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Pellegrini M. Accurate prognosis for localized prostate cancer through coherent voting networks with multi-omic and clinical data. Sci Rep 2023; 13:7875. [PMID: 37188913 DOI: 10.1038/s41598-023-35023-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/11/2023] [Indexed: 05/17/2023] Open
Abstract
Localized prostate cancer is a very heterogeneous disease, from both a clinical and a biological/biochemical point of view, which makes the task of producing stratifications of patients into risk classes remarkably challenging. In particular, it is important an early detection and discrimination of the indolent forms of the disease, from the aggressive ones, requiring post-surgery closer surveillance and timely treatment decisions. This work extends a recently developed supervised machine learning (ML) technique, called coherent voting networks (CVN) by incorporating a novel model-selection technique to counter the danger of model overfitting. For the challenging problem of discriminating between indolent and aggressive types of localized prostate cancer, accurate prognostic prediction of post-surgery progression-free survival with a granularity within a year is attained, improving accuracy with respect to the current state of the art. The development of novel ML techniques tailored to the problem of combining multi-omics and clinical prognostic biomarkers is a promising new line of attack for sharpening the capability to diversify and personalize cancer patient treatments. The proposed approach allows a finer post-surgery stratification of patients within the clinical high-risk category, with a potential impact on the surveillance regime and the timing of treatment decisions, complementing existing prognostic methods.
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Affiliation(s)
- Marco Pellegrini
- Institute of Informatics and Telematics (IIT), CNR, 56124, Pisa, Italy.
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Johnson H, Guo J, Zhang X, Zhang H, Simoulis A, Wu AHB, Xia T, Li F, Tan W, Johnson A, Dizeyi N, Abrahamsson PA, Kenner L, Feng X, Zou C, Xiao K, Persson JL, Chen L. Development and validation of a 25-Gene Panel urine test for prostate cancer diagnosis and potential treatment follow-up. BMC Med 2020; 18:376. [PMID: 33256740 PMCID: PMC7706045 DOI: 10.1186/s12916-020-01834-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heterogeneity of prostate cancer (PCa) contributes to inaccurate cancer screening and diagnosis, unnecessary biopsies, and overtreatment. We intended to develop non-invasive urine tests for accurate PCa diagnosis to avoid unnecessary biopsies. METHODS Using a machine learning program, we identified a 25-Gene Panel classifier for distinguishing PCa and benign prostate. A non-invasive test using pre-biopsy urine samples collected without digital rectal examination (DRE) was used to measure gene expression of the panel using cDNA preamplification followed by real-time qRT-PCR. The 25-Gene Panel urine test was validated in independent multi-center retrospective and prospective studies. The diagnostic performance of the test was assessed against the pathological diagnosis from biopsy by discriminant analysis. Uni- and multivariate logistic regression analysis was performed to assess its diagnostic improvement over PSA and risk factors. In addition, the 25-Gene Panel urine test was used to identify clinically significant PCa. Furthermore, the 25-Gene Panel urine test was assessed in a subset of patients to examine if cancer was detected after prostatectomy. RESULTS The 25-Gene Panel urine test accurately detected cancer and benign prostate with AUC of 0.946 (95% CI 0.963-0.929) in the retrospective cohort (n = 614), AUC of 0.901 (0.929-0.873) in the prospective cohort (n = 396), and AUC of 0.936 (0.956-0.916) in the large combination cohort (n = 1010). It greatly improved diagnostic accuracy over PSA and risk factors (p < 0.0001). When it was combined with PSA, the AUC increased to 0.961 (0.980-0.942). Importantly, the 25-Gene Panel urine test was able to accurately identify clinically significant and insignificant PCa with AUC of 0.928 (95% CI 0.947-0.909) in the combination cohort (n = 727). In addition, it was able to show the absence of cancer after prostatectomy with high accuracy. CONCLUSIONS The 25-Gene Panel urine test is the first highly accurate and non-invasive liquid biopsy method without DRE for PCa diagnosis. In clinical practice, it may be used for identifying patients in need of biopsy for cancer diagnosis and patients with clinically significant cancer for immediate treatment, and potentially assisting cancer treatment follow-up.
