Genes & genomics最新文献

Background: Identifying microbiome markers associated with ordered phenotypes, such as disease stages or severity levels, is crucial for understanding disease progression and advancing precision medicine. Despite this importance, most existing methods for differential abundance analysis are designed for binary group comparisons and do not incorporate ordinal information, limiting their ability to capture trends across ordered categories.

Objective: To develop and evaluate statistical methods that explicitly account for ordinal phenotype structure in microbiome data, addressing challenges such as sparsity and zero inflation, and improving the detection of meaningful microbial associations.

Methods: In this study, we propose and evaluate three novel approaches specifically tailored for microbiome association analysis with ordered groups: the binary optimal test, the linear trend test, and the proportional odds model-based permutation test (POMp). These methods explicitly account for the ordinal structure of phenotypes and address the sparsity and zero-inflation commonly observed in microbiome data through permutation-based inference. We applied the proposed methods to three publicly available gut microbiome datasets, including two related to obesity and one concerning colorectal cancer.

Results: All three proposed methods successfully identified differentially abundant features (DAFs) that exhibited stronger ordinal associations compared to those identified by existing methods. In particular, POMp consistently outperformed other approaches in terms of correlation with phenotype order, demonstrating its potential to identify biologically relevant markers.

Conclusion: The findings of this study highlight the importance of incorporating ordinal information in microbiome studies and provide robust statistical tools for advancing microbial biomarker discovery in complex disease contexts.

Background: Polypterus senegalus is a major actinopterygian fish that provides vital insights into vertebrate terrestrial adaptation. Advances in sequencing technologies have enabled improvements to the reference genome of P. senegalus, highlighting the need to expand research on this species.

Objective: In this study, we sought to construct high-quality, partially-phased, assemblies of the P. senegalus genome using high-fidelity long-read sequencing data.

Methods: First, partially-phased assemblies of P. senegalus genome using PacBio HiFi data. And then, our assemblies were compared with a previously published genome in terms of total length, contiguity, base-level accuracy, and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness, including resolution of repetitive regions and identification of telomere-telomere chromosomes.

Results: Compared with a previously published genome, our assemblies exhibit improved quality in overall quality. A total of 20,940 genes were annotated employing integrated short-read and long-read RNA sequencing data. Transcriptomics revealed the gene-expression relationships between 12 tissue types and the distinct expression patterns of genes associated with key evolutionary traits, such as aerial respiration, angiogenesis, and limb flexibility. Notably, several genes including Tcf21, Foxf1, and Tbx3a were coordinately expressed in the lungs and swim bladder, supporting shared origins and developmental patterns. Analyses of the correlations among tissues revealed physiological similarities between the lungs, kidneys, and spleen.

Conclusion: Our results provide a valuable genomic resource for P. senegalus and offer novel insights into the molecular basis of vertebrate organ evolution and adaptation.

Osteoarthritis (OA) is a common progressive joint disorder marked by synovial inflammation, cartilage degeneration, the formation of osteophytes, though its underlying molecular mechanisms remain unclear. This study integrated bioinformatics and experimental validation to identify key genes in OA synovium and their association with immune infiltration. Analysis of the GSE82107 dataset (10 OA, 7 controls) revealed 909 differentially expressed genes (525 upregulated, 384 downregulated). WGCNA identified the "midnightblue" module, and its intersection with DEGs yielded 122 genes enriched in cytokine-cytokine receptor interaction, JAK-STAT signaling, and autophagy pathways. Protein-protein interaction analysis highlighted FLT3LG, MC4R, CXCL10, CARTPT, and LHX2 as core genes (AUC 0.743-0.871). Immune infiltration analysis showed elevated M0 macrophages in OA, with CXCL10 showing a strong positive correlation with M1 macrophage infiltration (r = 0.74), and MC4R correlating with the presence of follicular helper T cells (r = 0.85). In vitro, OA-derived fibroblast-like synoviocytes exhibited CXCL10 upregulation, MC4R downregulation, and increased IL-6, IL-8, and TNF-α secretion, which were markedly reduced by CXCL10 knockdown or MC4R overexpression. Synovial tissue assays confirmed these expression patterns. CXCL10 and MC4R may represent promising diagnostic markers and therapeutic targets, offering new insights into OA immunopathogenesis and precision intervention.

