Integrative analyses of scRNA-seq and scATAC-seq reveal CXCL14 as a key regulator of lymph node metastasis in breast cancer

Abstract

The potentially different genetics and epigenetics in the primary tumors and metastases affect the efficacy of treatment in breast cancer patients. Nevertheless, the cellular and molecular mechanisms of breast cancer lymph node metastasis still remain elusive. Here, we employed single-cell RNA sequencing (scRNA-seq) to acquire the transcriptomic profiles of individual cells from primary tumours, negative, and positive lymph nodes. We also performed a single-cell assay for transposase-accessible chromatin (ATAC) sequencing (scATAC-seq) of the positive and negative lymph node samples to get the chromatin accessibility profile. We identified a novel cell subpopulation with an abnormally high expression level of CXCL14 in the positive lymph node of breast cancer patients. Cell trajectory analysis also revealed that CXCL14 was increased expressed in the late pseudo-time. Moreover. Based on a tissue microarray of 55 patients and the Oncomine database, We validated that CXCL14 expression was significantly higher in breast cancer patients with lymph node metastasis. Furthermore, scATAC-seq identified several transcription factors (TFs) that may be potential regulation factors for the lymph node metastasis of breast cancer. Thus, our findings will improve our current understanding of the mechanism for lymph node metastasis, and are potentially valuable in providing novel prognosis markers for lymphatic metastasis of breast cancer.

Single-cell RNA sequencing reveals cell heterogeneity and transcriptome profile of breast cancer lymph node metastasis

“…β2-microglobulin, which is encoded by B2M, is an essential component of MHC class I. Previous studies on pancreatic ductal adenocarcinoma, colorectal cancer, and melanoma showed that loss of B2M was an indicator of poor dismal prognosis, including lymph node metastasis, recurrence, and therapy resistance [ 11 , 24 , 25 ]. The high expression of B2M and MHC class I in metastases enabled a better chance for immune recognition and attack.…”

“…Previous studies reported gene expression characteristics of breast cancer lymph node metastasis [ 2 , 5 , 7 ]. Across multiple studies conducted over the years, including a tentative exploration of chromatin accessibility during lymph node metastasis derived from one breast cancer patient [ 24 ], no single best delineation has been identified to understand the transcriptome diversity of metastatic breast cancer at a single-cell level, nor were comparisons made between primary tumors and lymph node metastasis. The theme of self-renewing cancer cells, epithelial-mesenchymal transition, and tumor-immune escape seem to be recapitulated in research on many malignancies.…”

“…This single-cell transcriptome analysis is analogous to the results from other human malignancies and delineates the transcriptomic heterogeneity of tumors at the single-cell level [ 12 ]. Our findings suggest that the expression of genes including PTMA, STC2, CST3, and RAMP3 played contributory roles in lymph node metastasis at the single-cell level [ 24 , 26 , 28 , 31 , 32 ]. Furthermore, at the gene set level, the meta-program analysis will potentially be used for establishing panels predicting the metastasis and prognosis of breast cancer.…”

The Lymphatic System in Breast Cancer: Anatomical and Molecular Approaches

“…In breast cancer, the chemokine receptors CXCR4 and CCR7 have been involved in the process of the lymph node metastatization and the expression of their ligands CXCL12 and CCL21 by lymphatic endothelial cells attract tumours cells into lymphatic vessels [52,91]. Recently, Xu and colleagues [92] identified and validated a cell subpopulation of breast cancer cells with a high expression level of CXCL14 in the positive lymph nodes of breast cancer patients. The CXCL14 expression was significantly higher in breast cancer patients with lymph node metastasis, suggesting this protein as a new prognostic marker for lymphatic metastasis [92].…”

The Single-Cell Sequencing: A Dazzling Light Shining on the Dark Corner of Cancer

“…Moreover, the heterogeneity between the primary tumor and metastases in lymph nodes was assessed using scRNA-seq, and a novel cell subpopulation called CXCL14 cancer cells was identified in the positive lymph nodes of breast cancer patients. ATAC-seq of the positive and negative lymph node samples further revealed the chromatin accessibility profile and identified potential TFs related to CXCL14 cancer cells, including ZNF467, bZIP, EBF1, and PIT1, in the lymph node metastases of breast cancer ( 88 ).…”