A Liquid–Liquid Phase Separation-Related Index Associate with Biochemical Recurrence and Tumor Immune Environment of Prostate Cancer Patients
To identify liquid–liquid phase separation (LLPS)-related molecular clusters, and to develop and validate a novel index based on LLPS for predicting the prognosis of prostate cancer (PCa) patients. We download the clinical and transcriptome data of PCa from TCGA and GEO database. The LLPS-related ge...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/6/5515 |
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| author | Qi You Jia-Yin Chen Xiao-Hui Wu Yu-Ting Xue Jiang-Bo Sun Yong Wei Qing-Shui Zheng Xue-Yi Xue Dong-Ning Chen Ning Xu |
| author_facet | Qi You Jia-Yin Chen Xiao-Hui Wu Yu-Ting Xue Jiang-Bo Sun Yong Wei Qing-Shui Zheng Xue-Yi Xue Dong-Ning Chen Ning Xu |
| author_sort | Qi You |
| collection | DOAJ |
| description | To identify liquid–liquid phase separation (LLPS)-related molecular clusters, and to develop and validate a novel index based on LLPS for predicting the prognosis of prostate cancer (PCa) patients. We download the clinical and transcriptome data of PCa from TCGA and GEO database. The LLPS-related genes (LRGs) were extracted from PhaSepDB. Consensus clustering analysis was used to develop LLPS-related molecular subtypes for PCa. The LASSO cox regression analysis was performed to establish a novel LLPS-related index for predicting biochemical recurrence (BCR)-free survival (BCRFS). Preliminary experimental verification was performed. We initially identified a total of 102 differentially expressed LRGs for PCa. Three LLPS related molecular subtypes were identified. Moreover, we established a novel LLPS related signature for predicting BCRFS of PCa patients. Compared to low-risk patients in the training cohort, testing cohort and validating cohort, high-risk populations meant a higher risk of BCR and significantly poorer BCRFS. The area under receiver operating characteristic curve were 0.728, 0.762, and 0.741 at 1 year in the training cohort, testing cohort and validating cohort. Additionally, the subgroup analysis indicated that this index was especially suitable for PCa patients with age ≤ 65, T stage III-IV, N0 stage or in cluster 1. The <i>FUS</i>, which was the potential biomarker related to PCa liquid–liquid phase separation, was preliminarily identified and verified. This study successfully developed three LLPS-related molecular subtypes and identified a novel LLPS related molecular signature, which performed well in predicting BCRFS of PCa. |
| first_indexed | 2024-03-11T06:25:54Z |
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| id | doaj.art-4079ad809ab14e769a88b3c8bd7d8748 |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T06:25:54Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-4079ad809ab14e769a88b3c8bd7d87482023-11-17T11:35:03ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-03-01246551510.3390/ijms24065515A Liquid–Liquid Phase Separation-Related Index Associate with Biochemical Recurrence and Tumor Immune Environment of Prostate Cancer PatientsQi You0Jia-Yin Chen1Xiao-Hui Wu2Yu-Ting Xue3Jiang-Bo Sun4Yong Wei5Qing-Shui Zheng6Xue-Yi Xue7Dong-Ning Chen8Ning Xu9Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaDepartment of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, ChinaTo identify liquid–liquid phase separation (LLPS)-related molecular clusters, and to develop and validate a novel index based on LLPS for predicting the prognosis of prostate cancer (PCa) patients. We download the clinical and transcriptome data of PCa from TCGA and GEO database. The LLPS-related genes (LRGs) were extracted from PhaSepDB. Consensus clustering analysis was used to develop LLPS-related molecular subtypes for PCa. The LASSO cox regression analysis was performed to establish a novel LLPS-related index for predicting biochemical recurrence (BCR)-free survival (BCRFS). Preliminary experimental verification was performed. We initially identified a total of 102 differentially expressed LRGs for PCa. Three LLPS related molecular subtypes were identified. Moreover, we established a novel LLPS related signature for predicting BCRFS of PCa patients. Compared to low-risk patients in the training cohort, testing cohort and validating cohort, high-risk populations meant a higher risk of BCR and significantly poorer BCRFS. The area under receiver operating characteristic curve were 0.728, 0.762, and 0.741 at 1 year in the training cohort, testing cohort and validating cohort. Additionally, the subgroup analysis indicated that this index was especially suitable for PCa patients with age ≤ 65, T stage III-IV, N0 stage or in cluster 1. The <i>FUS</i>, which was the potential biomarker related to PCa liquid–liquid phase separation, was preliminarily identified and verified. This study successfully developed three LLPS-related molecular subtypes and identified a novel LLPS related molecular signature, which performed well in predicting BCRFS of PCa.https://www.mdpi.com/1422-0067/24/6/5515prostate cancerliquid–liquid phase separationbiochemical recurrencetumor immune microenvironment |
| spellingShingle | Qi You Jia-Yin Chen Xiao-Hui Wu Yu-Ting Xue Jiang-Bo Sun Yong Wei Qing-Shui Zheng Xue-Yi Xue Dong-Ning Chen Ning Xu A Liquid–Liquid Phase Separation-Related Index Associate with Biochemical Recurrence and Tumor Immune Environment of Prostate Cancer Patients International Journal of Molecular Sciences prostate cancer liquid–liquid phase separation biochemical recurrence tumor immune microenvironment |
| title | A Liquid–Liquid Phase Separation-Related Index Associate with Biochemical Recurrence and Tumor Immune Environment of Prostate Cancer Patients |
| title_full | A Liquid–Liquid Phase Separation-Related Index Associate with Biochemical Recurrence and Tumor Immune Environment of Prostate Cancer Patients |
| title_fullStr | A Liquid–Liquid Phase Separation-Related Index Associate with Biochemical Recurrence and Tumor Immune Environment of Prostate Cancer Patients |
| title_full_unstemmed | A Liquid–Liquid Phase Separation-Related Index Associate with Biochemical Recurrence and Tumor Immune Environment of Prostate Cancer Patients |
| title_short | A Liquid–Liquid Phase Separation-Related Index Associate with Biochemical Recurrence and Tumor Immune Environment of Prostate Cancer Patients |
| title_sort | liquid liquid phase separation related index associate with biochemical recurrence and tumor immune environment of prostate cancer patients |
| topic | prostate cancer liquid–liquid phase separation biochemical recurrence tumor immune microenvironment |
| url | https://www.mdpi.com/1422-0067/24/6/5515 |
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