Background: Parkinson's disease (PD) is a progressive neurodegenerative disorder marked by the loss of dopaminergic neurons, resulting in impaired motor control and cognitive decline. Despite current therapies, there remains a need for more effective and multifaceted treatment strategies.

Objective: This study explores the neuroprotective potential of exogenous Creatine in a Haloperidol-induced PD rat model, with a focus on reducing elevated homocysteine levels and targeting key proteins involved in PD pathology.

Method: We proposed a multitarget therapeutic approach, aiming to inhibit ADORA2A, alpha-synuclein, and monoamine Oxidase B (MAO-B) using the same bioactive compound. RNA-seq data from publicly available datasets (BioProject: PRJNA608432; GEO: GSE145814) were analyzed to identify dysregulated proteins and pathways associated with neuroactive ligand-receptor interaction, olfactory transduction, and phototransduction. Using computational methods, including RNA Seq analysis, molecular docking, MMGBSA, and ADME/T analyses, we screened for potential common ligand. Creatine showed a higher binding affinity for the target proteins compared to Levodopa (primarily used medication against PD), suggesting its therapeutic potential. In vivo experiments assessed the efficacy of Creatine through behavioural testing, redox status evaluation, biochemical markers, and histological analysis.

Result: The results potentially suggest that Creatine ameliorates motor deficits, reduces oxidative stress, and protects neuronal integrity in PD rats. Overall, our findings indicate that Creatine acts as a promising multitargeted approach, capable of modulating several PD-associated molecular mechanisms.

Conclusion: This approach may further be validated and pave the way for more effective, broad-spectrum treatments for Parkinson's disease, addressing both its motor and non-motor symptoms.

Background: Our previous research revealed that PRDI-BF1 and RIZ homology domain containing protein 14 (PRDM14) accelerated human non-small cell lung cancer (NSCLC) cell migration. However, the internal mechanism remains unclear.

Objective: Herein, we aimed to explore whether PRDM14 modulates NSCLS cell growth and metastasis via H3K27me3-mediated phosphatidylethanolamine-binding protein 1 (PEBP1)/Raf-1/MEK/ERK signaling.

Methods: PRDM14 overexpression plasmid (OE-PRDM14), siRNA targeting PRDM14 (si-PRDM14) or si-jumonji domain-containing protein 3 (si-JMJD3) were transfected to alter PRDM14 or JMJD3 expressions. Vemurafenib (VMF) was utilized to inhibit Raf-1/MEK/ERK signaling. Cell proliferation was tested via Edu staining and colony formation assay. Cell migration and invasion were evaluated through two-chamber transwell assay. The protein levels of polycomb repressive complex 2 (PRC2), tri-methylation at lysine 27 of histone H3 (H3K27me3) and PEBP1/Raf-1/MEK/ERK signaling were measured via western blotting. qPCR was used to test mRNA expressions of PEBP1, c-Fos, c-Jun and c-Myc.

Results: OE-PRDM14 promoted A549 cell proliferation, migration and invasion, elevated PRC2 and H3K27me3 expressions, lowered PEBP1 expression and activated Raf-1/MEK/ERK signaling. si-PRDM14 had contrary influences. VMF weakened the influences of OE-PRDM14 on A549 cell functions and Raf-1/MEK/ERK signaling, but had no significant effects on PEBP1 and H3K27me3 levels. si-JMJD3 accelerated the influences of PRDM14 overexpression on A549 cell functions, PEBP1 and H3K27me3 expressions, as well as Raf-1/MEK/ERK signaling.

Conclusions: PRDM14 promoted NSCLC proliferation, migration and invasion via modulating PRC2/H3K27me3-mediated PEBP1/Raf-1/MEK/ERK signaling activation. PRDM14 might be as a new target in NSCLC therapy.

Background: Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options, and paclitaxel resistance remains a major therapeutic challenge. Ferroptosis, an iron-dependent cell death mechanism, and microRNAs (miRNAs) like miR-325-3p have emerged as potential regulators of chemoresistance, but their roles in TNBC are poorly understood.

Objective: This study aimed to investigate whether ferroptosis and miR-325-3p modulate paclitaxel resistance in TNBC and to identify the underlying molecular mechanisms.

