Molecular Genetics and Genomics最新文献

Synodontis, of great edible and ornamental value, is the most species-rich genus of the catfish family Mochokidae, but comparative studies based on its mitogenome data are still lacking. Therefore, we sequenced and analyzed the complete mitogenomes of Synodontis decorus and Synodontis petricola and compared them with those of other Mochokidae or Synodontis species; these were determined to be 16,574 and 16,529 bp, respectively. A phylogenetic analysis further confirmed the position of Synodontis in Mochokidae and showed that the genus Synodontis is polyphyletic. These results are beneficial to a further understanding of the phylogenetic evolution of the Mochokidae family and Synodontis genus and provide a basis for species identification and conservation genetics.

Understanding gene function in vertebrate development requires tools that allow precise and timely manipulation of gene expression. Zebrafish (Danio rerio), with its transparent embryos and rapid development, offers an ideal model to study vertebrate biology. This review explores how morpholino oligonucleotides (MOs), a widely used tool for transient gene knockdown, have been employed to investigate the roles of carbonic anhydrases (CAs) and carbonic anhydrase-related proteins (CARPs) in zebrafish. CAs are metalloenzymes, while CARPs are inactive isozymes that play critical roles in pH regulation, ion transport, CO₂ metabolism, and protein interactions influencing diverse biological functions. Many of the MO knockdown studies presented here have been extensively conducted in our laboratory over the past decade, revealing novel roles for CAs in neural development, reproduction, and swim bladder formation. These studies also confirm roles previously reported in humans, such as pigmentation, acid-base homeostasis, neural development, and motor coordination. We discuss technical aspects of MO design, delivery, and validation, and address common challenges such as off-target effects, transient gene silencing, and the necessity of rescue experiments. In addition, the review includes a comparative analysis of MOs versus CRISPR/Cas9-based genome editing, underscoring their respective advantages and limitations for functional genomics. In conclusion, this review provides not only a methodological guide but also biological insights into CA function in zebrafish, highlighting how antisense technology continues to inform vertebrate development and disease modeling. The lessons learned here may inform the study of other gene families and support translational research in carbonic anhydrase-related human disorders.

Susceptibility to SARS-CoV-2 infection and severity of COVID-19 have high heterogeneity, but the underlying factors for such heterogeneity were largely unknown. This study aimed to investigate whether genetically determined immune phenotypes contribute to the variability in COVID-19 outcomes, by integrating large-scale GWAS data to assess genetic correlations, causal associations, and pleiotropic gene functions. Based on the summary statistics from GWAS analyses for immune phenotypes and COVID-19 outcomes, comprehensive analyses were performed to elucidate the associations between immune phenotypes and COVID-19 pairs. The genetic correlations between COVID-19 outcomes and immune phenotypes were commonly observed, and 60 immune phenotypes were significantly correlated with four COVID-19 outcomes (64 pairs) (FDR < 0.05). Treg T cell panel and B cell panel have relatively more significant pairs in number. Pairwise gene-based analyses identified numerous pleiotropic genes for significant pairs identified. The gene set enrichment analysis revealed the involvement of the identified pleiotropic genes in complex immune processes. We observed significant causal effects of six immune phenotypes from 4 trait panels on any one of the two COVID-19 outcomes, and of which CD19 on naïve-mature B cell was the only significant immune phenotype shared by the two COVID-19 outcomes. The findings greatly improved our understanding of the interaction between immune response and COVID-19 outcome, and also contribute to the detection of susceptible individuals and the design of therapeutic strategies from the perspectives of immunology. In conclusion, our study provides genetic evidence that immune phenotypes, particularly B cell and Treg traits, play a causal role in susceptibility to SARS-CoV-2 infection and progression to severe COVID-19.

Esophageal squamous cell carcinoma (ESCC) is a malignant cancer. At present, platinum-based chemotherapy drugs are mainly used to treat ESCC patients. However, certain patients have developed significant resistance to cisplatin, which greatly limits the effectiveness of treatment. Hence, it is urgent to probe the mechanism of cisplatin chemotherapy resistance in ESCC. To clarify the association between AL137246.1 level and cisplatin resistance in ESCC patients, a total of 30 pairs of cisplatin-sensitive and cisplatin-resistant ESCC tissues were collected, and 30 non-cancerous tissues were used as controls. Survival analysis was used to detect the relationship between AL137246.1 level and ESCC prognosis. Then, Eca109 and Kyse70 cells were treated with cisplatin to induce the ESCC cisplatin resistance model. For understanding the detailed molecular process involving AL137246.1 in the development of cisplatin resistance in ESCC, the binding relationship between GLI2 and ABCC1 promoter was determined by dual luciferase and ChIP assays. RIP was applied to test the interaction between AL137246.1 and GLI2. Cell viability and proliferation were detected by CCK8 and Edu assays, respectively. Cell apoptosis was detected by flow cytometry. The results indicated that AL137246.1 level was reduced in ESCC and indicated a poor prognosis of ESCC. AL137246.1 overexpression was associated with increased sensitivity to cisplatin in ESCC cells, which was reversed by ABCC1 upregulation. Mechanistically, GLI2 led to the transcriptional activation of ABCC1 in ESCC. In conclusion, AL137246.1 inhibited the expression of ABCC1 by binding to GLI2, thereby enhancing the sensitivity of ESCC to cisplatin. This study suggested that AL137246.1, as a potential molecular target, has important application prospects in improving the sensitivity of ESCC to cisplatin chemotherapy.

