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Yin W, Chen G, Li Y, Li R, Jia Z, Zhong C, Wang S, Mao X, Cai Z, Deng J, Zhong W, Pan B, Lu J. Identification of a 9-gene signature to enhance biochemical recurrence prediction in primary prostate cancer: A benchmarking study using ten machine learning methods and twelve patient cohorts. Cancer Lett 2024; 588:216739. [PMID: 38395379 DOI: 10.1016/j.canlet.2024.216739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
Prostate cancer (PCa) is a prevalent malignancy among men worldwide, and biochemical recurrence (BCR) after radical prostatectomy (RP) is a critical turning point commonly used to guide the development of treatment strategies for primary PCa. However, the clinical parameters currently in use are inadequate for precise risk stratification and informing treatment choice. To address this issue, we conducted a study that collected transcriptomic data and clinical information from 1662 primary PCa patients across 12 multicenter cohorts globally. We leveraged 101 algorithm combinations that consisted of 10 machine learning methods to develop and validate a 9-gene signature, named BCR SCR, for predicting the risk of BCR after RP. Our results demonstrated that BCR SCR generally outperformed 102 published prognostic signatures. We further established the clinical significance of these nine genes in PCa progression at the protein level through immunohistochemistry on Tissue Microarray (TMA). Moreover, our data showed that patients with higher BCR SCR tended to have higher rates of BCR and distant metastasis after radical radiotherapy. Through drug target prediction analysis, we identified nine potential therapeutic agents for patients with high BCR SCR. In conclusion, the newly developed BCR SCR has significant translational potential in accurately stratifying the risk of patients who undergo RP, monitoring treatment courses, and developing new therapies for the disease.
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Affiliation(s)
- Wenjun Yin
- Department of Andrology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China; Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China
| | - Guo Chen
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China
| | - Yutong Li
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China
| | - Ruidong Li
- Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA, 92521, USA
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Chuanfan Zhong
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Shuo Wang
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Xiangming Mao
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Zhouda Cai
- Department of Andrology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Junhong Deng
- Department of Andrology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Weide Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, 999078, Macau, China.
| | - Bin Pan
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510630, China.
| | - Jianming Lu
- Department of Andrology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China; Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China.
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Chien HW, Chuang CC, Hsieh YH, Lee CY, Yu NY, Yang SF. Tricetin suppresses the cell migration and BMP-6 expression through p38 signaling pathways in human retinal pigment epithelium cells. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38654487 DOI: 10.1002/tox.24294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 04/26/2024]
Abstract
Proliferative vitreoretinopathy (PVR) is a visual-threatening disease, which cause from the migration of retinal pigment epithelium (RPE). Tricetin, a family of flavonoids, can inhibit the metastasis of several cancers. Herein, we aim to evaluate the possible effect of tricetin on inhibiting ARPE-19 cells migration. The Boyden chamber assay, wound healing assay, RNA sequencing, and Western blot analysis were applied in our experiment. The results revealed that tricetin inhibited the cell migration abilities of ARPE-19 cells. Moreover, using RNA sequencing technology, we revealed that tricetin repressed bone morphogenetic protein-6 (BMP-6) gene expressions in ARPE-19 cells. Overexpression of BMP-6 resulted in significant restoration of cell migration capabilities of tricetin-treated ARPE-19 cells. Furthermore, tricetin suppressed the phosphorylation of the p38 signaling pathway. Moreover, blocking the p38 pathway also inhibits BMP-6 expression and migration in the ARPE-19 cells. In conclusion, this study revealed that tricetin inhibits the ARPE-19 cell migration mainly via the suppression of BMP-6 expression and p38 signaling pathway.
