Comparative and Functional Genomics最新文献

{"title":"A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species","authors":"Rongxuan Hu,&nbsp;Haifeng Huang,&nbsp;Ying Zhou,&nbsp;Yanshan Liu,&nbsp;Yaning Ren,&nbsp;Yuanfen Liao,&nbsp;Cunyin Yuan,&nbsp;Xiaohong Gu,&nbsp;Yubao Cui","doi":"10.1155/2024/3779688","DOIUrl":"10.1155/2024/3779688","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of <i>Dermatophagoides farinae</i>, a common allergenic mite species. <i>Methods</i>. We achieved a chromosome-level assembly of <i>D. farinae</i>’s genome by integrating PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, and Hi-C technology, followed by annotating allergens and mapping them to specific chromosomes. <i>Results</i>. A 62.43 Mb genome was assembled with a 0.52% heterozygosity rate and a 36.11 Merqury-estimated quality value. The assembled genome represents 92.1% completeness benchmarking universal single-copy orthologs with a scaffold N50 value of 7.11 Mb. Hi-C scaffolding of the genome resulted in construction of 10 pseudochromosomes. The genome comprises 13.01% (7.66 Mb) repetitive sequences and predicts 10,709 protein-coding genes, 96.57% of which are functionally annotated. Moreover, we identified and located 36 allergen groups on specific chromosomes, including allergens Der f 1, Der f 2, Der f 23, Der f 4, Der f 5, Der f 7, and Der f 21 located on chromosomes 2, 1, 7, 3, 4, 6, and 4, respectively. <i>Conclusion</i>. This comprehensive genomic data provides valuable insights into mite biology and evolutionary adaptations, potentially advancing <i>D. farinae</i> allergy research and treatment strategies.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/3779688","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete Genome Sequence Analysis of Bacillus subtilis MC4-2 Strain That against Tobacco Black Shank Disease","authors":"Chunlan Shi,&nbsp;Shuquan Zeng,&nbsp;Xi Gao,&nbsp;Mehboob Hussain,&nbsp;Mingchuan He,&nbsp;Xurong Niu,&nbsp;Congcong Wei,&nbsp;Rui Yang,&nbsp;Mingxian Lan,&nbsp;Yonghui Xie,&nbsp;Zhijiang Wang,&nbsp;Guoxing Wu,&nbsp;Ping Tang","doi":"10.1155/2024/8846747","DOIUrl":"10.1155/2024/8846747","url":null,"abstract":"<div>\u0000 <p>The MC4-2 bacterium strain was isolated and purified from the <i>Periplaneta americana</i> intestine as a biocontrol agent with good antagonistic effect against the pathogens of a soil-borne disease called tobacco black shank. The MC4-2 strain was found to have good broad-spectrum inhibition by plate stand-off test. Based on 16S rRNA and <i>gyrB</i> genes, ANI analysis, and other comparative genomics methods, it was determined that the MC4-2 strain was <i>Bacillus subtilis</i>. The complete genome sequence showed that the genome size was 4,076,630 bp, the average GC content was 43.78%, and the total number of CDSs was 4,207. Genomic prediction analysis revealed that a total of 145 genes were annotated by the CAZy, containing mainly GH and CE enzymes that break down carbohydrates such as glucose, chitin, starch, and alginate, and a large number of enzymes involved in glycosylation were present. A total of ten secondary metabolite clusters were predicted, six clusters of which were annotated as surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. The present investigation found the biological control mechanism of <i>B. subtilis</i> MC4-2, which provides a strong theoretical basis for the best use of this strain in biological control methods and provides a reference for the subsequent development of agents of this bacterium.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/8846747","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140300164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase 3 Expression and Its Correlation with Prognosis and Growth of Serous Ovarian Cancer: Correlation of DYRK3 with Ovarian Cancer Survival","authors":"Jia Sun,&nbsp;Yingzi Zhang,&nbsp;Aijie Li,&nbsp;Hao Yu","doi":"10.1155/2024/6683202","DOIUrl":"10.1155/2024/6683202","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Epithelial ovarian cancer, primarily serous ovarian cancer (SOC), stands as a predominant cause of cancer-related mortality among women globally, emphasizing the urgent need for comprehensive research into its molecular underpinnings. Within this context, the dual-specificity tyrosine phosphorylation-regulated kinase 3 (DYRK3) has emerged as a potential key player with implications for prognosis and tumor progression. <i>Methods</i>. This study conducted a meticulous retrospective analysis of 254 SOC cases from our medical center to unravel the prognostic significance of DYRK3. Survival analyses underscored DYRK3 as an independent adverse prognostic factor in SOC, with a hazard ratio of 2.60 (95% CI 1.67-4.07, <i>P</i> &lt; 0.001). Experimental investigations