , Middle Aged , Primary Cell Culture , Programmed Cell Death 1 Receptor/antagonists & inhibitors , RNA-Seq , Single-Cell Analysis , T-Box Domain Proteins/metabolism , T-Lymphocytes, Regulatory/metabolismABSTRACT
Cancer is characterized by pervasive epigenetic alterations with enhancer dysfunction orchestrating the aberrant cancer transcriptional programs and transcriptional dependencies. Here, we epigenetically characterize human colorectal cancer (CRC) using de novo chromatin state discovery on a library of different patient-derived organoids. By exploring this resource, we unveil a tumor-specific deregulated enhancerome that is cancer cell-intrinsic and independent of interpatient heterogeneity. We show that the transcriptional coactivators YAP/TAZ act as key regulators of the conserved CRC gained enhancers. The same YAP/TAZ-bound enhancers display active chromatin profiles across diverse human tumors, highlighting a pan-cancer epigenetic rewiring which at single-cell level distinguishes malignant from normal cell populations. YAP/TAZ inhibition in established tumor organoids causes extensive cell death unveiling their essential role in tumor maintenance. This work indicates a common layer of YAP/TAZ-fueled enhancer reprogramming that is key for the cancer cell state and can be exploited for the development of improved therapeutic avenues.
