Molecular Genetics and Genomics最新文献

Neurodevelopmental disorders (NDDs) exhibit complex genotype-phenotype associations that frequently result in inconclusive variant interpretations, contributing to suboptimal diagnostic yields (~ 40%). Koolen-de Vries syndrome (KdVS), an autosomal dominant NDD caused by KANSL1 haploinsufficiency, exemplifies this diagnostic challenge with its multisystem manifestations and lack of systematic genotype-phenotype associations. To address this gap, we constructed a comprehensive KdVS genotype-phenotype repository by systematically integrating all molecularly confirmed cases from global literature. Comprehensive phenotypic analysis revealed that core KdVS features include developmental delay/intellectual disability, characteristic craniofacial dysmorphism, hypotonia, and multisystem abnormalities. Phenotypic association analysis identified 249 significant correlations, demonstrating that KdVS clinical manifestations are highly interconnected rather than representing isolated features, such as the association between strabismus and hydrocephalus (OR = 14.26). Application of this repository to screen a Chinese rare disease cohort identified 53 KANSL1 variants. Among these, one de novo nonsense variant (NM_001193466.2: c.902T > G, p.Leu301Ter) was classified as pathogenic in a Chinese boy with classic KdVS features. The remaining 52 variants were categorized as variants of uncertain significance (VUS), approximately half of which were absent from gnomAD databases. Each VUS was comprehensively annotated with detailed clinical profiles to facilitate phenotype-driven reinterpretation. In conclusion, this study establishes KdVS as a highly interconnected multisystem disorder and demonstrates that deep phenotypic association analysis enhanced genetic diagnosis. This disease-specific repository approach provides a scalable framework for improving molecular diagnostics across rare NDDs.

Citrobacter koseri is a Gram-negative, multidrug-resistant bacterium linked to severe infections in immunocompromised individuals and neonates. It is especially linked to sepsis and meningitis, which often lead to CNS abscesses in newborns. Most infections happen randomly, but some are passed down from parent to child. There have also been reports of hospital-acquired outbreaks in neonatal care units. Even though diagnostic and treatment methods have improved, the death rate is still high. About one in three affected babies dies, and almost half of them suffer long-term neurological damage. As antibiotic resistance becomes more common, there is a growing need to look into new ways to treat diseases, such as vaccines and new drug targets. In order to address this issue, a thorough in-silico methodology integrating subtractive proteomics and reverse vaccinology was employed to pinpoint potential therapeutic targets from the core proteome. Five multi-epitope vaccine constructs were created using B- and T-cell epitopes from prioritized proteins, based on epitope prediction. Physicochemical and docking analysis identified constructs V1 and V5 as having strong binding affinities to Toll-like receptors TLR4 and TLR2, respectively. Furthermore, MD simulations validated the structural stability of docked complexes. In-silico immune simulations revealed that the constructs might induce robust immune responses. Additionally, potential drug target proteins were subjected to druggability analysis. This study presents a promising computational framework for combating C. koseri, though experimental and animal model validations are necessary to confirm the findings of this study.

The aim of this study was to identify the genetic cause of Branchio-oto-renal (BOR) syndrome using whole genome sequencing (WGS) in a previously unsolved case. We describe a novel, deep intronic variant in EYA1 that segregates with BOR syndrome in three generations in a Danish family. According to the prediction algorithm, SpliceAI, the variant creates a cryptic splice donor site in intron 7, resulting in inclusion of a pseudo-exon. We functionally assessed the intronic variant using an in-vitro splicing assay confirming a spliceogenic effect. The abnormally spliced EYA1 transcript is expected to undergo nonsense mediated decay resulting in haploinsufficiency. In conclusion, we identified the genetic cause of BOR syndrome in the family. To the best of our knowledge, this is the first report of a causative deep intronic variant in BOR syndrome. Our results demonstrate the clinical utility of WGS in cases with highly specific phenotypes.

There is ever increasing evidence for significant amounts of translation upstream of known AUG start codons in protein coding genes. Some of this translation is from upstream open reading frames (ORFs) that are unconnected to the main coding exons, but upstream initiation codons that are in-frame with coding exons can produce N-terminally extended protein isoforms. N-terminal extensions have much more proteomics support than the shorter proteins predicted to be produced from upstream ORFs. The upstream regions that produce N-terminal extensions have certain characteristics in common. They are highly GC-rich, most of the predicted start codons are non-AUG, and most do not conserve their reading frames beyond simians. The extended isoforms themselves are found significantly more frequently in dysregulated cells than in normal tissues. Approximately one in seven of these N-terminal extensions are upstream of signal peptides and would almost certainly block their recognition by the signal recognition particle. As a result, N-terminally extended isoforms containing exposed, hydrophobic signal peptides would be expected to accumulate in the cytoplasm. However, this analysis finds that those N-terminal extensions that would block signal recognition are practically not detected at the protein level even though the transcripts that would produce these extensions are found as expected in ribosome profiling experiments. This is a clear indication that these mislocated proteins are degraded after translation. Theprobable degradation of these extended proteins strongly suggests that their translation is a side effect of inefficient translation initiation.

