Comparative and Functional Genomics最新文献

{"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}

{"title":"IL1RN and PRRX1 as a Prognostic Biomarker Correlated with Immune Infiltrates in Colorectal Cancer: Evidence from Bioinformatic Analysis","authors":"Qi Wang,&nbsp;Xufeng Huang,&nbsp;Shujing Zhou,&nbsp;Yuntao Ding,&nbsp;Huizhi Wang,&nbsp;Weiye Jiang,&nbsp;Min Xu","doi":"10.1155/2022/2723264","DOIUrl":"10.1155/2022/2723264","url":null,"abstract":"<div>\u0000 <p>The extensive morbidity of colorectal cancer (CRC) and the inferior prognosis of terminal CRC urgently call for reliable prognostic biomarkers. For this, we identified 704 differentially expressed genes (DEGs) by intersecting three datasets, GSE41328, GSE37364, and GSE15960 from Gene Expression Omnibus database, to maximize the accuracy of the results. Preliminary analysis of the DEGs was then performed using online gene analysis datasets, such as DAVID, UCSC Cancer Genome Browser, CBioPortal, STRING, and UCSC Cancer Genome Browser. Cytoscape was utilized to visualize the protein perception interaction network of DEGs, and the bubble map of GO and KEGG enrichment function was demonstrated using the R package. The Molecular Complex Detection (MCODE), Biological Network Gene Oncology (BiNGO) plug-in in Cytoscape, was applied to further screen the DEGs to obtain 15 seed genes, which were <i>IL1RN</i>, <i>GALNT12</i>, <i>ADH6</i>, <i>SCN7A</i>, <i>CXCL1</i>, <i>FGF18</i>, <i>SOX9</i>, <i>ACACB</i>, <i>PRRX1</i>, <i>MZB1</i>, <i>SLC22A3</i>, <i>CNNM4</i>, <i>LY6E</i>, <i>IFITM2</i>, and <i>GDPD3</i>. Among them, <i>IL1RN</i>, <i>ADH6</i>, <i>SCN7A</i>, <i>ACACB</i>, <i>MZB1</i>, and <i>GDPD3</i> exhibited statistically significant survival differences, whereas limited studies were conducted in CRC. Based on the enrichment results of the “Gene Ontology“(GO) and “Kyoto Encyclopedia of Genes and genomes “(KEGG) as well as documented findings of key genes, we further emphasized the potential of <i>IL1RN</i> and <i>PRRX1</i> as markers of immune infiltrates in CRC and confirmed our hypothesis by compiling data from the UALCAN, Tumor Immune Estimation Resource, and TISIDB databases for these two genes. The above-mentioned genes might offer a valuable insight into the diagnosis, immunotherapeutic targets, and prognosis of CRC.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9726255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10723073","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 Insight into Paraptosis-Related Classification and Signature in Lower-Grade Gliomas","authors":"Xi-Feng Qian,&nbsp;Jia-Hao Zhang,&nbsp;Yue-Xue Mai,&nbsp;Xin Yin,&nbsp;Yu-Bin Zheng,&nbsp;Zi-Yuan Yu,&nbsp;Guo-Dong Zhu,&nbsp;Xu-Guang Guo","doi":"10.1155/2022/6465760","DOIUrl":"10.1155/2022/6465760","url":null,"abstract":"<div>\u0000 <p>Lower-grade gliomas (LGG) are the most common intracranial malignancies that readily evolve to high-grade gliomas and increase drug resistance. Paraptosis is defined as a nonapoptotic form of programmed cell death, which is gradually focused on patients with gliomas to develop treatment options. However, the specific role of paraptosis in LGG and its correlation is still vague. In this study, we first establish the novel paraptosis-based prognostic model for LGG patients. The relevant data of LGG patients were acquired from The Cancer Genome Atlas database, and we found that LGG patients could be divided into three different clusters based on paraptosis via consensus cluster analysis. Through least absolute shrinkage and selection operator regression analysis and multivariate Cox regression analysis, 10-paraptosis-related gene (PRG) signatures (CDK4, TNK2, DSTYK, CDKN3, CCR4, CASP9, HSPA5, RGR, LPAR1, and PDCD6IP) were identified to separate LGG patients into high- and