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He X, Hu S, Wang C, Yang Y, Li Z, Zeng M, Song G, Li Y, Lu Q. Predicting prostate cancer recurrence: Introducing PCRPS, an advanced online web server. Heliyon 2024; 10:e28878. [PMID: 38623253 PMCID: PMC11016622 DOI: 10.1016/j.heliyon.2024.e28878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
Background Prostate cancer (PCa) is one of the leading causes of cancer death in men. About 30% of PCa will develop a biochemical recurrence (BCR) following initial treatment, which significantly contributes to prostate cancer-related deaths. In clinical practice, accurate prediction of PCa recurrence is crucial for making informed treatment decisions. However, the development of reliable models and biomarkers for predicting PCa recurrence remains a challenge. In this study, the aim is to establish an effective and reliable tool for predicting the recurrence of PCa. Methods We systematically screened and analyzed potential datasets to predict PCa recurrence. Through quality control analysis, low-quality datasets were removed. Using meta-analysis, differential expression analysis, and feature selection, we identified key genes associated with recurrence. We also evaluated 22 previously published signatures for PCa recurrence prediction. To assess prediction performance, we employed nine machine learning algorithms. We compared the predictive capabilities of models constructed using clinical variables, expression data, and their combinations. Subsequently, we implemented these machine learning models into a user-friendly web server freely accessible to all researchers. Results Based on transcriptomic data derived from eight multicenter studies consisting of 733 PCa patients, we screened 23 highly influential genes for predicting prostate cancer recurrence. These genes were used to construct the Prostate Cancer Recurrence Prediction Signature (PCRPS). By comparing with 22 published signatures and four important clinicopathological features, the PCRPS exhibited a robust and significantly improved predictive capability. Among the tested algorithms, Random Forest demonstrated the highest AUC value of 0.72 in predicting PCa recurrence in the testing dataset. To facilitate access and usage of these machine learning models by all researchers and clinicians, we also developed an online web server (https://urology1926.shinyapps.io/PCRPS/) where the PCRPS model can be freely utilized. The tool can also be used to (1) predict the PCa recurrence by clinical information or expression data with high accuracy. (2) provide the possibility of PCa recurrence by nine machine learning algorithms. Furthermore, using the PCRPS scores, we predicted the sensitivity of 22 drugs from GDSC2 and 95 drugs from CTRP2 to the samples. These predictions provide valuable insights into potential drug sensitivities related to the PCRPS score groups. Conclusion Overall, our study provides an attractive tool to further guide the clinical management and individualized treatment for PCa.
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Affiliation(s)
| | | | - Chen Wang
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Yongjun Yang
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Zhuo Li
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Mingqiang Zeng
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Guangqing Song
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Yuanwei Li
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Qiang Lu
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
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Marin L, Casado F. Prediction of prostate cancer biochemical recurrence by using discretization supports the critical contribution of the extra-cellular matrix genes. Sci Rep 2023; 13:10144. [PMID: 37349324 PMCID: PMC10287745 DOI: 10.1038/s41598-023-35821-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
Due to its complexity, much effort has been devoted to the development of biomarkers for prostate cancer that have acquired the utmost clinical relevance for diagnosis and grading. However, all of these advances are limited due to the relatively large percentage of biochemical recurrence (BCR) and the limited strategies for follow up. This work proposes a methodology that uses discretization to predict prostate cancer BCR while optimizing the necessary variables. We used discretization of RNA-seq data to increase the prediction of biochemical recurrence and retrieve a subset of ten genes functionally known to be related to the tissue structure. Equal width and equal frequency data discretization methods were compared to isolate the contribution of the genes and their interval of action, simultaneously. Adding a robust clinical biomarker such as prostate specific antigen (PSA) improved the prediction of BCR. Discretization allowed classifying the cancer patients with an accuracy of 82% on testing datasets, and 75% on a validation dataset when a five-bin discretization by equal width was used. After data pre-processing, feature selection and classification, our predictions had a precision of 71% (testing dataset: MSKCC and GSE54460) and 69% (Validation dataset: GSE70769) should the patients present BCR up to 24 months after their final treatment. These results emphasize the use of equal width discretization as a pre-processing step to improve classification for a limited number of genes in the signature. Functionally, many of these genes have a direct or expected role in tissue structure and extracellular matrix organization. The processing steps presented in this study are also applicable to other cancer types to increase the speed and accuracy of the models in diverse datasets.
