Genome-wide association studies (GWASs) have identified many sources of genetic variation associated with bone mineral density (BMD), a clinical predictor of fracture risk and osteoporosis. Aside from the identification of causal genes, other difficult challenges to informing GWAS include characterizing the roles of predicted causal genes in disease and providing additional functional context, such as the cell-type predictions or biological pathways in which causal genes operate. Leveraging single-cell transcriptomics (scRNA-seq) can assist in informing BMD GWAS by linking disease-associated variants to genes and providing a cell-type context for which these causal genes drive disease. Here, we use large-scale scRNA-seq data from bone marrow-derived stromal cells cultured under osteogenic conditions (BMSC-OBs) from Diversity Outbred (DO) mice to generate cell type-specific networks and contextualize BMD GWAS-implicated genes. Using trajectories inferred from the scRNA-seq data that map cell state transitions, we identify networks enriched with genes that exhibit the most dynamic changes in expression across trajectories. We discover 21 network driver genes, which are likely to be causal for human BMD GWAS associations that colocalize with expression/splicing quantitative trait loci (eQTLs/sQTLs). These driver genes, including Fgfrl1 and Tpx2, along with their associated networks, are predicted to be novel regulators of BMD via their roles in the differentiation of mesenchymal lineage cells. In this work, we showcase the use of single-cell transcriptomics from mouse bone-relevant cells to inform human BMD GWAS and prioritize genetic targets with potential causal roles in the development of osteoporosis.

Splice-disrupting variants are estimated to account for one-third of disease-causing variants, yet many remain underrepresented in clinical databases due to limitations in detecting splicing changes beyond canonical splice sites. Short-read RNA sequencing (RNA-seq) has proved to be a valuable complement in clinical practice to address this gap, however, the added value of long-read RNA-seq is unclear. We evaluated the potential of PacBio long-read RNA-seq to detect pathogenic splicing events in rare disorders, comparing its performance to short-read RNA-seq. Participants from the UK (n = 23) and the Netherlands (n = 2) with suspected splice-altering variants underwent long-read RNA-seq following the Kinnex full-length RNA protocol. HiFi reads from the Revio instrument were processed using the Read Segmentation and Iso-Seq workflow and then classified and filtered using Pigeon. Detection of disease genes was comparable with short reads, with fibroblast capturing more transcripts overall. Novel isoforms accounted for ~14% of detected transcripts in both tissues, increasing following cycloheximide treatment in fibroblasts and decreasing following globin depletion in blood. Transcript abundance estimates showed strong concordance between short- and long-read platforms (Pearson r = 0.86 and 0.61 in blood and fibroblasts, respectively). LRS captured 21 confirmed known events, and revealed additional transcript-level effects in eight cases. This included intron retention, multiple exon skipping, leaky splicing, variant phasing, and isoform switching. These results demonstrate that long-read RNA-seq enhances detection and interpretation of clinically relevant splicing events, supporting its integration into diagnostic workflows for rare diseases.

BackgroundChronic obstructive pulmonary disease (COPD) is characterized by persistent airflow limitation, with its pathogenesis remaining elusive. Genetic factors are recognized as crucial factors in the pathogenesis of COPD.MethodsThis study employed transcriptome-wide association studies (TWAS) and single cell transcriptome analysis to identify predisposition genes and potential mechanisms for COPD. Cross-tissue TWAS analysis was performed using the FinnGen R10 database and sCCA weights built from the GTEx v8. Single-tissue and single-cell validations were conducted using a FUSION method based on functional summaries. SMR and colocalization analysis were carried out. C57BL/6 mice and Beas-2b cells were exposed to smoke to simulate COPD inflammation and verify the function of the genes. The regulatory effect of genes was verified by overexpression of plasmid and siRNA. Eventually, single-cell transcriptomics was conducted to investigate the expression of susceptibility genes in lung tissue cells, while GeneMANIA analysis enhanced our insights into the functional significance of these genes.ResultsA total of 125 susceptibility genes associated with COPD were identified by cross-tissue TWAS analysis. Single-tissue and single-cell TWAS, along with MAGMA validation, revealed two novel susceptibility genes, DNAJA4 and IREB2. SMR and colocalization analysis further confirmed these findings. Both mouse and cell experiments can prove that the occurrence of COPD is related to two genes. Both genes exhibit specific cell type enrichment in the lung tissue of COPD patients. The GeneMANIA analysis revealed that DNAJA4 and IREB2 potentially influence COPD risk by regulating protein folding and modification and metabolic processes, respectively.ConclusionWe identified two novel susceptibility genes (DNAJA4 and IREB2) that are causally associated with COPD. These results provide a new perspective on the genetics of COPD.

