Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types

Abstract

FoxP3+T regulatory (Treg) cells are central elements of immunologic tolerance. They are abundant in many tumors, where they restrict potentially favorable antitumor responses. We used a three-pronged strategy to identify genes related to the presence and function of Tregs in the tumor microenvironment. Gene expression profiles were generated from tumor-infiltrating Tregs (TITRs) of both human and mouse tumors and were compared with those of Tregs of lymphoid organs or normal tissues from the same individuals. A computational deconvolution of whole-tumor datasets from the Cancer Genome Atlas (TCGA) was performed to identify transcripts specifically associated with Tregs across thousands of tumors from different stages and locations. We identified a set of TITR-differential transcripts with striking reproducibility between tumor types in mice, between mice and humans, and between different human patients spanning tumor stages. Many of the TITR-preferential transcripts were shared with “tissue Tregs” residing in nonlymphoid tissues, but a tumor-preferential segment could be identified. Many of these TITR signature transcripts were confirmed by mining of TCGA datasets, which also brought forth transcript modules likely representing the parenchymal attraction of, or response to, tumor Tregs. Importantly, the TITR signature included several genes encoding effective targets of tumor immunotherapy. A number of other targets were validated by CRISPR-based gene inactivation in mouse Tregs. These results confirm the validity of the signature, generating a wealth of leads for understanding the role of Tregs in tumor progression and identifying potential targets for cancer immunotherapy.

Targeting Treg cells in cancer immunotherapy

“…). Tumor‐infiltrating Treg cells express high levels of specific chemokine receptors such as CCR4 and CCR8, which are also expressed by Th2 cells .…”

Treg programming and therapeutic reprogramming in cancer

“…However, the activation of Tregs can also drive the destabilization of Foxp3 expression and induce the production of pro‐inflammatory cytokines, revealing that maintenance of Treg identity is tenuous during activation. Treg activation within the context of the TME also imparts a unique transcriptional programme that distinguishes TI‐Tregs from Tregs present in normal tissues, indicating that Treg differentiation may adapt within cancers . Therefore, approaches that target the highly activated state of TI‐Tregs or their unique differentiation state within cancer may prove to be powerful mechanisms for specifically disrupting Tregs within tumours and reprogramming their functions.…”

“…Factors controlling Treg transcription, both transcription factors and the chromatin landscape, act in an independent and overlapping fashion to establish and maintain the Treg programme upon activation . TI‐Tregs exhibit a distinctive transcriptional programme compared with Tregs in other sites of the body, opening up the possibility to specifically disrupt the TI‐Treg transcriptome as a mechanism to enhance antitumour immunity …”

“…Treg activation within the context of the TME also imparts a unique transcriptional programme that distinguishes TI-Tregs from Tregs present in normal tissues, indicating that Treg differentiation may adapt within cancers. 9,10,14 Therefore, approaches that target the highly activated state of TI-Tregs or their unique differentiation state within cancer may prove to be powerful mechanisms for specifically disrupting Tregs within tumours and reprogramming their functions. We will begin our review by discussing the critical surface receptors that control Treg activation or contribute to their differentiated state in tumours.…”

Phosphoinositide 3‐kinase δ is a regulatory T‐cell target in cancer immunotherapy

“…Meanwhile, a greater understanding of the phenotypic profile of activated, highly suppressive effector Treg cells – describing the great majority of Treg cells within the tumour – is forming the basis for alternative approaches to Treg cell modulation. Although genetic aberrations that disrupt the development or maintenance of the homeostatic ‘resting’ Treg cell pool can result in catastrophic autoimmunity, effector Treg cells depend on a partially distinct set of transcriptional, metabolic and signalling conditions to maintain high functionality in specific contexts, such as the tumour microenvironment . Tumour‐infiltrating Treg cells adapt to an environment characterized by a myriad of cytokines and chemokines, low oxygen availability, and high glucose demand, among other factors .…”