Human molecular genetics最新文献

Bi-allelic mutations in GBA1, a gene that encodes the lysosomal enzyme β-glucocerebrosidase (GCase), cause Gaucher disease (GD). Although GD carriers do not exhibit clinical manifestations, GBA1 mutations are the highest risk factor for Parkinson's disease (PD) in GD patients and carriers of the disease [1-5]. GCase breaks down glucosylceramide (GluCer), a sphingolipid that accumulates in GD. GluCer is deacylated by the lysosomal enzyme acid ceramidase (ACDase) to glucosylsphingosine (GluSph) [6-8]. GluSph is neurotoxic and accumulates to high levels in neuronopathic GD brains [9, 10]. However, whether this metabolic pathway involving ACDase plays a role in GBA1-associated PD (GBA1/PD) is not known. In this report we used induced pluripotent stem cells (hiPSCs) from PD patients harboring heterozygote GBA1 mutations to examine the role of ACDase in promoting α-synuclein accumulation and aggregation, a hallmark of PD. Compared to isogenic controls, hiPSC-derived PD dopamine (DA) neurons had elevated levels of pathogenic α-synuclein species. There was also reduced nuclear localization of transcription factor EB (TFEB), impaired autophagy, and decreased levels of cathepsin D (CathD), a lysosomal protease involved in α-synuclein degradation [11]. Treatment of the mutant DA neurons with a number of different ACDase inhibitors, or CRISPR/Cas9 knockdown (KD) of the ASAH1 gene, reversed all the phenotypic abnormalities of the mutant DA neurons. We conclude that in GBA1/PD-DA neurons, ACDase contributes to deregulation of key nodes of the autophagy/lysosomal pathway (ALP) involved in α-synuclein clearance. Our results suggest that ACDase is a potential therapeutic target for treating GBA1-associated PD.

Orofacial clefts (OFCs) are one of the most common structural birth defects, with the prevalence of OFC varying across populations, and studies on the causes of OFCs in diverse populations are necessary, but still limited. We analyzed whole genome sequencing data on 419 parent-child trios from the Philippines, a population with a particularly high rate of OFC. To identify novel genes for OFCs, we studied both common variation and de novo variants (DNVs). We identified a significant enrichment in both loss-of-function (N = 62; P = 8.34 × 10-5) and protein-altering DNVs (N = 394; P = 1.49 × 10-7) among OFC probands. Among the genes individually enriched for DNVs was GRHL2 (P = 6.60 × 10-6), where there were two DNVs, a stop-gain and a frameshift deletion. We then queried OFC trios from other cohorts in the Gabriella Miller Kids First program (total N = 1254) and GeneMatcher and identified an 89 kb de novo deletion in GRHL2 and a de novo 8q22.3 microdeletion with one breakpoint in GRHL2. Additionally, within the common variant analyses we found significant gene x gene interactions with GRHL2. GRHL2 is a conserved transcription factor involved in embryonic development, with truncating mutations causing autosomal dominant progressive hearing loss and missense variants causing autosomal recessive ectodermal dysplasia. Heterozygous variation in its homolog, GRHL3, causes Van der Woude syndrome and isolated cleft palate. Additionally, mice deficient for either Grhl2 or Grhl3 have craniofacial anomalies, including facial and palatal clefts, strongly supporting GRHL2 as a risk locus for OFCs.

Alpha-fetoprotein (AFP), a fetal plasma protein, serves as a diagnostic marker for hepatocellular carcinoma (HCC) and germ cell tumors, with prior genome-wide association studies (GWAS) identifying AFP and PPIP5K1 as associated with its levels. The aim of this study was to identify novel genetic loci associated with serum AFP levels in the Taiwanese population and to elucidate their potential regulatory mechanisms, particularly in liver tissue, by integrating GWAS with expression quantitative trait loci (eQTL) analyses. We conducted a two-stage GWAS of serum AFP levels using participants from the Taiwan Biobank. The discovery cohort included 18 267 individuals, and findings were replicated in an independent sample of 21 994 individuals. Linear mixed models were used to assess genome-wide associations, adjusting for age, sex, and population structure via principal components. Quality control measures were applied to both genotyped and imputed SNPs. To explore functional implications, eQTL analyses were performed using publicly available liver tissue data, focusing on liver-specific regulatory effects. We identified 57 candidate genes across 10 genomic regions on chromosomes 2, 3, 4, 15, 17, and 22. For instance, SNPs in genes like SMC6, SENP7, and TP53BP1 demonstrated significant associations with AFP levels, contributing previously unreported genetic variations. eQTL analysis linked 55 of these genes in regulatory functions, especially within liver tissues, supporting their involvement in AFP expression. Our findings, integrating GWAS and eQTL approaches, enhance understanding of AFP heritability and suggest diagnostic and therapeutic potential for HCC, pending further validation in personalized medicine contexts.