Methods: Paclitaxel-resistant TNBC cell lines (MDA-MB-231/Pac, SUM159PT/Pac) were established and treated with ferroptosis modulators. miR-325-3p expression was assessed in resistant vs. sensitive TNBC tissues and cells. Functional assays (CCK-8, EdU, flow cytometry, TBARS, FerroOrange) evaluated cell viability, proliferation, apoptosis, and ferroptosis markers. GSTP1 was validated as a miR-325-3p target via dual-luciferase reporter assays and rescue experiments. In vivo xenograft models tested the therapeutic potential of miR-325-3p overexpression with/without GSTP1 restoration.

Results: Ferroptosis inducers (erastin, RSL3) sensitized resistant TNBC cells to paclitaxel, while inhibitors (deferiprone, NAC) attenuated this effect. MiR-325-3p was downregulated in paclitaxel-resistant tissues and cells. Its overexpression restored paclitaxel sensitivity by promoting apoptosis and ferroptosis (↑iron accumulation, ↑lipid peroxidation). GSTP1 was identified as a direct target of miR-325-3p. Rescue experiments confirmed that GSTP1 restoration partially reversed miR-325-3p-mediated ferroptosis and paclitaxel sensitization. In vivo, miR-325-3p overexpression suppressed tumor growth, while GSTP1 co-expression mitigated this effect.

Conclusion: The miR-325-3p/GSTP1 axis regulates paclitaxel resistance in TNBC by modulating ferroptosis. Targeting this axis represents a promising strategy to overcome chemoresistance.

Background: Dystrophinopathy is severe X-linked recessive muscle disease caused by mutations in DMD gene. There is an increasing number of deep intronic variants in DMD gene, and understanding the pathogenic mechanisms of intronic variants can help the diagnosis and treatment of patients with DMD.

Objective: To identify two novel splice site variants in two families affected with Dystrophinopathy.

Methods: Two children with Duchenne muscular dystrophy (DMD) caused by DMD gene variants diagnosed at Women and Children's Hospital of Ningbo University in April 2024 and August 2024 were selected as the subject. Genomic DNA was extracted from peripheral blood samples of the children and subjected to whole exome sequencing. Suspected splicing variant was verified by Sanger sequencing of family members. The splicing effects of the variant on DMD was assessed in a minigene assay, and X chromosome inactivation (XCL) analysis was performed for female carriers in 2 families.

Results: Two rare intronic variants were identified in DMD patients. One variant, NM_004006.3: c.9807 + 2dup of DMD identified in patient 1, leading to the retention of 21 intronic nucleotides, introducing a truncated protein (p.Ala3270_Met3685delinsValLysLeuPheThrPhe). The other variant, NM_004006.3: c.5739 + 326T > G of DMD identified in patient 2, resulted in the retention of 43 or 19 intronic nucleotides, introducing a truncated protein(p.Glu1914Metfs*3). X-chromosome inactivation (XCI) patterns identified the mother of patient 2 were moderately skewed with 83.1% (normal allele)/16.9% (mutant allele) when compared with the sister of patient 2 with 45.1%/54.9%.

Conclusion: Our study discovered two novel splicing mutation of DMD in two DMD patients, which expand the variant spectrum of DMD and provide precise genetic diagnosis of DMD for timely therapy. XCI may explained the asymptomatic of female carriers of DMD.

Background: Mesothelioma is a rare and aggressive cancer with limited therapeutic options and poor prognosis. Despite advancements in understanding its molecular mechanisms, effective biomarkers and therapeutic targets remain elusive.

Objective: This study utilizes a multi-omics approach to identify potential biomarkers and therapeutic targets for mesothelioma.

Methods: A multi-omics framework integrating druggable genomics, Mendelian randomization (MR), and single-cell RNA sequencing (scRNA-seq) was employed. Druggable genes were identified using expression quantitative trait loci data, and therapeutic targets were predicted through MR analysis. These targets were cross-referenced with mesothelioma-specific single-cell markers and validated by summary data-based MR and protein quantitative trait loci analysis. Gene Ontology, KEGG, and Gene Set Enrichment Analysis were used to explore functional mechanisms. Drug sensitivity was assessed with the GDSC2 dataset, and potential therapeutic compounds were identified through molecular docking simulations using the Drug Signature Database. Mediated MR analysis investigated 731 immune cells and 1,400 metabolites as mediators of the identified genes' effects on mesothelioma.

