Genetics research最新文献

{"title":"Pivotal Role of FBXW4 in Glioma Progression and Prognosis.","authors":"Kun Chen, Lei Pu, Yuzuo Hui","doi":"10.1155/2024/3005195","DOIUrl":"https://doi.org/10.1155/2024/3005195","url":null,"abstract":"<p><strong>Backgrounds: </strong>Glioma stands as one of the most formidable brain tumor types, with patient outcomes remaining bleak even in the face of advancements in treatment modalities. FBXW4, a constituent of the F-box and WD repeat domain-containing protein family, is recognized for its participation in diverse cellular activities, including those related to tumor dynamics. Yet, the therapeutic relevance and specific role of FBXW4 in the context of glioma are not well defined. This study aims to elucidate the functional dynamics and significance of FBXW4 in glioma cases.</p><p><strong>Methods: </strong>This research undertook a comprehensive analysis of FBXW4's expression patterns and clinical relevance in glioma by harnessing data from the TCGA and GTEx databases.</p><p><strong>Results: </strong>The investigation revealed a distinct downregulation of FBXW4 in glioma tissues compared to normal brain counterparts, with a pronounced correlation between FBXW4 levels and disease severity. Intriguingly, FBXW4 expression inversely related to WHO tumor grades, with the most advanced grade IV gliomas exhibiting the lowest FBXW4 levels, whereas grade II tumors demonstrated the highest. Cases presenting with IDH1/2 mutations or 1p/19q codeletions were also associated with elevated FBXW4 levels. Furthermore, diminished FBXW4 expression aligned with an increased risk of mortality.</p><p><strong>Conclusions: </strong>The findings suggest that FBXW4 holds promise as a prognostic marker and a potential therapeutic avenue in glioma management. Nonetheless, future research is imperative to decode the intricate signaling pathways involving FBXW4 and to understand its broader clinical ramifications in glioma treatment paradigms.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.4,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive Analysis of the Mechanism of Anoikis in Hepatocellular Carcinoma.","authors":"Dongqian Li,Qian Bao,Shiqi Ren,Haoxiang Ding,Chengfeng Guo,Kai Gao,Jian Wan,Yao Wang,MingYan Zhu,Yicheng Xiong","doi":"10.1155/2024/8217215","DOIUrl":"https://doi.org/10.1155/2024/8217215","url":null,"abstract":"BackgroundHepatocellular carcinoma (HCC), ranking as the second-leading cause of global mortality among malignancies, poses a substantial burden on public health worldwide. Anoikis, a type of programmed cell death, serves as a barrier against the dissemination of cancer cells to distant organs, thereby constraining the progression of cancer. Nevertheless, the mechanism of genes related to anoikis in HCC is yet to be elucidated.MethodsThis paper's data (TCGA-HCC) were retrieved from the database of the Cancer Genome Atlas (TCGA). Differential gene expression with prognostic implications for anoikis was identified by performing both the univariate Cox and differential expression analyses. Through unsupervised cluster analysis, we clustered the samples according to these DEGs. By employing the least absolute shrinkage and selection operator Cox regression analysis (CRA), a clinical predictive gene signature was generated from the DEGs. The Cell-Type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was used to determine the proportions of immune cell types. The external validation data (GSE76427) were procured from Gene Expression Omnibus (GEO) to verify the performance of the clinical prognosis gene signature. Western blotting and immunohistochemistry (IHC) analysis confirmed the expression of risk genes.ResultsIn total, 23 prognostic DEGs were identified. Based on these 23 DEGs, the samples were categorized into four distinct subgroups (clusters 1, 2, 3, and 4). In addition, a clinical predictive gene signature was constructed utilizing ETV4, PBK, and SLC2A1. The gene signature efficiently distinguished individuals into two risk groups, specifically low and high, demonstrating markedly higher survival rates in the former group. Significant correlations were observed between the expression of these risk genes and a variety of immune cells. Moreover, the outcomes from the validation cohort analysis aligned consistently with those obtained from the training cohort analysis. The results of Western blotting and IHC showed that ETV4, PBK, and SLC2A1 were upregulated in HCC samples.ConclusionThe outcomes of this paper underscore the effectiveness of the clinical prognostic gene signature, established utilizing anoikis-related genes, in accurately stratifying patients. This signature holds promise in advancing the development of personalized therapy for HCC.","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142261412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and Validation of Cytotoxicity-Related Features to Predict Prognostic and Immunotherapy Response in Patients with Clear Cell Renal Cell Carcinoma.","authors":"Junxiao Yu, Bowen Zhao, You Yu","doi":"10.1155/2024/3468209","DOIUrl":"10.1155/2024/3468209","url":null,"abstract":"<p><strong>Background: </strong>Clear cell renal cell carcinoma (ccRCC) is a renal cortical malignancy with a complex pathogenesis. Identifying ideal biomarkers to establish more accurate promising prognostic models is crucial for the survival of kidney cancer patients.