Pyroptosis-related lncRNAs: A novel prognosis signature of colorectal cancer
Pyroptosis is a newly discovered programmed cell death mechanism involved in tumorigenesis. Long non-coding RNAs (lncRNAs) have been implicated in colorectal cancer (CRC). However, the potential role of pyroptosis-related lncRNAs (PRLs) in CRC remains unelucidated. Therefore, we retrieved transcript...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Oncology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2022.983895/full |
| _version_ | 1797986498849538048 |
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| author | Xing Cai Xiaoqing Liang Kun Wang Yin Liu Mengdi Hao Huimin Li Xiaofang Dai Lei Ding |
| author_facet | Xing Cai Xiaoqing Liang Kun Wang Yin Liu Mengdi Hao Huimin Li Xiaofang Dai Lei Ding |
| author_sort | Xing Cai |
| collection | DOAJ |
| description | Pyroptosis is a newly discovered programmed cell death mechanism involved in tumorigenesis. Long non-coding RNAs (lncRNAs) have been implicated in colorectal cancer (CRC). However, the potential role of pyroptosis-related lncRNAs (PRLs) in CRC remains unelucidated. Therefore, we retrieved transcriptomic data of CRC patients from The Cancer Genome Atlas (TCGA). With the use of univariate and multivariate Cox proportional hazards regression models and the random forest algorithm, a new risk model was constructed based on eight PRLs: Z99289.2, FENDRR, CCDC144NL-ASL, TEX41, MNX1-AS1, NKILA, LINC02798, and LINC02381. Then, according to the Kaplan–Meier plots, the relationship of PRLs with the survival of CRC patients was explored and validated with our risk model in external datasets (Gene Expression Omnibus (GEO) databases; GEO17536, n = 177, and GSE161158, n = 250). To improve its clinical utility, a nomogram combining PRLs that could predict the clinical outcome of CRC patients was established. A full-spectrum immune landscape of CRC patients mediated by PRLs could be described. The PRLs were stratified into two molecular subtypes involved in immune modulators, immune infiltration of tumor immune microenvironment, and inflammatory pathways. Afterward, Tumor Immune Dysfunction and Exclusion (TIDE) and microsatellite instability (MSI) scores were analyzed. Three independent methods were applied to predict PRL-related sensitivity to chemotherapeutic drugs. Our comprehensive analysis of PRLs in CRC patients demonstrates a potential role of PRLs in predicting response to treatment and prognosis of CRC patients, which may provide a better understanding of molecular mechanisms underlying CRC pathogenesis and facilitate the development of effective immunotherapy. |
| first_indexed | 2024-04-11T07:34:44Z |
| format | Article |
| id | doaj.art-f5ddcd9023ca4f1e8a9e6ae6c455cced |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-04-11T07:34:44Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj.art-f5ddcd9023ca4f1e8a9e6ae6c455cced2022-12-22T04:36:48ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2022-11-011210.3389/fonc.2022.983895983895Pyroptosis-related lncRNAs: A novel prognosis signature of colorectal cancerXing Cai0Xiaoqing Liang1Kun Wang2Yin Liu3Mengdi Hao4Huimin Li5Xiaofang Dai6Lei Ding7Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing, ChinaDepartment of Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing, ChinaDepartment of Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing, ChinaDepartment of Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing, ChinaDepartment of Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing, ChinaCancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaDepartment of Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing, ChinaPyroptosis is a newly discovered programmed cell death mechanism involved in tumorigenesis. Long non-coding RNAs (lncRNAs) have been implicated in colorectal cancer (CRC). However, the potential role of pyroptosis-related lncRNAs (PRLs) in CRC remains unelucidated. Therefore, we retrieved transcriptomic data of CRC patients from The Cancer Genome Atlas (TCGA). With the use of univariate and multivariate Cox proportional hazards regression models and the random forest algorithm, a new risk model was constructed based on eight PRLs: Z99289.2, FENDRR, CCDC144NL-ASL, TEX41, MNX1-AS1, NKILA, LINC02798, and LINC02381. Then, according to the Kaplan–Meier plots, the relationship of PRLs with the survival of CRC patients was explored and validated with our risk model in external datasets (Gene Expression Omnibus (GEO) databases; GEO17536, n = 177, and GSE161158, n = 250). To improve its clinical utility, a nomogram combining PRLs that could predict the clinical outcome of CRC patients was established. A full-spectrum immune landscape of CRC patients mediated by PRLs could be described. The PRLs were stratified into two molecular subtypes involved in immune modulators, immune infiltration of tumor immune microenvironment, and inflammatory pathways. Afterward, Tumor Immune Dysfunction and Exclusion (TIDE) and microsatellite instability (MSI) scores were analyzed. Three independent methods were applied to predict PRL-related sensitivity to chemotherapeutic drugs. Our comprehensive analysis of PRLs in CRC patients demonstrates a potential role of PRLs in predicting response to treatment and prognosis of CRC patients, which may provide a better understanding of molecular mechanisms underlying CRC pathogenesis and facilitate the development of effective immunotherapy.https://www.frontiersin.org/articles/10.3389/fonc.2022.983895/fullpyroptosislong non coding RNAcolorectal cancerprognosisTCGA |
| spellingShingle | Xing Cai Xiaoqing Liang Kun Wang Yin Liu Mengdi Hao Huimin Li Xiaofang Dai Lei Ding Pyroptosis-related lncRNAs: A novel prognosis signature of colorectal cancer Frontiers in Oncology pyroptosis long non coding RNA colorectal cancer prognosis TCGA |
| title | Pyroptosis-related lncRNAs: A novel prognosis signature of colorectal cancer |
| title_full | Pyroptosis-related lncRNAs: A novel prognosis signature of colorectal cancer |
| title_fullStr | Pyroptosis-related lncRNAs: A novel prognosis signature of colorectal cancer |
| title_full_unstemmed | Pyroptosis-related lncRNAs: A novel prognosis signature of colorectal cancer |
| title_short | Pyroptosis-related lncRNAs: A novel prognosis signature of colorectal cancer |
| title_sort | pyroptosis related lncrnas a novel prognosis signature of colorectal cancer |
| topic | pyroptosis long non coding RNA colorectal cancer prognosis TCGA |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2022.983895/full |
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