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Affiliation(s)
- Hsiang-Wen Chien
- Department of Ophthalmology, Cathay General Hospital, Taipei, Taiwan
- Department of Ophthalmology, Sijhih Cathay General Hospital, New Taipei City, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
| | - Chih-Chun Chuang
- Department of Ophthalmology, Changhua Christian Hospital, Changhua, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Hsien Hsieh
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chia-Yi Lee
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Nobel Eye Institute, Taipei, Taiwan
| | - Nuo-Yi Yu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
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Li X, Zhao X, Yin R, Yuan M, Zhang Y, Li X. TGF-β2-induced alterations of m6A methylation in hTERT RPE-1 cells. Exp Eye Res 2024; 241:109839. [PMID: 38395214 DOI: 10.1016/j.exer.2024.109839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
N6-methyladenosine (m6A) is a major type of RNA modification implicated in various pathophysiological processes. Transforming growth factor β2 (TGF-β2) induces epithelial-mesenchymal transition (EMT) in retinal pigmental epithelial (RPE) cells and promotes the progression of proliferative vitreoretinopathy (PVR). However, the role of m6A methylation in the EMT of human telomerase reverse transcriptase (hTERT) retinal pigmental epithelium (RPE)-1 cells has not been clarified. Here, we extracted RNA from RPE cells subjected to 0 or 20 ng/mL TGF-β2 for 72 h and identified differentially methylated genes (DMGs) by m6A-Seq and differentially expressed genes (DEGs) by RNA-Seq. We selected the genes related to EMT by conjoint m6A-Seq/RNA-Seq analysis and verified them by qRT-PCR. We then confirmed the function of m6A methylation in the EMT of RPE cells by knocking down the methyltransferase METTL3 and the m6A reading protein YTHDF1. Sequencing yielded 5814 DMGs and 1607 DEGs. Conjoint analysis selected 467 genes altered at the m6A and RNA levels that are closely associated with the EMT-related TGF-β, AGE-RAGE, PI3K-Akt, P53, and Wnt signaling pathways. We also identified ten core EMT genes ACTG2, BMP6, CDH2, LOXL2, SNAIL1, SPARC, BMP4, EMP3, FOXM1, and MYC. Their RNA levels were evaluated by qRT-PCR and were consistent with the sequencing results. We observed that METTL3 knockdown enhanced RPE cell migration and significantly upregulated the EMT markers N-cadherin (encoded by CDH2), fibronectin (FN), Snail family transcription repressor (SLUG), and vimentin. However, YTHDF1 knockdown had the opposite effects and decreased both cell migration and the N-cadherin, FN, and SLUG expression levels. The present study clarified TGF-β2-induced m6A- and RNA-level differences in RPE cells, indicated that m6A methylation might regulate EMT marker expression, and showed that m6A could regulate TGF-β2-induced EMT.
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Affiliation(s)
- Xue Li
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China
| | - Xueru Zhao
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China
| | - Ruijie Yin
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China
| | - Min Yuan
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China
| | - Yongya Zhang
- Henan Provincial People's Hospital, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaohua Li
- Henan Provincial People's Hospital, Zhengzhou, China; Henan Eye Hospital, Henan Eye Institute, Henan Key Laboratory of Ophthalmology and Visual Science, Zhengzhou, China; People's Hospital of Zhengzhou University, Zhengzhou, China; People's Hospital of Henan University, Zhengzhou, China; Henan Academy of Innovations in Medical Science, Eye Institute, Zhengzhou, China.
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Jiang S, Yang X, Lin Y, Liu Y, Tran LJ, Zhang J, Qiu C, Ye F, Sun Z. Unveiling Anoikis-related genes: A breakthrough in the prognosis of bladder cancer. J Gene Med 2024; 26:e3651. [PMID: 38282152 DOI: 10.1002/jgm.3651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/10/2023] [Accepted: 11/26/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Bladder cancer (BLCA) is a prevalent malignancy worldwide. Anoikis remains a new form of cell death. It is necessary to explore Anoikis-related genes in the prognosis of BLCA. METHODS We obtained RNA expression profiles from the The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases for dimensionality reduction analysis and isolated epithelial cells, T cells and fibroblasts for copy number variation analysis, pseudotime analysis and transcription factor analysis based on R package. We integrated machine-learning algorithms to develop the artificial intelligence-derived prognostic signature (AIDPS). RESULTS The performance of AIDPS with clinical indicators was stable and robust in predicting BLCA and showed better performance in every validation dataset compared to other models. Mendelian randomization analysis was conducted. Single nucleotide polymorphism (SNP) sites of rs3100578 (HK2) and rs66467677 (HSP90B1) exhibited significant correlation of bladder problem (not cancer) and bladder cancer, whereasSNP sites of rs3100578 (HK2) and rs947939 (BAD) had correlation between bladder stone and bladder cancer. The immune infiltration analysis of the TCGA-BLCA cohort was calculated via the ESTIMATE (i.e. Estimation of STromal and Immune cells in MAlignantTumours using Expression data) algorithm which contains stromal, immune and estimate scores. We also found significant differences in the IC50 values of Bortezomib_1191, Docetaxel_1007, Staurosporine_1034 and Rapamycin_1084 among the high- and low-risk groups. CONCLUSIONS In conclusion, these findings indicated Anoikis-related prognostic genes in BLCA and constructed an innovative machine-learning model of AIDPS with high prognostic value for BLCA.