</p><p><strong>Methods: </strong>Seurat R package was used for single-cell RNA-sequencing (scRNA-seq) data filtering, dimensionality reduction, clustering, and differentially expressed genes analysis. Gene coexpression network analysis (WGCNA) was performed to identify the cytotoxicity-related module. The independent cytotoxicity-related risk model was established by the survival R package, and Kaplan-Meier (KM) survival analysis and timeROC with area under the curve (AUC) were employed to confirm the prognosis and effectiveness of the risk model. The risk and prognosis in patients suffering from ccRCC were predicted by establishing a nomogram. A comparison of the level of immune infiltration in different risk groups and subtypes using the CIBERSORT, MCP-counter, and TIMER methods, as well as assessment of drug sensitivity to conventional chemotherapeutic agents in risk groups using the pRRophetic package, was made.</p><p><strong>Results: </strong>Eleven ccRCC subpopulations were identified by single-cell sequencing data from the GSE224630 dataset. The identified cytotoxicity-related T-cell cluster and module genes defined three cytotoxicity-related molecular subtypes. Six key genes (SOWAHB, SLC16A12, IL20RB, SLC12A8, PLG, and HHLA2) affecting prognosis risk genes were selected for developing a risk model. A nomogram containing the RiskScore and stage revealed that the RiskScore contributed the most and exhibited excellent predicted performance for prognosis in the calibration plots and decision curve analysis (DCA). Notably, high-risk patients with ccRCC demonstrate a poorer prognosis with higher immune infiltration characteristics and TIDE scores, whereas low-risk patients are more likely to benefit from immunotherapy.</p><p><strong>Conclusions: </strong>A ccRCC survival prognostic model was produced based on the cytotoxicity-related signature, which had important clinical significance and may provide guidance for ccRCC treatment.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11379509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the Prognostic and Oncogenic Roles of Membrane-Associated Ring-CH-Type Finger 9 in Colorectal Cancer.","authors":"Jiayan Zhang, Qinghan Jiao, Zhigang Chen","doi":"10.1155/2024/9279653","DOIUrl":"10.1155/2024/9279653","url":null,"abstract":"<p><p><i>Backgroundsand Aims</i>. Colorectal cancer (CRC) represents a major global health challenge, necessitating comprehensive investigations into its underlying molecular mechanisms to enhance diagnostic and therapeutic strategies. This study focuses on elucidating the oncogenic role of Membrane-Associated Ring-CH-Type Finger 9 (MARCHF9), a RING-Type E3 ubiquitin transferase, in CRC. We aim to assess MARCHF9's clinical significance, functional impact on CRC progression, and its potential as a prognostic biomarker. <i>Methods</i>. We leveraged data from the Cancer Genome Atlas (TCGA) cohort to evaluate MARCHF9 expression profiles in CRC. In vitro experiments involved siRNA-mediated MARCHF9 knockdown in COAD cell lines (SW480 and LoVo). Cell proliferation and invasion assays were conducted to investigate MARCHF9's functional relevance. Survival analyses were performed to assess its prognostic role. <i>Results</i>. Our analysis revealed significantly elevated MARCHF9 expression in CRC tissues compared to normal colorectal tissues (<i>P</i> < 0.05). High MARCHF9 expression correlated with advanced clinical stages, distant metastases, and the presence of residual tumors in CRC patients. Survival analyses demonstrated that high MARCHF9 expression predicted unfavorable overall and disease-free survival outcomes (<i>P</i> < 0.05). In vitro experiments further supported its oncogenic potential, with MARCHF9 knockdown inhibiting COAD cell proliferation and invasion. <i>Conclusions</i>. This study unveils the oncogenic role of MARCHF9 in CRC, highlighting its clinical relevance as a potential biomarker and therapeutic target. MARCHF9's association with adverse clinicopathological features and its functional impact on cancer cell behavior underscore its significance in CRC progression. Further research is essential to elucidate precise mechanisms by which MARCHF9 enhances tumorigenesis and to explore its therapeutic potential in CRC management.