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Ren S, Li J, Dorado J, Sierra A, González-Díaz H, Duardo A, Shen B. From molecular mechanisms of prostate cancer to translational applications: based on multi-omics fusion analysis and intelligent medicine. Health Inf Sci Syst 2024; 12:6. [PMID: 38125666 PMCID: PMC10728428 DOI: 10.1007/s13755-023-00264-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Prostate cancer is the most common cancer in men worldwide and has a high mortality rate. The complex and heterogeneous development of prostate cancer has become a core obstacle in the treatment of prostate cancer. Simultaneously, the issues of overtreatment in early-stage diagnosis, oligometastasis and dormant tumor recognition, as well as personalized drug utilization, are also specific concerns that require attention in the clinical management of prostate cancer. Some typical genetic mutations have been proved to be associated with prostate cancer's initiation and progression. However, single-omic studies usually are not able to explain the causal relationship between molecular alterations and clinical phenotypes. Exploration from a systems genetics perspective is also lacking in this field, that is, the impact of gene network, the environmental factors, and even lifestyle behaviors on disease progression. At the meantime, current trend emphasizes the utilization of artificial intelligence (AI) and machine learning techniques to process extensive multidimensional data, including multi-omics. These technologies unveil the potential patterns, correlations, and insights related to diseases, thereby aiding the interpretable clinical decision making and applications, namely intelligent medicine. Therefore, there is a pressing need to integrate multidimensional data for identification of molecular subtypes, prediction of cancer progression and aggressiveness, along with perosonalized treatment performing. In this review, we systematically elaborated the landscape from molecular mechanism discovery of prostate cancer to clinical translational applications. We discussed the molecular profiles and clinical manifestations of prostate cancer heterogeneity, the identification of different states of prostate cancer, as well as corresponding precision medicine practices. Taking multi-omics fusion, systems genetics, and intelligence medicine as the main perspectives, the current research results and knowledge-driven research path of prostate cancer were summarized.
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Affiliation(s)
- Shumin Ren
- Department of Urology and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041 China
- Department of Computer Science and Information Technology, University of A Coruña, 15071 A Coruña, Spain
| | - Jiakun Li
- Department of Urology and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Julián Dorado
- Department of Computer Science and Information Technology, University of A Coruña, 15071 A Coruña, Spain
| | - Alejandro Sierra
- Department of Computer Science and Information Technology, University of A Coruña, 15071 A Coruña, Spain
- IKERDATA S.L., ZITEK, University of Basque Country UPVEHU, Rectorate Building, 48940 Leioa, Spain
| | - Humbert González-Díaz
- Department of Computer Science and Information Technology, University of A Coruña, 15071 A Coruña, Spain
- IKERDATA S.L., ZITEK, University of Basque Country UPVEHU, Rectorate Building, 48940 Leioa, Spain
| | - Aliuska Duardo
- Department of Computer Science and Information Technology, University of A Coruña, 15071 A Coruña, Spain
- IKERDATA S.L., ZITEK, University of Basque Country UPVEHU, Rectorate Building, 48940 Leioa, Spain
| | - Bairong Shen
- Department of Urology and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, 610041 China
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El-Melegy M, Mamdouh A, Ali S, Badawy M, El-Ghar MA, Alghamdi NS, El-Baz A. Prostate Cancer Diagnosis via Visual Representation of Tabular Data and Deep Transfer Learning. Bioengineering (Basel) 2024; 11:635. [PMID: 39061717 PMCID: PMC11274351 DOI: 10.3390/bioengineering11070635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
Prostate cancer (PC) is a prevalent and potentially fatal form of cancer that affects men globally. However, the existing diagnostic methods, such as biopsies or digital rectal examination (DRE), have limitations in terms of invasiveness, cost, and accuracy. This study proposes a novel machine learning approach for the diagnosis of PC by leveraging clinical biomarkers and personalized questionnaires. In our research, we explore various machine learning methods, including traditional, tree-based, and advanced tabular deep learning methods, to analyze tabular data related to PC. Additionally, we introduce the novel utilization of convolutional neural networks (CNNs) and transfer learning, which have been predominantly applied in image-related tasks, for handling tabular data after being transformed to proper graphical representations via our proposed Tab2Visual modeling framework. Furthermore, we investigate leveraging the prediction accuracy further by constructing ensemble models. An experimental evaluation of our proposed approach demonstrates its effectiveness in achieving superior performance attaining an F1-score of 0.907 and an AUC of 0.911. This offers promising potential for the accurate detection of PC without the reliance on invasive and high-cost procedures.