low-risk subgroups successfully. The Kaplan–Meier analysis and time-dependent receiver-operating characteristic showed that the performances of predicting overall survival (OS) were dramatically high. The parallel results were reappeared and verified by using the Chinese Glioma Genome Atlas and Gene Expression Omnibus databases. Independent prognostic analysis and nomogram construction implied that risk scores could be considered the independent factor to predict OS. Enrichment analysis indicated that immune-related biological processes were generally enriched, and different immune statuses were highly infiltrated in high-risk group. We also confirmed the potential relationship of 10-PRG signatures and drug sensitivity of Food and Drug Administration–approved drugs. In summary, our findings provide a novel knowledge of paraptosis status and crucial direction to further explore the role of PRG signatures in LGG.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9678488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40702382","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":"Expression and Prognostic Significance of PDIA3 in Cervical Cancer","authors":"Jing Zhang,&nbsp;Hui Li,&nbsp;Huling Li,&nbsp;Dandan Lin,&nbsp;Xiaoyan Wang,&nbsp;Kai Wang","doi":"10.1155/2022/4382645","DOIUrl":"10.1155/2022/4382645","url":null,"abstract":"&lt;div&gt;\u0000 &lt;p&gt;To investigate the expression of protein disulfide isomerase A3 (PDIA3/ERP57) in cervical cancer and its clinical prognostic significance as well as its function and possible action mechanism in the progression of cervical cancer. Based on TIMER2.0 database, the human protein map (Human Protein Atlas) was used to determine the expression level of PDIA3 protein for the analysis of PDIA3 expression in 39 The Cancer Genome Atlas (TCGA) tumors. The PDIA3 expression in cervical cancer tissues in the TCGA and Genotype-Tissue Expression databases was further verified based on the GEPIA2 database to analyze the relationship between the PDIA3 expression and the pathological stage of cervical cancer patients. Immunohistochemistry was used to detect the PDIA3 expression in cervical cancer tissue microarray, including 111 cancer tissue samples and 24 adjacent cancer tissue samples, and the relationship between PDIA3 protein expression and clinical characteristics of patients with cervical cancer was analyzed. The Kaplan–Meier method and log-rank test were used for survival analysis. Based on the cBioPortal database, the Spearman’s and Pearson’s methods were used to analyze the correlation between PDIA3 expression and DNA methylation. The correlation between PDIA3 expression and the infiltration levels of each immune cell in cervical cancer was evaluated. The STRING was used to construct protein interaction network. Based on LinkedOmics database, the Spearman’s method was used to analyze the co-expressed genes of PDIA3 in TCGA cervical cancer. The gene ontology functional enrichment analysis was performed on Top 50 differentially co-expressed genes based on DAVID database. The PDIA3 expression in cervical cancer tissues was significantly higher than that in normal tissues, which (&lt;i&gt;F&lt;/i&gt; = 2.74, PR (&gt;&lt;i&gt;F&lt;/i&gt;) = 0.0436) was significantly increased with the progression of tumor stage, and PDIA3 showed strong immunoreactivity in cervical cancer tissues. In cervical cancer patients, overall survival (&lt;i&gt;P&lt;/i&gt; = 0.014), disease-specific survival (&lt;i&gt;P&lt;/i&gt; = 0.013), disease-free interval (&lt;i&gt;P&lt;/i&gt; = 0.023), and progression-free interval (&lt;i&gt;P&lt;/i&gt; = 0.001) in those with high expression of PDIA3 were significantly lower than those with low expression, suggesting that high expression of PDIA3 was associated with poor