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Affiliation(s)
- Laura Marin
- Department of Engineering, Pontificia Universidad Catolica del Peru, Av. Universitaria 1801, San Miguel, 15088, Lima, Peru
- Institute of Omics Sciences and Applied Biotechnology, Pontificia Universidad Catolica del Peru, Av. Universitaria 1801, San Miguel, 15088, Lima, Peru
| | - Fanny Casado
- Institute of Omics Sciences and Applied Biotechnology, Pontificia Universidad Catolica del Peru, Av. Universitaria 1801, San Miguel, 15088, Lima, Peru.
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3
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Wei Z, Han D, Zhang C, Wang S, Liu J, Chao F, Song Z, Chen G. Deep Learning-Based Multi-Omics Integration Robustly Predicts Relapse in Prostate Cancer. Front Oncol 2022; 12:893424. [PMID: 35814412 PMCID: PMC9259796 DOI: 10.3389/fonc.2022.893424] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectivePost-operative biochemical relapse (BCR) continues to occur in a significant percentage of patients with localized prostate cancer (PCa). Current stratification methods are not adequate to identify high-risk patients. The present study exploits the ability of deep learning (DL) algorithms using the H2O package to combine multi-omics data to resolve this problem.MethodsFive-omics data from 417 PCa patients from The Cancer Genome Atlas (TCGA) were used to construct the DL-based, relapse-sensitive model. Among them, 265 (63.5%) individuals experienced BCR. Five additional independent validation sets were applied to assess its predictive robustness. Bioinformatics analyses of two relapse-associated subgroups were then performed for identification of differentially expressed genes (DEGs), enriched pathway analysis, copy number analysis and immune cell infiltration analysis.ResultsThe DL-based model, with a significant difference (P = 6e-9) between two subgroups and good concordance index (C-index = 0.767), were proven to be robust by external validation. 1530 DEGs including 678 up- and 852 down-regulated genes were identified in the high-risk subgroup S2 compared with the low-risk subgroup S1. Enrichment analyses found five hallmark gene sets were up-regulated while 13 were down-regulated. Then, we found that DNA damage repair pathways were significantly enriched in the S2 subgroup. CNV analysis showed that 30.18% of genes were significantly up-regulated and gene amplification on chromosomes 7 and 8 was significantly elevated in the S2 subgroup. Moreover, enrichment analysis revealed that some DEGs and pathways were associated with immunity. Three tumor-infiltrating immune cell (TIIC) groups with a higher proportion in the S2 subgroup (p = 1e-05, p = 8.7e-06, p = 0.00014) and one TIIC group with a higher proportion in the S1 subgroup (P = 1.3e-06) were identified.ConclusionWe developed a novel, robust classification for understanding PCa relapse. This study validated the effectiveness of deep learning technique in prognosis prediction, and the method may benefit patients and prevent relapse by improving early detection and advancing early intervention.
