Human Mutation最新文献

Accurate identification of the genetic determinants of rare diseases is essential for effective recurrence-risk management and informed reproductive decision-making. Although whole-exome sequencing (WES) and whole-genome sequencing (WGS) have significantly improved diagnostic capabilities, a subset of affected families still receives no definitive molecular diagnosis. RNA sequencing (RNA-seq) has emerged as a promising complementary diagnostic tool, yet its clinical implementation in the context of preconception genetic counseling remains underexplored. We used phytohemagglutinin-activated peripheral blood cells (PHACs) as a robust RNA source and enhanced conventional RNA-seq through the integration of three analytical innovations: (1) transcript isoform distribution (TID) analysis, (2) realignment against the MANE (Matched Annotation from NCBI and EMBL-EBI) reference transcriptome, and (3) pharmacological induction–based cryptic splicing detection. This optimized pipeline was applied to 55 rare-disease families with negative WES/WGS results who were undergoing preconception genetic counseling. Based on prior evaluations, families were grouped as VUS (n = 7), suspected-gene/variant-negative (n = 10), and unsolved/no-candidate (n = 38). PHACs showed reduced interindividual variability and higher RNA integrity than fresh PBMCs (median RIN: 9.77 vs. 8.97; p < 0.0001). The optimized workflow improved diagnostic yield by 2.2-fold (20% vs. 9%). Stratified analysis revealed positive rates of 71% (VUS), 40% (suspected-gene/variant-negative), and 5.2% (unsolved/no-candidate). Among the 11 positive cases, 10 received definitive diagnoses, leading to diverse reproductive decisions. This enhanced RNA-seq workflow provides a clinically applicable and scalable strategy for improving molecular diagnostics in reproductive and preconception settings, offering a valuable model for future clinical transcriptomics.

The extensive use of next-generation sequencing (NGS) multi-gene panels and advanced analysis algorithms have led to the identification of numerous genetic variants associated with breast, ovarian, and pancreatic cancer. Copynumber variations (CNVs), defined as deletions and duplications of specific DNA regions, account for up to 10% of pathogenic variants and can affect any of the cancer-predisposing genes. Despite this, CNVs’ contribution beyond BRCA1 and BRCA2 remains underexplored. This observational study analyzed data from 2949 patients, primarily affected by breast or ovarian cancer, who underwent NGS testing with a 22-gene hereditary cancer panel between 2018 and 2023, with a focus on CNV results. In line with comparison studies, a total diagnostic yield of 14.8% was observed with pathogenic variants in BRCA1, BRCA2, CHEK2, ATM, and PALB2 accounting for most of positive findings. In contrast, CNVs were found in 1.4% of patients, displaying a peculiar distribution pattern. PALB2 exhibited the highest frequency of pathogenic CNVs (66.7%), representing 62.2% of all PALB2 pathogenic variants. Notably, 24 out of 28 PALB2 CNV carriers shared the deletion of Exon 11. Further investigations revealed identical breakpoints and common geographical origins, and moreover, the same haplotype for some of the families suggests a relatively recent founder effect. Simultaneous sequence and copy number analyses resulted in likely higher positive predictive value of the test and, more interestingly, disclosed an unforeseen single contribution of CNVs in PALB2 gene, confirming geography as a key factor in shaping human genetic variations.

Information on the health-related consequences of rare chromosome disorders is often limited, posing challenges for both patients and their families. The Chromosome 6 Project aims to bridge this knowledge gap for structural aberrations involving chromosome 6 by providing parents of affected children with information on the expected phenotypes of their child. To achieve this, detailed phenotype and genotype data are collected directly from parents worldwide and supplemented with data from literature reports, resulting thus far in a dataset of over 500 individuals. This comprehensive data pool was used to develop Del2Phen, a software tool introduced in this paper that generates aberration-specific phenotype information for chromosome disorders. Del2Phen identifies individuals with a deletion or duplication similar to that of a new patient (index) and produces a clinical description for the index based on phenotypic features observed in these genotypically similar individuals. Genotypic similarity is determined using existing knowledge on the haploinsufficiency effect of genes and established gene–phenotype relationships. The optimal genotypic similarity parameters for chromosome 6 deletions were evaluated, which led to thorough and reliable clinical descriptions based on sufficiently large groups of individuals with highly similar deletions. Although currently optimised for chromosome 6 deletions, Del2Phen can also be applied to deletions involving other chromosomes and is easily adapted for use on duplications, given sufficient data are available. Del2Phen can already be used to expedite data analysis for chromosome disorders, thus aiding healthcare professionals in delivering appropriate clinical care. Lastly, this tool will be integrated into an interactive website designed for parents of children with a chromosome 6 aberration, providing essential health information in a timely and accessible manner.