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.4,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142055388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of Extracellular Matrix-Related Genes on the Tumor Microenvironment and Prognostic Indicators in Esophageal Cancer: A Comprehensive Analytical Study.","authors":"Yinghong Wu, Wenjie Hu, Zhihong Jia, Qiying Zhu, Jinghui Xu, Liang Peng, Renjie Wang","doi":"10.1155/2024/3577395","DOIUrl":"10.1155/2024/3577395","url":null,"abstract":"<p><p>Esophageal cancer is a major global health challenge with a poor prognosis. Recent studies underscore the extracellular matrix (ECM) role in cancer progression, but the full impact of ECM-related genes on patient outcomes remains unclear. Our study utilized next-generation sequencing and clinical data from esophageal cancer patients provided by The Cancer Genome Atlas, employing the R package in RStudio for computational analysis. This analysis identified significant associations between patient survival and various ECM-related genes, including IBSP, LINGO4, COL26A1, MMP12, KLK4, RTBDN, TENM1, GDF15, and RUNX1. Consequently, we developed a prognostic model to predict patient outcomes, which demonstrated clear survival differences between high-risk and low-risk patient groups. Our comprehensive review encompassed clinical correlations, biological pathways, and variations in immune response among these risk categories. We also constructed a nomogram integrating clinical information with risk assessment. Focusing on the TENM1 gene, we found it significantly impacts immune response, showing a positive correlation with T helper cells, NK cells, and CD8+ T cells, but a negative correlation with neutrophils and Th17 cells. Gene Set Enrichment Analysis revealed enhanced pathways related to pancreatic beta cells, spermatogenesis, apical junctions, and muscle formation in patients with high TENM1 expression. This research provides new insights into the role of ECM genes in esophageal cancer and informs future research directions.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.4,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11300105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of Bladder Cancer Staging Prediction Using Deep Residual Neural Network, Radiomics, and RNA-Seq from High-Definition CT Images.","authors":"Yao Zhou, Xingju Zheng, Zhucheng Sun, Bo Wang","doi":"10.1155/2024/4285171","DOIUrl":"10.1155/2024/4285171","url":null,"abstract":"<p><p>Bladder cancer has recently seen an alarming increase in global diagnoses, ascending as a predominant cause of cancer-related mortalities. Given this pressing scenario, there is a burgeoning need to identify effective biomarkers for both the diagnosis and therapeutic guidance of bladder cancer. This study focuses on evaluating the potential of high-definition computed tomography (CT) imagery coupled with RNA-sequencing analysis to accurately predict bladder tumor stages, utilizing deep residual networks. Data for this study, including CT images and RNA-Seq datasets for 82 high-grade bladder cancer patients, were sourced from the TCIA and TCGA databases. We employed Cox and lasso regression analyses to determine radiomics and gene signatures, leading to the identification of a three-factor radiomics signature and a four-gene signature in our bladder cancer cohort. ROC curve analyses underscored the strong predictive capacities of both these signatures. Furthermore, we formulated a nomogram integrating clinical features, radiomics, and gene signatures. This nomogram's AUC scores stood at 0.870, 0.873, and 0.971 for 1-year, 3-year, and 5-year predictions, respectively. Our model, leveraging radiomics and gene signatures, presents significant promise for enhancing diagnostic precision in bladder cancer prognosis, advocating for its clinical adoption.