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Affiliation(s)
- Ziwei Wei
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Dunsheng Han
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Cong Zhang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Shiyu Wang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jinke Liu
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Fan Chao
- Department of Urology, Zhongshan Hospital, Fudan University (Xiamen Branch), Xiamen, China
| | - Zhenyu Song
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Gang Chen, ; Zhenyu Song,
| | - Gang Chen
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Gang Chen, ; Zhenyu Song,
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Cheng D, Wang L, Qu F, Yu J, Tang Z, Liu X. Identification and construction of a 13-gene risk model for prognosis prediction in hepatocellular carcinoma patients. J Clin Lab Anal 2022; 36:e24377. [PMID: 35421268 PMCID: PMC9102505 DOI: 10.1002/jcla.24377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/09/2022] Open
Abstract
We attempted to screen out the feature genes associated with the prognosis of hepatocellular carcinoma (HCC) patients through bioinformatics methods, to generate a risk model to predict the survival rate of patients. Gene expression information of HCC was accessed from GEO database, and differentially expressed genes (DEGs) were obtained through the joint analysis of multi-chip. Functional and pathway enrichment analyses of DEGs indicated that the enrichment was mainly displayed in biological processes such as nuclear division. Based on TCGA-LIHC data set, univariate, LASSO, and multivariate Cox regression analyses were conducted on the DEGs. Then, 13 feature genes were screened for the risk model. Also, the hub genes were examined in our collected clinical samples and GEPIA database. The performance of the risk model was validated by Kaplan-Meier survival analysis and receiver operation characteristic (ROC) curves. While its universality was verified in GSE76427 and ICGC (LIRI-JP) validation cohorts. Besides, through combining patients' clinical features (age, gender, T staging, and stage) and risk scores, univariate and multivariate Cox regression analyses revealed that the risk score was an effective independent prognostic factor. Finally, a nomogram was implemented for 3-year and 5-year overall survival prediction of patients. Our findings aid precision prediction for prognosis of HCC patients.
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Affiliation(s)
- Daming Cheng
- Department of Hepatobiliary Surgery, Tangshan Gongren Hospital, Tangshan City, China
| | - Libing Wang
- Department of Hepatobiliary Surgery, Tangshan Gongren Hospital, Tangshan City, China
| | - Fengzhi Qu
- Department of Hepatobiliary Surgery, Tangshan Gongren Hospital, Tangshan City, China
| | - Jingkun Yu
- Department of Hepatobiliary Surgery, Tangshan Gongren Hospital, Tangshan City, China
| | - Zhaoyuan Tang
- Department of Hepatobiliary Surgery, Tangshan Gongren Hospital, Tangshan City, China
| | - Xiaogang Liu
- Department of Hepatobiliary Surgery, Tangshan Gongren Hospital, Tangshan City, China
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Zhao Y, Tao Z, Li L, Zheng J, Chen X. Predicting biochemical-recurrence-free survival using a three-metabolic-gene risk score model in prostate cancer patients. BMC Cancer 2022; 22:239. [PMID: 35246070 PMCID: PMC8896158 DOI: 10.1186/s12885-022-09331-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/24/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Biochemical recurrence (BCR) after initial treatment, such as radical prostatectomy, is the most frequently adopted prognostic factor for patients who suffer from prostate cancer (PCa). In this study, we aimed to construct a prognostic model consisting of gene expression profiles to predict BCR-free survival. METHODS We analyzed 70 metabolic pathways in 152 normal prostate samples and 494 PCa samples from the UCSC Xena dataset (training set) via gene set enrichment analysis (GSEA) to select BCR-related genes and constructed a BCR-related gene risk score (RS) model. We tested the power of our model using Kaplan-Meier (K-M) plots and receiver operator characteristic (ROC) curves. We performed univariate and multivariate analyses of RS using other clinicopathological features and established a nomogram model, which has stronger prediction ability. We used GSE70770 and DFKZ 2018 datasets to validate the results. Finally, we performed differential expression and quantitative real-time polymerase chain reaction analyses of the UCSC data for further verification of the findings. RESULTS A total of 194 core enriched genes were obtained through GSEA, among which 16 BCR-related genes were selected and a three-gene RS model based on the expression levels of CA14, LRAT, and MGAT5B was constructed. The outcomes of the K-M plots and ROC curves verified the accuracy of the RS model. We identified the Gleason score, pathologic T stage, and RS model as independent predictors through univariate and multivariate Cox analyses and constructed a nomogram model that presented better predictability than the RS model. The outcomes of the validation set were consistent with those of the training set. Finally, the results of differential expression analyses support the effectiveness of our model. CONCLUSION We constructed an RS model based on metabolic genes that could predict the prognosis of PCa patients. The model can be easily used in clinical applications and provide important insights into future research on the underlying mechanism of PCa.
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Affiliation(s)
- Yiqiao Zhao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Zijia Tao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Lei Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, People's Republic of China.
