Functional & Integrative Genomics最新文献

Avian influenza virus (AIV) remains a persistent threat to global poultry production and public health, owing to its ability to infect a wide range of avian and mammalian species. The global resurgence of H5N1 and the limitations associated with control measures in intensive poultry production have highlighted the need for a paradigm shift in disease management strategies. In this context, the development of AIV resilient poultry lines is gaining momentum as a promising strategy for long-term disease management. In this review, we discuss the ongoing threat of AIV to poultry production and explore genetic approaches to enhance resilience against avian influenza. We primarily focus on intracellular host restriction factors that inhibit viral replication, followed by an overview of virus-targeted strategies. We further discuss the use of genome-wide screening approaches to study host–pathogen interactions to identify high confidence host targets. Finally, we highlight studies that develop transgenic, or genome engineered chickens with the aim to enhance AIV resilience and their potential for transforming AIV control in poultry production.

The thermotolerant Acetobacter oryzifermentans strain AAB5, originally isolated from unripe grape vinegar was identified based on 16S rRNA, recA, and whole-genome sequencing. The genome of AAB5 spans 2,969,314 bp and encodes 2,986 coding sequences (CDSs). Genome annotation revealed numerous genes associated with the strain’s metabolic capacity, thermotolerance, and environmental stress responses. CRISPRCasFinder analysis identified four CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, and comparative genomic analysis showed that, unlike other members of the species, AAB5 harbors a type I-F CRISPR-Cas system. Additionally, a 17.7 kb prophage region was detected in its genome. To gain deeper insights into the fermentative potential of AAB5, we analysed its carbohydrate-active enzyme (CAZyme) genes, which are involved in the synthesis, metabolism, and recognition of complex carbohydrates. The genome encodes 69 CAZymes, predominantly glycosyltransferases (GTs), followed by glycoside hydrolases (GHs). These genes support capabilities such as bacterial cellulose production, biotransformation of waste materials, degradation of phenolic compounds, and utilization of complex carbohydrate sources including starch derivatives, glucans, and trehalose. The genomic architecture of strain AAB5 highlights its metabolic versatility and its potential to serve as a functional industrial culture for traditional vinegar fermentation.

Background A major complication of diabetes, diabetic foot ulcers (DFU), has been linked to mitochondrial dysfunction and oxidative stress. Here, we performed analysis of RNA sequencing data from publicly available databases, including single-cell assays, to identify dysregulated genes associated with these processes in DFU and the specific cell types involved. Methods Analysis of transcriptome sequencing was performed on GSE134431 and GSE80178 datasets from the GEO database to identify differentially expressed mitochondrial-related genes (DE-MRGs) in DFU samples relative to controls. LASSO and SVM-RFE algorithms were used to identify critical genes, and functional enrichment analyses were conducted to identify associated pathways. Results were validated in a cohort of DFU samples and controls processed at our institution, and single-cell RNA sequencing data from GSE245703 was used to determine expression of candidate genes in endothelial cells from DFU relative to non-DFU samples. SiRNA knockdown of one candidate gene, LETM2, was performed in human umbilical vein endothelial cells (HUVECs) exposed to H₂O₂ as a model system for oxidative stress. Results LETM2 emerged as key gene significantly associated with DFU from our integrated analysis of the DFU RNA sequencing datasets. Single-cell RNA sequencing data revealed increased expression of LETM2 in endothelial cells from DFU samples compared to controls. Transcriptome sequencing of RNA from HUVECs with LETM2 knockdown under oxidative stress conditions revealed corelated expression with other genes involved in mitochondrial function. HUVECs with LETM2 knockdown furthermore showed impaired mitochondrial fission and mitophagy, as well as decreased cell viability and increased apoptosis in vitro. Conclusions These findings indicate a role for LETM2 in preserving mitochondrial function in HUVECs under oxidative stress and underscore its potential as a therapeutic target for mitigating mitochondrial dysfunction in diabetic complications such as DFU.

Mild traumatic brain injury (mTBI) is a prevalent condition accounting for over 70% of all traumatic brain injury (TBI) cases, and it is a major cause of posttraumatic cognitive impairment. Ferroptosis, a form of regulated cell death characterized by iron-dependent lipid peroxidation, has been implicated in the pathophysiology of mTBI. However, its precise role in mTBI - induced cognitive dysfunction and potential therapeutic strategies remain unclear. This study aimed to investigate the neuroprotective effects of mesenchymal stem cell - derived exosomes (MSC - Exos) against ferroptosis and cognitive dysfunction following mTBI. We established an mTBI rat model and administered MSC - Exos at different doses. Behavioral assessments, histological and molecular biological analyses, and bioinformatics approaches were used. The results showed that mTBI rats exhibited cognitive impairments, increased lipid peroxidation, and reduced GPX4 expression. MSC - Exos treatment improved cognitive function in a dose - dependent manner, attenuated lipid peroxidation, and restored GPX4 expression. Transcriptomic and bioinformatic analyses revealed that MSC - Exos activated the PI3K/AKT/mTOR signaling pathway, which upregulated GPX4 expression and inhibited ferroptosis. In conclusion, MSC - Exos alleviate cognitive deficits after mTBI by inhibiting ferroptosis via PI3K/AKT/mTOR - mediated upregulation of GPX4, providing a novel therapeutic strategy for mTBI.

