BackgroundRisperidone is a widely used second-generation antipsychotic for schizophrenia, known for its clinical efficacy but also for long-term metabolic side effects, including weight gain and glucose-lipid dysregulation. Although its therapeutic effects have been well characterized, the molecular basis linking its benefits and adverse metabolic outcomes remains poorly understood.MethodsTo identify genes mediating both therapeutic and metabolic responses to risperidone, we conducted an integrative multiomics study combining large-scale genetic association data with transcriptomic and epigenetic profiling. Differentially expressed genes following risperidone exposure were intersected with schizophrenia- and metabolism-associated loci using summary data-based Mendelian randomization analysis based on GWAS summary statistics and eQTL data to uncover germline variants, germline susceptibility, and potential germline alteration. DNA methylation profiling from patient-derived peripheral blood mononuclear cells (PBMCs) was used for regulatory validation.ResultsWe identified 120 genes significantly modulated by risperidone, among which DKK3, EEF1A1, and PRKAA1 were causally associated with schizophrenia and metabolic traits through germline mutation-related regulatory evidence. Notably, DKK3 was downregulated after risperidone exposure and exhibited promoter hypermethylation, consistent with epigenetic regulation interacting with germline alteration and germline susceptibility. Functional correlation analysis revealed that lower DKK3 expression was associated with glycolipid dysregulation, supporting its role as a molecular bridge between antipsychotic action and metabolic liability.ConclusionOur findings identify DKK3 as a germline mutation-related and epigenetically regulated candidate that bridges risperidone ' s neuropsychiatric benefits with its metabolic risks. This work offers novel insight into the shared molecular basis of antipsychotic response and side effects and suggests DKK3 as a promising biomarker for personalized treatment strategies in schizophrenia informed by germline regulatory variation and potential germline alteration.

Approximately 30-40% of the human genome is anchored to the nuclear lamina (NL) through variably sized (10 kb-10 Mb) lamina-associated domains (LADs), which can be classified into two subtypes (T1 and T2) based on their level of lamina-association. The dynamics of LAD substructure in cells that remain postmitotic for long periods of time are poorly understood. Here, we developed Genome Organization with CUT and Tag (GO-CaT) to determine the T1- and T2-LAD substructure of postmitotic excitatory neurons isolated from the prenatal and adult human cortex. While T1-LADs exhibited epigenomic features characteristic of stable, cell type-invariant LADs including strong transcriptional repression, in prenatal neurons, T2-LADs were enriched for promoter-enhancer DNA interactions, intermediate levels of gene expression, and genetic risk associated with neurodevelopmental and cognitive disorders. In adult cortical neurons, T1-LADs were expanded in size and genomic coverage, incorporating the majority of the prenatal T2-LADs, sequestering genes involved in neurodevelopment. In contrast, the minority of prenatal T2-LADs that relocated to inter-LAD regions in adult neurons were enriched for processes related to synaptic function. Overall, these data provide evidence that LADs "mature" in postmitotic neurons, remodeling from a genomic architecture that is more permissive for the dynamics of transcription of development to one that is more restricted and focused on the decades-long transcriptional needs of adult brain neurons.

