HGG Advances最新文献

RNA polymerase III (RNA Pol III)-related disorders (POLR3-RDs) are a group of clinical entities characterized by causal variants in genes encoding RNA Pol III subunits, including POLR3A, POLR3B, POLR1C, POLR1D, POLR3D, POLR3E, POLR3F, POLR3GL, POLR3H, and POLR3K. These typically cause developmental phenotypes affecting the central nervous system; the eyes; connective tissues including bones, teeth, and endocrine axes; and the reproductive system. Similar phenotypes can be caused by variants in separate subunit genes (multigenic). In contrast, variants in the same gene can cause different phenotypes (pleiotropy), making genotype-phenotype correlation challenging. POLR3-RDs, though individually rare, have never been analyzed collectively. To bridge this gap, we developed an extensive database encompassing all published and unpublished cases of POLR3-RDs and conducted the first comprehensive genotype-phenotype correlation study across their entire spectrum. This work contributed new cases, representing 13% of all documented cases in the literature, along with 31 novel variants, accounting for 8% of all identified variants. This database was constructed by systematically reviewing the literature and integrating data from patients under the care of our international network of collaborators. The dataset includes genotype curation, bioinformatics, prior publications, and individual patient outcome information. By leveraging these comprehensive data, we were able to establish clear genotype-phenotype correlations for some pathogenic variants, which will help provide optimal clinical care and genetic counseling (including insights into disease phenotypes and progression) and offer valuable guidance for future clinical trial design and patient stratification.

Protein profiling and genetic findings can be integrated to define the genetic architecture of the circulating proteome in chronic diseases. Most self-identified African American (AA) individuals have both African and European genetic ancestry. Admixture mapping can detect genomic association regions in which causal variants exist with substantial differences in allele frequency or effect sizes between genetic ancestries. We performed admixture mapping of the circulating proteome in 1,989 participants from the Jackson Heart Study (JHS), investigating the relation of local African ancestry within genomic regions with levels of circulating proteins. We conditioned protein-local ancestry association models on variants previously found to be associated with those proteins in genome-wide association studies (GWASs). We replicated findings in 196 AA participants from the Multi-Ethnic Study of Atherosclerosis (MESA). 62 proteins were associated with local African ancestry. 21 of 62 remained statistically significant after conditioning on protein-associated variants observed in previous GWASs. 48 of 54 available protein-local ancestry associations were replicated in the MESA. Proteins associated with local African ancestry included chemokines, factors associated with vascular biology and inflammation, and other biologically interesting proteins. Admixture associations unexplained by previously reported protein-associated variants in conditional analysis suggest the existence of causal variants missed by standard GWAS techniques.

Congenital mirror movements (CMMs) are involuntary movements of one side of the body that mirror intentional movements of the opposite side. DCC, NTN1, RAD51, ARHGEF7, and DNAL4 have been associated with CMMs. Two-thirds of CMM-affected individuals remain without a genetic diagnosis, indicating that variants in additional genes need to be discovered. We report on a 27-year-old female with CMMs of the hands. Trio exome sequencing in the proband and healthy parents did not reveal a likely pathogenic variant in one of the CMM-associated genes but rather a de novo heterozygous frameshift variant c.523dup (p.Ser175Lysfs∗8) in the candidate RBM15. The variant results in only partial nonsense-mediated mRNA decay of RBM15 transcripts in the proband's lymphoblastoid cells. RBM15 encodes an RNA-binding protein involved in alternative splicing as well as other processes. Dcc alternative splicing generates Dcc_long and Dcc_short isoforms, which are important for commissural axon midline crossing. We tested whether Rbm15 regulates Dcc alternative splicing by using an in vitro minigene assay. Ectopic expression of Rbm15, similar to the splicing factors Nova1 and Nova2, promotes the production of Dcc_long transcripts. The possible link between Rbm15 and Dcc supports a role for Rbm15 in CMMs.

The hexanucleotide (G₄C₂) repeat expansion in the promoter region of C9orf72 is the most frequent genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). In this study, we conducted a genome-wide DNA methylation (DNAm) analysis using EPIC version 2 (EPICv2) arrays on an FTD cohort comprising 27 carriers and 250 non-carriers of the pathogenic C9orf72 repeat expansion from the Amsterdam Dementia Cohort. We identified differentially methylated CpGs probes associated with the pathogenic C9orf72 expansion and used these findings to create a DNAm least absolute shrinkage and selection operator (LASSO) predictor to identify repeat expansion carriers. Eight CpG sites at the C9orf72 locus were significantly differentially hypermethylated in repeat expansion carriers compared to non-carriers. The LASSO model predicted repeat expansion status with an average accuracy of 98.6%. The LASSO predictor was further validated in a separate, independent validation cohort containing 1,589 subjects with bipolar disorder, 580 first-degree relatives, and 289 independent control subjects with available EPICv2 data, identifying four C9orf72 repeat expansion carriers, subsequently confirmed by repeat-primed PCR. This result highlights the accuracy and generalizability of the DNAm predictor of C9orf72 repeat expansion carriers. The identification of a highly accurate DNAm biomarker for a repeat expansion locus associated with neurodegenerative disorders may provide great value for studying this locus. The approach holds significant promise for investigating this and other repeat expansion loci, particularly given the growing interest in epigenetic epidemiological studies involving large cohorts with available DNAm data.

