Achromatopsia caused by novel missense mutations in the CNGA3 gene

Structure-function analysis of CNGA3-associated achromatopsia patient variants complements clinical genomics in pathogenicity determination

BACKGROUND

Achromatopsia is an autosomal recessive genetic disease, and 95% of achromatopsia patients carry pathogenic mutations in the CNGA3 and CNGB3 genes. Once translated, these genes function together by forming a cone photoreceptor CNG channel protein complex.

RESULTS

There are 150 CNGA3 missense variants reported in achromatopsia patients, but the pathogenicity of 103 variants remains unknown due to inconclusive genetic information. Here, we present clinical features of a novel CNGA3 variant in an achromatopsia patient and demonstrate its pathogenicity by a three-dimensional (3D) proteoform-based structure-function analysis. We first identified six proteotypic groups using 47 pathogenic missense variants with distinctive functional consequences by mapping their spatial proximity in a 3D protein structure. This meta-analysis was further applied to 103 missense variants of unknown significance (VUS) found in patients with achromatopsia. Strikingly, 86.4% of VUS had similar/identical functional consequence to nearby pathogenic variants, which suggested their likely pathogenicity and potential molecular pathology. The distinct proteotypic consequence of CNGA3 mutants shown in our analysis strongly supported the notion that gene supplementation may be the most widely applicable therapeutic option for CNGA3-associated achromatopsia patients.

CONCLUSION

Thus, proteoform-based analysis can be a valuable approach for assessing novel variants and complement clinical genomics in its utilization.

Case Report: Novel CNGA3 compound heterozygous variants cause achromatopsia in three patients from a family

This study report a novel missense variant in the cyclic nucleotide-gated channel 3 (CNGA3) gene identified by targeted gene panel sequencing approach in a Chinese family with achromatopsia. The proband, a 24-year-old female, with normal intelligence, motor development and speech abilities exhibited nystagmus, amblyopia, photophobia, and indistinguishable colors. In addition, the two sisters of the proband had the same clinical symptoms, which means that three patients from a family with a monochromasia clinical diagnosis. Based on the family situation, the proband came to our hospital for facilitate genetic counseling. Genetic analysis using targeted gene panel sequencing was conducted to confirm causative variants. Compound heterozygous variants, including the novel missense c.524T>A (p.Ile175Asn) and the know missense variant c.829C>T (p.Arg277Cys), were identified in CNGA3. These variants represent the genetic defects associated with achromatopsia in this family.

CNGB3 Missense Variant Causes Recessive Achromatopsia in Original Braunvieh Cattle

Sporadic occurrence of inherited eye disorders has been reported in cattle but so far pathogenic variants were found only for rare forms of cataract but not for retinopathies. The aim of this study was to characterize the phenotype and the genetic aetiology of a recessive form of congenital day-blindness observed in several cases of purebred Original Braunvieh cattle. Electroretinography in an affected calf revealed absent cone-mediated function, whereas the rods continue to function normally. Brain areas involved in vision were morphologically normal. When targeting cones by immunofluorescence, a decrease in cone number and an accumulation of beta subunits of cone cyclic-nucleotide gated channel (CNGB3) in the outer plexiform layer of affected animals was obvious. Achromatopsia is a monogenic Mendelian disease characterized by the loss of cone photoreceptor function resulting in day-blindness, total color-blindness, and decreased central visual acuity. After SNP genotyping and subsequent homozygosity mapping with twelve affected cattle, we performed whole-genome sequencing and variant calling of three cases. We identified a single missense variant in the bovine CNGB3 gene situated in a ~2.5 Mb homozygous genome region on chromosome 14 shared between all cases. All affected cattle were homozygous carriers of the p.Asp251Asn mutation that was predicted to be deleterious, affecting an evolutionary conserved residue. In conclusion, we have evidence for the occurrence of a breed-specific novel CNGB3-related form of recessively inherited achromatopsia in Original Braunvieh cattle which we have designated OH1 showing an allele frequency of the deleterious allele of ~8%. The identification of carriers will enable selection against this inherited disorder. The studied cattle might serve as an animal model to further elucidate the function of CNGB3 in mammals.

