Comparative and Functional Genomics最新文献

{"title":"Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis","authors":"Dwijesh Chandra Mishra,&nbsp;Sayanti Guha Majumdar,&nbsp;Anuj Kumar,&nbsp;Jyotika Bhati,&nbsp;K. K. Chaturvedi,&nbsp;Ranjeet Ranjan Kumar,&nbsp;Suneha Goswami,&nbsp;Anil Rai,&nbsp;Neeraj Budhlakoti","doi":"10.1155/2023/1774764","DOIUrl":"10.1155/2023/1774764","url":null,"abstract":"<div>\u0000 <p>Climate change has become a major source of concern, particularly in agriculture, because it has a significant impact on the production of economically important crops such as wheat, rice, and maize. In the present study, an attempt has been made to identify differentially expressed heat stress-responsive long non-coding RNAs (lncRNAs) in the wheat genome using publicly available wheat transcriptome data (24 SRAs) representing two conditions, namely, control and heat-stressed. A total of 10,965 lncRNAs have been identified and, among them, 153, 143, and 211 differentially expressed transcripts have been found under 0 DAT, 1 DAT, and 4 DAT heat-stress conditions, respectively. Target prediction analysis revealed that 4098 lncRNAs were targeted by 119 different miRNA responses to a plethora of environmental stresses, including heat stress. A total of 171 hub genes had 204 SSRs (simple sequence repeats), and a set of target sequences had SNP potential as well. Furthermore, gene ontology analysis revealed that the majority of the discovered lncRNAs are engaged in a variety of cellular and biological processes related to heat stress responses. Furthermore, the modeled three-dimensional (3D) structures of hub genes encoding proteins, which had an appropriate range of similarity with solved structures, provided information on their structural roles. The current study reveals many elements of gene expression regulation in wheat under heat stress, paving the way for the development of improved climate-resilient wheat cultivars.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2023 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10079388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9265731","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":"Eight Aging-Related Genes Prognostic Signature for Cervical Cancer","authors":"Meilin Yin,&nbsp;Yanhua Weng","doi":"10.1155/2023/4971345","DOIUrl":"10.1155/2023/4971345","url":null,"abstract":"<div>\u0000 <p>This study searched for aging-related genes (ARGs) to predict the prognosis of patients with cervical cancer (CC). All data were obtained from Molecular Signatures Database, Cancer Genome Atlas, Gene Expression Integration, and Genotype Organization Expression. The R software was used to screen out the differentially expressed ARGs (DE-ARGs) between CC and normal tissues. A protein–protein interaction network was established by the DE-ARGs. The univariate and multivariate Cox regression analyses were conducted on the first extracted Molecular Complex Detection component, and a prognostic model was constructed. The prognostic model was further validated in the testing set and GSE44001 dataset. Prognosis was analyzed by Kaplan–Meier curves, and accuracy of the prognostic model was assessed by receiver operating characteristic area under the curve analysis. An independent prognostic analysis of risk score and some clinicopathological factors of CC was also performed. The copy-number variant (CNV) and single-nucleotide variant (SNV) of prognostic ARGs were analyzed by the BioPortal database. A clinical practical nomogram was established to predict individual survival probability. Finally, we carried out cell experiment to further verify the prognostic model. An eight-ARG prognostic signature for CC was constructed. High-risk CC patients had significantly shorter overall survival than low-risk patients. The receiver operating characteristic (ROC) curve validated the good performance of the signature in survival prediction. The Figo_stage and risk score served as independent prognostic factors. The eight ARGs mainly enriched in growth factor regulation and cell cycle pathway, and the deep deletion of FN1 was the most common CNV. An eight-ARG prognostic signature for CC was successfully constructed.