Genes & genomics最新文献

Introduction: Sjögren's syndrome (SS) is an autoimmune disorder affecting exocrine glands, causing dry mouth and eyes, with no effective treatment. While high-throughput sequencing has provided insights into its mechanisms, the role of alternative splicing (AS) in SS remains underexplored.

Objective: To investigate the relationship between immune infiltration in the salivary glands and AS events at the transcriptomic level, and to identify potential biomarkers that may be linked to the diagnosis and prognosis of SS.

Methods: Transcriptomic data from salivary glands were aligned to the GRCh38 genome using HISAT2. Isoform quantification was performed with StringTie, and differential isoform usage was analyzed with DEXSeq in the IsoformSwitchAnalyzeR pipeline. Further analyses were conducted to explore the relationship between AS events, clinical data and immune infiltration.

Results: 16 genes showed significant alternative splicing between biopsy-positive and biopsy-negative salivary glands. These genes were linked to immune regulation. Isoform usage ratios integrated with clinical data identified MAP4K1, SH2D3C, and ACAP1 isoforms as potential diagnostic biomarkers. Immune infiltration analysis showed a strong correlation between memory B cells, follicular helper T cells, and biopsy scores, with significant differences between biopsy-positive and biopsy-negative tissues. A correlation between immune infiltration and isoform usage provided insights into gene function and disease progression.

Conclusions: This study reveals the critical role of AS in SS, identifying 16 genes with differential isoform usage that may serve as biomarkers for diagnosis and prognosis. The link between immune infiltration and splicing suggests that AS influences immune responses in SS, providing opportunities for targeted therapies. These findings emphasize AS's importance in SS and offer new diagnostic and therapeutic avenues.

Background: Intelectin (ITLN) plays a pivotal role in innate immunity, inflammatory responses, and tumor progression. However, its physiological roles in caudate amphibians, such as Andrias davidianus, remain elusive.

Objective: A proto-type of intelectin (AdITLN1) from A. davidianus was characterized, following which an AdITLN1 homology model was generated to analyze its expression profiles and functional characterizations.

Methods: The intelectin1 gene (AdITLN1) was cloned, and its evolutionary relationship with ITLN1 from other species was explored. Additionally, a homology model was generated using Molecular Operating Environment (MOE) software, and the active binding pocket of AdITLN1 was identified. Infections with Aeromonas hydrophila were conducted to analyze changes in ITLN1 transcript levels in liver tissue. Finally, recombinant A. davidianus ITLN1 protein (rAdITLN1) was synthesized using prokaryotic expression, and its bacterial agglutination activity and impact on macrophage phagocytosis were examined.

Results: Multiple sequence alignment and phylogenetic analysis indicated that AdITLN1 shared the closest evolutionary relationship with amphibians, with its structure being similar to that of human intelectin1 and Xenopus Embryonic Epidermal Lectin. Moreover, AdITLN1 mRNA was expressed in a wide range of tissues and was significantly up-regulated post-A. hydrophila infection. Meanwhile, the AdITLN1 protein was successfully expressed and purified in Escherichia coli (E. coli) BL21 (DE3). The recombinant AdITLN1 (rAdITLN1) displayed strong agglutination activity against different Gram-negative and Gram-positive bacteria. Lastly, The phagocytosis of rAdITLN1-treated E. coli by macrophages was significantly enhanced.

Conclusion: The results of the present study demonstrated that AdITLN1 was a multifunctional immune protein with potent immunomodulatory activity. This study offers valuable insights into disease control in giant salamanders and the conservation of natural resources.

Background: Erythrocytes, derived from hematopoietic stem cells, are essential for oxygen transport, ensuring survival in all vertebrate animals. The process of erythropoiesis is associated with gene expression changes, but many key regulatory factors that govern erythroid differentiation remain to be fully understood.