prognosis. In cervical cancer, high expression of PDIA3 was associated with DNA methylation and negatively correlated with B cell memory (&lt;i&gt;r&lt;/i&gt; = −0.132, &lt;i&gt;P&lt;/i&gt; = 0.021), T cell regulatory (&lt;i&gt;r&lt;/i&gt; = −0.127, &lt;i&gt;P&lt;/i&gt; = 0.026), monocytes (&lt;i&gt;r&lt;/i&gt; = −0.204, &lt;i&gt;P&lt;/i&gt; = 0), and macrophages M2 (&lt;i&gt;r&lt;/i&gt; = −0.142, &lt;i&gt;P&lt;/i&gt; = 0.013), whereas positively correlated with levels of NK cell activated (&lt;i&gt;r&lt;/i&gt; = 0.162, &lt;i&gt;P&lt;/i&gt; = 0.005) and mast cells activated (&lt;i&gt;r&lt;/i&gt; = 0.119, &lt;i&gt;P&lt;/i&gt; = 0.037). The genes positively correlated with PDIA3 expression included HSPA5 and PPIB, which were mainly enriched in biological processes, such as","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9674421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40503082","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":"Detection of Complement C1q B Chain Overexpression and Its Latent Molecular Mechanisms in Cervical Cancer Tissues Using Multiple Methods","authors":"Si-Tong Lin,&nbsp;Zi-Qian Liang,&nbsp;Xiao-Yu Chen,&nbsp;Xin-Qing Ye,&nbsp;Yu-Yan Pang,&nbsp;Jia-Yuan Luo,&nbsp;Jun-Hong Chen,&nbsp;Yi-Wu Dang,&nbsp;Gang Chen","doi":"10.1155/2022/8775330","DOIUrl":"10.1155/2022/8775330","url":null,"abstract":"<div>\u0000 <p><i>Aim</i>. The aim of this study is to demonstrate the expression and clinicopathological significance of complement C1q B chain (<i>C1QB</i>) in cervical cancer. <i>Methods</i>. In total, 120 cervical cancer tissues, as well as 20 samples each of high-grade squamous intraepithelial lesions (HSILs), low-grade squamous intraepithelial lesions (LSILs), and benign cervical tissue, were collected to evaluate the expression of <i>C1QB</i> protein via immunohistochemical staining. We conducted an integrated analysis of <i>C1QB</i> mRNA expression in cervical cancer using public microarrays and RNA-seq data sets by calculating standard mean differences (SMDs). Simultaneously, we explored the relations of <i>C1QB</i> with clinicopathological parameters and the expression of P16, Ki-67, and P53. <i>Results</i>. The expression of <i>C1QB</i> protein was higher in cervical cancer samples than that in benign cervical tissue, LSIL, and HSIL samples (<i>p</i> &lt; 0.05). A combined SMD of 0.65 (95% CI: [0.52, 0.79], <i>p</i> &lt; 0.001) revealed upregulation of <i>C1QB</i> mRNA in cervical cancer. <i>C1QB</i> expression may also be related to the depth of infiltration, lymphovascular invasion, and perineural invasion in cervical cancer (<i>p</i> &lt; 0.05). We also found that <i>C1QB</i> protein expression was positively correlated with P16 and Ki-67 expression in cervical cancer (<i>p</i> &lt; 0.05). The gene set enrichment analysis showed that <i>C1QB</i> may participate in apoptosis and autophagy. A relationship was predicted between <i>C1QB</i> expression and drug sensitivity to cisplatin, paclitaxel, and docetaxel. <i>Conclusion</i>. We confirmed the overexpression of <i>C1QB</i> in cervical cancer at both mRNA and protein levels for the first time. <i>C1QB</i> may serve as an oncogene in the tumorigenesis of cervical cancer, but this possibility requires further study.