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2023 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9985510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10860890","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 Five-LLPS Gene Risk Score Prognostic Signature Predicts Survival in Hepatocellular Carcinoma","authors":"Wenwen Lai,&nbsp;Defu Li,&nbsp;Qiong Ge,&nbsp;Yehong Yan,&nbsp;Shiwen Luo,&nbsp;Quqin Lu","doi":"10.1155/2023/7299276","DOIUrl":"10.1155/2023/7299276","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Primary liver cancer, dominated by hepatocellular carcinoma (HCC), is one of the most common cancer types and the third leading cause of cancer death in 2020. Previous studies have shown that liquid–liquid phase separation (LLPS) plays an important role in the occurrence and development of cancer including HCC, but its influence on the patient prognosis is still unknown. It is necessary to explore the effect of LLPS genes on prognosis to accurately forecast the prognosis of HCC patients and identify relevant targeted therapeutic sites. <i>Methods</i>. Using The Cancer Genome Atlas dataset and PhaSepDB dataset, we identified LLPS genes linked to the overall survival (OS) of HCC patients. We applied Least Absolute Shrinkage and Selection Operator (LASSO) Cox penalized regression analysis to choose the best genes for the risk score prognostic signature. We then analysed the validation dataset and evaluated the effectiveness of the risk score prognostic signature. Finally, we performed quantitative real-time PCR experiments to validate the genes in the prognostic signature. <i>Results</i>. We identified 43 differentially expressed LLPS genes that were associated with the OS of HCC patients. Five of these genes (<i>BMX</i>, <i>FYN</i>, <i>KPNA2</i>, <i>PFKFB4</i>, and <i>SPP1</i>) were selected to generate a prognostic risk score signature. Patients in the low-risk group were associated with better OS than those in the high-risk group in both the training dataset and the validation dataset. We found that <i>BMX</i> and <i>FYN</i> had lower expression levels in HCC tumour tissues, whereas <i>KPNA2</i>, <i>PFKFB4</i>, and <i>SPP1</i> had higher expression levels in HCC tumour tissues. The validation demonstrated that the five-LLPS gene risk score signature has the capability of predicting the OS of HCC patients. <i>Conclusion</i>. Our study constructed a five-LLPS gene risk score signature that can be applied as an effective and convenient prognostic tool. These five genes might serve as potential targets for therapy and the treatment of HCC.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2023 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9977538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9393801","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 a Necroptosis-Related Prognostic Signature and Associated Regulatory Axis in Lung Adenocarcinoma","authors":"Libo Sun,&nbsp;Wenwen Li,&nbsp;Zhenhuan Zhao,&nbsp;Yanhua Zuo,&nbsp;Zhiwu Han","doi":"10.1155/2023/8766311","DOIUrl":"10.1155/2023/8766311","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Lung cancer is considered to be the second most aggressive and rapidly fatal cancer after breast cancer. Necroptosis, a novel discovered pattern of cell death, is mediated by Receptor-interacting serine/threonine-protein kinase 1 (RIPK1), Receptor-interacting serine/threonine-protein kinase 3 (RIPK3), and Mixed Lineage Kinase Domain Like Pseudokinase (MLKL). <i>Methods</i>. For the purpose of developing a prognostic model, Least absolute shrinkage and selection operator (LASSO) Cox regression analysis was conducted. Using Pearson’s correlation analysis, we evaluated the correlation between necroptosis-related markers and tumor immune infiltration. A bioinformatics analysis was conducted to construct a necroptosis-related regulatory axis. <i>Results</i>. There was a downregulation of most of necroptosis-related genes in lung adenocarcinoma (LUAD) versus lung tissues but an increase in PGAM5, HMGB1, TRAF2, EZH2 levels. We also summarized the Single Nucleotide Variant (SNV) and copy number variation (CNV) of necroptosis-related genes in LUAD. Consensus clustering identified two clusters in LUAD with distinct immune cell infiltration and ESTIMATEScore. Genes related to necroptosis were associated with necroptosis, Tumor necrosis factor (TNF) signaling pathway, and apoptosis according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Four prognostic genes (ALDH2, HMGB1, NDRG2, TLR2) were combined to develop a prognostic gene signature for LUAD patients, which was highly accurate in predicting prognosis. Univariate and multivariate analysis identified HMGB1, pT stage, and pN stage as independent factors impacting on LUAD patients’ prognosis. A significant correlation was found between the level of TLR2 and NDRG2 and clinical stage, immunity infiltration, and drug resistance. Additionally, the progression of LUAD might be regulated by lncRNA C5orf64/miR-582-5p/NDRG2/TLR2. <i>Conclusion</i>. The current bioinformatics analysis identified a necroptosis-related prognostic signature for LUAD and their relation to immunity infiltration. This result requires further investigation.