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Abdelwahed KS, Siddique AB, Qusa MH, King JA, Souid S, Abd Elmageed ZY, El Sayed KA. PCSK9 Axis-Targeting Pseurotin A as a Novel Prostate Cancer Recurrence Suppressor Lead. ACS Pharmacol Transl Sci 2021; 4:1771-1781. [DOI: 10.1021/acsptsci.1c00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 01/02/2023]
Affiliation(s)
- Khaldoun S. Abdelwahed
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, 1800 Bienville Drive, Monroe, Louisiana 71201, United States
| | - Abu Bakar Siddique
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, 1800 Bienville Drive, Monroe, Louisiana 71201, United States
| | - Mohammed H. Qusa
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, 1800 Bienville Drive, Monroe, Louisiana 71201, United States
| | - Judy Ann King
- Department of Pathology and Translational Pathobiology, LSU Health Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71103, United States
| | - Soumaya Souid
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, 1800 Bienville Drive, Monroe, Louisiana 71201, United States
| | - Zakaria Y. Abd Elmageed
- Department of Pharmacology, Edward Via College of Osteopathic Medicine, University of Louisiana at Monroe, Monroe, Louisiana 71203, United States
| | - Khalid A. El Sayed
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, 1800 Bienville Drive, Monroe, Louisiana 71201, United States
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A Novel Approach for the Discovery of Biomarkers of Radiotherapy Response in Breast Cancer. J Pers Med 2021; 11:jpm11080796. [PMID: 34442440 PMCID: PMC8399231 DOI: 10.3390/jpm11080796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 01/08/2023] Open
Abstract
Radiotherapy (RT) is an important treatment modality for the local control of breast cancer (BC). Unfortunately, not all patients that receive RT will obtain a therapeutic benefit, as cancer cells that either possess intrinsic radioresistance or develop resistance during treatment can reduce its efficacy. For RT treatment regimens to become personalised, there is a need to identify biomarkers that can predict and/or monitor a tumour's response to radiation. Here we describe a novel method to identify such biomarkers. Liquid chromatography-mass spectrometry (LC-MS) was used on conditioned media (CM) samples from a radiosensitive oestrogen receptor positive (ER+) BC cell line (MCF-7) to identify cancer-secreted biomarkers which reflected a response to radiation. A total of 33 radiation-induced secreted proteins that had higher (up to 12-fold) secretion levels at 24 h post-2 Gy radiation were identified. Secretomic results were combined with whole-transcriptome gene expression experiments, using both radiosensitive and radioresistant cells, to identify a signature related to intrinsic radiosensitivity. Gene expression analysis assessing the levels of the 33 proteins showed that 5 (YBX3, EIF4EBP2, DKK1, GNPNAT1 and TK1) had higher expression levels in the radiosensitive cells compared to their radioresistant derivatives; 3 of these proteins (DKK1, GNPNAT1 and TK1) underwent in-lab and initial clinical validation. Western blot analysis using CM samples from cell lines confirmed a significant increase in the release of each candidate biomarker from radiosensitive cells 24 h after treatment with a 2 Gy dose of radiation; no significant increase in secretion was observed in the radioresistant cells after radiation. Immunohistochemistry showed that higher intracellular protein levels of the biomarkers were associated with greater radiosensitivity. Intracellular levels were further assessed in pre-treatment biopsy tissues from patients diagnosed with ER+ BC that were subsequently treated with breast-conserving surgery and RT. High DKK1 and GNPNAT1 intracellular levels were associated with significantly increased recurrence-free survival times, indicating that these two candidate biomarkers have the potential to predict sensitivity to RT. We suggest that the methods highlighted in this study could be utilised for the identification of biomarkers that may have a potential clinical role in personalising and optimising RT dosing regimens, whilst limiting the administration of RT to patients who are unlikely to benefit.