Bone marrow-derived mesenchymal stem cell (BMSCs) delivery is a promising therapeutic strategy for bronchopulmonary dysplasia (BPD); however, its efficacy remains suboptimal. Recent studies have reported that extracellular vesicles derived from peroxiredoxin 6 (PRDX6)-downregulated mesenchymal stem cells (MSCs) exhibit diminished anti-inflammatory and anti-oxidant effects through a paracrine mechanism. Nevertheless, whether PRDX6 participates in BPD progression via paracrine signaling remains unclear. Herein, rat BMSCs were first isolated and characterized. The GFP-labeled lentivirus was used to overexpress PRDX6 in BMSCs. PRDX6-overexpressing BMSCs exhibited improved proliferation and migration abilities. Notably, mesencephalic astrocyte-derived neurotrophic factor (MANF) secretion was significantly increased (∼2.5-fold, p < 0.05) in PRDX6-overexpressed BMSCs. Further mechanistic studies revealed that PRDX6 bound to MANF, reducing its endoplasmic reticulum retention by displacing glucose-regulated protein 78, thereby promoting MANF secretion. Silencing MANF expression markedly attenuated the effects of PRDX6 overexpression. PRDX6-modified BMSCs were delivered intratracheally into BPD rat model, which was established by exposing rats in 85 % oxygen for 21 days. PRDX6 overexpression enhanced BMSCs recruitment to injured lung tissues, and significantly reduced apoptosis, inflammation, vascular loss, and pulmonary arterial remodeling. Concurrently, MANF levels in lung tissues, bronchoalveolar lavage fluid, and serum were elevated post-administration. These results suggest that PRDX6-mediated MANF secretion in BMSCs may not only enhance their proliferative and migratory capacities but also directly protect against lung injury. These findings provide a new strategy for amplifying the in vivo efficacy of BMSCs delivery on BPD.

Approximately 30-40% of the human genome is anchored to the nuclear lamina through variably sized (10 kb-10 Mb) lamina-associated domains (LADs). Previous work in cultured murine and human cell lines indicate that LADs are not homogenous but can be classified into two subtypes (T1 and T2) based on levels of lamina-association. Due in part to technical limitations, the LAD substructure of neurons maturing in vivo is poorly understood. Here, we developed Genome Organization with CUT and Tag (GO-CaT) to map LAD substructure in neurons isolated from the midgestational human cortex and adult human brain. GO-CaT with LaminB1 antibodies mapped LADs with high efficiency as compared to other methods, and in prenatal neurons, we distinguished T1- and T2-LADs based on levels of LaminB1 enrichment. While T1-LADs had the transcriptional and epigenomic characteristics of cell type-invariant LADs including strong transcriptional repression, T2-LADs had a distinct epigenomic state that included enrichment of promoter-enhancer DNA interactions and intermediate levels of gene expression. In prenatal neurons, T2-LADs defined genomic regions that play key roles in neuronal development and were enriched for neurological GWAS phenotypes including those of human cognitive disorders. In a population of adult brain neurons, most prenatal T2-LADs were repositioned to either inter-LAD regions or further sequestered into T1-LADs, perhaps representing the completed, life-long spatial genome architecture of human neurons. These studies highlight the utility of GO-CaT for LAD subdomain mapping in cells isolated from human tissues and illustrate how the substructure of LADs may contribute to neural development, neuronal maturation, and human brain disease. ### Competing Interest Statement The authors have declared no competing interest.

OBJECTIVE:To explore the genetic basis for a Chinese pedigree affected with Branchio-Oto syndrome (BOS).METHODS:A pedigree with BOS which had presented at the Genetics and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University in May 2021 was selected as the study subject. Clinical data of the pedigree was collected. Peripheral blood samples of the proband and her parents were collected. Whole exome sequencing (WES) was carried out for the proband. Multiplex ligation-dependent probe amplification (MLPA) was used to verify the result of WES, short tandem repeat (STR) analysis was used to verify the relationship between the proband and her parents, and the pathogenicity of the candidate variant was analyzed.RESULTS:The proband, a 6-year-old girl, had manifested severe congenital deafness, along with inner ear malformation and bilateral branchial fistulae. WES revealed that she has harbored a heterozygous deletion of 2 466 kb at chromosome 8q13.3, which encompassed the EYA1 gene. MLPA confirmed that all of the 18 exons of the EYA1 gene were lost, and neither of her parents has carried the same deletion variant. STR analysis supported that both of her parents are biological parents. Based on the guidelines from the American College of Medical Genetics and Genomics, the deletion was classified as pathogenic (PVS1+PS2+PM2_Supporting+PP4).CONCLUSION:The heterozygous deletion of EYA1 gene probably underlay the pathogenicity of BOS in the proband, which has provided a basis for the clinical diagnosis.