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Affiliation(s)
- Moumen El-Melegy
- Electrical Engineering Department, Assiut University, Assiut 71516, Egypt; (M.E.-M.); (A.M.); (S.A.)
| | - Ahmed Mamdouh
- Electrical Engineering Department, Assiut University, Assiut 71516, Egypt; (M.E.-M.); (A.M.); (S.A.)
| | - Samia Ali
- Electrical Engineering Department, Assiut University, Assiut 71516, Egypt; (M.E.-M.); (A.M.); (S.A.)
| | - Mohamed Badawy
- Radiology Department, Urology and Nephrology Center, Mansoura University, Mansoura 35516, Egypt; (M.B.); (M.A.E.-G.)
| | - Mohamed Abou El-Ghar
- Radiology Department, Urology and Nephrology Center, Mansoura University, Mansoura 35516, Egypt; (M.B.); (M.A.E.-G.)
| | - Norah Saleh Alghamdi
- Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Ayman El-Baz
- Bioengineering Department, University of Louisville, Louisville, KY 40292, USA
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Mukherjee A, Abraham S, Singh A, Balaji S, Mukunthan KS. From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies. Mol Biotechnol 2024:10.1007/s12033-024-01133-6. [PMID: 38565775 DOI: 10.1007/s12033-024-01133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.
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Affiliation(s)
- Arnab Mukherjee
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Suzanna Abraham
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Akshita Singh
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - K S Mukunthan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India.
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Liu CL, Jiang Y, Li HJ. Quality Consistency Evaluation of Traditional Chinese Medicines: Current Status and Future Perspectives. Crit Rev Anal Chem 2024:1-18. [PMID: 38252135 DOI: 10.1080/10408347.2024.2305267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Quality consistency evaluation of traditional Chinese medicines (TCMs) is a crucial factor that determines the safe and effective application in clinical settings. However, TCMs exhibit diverse, heterogeneous, complex, and flexible chemical compositions, as well as variability in preparation processes. These characteristics pose greater challenges in researching the consistency of TCMs compared to chemically synthesized and biological drugs. Therefore, it is paramount to develop effective strategies for evaluating the quality consistency of TCMs. From the starting point of quality properties, this review explores the strategy used to evaluate quality consistency in terms of chemistry-based strategy (chemical consistency) and the biology-based strategy (bioequivalence). Among them, the chemistry-based strategy is the mainstream, and biology-based strategy complements the chemistry-based strategy each other. Furthermore, the emerging chemistry-biology strategies (overall evaluation) is discussed, including individually combining strategy and integration strategy. Finally, this review provides insights into the challenges and future perspectives in this field. By highlighting current status and trends in TCMs quality consistency, this review aims to contribute to establishment of generally applicable chemistry-biology integrated evaluation strategy for TCMs. This will facilitate the advancement toward a higher stage of overall quality evaluation.
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Affiliation(s)
- Chun-Lu Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Yan Jiang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Hui-Jun Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
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Ali W, Xiao W, Hoang H, Cali V, Kajdacsy-Balla A. Carcinogenesis and Prognostic Utility of Arginine Methylation-Related Genes in Hepatocellular Cancer. Curr Issues Mol Biol 2023; 45:9422-9430. [PMID: 38132437 PMCID: PMC10742294 DOI: 10.3390/cimb45120591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 12/23/2023] Open
Abstract
Protein arginine methylation is among the most important post-translational modifications and has been studied in cancers such as those of the lung and breast. However, comparatively less has been investigated regarding hepatocellular carcinoma, with an annual incidence of almost one million cases. Through using in silico methods, this study examined arginine methylation-related gene expression and methylation levels, and alongside network and enrichment analysis attempted to find how said genes can drive tumorigenesis and offer possible therapeutic targets. We found a robust relationship among the selected methylation genes, with ⅞ showing prognostic value regarding overall survival, and a medley of non-arginine methylation pathways also being highlighted through the aforementioned analysis. This study furthers our knowledge of the methylation and expression patterns of arginine histone methylation-related genes, offering jumping points for further wet-lab studies.