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Manjang K, Yli-Harja O, Dehmer M, Emmert-Streib F. Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer. Front Genet 2021; 12:649429. [PMID: 34367234 PMCID: PMC8340016 DOI: 10.3389/fgene.2021.649429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/01/2021] [Indexed: 11/28/2022] Open
Abstract
High-throughput technologies do not only provide novel means for basic biological research but also for clinical applications in hospitals. For instance, the usage of gene expression profiles as prognostic biomarkers for predicting cancer progression has found widespread interest. Aside from predicting the progression of patients, it is generally believed that such prognostic biomarkers also provide valuable information about disease mechanisms and the underlying molecular processes that are causal for a disorder. However, the latter assumption has been challenged. In this paper, we study this problem for prostate cancer. Specifically, we investigate a large number of previously published prognostic signatures of prostate cancer based on gene expression profiles and show that none of these can provide unique information about the underlying disease etiology of prostate cancer. Hence, our analysis reveals that none of the studied signatures has a sensible biological meaning. Overall, this shows that all studied prognostic signatures are merely black-box models allowing sensible predictions of prostate cancer outcome but are not capable of providing causal explanations to enhance the understanding of prostate cancer.
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Affiliation(s)
- Kalifa Manjang
- Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Olli Yli-Harja
- Computational Systems Biology, Tampere University, Tampere, Finland.,Institute for Systems Biology, Seattle, WA, United States.,Faculty of Medicine and Health Technology, Institute of Biosciences and Medical Technology, Tampere University, Tampere, Finland
| | - Matthias Dehmer
- Department of Computer Science, Swiss Distance University of Applied Sciences, Brig, Switzerland.,Department of Mechatronics and Biomedical Computer Science, University for Health Sciences, Medical Informatics and Technology (UMIT), Hall, Austria.,College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Frank Emmert-Streib
- Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland.,Faculty of Medicine and Health Technology, Institute of Biosciences and Medical Technology, Tampere University, Tampere, Finland
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Wang TH, Lee CY, Lee TY, Huang HD, Hsu JBK, Chang TH. Biomarker Identification through Multiomics Data Analysis of Prostate Cancer Prognostication Using a Deep Learning Model and Similarity Network Fusion. Cancers (Basel) 2021; 13:cancers13112528. [PMID: 34064004 PMCID: PMC8196729 DOI: 10.3390/cancers13112528] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Around 30% of men treated with adjuvant therapy experience recurrences of prostate cancer (PC). Current monitoring of the relapse of PC requires regular postoperative prostate-specific antigen (PSA) value follow-up. Our study aims to identify potential multiomics biomarkers using modern computational analytic methods, deep learning (DL), similarity network fusion (SNF), and the Cancer Genome Atlas (TCGA) prostate adenocarcinoma (PRAD) dataset. Six significantly intersected omics biomarkers from the two models, TELO2, ZMYND19, miR-143, miR-378a, cg00687383 (MED4), and cg02318866 (JMJD6; METTL23) were collected for multiomics panel construction. The difference between the Kaplan–Meier curves of high and low recurrence-risk groups generated from the multiomics panels and clinical information achieve p-value = 2.97 × 10−15 and C-index = 0.713, and the prediction performance of five-year recurrence achieves AUC = 0.789. The results show that the multiomics panel provided valuable biomarkers for the early detection of high-risk recurrent patients, and integrating multiomics data gave us the power to detect the complex mechanisms of cancer among the interactions of different genetic and epigenetic factors. Abstract This study is to identify potential multiomics biomarkers for the early detection of the prognostic recurrence of PC patients. A total of 494 prostate adenocarcinoma (PRAD) patients (60-recurrent included) from the Cancer Genome Atlas (TCGA) portal were analyzed using the autoencoder model and similarity network fusion. Then, multiomics panels were constructed according to the intersected omics biomarkers identified from the two models. Six intersected omics biomarkers, TELO2, ZMYND19, miR-143, miR-378a, cg00687383 (MED4), and cg02318866 (JMJD6; METTL23), were collected for multiomics panel construction. The difference between the Kaplan–Meier curves of high and low recurrence-risk groups generated from the multiomics panel achieved p-value = 5.33 × 10−9, which is better than the former study (p-value = 5 × 10−7). Additionally, when evaluating the selected multiomics biomarkers with clinical information (Gleason score, age, and cancer stage), a high-performance prediction model was generated with C-index = 0.713, p-value = 2.97 × 10−15, and AUC = 0.789. The risk score generated from the selected multiomics biomarkers worked as an effective indicator for the prediction of PRAD recurrence. This study helps us to understand the etiology and pathways of PRAD and further benefits both patients and physicians with potential prognostic biomarkers when making clinical decisions after surgical treatment.