Spinal muscular atrophy (SMA) is a neuromuscular disease caused by biallelic variants of the survival motor neuron 1 (SMN1) gene. In this study, our aim was to make a molecular diagnosis in two patients with SMA carrying only one SMN1 copy number. Using ultra-long read sequencing (Ultra-LRS), 1415 bp deletion and 3348 bp deletion of the SMN1 gene were identified in patient 1 and the father of patient 2, respectively. Ultra-LRS revealed two novel deletions, starting from the SMN1 promoter to intron 1. It also accurately provided the location of the deletion breakpoints in the SMN1 gene: chr5 g.70,924,798-70,926,212 for a 1415 bp deletion; chr5 g.70,922,695-70,926,042 for a 3348 bp deletion. By analyzing the breakpoint junctions, we identified that these genomic sequences were composed of Alu sequences, including AluJb, AluYm1, AluSq, and AluYm1, indicating that Alu-mediated rearrangements are a mechanism of SMN1 deletion events. In addition, full-length SMN1 transcripts and SMN protein in patient 1 were significantly decreased (p < 0.01), suggesting that a 1415 bp deletion that included the transcription and translation initiation sites of the SMN1 gene had severe consequences for SMN expression. Ultra-LRS can easily distinguish highly homozygous genes compared to other detection technologies, which is useful for detecting SMN1 intragenic mutations, to quickly discover structural rearrangements and to precisely present the breakpoint positions. (c) 2023 Elsevier B.V. All rights reserved.

Objective:To detect and analyze the gene variation types of 64 unrelated pedigrees affected with autosomal dominant polycystic kidney disease (ADPKD), and explore the detection efficiency of multiple gene analysis techniques and variation characteristics.Methods:It was a cross-sectional study. The clinical data of 64 pedigrees with ADPKD from Nephrology Department or Genetic and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University from December 2017 to August 2020 were retrospectively analyzed. The blood samples of probands and other family members were collected. Genetic analysis was carried out by next generation sequencing, and suspected mutations were verified by multiplex ligation-dependent probe amplification, or long-range PCR combined with Sanger sequencing. Prenatal diagnosis for high-risk fetuses was performed by fetal villi or amniotic fluid cells after genotyping without maternal genomic DNA contamination.Results:Among detected 64 pedigrees, 57 pedigrees (89.06%) had genetic variants in PKD1/PKD2. A total of 49 pathogenic/likely pathogenic variants in PKD1/PKD2 were identified in 51 pedigrees (79.69%), including 14 nonsense variants (28.57%), 14 frameshift variants (28.57%), 11 missense variants (22.45%), 5 splicing variants (10.20%) and 5 deletion variants (10.20%). Of these variants, 87.76% (43/49) were in PKD1 and 12.24% (6/49) were in PKD2. Totally, 14 novel variants in PKD1/ PKD2 were identified, including 7 frameshift variants, 3 splicing variants, 2 nonsense variants, 1 deletion variant and 1 missense variant, of which 11 variants were in PKD1 and 3 variants were in PKD2. Twenty high-risk fetuses from 17 pedigrees received prenatal diagnosis, in whom 6 fetuses had PKD1 variation, and other 14 fetuses had no PKD1/ PKD2-genetic variation. Conclusions:The combination of next-generation sequencing, multiplex ligation-dependent probe amplification, and long-range PCR combined with Sanger sequencing can be helpful for rapid, efficient and accurate genetic diagnosis of ADPKD pedigrees. Point mutations are the most common types in PKD1/PKD2. Fourteen novel variants in PKD1/PKD2 extend its pathogenic variant spectrum and can provide basis for genetic counseling and prenatal diagnosis of ADPKD pedigrees.

