Breast cancer is a heterogeneous disease, and breast cancer cell lines are invaluable for studying this heterogeneity. However, the epigenetic diversity across these cell lines remains poorly understood. In this study, we performed genome-wide chromatin accessibility analysis on 23 breast cancer cell lines, including 2 estrogen receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative (ER+/HER2−), 3 ER+/HER2+, 3 HER2+, and 15 triple-negative breast cancer (TNBC) lines. These cell lines were classified into three groups based on their chromatin accessibility: the receptor-positive group (Group-P), TNBC basal group (Group-B), and TNBC mesenchymal group (Group-M). Motif enrichment analysis revealed that only Group-P exhibited coenrichment of forkhead box A1 (FOXA1) and grainyhead-like 2 (GRHL2) motifs, whereas Group-B was characterized by the presence of the GRHL2 motif without FOXA1. Notably, Group-M did not show enrichment of either FOXA1 or GRHL2 motifs. Furthermore, gene ontology analysis suggested that group-specific accessible regions were associated with their unique lineage characteristics. To investigate the epigenetic landscape regulatory roles of FOXA1 and GRHL2, we performed knockdown experiments targeting FOXA1 and GRHL2, followed by assay for transposase-accessible chromatin sequencing analysis. The findings revealed that FOXA1 maintains Group-P–specific regions while suppressing Group-B–specific regions in Group-P cells. In contrast, GRHL2 preserves commonly accessible regions shared between Group-P and Group-B in Group-B cells, suggesting that FOXA1 and GRHL2 play a pivotal role in preserving distinct chromatin accessibility patterns for each group. Specifically, FOXA1 distinguishes between receptor-positive and TNBC cell lines, whereas GRHL2 distinguishes between basal-like and mesenchymal subtypes in TNBC lines.

乳腺癌是一种异质性疾病，乳腺癌细胞系对于研究这种异质性非常有价值。然而，这些细胞系的表观遗传多样性仍然知之甚少。在这项研究中，我们对 23 个乳腺癌细胞系进行了全基因组染色质可及性分析，其中包括 2 个雌激素受体 (ER) 阳性/人表皮生长因子受体 2 (HER2) 阴性 (ER+/​​HER2−)、3 个 ER+/ HER2+、3 个 HER2+ 和 15 个三阴性乳腺癌 (TNBC) 系。根据染色质可及性将这些细胞系分为三组：受体阳性组（P组）、TNBC基底组（B组）和TNBC间充质组（M组）。基序富集分析显示，只有 P 组表现出叉头盒 A1 (FOXA1) 和grainyhead-like 2 (GRHL2) 基序的共富集，而 B 组的特征是存在 GRHL2 基序，但没有 FOXA1。值得注意的是，M 组没有显示出 FOXA1 或 GRHL2 基序的富集。此外，基因本体分析表明，特定群体的可访问区域与其独特的谱系特征相关。为了研究 FOXA1 和 GRHL2 的表观遗传景观调控作用，我们进行了针对FOXA1和GRHL2的敲低实验，然后进行了转座酶可及的染色质测序分析。研究结果表明，FOXA1 在 P 组细胞中维持 P 组特异性区域，同时抑制 B 组特异性区域。相比之下，GRHL2 保留了 B 组细胞中 P 组和 B 组之间共享的常见可及区域，这表明 FOXA1 和 GRHL2 在保留每个组的不同染色质可及性模式方面发挥着关键作用。具体来说，FOXA1 区分受体阳性细胞系和 TNBC 细胞系，而 GRHL2 区分 TNBC 系中的基底样亚型和间质亚型。