Journal of Human Genetics最新文献

The double homeobox 4 gene (DUX4) and its centromeric paralogue, DUX4C, reside in the subtelomeric region of chromosome 4 and have been implicated in facioscapulohumeral muscular dystrophy (FSHD) and cancers. However, the high sequence similarity between these genes, together with the widespread presence of DUX4-like paralogues across the human genome, has hindered accurate genotyping and expression profiling using short-read sequencing. To elucidate the genetic architecture and potential disease-associated functions of DUX4 and DUX4C, we first identified two distinct DUX4C haplotypes with expression quantitative trait effects-DUX4C-4qα and DUX4C-4qβ. We then integrated them with known DUX4 haplotypes to generate a reference genome, D4Ref-T2T, using long-read sequencing. Haplotype analysis indicated strong linkage disequilibrium between DUX4C and DUX4 haplotypes (r² = 0.86). We further characterized full-length DUX4C mRNA isoforms and established a corresponding transcriptome reference. Applying these resources to breast tumor, FSHD, and lymphoblastoid cell line datasets revealed that DUX4 is expressed in both breast tumor and FSHD tissues, whereas DUX4C shows expression only in breast tumors. Differential gene expression and Gene Ontology enrichment analyses further suggested that DUX4C expression is associated with activation of pathways involved in leukocyte differentiation, chemotaxis, and cell migration.

Press releases on genomic research play an important role in Japan. Not only do journalists use them as major sources of news stories, but the public also accesses them directly across various media platforms. Given the unique characteristics of genomic information, including ethical implications, it is essential to report research results in a responsible and comprehensive manner. To support individuals involved in communicating such results, we developed a press release guide for genomic research in collaboration with diverse stakeholders, including members of the public. This guide outlines 12 key items for scientific research press releases, five of which are tailored to genomic research: protect personal information; avoid detrimental behavior change; consider individuals involved; avoid prejudice or discrimination; and avoid "genetic determinism." For each item, supplementary explanations and guidance are presented in the form of "Note" and "For Media." Additionally, fresh insights gained through the discussions with the diverse stakeholders are incorporated into a new section titled "From a different viewpoint." Genomic research is increasingly integrated into clinical practice and society, which indicates that reports on genomic studies directly affect a broader audience. Furthermore, enhancing the reporting quality of genomic research is critical because of the distinctive characteristics of genomic information. Our guide provides practical support for those disseminating genomic research results and will be valuable in promoting communication among stakeholders with different roles and expectations.

Sarcoidosis is a heterogenous inflammatory disease with complex genetic susceptibilities. Multi-ethnic genome-wide association studies have validated the association of sarcoidosis susceptibilities with single nucleotide variants on interleukin 23 receptor gene (IL23R), which is highly expressed in adrenal gland and testis, but not in skeletal muscle. Here we report concomitant ectopic expression of a canonical IL23R transcript and alternative polyadenylation of intron 6 of IL23R, leading to novel aberrant transcripts containing two retrotransposons, LINE1 (L1PA16) and THE1A, in the 3' untranslated region (IL23R^L1-THE1A), in sarcoid myopathy (SM) compared with non-SM disease controls. RT-qPCR confirmed the expression of both transcripts in an additional sample set, including 14 SM and 29 non-SM. We also observed expression of both transcripts in T cells by single-nucleus RNA-sequencing. These findings should serve as an additional resource for investigating the role of IL23R transcript variants in the genetic background of sarcoidosis susceptibility and other inflammatory diseases.