Distal arthrogryposis (DA) is a group of nonprogressive congenital muscular disorders affecting distal limb joints, without concurrent neuromuscular disease. Ten different types of DAs are known, with many different genes involved. Dominant variants in TNNT3 (MIM ∗600692) cause DA type 2B2 (MIM #618435), a severe condition featuring dysmorphism, distal contractures, and deformities of hands and feet. TNNT3 encodes the fast skeletal troponin T, an essential component of the troponin complex that is necessary for calcium-coupled contraction initiation in the striated muscle. Recently, homozygous splicing variants in TNNT3 have been reported in two subjects with a distinctive congenital myopathy, only partially overlapping DA2B2. However, no functional evidence was provided. In this study, we investigated two patients presenting with myopathic conditions at different ends of the TNNT3 spectrum. One subject showed DA, whereas the second displayed a severe congenital myopathy featuring hypotonia, DA, and dysmorphism. Through exome sequencing, we identified the de novo missense change p.(Arg63His) in Subject #1 and biallelic TNNT3 variants in Subject #2, featuring a splicing and a stop gain variant. The p.(Arg63His) was predicted to affect the stability of troponin T3 in silico, and we confirmed this by western blot. Then, employing different biochemical approaches, we showed that the truncated variants identified in #2 (p.[Tyr13∗] and c.480+5G>A) lead to loss of the full-length protein. Our findings refine and expand the TNNT3 genotype–phenotype spectrum, suggesting that recessive TNNT3-related congenital myopathy should be considered a discrete entity caused by biallelic loss-of-function variants.

PHF20 encodes plant homeodomain finger protein 20 (PHF20), a component of the KAT8-containing nonspecific lethal (NSL) complex that deposits acetylation on histone H4 to activate gene expression. We report two unrelated individuals with developmental delay, microcephaly, and distinctive facial features, in whom exome sequencing and chromosomal microarray analysis revealed a homozygous deletion of PHF20 that segregated with the disease phenotype in their families. Breakpoint junction sequencing revealed an Alu–Alu-mediated deletion event. Western blot in cells from an affected individual showed undetectable PHF20, while levels of other NSL complex subunits were unaltered. Transcriptomic and epigenomic analysis revealed significant downregulation of gene pathways related to cell projection and neuronal development, associated with reduced histone H4K16 acetylation at these genes. In conclusion, our data suggest that homozygous deletion of PHF20 leads to a neurodevelopmental syndrome, potentially through targeted epigenetic dysregulation and altered gene expression essential for neuronal development. Identifying additional families with biallelic PHF20 variants will further delineate the phenotypic spectrum, and molecular studies in neuronal cell lines will be essential for understanding the disease mechanism.

Bladder cancer represents one of the most common malignancies globally, posing a severe threat to human health. Through compound library screening, we identified tetramethylcurcumin (FLLL31), a diketone analog of curcumin, as exhibiting significant inhibitory effects on the malignant biological behaviors of bladder cancer cells. Although possessing diverse biological activities, the application of FLLL31 in bladder cancer has not been reported previously. To investigate the function and mechanism of FLLL31, we assessed its impact on the proliferation, migration, and invasion of T24 and 5637 cells using CCK-8, EdU, colony formation, and Transwell. The in vivo efficacy of FLLL31 was evaluated by intraperitoneal injection in BALB/c-nu mice bearing subcutaneous xenografts. Utilizing RNA-seq, qRT-PCR, Western blotting, electron microscopy, flow cytometry, and JC-1 staining, we further explored the mechanism underlying FLLL31′s inhibition of malignant behaviors in bladder cancer cells. The results demonstrate that FLLL31 inhibits malignant bladder cancer behaviors by inducing apoptosis via the FOXO4/BCL6 axis. This pathway was further confirmed by the observation that lentiviral knockdown of either FOXO4 or BCL6 attenuated FLLL31-induced apoptosis. Mechanistically, FLLL31 upregulates FOXO4, leading to increased BCL6 expression. This subsequently suppresses the antiapoptotic protein Bcl-xL, thereby triggering apoptosis. These findings highlight the therapeutic potential of FLLL31 for bladder cancer and identify the FOXO4/BCL6 pathway as a promising novel target.

V. K. Jordan, B. Fregeau, X. Ge, et al., “Genotype–phenotype correlations in individuals with pathogenic RERE variants,” Human Mutation 2018, no. 39, 666–675, https://doi.org/10.1002/humu.23400.

In the article titled “Genotype–phenotype correlations in individuals with pathogenic RERE variants,” Table 1 contained an error in Row S3. The corrected data are now reflected in the revised Table 1 as follows.

We apologize for this error.

Cancer stem cells (CSCs) are a unique category of cells located within tumors, characterized by their exceptional self-renewal abilities and capacity to differentiate into different types of tumor cells. These cells are crucial in processes such as tumor metastasis, recurrence, and resistance to treatment. Nevertheless, their particular roles in bladder urothelial carcinoma (BLCA) require deeper exploration. This investigation firstly assessed the relationships between genes associated with CSCs and both the prognostic outcomes and responses to immunotherapy in patients with BLCA using cluster analysis methods. Among the genes linked to stem cells, CALR was identified as the most notable prognostic marker by the XGBoost algorithm. Additionally, the study explored the correlation between CALR and immune cell infiltration, as well as its interaction with mitomycin using molecular docking methods. In vitro experiments further validated that CALR affects BLCA stem cells. Utilizing multiple machine learning approaches, this study identified 14 essential stem cell–associated genes, underscoring their significance for BLCA diagnosis and potential therapeutic targeting. Critically, CALR demonstrates a strong correlation with prognostic outcomes and immunotherapy responses in BLCA, consistent with experimental findings indicating its elevated expression in BLCA and association with poor prognosis. Laboratory investigations have demonstrated that reducing CALR expression can lessen the stemness features of BLCA. Our results highlight the critical role of genes related to stem cells in BLCA and identify CALR as a promising target associated with stem cell functionality.