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.4,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11074870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variants in Candidate Genes for Phenotype Heterogeneity in Patients with the 22q11.2 Deletion Syndrome","authors":"N. Nunes, Beatriz Carvalho Nunes, M. Zamariolli, Diogo Cordeiro de Queiroz Soares, Leonardo Caires dos Santos, Anelisa Gollo Dantas, Vera Ayres Meloni, Sintia Iole Belangero, V. L. Gil-da-Silva-Lopes, Chong Ae Kim, M. I. Melaragno","doi":"10.1155/2024/5549592","DOIUrl":"https://doi.org/10.1155/2024/5549592","url":null,"abstract":"22q11.2 deletion syndrome (22q11.2DS) is a microdeletion syndrome with a broad and heterogeneous phenotype, even though most of the deletions present similar sizes, involving ∼3 Mb of DNA. In a relatively large population of a Brazilian 22q11.2DS cohort (60 patients), we investigated genetic variants that could act as genetic modifiers and contribute to the phenotypic heterogeneity, using a targeted NGS (Next Generation Sequencing) with a specific Ion AmpliSeq panel to sequence nine candidate genes (CRKL, MAPK1, HIRA, TANGO2, PI4KA, HDAC1, ZDHHC8, ZFPM2, and JAM3), mapped in and outside the 22q11.2 hemizygous deleted region. In silico prediction was performed, and the whole-genome sequencing annotation analysis package (WGSA) was used to predict the possible pathogenic effect of single nucleotide variants (SNVs). For the in silico prediction of the indels, we used the genomic variants filtered by a deep learning model in NGS (GARFIELD-NGS). We identified six variants, 4 SNVs and 2 indels, in MAPK1, JAM3, and ZFPM2 genes with possibly synergistic deleterious effects in the context of the 22q11.2 deletion. Our results provide the opportunity for the discovery of the co-occurrence of genetic variants with 22q11.2 deletions, which may influence the patients´ phenotype.","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140363326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HLA Gene Polymorphisms in Romanian Patients with Chronic Lymphocytic Leukemia.","authors":"Maria Tizu, Bogdan Calenic, Mihai Hârza, Bogdan M Cristea, Ion Maruntelu, Andreea M Caragea, Adriana Talangescu, Alina Dima, Alexandra E Constantinescu, Ileana Constantinescu","doi":"10.1155/2024/8852876","DOIUrl":"10.1155/2024/8852876","url":null,"abstract":"<p><strong>Materials and methods: </strong>This study included 66 patients with CLL, diagnosed between 2020 and 2022, and 100 healthy controls. HLA class I and class II genes (HLA-A/B/C, HLA-DQA1/DQB1/DPA1/DPB1, and HLA-DRB1/3/4/5) were investigated using next-generation sequencing technology.</p><p><strong>Results: </strong>Several HLA alleles were strongly associated with CLL. The most important finding was that HLA-DRB1^<i>∗</i>04:02:01 (<i>p</i>=0.001, OR = 1.05) and HLA-DRB3^<i>∗</i>02:01:01 (<i>p</i>=0.009, OR = 1.03) have a predisposing role in CLL development. Moreover, we identified that HLA-A^<i>∗</i>24:02:01 0.01 (<i>p</i>=0.01, OR = 0.38), HLA-DQA1^<i>∗</i>05:05:01 (<i>p</i>=0.01, OR = 0.56), HLA-DQB1^<i>∗</i>03:02:01 (<i>p</i>=0.03, OR = 0.40), and HLA-DRB4^<i>∗</i>01:03:01 (<i>p</i>=0.03, OR = 0.54 alleles have protective roles. Correlations between HLA expression and gender showed that women had a higher expression of protective HLA alleles when compared to men.</p><p><strong>Conclusions: </strong>Our data are the first to indicate that in Romanian patients with CLL, the HLA-A^<i>∗</i>24:02:01 and HLA-DQA1^<i>∗</i>05:05:01 alleles have a protective role against CLL development, whereas HLA-DRB1^<i>∗</i>04:02:01 and HLA-DRB3^<i>∗</i>02:01:01alleles are positively associated with CLL.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.4,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10917483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140049264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Comprehensive Identification and <i>In Silico</i> Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (<i>Hordeum vulgare</i> L.).","authors":"Fee Faysal Ahmed, Farah Sumaiya Dola, Md Shohel Ul Islam, Fatema Tuz Zohra, Nasrin Akter, Shaikh Mizanur Rahman, Md Abdur Rauf Sarkar","doi":"10.1155/2024/2924953","DOIUrl":"10.1155/2024/2924953","url":null,"abstract":"<p><p>Lectin receptor-like kinases (LecRLKs) are a significant subgroup of the receptor-like kinases (RLKs) protein family. They play crucial roles in plant growth, development, immune responses, signal transduction, and stress tolerance. However, the genome-wide identification and characterization of <i>LecRLK</i> genes and their regulatory elements have not been explored in a major cereal crop, barley (<i>Hordeum vulgare</i> L.). Therefore, in this study, integrated bioinformatics tools were used to identify and characterize the LecRLK gene family in barley. Based on the phylogenetic tree and domain organization, a total of 113 <i>LecRLK</i> genes were identified in the barley genome (referred to as <i>HvlecRLK</i>) corresponding to the <i>LecRLK</i> genes of <i>Arabidopsis thaliana</i>. These putative <i>HvlecRLK</i> genes were classified into three groups: 62 G-type <i>LecRLKs</i>, 1 C-type <i>LecRLK</i>, and 50 L-type <i>LecRLKs</i>. They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type <i>HvlecRLK</i> (96.8%), C-type <i>HvlecRLK</i> (100%), and L-type <i>HvlecRLK</i> (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of <i>AtlecRLK</i>. Notably, most of the <i>HvlecRLKs</i> (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that <i>HvlecRLK</i> gene pairs evolved through purifying selection and gene duplication was the major factor for the expansion of the HvlecRLK gene family. Exploration of gene ontology (GO) enrichment indicated that the identified <i>HvlecRLK</i> genes are associated with various cellular processes, metabolic pathways, defense mechanisms, kinase activity, catalytic activity, ion binding, and other essential pathways. The regulatory network analysis identified 29 transcription factor families (TFFs), with seven major TFFs including bZIP, C2H2, ERF, MIKC_MADS, MYB, NAC, and WRKY participating in the regulation of <i>HvlecRLK</i> gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type <i>HvleckRLK64</i> and <i>HvleckRLK86</i>. The promoter cis-acting regulatory element (CARE) analysis of barley identified a total of 75 CARE motifs responsive to light responsiveness (LR), tissue-specific (TS), hormone responsiveness (HR), and stress responsiveness (SR). The maximum number of CAREs was identified in <i>HvleckRLK11</i> (25 for LR), <i>HvleckRLK69</i> (17 for TS), and <i>HvleckRLK80</i> (12 for HR). Additionally, <i>HvleckRLK14, HvleckRLK16, HvleckRLK33, HvleckRLK50, HvleckRLK52, HvleckRLK56, and HvleckRLK110</i> were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 <i>HvlecRLK</i> genes and <i>HvlecRLK13</i> was the most targeted gene by 8 different miRNAs. Protein-protein in","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.4,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10914435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of the Expression of Infection-Related Long Noncoding RNAs among COVID-19 Patients: A Case-Control Study","authors":"Z. Firoozi, Elham Mohammadisoleimani, Farzaneh Bagheri, Atefeh Taheri, Babak Pezeshki, M. Naghizadeh, A. Daraei, Jalal Karimi, Yousef Gholampour, Y. Mansoori, Zahra Montaseri","doi":"10.1155/2024/3391054","DOIUrl":"https://doi.org/10.1155/2024/3391054","url":null,"abstract":"Background and Aims. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a worldwide pandemic, activates signaling cascades and leads to innate immune responses and secretion of multiple chemokines and cytokines. Long noncoding RNAs (lncRNAs) have a crucial role in inflammatory pathways. Through our search on the PubMed database, we discovered that existing research has primarily focused on examining the regulatory impacts of five lncRNAs in the context of viral infections. However, their role in regulating other conditions, including SARS-CoV-2, has not been explored. Therefore, this study aimed to investigate the expression pattern of lncRNAs in the peripheral blood mononuclear cells (PBMC) and their potential roles in SARS-CoV-2 infection. Potentially significant competing endogenous RNA (ceRNA) networks of these five lncRNAs were found using online in-silico techniques. Methods. Ethylenediaminetetraacetic acid (EDTA) blood samples of the control group consisted of 45 healthy people, and a total of 53 COVID-19-infected patients in case group, with a written informed consent, was collected. PBMCs were extracted, and then, the RNA extraction and complementary DNA (cDNA) synthesis was performed. The expression of five lncRNAs (lnc ISR, lnc ATV, lnc PAAN, lnc SG20, and lnc HEAL) was assessed by real-time PCR. In order to evaluate the biomarker roles of genes, receiver operating characteristic (ROC) curve was drawn. Results. Twenty-four (53.3%) and 29 (54.7%) of healthy and COVID-19-infected participants were male, respectively. The most prevalent symptoms were as follows: cough, general weakness, contusion, headache, and sore throat. The results showed that three lncRNAs, including lnc ISR, lnc ATV, and lnc HEAL, were expressed dramatically higher in the case group compared to healthy controls. According to ROC curve analysis, lnc ATV has a higher AUC and is a better biomarker to differentiate COVID-19 patients from the healthy controls. Then, using bioinformatics methods, the ceRNA network of these lncRNAs enabled the identification of mRNAs and miRNAs with crucial functions in COVID-19. Conclusion. The considerable higher expression of ISR, ATV, and HEAL lncRNAs and the significant area under curve (AUC) in ROC curve demonstrate that these RNAs probably have a potential role in controlling the host innate immune responses and regulate the viral replication of SARS-CoV-2. However, these assumptions need further in vitro and in vivo investigations to be confirmed.","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139775907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}