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2023 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10643042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48606981","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":"An Investigation of the Prognostic Role of Genes Related to Lipid Metabolism in Head and Neck Squamous Cell Carcinoma","authors":"Ling Qian,&nbsp;Chenyu Zhou,&nbsp;Keyi Wang,&nbsp;Liuyang Li,&nbsp;Wenhui Xia,&nbsp;Yuan Fan","doi":"10.1155/2023/9708282","DOIUrl":"10.1155/2023/9708282","url":null,"abstract":"<div>\u0000 <p>Head and neck squamous cell carcinoma (HNSCC) has become a prevalent malignancy, and its incidence and mortality rate are increasing worldwide. Accumulating evidence has indicated that lipid metabolism-related genes (LMRGs) are involved in the occurrence and development of HNSCC. This study investigated the latent association of lipid metabolism with HNSCC and established a prognostic signature based on LMRGs. A prognostic risk model composed of eight differentially expressed LMRGs (<i>PHYH</i>, <i>CYP4F8</i>, <i>INMT</i>, <i>ELOVL6</i>, <i>PLPP3</i>, <i>BCHE</i>, <i>TPTE</i>, and <i>STAR</i>) was constructed through The Cancer Genome Atlas database. Then, ELOVL6 expression was validated in oral squamous cell carcinoma (OSCC), which is a common type of HNSCC, by immunohistochemical analysis. ELOVL6 expression in the OSCC II/III group was significantly higher than that in the other three groups (normal, dysplasia, and OSCC I), and OSCC patients with high ELOVL6 expression had poorer survival than those with low ELOVL6 expression. In summary, the LMRG-based prognostic feature had prognostic predictive capacity. ELOVL6 may be a potential prognostic factor for HNSCC patients.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2023 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9937776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10767431","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 Review of the GSTM1 Null Genotype Modifies the Association between Air Pollutant Exposure and Health Problems","authors":"Dwi Aris Agung Nugrahaningsih,&nbsp;Hevi Wihadmadyatami,&nbsp;Sitarina Widyarini,&nbsp;Rahmi Ayu Wijayaningsih","doi":"10.1155/2023/4961487","DOIUrl":"10.1155/2023/4961487","url":null,"abstract":"<div>\u0000 <p>Air pollution is one of the significant environmental risks known as the cause of premature deaths. It has deleterious effects on human health, including deteriorating respiratory, cardiovascular, nervous, and endocrine functions. Exposure to air pollution stimulates reactive oxygen species (ROS) production in the body, which can further cause oxidative stress. Antioxidant enzymes, such as glutathione S-transferase mu 1 (<i>GSTM1</i>), are essential to prevent oxidative stress development by neutralizing excess oxidants. When the antioxidant enzyme function is lacking, ROS can accumulate and, thus, cause oxidative stress. Genetic variation studies from different countries show that <i>GSTM1</i> null genotype dominates the <i>GSTM1</i> genotype in the population. However, the impact of the <i>GSTM1</i> null genotype in modifying the association between air pollution and health problem is not yet clear. This study will elaborate on <i>GSTM1</i>’s null genotype role in modifying the relationship between air pollution and health problems.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2023 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9925255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10728446","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":"LncRNA MIAT Upregulates NEGR1 by Competing for miR-150-5p as a Competitive Endogenous RNA in SCIRI Rats","authors":"Zheng Wang,&nbsp;Jianguang Liu,&nbsp;Qiuxiang Yang,&nbsp;Mengjie Ma","doi":"10.1155/2022/2942633","DOIUrl":"10.1155/2022/2942633","url":null,"abstract":"<div>\u0000 <p><i>Objective</i>. Spinal cord ischemia–reperfusion injury (SCIRI) can cause a pathological state of irreversible delayed death of neurons in the spinal cord tissue and a range of complications, such as spinal cord dysfunction and motor function impairment. This study aimed to determine whether the long-stranded non-coding ribonucleic acid (lncRNA), myocardial infarction-associated transcript (MIAT), could upregulate neuronal growth regulator 1 (NEGR1) by competing for miR-150-5p as a competitive endogenous RNA in a rat SCIRI model. <i>Methods</i>. The MIAT knockdown vector or the corresponding blank vector was injected into the spinal cord of healthy sprague Dawley (SD) rats. Administration of the MIAT knockdown vector led to the establishment of the SCIRI rat model. Basso, Beattie &amp; Bresnahan locomotor rating scale (BBB) assessment of hind limb motion. Pathological changes in the spinal cord were observed via hematoxylin and eosin staining and eosin