Genotypes and phenotypes of genes associated with achromatopsia: A reference for clinical genetic testing

PURPOSE

Achromatopsia is a congenital autosomal recessive cone disorder, and it has been found to be associated with six genes. However, pathogenic variants in these six genes have been identified in patients with various retinal dystrophies with the exception of achromatopsia. Thus, this study aims to investigate the contribution of these genes in hereditary retinal diseases and the potential genotype-phenotype correlations.

METHODS

Biallelic variants in six achromatopsia-related genes, namely, CNGA3, CNGB3, GNAT2, ATF6, PDE6C, and PDE6H, were analyzed based on data obtained from 7,195 probands with different eye conditions. A systematic genotype-phenotype analysis of these genes was performed based on these data, along with the data reported in the literature.

RESULTS

Biallelic potential pathogenic variants (PPVs) in five of the six genes were identified in 119 probands with genetic eye diseases. The variants in CNGA3 were the most common and accounted for 81.5% (97/119). Of the 119 probands, 62.2% (74/119) have cone-rod dystrophy, whereas only 25.2% (30/119) have achromatopsia. No biallelic pathogenic variants in these genes were identified in patients with rod-dominant degeneration. A systematic review of genotypes and phenotypes revealed certain characteristics of each of the six genes, providing clues for the pathogenicity evaluation of the variants of the genes.

CONCLUSIONS

PPVs in the six genes were identified in various inherited retinal degeneration diseases, most of which are cone-dominant diseases but no rod-dominant diseases based on the data from a cohort of 7,195 probands with different eye conditions. The systematic genotype-phenotype analysis of these genes will be useful in drafting guidelines for the clinical genetic diagnostic application for the investigated genes.

Abnormal expression of mRNA, microRNA alteration and aberrant DNA methylation patterns in rectal adenocarcinoma

Aim

Rectal adenocarcinoma (READ) is a malignancy cancer with the high morbidity and motility worldwide. Our study aimed to explore the potential pathogenesis of READ through integrated analysis of gene expression profiling and DNA methylation data.

Methods

The miRNA, mRNA expression profiling and corresponding DNA methylation data were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed mRNAs/ miRNAs/methylated regions (DEmRNA/DEmiRNAs) were identified in READ. The negatively correlation of DEmiRNA-DEmRNAs and DNA methylation-DEmRNAs were obtained. DEmRNAs expression was validated through quantitative real-time polymerase chain reaction (qRT-PCR) and microarray expression profiling analyses.

Results

1192 dysregulated DEmRNAs, 27 dysregulated DEmiRNAs and 6403 aberrant methylation CpG sites were screened in READ compared to normal controls. 1987 negative interaction pairs among 27 DEmiRNAs and 668 DEmRNAs were predicted. 446 genes with aberrant methylation were annotated. Eventually, 50 DEmRNAs (39 down- and 11 up-regulated DEmRNAs) with hypermethylation, synchronously negatively targeted by DEmiRNAs, were identified through the correlation analysis among 446 genes with aberrant methylation and 668 DEmRNAs. 50 DEmRNAs were significantly enriched in cAMP signaling pathway, circadian entrainment and glutamatergic synapse. The validation results of expression levels of DEmRNAs through qRT-PCR and microarray analyses were compatible with our study.

Conclusion

7 genes of SORCS1, PDZRN4, LONRF2, CNGA3, HAND2, RSPO2 and GNAO1 with hypermethylation and negatively regulation by DEmiRNAs might contribute to the tumorigenesis of READ. Our work might provide valuable foundation for the READ in mechanism elucidation, early diagnosis and therapeutic target identification.