PO.MCB08.04 · 分子与细胞生物学
利用单核多组学对子宫内膜癌风险基因进行细胞类型特异性定位
Cell type-specific mapping of endometrial cancer risk genes using single-nucleus multi-omics
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
子宫内膜癌是一种常见的妇科恶性肿瘤,2020年全球新诊断病例超过410,000例。子宫内膜癌全基因组关联研究(GWAS)已鉴定出21个稳健的易感区域,其中大多数位于非编码区,推测通过细胞类型特异性调控元件发挥作用。然而,块状组织和细胞系模型无法完全解析这些调控程序。本项目采用单核多组学(RNA+ATAC)图谱分析,能够在同一细胞核内同时测量染色质可及性和基因表达,从而在子宫内膜肿瘤中生成细胞类型特异性的增强子-基因图谱。通过将这些图谱与GWAS数据整合,我们旨在鉴定一套全面的候选子宫内膜癌风险基因。我们使用10X Multimodal GEX+ATAC单核测序试剂盒,对通过澳大利亚国家子宫内膜癌研究(ANECS,一项基于人群、具有丰富临床数据的子宫内膜癌病例对照研究)获得的存档子宫内膜肿瘤中的开放染色质和基因表达图谱进行定位。文库在NextSeq2000平台上测序,随后使用Cell Ranger、Seurat和Signac进行数据处理,以实现细胞类型解析的增强子-基因定位。探索性增强子-基因定位采用Signac中的共可及性和基因表达相关性分析进行。将来自21个子宫内膜癌GWAS位点的可信风险变异与增强子进行交集,以鉴定候选致病风险变异及相应靶基因。约25,000个细胞核被成功分析并聚类为主要的子宫内膜细胞类型,包括上皮细胞(纤毛和非纤毛)、成纤维细胞和免疫细胞。使用Signac共可及性分析进行的初步增强子-基因定位发现,位于13q22.1位点的子宫内膜癌风险变异位于上皮细胞增强子内,并与KLF5表达相关。我们生成了首个子宫内膜癌单核多模态图谱,能够将子宫内膜癌风险变异直接与细胞类型特异性调控元件和靶基因(包括KLF5,一种调控子宫上皮重塑并在实验模型中促进子宫内膜癌细胞增殖的转录因子)相关联。这项工作是一项正在进行的初步研究,更多肿瘤和位点正在分析中,以揭示细胞类型特异性的子宫内膜癌风险基因。
查看英文原文 English abstract
Endometrial cancer is a common gynecological malignancy with more than 410,000 new cases diagnosed worldwide in 2020. Endometrial cancer genome-wide association study (GWAS) have identified 21 robust susceptibility regions, most of which lie in non-coding regions and are presumed to act through cell type-specific regulatory elements. However, bulk tissue and cell-line models cannot fully resolve these regulatory programs. This project uses single-nucleus multi-omic (RNA+ATAC) profiling, enabling simultaneous measurement of chromatin accessibility and gene expression within the same nucleus, to generate cell type-specific enhancer-gene maps in endometrial tumors. By integrating these maps with GWAS data, we aim to identify a comprehensive set of candidate endometrial cancer risk genes. We used the 10X Multimodal GEX+ATAC single nucleus sequencing kit to map open chromatin and gene expression profiles in archival endometrial tumors available through the Australian National Endometrial Cancer Study (ANECS), a population-based case-control study of endometrial cancer with extensive clinical data. Libraries were sequenced on the NextSeq2000 platform before data processing using Cell Ranger, Seurat and Signac for cell-type-resolved enhancer-gene mapping. Exploratory enhancer-gene mapping was performed using co-accessibility and gene expression correlation analysis in Signac. Credible risk variants from 21 endometrial cancer GWAS loci were intersected with enhancers to identify candidate causal risk variants and corresponding target genes. Approximately 25,000 nuclei were successfully profiled and clustered into major endometrial cell types, including epithelial (ciliated and unciliated), fibroblast and immune cells. Initial enhancer-gene mapping using Signac co-accessibility analysis identified endometrial cancer risk variants at the 13q22.1 locus residing within epithelial cell enhancers that correlate with KLF5 expression. We have generated the first single-nucleus multimodal map of endometrial cancer, enabling direct linkage of endometrial cancer risk variants to cell type-specific regulatory elements and target genes, including KLF5 , a transcription factor that regulates uterine epithelial remodeling and promotes endometrial cancer cell proliferation in experimental models. This work represents an ongoing pilot study, with further tumors and loci being analyzed to reveal cell type-specific endometrial cancer risk genes.
利益披露 Disclosure
P. Bajwa, None..
C. Chapman, None..
D. Glubb, None..
T. O'Mara, None.