Genes & genomics最新文献

Background: Dry eye disease (DED) is an ocular illness caused by insufficient tear secretion or poor tear quality, and inflammation is a key factor in its pathogenesis. Previous studies have shown that miRNAs are important regulatory factors in DED.

Objective: The purpose of this study was to explore the potential mechanism by which miR-214-3p influenced the DED process by regulating the macrophage inflammatory response.

Methods: We induced THP-1 cells to differentiate into M0 macrophages with 100 ng/mL phorbol-12-myristate-13-acetate (PMA) and then added 15 ng/mL lipopolysaccharide (LPS) to induce inflammation. The expression of related genes and proteins was detected via RT‒qPCR, Western blotting, ELISA and immunofluorescence staining; cell viability was measured using the CCK-8 assay; and flow cytometry was used to detect ROS levels.

Results: In tear and serum samples from DED patients, the levels of miR-214-3p, IL-10, and Arg1 were decreased, and the levels of IL-6, TNF-α, IL-1β, and iNOS expression were increased. Moreover, the overexpression of miR-214-3p attenuated the effect of LPS and inhibited M1 polarization and inflammation in macrophages. Mechanistically, miR-214-3p inhibited macrophage ferroptosis by downregulating TFRC expression, thereby inhibiting macrophage M1 polarization and inflammation and alleviating the progression of DED.

Conclusions: Our study indicated that the upregulation of miR-214-3p expression might be a new target for DED therapy.

Background: Cervical cancer is the fourth most common cancer worldwide in females. This occurs primarily due to the infection of high-risk Human Papilloma Virus (HPV), although in advanced stages it requires support from host cellular factors. BRN3A is one such host cellular factors, whose expression remains high in cervical cancers and upregulates tumorigenic HPV gene expression. The effect of BRN3A on HPV-mediated cervical cancer and the underlying mechanism remains obscure.

Objective: To investigates the effect of BRN3A on cancer-promoting biological processes in HPV-positive uterine cervix cancer cells.

Methods: We have altered the expression of BRN3A through over-expression (OE) and knock-down (KD) constructs in cervical cancer cell line, SiHa, and did transcriptome profiling through next-generation RNA-sequencing, validation through RT-PCR and BRN3A binding study with in silico promoter study and ChIP PCR methods.

Results: This study revealed a substantial change in the expression of several genes associated with cancer-promoting biological processes including viral processes, immune response, cell-death, cell-proliferation, different signaling pathways, etc. Additionally, promoter analysis through in silico mode revealed that a total of 32.7% of genes possess BRN3A binding sites at their promoters. Physical interaction of BRN3A with IFITM1, OAS3, ISG15, BCL2L1 and HSP90AB1 genes was also confirmed.

Conclusions: The present study identified molecular targets of BRN3A and provided new insight into the pathogenesis of cervical cancer. According to our knowledge, this is the first report on the effect on eukaryotic transcriptomes after over-expression and knocking down BRN3A.

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: Next-generation sequencing has revolutionized genome science over the last two decades. Indeed, the wealth of sequence information on our genome has deepened our understanding on cancer. Cancer is a genetic disease caused by genetic or epigenetic alternations that affect the expression of genes that control cell functions, particularly cell growth and division. Utilization of next-generation sequencing in cancer gene panels has enabled the identification of actionable gene alterations in cancer patients to guide personalized precision medicine.

Objective: The aim is to provide information that can identify actionable gene alterations, enabling personalized precision medicine for cancer patients.

Results & discussion: Equipped with next-generation sequencing techniques, international collaboration programs on cancer genomics have identified numerous mutations, gene fusions, microsatellite variations, copy number variations, and epigenetics changes that promote the transformation of normal cells into tumors. Cancer classification has traditionally been based on cell type or tissue-of-origin and the morphological characteristics of the cancer. However, interactive genomic analyses have currently reclassified cancers based on systemic molecular-based taxonomy. Although all cancer-causing genes and mechanisms have yet to be completely understood or identified, personalized or precision medicine is now currently possible for some forms of cancer. Unlike the "one-size-fits-all" approach of traditional medicine, precision medicine allows for customized or personalized treatment based on genomic information.

Conclusion: Despite the availability of numerous cancer gene panels, technological innovation in genomics and expansion of knowledge on the cancer genome will allow precision oncology to manage even more types of cancers.

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: Cyanobacteria, particularly Synechocystis sp. PCC 6803, serve as model organisms for studying acclimation strategies that enable adaptation to various environmental stresses. Understanding the molecular mechanisms underlying these adaptations provides insight into how cells adjust gene expression in response to challenging conditions.

Objective: To analyze the transcriptome data of Synechocystis sp. PCC 6803 under light, salinity, and iron stress conditions and to identify hub genes potentially involved in stress response, specifically comparing the findings with Geminocystis sp. NIES-3708.

Methods: A comprehensive bioinformatics approach was applied, integrating meta-analysis, weighted gene co-expression network analysis (WGCNA), and a Random Forest (RF) machine learning algorithm. These approaches underscore the robustness of our findings, allowing for a more nuanced understanding of gene interactions and their functional relevance in stress responses. This methodology was used to identify key hub genes in Synechocystis sp. PCC 6803 that may have conserved roles in Geminocystis sp. NIES-3708. A total of four potential hub genes, including slr1392, slr1484, sll1549, and sll1863, were identified. Among these, only sll1549 had a homolog (GM3708_2556) with 71% sequence similarity and 70% query coverage in Geminocystis sp. NIES-3708. The expression of GM3708_2556 was further evaluated under nitrate, salt, and combined salinity-nitrate stress conditions using RT-qPCR.

