Human molecular genetics最新文献

The Meta-Analysis of Glucose and Insulin-related traits Consortium (MAGIC) identified 242 loci associated with glycaemic traits fasting insulin (FI), fasting glucose (FG), 2 h-Glucose (2hGlu), and glycated haemoglobin (HbA1c). However, for the majority, the causal variant(s) remain(s) unknown. Modelling multiple traits and integrating functional annotations have each been shown to improve fine-mapping resolution. Here, we aimed to determine whether combining these techniques would further improve fine-mapping resolution. Using single-trait fine-mapping results from FINEMAP as input, we performed multi-trait fine-mapping with flashfm at 50 loci significantly associated with more than one glycaemic trait. We used fGWAS to build models of enriched annotations by considering 32 cell-type specific and 28 static annotations. We used these models to define prior probabilities to perform annotation informed fine-mapping with both FINEMAP (single-trait) and flashfm (multi-trait). Multi-trait fine-mapping of 106 locus-trait associations significantly (P = 1.23 × 10-17) reduced the median size of the credible sets accounting for 99% of the posterior probability of being causal (99CS) to 21.5 variants compared to the 60.5 variants in single-trait fine-mapping. Annotation informed single-trait fine-mapping of 211 locus-trait associations reduced (P = 4.24 × 10-12) the median 99CS size from 72 in agnostic single-trait fine-mapping to 52 variants. Annotation informed multi-trait fine-mapping of 110 locus-trait associations led to a further significant (P = 2.69 × 10-18) decrease in median 99CS size to 14.5 variants compared to 51.0 in annotation informed single-trait fine-mapping. In conclusion, by applying combined multi-trait and annotation informed fine-mapping to 50 loci, we refined the number of potential causal variants by 71.1% compared to single-trait agnostic fine-mapping.

ZBTB24 is a member of a protein family containing a Broad-Complex, Tramtrack, and Bric a Brac (BTB) domain, which functions in protein-protein interactions. ZBTB24, a transcription factor, binds its DNA targets through its C-terminal zinc finger (ZF) domain. Biallelic ZBTB24 pathogenic variants lead to the rare autosomal recessive Immunodeficiency, Centromeric instability and Facial anomalies type 2 (ICF2) syndrome. The majority of ICF2 patients carry biallelic loss-of-function variants in ZBTB24. The remaining patients harbor missense variants in the ZF domain that compromise the ability of ZBTB24 to transcriptionally activate CDCA7, the gene responsible for ICF subtype 3 syndrome. Although an ICF2 patient with compound heterozygous pathogenic variants, including a missense variant (p.Ser59Gly) in the BTB domain, has been reported, no ICF2 patients with biallelic missense variants in any ZBTB24 domains other than the zinc finger domain have been described. Similar to all subtypes of ICF syndrome, ZBTB24 pathogenic variants lead to significant DNA hypomethylation throughout the genome. Here we describe a patient with severe infections initiating during her first year of life, significant developmental delay and an abnormal facial shape, who carries a homozygous p.Val43Leu substitution in the BTB domain of ZBTB24. The patient's peripheral blood cells demonstrate whole genome DNA hypomethylation with patterns identical to those found in verified ICF2 patients. Both the p.Val43Leu and p.Ser59Gly variants cause significant ZBTB24 protein instability. Thus, we demonstrate that pathogenic missense variants in the BTB domain of ZBTB24 can functionally act as loss-of-function variants that result in ICF2 syndrome.

The causal effect of lower plasma sclerostin on cardiovascular disease (CVD) risk has previously been examined with the aim of investigating potential side effects of pharmacological sclerostin inhibition for treatment of osteoporosis. We explored the relationship between plasma sclerostin levels and CVDs and bone phenotypes using Mendelian randomization (MR) and correlation between plasma sclerostin levels and these outcomes. We used variants identified in genome-wide association studies of plasma sclerostin levels in large proteomic datasets from the UK Biobank (Olink) and Iceland (SomaScan) as instruments in two separate MR analyses. These analyses did not provide evidence of association between the effects of sequence variants on plasma sclerostin levels and their effects on CVDs and CVD risk factors (P > 0.05). Several of the instruments had heterogenic effects on bone phenotypes and causal estimates in MR were non-significant (P > 0.05/8). Plasma sclerostin levels correlated positively with coronary artery disease, myocardial infarction and CVD risk factors. Our results do not provide evidence supporting the hypothesis that lower plasma sclerostin levels increase CVD risk and suggest that plasma sclerostin levels are not a good surrogate for pharmacological inhibition.

