Abstract 2542: Unraveling heterogeneity of tumor microenvironment of TNBC patients by meta-analysis of 6 breast cancer scRNAseq studies
Authors: Kim Kyungsoo , Ahn Sung Gwe , Bae Soong June , Chu Chihhao , Ji Jung Hwan , Kim Jee Hung , Jeong Joon 
Published: June 2022

Breast cancer can be classified into several types. Among them, triple-negative breast cancer (TNBC) is breast cancer that does not express estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Since targeted therapy for breast cancer relies on the three receptors, treatment outcomes have been worst in TNBCs. However, clinical benefit of immune-checkpoint inhibitors (ICIs) with chemotherapy over chemotherapy alone was demonstrated in the KEYNOTE-355 and IMPASSION-130 trials in terms of overall survival, opening new avenue for patients with metastatic PD-L1+ TNBC. After several studies with ICIs, researchers found that the tumor microenvironment affects the response rate of immunotherapies.

Therefore, to unravel the heterogeneity of tumor microenvironment of TNBC patients, we collected 28 TNBC samples from 6 public single cell RNA sequencing breast cancer studies.

Results: From 124,301 cells populating tumors and tumor-microenvironment (TMEs), we first identified epithelial cells separately. Using epithelial cells alone, we identified the Baylor-proposed TNBC molecular subtype of each patient. This approach with epithelial cells revealed that 3 basal-like immune-activated (BLIA), 11 basal-like immune-suppressed (BLIS), 5 luminal- androgen receptor (LAR), and 9 unclassified subtypes. By comparing cell number and cell-cell interactions, the heterogeneity of TME-consisting cell populations between the TNBC subtypes was analyzed. Analysis of tumor-infiltrating lymphocytes revealed their difference in activation, expansion, and exhaustion programs across patients. Among the subtypes, the LAR subtype had less amount of exhausted CD8+ T cells and regulatory T cells. This finding was consistent with cell-cell interaction analysis. In the case of the LAR subtype, the interaction between regulatory T cells and CD8 T cells was less active than other subtypes. Also, the interaction between cytotoxic cells (T cells and NK cells) and regulatory T cells was less active in the LAR subtype. Additionally, tumor cells in the LAR subtype seem to inhibit cytotoxic cells to a lesser extent. When we repeated our analyses using whole cells including epithelial and immune-stromal cells, the molecular subtypes of each subject were changed (7 of 19, 36.8%). 4 of 11 BLIS were changed to BLIA, 1 of 11 BLIS were changed to mesenchymal (MES), and 2 of 5 LAR were changed to MES. Characteristics of immune cells in the epithelial-based LAR subtype were conserved in the whole cells-based MES.

Conclusions:This extensive meta-analysis of public single cell RNA sequencing analysis enhances our knowledge about the heterogeneity and dynamics of the tumor microenvironment. These results offer insights about potential diagnostic and therapeutic targets for TNBC depending on their subtypes.

Citation Format: Kyungsoo Kim, Sung Gwe Ahn, Soong June Bae, Chihhao Chu, Jung Hwan Ji, Jee Hung Kim, Joon Jeong. Unraveling heterogeneity of tumor microenvironment of TNBC patients by meta-analysis of 6 breast cancer scRNAseq studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2542.