OBJECTIVE:To explore the clinical and genetic characteristics of three children with KBG syndrome.METHODS:Clinical data of the three children from two families who have presented at the First Affiliated Hospital of Zhengzhou University between October 2019 and September 2020 and their family members were collected. Trio-whole exome sequencing (trio-WES) and Sanger sequencing were carried out.RESULTS:All children had feeding difficulties, congenital heart defects and facial dysmorphism. The sib- pair from family 1 was found to harbor a novel de novo heterozygous c.6270delT (p.Q2091Rfs*84) variant of the ANKRD11 gene, whilst the child from family 2 was found to harbor a novel heterozygous c.6858delC (p.D2286Efs*51) variant of the ANKRD11 gene, which was inherited from his mother who had a mild clinical phenotype.CONCLUSION:The heterozygous frameshift variants of the ANKRD11 gene probably underlay the disease in the three children. Above findings have enriched the spectrum of the ANKRD11 gene variants.

OBJECTIVE:To explore the genetic basis for a Chinese pedigree featuring congenital profound syndromic deafness and chronic constipation, and provide prenatal diagnosis for a high-risk fetus.METHODS:Whole-exome sequencing was carried out to analyze the sequences of genes associated with hereditary deafness, and multiplex ligation-dependent probe amplification (MLPA) was used to verify the candidate variant in the proband's parents and the fetus.RESULTS:The proband was found to have harbored a heterozygous deletion of SOX10, a pathogenic gene associated with Waardenburg syndrome type 4C (WS4C). The same deletion was found in her mother (with profound syndromic deafness and chronic constipation) and the fetus, but not in her father with normal hearing. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the SOX10 gene deletion was predicted to be a pathogenic variant (PVS1+PM2_Supporting+PP1+PP4).CONCLUSION:The pedigree was diagnosed with WS4C, which has conformed to an autosomal dominant inheritance. Deletion of the entire SOX10 gene, as a loss-of-function variant, probably underlay its pathogenesis. Above finding has facilitated genetic counseling and prenatal diagnosis for this family.

Gene mutations among HGSOCs reveal DNAH5 as a FT-derived HGSOC exclusively mutated gene

OBJECTIVE:To explore the clinical and genetic features of a child with autosomal dominant mental retardation type 40 (MRD40) due to variant of the CHAMP1 gene.METHODS:Clinical characteristics of the child were analyzed. Genetic testing was carried out by low-depth high-throughput and whole genome copy number variant sequencing (CNV-seq) and whole exome sequencing (WES). A literature review was also carried out for the clinical phenotype and genetic characteristics of patients with MRD40 due to CHAMP1 gene variants.RESULTS:The child, a 11-month-old girl, has presented with intellectual and motor developmental delay. CNV-seq revealed no definite pathogenic variants. WES has detected the presence of a heterozygous c.1908C>G (p.Y636*) variant in the CHAMP1 gene, which was carried by neither parent and predicted to be pathogenic. Literature review has identified 33 additional children from 12 previous reports. All children had presented with developmental delay and mental retardation, and most had dystonia (94.1%), delayed speech and/or walking (85.2%, 82.4%) and ocular abnormalities (79.4%). In total 26 variants of the CHAMP1 gene were detected, with all nonsense variants being of loss-of-function type, located in exon 3, and de novo in origin.CONCLUSION:The heterozygous c.1908C>G (p.Y636*) variant of the CHAMP1 gene probably underlay the WRD40 in this child. Genetic testing should be considered for children featuring global developmental delay, mental retardation, hypertonia and facial dysmorphism.

OBJECTIVE:To explore the genetic basis for a Chinese pedigree affected with congenital deafness pedigree in conjunct with enlarged vestibular aqueduct.METHODS:Whole-exome sequencing was carried out for the proband to analyze the genes associated with hereditary deafness. Candidate variant was verified by Sanger sequencing of the proband's parents and her younger brother.RESULTS:The proband was found to harbor compound heterozygous variants including c.748dupG (p.Asp250Glyfs*30Asn) (pathogenic, PVS1+PM2+PP4) and c.879C>A (p.Ser293Arg) (likely pathogenic, PM2+PM3+PP1+PP4) of the FOXI1 gene, which has been associated with enlarged vestibular aqueduct (OMIM 600791). Both variants were unreported previously. The variants were respectively inherited from proband's parents whom had normal hearing. Her younger brother was heterozygous for the c.748dupG variant but also had normal hearing.CONCLUSION:The compound heterozygous variants of the FOXI1 gene probably underlay the pathogenicity of congenital deafness and enlarged vestibular aqueduct in the proband. The co-segregation of the two variants with the hearing loss has facilitated genetic counseling and prenatal diagnosis for this pedigree.