Microorganisms rapidly adapt to non-lethal stress through mutations, a process central to microbial evolution. In this study, we investigate the molecular mechanism of adaptive mutagenesis in the bacterial strain Escherichia coli K-12 harboring a frameshift lac mutation. A non-random mutational spectrum, featuring a prominent - 1 bp deletion hot-spot is an intriguing unsolved phenomenon seen in the revertants of starving cells of this strain. The very-short-patch mismatch repair, a stationary-phase specific DNA repair pathway, has been hypothesized to create this hot-spot. To test this, we independently inactivated two main players of this pathway: dcm involved in DNA cytosine methylation and vsr encoding a sequence-specific DNA repair endonuclease. Contrary to the prediction of our hypothesis, the stationary-phase mutational spectra of Δdcm and Δvsr strains were indistinguishable from that of the wild-type strain, i.e., the frequency of mutations at the hot-spot remained unchanged. Unexpectedly, both Δdcm and Δvsr strains showed a two-fold increase in stationary-phase reversion frequency with respect to the wild-type strain. This result differed from an earlier finding where simultaneous deletion of both genes had no effect. We conclude that the adaptive mutation hot-spot is not caused by very-short-patch mismatch repair. Instead, our data suggest that dcm and vsr independently influence adaptive mutagenesis rate, possibly through previously unrecognized 'moonlighting' functions. Future work will aim to uncover the mechanism behind this unique adaptive mutational spectrum, advancing our understanding of stress-induced mutagenesis.

Cardiovascular diseases are the leading causes of mortality globally, of which coronary artery disease (CAD) is the most frequent. Several epigenomics and transcriptomics studies of CAD have been conducted, however, only a few studies have utilized the statically powerful discordant twin pair design, which reduces the confounding introduced by genetics. Finally, no study has investigated the link between the DNA methylation position and gene expression levels. The present study aims at filling this knowledge gap, to present novel biomarkers of CAD. We investigated 44 Danish twin pairs that were discordant for incident CAD, for whom, both genome-wide DNA methylation (CpG) and gene expression (probe) data were available. We identified CpGs and probes, which were more different within the twin pairs than expected by change, and investigated these by Cox regression analysis. CpGs and probes belonging to the same gene were divided into groups based on their directions of effect, and these genes were investigated by gene set enrichment and interaction network analyses. Overall, we found that CAD co-twins showed DNA methylation patterns leading to up-regulated gene expression; especially with demethylation of promoters and methylation of gene bodies, compared to their non-CAD co-twin. Generally, we found that the largest biological group of up-regulated pathways related to immune-inflammation processes, whereas down-regulated pathways related to muscle system biology, among others. Hence, the present study uncovers a specific pattern between DNA methylation position and gene expression levels relating to CAD, pointing to a need for additional studies. However, such multi-omics designs are surprisingly rare.

Objective: Temozolomide (TMZ) resistance is a major cause of treatment failure in glioblastoma (GBM). This study investigates the role and mechanism of the RNA-binding protein RNA-binding motif protein 7 (RBM7) and F-box and leucine-rich repeat protein 16 (FBXL16) in TMZ resistance in GBM, focusing on mitochondrial dysfunction and ferroptosis. TMZ-resistant GBM cell lines (TR/U87) were established through gradient induction. Cell viability and proliferation were assessed using the Cell Counting Kit-8 assay and colony formation assays. Western blot analysis and immunohistochemistry were performed to measure FBXL16, activating transcription factor 4, and peroxisome proliferator-activated receptor gamma coactivator 1-alpha protein expression. Transwell assays evaluated TR/U87 cell migration and invasion. Co-immunoprecipitation and RNA immunoprecipitation assays verified the interaction between RBM7 and FBXL16. An actinomycin D assay analyzed FBXL16 mRNA stability. Flow cytometry was used to detect reactive oxygen species, iron levels, and apoptosis. A nude mouse xenograft model was used to validate in vivo effects. RBM7 was highly expressed in TMZ-resistant cells. Knockdown of RBM7 suppressed TR/U87 cell proliferation and migration, induced mitochondrial structural damage, and triggered ferroptosis. Mechanistically, RBM7 interacted with FBXL16 and reduced its mRNA stability. FBXL16 knockdown reversed RBM7 deficiency-induced ferroptosis and chemosensitivity. In vivo experiments confirmed that RBM7 knockdown combined with TMZ significantly inhibited tumor growth. RBM7 promotes TMZ resistance by suppressing mitochondrial dysfunction and ferroptosis through destabilization of FBXL16. Targeting the RBM7-FBXL16 axis may represent a novel strategy to overcome GBM chemoresistance.

Harvest index (HI), a key yield-related trait in wheat, is influenced by genetic, phenological, environmental, and stress factors. In the Indo-Gangetic Plains (IGP) of India, spot blotch (SB) poses a major biotic stress, reducing grain yield by affecting photosynthesis and HI. Identifying stable wheat genotypes and genomic regions controlling these traits are essential for developing resilient wheat for the IGP. We evaluated 1500 elite wheat lines in four environments at IGP, including SB and disease-free (DF) conditions. On average, in the SB condition HI (%) reduced by 4.3% compared to its DF environment. Genome-wide association studies identified important SNPs:1A_494392059, 1A_495192503, 2A_32931719, 3B_10249157, 3B_10644041, 3B_6127880, 5B_538548049, 6A_96651968, 7A_49592941 and 7D_326728664, and a favourable haplotype TTGTCG (n = 303), which showed higher average HI (39.75%) under SB conditions. Additionally, most of candidate genes associated with the identified SNPs were involved in senescence and disease resistance. Stability analysis using AMMI and genotype selection index identified a set of genotypes with consistently high and stable HI under both SB and DF conditions. Further, genotypes with favourable alleles at all these identified significant MTAs, and stable genotypes identified for HI shared common genetic contributors, including the SR50 gene and prominent wheat varieties such as KACHU, PASTOR, and PRL. These genetic backgrounds play a pivotal role in conferring both disease resistance and yield stability, highlighting their importance in wheat breeding programs for IGP. Further, Genomic predictions using genome-wide markers demonstrated moderate predictive accuracy, ranging from 0.22 to 0.39, with higher accuracy observed under SB conditions. The stable genotypes and genomic regions identified in this study could serve as important resources and knowledge for developing resilient genotypes adapted to the IGP.