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Affiliation(s)
- Tzu-Hao Wang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (T.-H.W.); (C.-Y.L.)
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Cheng-Yang Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (T.-H.W.); (C.-Y.L.)
- Office of Information Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Tzong-Yi Lee
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China; (T.-Y.L.); (H.-D.H.)
- School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Hsien-Da Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China; (T.-Y.L.); (H.-D.H.)
- School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Justin Bo-Kai Hsu
- Department of Medical Research, Taipei Medical University Hospital, Taipei 110, Taiwan
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
- Correspondence: (J.B.-K.H.); (T.-H.C.)
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; (T.-H.W.); (C.-Y.L.)
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
- Correspondence: (J.B.-K.H.); (T.-H.C.)
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10
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Zhu P, Gu S, Huang H, Zhong C, Liu Z, Zhang X, Wang W, Xie S, Wu K, Lu T, Zhou Y. Upregulation of glucosamine-phosphate N-acetyltransferase 1 is a promising diagnostic and predictive indicator for poor survival in patients with lung adenocarcinoma. Oncol Lett 2021; 21:488. [PMID: 33968204 PMCID: PMC8100941 DOI: 10.3892/ol.2021.12750] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/19/2021] [Indexed: 12/30/2022] Open
Abstract
Lung adenocarcinoma, a type of non-small cell lung cancer, is the leading cause of cancer death worldwide. Great efforts have been made to identify the underlying mechanism of adenocarcinoma, especially in relation to oncogenes. The present study by integrating computational analysis with western blotting, aimed to understand the role of the upregulation of glucosamine-phosphate N-acetyltransferase 1 (GNPNAT1) in carcinogenesis. In the present study, publicly available gene expression profiles and clinical data were downloaded from The Cancer Genome Atlas to determine the role of GNPNAT1 in lung adenocarcinoma (LUAD). In addition, the association between LUAD susceptibility and GNPNAT1 upregulation were analyzed using Wilcoxon signed-rank test and logistic regression analysis. In LUAD, GNPNAT1 upregulation was significantly associated with disease stage [odds ratio (OR)=2.92, stage III vs. stage I], vital status (dead vs. alive, OR=1.89), cancer status (tumor status vs. tumor-free status, OR=1.85) and N classification (yes vs. no, OR=1.75). Cox regression analysis and the Kaplan-Meier method were utilized to evaluate the association between GNPNAT1 expression and overall survival (OS) time in patients with LUAD. The results demonstrated that patients with increased GNPNAT1 expression levels exhibited a reduced survival rate compared with those with decreased expression levels (P=8.9×10−5). In addition, Cox regression analysis revealed that GNPNAT1 upregulation was significantly associated with poor OS time [hazard ratio (HR): 1.07; 95% confidence interval (CI): 1.04–1.10; P<0.001]. The gene set enrichment analysis revealed that ‘cell cycle’, ‘oocyte meiosis’, ‘pyrimidine mediated metabolism’, ‘ubiquitin mediated proteolysis’, ‘one carbon pool by folate’, ‘mismatch repair progesterone-mediated oocyte maturation’ and ‘basal transcription factors purine metabolism’ were differentially enriched in the GNPNAT1 high-expression samples compared with GNPNAT1 low-expression samples. The aforementioned pathways are involved in the pathogenesis of LUAD. The findings of the present study suggested that GNPNAT1 upregulation may be considered as a promising diagnostic and prognostic biomarker in patients with LUAD. In addition, the aforementioned pathways may be pivotal pathways perturbed by the abnormal expression of GNPNAT1 in LUAD. The findings of the present study demonstrated the therapeutic value of the regulation of GNPNAT1 in lung adenocarcinoma.