Background Balanced reciprocal translocation is one of the most common chromosomal abnormalities in humans that may lead to infertility, recurrent pregnancy loss, or having children with physical or mental abnormalities. Karyotyping and FISH are traditional detection approaches with a low resolution. Bionano optical genome mapping (OGM) developed in recent years can be used to analyze chromosomal abnormalities at a higher resolution, providing the possibility of more in-depth analyses of balanced chromosome translocations. Methods To evaluate the feasibility of OGM to detect chromosome balanced translocations, 10 genetic outpatients were collected and detected simultaneously by karyotype analysis, FISH, CNV-seq, and Bionano OGM in this study. Results The results showed that the karyotypes of the patients were detected by karyotype analysis, FISH, and Bionano OGM, but one patient with karyotype t(Y,19) was not correctly detected by OGM. There were not find any chromosome abnormality by CNV-seq. More importantly, OGM allowed the location of the mutation to the gene level, which is important for aiding diagnoses, compared to karyotype analysis, and FISH. Conclusions This study shows that OGM can be a high adjunctive diagnostic method for detecting balanced chromosome translocations, but the accuracy and precision of OGM detecting mutations need to be gradually improved in telomere and centromere regions.

OBJECTIVE:To explore the clinical features and genetic basis for a child with Bainbridge-Ropers syndrome (BRPS).METHODS:Clinical data of the child were retrospectively analyzed. Copy number variation sequencing (CNV-seq) and trio based whole exome sequencing (trio-WES) were carried out. Prenatal diagnosis was provided for a at risk fetus from the pedigree, and genotype phenotype correlation was summarized through a literature review.RESULTS:The proband, a 6-year-old boy, has presented with feeding difficulties, specific craniofacial features, global developmental delay and intellectual disability, which has not improved after rehabilitation treatment. CNV-seq analysis of the patient showed no obvious abnormalities. A de novo heterozygous truncating variation, c.1448dupT (p.T484Nfs*5), was identified in the ASXL3 gene by trio-WES, which was a previously reported pathogenic variant. So far 14 Chinese patients with BRPS and ASXL3 variants have been reported. All patients have shown specific craniofacial features and delayed motor and speech development, and harbored 12 loss of function ASXL3 variants, which were de novo in origin and have clustered in exons 11 and 12 of the ASXL3 gene.CONCLUSION:The heterozygous frameshift c.1448dupT (p.T484Nfs*5) variant of the ASXL3 gene probably underlay the disorder in this patient. BRPS should be considered in infants with feeding difficulties, special craniofacial features, global developmental delay and hand anomalies, and WES can help to delineate the pathogenesis and establish the definite diagnosis.

Expanded carrier screening (ECS) has become an increasingly common technique to assess the genetic risks of individuals in the prenatal or preconception period. Unexpected variants unrelated to referral are being increasingly detected in asymptomatic individuals through ECS. In this study, we reported an asymptomatic male with duplication of exons 56–61 in the DMD gene through ECS using whole-exome sequencing (WES), which was also detected in a male patient diagnosed with typical Duchenne muscular dystrophy (DMD). Breakpoint analysis was then performed to explore the potential mechanisms of phenotypic differences using long-read sequencing (LRS), PacBio single-molecule real-time (PacBio SMRT) target sequencing, and Sanger sequencing. Complex structural variations (SVs) on chromosome X were identified in the asymptomatic male, which revealed that the duplication occurred outside the DMD gene; whereas, the duplication in the patient with DMD was a tandem repeat. The phenotypic differences between the two men could be explained by the different breakpoint junctions. To the best of our knowledge, this is the first report of a breakpoint analysis of DMD duplication in two men with different phenotypes. Breakpoint analysis is necessary when the clinical phenotypes are inconsistent with genotypes, and it applies to prenatal testing.