Identification of ultra-rare disruptive variants in voltage-gated calcium channel-encoding genes in Japanese samples of schizophrenia and autism spectrum disorder

Chenyao Wang,Takeo Yoshikawa,Branko Aleksić ,Sayaka Takemoto-Kimura,Takeshi Kawabata,Takashi Yoshida,Takashi Okada,Minoru Wakamori,H Fujii ,Yoshimi Iwayama,Shin-Ichiro Horigane,Haruhiko Bito,Yukako Nakamura,Shuhei Ueda,Daisuke Mori,Hiroki Kimura,Masashi Ikeda,Itaru Kushima,Nakao Iwata,Kanako Ishizuka,Norio Ozaki

doi:10.1038/s41398-022-01851-y

Abstract

Several large-scale whole-exome sequencing studies in patients with schizophrenia (SCZ) and autism spectrum disorder (ASD) have identified rare variants with modest or strong effect size as genetic risk factors. Dysregulation of cellular calcium homeostasis might be involved in SCZ/ASD pathogenesis, and genes encoding L-type voltage-gated calcium channel (VGCC) subunits Cav1.1 (CACNA1S), Cav1.2 (CACNA1C), Cav1.3 (CACNA1D), and T-type VGCC subunit Cav3.3 (CACNA1I) recently were identified as risk loci for psychiatric disorders. We performed a screening study, using the Ion Torrent Personal Genome Machine (PGM), of exon regions of these four candidate genes (CACNA1C, CACNA1D, CACNA1S, CACNA1I) in 370 Japanese patients with SCZ and 192 with ASD. Variant filtering was applied to identify biologically relevant mutations that were not registered in the dbSNP database or that have a minor allele frequency of less than 1% in East-Asian samples from databases; and are potentially disruptive, including nonsense, frameshift, canonical splicing site single nucleotide variants (SNVs), and non-synonymous SNVs predicted as damaging by five different in silico analyses. Each of these filtered mutations were confirmed by Sanger sequencing. If parental samples were available, segregation analysis was employed for measuring the inheritance pattern. Using our filter, we discovered one nonsense SNV (p.C1451* in CACNA1D), one de novo SNV (p.A36V in CACNA1C), one rare short deletion (p.E1675del in CACNA1D), and 14 NSstrict SNVs (non-synonymous SNV predicted as damaging by all of five in silico analyses). Neither p.A36V in CACNA1C nor p.C1451* in CACNA1D were found in 1871 SCZ cases, 380 ASD cases, or 1916 healthy controls in the independent sample set, suggesting that these SNVs might be ultra-rare SNVs in the Japanese population. The neuronal splicing isoform of Cav1.2 with the p.A36V mutation, discovered in the present study, showed reduced Ca2+-dependent inhibition, resulting in excessive Ca2+ entry through the mutant channel. These results suggested that this de novo SNV in CACNA1C might predispose to SCZ by affecting Ca2+ homeostasis. Thus, our analysis successfully identified several ultra-rare and potentially disruptive gene variants, lending partial support to the hypothesis that VGCC-encoding genes may contribute to the risk of SCZ/ASD.

Highlights

Schizophrenia (SCZ) is a severe, chronic, and common psychiatric disorder that is characterized by psychotic symptoms such as hallucinations and delusions; the prevalence of SCZ is estimated to be 1% [1]
voltage-gated calcium channel (VGCC) are composed of a pore-forming α1 subunit and auxiliary α2δ and β subunits⊡ The α1 subunit is encoded by CACNA1 genes, including CACNA1C and CACNA1D; both of these genes have been associated with SCZ/autism spectrum disorder (ASD), as elucidated by several previous genetic and biological studies [5, 9,10,11,12]
We successfully discovered one de novo single nucleotide variants (SNVs) (p.A36V in CACNA1C) that was present resistance was electronically compensated to 60% and both the leakage and the remaining capacitance were subtracted by -P/5 method

Summary

Introduction

Schizophrenia (SCZ) is a severe, chronic, and common psychiatric disorder that is characterized by psychotic symptoms such as hallucinations and delusions; the prevalence of SCZ is estimated to be 1% [1]. SCZ/ASD both have been implicated to have a high heritability that is estimated as 60–90% from population-based and twin studies [3, 4]. Genomic studies coupled with large-scale collaborative projects have identified hundreds of common and rare mutations that contribute to SCZ/ASD [5,6,7,8]. VGCCs are composed of a pore-forming α1 subunit and auxiliary α2δ and β subunits⊡ The α1 subunit is encoded by CACNA1 genes, including CACNA1C and CACNA1D; both of these genes have been associated with SCZ/ASD, as elucidated by several previous genetic and biological studies [5, 9,10,11,12].

Methods

Results

Conclusion