Genes & genomics最新文献

Background: Defensins, small cationic peptides with strong antimicrobial activity, are key effectors of innate immunity. α-defensins, human neutrophil peptides, are produced primarily by neutrophils and serve as an essential component of the airway defense system against invading pathogens. However, accumulating evidence indicates that α-defensins released from human neutrophils are markedly elevated in various lung diseases, where excessive α-defensins exert cytotoxic effects on epithelial and immune cells.

Objective: We investigated how α-defensins influence macrophage inflammatory responses and aimed to elucidate the molecular mechanisms underlying α-defensin-induced macrophage activation.

Methods: Through RNA-seq analysis, we identified key molecules potentially involved in α-defensin-induced inflammatory signaling and validated these candidates using qRT-PCR and western blotting.

Results: Our results show that α-defensins significantly upregulate both the gene expression and protein levels of RNF31 in macrophages, leading to enhanced phosphorylation of NF-κB p65 and increased production of pro-inflammatory cytokines. Furthermore, when co-cultured with lung epithelial cells, α-defensin-stimulated macrophages induced NLRP3 expression in epithelial cells, suggesting that macrophage-epithelial crosstalk contributes to α-defensin-driven airway inflammation.

Conclusion: Together, our results reveal that α-defensins promote macrophage-driven inflammation through RNF31-dependent NF-κB activation and subsequent macrophage-epithelial communication, providing new insight into the inflammatory mechanisms of lung injury. These findings uncover a previously unrecognized α-defensin-RNF31 signaling pathway that amplifies macrophage-mediated airway inflammation, highlighting RNF31 as a potential therapeutic target for inflammatory lung diseases.

Background: Bladder cancer (BCa) is the most frequently seen malignancy of the urinary tract. However, its molecular mechanisms and therapeutic targets are not well established.

Objective: This study aims to investigate the mechanism by which tissue specific transplantation antigen P35B (TSTA3) mediates the suppression of epithelial-mesenchymal transition (EMT) in BCa through targeted regulation of lysosome-associated membrane protein 2 (LAMP2) expression via the mitogen-activated protein kinase (MAPK) signaling pathway.

Methods: Public datasets were analyzed to predict TSTA3 expression and prognosis in BCa. TSTA3 and LAMP2 expression levels were examined in 30 paired BCa and adjacent normal tissues, followed by Pearson correlation analysis of their mRNA levels. TSTA3 expression was quantified in T24, BIU-87 and simian virus 40-immortalized human urothelial cell line-1 (SV-HUC-1). T24 and BIU-87 cells were subjected to TSTA3 knockdown or overexpression. Cell proliferation, migration/invasion (Transwell), apoptosis (flow cytometry), EMT markers (immunofluorescence), and LAMP2/MAPK pathway proteins were evaluated.

Results: TSTA3 upregulation was demonstrated in public databases, BCa patient tissues, and cell strains. TSTA3 knockdown in T24 cells substantially suppressed proliferation, colony formation, invasion, migration, and apoptosis while increasing E-cadherin and decreasing Vimentin expression, whereas TSTA3 overexpression in BIU-87 cells promoted malignant phenotypes. TSTA3 and LAMP2 mRNA levels showed a strongly negative correlation in BCa patients. LAMP2 knockdown reversed the tumor-suppressive effects of TSTA3 silencing. Inhibition of the MAPK pathway rescued the functional deterioration of T24 cells caused by TSTA3 overexpression.

Conclusions: TSTA3 promotes BCa proliferation, migration, invasion, and EMT by regulating LAMP2 to activate the MAPK pathway.

Background: Understanding the molecular regulation of gestation is crucial for improving reproductive efficiency in Hanwoo cattle, yet the systemic changes occurring throughout pregnancy remain undefined.

Objective: To identify molecular mechanisms underlying pregnancy progression and develop potential biomarkers for early detection through transcriptome profiling.

Methods: Whole blood samples were collected from 15 Hanwoo cows at five physiological stages: non-pregnant, and at 2-, 4-, 16- and 40-week of gestation. RNA sequencing was performed to identify differentially expressed genes (DEGs), and their functional roles were predicted using Gene Ontology and pathway enrichment analyses. Additionally, time-series clustering was conducted to track expression patterns, and validation of candidate early pregnancy biomarkers was performed via qRT-PCR.