involved DYRK3 knockdown in serous ovarian cancer cell lines (CAOV3 and OVCAR-3) through a shRNA strategy, revealing substantial decreases in cell growth and invasion capabilities. Bioinformatics analyses further hinted at DYRK3’s involvement in modulating the tumor immune microenvironment. In vivo experiments with DYRK3-knockdown cell lines validated these findings, demonstrating a notable restriction in the growth of ovarian cancer xenografts. <i>Results</i>. Our findings collectively illuminate DYRK3 as a pivotal tumor-promoting oncogene in SOC. Beyond its adverse prognostic implications, DYRK3 knockdown exhibited promising therapeutic potential by impeding cancer progression and potentially influencing the tumor immune microenvironment. <i>Conclusions</i>. This study establishes a compelling foundation for further research into DYRK3’s intricate role and therapeutic potential in ovarian cancer treatment. As we unravel the complexities surrounding DYRK3, our work not only contributes to the understanding of SOC pathogenesis but also unveils new prospects for targeted therapeutic interventions, holding promise for improved outcomes in ovarian cancer management.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/6683202","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140155485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes","authors":"Biigba Yakubu,&nbsp;Edwin Moses Appiah,&nbsp;Andrews Frimpong Adu","doi":"10.1155/2024/5536117","DOIUrl":"10.1155/2024/5536117","url":null,"abstract":"<div>\u0000 <p>The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). <i>Conclusion</i>. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium’s antibiotic resistance.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/5536117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140026117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel Splicing Mutation Leading to Wiskott-Aldrich Syndrome from a Family","authors":"Lingyu Wang,&nbsp;Jie Zhang,&nbsp;Linna Lu,&nbsp;Juan Ren,&nbsp;Yaofang Zhang,&nbsp;Lidong Zhao,&nbsp;Wukang Shen,&nbsp;Xucheng Hu,&nbsp;Shuai Fang,&nbsp;Xiaomei Lu,&nbsp;Gang Wang,&nbsp;Linhua Yang","doi":"10.1155/2024/2277956","DOIUrl":"10.1155/2024/2277956","url":null,"abstract":"<div>\u0000 <p>Wiskott-Aldrich syndrome (WAS) is a rare X-linked recessive genetic disease characterized by clinical symptoms such as eczema, thrombocytopenia with small platelets, immune deficiency, prone to autoimmune diseases, and malignant tumors. This disease is caused by mutations of the <i>WAS</i> gene encoding WASprotein (WASP). The locus and type of mutations of the <i>WAS</i> gene and the expression quantity of WASP were strongly correlated with the clinical manifestations of patients. We found a novel mutation in the <i>WAS</i> gene (c.931 + 5G &gt; C), which affected splicing to produce three abnormal mRNA, resulting in an abnormally truncated WASP. This mutation led to a reduction but not the elimination of the normal WASP population, resulting in causes X-linked thrombocytopenia (XLT) with mild clinical manifestations. Our findings revealed the pathogenic mechanism of this mutation.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/2277956","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139919565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overexpression of FERM Domain Containing Kindlin 2 (FERMT2) in Fibroblasts Correlates with EMT and Immunosuppression in Gastric Cancer","authors":"Sheng-yan Yin,&nbsp;Yuan-jie Liu,&nbsp;Jie-pin Li,&nbsp;Jian Liu","doi":"10.1155/2024/4123737","DOIUrl":"10.1155/2024/4123737","url":null,"abstract":"<div>\u0000 <p>The mesenchymal feature, dominated by epithelial mesenchymal transition (EMT) and stromal cell activation, is one of the main reasons for the aggressive nature of tumors, yet it remains poorly understood. In gastric cancer (GC), the fermitin family homolog-2 (<i>FERMT2</i>) is involved in macrophage signaling, promoting migration and invasion. However, the function of <i>FERMT2</i> in fibroblasts remains unclear. Here, we demonstrated that downregulation of <i>FERMT2</i> expression can block EMT in GC cells by inhibiting fibroblast activation in vitro. Furthermore, we found that, in addition to the known pathways, fibroblast-derived <i>FERMT2</i> promotes M2-like macrophage growth and that in human GC samples, there is a strong positive correlation between FERMT2 and CD163 and CD206 levels. Notably, high <i>FERMT2</i> expression was significantly associated with poor clinical outcomes and was upregulated in patients with advanced disease. Taken together, our results provide evidence that the fibroblast-FERMT2-EMT-M2 macrophage axis plays a critical role in the GC mesenchymal phenotype and may be a promising target for the treatment of advanced GC.