staining. Quantitative polymerase chain reaction was performed to determine the expression levels of the candidate microRNAs and predicted candidate genes, and the relationship between them. Terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling assay (TUNEL) staining was used to detect apoptosis in the spinal cord tissue of rats in each group. Western blotting was performed to determine the expression of the apoptosis-related proteins, caspase-9, caspase-3, and BCL2-Associated X (Bax)/B-cell lymphoma-2 (Bcl-2). The luciferase reporter gene was used to assess the interaction among the lncRNA, MIAT, and miR-150-5, and the interaction between miR-150-5 and NEGR1. <i>Results</i>. The sh-lncRNA, MIAT, improved exercise status, and pathological changes in the spinal cord of SCIRI rats, inhibited apoptosis, increased the expression of miR-150-5p, and reduced the expression of NEGR1. Compared with mimics-NC, the transfection of miR-150-5p significantly decreased the relative fluorescence activity ratio of MIAT 3′-untranslated region (3′-UTR) wild-type Human embryonic kidney cells 293 (HEK-293 cells). Compared with mimics-negative control (NC), the transfection of miR-150-5p significantly decreased the relative fluorescence activity ratio of NEGR1 3′-UTR wild-type HEK-293 cells. <i>Conclusion</i>. MIAT can affect the symptoms of SCIRI in rats. Furthermore, as a competitive endogenous RNA, MIAT upregulates NEGR1 by competing with miR-150-5p in SCIRI rats.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9812626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10858494","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 Genomic Analysis of Bacillus megaterium HT517 Reveals the Genetic Basis of Its Abilities to Promote Growth and Control Disease in Greenhouse Tomato","authors":"Wei Yang,&nbsp;Yingnan Zhao,&nbsp;Yang Yang,&nbsp;Minshuo Zhang,&nbsp;Xiaoxi Mao,&nbsp;Yanjie Guo,&nbsp;Xiangyu Li,&nbsp;Bu Tao,&nbsp;Yongzhi Qi,&nbsp;Li Ma,&nbsp;Wenju Liu,&nbsp;Bowen Li,&nbsp;Hong J. Di","doi":"10.1155/2022/2093029","DOIUrl":"10.1155/2022/2093029","url":null,"abstract":"<div>\u0000 <p><i>Bacillus megaterium</i> is well known as a plant growth-promoting rhizobacterium, but the relevant molecular mechanisms remain unclear. This study aimed to elucidate the effects of <i>B. megaterium</i> HT517 on the growth and development of and the control of disease in greenhouse tomato and its mechanism of action. A pot experiment was conducted to determine the effect of <i>B. megaterium</i> on tomato growth, and this experiment included the HT517 group (3.2 × 10⁸ cfu/pot) and the control group (inoculated with the same amount of sterilized suspension). An antagonistic experiment and a plate confrontation experiment were conducted to study the antagonistic effect of <i>B. megaterium</i> and <i>Fusarium oxysporum f.</i>sp. <i>lycopersici</i>. Liquid chromatography–mass spectrometry was used to determine the metabolite composition and metabolic pathway of HT517. PacBio+Illumina HiSeq sequencing was utilized for map sequencing of the samples. An in-depth analysis of the functional genes related to the secretion of these substances by functional bacteria was conducted. HT517 could secrete organic acids that solubilize phosphorus, promote root growth, secrete auxin, which that promotes early flowering and fruiting, and alkaloids, which control disease, and reduce the incidence of crown rot by 51.0%. The complete genome sequence indicated that the strain comprised one circular chromosome with a length of 5,510,339 bp (including four plasmids in the genome), and the GC content accounted for 37.95%. Seven genes (<i>pyk</i>, <i>aceB</i>, <i>pyc</i>, <i>ackA</i>, <i>gltA</i>, <i>buk</i>, and <i>aroK</i>) related to phosphate solubilization, five genes (<i>trpA</i>, <i>trpB</i>, <i>trpS</i>, <i>TDO2</i>, and <i>idi</i>) related to growth promotion, eight genes (<i>hpaB</i>, <i>pheS</i>, <i>pheT</i>, <i>ileS</i>, <i>pepA</i>, <i>iucD</i>, <i>paaG</i>, and <i>kamA</i>) related to disease control, and one gene cluster of synthetic surfactin were identified in this research. The identification of molecular biological mechanisms for extracellular secretion by the HT517 strain clarified that its organic acids solubilized phosphorus, that auxin promoted growth, and that alkaloids controlled tomato diseases.