Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer

被引：19

作者：

Ye, Ying ^{[1
,2
]}

Feng, Weiyi ^{[1
,2
]}

Zhang, Jialiang ^{[1
,2
]}

Zhu, Kaiyu ^{[1
,2
]}

Huang, Xudong ^{[1
,2
]}

Pan, Ling ^{[1
,2
]}

Su, Jiachun ^{[1
,2
]}

Zheng, Yanfen ^{[1
,2
]}

Li, Rui ^{[1
,2
]}

Deng, Shuang ^{[1
,2
]}

Bai, Ruihong ^{[1
,2
]}

Zhuang, Lisha ^{[1
,2
]}

Wei, Lusheng ^{[3
]}

Deng, Junge ^{[1
,2
]}

Li, Mei ^{[4
]}

Chen, Rufu ^{[5
,6
]}

Lin, Dongxin ^{[1
,2
,7
,8
]}

Zuo, Zhixiang ^{[1
,2
]}

Zheng, Jian ^{[1
,2
,8
]}

机构：

[1] Sun Yat Sen Univ, Canc Ctr, State Key Lab Oncol South China, Guangzhou, Peoples R China

[2] Collaborat Innovat Ctr Canc Med, Guangzhou, Peoples R China

[3] Sun Yat Sen Univ, Sun Yat Sen Mem Hosp, Dept Pancreaticobiliary Surg, Guangzhou, Peoples R China

[4] Sun Yat Sen Univ, Dept Pathol, Canc Ctr, Guangzhou, Peoples R China

[5] Guangdong Prov Peoples Hosp, Guangzhou, Peoples R China

[6] Guangdong Acad Med Sci, Guangzhou, Peoples R China

[7] Chinese Acad Med Sci & Peking Union Med Coll, Dept Etiol & Carcinogenesis, Natl Canc Ctr, Natl Clin Res Ctr,Canc Hosp, Beijing, Peoples R China

[8] Nanjing Med Univ, Collaborat Innovat Ctr Canc Med, Jiangsu Key Lab Canc Biomarkers Prevent & Treatme, Nanjing, Peoples R China

来源：

GENOME MEDICINE | 2021年 / 13卷 / 01期

基金：

中国国家自然科学基金;

关键词：

m(6)A modification; Circular RNA; m(6)A-seq; Pancreatic cancer; METHYLATION; REVEALS; TRANSLATION; LANDSCAPE; PACKAGE; WRITERS; N6-METHYLADENOSINE; DIFFERENTIATION; BIOGENESIS; WIDESPREAD;

D O I：

10.1186/s13073-021-01002-w

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Background: N-6-methyladenosine (m(6)A) is the most abundant modification of RNA in eukaryotic cells and play critical roles in cancer. While most related studies focus on m(6)A modifications in linear RNA, transcriptome-wide profiling and exploration of m(6)A modification in circular RNAs in cancer is still lacking. Methods: For the detection of m(6)A modification in circRNAs, we developed a new bioinformatics tools called Circm6A and applied it to the m(6)A-seq data of 77 tissue samples from 58 individuals with pancreatic ductal adenocarcinoma (PDAC). Results: Circm6A performs better than the existing circRNA identification tools, which achieved highest F1 score among these tools in the detection of circRNAs with m(6)A modifications. By using Circm6A, we identified a total of 8807 m(6)A-circRNAs from our m(6)A-seq data. The m(6)A-circRNAs tend to be hypermethylated in PDAC tumor tissues compared with normal tissues. The hypermethylated m(6)A-circRNAs were associated with a significant gain of circRNA-mRNA coexpression network, leading to the dysregulation of many important cancer-related pathways. Moreover, we found the cues that hypermethylated m(6)A-circRNAs may promote the circularization and translation of circRNAs. Conclusions: These comprehensive findings further bridged the knowledge gaps between m(6)A modification and circRNAs fields by depicting the m(6)A-circRNAs genomic landscape of PDAC patients and revealed the emerging roles played by m(6)A-circRNAs in pancreatic cancer. Circm6A is available at https://github.com/canceromics/circm6a.

引用

页数：19

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