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Affiliation(s)
- Waleed Ali
- Albert Einstein College of Medicine, The Bronx, NY 10461, USA; (W.A.); (W.X.); (H.H.); (V.C.)
| | - Weirui Xiao
- Albert Einstein College of Medicine, The Bronx, NY 10461, USA; (W.A.); (W.X.); (H.H.); (V.C.)
| | - Henry Hoang
- Albert Einstein College of Medicine, The Bronx, NY 10461, USA; (W.A.); (W.X.); (H.H.); (V.C.)
| | - Vincent Cali
- Albert Einstein College of Medicine, The Bronx, NY 10461, USA; (W.A.); (W.X.); (H.H.); (V.C.)
| | - Andre Kajdacsy-Balla
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
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Li W, Huang Q, Peng Y, Pan S, Hu M, Wang P, He Y. A deep learning approach based on multi-omics data integration to construct a risk stratification prediction model for skin cutaneous melanoma. J Cancer Res Clin Oncol 2023; 149:15923-15938. [PMID: 37673824 DOI: 10.1007/s00432-023-05358-x] [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: 06/27/2023] [Accepted: 08/26/2023] [Indexed: 09/08/2023]
Abstract
PURPOSE Skin cutaneous melanoma (SKCM) is a highly aggressive melanocytic carcinoma whose high heterogeneity and complex etiology make its prognosis difficult to predict. This study aimed to construct a risk subtype typing model for SKCM. METHODS The study proposes a deep learning framework combining early fusion feature autoencoder (AE) and late fusion feature AE for risk subtype prediction of SKCM. The deep learning framework integrates mRNA, miRNA, and DNA methylation data of SKCM patients from The Cancer Genome Atlas (TCGA), and clusters the screened multi-omics features associated with survival prognosis to identify risk subtypes. Differential expression analysis and functional enrichment analysis were performed between risk subtypes, while SVM classifiers were constructed between differentially expressed genes (DEGs) obtained by Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression screening and risk subtype labels inferred from multi-omics data, and the predictive robustness of risk subtypes inferred from the risk subtype classification prediction model was validated using two independent datasets. RESULTS The deep learning framework that combined early fusion feature AE with late fusion feature AE distinguished the two best risk subtypes compared to the multi-omics integration approach with single strategy AE or PCA. A promising C-index (C-index = 0.748) and a significant difference in survival (log-rank P value = 4.61 × 10-9) were found between the identified risk subtypes. The DEGs with the top significance values together with differentially expressed miRNAs provided the biological interpretation of risk subtypes on SKCM. Finally, the framework was applied to predict risk subtypes in two independent test datasets of SKCM patients, all of which showed good predictive power (C-index > 0.680) and significant survival differences (log-rank P value < 0.01). CONCLUSION The SKCM risk subtypes identified by integrating multi-omics data based on deep learning can not only improve the understanding of the molecular mechanisms of SKCM, but also provide clinicians with assistance in treatment decisions.
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Affiliation(s)
- Weijia Li
- Department of Epidemiology and Medical Statistics, Institute of Medical Systems Biology, Guangdong Medical University, Dongguan, Guangdong, China
| | - Qiao Huang
- Department of Epidemiology and Medical Statistics, Institute of Medical Systems Biology, Guangdong Medical University, Dongguan, Guangdong, China
| | - Yi Peng
- Department of Epidemiology and Medical Statistics, Institute of Medical Systems Biology, Guangdong Medical University, Dongguan, Guangdong, China
| | - Suyue Pan
- Department of Epidemiology and Medical Statistics, Institute of Medical Systems Biology, Guangdong Medical University, Dongguan, Guangdong, China
| | - Min Hu
- Department of Epidemiology and Medical Statistics, Institute of Medical Systems Biology, Guangdong Medical University, Dongguan, Guangdong, China
| | - Pu Wang
- Department of Epidemiology and Medical Statistics, Institute of Medical Systems Biology, Guangdong Medical University, Dongguan, Guangdong, China
| | - Yuqing He
- Department of Epidemiology and Medical Statistics, Institute of Medical Systems Biology, Guangdong Medical University, Dongguan, Guangdong, China.
- Dongguan Liaobu Hospital, Dongguan, Guangdong, China.