The MRE11 DNA nuclease plays central roles in the repair of DNA double-strand breaks (DSBs) as a core component of the MRE11-RAD50-NBS1 (MRN) complex. MRN localizes to chromosomal DSBs and recruits and activates the DSB repair protein kinase, ATM, which phosphorylates downstream substrates to elicit cellular DNA damage responses. Pathogenic variants in MRE11 cause the genome instability disorder ataxia-telangiectasia-like disorder (ATLD). The first ATLD patient allele identified, ATLD1, is a nonsense mutation that deletes 76 residues from the MRE11 C-terminus and markedly reduces levels of MRE11-ATLD1 and the entire MRN complex. The MRE11 C-terminus has been demonstrated to function in DNA binding, mediate protein interactions, and undergo post-translational modifications that regulate the MRE11 nuclease. We previously demonstrated that transgenic mice expressing reduced wildtype MRN levels exhibit severe phenotypes, including small body size, anemia, and DNA DSB repair defects. Thus, it is currently unknown whether low MRE11-ATLD1 levels, loss of the C-terminus, or both cause disease-associated phenotypes. In this study, we generated transgenic mouse models that express near endogenous or significantly reduced levels of MRE11-ATLD1 to determine the in vivo importance of the MRE11 C-terminus. We observe that low MRE11-ATLD1 expression leads to anemia, bone marrow failure, extramedullary hematopoiesis, and impaired lymphocyte development, similar to mice expressing low wildtype MRE11. In contrast, higher MRE11-ATLD1 expression results in a subset of moderate phenotypes, indicating that loss of the C-terminus has limited impact on MRN functions in vivo. These findings provide a foundation for predicting the clinical presentation and severity of ATLD patient phenotypes.

Gout is a prevalent and painful form of inflammatory arthritis associated with hyperuricemia, which leads to monosodium urate crystal deposition in joints and surrounding tissues, triggering acute inflammatory responses. This disease is also closely linked to serious comorbidities, including cardiovascular diseases, chronic kidney diseases, diabetes, and increased mortality risk, significantly impacting global health. In this study, we conducted a comprehensive genome-wide association study (GWAS) based on the UK Biobank pain questionnaire 2019, comprising 10 474 gout cases and 140 068 controls, identifying 13 loci associated with gout. These findings were further explored in the FinnGen cohort, with 10 loci being replicated significantly. Sex-stratified analyses revealed notable differences, with 16 loci identified in males and two loci identified in females, reflecting both shared and sex -stratified genetic influences on gout susceptibility. In addition, genetic correlation analyses demonstrated strong associations between gout and traits related to urate levels, specific medication use, and metabolic functions. Transcriptome-wide association studies highlighted several genes, such as SLC16A9 and ASAH2B, which showed significant expression patterns across various tissues, implicating metabolic and immune pathways in gout. Phenome-wide association studies of significant single nucleotide polymorphisms revealed links to metabolic, immunological, and skeletal traits, underscoring the multi-faceted nature of gout. These results contribute valuable insights into the genetic architecture and biological mechanisms underlying gout, suggesting potential avenues for tailored interventions.

Smith-Lemli-Opitz syndrome (SLOS) is a rare, autosomal recessive disorder characterized by congenital malformations, intellectual disability, and behavioral abnormalities. SLOS results from mutations in the DHCR7 gene, leading to impaired cholesterol biosynthesis due to dysregulation of 7-dehydrocholesterol reductase. Cholesterol plays crucial roles in neurophysiology, including synaptic formation and neurotransmitter receptor regulation, which likely contribute to neurological manifestations in SLOS patients. While astrocytes are the main cholesterol producing cells in the brain, their specific role in SLOS pathogenesis remains unclear. In this study, we utilized induced pluripotent stem cell (iPSC)-derived astrocytes from a SLOS patient with DHCR7 c.C278T mutation and the isogenic control. We found decreased lipid droplet formation in SLOS iPSC astrocytes compared to controls, accompanied with diminished efflux of cholesterol and apolipoprotein E. Lipidomics revealed reduced cholesterol and cholesterol esters, as well as altered profiles of other lipids in SLOS iPSC astrocytes. While RNA-sequencing identified various genes and pathways affected by the disease status, those related to mitochondria functions were top-ranked. Mitochondrial electron transport chain oxidative phosphorylation gene expression decreased in SLOS iPSC astrocytes, alongside impaired mitochondrial respiration. Furthermore, SLOS iPSC astrocytes less effectively mediated neuroprotection on iPSC neurons than control astrocytes in serum-starvation conditions. SLOS iPSC astrocytes also poorly contributed to synaptic networks when co-cultured with iPSC neurons. Overall, our findings provide mechanistic insights into how DHCR7 disruption impacts astrocyte function, contributing to SLOS neuropathology by dysregulating lipid metabolism, mitochondrial respiration, and impaired neuroprotection.