ABSTRACT VariantMatcher is a web‐based platform developed to share variant‐level genomic data and phenotypic information. Here, we describe the experience of a clinical laboratory in Brazil, DASA, utilizing VariantMatcher to enhance variant classification in a clinical setting. We retrospectively analyzed 3025 molecular genetic test results to identify variants classified as variants of uncertain significance (VUS). Of 2302 reported variants, 1679 were classified as VUS. Next, we selected the 542 VUS not described in gnomAD to investigate their presence in VariantMatcher. Of these 542, 80 variants were present in VariantMatcher. Sixty‐three of them were identified in individuals with a phenotypic overlap. Further investigation of the phenotypic features of individuals with the same variants led to the reclassification of 20 (32%) of the 63 variants. Notably, most of the reclassifications helped rule out the queried variant as causative for the phenotype being investigated, particularly for autosomal or X‐linked dominant diseases with early onset and complete penetrance. Our experience supports the benefits of data sharing in the clinical setting, which can improve variant classification accuracy and provide more precise guidance for informed clinical decision‐making.

A De Novo Variant in Calponin2 Causes Intestinal Pseudo-obstruction: Evidence from Patient and Mouse Model.

Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of cortical and spinal motor neurons. Mendelian germline mutations often cause familial ALS (fALS) but only approximately 10% of sporadic ALS cases (sALS). We leveraged DNA and single-cell RNA sequencing data from autopsy tissue to explore the presence of somatic mosaic variants in sALS cases. Deep targeted panel sequencing of known ALS disease genes in motor cortex tissue revealed an enrichment of low allele frequency variants in sALS, but not in fALS with an identified monogenic cause. In silico analysis predicted increased pathogenicity of mosaic mutations in various known ALS mutational hot-spots. In particular, we identified the somatic FUS variant p.E516X, located in an established hotspot for germline ALS mutations, which leads to nucleo-cytoplasmic mislocalization and aggregation typical for ALS FUS pathology. Additionally, we performed somatic variant calling on single-cell RNA-sequencing data from sALS tissue and revealed a specific accumulation of somatic variants in excitatory neurons, reinforcing a neuron-autonomous disease initiation. Collectively, this study indicates that somatic mutations within the motor cortex, especially in excitatory neurons, may contribute to sALS development.

Cervical cancer (CC) is the most common gynecological malignancy and is strongly linked to human papillomavirus (HPV) infection. Currently, immune checkpoint blockade therapy has shown limited clinical benefits for CC, highlighting the need to find more effective therapeutic targets. LILRB4, a member of the leukocyte immunoglobulin-like receptor superfamily, is considered a key mediator of cancer immunosuppression. However, its role in the CC immune microenvironment remains unclear. Here, LILRB4 expression was upregulated in CC tissues, and high expression levels were positively associated with advanced disease and immunosuppressive genes in tumors. In an immunocompetent mouse model, LILRB4 expression in CC tumors increased with tumor growth, whereas blocking LILRB4 reduced tumor growth. Flow cytometry analysis revealed that blockade of LILRB4 reduced CD8+ T-cell exhaustion within tumors. Additionally, blockade of LILRB4 decreased the number of tumor‑infiltrating myeloid cells (TIMs), including myeloid‑derived suppressor cells (MDSCs) and M2 tumor‑associated macrophages (M2‑TAMs). Cell coculture experiments demonstrated that blockade of LILRB4 prevented CD8+ T-cell exhaustion by reducing the numbers of MDSCs and TAMs. Furthermore, HPV16 upregulated ApoE expression through transcriptional regulation, and LILRB4 mediated the suppression of CD8+ T cells by ApoE. Overall, the HPV16/ApoE/LILRB4 axis induced TIM-mediated suppression of CD8+ T cells, creating an immunosuppressive microenvironment that promoted CC progression.

Moyamoya disease (MMD) has a strong genetic basis, with the rare RNF213 variant (rs112735431) representing a major risk factor, while the broader genetic architecture and disease-relevant vascular cell types remain incompletely understood. We conducted a genome-wide association study in Japanese individuals (n=47 656; 401 MMD cases and 47 255 controls). Population-level features at MMD risk loci were examined by regional allele frequency and haplotype analyses. We performed single-nucleus RNA-seq of superficial temporal arteries from patients with MMD (n=3). Cell type-specific enrichment of genome-wide association study signals was assessed using the Single-Cell Disease Relevance Score. Endothelial signatures were validated by integration with publicly available single-cell data sets from controls (n=5) and immunohistochemistry for candidate markers (n=1). Beyond rs112735431, we identified a genome-wide significant signal in the HDAC9-TWIST1 region (P=3.3×10-14; odds ratio, 1.77). Conditional analysis on rs112735431 revealed a protective RNF213 missense variant, p.Asn1331Gly (rs8074015; P=3.7×10-9; odds ratio, 0.53), whose minor allele was mutually exclusive with rs112735431-A on haplotypes. Population analysis revealed geographic variation and extended haplotype structure of the rs112735431-A allele in Japan. Single-nucleus RNA-seq identified a mesenchymal-like endothelial cell (MEC) population with selective FN1 expression. Genome-wide association study-prioritized disease genes were strongly enriched in MECs. MECs showed mesenchymal pathway activation with a regulatory program distinct from canonical endothelial states. The proportion of MECs was markedly increased in MMD (72% versus 28% in controls), and FN1 expression in endothelial regions was confirmed by immunohistochemistry. Our findings identify a protective RNF213 variant that is mutually exclusive with the known rs112735431-A allele. Genetic risk converges on an MEC state markedly expanded in MMD.

SOX17 variants are associated with severe pulmonary arterial hypertension with and without congenital heart disease.

Cytoskeletal-related genes function as checkpoints for the maintenance of VSMC contractile phenotype and prevent pathological remodeling in arterial diseases.

Role of miR-338-3p and miR-378a-3p as regulators in Crohn's disease pathogenesis: Potential therapeutic implications in inflammatory bowel disease.

Proteases are essential enzymes that, through the breakdown of proteins, regulate many aspects of tissue homeostasis including barrier function, cellular signaling, and tissue repair mechanisms in organisms. Disease gene discovery in a number of monogenic skin diseases has deepened the knowledge of how proteases and protease inhibitors can regulate skin homeostasis, keratinocyte desmosome-mediated cell adhesion, and epidermal barrier function. This short review details the association of protease dysregulation with monogenic skin diseases, postulated disease mechanisms, and emerging therapeutic strategies.

Since the completion of the Human Genome Project, genome-based medicine has progressed from a predominantly research- driven endeavor to a field of increasing clinical relevance. In Korea, the Korea National Institute of Health (KNIH) has played a central role in the establishment of the necessary research infrastructure that supports the secure and responsible use of genomic and clinical data. These efforts have enabled the generation of comprehensive genomic datasets representative of the Korean population and, together with the Korea Biobank Array optimized for population-specific variants, have strengthened discovery-driven research and accelerated advances in disease gene identification and risk prediction. More recently, KNIH has expanded analyses based on whole-genome sequencing data to support clinical translation, enabling more comprehensive variant detection and facilitating the application of genomic information to disease diagnosis and precision medicine research. These national genomic resources provide an important foundation for improving the diagnosis and management of genetically mediated conditions, including pediatric kidney diseases, where early etiologic diagnosis can substantially influence clinical decision-making and long-term outcomes. Further strengthening of institutional and regulatory frameworks will be essential to support routine clinical implementation and maximize the public health impact of genomics in Korea.

Genomic sequencing has transformed the diagnostic approach for mitochondrial disease, yet integration into standard clinical practice is limited by access and funding. We conducted a post-implementation evaluation of genome sequencing (GS) for mitochondrial disease in Australia, which became publicly funded through the Medicare Benefits Scheme (MBS) in November 2023, to allow for broader access to testing. Test request data, including demographics, phenotypic information, and the diagnostic outcomes, were collected from November 2023 to May 2025 from the Victorian Clinical Genetics Services, the current laboratory provider of the MBS-funded service. Test uptake was 26% of predicted, with lower test rates in regional and remote areas. Over the first 19 months, 300 individuals suspected of mitochondrial disease underwent GS with a median turnaround time of 84 days (8 days-218 days). The diagnostic yield was 20%, with 56% of diagnoses in known mitochondrial disease genes. Of these, 70% (24 of 34) were in mitochondrial DNA. Seventeen diagnoses were in individuals who had prior non-diagnostic testing (exome sequencing or gene panel). We demonstrate that publicly-funded GS can deliver meaningful diagnostic outcomes for mitochondrial disease on a national scale. To maximise its impact, attention must now shift towards ensuring equitable access, particularly for regional and remote areas, and embedding sustainable mainstreaming models that support both genetic and non-genetic clinicians.

Reliably predicting the molecular impact of premature termination codons (PTCs) is essential for the clinical interpretation of "loss-of-function" variants in human disease. Measures of selective constraint can identify genes and genomic regions which are intolerant to deleterious genetic variation. However, existing loss-of-function constraint metrics do not comprehensively account for nonsense-mediated mRNA decay (NMD), a quality control pathway which critically regulates PTCs. Here, we use sequencing data from 730,947 individuals to develop an NMD-informed regional nonsense constraint metric. We find 2764 genes with significant regional nonsense constraint, including 641 known autosomal dominant disease genes. Using sequencing data in 32,260 trios from three rare disease cohorts, we find that de novo nonsense and frameshift variants are 9.5-fold enriched and associated with up to 5.9-fold higher odds of diagnosis in constrained regions versus unconstrained regions. We use these data to identify 22 candidate disease genes with clusters of de novo variants in constrained regions. These findings enhance clinical variant interpretation, deliver mechanistic insights in human disease, and empower the discovery of novel disease genes.

Hidradenitis suppurativa (HS) is an underdiagnosed chronic, immune-mediated inflammatory skin disease that causes severe pain, drainage, and scarring, leading to significant physical and psychosocial burdens. HS is characterized by heterogenous molecular changes that are poorly understood, posing a significant challenge for drug development. Therapeutic options remain limited, and many patients experience disease relapse despite treatment. Therefore, precision medicine approaches are urgently needed to identify new therapies for HS. Here, we combine integrative transcriptomics, large-scale drug perturbational datasets, and translational immunology to identify sirolimus, pioglitazone, and fulvestrant as novel therapies for HS that can directly target and reverse the HS disease gene signature in immune cell types relevant to HS pathogenesis. Using a novel ex vivo HS skin model, sirolimus, pioglitazone, and fulvestrant inhibited T cell proliferation and activation, and suppressed the production of pro-inflammatory cytokines from HS skin. These results show that unbiased data-driven precision medicine approaches can identify novel therapies for HS and can serve more generally as a model approach for therapeutic discovery in other chronic inflammatory diseases.

As the world grapples with escalating global health and environmental crises, existing Western bioethics frameworks tend to fall short in addressing the complex interdependencies between human, animal, and ecological health, as well as the diverse cultural and belief systems in many parts of the world. Eco-bio-communitarianism, a bioethics framework informed by an African indigenous worldview, provides a commonsensical, practical, and comprehensive approach that can bring about positive change in global and public health. The framework promotes the principles of planetary kinship, relational interdependence, non-anthropocentricity, eco-bio-centricity, and cosmic humility. Unlike mainstream bioethics, which is frequently driven by individual autonomy and biomedical reductionism, eco-bio-communitarianism situates health within a broader moral ecology that recognizes the interconnectedness of all life forms, including humans, non-human species, ecosystems, and cultures. This paper showcases the practical application and utility of eco-bio-communitarianism through a series of case studies addressing and examining zoonotic disease management, biotechnology governance, and gene therapy. Far from dismissing Western bioethics models, eco-bio-communitarianism invites a pluralistic and decolonial expansion of global bioethics, one that respects cultural specificities and advances ecological responsibility and relational justice, while urging public health practitioners, policymakers, and global health actors to embrace a more inclusive, relational, and culturally attuned perspective to global health and the biomedical sciences.

