Prioritizing de novo potential non-canonical splicing variants in neurodevelopmental disorders

Kuokuo Li; Jifang Xiao; Zhengbao Ling; Tengfei Luo; Jingyu Xiong; Qian Chen; Lijie Dong; Yijing Wang; Xiaomeng Wang; Zhaowei Jiang; Lu Xia; Zhen Yu; Rong Hua; Rui Guo; Dongdong Tang; Mingrong Lv; Aojie Lian; Bin Li; GuiHu Zhao; Xiaojin He; Kun Xia; Yunxia Cao; Jinchen Li

doi:10.1016/j.ebiom.2023.104928

Prioritizing de novo potential non-canonical splicing variants in neurodevelopmental disorders

EBioMedicine. 2024 Jan:99:104928. doi: 10.1016/j.ebiom.2023.104928. Epub 2023 Dec 18.

Authors

Kuokuo Li¹, Jifang Xiao², Zhengbao Ling³, Tengfei Luo³, Jingyu Xiong³, Qian Chen², Lijie Dong⁴, Yijing Wang⁵, Xiaomeng Wang⁴, Zhaowei Jiang³, Lu Xia³, Zhen Yu¹, Rong Hua¹, Rui Guo¹, Dongdong Tang¹, Mingrong Lv¹, Aojie Lian⁶, Bin Li², GuiHu Zhao², Xiaojin He⁷, Kun Xia⁸, Yunxia Cao⁹, Jinchen Li¹⁰

Affiliations

¹ Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
² Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China.
³ Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
⁴ Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China.
⁵ Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China.
⁶ National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.
⁷ Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China; Anhui Provincial Human Sperm Bank, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China. Electronic address: hxj0117@126.com.
⁸ Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. Electronic address: xiakun@sklmg.edu.cn.
⁹ Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China. Electronic address: caoyunxia6@126.com.
¹⁰ Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Bioinformatics Center, Furong Laboratory, Central South University, Changsha, Hunan, China. Electronic address: lijinchen@csu.edu.cn.

Abstract

Background: Genomic variants outside of the canonical splicing site (±2) may generate abnormal mRNA splicing, which are defined as non-canonical splicing variants (NCSVs). However, the clinical interpretation of NCSVs in neurodevelopmental disorders (NDDs) is largely unknown.

Methods: We investigated the contribution of NCSVs to NDDs from 345,787 de novo variants (DNVs) in 47,574 patients with NDDs. We performed functional enrichment and protein-protein interaction analysis to assess the association between genes carrying prioritised NCSVs and NDDs. Minigene was used to validate the impact of NCSVs on mRNA splicing.

Findings: We observed significantly more NCSVs (p = 0.02, odds ratio [OR] = 2.05) among patients with NDD than in controls. Both canonical splicing variants (CSVs) and NCSVs contributed to an equal proportion of patients with NDD (0.76% vs. 0.82%). The candidate genes carrying NCSVs were associated with glutamatergic synapse and chromatin remodelling. Minigene successfully validated 59 of 79 (74.68%) NCSVs that led to abnormal splicing in 40 candidate genes, and 9 of the genes (ARID1B, KAT6B, TCF4, SMARCA2, SHANK3, PDHA1, WDR45, SCN2A, SYNGAP1) harboured recurrent NCSVs with the same variant present in more than two unrelated patients with NDD. Moreover, 36 of 59 (61.02%) NCSVs are novel clinically relevant variants, including 34 unreported and 2 clinically conflicting interpretations or of uncertain significance NCSVs in the ClinVar database.

Interpretation: This study highlights the common pathology and clinical importance of NCSVs in unsolved patients with NDD.

Funding: The present study was funded by grants from the National Natural Science Foundation of China, China Postdoctoral Science Foundation, the Hunan Youth Science and Technology Innovation Talent Project, the Provincial Natural Science Foundation of Hunan, The Scientific Research Program of FuRong laboratory, and the Natural Science Project of the University of Anhui Province.

Keywords: De novo variants; Minigene; Neurodevelopmental disorders; Non-canonical splicing.

MeSH terms

Adolescent
Carrier Proteins / genetics
Exons
Histone Acetyltransferases / genetics
Humans
Mutation
Neurodevelopmental Disorders* / genetics
RNA Splicing / genetics
RNA, Messenger

Substances

RNA, Messenger
KAT6B protein, human
Histone Acetyltransferases
WDR45 protein, human
Carrier Proteins