HGG Advances最新文献

Pleiotropy, the phenomenon where a genetic region confers risk to multiple traits, is widely observed, even among seemingly unrelated traits. Knowledge of pleiotropy can improve understanding of biological mechanisms of diseases/traits, and can potentially guide identification of molecular targets or help predict side effects in drug development. However, statistical approaches for identifying pleiotropy genome-wide are limited, particularly for two correlated traits or case-control traits with unknown sample overlap or for disease traits from family studies. We proposed PLACO+, an improved version of our pleiotropic analysis under composite null hypothesis method based on GWAS summary statistics from two traits. PLACO+ uses an inflated variance model to allow for fractions of variants to be associated with none or only one trait under the null. It is genome-wide scalable, where analytical p value is computed as a weighted sum of extreme tail probabilities of bivariate normal product distribution. Simulations for both population-based and family-based designs demonstrate well-calibrated type I errors at stringent levels and substantially improved power of PLACO+ over conventional approaches. We illustrate PLACO+ on inflammatory bowel disease subtypes with shared controls and on correlated lipid traits with unknown sample overlap. In particular, PLACO+ revealed pleiotropic regions between triglyceride and high-density lipoprotein levels that conventional approaches missed and all of which were replicated in a larger GWAS of these lipid traits. This further demonstrates the utility of PLACO+ in discovering genetic associations of traits with modest sample sizes by leveraging information from another correlated trait.

The treatment of defective glycosylation in clinical practice has been limited to patients with rare and severe phenotypes associated with congenital disorders of glycosylation (CDGs). Carried by approximately 5% of the human population, the discovery of the highly pleiotropic, missense variant in a manganese transporter ZIP8 has exposed under-appreciated roles for Mn homeostasis and aberrant Mn-dependent glycosyltransferases activity leading to defective N-glycosylation in complex human diseases. Here, we test the hypothesis that aberrant N-glycosylation contributes to the disease pathogenesis of ZIP8 A391T-associated Crohn disease. Analysis of N-glycan branching in intestinal biopsies demonstrates perturbation in active Crohn disease and a genotype-dependent effect characterized by increased truncated N-glycans. A mouse model of ZIP8 391-Thr recapitulates the intestinal glycophenotype of patients carrying ZIP8 variants. Borrowing from therapeutic strategies employed in the treatment of patients with CDGs, oral monosaccharide therapy with N-acetylglucosamine ameliorates the epithelial N-glycan defect, bile acid dyshomeostasis, intestinal permeability, and susceptibility to chemical-induced colitis in a mouse model of ZIP8 391-Thr. Together, these data support ZIP8 391-Thr alters N-glycosylation to contribute to disease pathogenesis, challenging the clinical paradigm that CDGs are limited to patients with rare diseases. Critically, the defect in glycosylation can be targeted with monosaccharide supplementation, providing an opportunity for genotype-driven, personalized medicine.

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.

Variants in SLC6A1 result in a rare neurodevelopmental disorder characterized by a variable clinical presentation of symptoms including developmental delay, epilepsy, motor dysfunction, and autism spectrum disorder. SLC6A1 haploinsufficiency has been confirmed as the predominant pathway of SLC6A1-related neurodevelopmental disorder (SLC6A1-NDD); however, the molecular mechanism underlying the variable clinical presentation remains unclear. Here, through work of the Undiagnosed Diseases Network, we identify an individual with an inherited p.A334S variant of uncertain significance. To resolve this variant and better understand the variable expressivity associated with SLC6A1, we assess the phenotypes of the proband in comparison with a cohort of 13 individuals diagnosed with SLC6A1-NDD. We then create an allelic series in Drosophila melanogaster to functionally characterize these variants. Informatic clustering based on these clinical findings points to significant clinical overlap between the unsolved individual and confirmed SLC6A1-NDD. We confirm phenotypes in flies expressing SLC6A1 variants consistent with a partial loss-of-function mechanism. We conclude that the p.A334S variant is a hypomorphic allele and begin to elucidate the underlying variability in SLC6A1-NDD. These insights will inform clinical diagnosis, prognosis, intervention, and inform therapeutic design for those living with SLC6A1-NDD.

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.

Single-nucleotide variants (SNVs) and small insertions or deletions (indels) underlie most rare monogenic disorders, yet therapeutic strategies to precisely correct these mutations remain limited. Prime editing enables the repair of such pathogenic variants without introducing double-stranded breaks. Here, we applied CRISPR prime editing to model and correct a de novo GDF11 nonsense mutation (Tyr336∗) identified in a participant from the Undiagnosed Diseases Network with growth delay and multisystem abnormalities. Using HEK293T cells, we generated heterozygous (HET) GDF11 Tyr336∗ clones, which exhibited reduced GDF11 protein levels due to post-translational degradation likely mediated by endoplasmic reticulum- and Golgi-associated quality control pathways. These cells displayed marked Golgi abnormalities, including an increased number of compact, irregularly shaped Golgi structures, findings consistent with Golgi fragmentation and stress. Transcriptomic profiling of HET cells revealed a broad dysregulation of gene networks, including downregulation of metabolic and Golgi-linked biosynthetic genes, and upregulation of cell-adhesion and extracellular matrix genes. These transcriptional shifts paralleled the participant's developmental, neural, and cardiovascular phenotypes. To correct the mutation, we tested multiple bespoke prime editing strategies and identified PE7, in combination with a prime editing guide RNA designed by Pridict, as the most effective ribonucleoprotein complex for rescue. Editing efficiency was further enhanced by introducing an additional silent protospacer-adjacent motif-disrupting mutation, likely preventing both Cas9 re-binding and mismatch repair. Together, these findings support a haploinsufficiency mechanism for the GDF11 Tyr336∗ allele and establish a generalizable framework for disease modeling and allele-specific correction of pathogenic variants in human cells.