Objective: This study investigates the role of TWS119, a known GSK3β inhibitor, in inducing erythropoiesis in K562 erythroleukemia cells and explores the impact of Replication initiation determinant protein (RepID) depletion on the process.

Methods: K562 cells were treated with TWS119 and erythropoiesis markers including various erythrocytic phenotypes were assessed. Chromatin-immunoprecipitation analysis was employed to examine the changes in chromatin structure and gene expression regulation. The impact of RepID depletion on TWS119-induced erythropoiesis was also evaluated by analyzing globin promoter euchromatinization and NRF2 binding.

Results: TWS119 treatment led to erythrocytic phenotypes in K562 cells, such as red pellet formation, enucleation, and nucleus condensation, along with the upregulation of erythropoiesis markers. Furthermore, RepID depletion accelerated TWS119-mediated erythropoiesis. Chromatin-immunoprecipitation analysis revealed euchromatinization of the globin promoter and enhanced NRF2 binding in RepID-depleted cells, suggesting a mechanism of gene expression regulation during erythropoiesis.

Conclusion: This study demonstrates that TWS119 can induce erythropoiesis in K562 cells, and that RepID depletion enhances this process by modulating chromatin structure and facilitating transcription factor binding. These findings highlight a RepID-dependent mechanism in the regulation of gene expression during erythropoiesis.

Background: Mind bomb 1 (MIB1) is an E3 ubiquitin ligase that promotes the polyubiquitination-mediated degradation of NOTCH ligands and plays an important role in various cancers by enhancing tumor cell proliferation. Also, MIB1 inhibited the cell cycle progression by transcriptional repression of P21 in HCT116 cells. Fibroblast growth factor receptor 1 (FGFR1) is a receptor tyrosine kinase (RTK) that plays a significant role in the progression of various cancers. However, the regulatory mechanisms underlying FGFR1-associated signaling in colon cancer remain unclear.

Objective: We investigated whether MIB1 regulates protein stability of FGFR1 and impairs cell proliferation in HCT116 cells.

Methods: We conducted immunoprecipitation assay to identify correlation of MIB1 and FGFR1. We also tested mRNA level of FGFR1 in MIB1-depleted HCT116 cells using reverse transcription-quantitative polymerase chain reaction. Furthermore, we transfected HA-MIB1 and FLAG-FGFR1 and analyzed the downstream signaling cascades by western blotting. Cell viability was assessed using colony formation assays and MTT assay.

Results: FGFR1 interacts with MIB1 and controls FGFR1 protein level in HCT116 cells. Transcriptome analysis revealed that the mRNA levels of FGFR1 increased when MIB1 was depleted in HCT116 cells. Moreover, histone deacetylase 3 (HDAC3) is involved in histone deacetylation and transcriptional repression, mediating the interaction between MIB1 and FGFR1.

Conclusion: These findings suggest the importance of MIB1-mediated transcriptional repression of FGFR1 and its potential therapeutic target in colon cancer.

Background: Increasing evidence suggests that lactate is an essential compound in the tumor microenvironment, and especially for macrophage cells. However, the mechanism by which lactate affects macrophages remains unclear.

Objective: This study investigated whether and how lactate affects macrophage polarization in lung adenocarcinoma (LUAD).

Methods: Clinical samples of LUAD and paracancerous tissue were obtained for evaluation of lactate dehydrogenase A (LDHA) expression. LUAD cell lines and THP-1 induced macrophages were used in this study. Quantitative real-time PCR (QPCR), western blotting, and immunohistochemical (IHC) staining were performed to detect gene expression. Flow cytometry and ELISA assays were used to detect the levels of M1 macrophage and M2 macrophage biomarkers.