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10864055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139729571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of ZIC2 as a Potential Biomarker Linked with the Clinical Progression and Immune Infiltration of Oral Cancer: A Multicenter Study","authors":"Li Gao,&nbsp;Shi-Bai Yan,&nbsp;Fang-Cheng Jiang,&nbsp;Zhi-Guang Huang,&nbsp;Dong-Ming Li,&nbsp;Yu-Lu Tang,&nbsp;Jia-Yuan Luo,&nbsp;Gang Chen,&nbsp;Dan-Ming Wei","doi":"10.1155/2024/3256694","DOIUrl":"10.1155/2024/3256694","url":null,"abstract":"<div>\u0000 <p><i>Aim</i>. To investigate the specific expression profile, clinicopathological significance and mechanism of Zic family member 2 (ZIC2) in oral cancer were unclear. <i>Patients and Methods</i>. We explored the expression pattern and clinicopathological significance of ZIC2 in oral cancer through performing in-house tissue microarray and integrated analysis global RNA-seq and microarrays containing large samples. The molecular basis of ZIC2 in oral cancer was further investigated in the aspects of transcription network and immune correlations. We also performed in vitro experiments and calculated drug sensitivity of oral cancer with different ZIC2 expression levels in response to hundreds of compounds. <i>Results</i>. All data unanimously proved the significant overexpression of ZIC2 in oral cancer. The upregulation of ZIC2 was remarkably associated with the malignant clinical progression of oral cancer. ZIC2 was predicted to be targeted by miRNAs such as miR-3140, miR-4999, and miR-1322. The infiltration level of CD8+ T and central memory cells was positively related to the overexpression of ZIC2. Oral cancer patients with higher ZIC2 expression showed higher drug sensitivity to two compounds including AZD8186 and ERK_2240. <i>Conclusions</i>. We demonstrated the upregulation of ZIC2 in oral cancer and its promoting effect on the clinical advancement of oral cancer. The potential clinical value of ZIC2 in oral cancer deserves attention.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/3256694","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139552681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physiological Characteristic Changes and Transcriptome Analysis of Maize (Zea mays L.) Roots under Drought Stress","authors":"Chenglin Zou,&nbsp;Hua Tan,&nbsp;Kaijian Huang,&nbsp;Ruining Zhai,&nbsp;Meng Yang,&nbsp;Aihua Huang,&nbsp;Xinxing Wei,&nbsp;Runxiu Mo,&nbsp;Faqian Xiong","doi":"10.1155/2024/5681174","DOIUrl":"10.1155/2024/5681174","url":null,"abstract":"<div>\u0000 <p>Water deficit is a key limiting factor for limiting yield in maize (<i>Zea mays L.</i>). It is crucial to elucidate the molecular regulatory networks of stress tolerance for genetic enhancement of drought tolerance. The mechanism of drought tolerance of maize was explored by comparing physiological and transcriptomic data under normal conditions and drought treatment at polyethylene glycol- (PEG-) induced drought stress (5%, 10%, 15%, and 20%) in the root during the seedling stage. The content of saccharide, SOD, CAT, and MDA showed an upward trend, proteins showed a downward trend, and the levels of POD first showed an upward trend and then decreased. Compared with the control group, a total of 597, 2748, 6588, and 5410 differentially expressed genes were found at 5%, 10%, 15%, and 20% PEG, respectively, and 354 common DEGs were identified in these comparisons. Some differentially expressed genes were remarkably enriched in the MAPK signaling pathway and plant hormone signal transduction. The 50 transcription factors (TFs) divided into 15 categories were screened from the 354 common DEGs during drought stress. Auxin response factor 10 (ARF10), auxin-responsive protein IAA9 (IAA9), auxin response factor 14 (ARF14), auxin-responsive protein IAA1 (IAA1), auxin-responsive protein IAA27 (IAA27), and 1 ethylene response sensor 2 (ERS2) were upregulated. The two TFs, including bHLH 35 and bHLH 96, involved in the MAPK signal pathway and plant hormones pathway, are significantly upregulated in 5%, 10%, 15%, and 20% PEG stress groups. The present study provides greater insight into the fundamental transcriptome reprogramming of grain crops under drought.