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Affiliation(s)
- Shen Jiang
- Jilin Cancer Hospital, Changchun, Jilin, China
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Xiping Yang
- Jilin Cancer Hospital, Changchun, Jilin, China
| | - Yang Lin
- Jilin Cancer Hospital, Changchun, Jilin, China
| | - Yunfei Liu
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Lisa Jia Tran
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Jing Zhang
- Division of Basic Biomedical Sciences, The University of South Dakota Sanford School of Medicine, Vermillion, South Dakota, USA
| | - Chengjun Qiu
- Department of Urology, The First People's Hospital of Jiangxia District, Wuhan, Hubei, China
| | - Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhou Sun
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Department of Urology, The First People's Hospital of Jiangxia District, Wuhan, Hubei, China
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Ljunggren M, Zhou X, Theorell-Haglöw J, Janson C, Franklin KA, Emilsson Ö, Lindberg E. Sleep Apnea Indices Associated with Markers of Inflammation and Cardiovascular Disease: A Proteomic Study in the MUSTACHE Cohort. Ann Am Thorac Soc 2024; 21:165-169. [PMID: 37788298 PMCID: PMC10867909 DOI: 10.1513/annalsats.202305-472rl] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/03/2023] [Indexed: 10/05/2023] Open
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Wang G, Ding B, Sun L, Guo J, Wang S, Li W, Zhang Y, Lv J, Qiu W. Construction and Validation of a Necroptosis-Related Signature Associated With the Immune Microenvironment in Liver Hepatocellular Carcinoma. Front Genet 2022; 13:859544. [PMID: 35480307 PMCID: PMC9037783 DOI: 10.3389/fgene.2022.859544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022] Open
Abstract
Background: Liver hepatocellular carcinoma (LIHC) is a widespread and often deadly neoplasm. There is increasing evidence that necroptosis mediates numerous tumor-associated behaviors, as well as the regulation of the tumor microenvironment, suggesting its use as a biomarker for tumor prognosis. Methods: Data on mRNA expression and necroptosis regulators were acquired from the TCGA and KEGG databases, respectively. Clinical liver hepatocellular carcinoma (LIHC) patient data and information on the expression of necroptosis regulators were processed by unsupervised cluster analysis was performed on LIHC patients together with necroptotic regulator expression and, differentially expressed necroptosis-related genes (DENRGs) were identified by comparing the two clusters. A signature based on eight DENRGs was constructed and verified through independent data sets, and its relationship with the tumor microenvironment was investigated. Results: Unsupervised cluster analysis demonstrated inherent immune differences among LIHC patients. In all, 1,516 DENRGs were obtained by comparison between the two clusters. In the training set, the final eight genes obtained by univariate, LASSO, and multivariate Cox regression were utilized for constructing the signature. The survival and receiver operating characteristic (ROC) curve achieved satisfactory results in both sets. The high-risk group was characterized by greater immune infiltration and poor prognosis. The results of survival analysis based on the expression of eight DENRGs further confirmed the signature. Conclusion: We established and validated a risk signature based on eight DERNGs related to the tumor microenvironment. This provides a possible explanation for the different clinical effects of immunotherapy and provides a novel perspective for predicting tumor prognosis in LIHC.
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Affiliation(s)
- Gongjun Wang
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Baoning Ding
- School of Statistics, Shandong University of Finance and Economics, Jinan, China
| | | | - Jing Guo
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shasha Wang
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenqian Li
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuqi Zhang
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jing Lv
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Wensheng Qiu, Jing Lv,
| | - Wensheng Qiu
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Wensheng Qiu, Jing Lv,
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