Morphine is a potent analgesic and exhibits significant efficacy in alleviating severe pain. However, prolonged use can lead to drug dependency. Moreover, there are individual variations in response to and tolerance of morphine, indicating potential genetic regulation. Nevertheless, the mechanisms underlying these phenomena remain unclear. Therefore, we aimed to systematically dissect the genetic regulatory network for morphine response. We used quantitative trait locus mapping to identify genetic regions associated with morphine-related traits. Candidate genes for each locus were further filtered based on multiple criteria, including gene-trait association, cis-regulation, genetic variation, and potential function. The results showed that morphine response-related behavioral traits were significantly influenced by genetic background. Using the GEMMA and HK algorithms, we identified 18 genomic loci associated with dozens of morphine response-related traits. This includes loci previously studied on chromosome 10, together with a locus on chromosome 5 (0-20 Mb) identified in our analysis which showed the most association outside chromosome 10. Additionally, we identified six candidate functional genes (Cacna2d1, Myo7a, Elovl4, Oprm1, Cdk12, and Ccdc88c) that passed the filtering criteria. Oprm1 encodes the μ-opioid receptor, while Cacna2d1, Cdk12, and Elovl4 are closely associated with neurons. Myo7a and Ccdc88c may mediate anxiety and cognitive dysfunction caused by morphine dependence. Furthermore, Oprm1, Cacna2d1, and Ccdc88c are associated with opioid use disorders, nerve measurements, and brain volume in humans. In summary, our study describes the genetic regulation landscape of morphine response in BXD mice and identifies six candidate genes, providing valuable opportunities for further exploration.

Polygenic scores (PGSs) have shown promise in advancing precision medicine by capturing the additive effects of common genetic variants to assess inherited disease risk. However, their predictive accuracy remains limited in non-European populations. We enhanced our previously developed Bayesian polygenic model, "select and shrink with summary statistics" (S4), by introducing a multi-ancestry extension (S4-Multi) to improve prediction accuracy across African, American, East Asian, European, and South Asian ancestries. By leveraging simulated data and biobank cohorts from UK Biobank, FinnGen, Biobank Japan, the All of Us Research Program, and the Global Biobank Meta-Analysis Initiative, we benchmarked S4-Multi against leading methods for predicting type 2 diabetes, breast cancer, colorectal cancer, asthma, and stroke. In simulation tests, S4-Multi outperformed its single-ancestry version, achieving over 1.6 times greater accuracy in non-European populations, and matched or exceeded top-performing methods across all tested ancestry groups. In biobank tests, S4-Multi matched the performance of the best methods, varying by ancestry and phenotype. We find that S4-Multi achieves comparable performance using 9%-77% fewer genetic variants than competing models, highlighting potential for robust performance in clinical settings with limited available genomic data.

Microcephaly is a neurodevelopmental anomaly characterized by reduced head circumference and impaired brain growth, often accompanied by intellectual disability (ID), developmental delays, and seizures. While numerous genes have been implicated in microcephaly, the role of the SCF (Skp1-Cul1-F-box protein) ubiquitin ligase complex, particularly its core component CUL1, remains poorly understood. In this study, we identified heterozygous de novo and inherited variants in the CUL1 gene in four unrelated families with severe microcephaly, ID, and developmental delays. To investigate the functional consequences of CUL1 loss of function, we developed a zebrafish model with knockdown of cul1a&b, which exhibited significant reductions in central nervous system size and behavioral defects, mirroring the clinical phenotypes observed in patients. These findings establish CUL1 as a novel gene associated with severe neurodevelopmental disorders (NDDs) and highlight its critical role in brain development. Our study provides genotype-phenotype correlations for CUL1 in NDDs, expanding the genetic spectrum of disorders linked to the SCF complex and underscoring its importance in neurodevelopment.

Ribosomes are ribonucleoproteins that are responsible for protein synthesis. They consist of ribosomal proteins and ribosomal RNAs (rRNAs). Pre-rRNAs are co-transcriptionally processed and chemically modified. The 2'-O-methylation of rRNAs is guided by box C/D small nucleolar ribonucleoprotein particles (snoRNPs), which are composed of a box C/D snoRNA and the core proteins NOP56, NOP58, SNU13, and the methyltransferase fibrillarin. Catalytically active box C/D snoRNPs function in nucleoli. We performed trio whole-exome sequencing in a proband with a severe neurodevelopmental disorder including global developmental delay, microcephaly, seizures, and ophthalmological and brain abnormalities and his healthy parents and identified the homozygous synonymous variant c.516G>A; p.Leu172= in NOP58. In fibroblasts of the proband, we demonstrated skipping of exon 7 in most NOP58 mRNAs, while ∼20% canonically spliced NOP58 transcripts were detected in the proband compared with control cells. NOP58 protein levels were reduced to ∼12% in proband cells that concomitantly reduced fibrillarin levels. Analysis of nucleoli in proband-derived fibroblasts revealed changes in the number of nucleolar condensates and in nucleolar morphology. We found reduced levels of three box C/D snoRNAs required for 2'-O-methylation and of one box C/D snoRNA important for 2'-O-methylation and pre-rRNA processing. Analysis of pre-rRNA maturation by RT-qPCR revealed increased 45S and 21S pre-rRNA levels, whereas the amplification signal for the 47S, 32S, and 26S pre-rRNAs was substantially decreased in proband compared with control cells. Together, our data unveil that the homozygous NOP58 variant c.516G>A represents a hypomorphic allele and underlies the neurodevelopmental phenotype in the proband, likely by impairing pre-rRNA maturation.