Abstract PR05: Single-cell transcriptomics reveals shared and subtype-specific vulnerabilities of the tumor-microenvironment ecosystems in peripheral T-cell lymphomas
Authors: Wen-Hsuan Wendy Lin, Anqi W Wang, Bobby B Shih, Jean-Baptiste F Reynier, Laura Quevedo Palacio, Craig Soderquist, Ryan D Najac, Cindy Ma, Govind Bhagat, Adolfo A Ferrando, Raul Rabadan, Teresa Palomero
Journal: Blood Cancer Discovery (2024)

Abstract Peripheral T-cell lymphomas (PTCL) are heterogeneous and highly aggressive hematologic malignancies with dismal outcomes, highlighting the need for novel targeted therapies. PTCLs are characterized by complex tumor-microenvironment (TME) ecosystems with low tumor cell content, admixed with rich immune infiltrates and stromal elements correlated with clinical outcomes. Direct targeting of the TME is an attractive strategy for PTCLs; however, the specific mechanisms that regulate the interdependence between lymphoma and TME remain poorly understood, hampering the development of TME-directed therapies. Our previous work based on driver genetic alterations in PTCL patients and genetic mouse models identified an important role of these driver mutations in remodeling the TME (Cortes et al., 2022). To address the specific role and mechanisms of tumor cell-TME interactions in the pathogenesis of PTCL, we developed a novel experimental platform and cutting-edge computational methodologies using single-nucleus RNAseq analysis to comprehensively profile lymphoma cells and their microenvironment from 27 PTCL patient samples of two major nodal pathologic subtypes, including 18 Nodal T follicular helper cell lymphomas (TFHcL) and 9 PTCL, not otherwise specified (PTCL, NOS). Our approach allowed the identification and in-depth characterization of tumor cells, lymphoid and myeloid TME, and vascular endothelium and non-endothelial stromal cells, which were challenging to capture with conventional single-cell RNAseq. The malignant T-cells in PTCL, NOS were grouped into patient-specific clusters demonstrating significant inter-tumor heterogeneity associated with diverse and frequently complex chromosomal abnormalities identified by copy number variation (CNV) analysis. In contrast, malignant TFHcL cells show a low degree to no apparent chromosomal abnormalities and divide into two major transcriptional subclusters, with tumor cells from the same patient falling into one of the two subclusters. Additionally, genomic profiles of TFHcL tumors revealed that the inter-tumor transcriptional heterogeneity of TFHcL tumor cells was strongly associated with the driver RHOA G17V mutation status. To profile oncogenic pathways critical for PTCL growth, we compared PTCL tumor cells to normal CD4 T-cells from reactive lymphoid tissue. PTCL, NOS and TFHcL tumor cells were equally enriched in the TCR signaling pathway, mitosis, and cell cycle related genes. However, exploitation of KRAS and cytokine-driven inflammatory signals was prevalent in TFHcL but not PTCL, NOS tumor cells. Analysis of the immune TME identified an increase in T regulatory cells, CD8 T-cells, immunoblasts, and macrophages in TFHcL. Furthermore, while dysregulated B-cells with heightened cytokine-driven inflammatory signals were unique to TFHcL, inflammatory macrophages and classic dendritic cells (cDC) were prominent in the TME of both subtypes. Our results uncover shared and subtype-specific pathogenic features in PTCL and pave the way for designing novel precision therapies for PTCL patients. Citation Format: Wen-Hsuan Wendy Lin, Anqi W Wang, Bobby B Shih, Jean-Baptiste F Reynier, Laura Quevedo Palacio, Craig Soderquist, Ryan D Najac, Cindy Ma, Govind Bhagat, Adolfo A Ferrando, Raul Rabadan, Teresa Palomero. Single-cell transcriptomics reveals shared and subtype-specific vulnerabilities of the tumor-microenvironment ecosystems in peripheral T-cell lymphomas [abstract]. In: Proceedings of the Fourth AACR International Meeting on Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2024 Jun 19-22; Philadelphia, PA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(3_Suppl):Abstract nr PR05.