Results: Transcript levels of GM3708_2556 increased significantly under salt stress (3.35-fold, p-value < 0.05) and combined salinity-nitrate stress (2.24-fold, p-value < 0.05) compared to control conditions, while no significant change was observed under nitrate stress alone. These results suggest that GM3708_2556 may play a crucial role in the organism's response to salt stress, with potential interactions in nitrate metabolism.

Conclusion: This study highlights the gene GM3708_2556 as a significant factor in salt stress response, with implications for conserved functional roles across cyanobacterial species. Furthermore, the findings have potential relevance to biotechnology, particularly in engineering stress-resistant cyanobacterial strains for applications in sustainable agriculture and bioenergy production.

Background: This study explores the cross-fertilization of transgenic tobacco plants to produce dual-specific monoclonal antibodies (mAbs) targeting Ebola virus-like particles and HER2 proteins. We generated F₁ plants by hybridizing individual transgenic lines expressing the anti-HER2 breast cancer VHH mAb (HV) and the H-13F6 human anti-Ebola large single chain mAb (EL).

Objective: Hybridizing transgenic plants to express dual-antibodies between different structures VHH and LSCK indicate the potential of transgenic plants as a cost-effective and scalable production system for dual targeting mAbs.

Methods: We performed polymerase chain reaction (PCR) analysis to confirm the integration of EL and HV genes in the F₁ progeny. The reverse-transcription (RT)-PCR and immunoblotting were performed to confirm the expression of transgenes. Indirect enzyme-linked immunosorbent assay was conducted to confirm the functionality of purified EL and HV mAb.

Results: A PCR analysis confirmed the successful integration of both EL and HV mAb genes in the F₁ progeny. Additionally, (RT)-PCR and immunoblotting validated the expression of these transgenes, with EL and HV mAbs purified from the F₁ plants. Indirect enzyme-linked immunosorbent assay (ELISA) demonstrated that EL × HV mAb proteins maintained binding activity to Ebola virus-specific antigens, comparable to that of the EL mAb protein, while also exhibiting binding activity against HER2 proteins similar to that of the HV mAb.

Conclusion: This study indicates the potential for transgenic plants to produce dually targeting mAbs, suggesting a promising application in enabling the co-expression of antibodies targeting two different diseases in a single plant.

Background: The clinical course of high-risk neuroblastoma patients remains suboptimal, and the dynamic and reversible nature of cellular senescence provides an opportunity to develop new therapies.

Objective: This study aims to identify unique markers of cellular senescence in neuroblastoma and to explore their clinical significance.

Methods: The impact of multiple genetic regulatory mechanisms on cellular senescence-associated genes (CSAGs) was first assessed. We identified cellular senescence-associated subtypes by hierarchical clustering and explored the intrinsic differences between subtypes. We screened key CSAGs based on PPI networks and clinical significance. Subsequently, we constructed the cellular senescence-related risk score (CSRS) by LASSO regression and stepwise Cox regression, and validated its performance and stability through multiple methods. Finally, we performed single-cell analysis and constructed the nomogram.

Results: The expression of CSAGs was influenced by copy number variation and DNA methylation. We found that significant differences between cellular senescence-associated subtypes in immune infiltration and overall prognosis. AURKA, CDK4, TERT were key genes in the cellular senescence process. CSRS showed superior and robust predictive performance in several cohorts and could serve as an independent prognostic factor in neuroblastoma. The senescence signature was also meaningful at the single-cell level and the nomogram was shown to have high accuracy and high clinical benefit.

Conclusions: We comprehensively evaluated the significance of cellular senescence in neuroblastoma and concluded that it was significantly associated with immune characteristics and overall prognosis. Based on the expression levels of CSAGs, we developed the CSRS, which was a reliable tool to contribute to prognostic assessment and clinical decision making.

Background: Hearing loss adversely impacts language development, acquisition, and the social and cognitive maturation of affected children. The hearing loss etiology mainly includes genetic factors and environmental factors, of which the former account for about 50-60%.

Objective: This study aimed to investigate the genetic basis of autosomal recessive non-syndromic hearing loss (NSHL) by identifying and characterizing novel variants in the CDH23 gene. Furthermore, it seeks to determine the pathogenic potential of the noncanonical splice site variant c.2398-6G > A.

Methods: Comprehensive clinical evaluation and whole-exome sequencing (WES) were performed on the girl. The WES analysis revealed two novel variants in the CDH23 gene, associated with nonsyndromic deafness 12 (DFNB12). To further explore the pathogenicity of these variants, functional studies involving in vivo splicing analysis were performed on the novel noncanonical splice site variant, c.2398-6G > A, which was initially classified as a variant of uncertain significance (VUS).

Results: Whole-exome sequencing of the patient identified two compound heterozygous variants in CDH23: c.2398-6G > A, a noncanonical splice site variant, and c.6068C > A (p. Ser2023Ter), a nonsense mutation. In vitro splicing assays demonstrated that c.2398-6G > A caused aberrant splicing, leading to a frameshift (p. Val800Alafs*6) and the production of a truncated protein, as confirmed by structural protein analysis. The study revealed novel mutations as likely pathogenic, linking both variants to autosomal recessive NSHL.

Conclusions: Our analyses revealed novel compound heterozygous mutations in CDH23 associated with autosomal recessive NSHL, thereby expanding the mutational landscape of CDH23-related hearing loss and increasing knowledge about the CDH23 splice site variants.