Results: LDHA was highly expressed in the LUAD tissues. Culture medium supernatants derived from LUAD cells (CM) promoted macrophage M2 polarization, and lactate levels were elevated in the CM. Inhibition of LDHA in LUAD cells decreased lactate levels and suppressed M2 macrophage polarization. Moreover, overexpression of GPR132 in macrophages promoted, while GPR132 knockdown in macrophages suppressed M2 macrophage polarization and cAMP (Cyclic Adenosine 3',5'-Monophosphate)/PKA (Protein Kinase) pathway activation induced by lactate. The effect of GPR132 overexpression was reversed by a PKA inhibitor (H-89).

Conclusion: Collectively, our results confirmed that lactate released by LUAD cells promoted M2 macrophage polarization via the GPR132/cAMP/PKA pathway.

Background: Colorectal cancer (CRC) is a significant global health issue, with early detection being critical to improving patient survival. Dysregulation of the glycolysis pathway plays a pivotal role in CRC progression, but specific gene-level mechanisms remain underexplored.

Objective: This study aimed to investigate the role of glycolysis-related genes in CRC development and identify potential diagnostic and prognostic biomarkers.

Methods: We utilized The Cancer Genome Atlas (TCGA) dataset to perform differential expression analysis of glycolysis-related genes in CRC. Protein-protein interaction (PPI) network analysis was conducted to identify central hub genes. The diagnostic potential of selected genes was evaluated using ROC curve analysis, while their expression levels were validated through RT-qPCR.

Results: IER3 and AGRN were identified as significantly upregulated genes associated with reduced survival rates in CRC patients. PPI analysis revealed their roles as central hub genes within the glycolysis pathway. ROC curve analysis demonstrated their ability to distinguish CRC patients from healthy individuals. Validation through RT-qPCR confirmed their significant overexpression in CRC samples, highlighting their involvement in disease progression.

Conclusion: IER3 and AGRN are critical components of the glycolysis pathway, driving CRC development and progression while also showing potential as biomarkers for predicting outcomes, diagnosing CRC, and serving as treatment targets.

Background: TCP proteins are plant-specific transcription factors that play essential roles in various developmental processes, including leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, a comprehensive analysis of genome-wide TCP genes and their expression patterns in melon is yet to be done.

Objective: The present study aims to identify and analyze the TCP genes in the melon genome and understand their putative functions.

Methods: The chromosomal location, gene structure, conserved motifs, protein domains, structural homology, cis-regulating elements, transcript expression patterns, and potential protein-protein interactions were analyzed using various databases and webtools.

Results: A total of 29 putative TCP genes are identified in melon. These genes were classified into two classes: Class-I (13 genes) and Class-II (16 genes). The results revealed that the putative CmTCP genes are distributed across nine of the twelve melon chromosomes and exhibit diverse expression patterns in different tissues which mostly indicates their potential role in floral organ development, lateral branching, growth and development. Phylogenetic analysis suggests that some CmTCP genes may have similar functions to their homologs in other plant species, while others may have undergone functional diversification.

Conclusion: This study paves the way for future investigations into the specific roles of individual CmTCP genes in melon and for elucidating the mechanisms by which TCP proteins regulate leaf elongation, floral development, and lateral branching.

Background: Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) are standard treatments for non-small cell lung cancer (NSCLC) patients with EGFR mutations; however, drug resistance limits their efficacy. Cytoskeleton-associated protein 4 (CKAP4) has been linked to cancer progression, but its role in EGFR-TKI resistance remains unclear.

Objective: This study investigates the clinical relevance of CKAP4 as a therapeutic target to overcome EGFR-TKI resistance in lung adenocarcinoma (LUAD) patients.

Methods: GEO datasets were analyzed to identify 24 differentially expressed genes associated with EGFR-TKI resistance, with CKAP4 selected via functional annotation and scoring using the VarElect tool. The prognostic significance of CKAP4 was evaluated using public databases, and its upregulation was confirmed in osimertinib-tolerant H1975 cells through quantitative reverse transcription-polymerase chain reaction.