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Affiliation(s)
- Pengyuan Zhu
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China.,School of Medicine, Nantong University, Nantong, Jiangsu 226001, P.R. China.,Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
| | - Shaorui Gu
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
| | - Haitao Huang
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Chongjun Zhong
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Zhenchuan Liu
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
| | - Xin Zhang
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
| | - Wenli Wang
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
| | - Shiliang Xie
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
| | - Kaiqin Wu
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
| | - Tiancheng Lu
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
| | - Yongxin Zhou
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, P.R. China
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11
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Eigentler A, Tymoszuk P, Zwick J, Schmitz AA, Pircher A, Kocher F, Schlicker A, Lesche R, Schäfer G, Theurl I, Klocker H, Heidegger I. The Impact of Cand1 in Prostate Cancer. Cancers (Basel) 2020; 12:cancers12020428. [PMID: 32059441 PMCID: PMC7072594 DOI: 10.3390/cancers12020428] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 02/07/2023] Open
Abstract
Evidence has accumulated asserting the importance of cullin-RING (really interesting new gene) ubiquitin ligases (CRLs) and their regulator Cullin-associated neural-precursor-cell-expressed developmentally down-regulated 8 (NEDD8) dissociated protein 1 (Cand1) in various cancer entities. However, the role of Cand1 in prostate cancer (PCa) has not been intensively investigated so far. Thus, in the present study, we aimed to assess the relevance of Cand1 in the clinical and preclinical setting. Immunohistochemical analyses of radical prostatectomy specimens of PCa patients showed that Cand1 protein levels are elevated in PCa compared to benign areas. In addition, high Cand1 levels were associated with higher Gleason Scores, as well as higher tumor recurrence and decreased overall survival. In line with clinical findings, in vitro experiments in different PCa cell lines revealed that knockdown of Cand1 reduced cell viability and proliferation and increased apoptosis, therefore underlining its role in tumor progression. We also found that the cyclin-dependent kinase inhibitor p21 is significantly upregulated upon downregulation of Cand1. Using bioinformatic tools, we detected genes encoding for proteins linked to mRNA turnover, protein polyubiquitination, and proteasomal degradation to be significantly upregulated in Cand1high tumors. Next generation sequencing of PCa cell lines resistant to the anti-androgen enzalutamide revealed that Cand1 is mutated in enzalutamide-resistant cells, however, with little functional and clinically relevant impact in the process of resistance development. To summarize the present study, we found that high Cand1 levels correlate with PCa aggressiveness.
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Affiliation(s)
- Andrea Eigentler
- Department of Urology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.E.); (J.Z.); (H.K.)
| | - Piotr Tymoszuk
- Laboratory for Immunotherapy, Department of Internal Medicine II, Medical University of Innsbruck, 6020 Innsbruck, Austria; (P.T.); (I.T.)
| | - Johanna Zwick
- Department of Urology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.E.); (J.Z.); (H.K.)
| | - Arndt A. Schmitz
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany (A.S.); (R.L.)
| | - Andreas Pircher
- Department of Internal Medicine V, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.P.); (F.K.)
| | - Florian Kocher
- Department of Internal Medicine V, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.P.); (F.K.)
| | - Andreas Schlicker
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany (A.S.); (R.L.)
| | - Ralf Lesche
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany (A.S.); (R.L.)
| | - Georg Schäfer
- Department of Pathology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Igor Theurl
- Laboratory for Immunotherapy, Department of Internal Medicine II, Medical University of Innsbruck, 6020 Innsbruck, Austria; (P.T.); (I.T.)
| | - Helmut Klocker
- Department of Urology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.E.); (J.Z.); (H.K.)
| | - Isabel Heidegger
- Department of Urology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.E.); (J.Z.); (H.K.)