Lactylation is a post-translational modification that can influence the onset and progression of various diseases.However, its role in Idiopathic Pulmonary Fibrosis (IPF) has not been systematically investigated. Single-cell sequencing and bulk RNA sequencing techniques were utilized to assess lactylation levels in IPF patients and health people. The clinical significance of lactylation was explored through survival and correlation analyses. Optimal feature genes of lactylation were identified using correlation analysis, multiple machine learning algorithms, Cox regression analysis and Mendelian randomization. The potential mechanisms of these Optimal feature genes were inferred through pseudotime analysis and gene pathway activity analysis, followed by experimental validation. Cell-cell communication and metabolic assessments were employed to explore the reasons for elevated lactylation levels in IPF, and relevant findings were verified through in vitro cellular experiments. Both single-cell sequencing and bulk RNA sequencing consistently demonstrated elevated lactylation levels in the IPF patients. High lactylation levels were associated with worse lung function and poorer prognosis. Through the integration of five machine learning algorithms, Cox regression analysis and Mendelian randomization, two optimal feature genes IGFBP7 and CCT2 were identified. These optimal feature genes were found to be significantly highly expressed in vascular endothelial cells, and this conclusion was experimentally validated. Pseudotime analysis results combined with RNA interference (RNAi) and wound healing assays demonstrated that both optimal feature genes promoted endothelial-mesenchymal transition (EndMT) in endothelial cells. Through cell-cell communication analysis, we discovered that TGF-β can promote metabolic reprogramming in endothelial cells, leading to increased lactate production and ultimately elevated expression of the optimal feature genes. Lactylation levels are significantly increased in IPF patients. TGF-β can induce metabolic reprogramming in endothelial cells, leading to high expression of IGFBP7 and CCT2, thereby promoting EndMT.

Non-coding RNAs (ncRNAs) are showing great potential as clinical indicators and are becoming essential regulators in gastrointestinal (GI) cancers. The computational discovery and subsequent confirmation of specific ncRNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in the pathophysiology of GI cancer (GIC) is the primary focus of this study. We reviewed a rigorous, multi-step validation workflow that includes RNA sequencing and bioinformatic analysis for initial discovery, quantitative PCR for confirmation in tissue and liquid biopsies, and receiver operating characteristic (ROC) and survival analyses for evaluating clinical usefulness. We highlight, as a specific result, that a panel of lncRNAs (e.g., H19, NEAT1, OIP5-AS, MALAT1) and miRNAs (e.g., miR-21, miR-92a) have been consistently validated with excellent diagnostic accuracy and are strongly associated with poor overall survival. According to our findings, these computationally generated ncRNA signatures are practical tools for GIC prognosis and early diagnosis, opening the door for their incorporation into personalized oncology.

Graphical abstract

The process of finding gastrointestinal cancer biomarkers based on non-coding RNA (ncRNA) is shown in this graphical abstract. The first step is to utilize high-throughput RNA sequencing to identify various ncRNAs, including microRNA (miRNA), circular RNA (circRNA), and long non-coding RNA (lncRNA). After potential biomarkers have been identified through computational approaches and bioinformatics analysis, they are validated using focused techniques such as quantitative PCR (qPCR). Lastly, diagnostic and prognostic assessment is done to determine the clinical value of these validated biomarkers.

Glycoside hydrolase family 1 (GH1) proteins are widely distributed in plants and function as β-glucosidases involved in cell wall metabolism, signal transduction, and stress responses. They enhance plant tolerance to abiotic stresses by optimizing osmotic regulation, mediating the activation of secondary metabolites, and mitigating ion toxicity. In this study, we identified a total of 153 GH1 gene family members across four cotton species: Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii. Phylogenetic analysis classified the GH1 genes into five distinct subgroups. Further analysis of gene structure and conserved motifs revealed that genes within the same subgroup share highly similar exon-intron organizations and consistent motif distributions, suggesting functional conservation among subgroup members. Chromosomal localization combined with MCScanX-based collinearity analysis indicates that segmental duplication is the primary mechanism driving the expansion of the GH1 gene family. Furthermore, promoter fanalysis revealed multiple stress-related cis-regulatory elements, including ABRE and MBSI, indicating potential regulation by abscisic acid (ABA) and stress-responsive transcription factors. RT–qPCR analysis of ten representative GH1 genes under 200 mM NaCl treatment revealed distinct expression patterns, with four genes significantly upregulated and five significantly downregulated relative to the control group. Additionally, functional verification through virus-induced gene silencing (VIGS) demonstrated that silencing Gohir.A02G106100 resulted in reduced plant height and shoot fresh weight compared to the controls. The findings indicated that plants with silenced Gohir.A02G106100 exhibited significantly greater sensitivity to salt stress than the negative control plants, suggesting that this gene may play a role in cotton’s response to salt stress.