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9810399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10549480","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":"Molecular Characterization and Clinical Characteristics of m5C-Based RNA Methylation in Spinal Cord Injury: Validated by qPCR","authors":"Liang Cao,&nbsp;Wen Jun Pi,&nbsp;Qiang Zhang,&nbsp;Qing Li","doi":"10.1155/2022/5433860","DOIUrl":"10.1155/2022/5433860","url":null,"abstract":"<div>\u0000 <p>Aberrant patterns of 5-methylcytosine (m5C)-based ribonucleic acid (RNA) methylation have critical roles in various human diseases, but their importance in spinal cord injury (SCI) is largely unknown. We explore the expression patterns and potential roles of m5C-based regulators of RNA modification after SCI. We analyzed 16 m5C-based regulators of RNA modification in tissues with SCI and normal rats from the Gene Expression Omnibus database. We constructed a “gene signature” of m5C-based regulators of RNA modification to predict the prognosis of SCI using least absolute shrinkage and selection operator regression and random-forest strategy. We found that the m5C-related genes, deoxyribonucleic acid (DNA) methyltransferase1 (<i>Dnmt1</i>), methyl-CpG binding domain protein 2 (<i>Mbd2</i>), ubiquitin-like with PHD and ring finger domains 1 (<i>Uhrf1</i>), uracil-<i>N</i>-glycosylase (<i>Ung</i>), and zinc finger and BTB(brica-brac, tramtrack, and broad) domain containing 38 (<i>Zbtb38</i>) had high expression, and zinc finger and BTB domain containing 4 (<i>Zbtb4</i>) had low expression in SCI. Analysis of the correlation between the gene sets of m5C-based regulators of RNA modification and immune-cell infiltration and immune response revealed Dnmt1, DNA methyltransferases 3A (Dnmt3a), Mbd2, and Ung to be positive regulators of the immune microenvironment, and Zbtb4 may negatively regulate the immune environment. Then, two molecular subtypes were identified based on 16 m5C-regulated genes. Functional-enrichment analysis of differentially expressed genes between different patterns of m5C-based modification was undertaken. Through the creation of a protein–protein interaction network, we screened 11 hub genes. We demonstrated their importance between SCI group and sham group using real-time reverse transcription-quantitative polymerase chain reaction in rat model. Expression of hub genes did not correlate with mitophagy but was positively correlated with endoplasmic reticulum stress (ERS), which suggested that there may be differences in ERS between different patterns of m5C-based modification. This present study explored and discovered the close link between m5C regulators-related genes and SCI. We also hope our findings may contribute to further mechanistic and therapeutic research on the role of key m5C regulators after SCI.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9794433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10802282","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":"The Novel Action of miR-193b-3p/CDK1 Signaling in HCC Proliferation and Migration: A Study Based on Bioinformatic Analysis and Experimental Investigation","authors":"Xue Pang,&nbsp;Wei Wan,&nbsp;Xingxing Wu,&nbsp;Yu Shen","doi":"10.1155/2022/8755263","DOIUrl":"10.1155/2022/8755263","url":null,"abstract":"<div>\u0000 <p>Hepatocellular carcinoma (HCC) is a common human malignancy with high mortality and dismal prognosis. A growing number of novel targets underlying HCC pathophysiology have been detected using microarray high throughput screening platforms. This study carried out bioinformatics analysis to explore underlying biomarkers in HCC and assessed the potential action of the miR-193b-3p/CDK1 signaling pathway in HCC progression. A total of 241 common differentially expressed genes (DEGs) were screened from GSE33294, GSE104310, and GSE144269. Functional analysis results implicated that DEGs are significantly associated with “cell cycle,” “cell division,” and “proliferation.” The protein–protein interaction network analysis extracted ten hub genes from common DEGs. Ten hub genes were significantly overexpression in HCC tissues. Kaplan–Meier survival analysis revealed that 10 hub genes were linked with a poorer prognosis in HCC patients. Functional assays showed that CDK1 knockdown repressed HCC cell proliferation and migration. Luciferase reporter assay showed that miR-193b-3p could target CDK1 3′ untranslated region, and miR-193b-3p negatively modulated CDK1. Enforced CDK1 expression attenuated miR-193b-3p-modulated suppressive actions on HCC cell proliferation and migration. To summarize, we performed a comprehensive bioinformatics analysis and identified 10 hub genes linked to the prognosis in HCC patients. Functional analysis revealed that CDK1, negatively regulated by miR-193b-3p, may act as an oncogene to promote HCC cell proliferation and migration and may predict poor prognosis of HCC patients. However, the role of CDK1/miR-193b-3p may still require further investigation.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9806689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10489247","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}