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9613392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40439088","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":"ALDH1A3–Linc00284 Axis Mediates the Invasion of Colorectal Cancer by Targeting TGFβ Signaling via Sponging miR-361-5p","authors":"Chunlin Ke,&nbsp;Minmin Shen,&nbsp;Peirong Wang,&nbsp;Zhihua Chen,&nbsp;Suyong Lin,&nbsp;Feng Dong","doi":"10.1155/2022/6561047","DOIUrl":"10.1155/2022/6561047","url":null,"abstract":"<div>\u0000 <p>ALDH1A3 and Linc00284 involve in colorectal cancer (CRC) development; however, the regulatory mechanism is still unclear. In this study, we collected clinicopathological characteristics and tissue samples from 73 CRC patients to analyze the expression of ALDH1A3, Linc00284, TGF<i>β</i> signaling and miR-361-5p using qPCR, Western blotting, and ELISA. Multiple CRC cell lines were evaluated in this study, and the highest level of ALDH1A3 was observed in SW480 cells. To investigate the regulatory mechanism, RIP and luciferase assays were used to validate the interaction between Linc00284, miR-361-5p, and TGF<i>β</i>. Proliferation, viability, migration, and invasion assays were performed to profile the effects of the ALDH1A3–Linc00284 axis in CRC cell functions, which was upregulated in CRC tissues. Knockdown ALDH1A3 or Linc00284 significantly reduced TGF<i>β</i> expression and suppressed the EMT process, while overexpression had opposite effects. miR-361-5p targeted TGF<i>β</i> directly, which negatively correlated with ALDH1A3–Linc00284 expression and CRC progression. Mechanistically, upregulation of ALDH1A3–Linc00284 promotes colorectal cancer invasion and migration by regulating miR-361-5p/TGF<i>β</i> signaling pathway. Dysregulation of the ALDH1A3–Linc00284-miR-361-5p-TGF<i>β</i> axis causes CRC invasion, which might provide a new insight into the treatment of CRC.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9584677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40664292","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":"Comparison of In Silico Tools for Splice-Altering Variant Prediction Using Established Spliceogenic Variants: An End-User’s Point of View","authors":"Woori Jang,&nbsp;Joonhong Park,&nbsp;Hyojin Chae,&nbsp;Myungshin Kim","doi":"10.1155/2022/5265686","DOIUrl":"10.1155/2022/5265686","url":null,"abstract":"<div>\u0000 <p>Assessing the impact of variants of unknown significance on splicing has become a critical issue and a bottleneck, especially with the widespread implementation of whole-genome or exome sequencing. Although multiple <i>in silico</i> tools are available, the interpretation and application of these tools are difficult and practical guidelines are still lacking. A streamlined decision-making process can facilitate the downstream RNA analysis in a more efficient manner. Therefore, we evaluated the performance of 8 <i>in silico</i> tools (Splice Site Finder, MaxEntScan, Splice-site prediction by neural network, GeneSplicer, Human Splicing Finder, SpliceAI, Splicing Predictions in Consensus Elements, and SpliceRover) using 114 <i>NF1</i> spliceogenic variants, experimentally validated at the mRNA level. The change in the predicted score incurred by the variant of the nearest wild-type splice site was analyzed, and for type II, III, and IV splice variants, the change in the prediction score of <i>de novo</i> or cryptic splice site was also analyzed. SpliceAI and SpliceRover, tools based on deep learning, outperformed all other tools, with AUCs of 0.972 and 0.924, respectively. For <i>de novo</i> and cryptic splice sites, SpliceAI outperformed all other tools and showed a sensitivity of 95.7% at an optimal cut-off of 0.02 score change. Our results show that deep learning algorithms, especially those of SpliceAI, are validated at a significantly higher rate than other <i>in silico</i> tools for clinically relevant <i>NF1</i> variants. This suggests that deep learning algorithms outperform traditional probabilistic approaches and classical machine learning tools in predicting the <i>de novo</i> and cryptic splice sites.