Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain

Abstract

Background: Few somatic mutations have been linked to breast cancer metastasis, whereas transcriptomic differences among primary tumors correlate with incidence of metastasis, especially to the lungs and brain. However, the epigenomic alterations and transcription factors (TFs) which underlie these alterations remain unclear. Methods: To identify these, we performed RNA-seq, Chromatin Immunoprecipitation and sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) of the MDA-MB-231 cell line and its brain (BrM2) and lung (LM2) metastatic sub-populations. We incorporated ATAC-seq data from TCGA to assess metastatic open chromatin signatures, and gene expression data from human metastatic datasets to nominate transcription factor biomarkers. Results: Our integrated epigenomic analyses found that lung and brain metastatic cells exhibit both shared and distinctive signatures of active chromatin. Notably, metastatic sub-populations exhibit increased activation of both promoters and enhancers. We also integrated these data with chromosome conformation capture coupled with ChIP-seq (HiChIP) derived enhancer-promoter interactions to predict enhancer-controlled pathway alterations. We found that enhancer changes are associated with endothelial cell migration in LM2, and negative regulation of epithelial cell proliferation in BrM2. Promoter changes are associated with vasculature development in LM2 and homophilic cell adhesion in BrM2. Using ATAC-seq, we identified a metastasis open-chromatin signature that is elevated in basal-like and HER2-enriched breast cancer subtypes and associates with worse prognosis in human samples. We further uncovered TFs associated with the open chromatin landscapes of metastatic cells and whose expression correlates with risk for metastasis. While some of these TFs are associated with primary breast tumor subtypes, others more specifically correlate with lung or brain metastasis. Conclusions: We identify distinctive epigenomic properties of breast cancer cells that metastasize to the lung and brain. We also demonstrate that signatures of active chromatin sites are partially linked to human breast cancer subtypes with poor prognosis, and that specific TFs can independently distinguish lung and brain relapse.

Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection

“…Tumor metastasis is the leading cause of death in cancer patients (39). ATAC-seq can be used to detect open chromatin in metastatic tissue, thus predicting the risk of tumor metastasis (24). Targeted therapy for cancer has made a leap from the macroworld to the microworld, which improved the efficiency of chemotherapy.…”

“…Second, ATAC-seq can be used to analyze immune cells and explore cancer immunotherapy (23). Third, ATACseq can be used to predict the risk of tumor metastasis by detecting metastasis-related open chromatin (24). Finally, ATACseq can be used to explore the target of cancer treatment by studying drugs as inhibitors of transcription factors (25).…”

An Information Theoretical Multilayer Network Approach to Breast Cancer Transcriptional Regulation

“…Instead, we speculate the pattern is related to promoter accessibility because of ATAC-seq data groups tumors in Basal and non-basal networks (Corces et al, 2018 ). Further characterization finds a pro-metastasis open-chromatin signature elevated in the Basal subtype (Cai et al, 2020 ). By its side, protein level measures integrated with copy number normalized gene expression suggest TF-genes as relevant drivers of this subtype (Koh et al, 2019 ).…”

Derivation and Application of Molecular Signatures to Prostate Cancer: Opportunities and Challenges

“…Changes in chromatin accessibility alter the binding ability of TFs playing a significant role in CRPC because AR-regulated, bromodomain-containing proteins such as BRD2 mediate chromatin relaxation, thus leading to the identification of a bromodomain-related gene stratification signature, BROMO-10 [ 41 ]. Integrative analyses in lung and brain metastatic cells of breast origin utilizing ATAC-seq TCGA data, ChIP-seq, and chromosome conformation capture showed distinct chromatin accessibility signatures (metATAC) of active chromatin, identifying TFs such as TFAP2C as markers of metastatic progression [ 51 ]. Chromatin dysregulation studies have uncovered important regulators of TF activity such as the chromatin remodeler gene CHD1.…”