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Affiliation(s)
| | - Jinan Guo
- Department of Urology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen Urology Minimally Invasive Engineering Centre, Shenzhen, China.,Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Clinical Medical Research Centre, The Second Clinical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Xuhui Zhang
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Heqiu Zhang
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Athanasios Simoulis
- Department of Clinical Pathology and Cytology, Skåne University Hospital, Malmö, Sweden
| | - Alan H B Wu
- Clinical Laboratories, San Francisco General Hospital, San Francisco, CA, USA
| | - Taolin Xia
- Department of Urology, Foshan First People's Hospital, Foshan, China
| | - Fei Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wanlong Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Nishtman Dizeyi
- Department of Translational Medicine, Lund University, Clinical Research Centre, Malmö, Sweden
| | - Per-Anders Abrahamsson
- Department of Translational Medicine, Lund University, Clinical Research Centre, Malmö, Sweden
| | - Lukas Kenner
- Department of Experimental Pathology, Medical University Vienna & Unit of Laboratory Animal Pathology, University of Veterinary Medicine, Vienna, Austria
| | - Xiaoyan Feng
- Department of Bio-diagnosis, Institute of Basic Medical Sciences, Beijing, China
| | - Chang Zou
- Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Clinical Medical Research Centre, The Second Clinical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Kefeng Xiao
- Department of Urology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen Urology Minimally Invasive Engineering Centre, Shenzhen, China.,Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Clinical Medical Research Centre, The Second Clinical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China
| | - Jenny L Persson
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden. .,Division of Experimental Cancer Research, Department of Translational Medicine, Lund University, 205 02, Malmö, Sweden. .,Department of Biomedical Sciences, Malmö University, Malmö, Sweden.
| | - Lingwu Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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Ge S, Sun C, Hu Q, Guo Y, Xia G, Mi Y, Zhu L. Differential expression profiles of circRNAs in human prostate cancer based on chip and bioinformatic analysis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:1045-1052. [PMID: 32509077 PMCID: PMC7270690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Increasing evidence suggests that circRNAs are involved in the pathogenesis of multiple kinds of cancer. Nevertheless, the differential expression of circRNAs in prostate cancer (PCA) is rarely reported. MATERIAL/METHOD In our present analyses, circRNAs expression profiles were identified in PCA, based on 5 pairs of PCA and matched non-PCA tissues using circRNA chips. RESULTS A number of 749 differential circRNAs were expressed between PCA tumor and paracancerous tissues (Fold Change, FC ≥ 2.0 and P < 0.05): 261 were upregulated, whereas 487 were downregulated in PCA tissues. Gene ontology and KEGG pathway analyses indicated that many of the circRNAs are related to carcinogenesis. Circ_0033074 and circ_0016064 both showed changes of maximum magnitude among differentially expressed circRNAs. CONCLUSIONS Our study detected a relative comprehensive differential map of circRNAs in PCA, which may become novel biomarkers for diagnosis, treatment and follow-up in the future.