Results: A total of 2,029 DEGs were identified across the gestation period. Early pregnancy (2-4 weeks) was characterized by immune tolerance mechanisms and the downregulation of TLR9 signaling, with ADGRE3 and OCSTAMP identified as key genes for uterine receptivity. Mid-pregnancy (16 weeks) exhibited significant upregulation of NOTCH2 and SMAD4, essential for placental maturation. Late pregnancy (40 weeks) revealed ECM remodeling and immune suppression. Validated biomarkers for early pregnancy, including HBB, HBQ1, and ADGRE3, showed strong consistency between RNA-seq and qRT-PCR data.

Conclusion: This study provides comprehensive insights into the transcriptional dynamics during pregnancy in Hanwoo cattle and suggests practical biomarkers for early pregnancy diagnosis.

Background: Hyperglycemia in type 1 diabetes (T1D) disrupts immune function, yet it remains unclear whether hyperglycemia-induced immunological defects in the bone marrow (BM) persist in BM-derived M1 and M2 macrophages.

Objective: We investigated the immunological and metabolic features of BM-derived M1 and M2 macrophages from prediabetic and diabetic non-obese diabetic (NOD) mice to determine the impact of hyperglycemic memory on polarized macrophages.

Methods: Macrophages were differentiated from BM cells of prediabetic and diabetic NOD mice and subsequently polarized with lipopolysaccharide (LPS; M1 macrophages) or interleukin-4 (IL-4; M2 macrophages). Transcriptomic profiles were assessed using RNA sequencing and gene set enrichment analysis of differentially expressed genes (DEGs). In parallel, glycolysis, oxygen consumption, and cytokine production were evaluated.

Results: Hyperglycemia induced pronounced transcriptomic alterations in both M1 and M2 macrophages, modifying immune and metabolic gene expression. Immune pathways, including inflammatory responses and cytokine production, were consistently suppressed in both subsets from diabetic mice compared with those from prediabetic mice. Metabolically, M1 macrophages preserved mitochondrial and glycolytic activity under diabetic conditions, whereas M2 macrophages exhibited impaired oxidative phosphorylation and glycolysis, resulting in diminished energy production. Functionally, both subsets from diabetic mice secreted lower levels of inflammatory cytokines upon stimulation relative to prediabetic counterparts.

Conclusion: These findings demonstrate that hyperglycemia imprints persistent transcriptomic and functional defects in BM-derived M1 and M2 macrophages. This work provides new insights into how chronic hyperglycemia contributes to impaired host defense and dysregulated inflammation in diabetes.

Background: Rhododendron possesses significant ornamental and economic value; however, its limited heat tolerance severely hinders its broader development and application. Heat shock transcription factors (Hsfs) are extensively involved in various abiotic stress responses and play essential roles in plant thermotolerance and other physiological processes.

Objective: To identify Hsf genes in the genome of Rhododendron molle (R. molle) and investigate their regulatory mechanisms underlying heat tolerance in R. molle.

Methods: The Hsf gene family was systematically identified using the genomic data of R. molle, and the expression levels of RmHsf genes under heat stress were analyzed through Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR).

Results: The RmHsf gene family consists of 25 members distributed across 12 chromosomes. Phylogenetic analysis demonstrated that the RmHsf genes are classified into three subfamilies: A, B and C. Most genes within the same subfamily share similar conserved motifs and gene structures. The cis-acting elements in the promoter regions of RmHsf genes are associated with plant hormone signaling and stress response pathways. Collinearity analysis revealed that the expansion of the RmHsf gene family primarily occurred through segmental and tandem duplication events. RT-qPCR results showed that RmHsfA2, RmHsfA3, RmHsfA7a, and RmHsfA7b were significantly upregulated under heat stress, suggesting that they may serve as key genes in the heat stress response of R. molle. Among them, RmHsfA2 and RmHsfA3 were notably induced by exogenous ethylene.