- Correspondence: ; Tel: 0043-512-504-24-808
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12
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Lin X, Kapoor A, Gu Y, Chow MJ, Xu H, Major P, Tang D. Assessment of biochemical recurrence of prostate cancer (Review). Int J Oncol 2019; 55:1194-1212. [PMID: 31638194 PMCID: PMC6831208 DOI: 10.3892/ijo.2019.4893] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/24/2019] [Indexed: 12/12/2022] Open
Abstract
The assessment of the risk of biochemical recurrence (BCR) is critical in the management of males with prostate cancer (PC). Over the past decades, a comprehensive effort has been focusing on improving risk stratification; a variety of models have been constructed using PC-associated pathological features and molecular alterations occurring at the genome, protein and RNA level. Alterations in RNA expression (lncRNA, miRNA and mRNA) constitute the largest proportion of the biomarkers of BCR. In this article, we systemically review RNA-based BCR biomarkers reported in PubMed according to the PRISMA guidelines. Individual miRNAs, mRNAs, lncRNAs and multi-gene panels, including the commercially available signatures, Oncotype DX and Prolaris, will be discussed; details related to cohort size, hazard ratio and 95% confidence intervals will be provided. Mechanistically, these individual biomarkers affect multiple pathways critical to tumorigenesis and progression, including epithelial-mesenchymal transition (EMT), phosphatase and tensin homolog (PTEN), Wnt, growth factor receptor, cell proliferation, immune checkpoints and others. This variety in the mechanisms involved not only validates their associations with BCR, but also highlights the need for the coverage of multiple pathways in order to effectively stratify the risk of BCR. Updates of novel biomarkers and their mechanistic insights are considered, which suggests new avenues to pursue in the prediction of BCR. Additionally, the management of patients with BCR and the potential utility of the stratification of the risk of BCR in salvage treatment decision making for these patients are briefly covered. Limitations will also be discussed.
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Affiliation(s)
- Xiaozeng Lin
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Anil Kapoor
- The Research Institute of St. Joe's Hamilton, St. Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yan Gu
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Mathilda Jing Chow
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Hui Xu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Pierre Major
- Division of Medical Oncology, Department of Oncology, McMaster University, Hamilton, ON L8V 5C2, Canada
| | - Damu Tang
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
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13
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Pudova EA, Lukyanova EN, Nyushko KM, Mikhaylenko DS, Zaretsky AR, Snezhkina AV, Savvateeva MV, Kobelyatskaya AA, Melnikova NV, Volchenko NN, Efremov GD, Klimina KM, Belova AA, Kiseleva MV, Kaprin AD, Alekseev BY, Krasnov GS, Kudryavtseva AV. Differentially Expressed Genes Associated With Prognosis in Locally Advanced Lymph Node-Negative Prostate Cancer. Front Genet 2019; 10:730. [PMID: 31447885 PMCID: PMC6697060 DOI: 10.3389/fgene.2019.00730] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
Older age is one of the main risk factors for cancer development. The incidence of prostate cancer, as a multifactorial disease, also depends upon demographic factors, race, and genetic predisposition. Prostate cancer most frequently occurs in men over 60 years of age, indicating a clear association between older age and disease onset. Carcinogenesis is followed by the deregulation of many genes, and some of these changes could serve as biomarkers for diagnosis, prognosis, prediction of drug therapy efficacy, as well as possible therapeutic targets. We have performed a bioinformatic analysis of a The Cancer Genome Atlas (TCGA) data and RNA-Seq profiling of a Russian patient cohort to reveal prognostic markers of locally advanced lymph node-negative prostate cancer (lymph node-negative LAPC). We also aimed to identify markers of the most common molecular subtype of prostate cancer carrying a fusion transcript TMPRSS2-ERG. We have found several genes that were differently expressed between the favorable and unfavorable prognosis groups and involved in the enriched KEGG pathways based on the TCGA (B4GALNT4, PTK6, and CHAT) and Russian patient cohort data (AKR1C1 and AKR1C3). Additionally, we revealed such genes for the TMPRSS2-ERG prostate cancer molecular subtype (B4GALNT4, ASRGL1, MYBPC1, RGS11, SLC6A14, GALNT13, and ST6GALNAC1). Obtained results contribute to a better understanding of the molecular mechanisms behind prostate cancer progression and could be used for further development of the LAPC prognosis marker panel.
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Affiliation(s)
- Elena A. Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Lukyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kirill M. Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Dmitry S. Mikhaylenko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrew R. Zaretsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Maria V. Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda N. Volchenko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Gennady D. Efremov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Kseniya M. Klimina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A. Belova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina V. Kiseleva
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrey D. Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Boris Y. Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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