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Affiliation(s)
- Shengyang Ge
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai, P. R. China
| | - Chuanyu Sun
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai, P. R. China
| | - Qingfeng Hu
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai, P. R. China
| | - Yijun Guo
- Department of Urology, Shanghai Jing’an District Central Hospital (Jing’an Branch of Huashan Hospital Affiliated to Fudan University)Shanghai, P. R. China
| | - Guowei Xia
- Department of Urology, Huashan Hospital, Fudan UniversityShanghai, P. R. China
| | - Yuanyuan Mi
- Department of Urology, Affiliated Hospital of Jiangnan UniversityWuxi, P. R. China
| | - Lijie Zhu
- Department of Urology, Affiliated Hospital of Jiangnan UniversityWuxi, P. R. China
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Liang CY, Huang ZG, Tang ZQ, Xiao XL, Zeng JJ, Feng ZB. FOXO1 and hsa-microRNA-204-5p affect the biologic behavior of MDA-MB-231 breast cancer cells. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:1146-1158. [PMID: 32509089 PMCID: PMC7270695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
RNA molecules and targeting microRNA (miRNA) have been reported as novel focuses in recent research on breast cancer. This study aimed to probe the expression of FOXO1 in the MDA-MB-231 cell line and to explore the target effects of FOXO1 with hsa-microRNA-204-5p (miR-204) on the biologic behavior of MDA-MB-231 cells. The expression of FOXO1 mRNA and protein in MDA-MB-231 cells were derived and verified from the public databases, literature, and experimental assays, then the downregulation of FOXO1 was confirmed in the MDA-MB-231 cell line. The target binding of FOXO1 and miR-204 was predicted by miRWalk and confirmed by luciferase reporter assays. MiR-204 targeted the 3' untranslated region of FOXO1 and reduced FOXO1 expression in miR-204-transfected cells, resulting in cell growth amplification but inhibition of cell migration and apoptosis, which were assessed using the MTT method, wound healing assays, and flow cytometry, respectively. The protein levels of serine-threonine kinase (AKT), c-jun N-terminal kinase (JNK), extracellular regulatory protein kinase (ERK), and the phosphorylated protein kinases (P-AKT, P-JNK, and P-ERK) were measured by western blot. It was found that AKT, JNK, and ERK remained constant, but P-AKT, P-JNK, and P-ERK were upregulated after miR-204 transfection. In summary, the expression of FOXO1 was downregulated in MDA-MB-231 cells; and the target binding of miR-204 and FOXO1 affected phosphatidylinositol 3-kinase (PI3K)/AKT and mitogen-activated protein kinase (MAPK) signal pathways, leading to different alterations of cellular activity in MDA-MB-231 cells.
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Affiliation(s)
- Chang-Yu Liang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Zhong-Qing Tang
- Department of Pathology, Gongren Hospital of WuzhouWuzhou, Guangxi, P. R. China
| | - Xiao-Ling Xiao
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Jing-Jing Zeng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi, P. R. China
| | - Zhen-Bo Feng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, Guangxi, P. R. China
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[Mass spectrometry-applications in pathology]. DER PATHOLOGE 2019; 40:277-281. [PMID: 31713660 DOI: 10.1007/s00292-019-00692-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Currently, more complex and extensive diagnostic pathology work-up of sometimes only limited sample material is necessary to ensure optimal patient treatment. This often includes genomic analyses. However, dynamic changes within an organism or tumor can be better reflected at the protein level. Therefore, proteomic technologies would seem to be the solution. OBJECTIVES To evaluate the application of different proteomic techniques to analyze body fluids and tissue samples with regards to implementation in diagnostics. MATERIALS AND METHODS All studies utilized mass spectrometry-based methods in order to achieve differentiation of a number of different patient groups in various diseases. RESULTS Whereas classical proteomic methods are particularly suitable for analyzing serum samples in order to diagnose bladder cancer or chronic hepatitis C, tissue analyses would require prior tissue lyses, thus erasing possible information to be obtained from histology. Imaging mass spectrometry offers a solution as it allows for the analysis of an intact tissue section. Possible applications and the added benefit of this method could be shown using various examples of tumors (prostate cancer, Hodgkin's lymphoma, cervical cancer, and different types of adenocarcinomas). CONCLUSIONS Mass spectrometry-based technologies allow diagnostic confirmation with high sensitivity and specificity. In comparison to routine diagnostic approaches, results can be achieved faster, using less sample material, and with comparable accuracy.