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by reduced levels of the survival motor neuron (SMN) protein, an essential component of the RNA splicing machinery. Although disruption of alternative splicing is a well-established hallmark of SMA, the specific splicing events that contribute to disease pathogenesis remain poorly understood. We utilised an established Caenorhabditis elegans SMA model to investigate global splicing changes using poly(A)+ RNA-seq and custom transcriptome assembly. Zygotic loss of smn-1 led to extensive transcriptomic changes, including over 1000 alternative splicing events, many of which were functionally tied to larval development. Exon skipping and intron retention were the most prevalent splicing alterations, and sequence motif analysis indicated a general shift from strong to weak splice site usage; however, no single motif accounted for the majority of observed splicing changes. Notably, we identified an overlap between smn-1 dependent splicing and those regulated by U6 snRNA m6A methylation. Our findings reinforce the conserved, broad role of SMN in maintaining splicing fidelity and reveal specific sequence biases associated with splicing errors in SMA.

Copy number variations (CNVs) in the distal 1q21.1 region, both deletion (1q del) and duplication (1q dup) are associated with various neurodevelopmental and neuropsychiatric disorders such as autism spectrum disorder, intellectual disability, epilepsy, and schizophrenia. Besides common phenotypes, 1q del and 1q dup manifest opposite clinical phenotypes, e.g. microcephaly in 1q del and macrocephaly in 1q dup. However, molecular and cellular mechanisms underlying these phenotypes are still elusive. Here, to identify molecular mechanisms associated with neurodevelopmental phenotypes from the viewpoint of neurogenesis and neurodevelopment, we generate isogenic human ES cell (hESC) lines with reciprocal 1q21.1 CNVs using CRISPR/Cas9 system and differentiate them into 2-dimensional (2-D) neurons and neural progenitor cell (NPC) spheroids. Our study recapitulates reciprocal brain size in the NPC spheroids and shows dosage-dependent differentiation changes i.e. more GABAergic components in 1q del and more proliferative state in 1q dup. These results demonstrate that 1q21.1 CNVs dramatically affect cell fate in the early neurodevelopmental periods. This is the first isogenic cell model of human 1q21.1 CNVs, and our findings provide new insights into the underlying mechanisms of neurodevelopmental disorders.

Facioscapulohumeral muscular dystrophy (FSHD) is caused by aberrant expression of the double homeobox transcription factor DUX4 in skeletal muscle. Because direct measurement of DUX4 in FSHD muscle is technically challenging, DUX4-regulated transcripts in muscle biopsies have been used as surrogates; however, this approach is invasive, limited to a single muscle, and less suitable for repeated monitoring. Thus, we sought to identify DUX4-regulated circulating biomarkers that could integrate DUX4 activity across all affected muscles and enable more frequent measurement. We performed mass spectrometry on conditioned media from DUX4-inducible immortalized human myoblasts (MB135iDUX4) and identified a top candidate-KHDC1L, the protein product of a DUX4-regulated mRNA previously shown to correlate with DUX4 expression in muscle. Western blotting confirmed KHDC1L release into the supernatant of DUX4-expressing cells. Plasma profiling demonstrated elevated KHDC1L levels in individuals with FSHD compared to healthy controls, supporting its role as a circulating readout of DUX4 activity. These findings suggest that plasma KHDC1L is a potential pharmacodynamic marker of DUX4 activity, providing a minimally invasive tool for disease monitoring and a potential response marker to evaluate emerging FSHD therapies.