Branched-chain amino acid transaminase-1 (BCAT1) initiates the catabolism of branched-chain amino acids (BCAAs), which are essential for neurologic function. However, the role of BCAT1 in neurodevelopment is largely unknown. Here, we identify compound heterozygous BCAT1 variants in a patient with a severe progressive neurodevelopmental syndrome. To investigate the functional consequences, we established patient variant (BCAT1: c.792T>A p.Phe264Leu; c.1042G>A p.Glu348Lys) and BCAT1 knockout hiPSC models. Both disease models show profound defects in cortical neuron differentiation and neurite outgrowth. Furthermore, metabolic analysis revealed evidence of mitochondrial dysfunction associated with increased levels of tricarboxylic acid (TCA) cycle intermediates, glutamate, and glutamine. This increase is linked to altered oxygen consumption rates, superoxide production, and upregulation of UCP2 in BCAT1 disease neurons, suggesting a downstream impact on electron transport chain homeostasis. These findings establish a regulatory role for BCAT1 in mitochondrial function and further define a role for genomic variants in BCAT1 in neurometabolic disorders.

The Navajo Nation is reevaluating a moratorium on genetic research that was authorized in 2002. While the moratorium was instituted due to cultural concerns and the lack of a Navajo genetic research policy, there remains limited empirical work assessing the perspectives of Diné (Navajo) people and other interest holders regarding genetic research. To address this gap, this study examines the perspectives of research project leaders with protocols approved by the Navajo Nation Human Research Review Board (NNHRRB) as this group is aware of research expectations and cultural considerations. An online survey was designed to gauge researchers' interest in adding a genetic component to their research if the moratorium were lifted, while also examining potential benefits, risks, and ethical considerations. Survey participants (n = 36) included 27% Diné researchers and 73% non-Diné researchers, and 50% of researchers (n = 18) had collected human biospecimens in their research (e.g., blood, tissue). Our results indicate that, if the moratorium on genetic research ended, 42% of researchers (n = 15) would be unsure about adding a genetic component to their projects, while 31% (n = 11) of researchers were interested. Participants were asked to rank ethical considerations related to five broad topics: community engagement; dissemination of results and data; privacy and rights; health, safety, and equity; and discrimination and mistrust. Participants ranked "ensure that no research participants are harmed" and "give presentations to the community" as very important, whereas "sharing data with other researchers" was of low importance. We provide valuable perspectives to guide potential genetic policy development for the Navajo Nation.

Treacher Collins syndrome (TCS) is a craniofacial genetic disorder caused by loss-of-function variants in TCOF1, POLR1B, POLR1C, or POLR1D. Here, we describe two previously undiagnosed paternal half-siblings affected with clinical TCS, and their apparently unaffected father. Diagnostic short-read RNA sequencing) identified aberrant expression of TCOF1 and optical genome mapping detected a large genomic insertion therein. Long-read genome sequencing (lrGS) resolved a deep intronic 3.5 kb SINE-VNTR-Alu (SVA) retrotransposon insertion in intron 17 of TCOF1. Long-read RNA sequencing (lrRNA-seq) demonstrated that the insertion was partially exonized inducing isoform switch to the shorter non-canonical TCOF1 isoform c. SVA insertion was confirmed in both half-siblings, and we detected mosaicism in the father. This work demonstrates the potential of lrRNA-seq and lrGS, to identify pathogenic variants in unexplained genetic disorders.

DNA variants affecting pre-mRNA splicing are an important cause of genetic disorders and remain challenging to interpret without experimental data. Although variant classification guidelines recommend experimental characterization of variant splicing effects, the added value of routine diagnostic investigation of patient mRNA splicing has not been systematically described. Here, we assessed the utility of pre-mRNA splicing analysis in a diagnostic setting for 202 suspected splice-altering variants from individuals referred for genetic testing. Pre-mRNA splicing was assessed in patient cells by RT-PCR, followed by agarose gel electrophoresis and Sanger sequencing and/or exon trapping assays. An effect on pre-mRNA splicing was demonstrated in 63% (n = 128/202) of the tested variants. Among the 177 variants initially classified as variants of uncertain significance (VUS), 54% (n = 96/177) were reclassified based on pre-mRNA splicing analysis, including 48% (n = 85/177) that were upgraded to likely pathogenic or pathogenic. We benchmarked the splice prediction algorithms SpliceAI, SQUIRLS, SPiP, and Pangolin, the tools integrated in Alamut on this clinically relevant and experimentally validated dataset, and the CAGI6 splicing VUS dataset and found variable performance dependent on variant type and location. No single tool classified all variants equally well. We describe several examples of hard-to-predict effects and unexpected results highlighting the limitations of prediction tools, including a not previously described variant type affecting U12-splice site subtype. In summary, we provide a framework for RNA-based analysis in a molecular diagnostic setting, demonstrate the added value of routine testing of RNA from individuals with suspected splice-altering variants, and highlight the limitations of in silico prediction tools.

Eye diseases, including cataracts, glaucoma, diabetes retinopathy, and age-related macular degeneration, are major global health challenges and leading causes of blindness. This study leveraged genome-wide association studies (GWASs) involving over 100,000 individuals, integrating data from the Taiwan Biobank and National Health Insurance Research Database, to identify genetic loci associated with disease onset. Our findings suggest that these conditions are influenced by multifactorial etiologies, as pleiotropic loci including rs10811660, rs4710941, rs2283228, and rs7646518 were identified, linking ocular diseases to metabolic conditions. Notably, a strong genetic correlation was observed between cataract and depression. Mendelian randomization analysis further demonstrated a causal effect of depression on cataract risk, implicating shared biological pathways, particularly oxytocin signaling, in disease pathophysiology. This finding revealed a functional genetic variant near the OXTR gene, highlighting its potential as a causal candidate for genetic diagnosis in precision health. By bridging the gap between genetic discovery and clinical application, this research offers critical insights into shared genetic mechanisms across diverse health domains, paving the way for innovative diagnostic and therapeutic strategies.