β-Thalassemia is a prevalent autosomal recessive genetic disorder caused by mutations in the β-globin gene, leading to impaired hemoglobin production and chronic anemia. While traditional treatments such as regular blood transfusions, iron chelation, and supportive care have significantly improved patient survival, these methods remain palliative. The availability of curative options is limited, with allogeneic hematopoietic stem cell transplantation (HSCT) presenting risks due to donor constraints and procedure-related complications. Recent advances in the molecular understanding of β-thalassemia have opened the door to novel therapeutic strategies. Gene therapy approaches, including lentiviral vector-mediated β-globin gene addition and CRISPR/Cas9-mediated genome editing targeting the BCL11A enhancer, have shown promising results in clinical trials and have gained regulatory approval in several regions. Pharmacological interventions, such as luspatercept, which enhances erythroid maturation, and other fetal hemoglobin inducers, offer valuable alternatives for patients who are ineligible for gene-based therapies. This review explores the current landscape of β-thalassemia, including its epidemiology, pathophysiology, and clinical manifestations, while highlighting recent advances in treatment options. We critically evaluate the clinical data emerging from gene therapies and other innovative treatments, address the ongoing challenges, and outline future directions for enhancing patient outcomes through personalized and accessible care strategies.

MicroRNAs (miRNAs) are key regulators of gene expression in plant responses to abiotic stresses, including heat stress. High temperatures during the critical developmental stages of wheat (Triticum aestivum L.) drastically limit growth and production. Recent research has found that specific miRNAs regulate molecular complexes and physiological responses by targeting transcription factors, heat shock proteins, and signaling components, thereby modulating heat stress tolerance pathways. This review highlights current knowledge about heat-responsive miRNAs in wheat, including their validated targets and functional involvement in thermotolerance. In addition, we summarized the potential CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats /CRISPR associated protein 9) genome editing tool for precise alteration of miRNA genes or their targets, degradome profiling, the secondary structure of miRNA, and how interplay of miRNAs with HSFs and HSPs in target gene regulation to improve heat resilience. A comprehensive understanding of miRNA-regulated networks presents novel possibilities for developing climate-resilient wheat varieties, thereby ensuring food security in the face of global warming.

Diabetic nephropathy (DN) is a leading complication of diabetes mellitus. Engineered exosomes have shown promise in disease treatment by enabling targeted cargo delivery. RNA-binding motif protein 15 (RBM15) accelerates the progression of DN. This study developed siRBM15-loaded exosomes and evaluated their therapeutic efficacy and mechanisms. Exosomes were isolated from human umbilical cord MSCs (hucMSCs) and loaded with siRBM15 (siRBM15-Exo) by electroporation. Human glomerular mesangial cells (HGMCs) were exposed to high glucose (HG). A rat model of DN was generated by streptozotocin induction. The effects on cell pathological responses were evaluated by detecting α-SMA and collagen IV expression, TNF-α and IL-1β levels, ROS and MDA levels, SOD activity, the percentage of SA-β-gal positive cells, and senescence-associated factors p53 and p21. The impact on DN rats was assessed by measuring pathological changes and inflammation. Myostatin (MSTN) and RBM15 were overexpressed in DN kidneys and HG-stimulated HGMCs. MSTN depletion reduced the production of the related markers of fibrosis, inflammation, oxidative stress, and senescence in HG-stimulated HGMCs. Mechanistically, RBM15 stabilized MSTN mRNA via m6A methylation. Reintroducing MSTN reversed these protective effects of RBM15 silencing on HG-induced pathological responses in HGMCs. Furthermore, siRBM15-Exo attenuated HG-induced fibrotic, inflammatory, oxidative, and senescent responses in HGMCs and mitigated inflammation and pathological changes in DN rats. SiRBM15-Exo downregulated MSTN in HG-stimulated HGMCs. Our study shows that the siRBM15-Exo effectively suppress MSTN expression to alleviate DN progression, providing promising translational potential for DN therapy.

Graphical Abstract

SiRBM15-loaded engineered MSC exosomes (siRBM15-Exo) effectively reduce MSTN expression through m6A-dependent mechanisms, thereby attenuating DN progression by suppressing inflammation, ferroptosis, oxidative stress, and senescence.