Mutations in the PTEN gene have been implicated in autism spectrum disorders (ASD), particularly among individuals with comorbid macrocephaly. In our previous study, we demonstrated that the PTEN p.Ile135Leu variant, in an ASD-related genetic background dependent fashion, disrupts both cortical neurogenesis and gliogenesis. While abnormal cerebellar development is a recognized feature of ASD, the specific cellular targets and timing of disruptions during cerebellar differentiation and development remain poorly understood. To investigate these aspects, we applied our previously established cerebellar organoid protocol and used isogenic human iPSC lines harboring this PTEN-variant. We examined the expression of Purkinje cells, granule cells, interneurons, and glial cells prior to 22 weeks of differentiation, assessed genes expression at 8 weeks, and evaluated spontaneous spikes activity in Purkinje cells after 11 weeks. We observed that cell-type-specific expression patterns differed between the PTEN p.Ile135Leu variant in control versus ASD-genetic backgrounds. However, these background differences were diminished in PTEN knockout lines across both backgrounds. Our single-cell RNA sequencing (scRNA-seq) dataset revealed that the PTEN p.Ile135Leu variant increased the number of interneuron progenitor cells, whereas PTEN knockout led to an expansion of meningeal-like cells in both genetic contexts. Moreover, both the PTEN p.Ile135Leu variant and PTEN knockout abolished spontaneous simple spikes activity in Purkinje cells across both backgrounds, including PTEN-corrected patient-derived lines. Together, these findings provide direct evidence linking PTEN dysfunction and genetic background to altered cerebellar differentiation and neuronal network activity in human cerebellar organoids.

Fetal hemoglobin (HbF) modulates the clinical severity of sickle cell disease (SCD) by inhibiting the polymerization of sickle hemoglobin. Elevated HbF levels are associated with milder disease phenotypes, fewer Vaso-occlusive crises, and reduced organ damage. Understanding the molecular regulation of HbF expression is critical for the development of new therapeutic strategies, including pharmacologic agents and gene-based interventions aimed at ameliorating the course of SCD. We investigated transcriptomic expression in erythroid cells during the transition from the neonatal period to early childhood to identify genes associated with HbF regulation. Reticulocyte transcriptomes were compared between samples obtained at birth (cord blood), when HbF levels ranged from 72.6% to 90%, and at 18 months of age (whole blood), when HbF levels declined to 5.9%-10.3%. Reticulocytes were enriched, RNA extracted, and high-throughput RNA sequencing was performed, followed by differential gene expression and network analyses. Analysis of 20 346 genes revealed 1245 differentially expressed genes, of which 631 genes were upregulated in cord blood reticulocytes. The differentially expressed genes were significantly enriched in pathways related to cell signaling, proliferation, differentiation, metabolism, immune functionality, and erythropoiesis. Developmental shifts in the erythroid transcriptome uncover key biological processes that may regulate HbF expression. These findings offer a valuable panel of candidate genes for future functional studies and highlight new potential molecular targets for therapeutic modulation of HbF in sickle cell disease.

FOXP1 (Forkhead-box protein P1) is a crucial transcription factor in neural development and is associated with schizophrenia (SCZ). FOXP1-regulated genes may contribute to genetic risk of SCZ and this may vary across different stages of neurodevelopment. We analyzed RNA-seq transcriptomic data from mouse and human models of FOXP1 loss-of-function across prenatal and postnatal developmental stages, including neural stem cells from embryonic mice (E14.5) and human brain organoids (equivalent to second trimester), and cortical tissues from different mouse postnatal stages P0, P7, and P47. P0 in mice corresponds to the third trimester in humans, while P7 and P47 represent early childhood and adolescence, respectively. Linkage disequilibrium score regression assessed if FOXP1-regulated genes were enriched for SCZ heritability. Gene-set enrichment analysis investigated if FOXP1-regulated genes were enriched for SCZ-associated genes reported as differentially expressed in single cortical cell studies. SynGO analysis mapped FOXP1-regulated genes to synaptic locations and functions. FOXP1-regulated genes were enriched for SCZ heritability, with significant results for E14.5, P7 and P47 but not P0. The P7 gene-set showed the strongest enrichment for SCZ-associated genes from single cortical cell studies. FOXP1-regulated genes at both P7 and P47 were involved in multiple synaptic functions and were mainly enriched within glutamatergic excitatory neurons, with P47 also showing enrichment within GABAergic inhibitory neurons. Prenatal FOXP1-regulated genes were enriched in progenitor cells and also mapped to the synapse. Genetic risk for SCZ within FOXP1-regulated genes follows a dynamic trajectory across developmental stages, showing strongest effects at a timepoint that maps to early childhood.