Taxonomic and functional analysis outcomes are greatly influenced by the algorithms and databases used by different software. The present study evaluated three widely used software; MG-RAST, MEGAN6 and Kraken2 for the analysis of the shotgun metagenomic data of saffron cormosphere. Kraken2 outperformed other two for taxonomy. It gave significantly higher alpha diversity values, indicating greater taxonomic diversity and evenness compared to MG-RAST and MEGAN6. The limitation of the Kraken2 is that it does not support functional analysis which both MG-RAST and MEGAN6 can do in addition to taxonomical analysis. Additionally, they can analyse sequence data generated by different sequencing methods such as Sanger, Illumina and PacBio. MG-RAST is comparatively easy to use and integrates large number of databases than MEGAN6, however data processing is relatively slow. Additionally, MEGAN6 has a feature of extraction of genes automatically, that allows user to study sub set of specific genes, though in MG-RAST, it can be done manually and the process is cumbersome. The difference in the outcome of these three software can be attributed to differences in the databases, algorithms, and parameters used by the three software. A combined approach using the results from more than one software can be considered to create a more comprehensive taxonomy and functional profile until a factotum software is developed.

Aging is a major biological process underlying increased risk of chronic and neurodegenerative diseases, yet its molecular mechanisms remain incompletely defined. Our study systematically investigates the conserved functions and pathways of W06A7.4 in Caenorhabditis elegans and its human homolog TMEM144 in the regulation of aging, combining genetic manipulation in model organisms, analysis of human clinical samples, and functional assays in cell lines. The results demonstrate that W06A7.4 promotes longevity in C. elegans through synergistic effects with dietary restriction, reduction of oxidative damage, modulation of IIS and mTOR signaling, and maintenance of mitochondrial membrane potential. In human samples and cellular models, TMEM144 expression increases with age and in Alzheimer's disease. Our results suggest that TMEM144 may be involved in the regulation of glucose transport and mitochondrial respiration via the downstream protein TIMMDC1. These findings advance our understanding of evolutionarily conserved aging pathways and identify W06A7.4/TMEM144 as promising molecular targets for anti-aging and neurodegenerative disease interventions.

Antimicrobial resistance (AMR) presents a critical global challenge, causing over 1.27 million deaths annually, with projections reaching 10 million by 2050. Among the most concerning contributors are Enterobacteriaceae, particularly Escherichia coli and Klebsiella pneumoniae, which harbour Extended-Spectrum β-Lactamase (ESBL) genes-enzymes that hydrolyse β-lactam antibiotics and confer resistance-such as bla-CTX-M, bla-SHV, and bla-TEM. These genes confer resistance to β-lactam antibiotics, including penicillins and cephalosporins, limiting treatment options for urinary tract infections, bloodstream infections, and pneumonia. The World Health Organisation has classified these pathogens as critical targets for new drug development. In this study, we comprehensively analysed all known variants of bla-CTX-M, bla-SHV, and bla-TEM genes along with their wild-type sequences. Using a multi-step computational approach, we assessed guanine-cytosine (GC) content, single nucleotide polymorphisms (SNPs; single-base changes in DNA), insertion and deletion (InDel) variants (mutations involving nucleotide addition or removal), codon usage patterns, transcription factor binding sites (TFBS; DNA regions regulating gene expression), amino acid composition, protein stability, mutational hotspots, nucleotide and amino acid mutation frequencies, hydrophobicity, isoelectric point, aromaticity, aliphatic index, and molecular flexibility. The integrated dataset maps conserved regions and identifies residues frequently associated with resistance phenotypes. Our findings provide a framework for predicting resistance-associated mutation patterns and identifying genomic regions suitable for resistance-free drug targeting. These insights support prioritising drug target sites, optimising screening libraries, and generating high-quality datasets for machine learning-based precision drug design.