Non-invasive prenatal testing (NIPT) is a screening method that detects fetal chromosomal trisomies from cell-free DNA in maternal blood. Because NIPT uses whole-genome sequencing with next-generation sequencing for data processing, it can also detect maternal genomic information. Although most copy number variations (CNVs) are benign, some have been reported to be associated with pathological phenotypes and are attracting increasing attention. However, most CNV studies have been conducted in Western populations, and large-scale studies in Japanese cohorts remain scarce. This study represents the first multicenter, large-scale cohort investigation of maternal CNVs in Japanese pregnant women. We analyzed 46,082 participants to establish a reliable threshold for maternal CNV detection and to evaluate their clinical significance. Maternal CNVs were validated using array comparative genomic hybridization, and receiver operating characteristic curve analysis identified 0.8 Mbp as the minimum threshold achieving 100% specificity. Applying this criterion, maternal CNVs were identified in 2907 cases (6.3%), with the most frequent being a duplication at chr8: 3,842,478-6,092,478 (hg38, allele frequency 2.67%). Comparison with public genomic databases, including the Tohoku Medical Megabank Organization (ToMMo) and the Genome Aggregation Database (gnomAD), confirmed that all CNVs detected in this study had been previously reported, with particularly high concordance in ToMMo. Notably, several very rare CNVs were also identified. These findings demonstrate that NIPT can reliably detect maternal CNVs ≥0.8 Mbp, which appear to represent benign genomic variants that are unlikely to affect fertility or early miscarriage.

Spinocerebellar ataxia type 41 (SCA41) is a rare autosomal dominant cerebellar ataxia caused by mutations in the transient receptor potential canonical 3 (TRPC3) gene. We report a case of a patient with SCA41 whose clinical manifestations were initially suspected to be multiple system atrophy cerebellar-type (MSA-C). Whole-exome sequencing (WES) revealed a c.1955A>G (p.K652R) mutation in the TRPC3 gene of this patient. After treatment with transcranial magnetic stimulation and rehabilitation training, the patient reported a slight improvement in unsteady gait compared with before. This is the first report of SCA41 caused by the c.1955A>G variant in the TRPC3 gene, which expands the mutation spectrum of the TRPC3 gene. Clinicians should have sufficient awareness of SCA41, as SCA and MSA-C share overlapping clinical phenotypes and imaging features, which may easily lead to misdiagnosis, and genetic testing plays a crucial role in differentiating between the two disorders.

Recent studies have revealed de novo or germline-derived GNAS-Gsα variants with constitutive ligand-independent gain-of-function (GOF) effects on specific G-protein-coupled receptor signalings in patients with nephrogenic syndrome of inappropriate antidiuresis (NSIAD), osteolytic bone disorder with metaphyseal dysplasia, and peripheral precocious puberty. We encountered a Japanese girl with NSIAD and osteolytic bone disorder with metaphyseal dysplasia. Whole genome sequencing identified a de novo ″likely pathogenic″ heterozygous GNAS-Gsα missense variant (NM_000516.7:c.163 A > G:p.(Thr55Ala)) which occurred on the paternally inherited allele. Luciferase assays for p.Thr55Ala showed ligand-independent GOF effects on AVPR2 and PTH1R signalings, and a ligand-dependent loss-of-function (LOF) effect on PTH1R signaling. Protein structural analysis for p.Thr55Ala indicated disruption of the hydrogen bond between p.Thr55 side chain and the α-phosphate group of the bound nucleotide in both GDP-bound inactive form and GTP-bound active form and resultantly reduced affinity of the variant-positive Gsα protein for both GDP and GTP, consistent with the ligand-independent GOF and ligand-dependent LOF effects. The results, in conjunction with the previous findings, indicate that GNAS-Gsα variants with constitutive GOF effects cause clinically distinctive congenital rare disorders including NSIAD and characteristic bone disorder.

