Dataset Information

GRHL2 motif is associated with intratumor heterogeneity of cis-regulatory elements in luminal breast cancer.

ABSTRACT: In breast cancer patients, tumor heterogeneity is associated with prognosis and therapeutic response; however, the epigenetic diversity that exists in primary tumors remains unknown. Using a single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq), we obtained the chromatin accessibility profiles of 12,452 cells from 16 breast cancer patients including 11 luminal, 1 luminal-HER2, 1 HER2⁺, and 3 triple-negative subtypes. Via this profiling process, tumors were classified into cancer cells and the tumor microenvironment, highlighting the heterogeneity of disease-related pathways including estrogen receptor (ER) signaling. Furthermore, the coexistence of cancer cell clusters with different ER binding motif enrichments was identified in a single ER⁺ tumor. In a cluster with reduced ER motif enrichment, we identified GRHL2, a transcription factor, as the most enriched motif, and it cooperated with FOXA1 to initiate endocrine resistance. Coaccessibility analysis revealed that GRHL2 binding elements potentially regulate genes associated with endocrine resistance, metastasis, and poor prognosis in patients that received hormonal therapy. Overall, our study suggests that epigenetic heterogeneity could lead to endocrine resistance and poor prognosis in breast cancer patients and it offers a large-scale resource for further cancer research.

SUBMITTER: Kumegawa K

PROVIDER: S-EPMC9177858 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

GRHL2 motif is associated with intratumor heterogeneity of cis-regulatory elements in luminal breast cancer.

Kumegawa Kohei K Takahashi Yoko Y Saeki Sumito S Yang Liying L Nakadai Tomoyoshi T Osako Tomo T Mori Seiichi S Noda Tetsuo T Ohno Shinji S Ueno Takayuki T Maruyama Reo R

NPJ breast cancer 20220608 1

In breast cancer patients, tumor heterogeneity is associated with prognosis and therapeutic response; however, the epigenetic diversity that exists in primary tumors remains unknown. Using a single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq), we obtained the chromatin accessibility profiles of 12,452 cells from 16 breast cancer patients including 11 luminal, 1 luminal-HER2, 1 HER2<sup>+</sup>, and 3 triple-negative subtypes. Via this profiling process, tumors were cla ...[more]

PMID: 35676392

Similar Datasets

Project description:The transcription factor Grainyhead-like 2 (GRHL2) is a critical transcription factor for epithelial tissues that has been reported to promote cancer growth in some and suppress aspects of cancer progression in other studies. We investigated its role in different breast cancer subtypes. In breast cancer patients, GRHL2 expression was increased in all subtypes and inversely correlated with overall survival in basal-like breast cancer patients. In a large cell line panel, GRHL2 was expressed in luminal and basal A cells, but low or absent in basal B cells. The intersection of ChIP-Seq analysis in 3 luminal and 3 basal A cell lines identified conserved GRHL2 binding sites for both subtypes. A pathway analysis of ChIP-seq data revealed cell-cell junction regulation and epithelial migration as well as epithelial proliferation, as candidate GRHL2-regulated processes and further analysis of hub genes in these pathways showed similar regulatory networks in both subtypes. However, GRHL2 deletion in a luminal cell line caused cell cycle arrest while this was less prominent in a basal A cell line. Conversely, GRHL2 loss triggered enhanced migration in the basal A cells but failed to do so in the luminal cell line. ChIP-Seq and ChIP-qPCR demonstrated GRHL2 binding to CLDN4 and OVOL2 in both subtypes but not to other GRHL2 targets controlling cell-cell adhesion that were previously identified in other cell types, including CDH1 and ZEB1. Nevertheless, E-cadherin protein expression was decreased upon GRHL2 deletion especially in the luminal line and, in agreement with its selectively enhanced migration, only the basal A cell line showed concomitant induction of vimentin and N-cadherin. To address how the balance between growth reduction and aspects of EMT upon loss of GRHL2 affected in vivo behavior, we used a mouse basal A orthotopic transplantation model in which the GRHL2 gene was silenced. This resulted in reduced primary tumor growth and a reduction in number and size of lung colonies, indicating that growth suppression was the predominant consequence of GRHL2 loss. Altogether, these findings point to largely common but also distinct roles for GRHL2 in luminal and basal breast cancers with respect to growth and motility and indicate that, in agreement with its negative association with patient survival, growth suppression is the dominant response to GRHL2 loss.

Project description:Background: Cis-regulatory elements (CREs) control oncogene expression and malignant phenotypes. The high clinicopathological heterogeneity of cancer cannot be explained by gene expression alone, being attributed to CRE heterogeneity. However, characterizing cancer-associated CRE is challenging. To address this issue, we performed a single-cell epigenomic analysis of clinical specimens. Methods: To map the multicellular ecosystem of BC and identify candidate CREs (cCREs), we performed a single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) of 38 prospectively collected breast cancer (BC) samples with various clinicopathological characteristics. Results: First, we performed single-cell chromatin accessibility profiling of a high-quality set of 22,775 cells from BC samples. Cells were accurately annotated using marker gene accessibility and integration with existing single-cell RNA sequencing data. By predicting copy number variants, epithelial cells were classified into non-malignant and malignant cells. The chromatin accessibility patterns exhibited by malignant cells were consistent with the clinicopathological features of each tumor. We identified 224,585 cCREs across the BC ecosystem. By identifying cluster-specific differentially accessible cCREs (DA-cCREs) and constructing a putative enhancer-promoter network, we mapped the cis-regulatory landscape for cancer cells and the tumor microenvironment. In this dataset, we identified changes in the cis-regulatory landscape associated with cancer progression. In particular, estrogen receptor (ER)-positive tumors have increased accessibility of ER binding motifs during the cell transition from non-cancerous to cancerous and increased accessibility of Kruppel like factor motifs during the transition from cancerous to metastatic. Furthermore, the accessibility of putative enhancers targeting the same gene differed within or between tumors, highlighting intra- and inter-cis-regulatory tumor heterogeneity. Conclusions: This study provides a valuable resource for future epigenetic research on BC and highlights the diverse regulatory landscape within or among tumor(s), suggesting that cCREs regulate tumor progression and intra- and inter-tumor heterogeneity.

Dataset Information

GRHL2 motif is associated with intratumor heterogeneity of cis-regulatory elements in luminal breast cancer.

Publications

GRHL2 motif is associated with intratumor heterogeneity of cis-regulatory elements in luminal breast cancer.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets