The widespread implementation of low-dose computed tomography (LDCT) has markedly increased the detection of pulmonary nodules, yet their genetic determinants remain poorly understood. We conducted a genome-wide association study (GWAS) of 36 175 LDCT-screened individuals from Zhejiang and Jiangsu provinces in China, assessing fourteen pulmonary nodule phenotypes defined using a convolutional neural network-based computer-aided detection (CNN-CAD) system. We identified eleven independent single-nucleotide polymorphisms (SNPs) at nine loci associated with nodule phenotypes. Functional annotation prioritized six candidate genes with either missense variants or strong colocalization evidence, including TP63 at 3q28, PLA2G4F at 15q15.1, HLA-DRB6 and CYP21A2 at 6p21.32, TNFSF11 at 13q14.11, and TNFRSF11B at 8q24.12. These genes were enriched in pathways related to cell adhesion, chemotaxis, cytokine activity, and lymphocyte activation. Several of the identified variants-associated with non-solid components, nodule size, and the number of positive nodules-were also significantly associated with increased malignancy probability of pulmonary nodules. Genetic correlation analysis revealed a substantial shared genetic basis between purely ground-glass nodules (pGGNs) and lung adenocarcinoma (LUAD) (rg = 0.79; 95% CI, 0.16-1.42; P = 0.014), and Mendelian randomization (MR) further supported a potential causal relationship, with an odds ratio (OR) of 51.1 (95% CI: 1.13-2035.31). These findings offer novel insights into the genetic architecture of pulmonary nodules and highlight a substantial genetic overlap between pGGNs and LUAD, which may inform risk prediction and precision prevention in lung cancer screening.

IntroductionCharcot Marie Tooth neuropathies arise from diverse genetic disturbances that impair axonal structure or myelin integrity. Variants in NEFL, encoding the light chain of neurofilaments, represent a rare cause of CMT and may disrupt filament assembly, axonal transport, and cytoskeletal stability. Because NEFL variants are uncommon and phenotypes variable, the pathogenic relevance of individual substitutions is often difficult to determine. Here, we identified a previously unreported missense variant, p.(Leu97Ile), in three affected individuals. In two, a second variant, p.(Arg206Ser), was present in cis. We therefore aimed to investigate the pathogenic impact of this allele constellation using clinical, biochemical, and structural approaches.MethodsNeurological examination, CMTNS scoring, and electrophysiological studies were performed. Exome sequencing established the genotype. Variant effects were assessed using serum biomarkers, in silico modelling and quantitative immunofluorescence of patient-derived fibroblasts.ResultsPatients showed differing clinical presentations, including moderate adult-onset neuropathy to severe early-onset disease and neuromuscular abnormalities in childhood. Neurophysiology revealed mixed features, and conduction slowing in the child supported classification within the CMT1F spectrum. All carriers exhibited elevated serum NfL; CK was increased in the adult patients. Descriptive biomarker differences between the patients were observed for GDF15, FGF21, Periaxin, and NCAM1. Fibroblasts displayed increased cytoplasmic NfL without altered nuclear metrics. Structural modelling predicted destabilizing effects of both substitutions, with the cis combination producing the strongest deviation.DiscussionIntegrated clinical, biochemical, and structural evidence support pathogenicity of p.(Leu97Ile) and suggest that p.(Arg206Ser) in cis augments its biological impact. These findings expand the genetic and phenotypic spectrum of NEFL-associated CMT1F.

Biobanks have redefined how we study complex diseases, integrating genomic and phenotype data on an unprecedented scale. Population-based biobanks like the UK Biobank have provided powerful tools for epidemiology and polygenic risk stratification, while academic medical biobanks, enriched for advanced and rare diseases, leverage longitudinal electronic health records and deep phenotyping to uncover novel insights into disease mechanisms. A pivotal innovation in this space is the recall-by-genotype (RbG) study design, where individuals are recruited based on genetic variants of interest for detailed (deep) phenotypic investigation. This genome-first approach has enabled groundbreaking studies, from identifying genetic modifiers of rare conditions to leveraging polygenic risk scores for precision medicine. These studies demonstrate the potential of the RbG design to bridge genotype-phenotype relationships and drive biomedical discovery. However, most biobank studies remain underpowered in diverse populations, limiting the research and applicability of these findings. Expanding diversity in biobank datasets is not just a challenge but also an opportunity to make genomic advances equitable and impactful for all. Here, we review the transformative role of RbG studies, explore their application in academic medical biobanks, and discuss their potential to advance the frontier of precision medicine.

Melanocortin-2 receptor accessory protein-2 (MRAP2) modulates the activity of hypothalamic melanocortin-4 (MC4R) and growth hormone-secretagogue (GHSR) receptors, which suppress and promote appetite, respectively. We investigate whether obesity-associated variants of MRAP2 alter their ability to modulate MC4R and GHSR signalling as a possible mechanistic link to the development of obesity. Functional effects of five obesity-associated MRAP2 variants were analysed in HEK293 cells by co-expressing wild-type or variant MRAP2 with MC4R or GHSR. Endpoints included cell-surface and total expression, and ligand-induced second-messenger responses, β-arrestin-2 recruitment, and alternative G-protein activation. MRAP2 decreased basal MC4R cell-surface expression while GHSR cell-surface expression was not affected. In MC4R/MRAP2 expressing cells, maximal α-MSH-induced cAMP and β-arrestin-2 recruitment responses were increased. Similarly, ghrelin-induced Ca2+-mobilization in GHSR/MRAP2 expressing cells was increased, but β-arrestin-2 recruitment was suppressed. MRAP2 did not bias G-protein activation by either receptor, although previous reports show MRAP2 biases MC4R signalling towards Gαq/11. The variants did not significantly affect the ability of MRAP2 to modulate MC4R and GHSR signalling. Our results indicate that MRAP2 potentiates the ligand responsiveness of MC4R and GHSR, but has differential effects on β-arrestin-2 recruitment. The MRAP2 variants had no significant effects on the signalling endpoints tested. This suggests that, despite their association with obesity, the variants may be functionally benign, or that the absence of effects reflects limitations inherent to our cellular model. In addition, since MRAP2 can modulate multiple receptors and differentially modulate their signalling, we cannot rule out their influence on body weight regulation via other mechanisms.

BackgroundDown syndrome (DS), caused by trisomy of chromosome 21, is associated with a high prevalence of congenital non-autoimmune thyroid dysfunction, typically characterized by an elevated serum thyroid stimulating hormone (TSH) concentration. Early-life observational studies and fetal cordocentesis data, consistently reporting elevated TSH levels, suggest a developmental origin. However, the underlying pathophysiological mechanism remains unclear. This study aimed to investigate the molecular and developmental features underlying thyroid dysfunction in DS.MethodsThyroid tissue of fetuses with DS (n = 4) and fetuses without a genetic/developmental abnormality (n = 5) were analyzed using histology, bulk RNA sequencing (RNA-seq), and DNA methylation (DNAm) profiling.ResultsHistological analysis revealed underdevelopment of DS fetal thyroid tissue, with smaller follicles and greater heterogeneity. RNA-seq identified 1035 differentially expressed genes (DEGs) distributed across the genome. Notably, three thyroid-relevant genes, FOXE1, IYD, and DIO2, were significantly downregulated in DS tissue. Gene set enrichment analysis (GSEA) showed widespread disruption of cellular processes. DNAm analysis identified 266 differentially methylated regions (DMRs), several of which overlapped with loci previously implicated in DS. Integration of expression and DNAm data revealed 20 significant integrative methylation–expression analysis associations, indicating cis-regulatory DNAm effects on gene expression.ConclusionsThese findings suggest that congenital thyroid dysfunction in DS represents a DS-specific form of thyroid dysfunction, characterized by impaired thyroid development and altered expression and regulation of genes involved in thyroid function and general cellular processes. The genome-wide molecular changes observed likely result from gene dosage effects and systemic (epi)genomic disturbances caused by trisomy 21.

Polyglucosan body myopathy type 1 (PGBM1) is a rare glycogen storage disorder characterized by the abnormal accumulation of polyglucosan bodies in various tissues, particularly skeletal muscle. Caused by pathogenic variants in the RBCK1 gene, PGBM1 presents significant diagnostic challenges due to its rarity and potentially cryptic genetic mechanisms. This report describes a 12-year-old boy presenting with progressive lower limb weakness. Muscle biopsy revealed polyglucosan myopathy changes, including PAS-positive, diastase-resistant inclusions predominantly within glycogen-depleted muscle fibers. A definitive molecular diagnosis was achieved through the integration of whole-genome sequencing and RNA sequencing, which uncovered an Alu mediated homozygous intergenic inversion involving exons 1-4 of the RBCK1 gene. Based on previously reported cases of RBCK1-related PGBM1 and our patient, we observed a recurrent recombination between the RBCK1 and TRIB3 genes. This suggests that the 20p13 region is a potential structural rearrangement hotspot.

Calmodulin is an intracellular Ca2+ sensor that regulates numerous cellular processes through binding effector proteins and changing their activity. Humans have three calmodulin paralogs, CALM1, CALM2 and CALM3, encoding identical proteins, and missense variants in all three are included in the ACMG recommendations for reporting of secondary findings related to early onset sudden cardiac death caused by arrhythmias long QT syndrome and CPVT. Recently, a subset of individuals with de novo variants in calmodulin genes were described who also presented with neurologic phenotypes. Here we report two individuals with the same de novo variant c.419A > T in CALM1 or CALM2 that may generate a 5' splice donor gain and/or a missense change p.E140V. These individuals share hypotonia, motor delay, intellectual disability, and abnormal electroencephalograms but lack cardiac arrhythmia/electrocardiogram abnormalities of previously described CALM-associated disease, suggesting the variant causes phenotypic expansion beyond the known Mendelian phenotypes. RNA-seq of the CALM1 proband blood's sample revealed that most transcripts from the variant allele showed usage of the new splice site or intron retention, without NMD, resulting in frameshifted C-terminal truncations, while a minority resulted in production of the p.E140V missense protein. We modeled the CALM1/2 p.E140V variant as well as a known arrhythmia variant, CALM1 p.E141G, using the C. elegans ortholog cmd-1. We found that cmd-1 E140V displayed both qualitative and quantitative differences in phenotype from E141G, indicating distinct genetic mechanisms. Together, these findings support CALM1/2 phenotypic expansion, with c.419A > T p.E140V resulting in neurologic, but not arrhythmia phenotypes.

Mutations in TULP1 are associated with early-onset forms of inherited retinal degenerations (IRDs). Evidence from Tulp1-/- mice indicates that TULP1 plays a role in photoreceptor protein trafficking. Here we generated two novel knock-in mouse models, each expressing the ortholog to a human IRD-causing homozygous missense TULP1 mutation to: 1) better recapitulate IRD patients' gene dosage and spatiotemporal degeneration, 2) determine the pathological disease mechanism, and 3) evaluate mutations affecting different domains of the protein. The Tulp1F492L model carries a mutation affecting a conserved amino acid in the C-terminal tubby domain, whereas the Tulp1D89Y model carries the only homozygous mutation located outside the tubby domain. In both mutant retinas, TULP1F492L and TULP1D89Y protein levels and distribution were comparable to WT. Surprisingly, variable retinal phenotypes were observed in the two mutant lines. The Tulp1F492L model displayed rapid photoreceptor degeneration, rod and cone opsin mistrafficking, and abnormal shaped ribbon synapses, similar to Tulp1-/- mice. In contrast, these abnormalities were not seen in the Tulp1D89Y model; indeed, retinal morphology and function was preserved up to 12months, although we noted less RPE pigmentation and dilated structures in the outer plexiform layer at this timepoint. Moreover, building on our prior in vitro results, we observed activation of the IRE1 branch of the endoplasmic reticulum (ER)-unfolded protein response (UPR) complex in Tulp1-/- and Tulp1F492L retinas, identifying ER stress as a key disease mechanism leading to photoreceptor death and as a potential therapeutic target in TULP1-associated forms of IRD.

Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited disorder caused by mutations in PKD1 or PKD2. The PAX2 and PAX8 genes encode transcription factors required for kidney development, but their role in ADPKD remains unclear. We hypothesized that PAX2 and PAX8 contribute to ADPKD cystogenesis through distinct and overlapping mechanisms. Using immunofluorescence, PAX2 and PAX8 expression was assessed in human ADPKD kidney tissues. Nuclear PAX2 expression, and cytoplasmic PAX8 expression were found to be up-regulated in cyst-lining epithelial cells. Furthermore, using siRNA-mediated knockdown of PAX2 and PAX8, significantly reduced 3D spheroid growth was observed in MDCK, WT9-7, and WT9-12 renal epithelial cell line models. RNA sequencing after individual and combined knockdown of PAX2 and PAX8 in WT9-7 and WT9-12 cells identified differentially expressed genes and enriched pathways, revealing that PAX2 regulates pathways related to embryonic development, endoplasmic reticulum stress, and cilia. In contrast, PAX8 regulates cell cycle and adhesion pathways, while dual knockdown of PAX2 and PAX8 impacted extracellular matrix organization pathways. Several genes, including AGO2 and WWTR1, which were previously found to exhibit expression changes in human ADPKD tissues were co-regulated by both factors, suggesting their upregulation in ADPKD may be due to PAX co-expression. Overall, we found PAX2 and PAX8 regulated both unique and overlapping gene networks known to promote ADPKD cystic epithelial growth. Their differential expression patterns and combined impact on extracellular matrix remodelling highlight their potential as therapeutic targets. These findings advance our understanding of ADPKD pathogenesis, and suggest potential avenues for targeted intervention.