The importance of 5'-untranslated region (5'-UTR) variants in genetic diseases has become increasingly recognized. However, systematic frameworks for interpreting their pathogenic mechanisms remain underdeveloped. We performed genome sequencing (GS) or reanalyzed exome sequencing (ES) data from patients with neurodevelopmental disorders in whom no pathogenic variants had previously been identified, and searched for variants affecting upstream open reading frames (uORFs) in the 5'-UTR using UTRannotator, a tool for annotating 5'-UTR variants. We identified one patient with a maternally inherited single nucleotide duplication upstream of ATRX (c.-138dup), which is predicted to result in the formation of an out-of-frame uORF overlapping the coding sequence (CDS). The patient exhibited the core features of ATRX-related disorders. RNA sequencing of urine-derived cells (UDCs) revealed reduced ATRX expression in the patient. Luciferase reporter assays demonstrated that wild-type and mutant ATRX 5'-UTR sequences conferred significantly increased and decreased luciferase activity compared with the parental pGL3-promoter vector, respectively, suggesting that the c.-138dup variant may disrupt an enhancer-like regulatory element and impair translation. We also identified another patient with a de novo single nucleotide variant upstream of POU3F3 (c.-303C>A), which introduces a novel uORF overlapping the CDS in-frame. This patient showed phenotypes consistent with POU3F3-related disorder. Although immunoblotting using UDCs revealed no elongated POU3F3 proteins, the luciferase assay showed reduced activity with mutant 5'-UTR compared to the wild-type. Our study demonstrates that integrating GS or ES with UTRannotator is useful for identifying candidate 5'-UTR variants; however, the potential impact of predicted non-coding variants still requires careful experimental evaluation.

Lipocalin-2 (LCN2) level, leukocyte count (LC), and renal function are key biomarkers linked to inflammation and metabolism. We aimed to explore the genetic determinants, causal associations, and long-term outcome effects of LCN2 levels. Phenotypic associations, genome-wide association studies (GWASs), linkage disequilibrium score regression (LDSC), and Mendelian randomization (MR) analyses for genetic correlation and causal associations between LCN2, LC, and estimated glomerular filtration rate (eGFR) were performed in 8208, 117,666, and 117,666 Taiwan Biobank participants, respectively. Long-term outcome analyses were performed for LCN2 in 481 patients with coronary artery disease (CAD). Elevated LCN2 levels were associated with older age, male sex, and altered metabolic parameters. GWAS of LCN2 levels identified genome-wide significant loci on LCN2, GSDMA, and MYB. LDSC revealed a limited number of shared loci between LCN2 level, LC and eGFR rather than broad polygenic overlap. MR analyses showed weighted genetic risk scores for LC and eGFR were significantly associated with LCN2 levels, which remain significant even at multivariate analysis (p = 0.0123 and p = 0.0010, respectively). Sensitivity analyses confirmed the robustness of causal estimates. Kaplan-Meier survival and Cox regression analyses further indicated that elevated LCN2 level, especially when combined with C-reactive protein levels, is an independent predictor of all-cause mortality and combined cerebral and cardiovascular event rates in CAD patients. Taken together, these results indicate that circulating LCN2 is largely a downstream marker of immune activation and impaired renal function. Elevated LCN2 levels independently predict poor long-term outcomes of CAD.

The accurate removal of intronic sequences from pre-mRNA by the spliceosome is essential for correct gene expression, with small nuclear RNAs (snRNAs) such as U4 playing structural and regulatory roles in catalyzing this. De novo variants in the highly constrained critical region including the T-loop region of RNU4-2 have been linked to ReNU syndrome, a neurodevelopmental disorder, but the broader mutational spectrum remains uncharacterized. Here, we show that, in a cohort of unresolved cases with neurodevelopmental disorder, monoallelic and biallelic RNU4-2 variants were identified in 16 affected individuals, expanding the genetic basis beyond the critical region: 12 with de novo T-loop variants and 4 from two families with compound heterozygous variants in non-critical regions (stem II, the k-turn, and the Sm-binding site). Previously reported functional mapping by saturation genome editing confirmed that most of the variant positions in this study are highly functionally constrained. Clinically, individuals with biallelic variants exhibited developmental delay and intellectual disability that were similar to but milder than those with monoallelic variants, notably lacking extracerebral organ involvement. These results suggest that pathogenic RNU4-2 variants act in both dominant and recessive manners, and that non-critical regions may also harbor disease-causing variants. More broadly, this study underscores the diagnostic importance of non-coding RNA genes in neurodevelopmental disorders and demonstrates the need to distinguish pathogenic variants from benign ones, together with their inheritance patterns.