A Single-Cell Immune Atlas of Triple Negative Breast Cancer Reveals Novel Immune Cell Subsets

Abstract

26Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer 27 subtype, which recently attracts great interest for immune therapeutic development. In 28 this context, in-depth understanding of TNBC immune landscape is highly demanded. 29 Here we report single-cell RNA sequencing results of 9683 tumor-infiltrated immune 30 cells isolated from 14 treatment naïve TNBC tumors, where 22 immune cell subsets, 31 including T cells, macrophages, B cells, and DCs have been characterized. We 32 identify a new T cell subset, CD8 + CXCL8 + naïve T cell, which associates with poor 33 survival. A novel immune cell subset comprised of TCR + macrophages, is found to be 34 widely distributed in TNBC tumors. Further analyses reveal an up-regulation of 35 molecules associated with TCR signaling and cytotoxicity in these immune cells, 36 indicating TCR signaling activation. Altogether, our study provides a valuable 37 resource to understand the immune ecosystem of TNBC. The novel immune cell 38 subsets reported herein might be functionally important in cancer immunity. 39 40 SIGNIFICANCE：This work demonstrates a single-cell transcriptome atlas of 41 immune cells in treatment naïve TNBC tumors, revealing novel immune cell subsets. 42This study provides a valuable resource to understand the immune ecosystem of 43 TNBC, which will be helpful for the immunotherapeutic strategy design of TNBC. 44 45 85TNBC tumors are typically more aggressive and difficult to treat than hormone 86 receptor-positive tumors, and are associated with a higher risk of early relapse. The 87 lack of estrogen receptor, progesterone receptor, and HER2 expression precludes the 88 use of targeted therapies, and the only approved systemic treatment option is 89 chemotherapy. Responses to chemotherapy occur, but are often short lived and 90 frequently accompanied by considerable toxicity. Gene profiling studies reveal that 91 TNBCs are highly heterogeneous and a large proportion of them demonstrate DNA 92 Repair Deficiency Signature (18)(19)(20). Recent data showed impressive activity of 93 PD-1/PD-L1 blockade therapy in metastatic TNBC patients who were chemotherapy 94 naïve, suggesting early intervention of immunotherapy can bring more benefit (21). 95Clinical trials applying checkpoint inhibitors in the neo-adjuvant setting of TNBC are 96 ongoing. Although need to be confirmed in a larger cohort, these results are consistent 97 with the notion that immunotherapy agents are most efficient at low tumor burden and 98 in patients naïve of immune-modulatory chemotherapy agents. To better understand 99 the immune ecosystem of TNBC, we analyzed the full-length single-cell RNA 100 sequencing data of 9,683 tumor-infiltrated immune cells isolated from treatment naïve 101 TNBC tumors. We identified 22 unique immune cell subsets, including T cells, 102 macrophages, B cells, and DCs. Using combined expression and TCR-based analyses, 103 we were able to indicate the function and developmental path of T cell subsets. We 104 found a novel T c...

The Influence of Cancer Molecular Subtypes and Treatment on the Mutation Spectrum in Metastatic Breast Cancers

“…Since studies on WES did not fully address the questions related to mBCs, there is a need to further explore this entity thanks to new technologies including single-cell sequencing, proteomics, and Assay for Transposase-Accessible Chromatin using sequencing (ATACseq). Preliminary studies have enabled to specify immune ecosystem of TNBC (83) and suggest that subclonal resistant cells pre-exist and can be selected by treatment (84). This approach is nevertheless dependent on the sampling, just as bulk sequencing approaches.…”

Organotypic 3D decellularized matrix tumor spheroids for high-throughput drug screening

“…As demonstrated through high-resolution CLSM micrographs clustering of both cancer and stromal populations into non-uniform agglomerates and randomly distributed cells within both models was observable. Triple-negative breast cancer naturally showcases stromal/cancer cell clusters with semi-defined borders in which direct cell-cell interactions between cancer, stromal and immune cells are found to be highly recurrent [71,72]. Following the characterization of dECM-Spheroids size/shape, necrotic core establishment, cell viability, and spatiotemporal distribution of cancer cells and fibroblasts in coculture models, their utility to serve as a living platform for studying metastatic breast cancer cells invasion in vitro was investigated.…”

Spatial heterogeneity of infiltrating T cells in high-grade serous ovarian cancer revealed by multi-omics analysis

“…This may contribute to an elevated CD8_C03 (Tex) terminal exhausted signature score being associated with better prognosis in TCGA ovarian cohort. This may not be unique to ovarian cancer as Zhang and co-workers 47 reported that CD8-CXCL13 and CD4-CXCL13 T cells, which are proposed to represent exhausted T cells, predict effective responses to PD-L1 blockade in breast cancer. However, other studies suggest that dysfunctional T cells can no longer be reversed and activated by PD-1 therapy.…”