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9584665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40652060","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 BANCR Promotes Endometrial Stromal Cell Proliferation and Invasion in Endometriosis via the miR-15a-5p/TRIM59 Axis","authors":"Lixue Liu,&nbsp;Ru Bai,&nbsp;Debang Li,&nbsp;Bai Dai,&nbsp;Ya Tuo","doi":"10.1155/2022/9083822","DOIUrl":"10.1155/2022/9083822","url":null,"abstract":"<div>\u0000 <p>Long non-coding RNA (LncRNA) emerges as a regulator in various diseases, including endometriosis (EM). This study aims to uncover the role of <i>long non-coding RNA BRAF-activated non-protein coding RNA</i> (<i>lncRNA BANCR</i>)-mediated competing endogenous RNA mechanism in endometrial stromal cell (ESC) proliferation and invasion in EM by regulating <i>miR-15a-5p</i>/TRIM59. ESCs were isolated from eutopic and ectopic endometrial tissues, followed by the determination of Cytokeratin 19 and Vimentin expressions in cells. Then, expressions of <i>lncRNA BANCR</i>, <i>microRNA (miR)-15a-5p</i>, and tripartite motif-containing 59 (TRIM59) in tissues and cells were determined by real-time quantitative polymerase chain reaction or Western blot assay, and cell proliferation and invasion were evaluated by cell counting kit-8 and transwell assays. After that, the subcellular localization of <i>lncRNA BANCR</i> and binding of <i>miR-15a-5p</i> to <i>lncRNA BANCR</i> or TRIM59 were analyzed. <i>LncRNA BANCR</i> was upregulated in ectopic endometrial tissues and ectopic ESCs (Ect-ESCs). Silencing <i>lncRNA BANCR</i> suppressed Ect-ESC proliferation and invasion. <i>LncRNA BANCR</i> inhibited <i>miR-15a-5p</i> to promote TRIM59 expression. <i>miR-15a-5p</i> downregulation or TRIM59 overexpression both reversed the effects of silencing <i>lncRNA BANCR</i> on Ect-ESC proliferation and invasion. In summary, our findings suggested that <i>lncRNA BANCR</i> facilitated Ect-ESC proliferation and invasion by inhibiting <i>miR-15a-5p</i> and promoting TRIM59.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9576446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40646889","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":"Expression Profiles of Differentially Expressed Circular RNAs and circRNA–miRNA–mRNA Regulatory Networks in SH-SY5Y Cells Infected with Coxsackievirus B5","authors":"Jing Li,&nbsp;Heng Yang,&nbsp;Huaran Shi,&nbsp;Jihong Zhang,&nbsp;Wei Chen","doi":"10.1155/2022/9298149","DOIUrl":"10.1155/2022/9298149","url":null,"abstract":"<div>\u0000 <p>Coxsackievirus B5 (CVB5) is the causative agent of hand, foot, and mouth disease (HFMD) that can cause neurological complications and fatalities. Circular RNA (circRNA) has been shown to play an important role in regulating pathogenic processes. However, the functions of circRNA in response to CVB5 infection remain unclear. In our research, RNA-seq was employed to analyze the expression profiles of circRNAs in SH-SY5Y cells with or without CVB5 infection. Out of 5,665 circRNAs identified to be expressed in SH-SY5Y cells, 163 circRNAs were found to be differentially expressed significantly. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the differentially expressed circRNAs were mainly involved in ubiquitin-mediated proteolysis and signaling pathways during CVB5 infection. Additionally, RT-qPCR was used to validate the RNA-seq data, and a circRNA–miRNA–mRNA interaction network was constructed based on two circRNAs, such as hsa_circ_0008378 and novel_circ_0014617, which were associated with the regulation of innate immune response in host cells. Additionally, we confirmed the two circRANs up-regulated the key factors in the IFN-I signaling pathway, hampering viral replication. Our data provide a new perspective that facilitates further understanding of the virus-host mechanism.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9577011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40563360","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}