Biallelic variants in PRKN cause autosomal recessive Parkinson's disease (PD) with a median age at onset of 31 years. When evaluating the 16 previously published carriers of a homozygous deletion of Exon 2 from the International Parkinson's Disease and Movement Disorder Society Gene Database (MDSGene) database, the median age at onset is later (39.5 years) than in carriers of other PRKN pathogenic variants. We investigated whether these carriers show delayed disease onset compared with carriers of other pathogenic PRKN variants and explored the underlying molecular mechanism. We compared 26 homozygous PRKN Exon 2 deletion carriers with carriers of other pathogenic variants. Using human-induced pluripotent stem cell (hiPSC)-derived neuronal cell models from an unaffected 86-year-old carrier, genome-edited control lines, neuroblastoma cell lines, and in silico prediction, we investigated the underlying mechanism. Patients with PRKN Exon 2 deletions showed a later age at onset compared with carriers of other pathogenic variants. We discovered elevated levels of an N-terminally truncated Parkin proteoform lacking amino acids 1-79 due to internal translation initiation. This truncated protein partially retained ubiquitin ligase activity at endogenous levels. Treatment with Parkin modulator BIO-2007817 enhanced this residual function but reduced endogenous full-length Parkin activity. Residual truncated Parkin function provides a molecular explanation for a delayed disease onset in PRKN Exon 2 deletion carriers. Whereas this retained activity can be pharmacologically enhanced, the modulator's inhibitory effect on endogenous full-length Parkin may mandate strict patient stratification based on genotype. This finding offers mutation-specific counseling opportunities and highlights a potential therapeutic approach for appropriately selected patients with PARK-PRKN. ANN NEUROL 2026.

We develop Spatial Perturb-Seq, an in vivo CRISPR technology that interrogates multiple genes within single cells of intact tissues, compatible with both sequencing-based and probe-based spatial technologies. We apply Spatial Perturb-Seq to knock out risk genes for neurodegenerative diseases in the mouse brain, uncovering cell autonomous and cell-cell microenvironmental effects within the spatially intact tissue. Spatial Perturb-Seq functionally screens multiple genes in situ and in vivo, bypasses cell processing steps that skew cell type representation, identifies intracellular and intercellular effects of knockouts, and identifies candidate genes underlying dysregulated neuronal intercellular communication pathways.

Monogenic disorders are a major cause of fetal structural anomalies. Most genetic diagnoses involve de novo, biallelic or X linked variants; however, inherited variants in autosomal dominant disease genes have been detected across multiple studies. The overall contribution of such variants to fetal structural anomalies is unclear and variant filtering strategies may exclude them. In this study, we aimed to characterise the inherited variants in autosomal dominant disease genes detected by prenatal exome sequencing in a large, well-phenotyped cohort. The outcomes of prenatal exome sequencing for fetuses with structural anomalies referred to our laboratory from April 2019 to February 2025 were reviewed. Prenatal exome sequencing was carried out in 1185 fetuses, resulting in a diagnosis in 30.0% of cases. Autosomal dominant disorders accounted for 59.9% of diagnoses and a risk of recurrence was identified for 19.2% of these. Autosomal dominant conditions with an increased risk for recurrence were therefore identified in 3.5% of fetuses referred for sequencing, and accounted for 11.5% of prenatal exome sequencing diagnoses. Recurrent diagnoses involving inherited variants included rasopathies and type I/II collagen disorders. Inherited variants in autosomal dominant disease genes are a significant contributor to fetal structural anomalies and may have implications for parents' own health as well as management of the current pregnancy and reproductive options. The requirements for genomic counselling, clinical assessment and genetic testing of parents and family members following an inherited finding must be taken into account when planning delivery of a prenatal sequencing service.