Results: CYTL1 and H6PD were identified as potential biomarkers and therapeutic targets for mesothelioma. CYTL1 was associated with poor prognosis and reduced drug sensitivity, while H6PD showed the opposite trend. Although molecular docking results for H6PD were unfavorable, compounds targeting CYTL1 were identified. Immune cells did not mediate the effects of either gene on mesothelioma progression, despite their prognostic associations. Metabolic mediation analysis revealed that CYTL1 influences mesothelioma via levulinoylcarnitine levels, whereas H6PD regulates tumor metabolism through the mannose-to-mannitol-to-sorbitol ratio and glutamate-to-5-oxoproline ratio.

Conclusion: This study identifies CYTL1 and H6PD as key regulators of tumor metabolism in mesothelioma. CYTL1 is a promising therapeutic target, warranting further investigation, while H6PD remains a potential candidate despite unfavorable docking results. These findings demonstrate the value of multi-omics approaches in identifying novel therapeutic targets for mesothelioma.

Background: Early-life stress (ELS) is a significant risk factor for the development of numerous metabolic and physiological disorders later in life.

Objective: This study aims to investigate the effects of early-life stress on mitochondrial biogenesis, thermogenesis-related genes, and developmental signalling pathways in the stomach and duodenum of offspring.

Methods: This study consists of three groups: the first is the control group, and the second and third groups were randomly exposed to unpredictable maternal separation (MS) for three hours a day on postnatal days (PND) 1-14. The third group was exposed to unpredictable maternal stress (MSUS) in addition to MS. Mice were sacrificed at PND35. Total RNA was extracted from the tissues (corpus region of the stomach and the start zone of the duodenum) via the phenol‒chloroform technique. The expression levels of miR-34c-5p, Notch1, Prdm16, Ppargc1a, and Ucp1 were measured via Rotor-Gene Q.

Results: Although the expression of miR-34c-5p remained unchanged between the groups, the mRNA expression of genes associated with mitochondrial biogenesis and thermogenesis increased significantly with increasing stress in females. In males, the expression also increased significantly in the MS but returned to control levels in the MSUS.

Conclusions: ELS can stimulate Ucp1-mediated thermogenesis in gastrointestinal tissues by promoting mitochondrial biogenesis, which is driven by Prdm16 and mediated by Ppargc1a. ELS might initiate mitochondrial biogenesis to accommodate the growing energy demands of the digestive system. However, increased stress alters mitochondrial biogenesis and thermogenesis-related gene expression in a sex-specific manner.

Background: Immunoglobulin A nephropathy (IgAN) represents the most prevalent form of primary glomerulonephritis. Long noncoding RNAs (lncRNAs) play critical roles in the initiation and progression of various diseases, including kidney disorders. However, the involvement of lncRNAs in IgAN remains underexplored. This study aims to investigate the potential role of lncRNAs in IgAN by constructing a comprehensive lncRNA-miRNA-mRNA regulatory network.

Methods: An IgAN mouse model was established for the study. The expression profiles of lncRNAs and mRNAs were obtained via RNA sequencing (RNA-seq) to identify differentially expressed mRNAs and lncRNAs. A lncRNA-mediated competing endogenous RNA (ceRNA) regulatory network was subsequently constructed through bioinformatics analysis, and pathway enrichment was explored through functional analyses. Validation of lncRNAs, miRNAs, and mRNAs was performed via Real-time quantitative polymerase chain reaction (RT-qPCR).

Results: Histological analysis using hematoxylin and eosin (HE) staining and immunofluorescence confirmed the successful development of the IgAN mouse model. Enzyme-linked immunosorbent assay (ELISA) and biochemical index testing indicated significant increases in renal function markers, including Immunoglobulin A (IgA), Blood Urea Nitrogen (BUN), and Creatinine (CRE). RNA-seq analysis revealed 388 differentially expressed lncRNAs and 256 differentially expressed mRNAs. A bioinformatics-based ceRNA network, focused on inflammation and immune response, was successfully constructed, comprising 19 lncRNAs, 7 mRNAs, and 5 miRNAs. Functional enrichment analysis identified significant involvement of these lncRNAs in the MAPK, Ras, and PI3K-Akt signaling pathways. Finally, the RT-qPCR validation data agreed with the RNA-seq.

Conclusion: This study identified a novel lncRNA/miRNA/mRNA regulatory network involved in the pathogenesis of IgAN.