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/5681174","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139484125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Mid-Density Single-Nucleotide Polymorphism Panel for Molecular Applications in Cowpea (Vigna unguiculata (L.) Walp)","authors":"Patrick Obia Ongom,&nbsp;Christian Fatokun,&nbsp;Abou Togola,&nbsp;Ana Luisa Garcia-Oliveira,&nbsp;Eng Hwa Ng,&nbsp;Andrzej Kilian,&nbsp;Stefano Lonardi,&nbsp;Timothy J. Close,&nbsp;Ousmane Boukar","doi":"10.1155/2024/9912987","DOIUrl":"10.1155/2024/9912987","url":null,"abstract":"<div>\u0000 <p>Molecular markers are increasingly being deployed to accelerate genetic gain in crop plants. The objective of this study was to assess the potential of a mid-density genotyping panel for molecular applications in cowpea breeding. A core set of 2,602 targeted diversity array technology (DArTag) single-nucleotide polymorphisms (SNPs) was designed from an existing 51,128 Cowpea iSelect Consortium Array. The panel’s usefulness was assessed using 376 genotypes from different populations of known genetic backgrounds. The panel was informative, with over 78% of SNPs exceeding a minor allele frequency of 0.20. The panel decoded three stratifications in the constituted population, as was expected. Linkage disequilibrium (LD) decay was correctly depicted as slower in a biparental subset than in other populations. A known flower and seed coat color gene region was located on chromosome Vu07, suggesting that the mid-density panel may be used to hypothesize genomic regions underlying target traits in cowpea. Unexpected heterozygosity was detected in some lines and highly among F₁ progenies, divulging the panel’s potential application in germplasm purity and hybridity verification. The study unveils the potential of an excellent genomic resource that can be tapped to enhance the development of improved cowpea cultivars.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/9912987","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139411242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription Analysis of the THBS2 Gene through Regulation by Potential Noncoding Diagnostic Biomarkers and Oncogenes of Gastric Cancer in the ECM-Receptor Interaction Signaling Pathway: Integrated System Biology and Experimental Investigation","authors":"Ali Barani,&nbsp;Kamyar Beikverdi,&nbsp;Benyamin Mashhadi,&nbsp;Naeimeh Parsapour,&nbsp;Mohammad Rezaei,&nbsp;Pegah Javid,&nbsp;Mansoureh Azadeh","doi":"10.1155/2023/5583231","DOIUrl":"10.1155/2023/5583231","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Gastric cancer (GC) is the second most frequent cause of cancer-related death worldwide and the fourth most common malignancy. Despite significant improvements in patient survival over the past few decades, the prognosis for patients with GC remains dismal because of the high recurrence rate. In this comprehensive system biology and experimental investigation, we aimed to find new novel diagnostic biomarkers of GC through a regulatory RNA interaction network. <i>Methods</i>. Gene expression, coexpression, and survival analyses were performed using microarray and RNAseq datasets (analyzed by RStudio, GEPIA2, and ENCORI). RNA interaction analysis was performed using miRWalk and ENCORI online databases. Gene set enrichment analysis (GSEA) was performed to find related signaling pathways of up- and downregulated genes in the microarray dataset. Gene ontology and pathway enrichment analysis were performed by the enrichr database. Protein interaction analysis was performed by STRING online database. Validation of expression and coexpression analyses was performed using a qRT-PCR experiment. <i>Results</i>. Based on bioinformatics analyses, <i>THBS2</i> (FC: 7.14, FDR &lt; 0.0001) has a significantly high expression in GC samples. lncRNAs <i>BAIAP2-AS1</i>, <i>TSIX</i>, and <i>LINC01215</i> have RNA interaction with <i>THBS2</i>. <i>BAIAP2-AS1</i> (FC: 1.44, FDR: 0.018), <i>TSIX</i> (FC: 1.34, FDR: 0.038), and <i>LINC01215</i> (FC: 1.19, FDR: 0.046) have significant upregulation in GC samples. <i>THBS2</i> has a significant role in the regulation of the ECM-receptor signaling pathway. miR-4677-5p has a significant RNA interaction with <i>THBS2</i>. The expression level of <i>THBS2</i>, <i>BAIAP2-AS1</i>, <i>TSIX</i>, and <i>LINC01215</i> has a nonsignificant negative correlation with the survival rate of GC patients (HR: 0.28, logrank <i>p</i>: 0.28). qRT-PCR experiment validates mentioned bioinformatics expression analyses. <i>BAIAP2-AS1</i> (AUC: 0.7136, <i>p</i> value: 0.0096), <i>TSIX</i> (AUC: 0.7456, <i>p</i> value: 0.0029), and <i>LINC01215</i> (AUC: 0.7872, <i>p</i> value: 0.0005) could be acceptable diagnostic biomarkers of GC. <i>Conclusion</i>. <i>BAIAP2-AS1</i>, lncRNA <i>LINC01215</i>, lncRNA <i>TSIX</i>, and miR-4677-5p might modulate the ECM-receptor signaling pathway via regulation of <i>THBS2</i> expression level, as the high-expressed noncoding RNAs in GC. Furthermore, mentioned lncRNAs could be considered potential diagnostic biomarkers of GC.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2023 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2023/5583231","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138944984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}