Analysis of epigenetic characteristics in colonic tumors of Apcmin/+via spatial ATAC-seq technology
10.3969/j.issn.1674-8115.2025.10.001
- VernacularTitle:基于空间ATAC-seq技术的Apcmin/+小鼠结肠肿瘤表观特征分析
- Author:
Lebin LIANG
1
;
Huifang CHEN
1
;
Shujing LAI
1
;
Liang GU
1
;
Bing SU
1
Author Information
1. 上海交通大学基础医学院免疫学与微生物学系,上海市免疫学研究所,上海 200025
- Publication Type:Journal Article
- Keywords:
colorectal cancer(CRC);
spatial ATAC-seq;
epigenetics;
single-cell RNA-seq
- From:
Journal of Shanghai Jiaotong University(Medical Science)
2025;45(10):1261-1270
- CountryChina
- Language:Chinese
-
Abstract:
Objective·To investigate the spatial epigenetic characteristics of spontaneous colon tumors in Apcmin/+mice.Methods·A spatial assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq)technology platform was established using an eight-month-old male Apcmin/+mouse model with spontaneous colon tumors.One tumor from a mouse was harvested and embedded in OCT compound for serial cryosectioning;one tissue section was stained with hematoxylin-eosin(H-E)to observe its histological characteristics,while an adjacent section was processed using spatial ATAC-seq technology to generate spatially resolved DNA libraries,followed by sequencing to obtain spatial chromatin accessibility data.Another tumor from the same mouse was digested into a single-cell suspension,in which viable single cells were sorted by flow cytometry and processed for single-cell RNA sequencing.The results were integrated with spatial chromatin accessibility data to jointly analyze the epigenetic characteristics of the colon tumor microenvironment.Results·A stable spatial ATAC-seq platform was successfully established,dividing the tumor into malignant,non-malignant,and malignant-non-malignant boundary regions.Transcription factors enriched in malignant regions included NK2 homeobox 5(NKX2-5)and transcription factor 3(TCF3).Analysis of transcription factor enrichment in the 3 regions revealed two distinct expression trends:one showing a gradual decrease from malignant to boundary to non-malignant regions,and the other exhibiting high expression in malignant and boundary regions but low expression in non-malignant regions.Gene analysis across regions revealed significant upregulation of hypoxia response,transforming growth factor(TGF),and Kirsten rat sarcoma viral oncogene homolog(KRAS)signaling pathways in malignant regions,with cell cycle-related functions markedly enhanced.Analysis of cell-cell interactions in the tumor microenvironment revealed significant differences in interaction strength:strong interactions within non-malignant regions,moderate interactions between boundary and non-malignant regions,and weak interactions between malignant and boundary regions as well as between malignant and non-malignant regions.Conclusion·Colon tumors in Apcmin/+mice exhibit high spatial heterogeneity;malignant regions were enriched with transcription factors including TCF3,and cell interactions between malignant regions and boundary/non-malignant regions were relatively weak.