Conclusion: This study conducted a comprehensive genome-wide analysis of the Hsf gene family in R. molle, laying a solid foundation for functional validation of Hsf genes and the breeding of heat-tolerant cultivars.

Background: Acute myeloid leukemia (AML) is characterized by extensive immunometabolic rewiring that drives leukemic progression and fosters immune evasion.

Objective: This study investigates regulatory role of CD36 as an immunometabolic mediator in AML pathogenesis.

Methods: Integrated bulk transcriptomics, single-cell RNA sequencing, and in-vitro validation were performed. Macrophage co-localization was validated using colorectal cancer (CRC) spatial transcriptomics.

Results: CD36 was identified as a central hub in preserved immunometabolic modules, enriched for TLR signaling, lipid metabolism, antigen-presenting pathways, and cytokine-cytokine receptor interactions. Drug sensitivity analysis revealed that high CD36 expression showed greater sensitivity to venetoclax and GSK626616AC. CD36 drives AML immune cycle and revealed a strong association with AML functional states, including inflammation, differentiation, apoptosis, invasion, quiescence, and hypoxia. Single-cell analysis indicated CD36 upregulation in monocyte and macrophage clusters, facilitating ligand-receptor communication with T cells, which emphasizes CD36's role in shaping immune microenvironment. Spatial transcriptomics analysis of colorectal cancer confirmed a significant CD36-CD68 colocalization in macrophages. CD36 also influenced monocyte to macrophage differentiation in AML cells. CD36 deficiency significantly reduces AML cells' proliferation and leads to G0/G1 phase expansion, accompanied by E2F4/E2F5/RB1 modulation. Hallmark enrichment analysis unveiled that CD36-high expression leukemic cells, CD36 immune signatures, and monocytes/macrophages showed enrichment in key immune and inflammatory pathways, including TNFα/NF-κB, IL6/JAK/STAT3, and IL2/STAT5 signaling, mTORC1 activation, interferon alpha and gamma responses, and reactive oxygen species pathways.

Conclusion: Integration of transcriptomics and spatial validation revealed robust CD36-mediated immunometabolic signaling in AML, which further requires comprehensive in-vitro and in-vivo validation.

Background: Acute myocardial infarction (AMI) is a leading cause of mortality worldwide, with sterile inflammation and immune dysregulation driving cardiac injury. Itaconate, a mitochondria-derived immunometabolite synthesized by ACOD1, has emerged as a key regulator of myeloid cell function, exhibiting anti-inflammatory and metabolic effects. However, its role and downstream targets in sterile myocardial inflammation remain poorly understood.

Objective: This study aimed to systematically dissect the immunometabolic role of itaconate in AMI by identifying itaconate-responsive genes, uncovering their cell-type specificity and functional dynamics, and evaluating their diagnostic and therapeutic potential.

Methods: We established a novel systems-level framework that integrates bulk and single-cell/single-nucleus transcriptomics, network pharmacology, machine learning-based feature selection, and molecular docking. This multi-layered strategy was applied to human and murine datasets covering infarcted cardiac tissue and peripheral immune compartments to identify robust, itaconate-responsive immune targets in AMI.

Results: Single-cell data show that ACOD1 induction is disease-specific and characteristic of AMI. And we identified 36 itaconate-associated genes enriched in myeloid populations and dynamically regulated during infarction. Among them, MMP9, TLR2, and ANPEP were consistently prioritized by multiply machine learning algorithms, showed robust diagnostic performance across independent cohorts, and exhibited potential binding to itaconate in silico. Single-cell analyses confirmed spatial and temporal regulation of these targets in infarcted myocardium. Functional analyses revealed that 4-octyl-itaconate (4-OI) induced dose- and context-dependent transcriptional programs in myeloid cells, including NRF2 and ATF3 activation.

Conclusions: This study identifies a core immunometabolic program downstream of itaconate in myeloid cells and highlights MMP9, TLR2, and ANPEP as key effectors linking metabolic sensing to inflammation and tissue remodeling in AMI. Our integrative approach offers new insights into context-specific immunomodulation and supports the development of metabolite-guided therapeutic strategies for cardiovascular inflammation.