Integrated genomic analysis identifies novel low-frequency cis-regulatory variant rs2279658 associated with VSD risk in Chinese children

Lihui Jin; Zhenyuan Han; Zhongli Jiang; Jieru Lu; Yizhuo Wu; Bingqian Yan; Weibin Zhang; Xuedong Lin; Lvyan Jiang; Pengjun Zhao; Kun Sun

doi:10.3389/fcell.2022.1062403

Integrated genomic analysis identifies novel low-frequency cis-regulatory variant rs2279658 associated with VSD risk in Chinese children

Front Cell Dev Biol. 2022 Dec 8:10:1062403. doi: 10.3389/fcell.2022.1062403. eCollection 2022.

Authors

Lihui Jin¹, Zhenyuan Han², Zhongli Jiang³, Jieru Lu^{1

4}, Yizhuo Wu^{1

5}, Bingqian Yan⁶, Weibin Zhang⁷, Xuedong Lin⁸, Lvyan Jiang⁹, Pengjun Zhao¹, Kun Sun¹

Affiliations

¹ Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
² Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China.
³ Department of Statistics, College of Science, Purdue University, West Lafayette, IN, United States.
⁴ Children's Heart Center, Institute of Cardiovascular Development and Translational Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.
⁵ Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
⁶ Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
⁷ Department of Dermatology, People's Hospital of Zhengzhou, Zhengzhou, China.
⁸ Department of Gastroenterology, Wenzhou Hospital of Chinese Medicine, Wenzhou, China.
⁹ Ping'an Community Healthcare Center Hospital, Shanghai, China.

Abstract

VSD combined with other cardiac or extracardiac malformations (defined as "complex VSD" by us) is one of the major causes of perinatal morbidity and mortality. Functional non-coding SNPs (cis-regulatory SNPs) have not been systematically studied in CHDs, including complex VSD. Here we report an exome-wide association analysis using WES data of 60 PA/VSD cases, 20 TOF cases and 100 controls in Chinese children. We identify 93 low-frequency non-coding SNPs associated with complex VSD risk. A functional genomics pipeline integrating ATAC-seq, ChIP-seq and promoter CHi-C recognizes the rs2279658 variant as a candidate cis-regulatory SNP. Specifically, rs2279658 resides in a cardiac-specific enhancer bound by FOXH1 and PITX2, and would abrogate binding of these two transcription factors to the identified enhancer during cardiac morphogenesis. COQ2 and FAM175A are predicted to be target genes for "rs2279658-FOXH1 or PITX2" pairs in the heart. These findings highlight the importance of cis-regulatory SNPs in the pathogenesis of complex VSD and broaden our understanding of this disease.

Keywords: VSD; cis-regulatory SNP; cis-regulatory region; exome-wide association analysis; in vitro cardiac differentiation; rs2279658.