Several genome wide association studies (GWASs) of orofacial cleft have been conducted. However only a few such studies to date have combined all cleft cases, focused on subtypes other than non-syndromic cleft lip with/without cleft palate, or investigated subtype heterogeneity. We conducted a GWAS of orofacial clefts within 2268 cases from the Cleft Collective and 7913 population-based controls; we performed analyses of all orofacial clefts, plus 7 subgroups. We replicated our findings in a meta-analysis of independent samples and investigated patterns of correlation across subgroups. We identified 27 regions at genome-wide significance, 8 of which were novel. We also conducted the first GWAS of Pierre Robin Sequence, despite the small sample size (n cases = 237), we found one genome wide significant SNP (P < 5 × 10-8), and another 21 suggestive associations (P < 10-5). Novel loci include those mapping to LHX8 and TSBP1 (combined clefts), ARHGEF18 and ARHGEF19 (cleft lip with/without palate), FBN2 (cleft lip only), SLC35B3 (cleft palate only), CASC20 (Pierre Robin Sequence) and CHRM2 (non-syndromic cleft palate only). Several novel hits were in regions previously associated with facial morphology in GWAS or were in regions involved in key developmental processes, including neural crest cell migration and craniofacial development. We identified genetic loci with similar effects across all subgroups and some loci which were subtype specific, we also identified 3 loci with opposing effects on cleft lip and Pierre Robin sequence. Our findings highlight the merit of including all orofacial cleft subtypes in GWAS studies and investigating heterogeneity of effects across subtypes.

RBM20 is one of the genes predisposing to dilated cardiomyopathy (DCM). Several dozen variants associated with DCM have been reported so far. Variants in the arginine/serine-rich domain and the RNA recognition motif domain have been well studied, but the pathogenicity of variants outside of these areas remains unknown. A patient with the Q373fs-RBM20 variant without a typical DCM phenotype was identified in a sudden death cohort. The Q374fs-Rbm20 mouse model was generated to determine the significance of this variant. In mouse experiments, cardiac dysfunction, such as reduced fractional shortening and an extended duration of QRS and the corrected QT interval, were observed in Q374fs-Rbm20 mice by ultrasound echocardiography and electrocardiography. RNA sequencing analysis showed that Q374fs-Rbm20 mice had different splicing patterns, such as Ttn, Ldb3, Camk2d, Obscn, and Ryr2. Casq1, Mybpc2, and Myot expression was also upregulated in Q374fs-Rbm20 mice. A pathway analysis indicated the involvement of some of the 1770 differentially expressed genes in cytoplasmic ribosomal proteins, calcium regulation in cardiac cells, and striated muscle contraction. Our findings suggest that the Q374fs-Rbm20 variant changes gene splicing, affects genes involved in sarcomere structure and calcium handling genes, and presents with cardiac dysfunction.

Variants in the SLC52A3 gene have been associated with riboflavin transporter deficiency type 3 (RTD3), a severe neurodegenerative disorder, typically inherited in an autosomal recessive manner. In this study, two SLC52A3 variants (NM_033409.4: c.62A > G [p.Asn21Ser] and c.161G > A [p.Gly54Glu]) were identified in a family with hereditary hearing loss through whole-exome sequencing. The compound heterozygous proband exhibited only late-onset, progressive, and symmetric sensorineural hearing loss over 23 yr, along with unilateral facial muscle spasm. A heterozygous carrier of the c.62A > G variant also exhibited optic nerve dysfunction, while no other neurological abnormalities were observed in the family. Although the proband's decreased serum riboflavin level has been improved through supplementation, no significant clinical improvement was observed. These findings further support the phenotypic variability, incomplete penetrance, and a potential autosomal dominant inheritance pattern of RTD3. We also underscore the importance of early genetic testing, timely and sustained riboflavin supplementation, and long-term follow-up in affected individuals.

Huntington's disease (HD) is driven by somatic expansion of the HTT CAG repeat, with onset modified by genetic factors. One such modifier, 8AM1, maps to chromosome 8 near RRM2B, a gene not directly involved in the machinery that lengthens the repeat. To investigate this locus, we performed capture sequencing and identified variants at both the 5' and 3' ends of RRM2B with expected minor allele frequencies. A polymorphic frameshift variant (rs1037699) in an alternate exon 1 disrupts expression of a previously uncharacterized RRM2B isoform 2, but not isoform 1. Functional analyses in RRM2B knock-out cells and 8AM1 heterozygous LCLs suggest that isoform 2 may function at mitochondria. Several 3' variants, including a 21 bp 3'UTR deletion (rs200678743) and peak tag-SNV (rs79136984), act as cis expression quantitative trait loci. Analysis of HD onset data (n = 12,982) revealed that 5' and 3' variants contribute independently to the 8AM1 modifier effect, with full impact observed only in the absence of the frameshift variant. Knockdown of both isoforms increased neurodegeneration in HD neurons derived from pre-symptomatic patient fibroblasts, supporting an intersection of RRM2B biology and HD pathogenesis. We conclude that the 8AM1 haplotype, present in ~ 14% of Europeans, modifies RRM2B expression in a cell- and context-dependent manner, thereby accelerating HD onset in mutation carriers.