Results: Integrated bioinformatics analysis identified CKAP4 as strongly associated with EGFR-TKI resistance. Elevated CKAP4 expression was particularly linked to poorer clinical outcomes in LUAD patients. Notably, osimertinib-tolerant cells exhibited high CKAP4 expression, correlating positively with increased half-maximal inhibitory concentrations of EGFR-TKIs. LUAD patients with upregulated CKAP4 showed significantly reduced overall and relapse-free survival.

Conclusion: This study underscores the prognostic value of CKAP4 in EGFR-mutated LUAD and highlights its potential as a therapeutic target to counter EGFR-TKI resistance.

Background: Soil salinity has been a serious threat to agricultural production worldwide, including soybeans. Glycine soja, the wild ancestor of cultivated soybeans, harbors high genetic diversity and possesses attractive rare alleles.

Objective: We conducted a transcriptome analysis of G. soja subjected to salt stress to profile the transcriptomes and identify salt-responsive genes.

Methods: G. soja was subjected to salt stress at 0, 24, and 48 h. RNA was sequenced using the Illumina NovaSeq 6000 platform. Transcriptome sequencing was used to identify differentially expressed genes (DEGs) and differential alternative splicing genes (DASGs) and to analyze alterations in salt-responsive genes.

Results: A total of 249 and 1890 DEGs were identified at 24 and 48 h under salt stress, respectively. Among the DEGs, 45 and 252 transcription factors, including bHLH, MYB, and WRKY, were identified at 24 and 48 h, respectively. Additionally, 602 and 1850 DASGs were identified at 24 and 48 h, respectively. For DASGs, significant GO term enrichments included 'mRNA processing', 'Chromatin organization', 'Nucleus', and 'Transcription cofactor activity' at 48 h. The KEGG pathways, 'Spliceosome' and the 'mRNA surveillance pathway', were significantly enriched in DASGs at 48 h. Salt-responsive genes were identified in DEGs and/or DASGs, specifically GsJ3, GsACA12, GsACA13, GsHSFA2-like, and GsHSF30-like.

Conclusion: Through the analysis of DEGs, DASGs, and transcription factor predictions, we identified key factors involved in the salt stress response and tolerance of G. soja, which could contribute to salt-tolerant soybean cultivar through genetic engineering strategies.

Background: Vegetable oils are primarily composed of unsaturated fatty acids. Soybean [Glycine max (L.) Merr.] oil, accounting for 28% of the global production of vegetable oil, contains mainly two saturated fatty acids (palmitic acid and stearic acid) and three unsaturated fatty acids (oleic acid, linoleic acid, and linolenic acid) in seeds.

Objective: The five fatty acids determine soybean oil quality. We aimed to identify genetic relationship between genomics and fatty acid contents in soybean mutant pool.

Methods: This study used a mutant diversity pool (MDP) comprising 192 soybean lines. A genome-wide association study (GWAS) was conducted with the diverse fatty acid contents in MDP and 17,631 filtered SNPs from genotyping-by-sequencing (GBS).

Results: The GWAS revealed nine significant SNPs within intragenic regions that were associated with fatty acid composition. These SNPs corresponded to six genes (Glyma.03g042500, Glyma.07g069200, Glyma.13g150200, Glyma.14g223100, Glyma.15g084700, and Glyma.15g274000), of which three (Glyma.03g042500, Glyma.13g150200, and Glyma.15g274000) were predicted to be candidate genes influencing oleic acid, linoleic acid, and linolenic acid contents. Analyses of SNP allelic effects revealed the largest and smallest significant differences in fatty acid contents were 5.53% (linolenic acid) and 0.4% (stearic acid), respectively.

Conclusion: The present study detected significant phenotypic variations and genetic associations underlying the fatty acid composition of soybean seeds in MDP lines. The mutant seeds differed from the original cultivars in terms of fatty acids composition, with the allelic effects of significant SNPs influencing the fatty acid content in seeds. These findings may be useful for enhancing breeding strategies to optimize soybean oil quality for various uses.