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Rong MH, Cai KT, Lu HP, Guo YN, Huang XY, Zhu ZH, Tang W, Huang SN. Overexpression of MiR-452-5p in hepatocellular carcinoma tissues and its prospective signaling pathways. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:4041-4056. [PMID: 31933800 PMCID: PMC6949781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The implication of miR-452-5p and its prospective machinery in hepatocellular carcinoma (HCC) remains largely unknown. For this reason, this study aimed to inspect the clinical implication of miR-452-5p expression in HCC tissues with multiple detection approaches, to analyze its potential function via in silico methods, and to validate this using a dual-luciferase reporter assay. METHODS The assessment of the expression level of miR-452-5p in HCC was conducted via four methods: 1) in-house real-time quantitative PCR (RT-qPCR), 2) miRNA-sequencing (miRNA-seq) from The Cancer Genome Atlas (TCGA), 3) miRNA microarrays from the Gene Expression Omnibus (GEO), and 4) comprehensive meta-analyses calculating the standard mean difference (SMD) and summary of receiver operator characteristic (sROC). Following the target prediction, one of the potential targets of miR-452-5p was validated through a dual-luciferase reporter assay. RESULTS MiR-452-5p was consistently elevated in HCC tissues via various detection methods, including in-house RT-qPCR, miRNA-seq, and miRNA microarrays. The final SMD was 0.842 for 820 cases of HCC samples. Simultaneously, the area under curve (AUC) of the sROC was 0.80 (0.76-0.83). The 1,135 predicted targets of miR-452-5p were enriched in the pathways of cytokine-cytokine receptor interaction, carbon metabolism, and complement and coagulation cascades. Among these predicted targets, CDKN1B was verified to be a real target of miR-452-5p. CONCLUSION The overexpression of miR-452-5p may play a pivotal role in the carcinogenesis of HCC via targeting multiple signaling pathways and genes. The function and molecular machinery of miR-452-5p in HCC requires further in-depth exploration.
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Affiliation(s)
- Min-Hua Rong
- Research Department, Affiliated Cancer Hospital, Guangxi Medical University71 Hedi Road, Nanning 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Kai-Teng Cai
- Research Department, Affiliated Cancer Hospital, Guangxi Medical University71 Hedi Road, Nanning 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Hui-Ping Lu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical UniversityNanning 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Yi-Nan Guo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical UniversityNanning 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Xiong-Yan Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical UniversityNanning 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Zhan-Hui Zhu
- Research Department, Affiliated Cancer Hospital, Guangxi Medical University71 Hedi Road, Nanning 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Wei Tang
- Department of Breast Surgery, Affiliated Cancer Hospital, Guangxi Medical University71 Hedi Road, Nanning 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Su-Ning Huang
- Department of Radiotherapy, Affiliated Cancer Hospital, Guangxi Medical University71 Hedi Road, Nanning 530021, Guangxi Zhuang Autonomous Region, P. R. China
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Zhang Z, Qiao J, Zhang D, Zhu W, Zhu J, Leng X, Li S. Noncoding RNAs Act as Tumor-Derived Molecular Components in Inducing Premetastatic Niche Formation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9258075. [PMID: 31309120 PMCID: PMC6594336 DOI: 10.1155/2019/9258075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/04/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022]
Abstract
Cancer metastasis has been demonstrated as it is the culmination of a cascade of priming steps. Increasing evidence has shown that tumor-derived molecular components (TDMCs) are known as extra cellular vesicle and nonvesicle factors and serve as versatile intercellular communication vehicles which can mediate signaling in the tumor microenvironment while creating the premetastatic niche. Noncoding RNAs (ncRNAs) as one of the TDMCs have been proved in participating in the formation of the premetastatic niche. Understanding the premetastatic niche formation mechanisms through TDMCs, especially ncRNAs may open a new avenue for cancer metastasis therapeutic strategies. In this review, recent findings regarding ncRNAs function were summarized, and then the interaction with the premetastatic niche formation was studied, which highlight the potential of using ncRNAs for cancer diagnosis and therapeutic effect.
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Affiliation(s)
- Zhedong Zhang
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jiao Qiao
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, 250021, China
| | - Dafang Zhang
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Weihua Zhu
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jiye Zhu
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xisheng Leng
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Shu Li
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, 100044, China
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