Diamond-Blackfan anaemia (DBA) is a rare inherited disorder marked by early-onset macrocytic anaemia and erythroid hypoplasia, resulting from mutations in ribosomal protein genes. Despite growing genetic insights, data on functional validation remain limited in India; here we report a novel RPS10 mutation with functional validation and provide genotype-phenotype correlation by integrating our findings with all previously reported RPS10 variants. A clinically suspected Diamond-Blackfan anaemia (DBA) case was evaluated through haematological profiling, bone marrow examination, and erythrocyte adenosine deaminase (eADA) activity measurement. Whole exome sequencing (WES) was followed by Sanger sequencing to identify and validate a novel pathogenic variant. Gene expression of ribosomal and regulatory genes was analysed by quantitative RT-PCR, and rRNA processing analysis was carried out to assess functional impact. The proband presented with severe macrocytic anaemia, reticulocytopenia, and erythroid hypoplasia consistent with Diamond-Blackfan anaemia (DBA). Whole exome sequencing identified a novel heterozygous nonsense variant in RPS10 (c.206G > A; p.Trp69Ter), and Sanger sequencing confirmed the variant as de novo. Gene expression analysis revealed significant upregulation of TP53 and downregulation of RPS10 and GATA1, indicating ribosomal dysfunction and activation of the p53 pathway. Additionally, the rRNA processing defect validated the pathogenicity of the novel RPS10 variant. This study identifies a novel de novo nonsense variant in RPS10 associated with Diamond-Blackfan anaemia, with supporting functional evidence of haploinsufficiency and p53 pathway activation. These findings expand the mutational spectrum of RPS10 and underscore the diagnostic value of integrating genomic and functional analyses in rare haematological disorders, while also contributing to ongoing efforts to delineate genotype-phenotype correlations in DBA.

Moraxella catarrhalis is a Gram-negative diplococcus bacterium and a common respiratory pathogen, implicated in 15-20% of otitis media (OM) cases in children and chronic obstructive pulmonary disease (COPD) in adults. The rise of drug-resistant Moraxella catarrhalis has highlighted the urgent need for the potent vaccine strategies to reduce its clinical burden. Despite a mortality rate of 13%, there is no FDA-approved vaccine for this pathogen. The aim of this study was to computationally identify novel antigens and design a multi-epitope peptide-based vaccine candidate against M. catarrhalis using an immunoinformatics-driven subtractive proteomics and reverse vaccinology approaches. The core proteome of 12 M. catarrhalis genomes were analyzed, identifying 360 host non-homologous proteins. Subsequent screening revealed 30 metabolic pathway-dependent and 7 independent drug targets, along with 7 membrane and extracellular proteins as potential vaccine candidates. A prioritized protein target (WP_081569984.1) was selected for vaccine design. The predicted B-cell, MHC-I, and MHC-II epitopes were linked using adjuvants and linkers to construct four vaccine candidates (V1-V4). These constructs were assessed for physicochemical properties, allergenicity, antigenicity, secondary structures, and immune receptor interactions. As a result, V1 emerged as the most promising candidate. Molecular docking and molecular dynamics (MD) simulations evaluated the interactions of V1 with human toll-like receptors (TLR2 and TLR3). MD trajectories including RMSD, RMSF, Radius of gyration (Rg), SASA, binding free energy (MM-PBSA), PCA, free energy landscapes, and DCCM, showed a strong interaction of vaccine with the TLR recptors. Immune simulations predicted significant immune responses against the proposed vaccine. Additionally, the vaccine construct was in-silico tested in an E. coli plasmid vector (pET-28a(+) for its cloning potential. These findings highlight the potential of the proposed multi-epitope vaccine V1 as a safe and effective preventive strategy against M. catarrhalis-associated infections, and additionally laid the groundwork for future in vitro, in vivo, and clinical studies to validate its immunogenicity and protective efficacy.

Accurate variant calling is essential for next-generation sequencing (NGS)-based diagnosis of rare diseases, yet most benchmarking studies have focused on standard cell lines or trio-based samples, with limited relevance to sporadic cases. Here, we systematically compared the performance of DeepVariant and GATK HaplotypeCaller in two Chinese cohorts of patients with sporadic epilepsy (EP) and autism spectrum disorder (ASD). DeepVariant exhibited higher precision and sensitivity in detecting single nucleotide variants (SNVs), while GATK showed a distinct advantage in identifying rare variants, which are often key to understanding the genetic basis of rare diseases. Comparative analyses based on disease-related gene panels further highlighted differences in the identification of potentially deleterious variants. These findings reveal important trade-offs between variant callers and emphasize the need to tailor variant-calling strategies to specific research and clinical contexts. Our study provides practical vision for optimizing germline variant detection pipelines in sporadic neurodevelopmental disorders, offering broader insights for precision medicine applications.