Screening of pyroptosis-related long non-coding RNAs and genes that influence prognosis for colon cancer
Objective To screen long non-coding RNAs (lncRNAs) and genes which are associated with pyroptosis and may potentially affect the prognosis of colon cancer by bioinformatics. Methods The gene microarray and clinical data of colon cancer patients were downloaded from TCGA database, and the obtained 44...
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| Format: | Article |
| Language: | zho |
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Editorial Office of Journal of Army Medical University
2023-04-01
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| Series: | 陆军军医大学学报 |
| Subjects: | |
| Online Access: | http://aammt.tmmu.edu.cn/html/202210142.htm |
| _version_ | 1797845648584736768 |
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| author | MA Zhan LOU Shuping JIANG Zheng |
| author_facet | MA Zhan LOU Shuping JIANG Zheng |
| author_sort | MA Zhan |
| collection | DOAJ |
| description | Objective To screen long non-coding RNAs (lncRNAs) and genes which are associated with pyroptosis and may potentially affect the prognosis of colon cancer by bioinformatics. Methods The gene microarray and clinical data of colon cancer patients were downloaded from TCGA database, and the obtained 446 patients were divided into training set (n=224) and validation set (n=222) by stratified random sampling. Differentially expressed pyroptosis-related lncRNAs were subsequently screened out by co-expression analysis and difference analysis. According to the median score of risk assessment, the patients were divided into high- and low-risk score groups. In the training set, the prognosis model was constructed with univariate and multivariate COX analyses and LASSO regression analysis, and then the model was evaluated through Kaplan-Meier survival analysis, ROC curve, univariate and multivariate COX regression. A nomogram was then plotted to predict the survival of the samples, and the model was further verified using the data from the validation set as well as the whole set. Moreover, co-expression analysis, mutation and difference analyses were performed to screen pyroptosis-related genes, and immunohistochemical assay was adopted to further confirm the screening results. Results A total of 5 prognosis-related lncRNAs (MIR181A2HG, AP003555.1, LINCO2257, ALMS1-IT1 and AL137782.1) were filtered out. The survival rate of colon cancer patients with the high-risk score group was lower than that in the low-risk score group (P < 0.05), indicating the risk score as an independent prognostic factor (P < 0.01). A nomogram including age, sex, TMN stage, risk score and other related factors was generated, which performed well in predicting survival rate of 1, 3 and 5 years. In addition, 5 pyroptosis-related genes (SCAF11, IL1A, PJVK, CHMP2A and CHMP6) were also obtained, from which SCAF11 was selected for immunohistochemical assay, presenting high expression in colon cancer tissues. Conclusion A prognostic model is successfully constructed. Five pyroptosis-related lncRNAs and 5 pyroptosis-related genes are screened out. Immunohistochemical assay has verified that the expression of SCAF11 is higher in colon cancer tissues than paracancer tissues.
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| first_indexed | 2024-04-09T17:42:24Z |
| format | Article |
| id | doaj.art-0679f40c4f2c4a5e961dffd55e032005 |
| institution | Directory Open Access Journal |
| issn | 2097-0927 |
| language | zho |
| last_indexed | 2024-04-09T17:42:24Z |
| publishDate | 2023-04-01 |
| publisher | Editorial Office of Journal of Army Medical University |
| record_format | Article |
| series | 陆军军医大学学报 |
| spelling | doaj.art-0679f40c4f2c4a5e961dffd55e0320052023-04-17T01:30:34ZzhoEditorial Office of Journal of Army Medical University陆军军医大学学报2097-09272023-04-0145766767610.16016/j.2097-0927.202210142Screening of pyroptosis-related long non-coding RNAs and genes that influence prognosis for colon cancerMA Zhan0LOU Shuping1JIANG Zheng2Department of Gastroenterology, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang Province, 322000Department of Infection Management, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang Province, 322000Department of Gastroenterology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, ChinaObjective To screen long non-coding RNAs (lncRNAs) and genes which are associated with pyroptosis and may potentially affect the prognosis of colon cancer by bioinformatics. Methods The gene microarray and clinical data of colon cancer patients were downloaded from TCGA database, and the obtained 446 patients were divided into training set (n=224) and validation set (n=222) by stratified random sampling. Differentially expressed pyroptosis-related lncRNAs were subsequently screened out by co-expression analysis and difference analysis. According to the median score of risk assessment, the patients were divided into high- and low-risk score groups. In the training set, the prognosis model was constructed with univariate and multivariate COX analyses and LASSO regression analysis, and then the model was evaluated through Kaplan-Meier survival analysis, ROC curve, univariate and multivariate COX regression. A nomogram was then plotted to predict the survival of the samples, and the model was further verified using the data from the validation set as well as the whole set. Moreover, co-expression analysis, mutation and difference analyses were performed to screen pyroptosis-related genes, and immunohistochemical assay was adopted to further confirm the screening results. Results A total of 5 prognosis-related lncRNAs (MIR181A2HG, AP003555.1, LINCO2257, ALMS1-IT1 and AL137782.1) were filtered out. The survival rate of colon cancer patients with the high-risk score group was lower than that in the low-risk score group (P < 0.05), indicating the risk score as an independent prognostic factor (P < 0.01). A nomogram including age, sex, TMN stage, risk score and other related factors was generated, which performed well in predicting survival rate of 1, 3 and 5 years. In addition, 5 pyroptosis-related genes (SCAF11, IL1A, PJVK, CHMP2A and CHMP6) were also obtained, from which SCAF11 was selected for immunohistochemical assay, presenting high expression in colon cancer tissues. Conclusion A prognostic model is successfully constructed. Five pyroptosis-related lncRNAs and 5 pyroptosis-related genes are screened out. Immunohistochemical assay has verified that the expression of SCAF11 is higher in colon cancer tissues than paracancer tissues. http://aammt.tmmu.edu.cn/html/202210142.htmpyroptosiscolon cancerprognostic modelbioinformatics |
| spellingShingle | MA Zhan LOU Shuping JIANG Zheng Screening of pyroptosis-related long non-coding RNAs and genes that influence prognosis for colon cancer 陆军军医大学学报 pyroptosis colon cancer prognostic model bioinformatics |
| title | Screening of pyroptosis-related long non-coding RNAs and genes that influence prognosis for colon cancer |
| title_full | Screening of pyroptosis-related long non-coding RNAs and genes that influence prognosis for colon cancer |
| title_fullStr | Screening of pyroptosis-related long non-coding RNAs and genes that influence prognosis for colon cancer |
| title_full_unstemmed | Screening of pyroptosis-related long non-coding RNAs and genes that influence prognosis for colon cancer |
| title_short | Screening of pyroptosis-related long non-coding RNAs and genes that influence prognosis for colon cancer |
| title_sort | screening of pyroptosis related long non coding rnas and genes that influence prognosis for colon cancer |
| topic | pyroptosis colon cancer prognostic model bioinformatics |
| url | http://aammt.tmmu.edu.cn/html/202210142.htm |
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