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Ranjbari S, Arslanturk S. Integration of incomplete multi-omics data using Knowledge Distillation and Supervised Variational Autoencoders for disease progression prediction. J Biomed Inform 2023; 147:104512. [PMID: 37813325 DOI: 10.1016/j.jbi.2023.104512] [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: 06/10/2023] [Revised: 08/31/2023] [Accepted: 10/03/2023] [Indexed: 10/11/2023]
Abstract
OBJECTIVE The rapid advancement of high-throughput technologies in the biomedical field has resulted in the accumulation of diverse omics data types, such as mRNA expression, DNA methylation, and microRNA expression, for studying various diseases. Integrating these multi-omics datasets enables a comprehensive understanding of the molecular basis of cancer and facilitates accurate prediction of disease progression. METHODS However, conventional approaches face challenges due to the dimensionality curse problem. This paper introduces a novel framework called Knowledge Distillation and Supervised Variational AutoEncoders utilizing View Correlation Discovery Network (KD-SVAE-VCDN) to address the integration of high-dimensional multi-omics data with limited common samples. Through our experimental evaluation, we demonstrate that the proposed KD-SVAE-VCDN architecture accurately predicts the progression of breast and kidney carcinoma by effectively classifying patients as long- or short-term survivors. Furthermore, our approach outperforms other state-of-the-art multi-omics integration models. RESULTS Our findings highlight the efficacy of the KD-SVAE-VCDN architecture in predicting the disease progression of breast and kidney carcinoma. By enabling the classification of patients based on survival outcomes, our model contributes to personalized and targeted treatments. The favorable performance of our approach in comparison to several existing models suggests its potential to contribute to the advancement of cancer understanding and management. CONCLUSION The development of a robust predictive model capable of accurately forecasting disease progression at the time of diagnosis holds immense promise for advancing personalized medicine. By leveraging multi-omics data integration, our proposed KD-SVAE-VCDN framework offers an effective solution to this challenge, paving the way for more precise and tailored treatment strategies for patients with different types of cancer.
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Affiliation(s)
- Sima Ranjbari
- Department of Computer Science, Wayne State University, Detroit, 48202, MI, USA.
| | - Suzan Arslanturk
- Department of Computer Science, Wayne State University, Detroit, 48202, MI, USA.
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Miranda J, Paules C, Noell G, Youssef L, Paternina-Caicedo A, Crovetto F, Cañellas N, Garcia-Martín ML, Amigó N, Eixarch E, Faner R, Figueras F, Simões RV, Crispi F, Gratacós E. Similarity network fusion to identify phenotypes of small-for-gestational-age fetuses. iScience 2023; 26:107620. [PMID: 37694157 PMCID: PMC10485038 DOI: 10.1016/j.isci.2023.107620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/19/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023] Open
Abstract
Fetal growth restriction (FGR) affects 5-10% of pregnancies, is the largest contributor to fetal death, and can have long-term consequences for the child. Implementation of a standard clinical classification system is hampered by the multiphenotypic spectrum of small fetuses with substantial differences in perinatal risks. Machine learning and multiomics data can potentially revolutionize clinical decision-making in FGR by identifying new phenotypes. Herein, we describe a cluster analysis of FGR based on an unbiased machine-learning method. Our results confirm the existence of two subtypes of human FGR with distinct molecular and clinical features based on multiomic analysis. In addition, we demonstrated that clusters generated by machine learning significantly outperform single data subtype analysis and biologically support the current clinical classification in predicting adverse maternal and neonatal outcomes. Our approach can aid in the refinement of clinical classification systems for FGR supported by molecular and clinical signatures.
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Affiliation(s)
- Jezid Miranda
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
- Department of Obstetrics and Gynecology, Faculty of Medicine, Universidad de Cartagena, Cartagena de Indias, Colombia
| | - Cristina Paules
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
- Aragon Institute of Health Research (IIS Aragon), Obstetrics Department, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | - Guillaume Noell
- University of Barcelona, Biomedicine Department, IDIBAPS, Centre for Biomedical Research on Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Lina Youssef
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | | | - Francesca Crovetto
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Nicolau Cañellas
- Metabolomics Platform, IISPV, DEEiA, Universidad Rovira i Virgili, Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Tarragona, Spain
| | - María L. Garcia-Martín
- BIONAND, Andalusian Centre for Nanomedicine and Biotechnology, Junta de Andalucía, Universidad de Málaga, Málaga, Spain
| | | | - Elisenda Eixarch
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Rosa Faner
- University of Barcelona, Biomedicine Department, IDIBAPS, Centre for Biomedical Research on Respiratory Diseases (CIBERES), Barcelona, Spain
| | - Francesc Figueras
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Rui V. Simões
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
- Institute for Research & Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - Fàtima Crispi
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Eduard Gratacós
- BCNatal – Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), IDIBAPS, University of Barcelona, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
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Tabrizi-Nezhadi P, MotieGhader H, Maleki M, Sahin S, Nematzadeh S, Torkamanian-Afshar M. Application of Protein-Protein Interaction Network Analysis in Order to Identify Cervical Cancer miRNA and mRNA Biomarkers. ScientificWorldJournal 2023; 2023:6626279. [PMID: 37746664 PMCID: PMC10513823 DOI: 10.1155/2023/6626279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023] Open
Abstract
Cervical cancer (CC) is one of the world's most common and severe cancers. This cancer includes two histological types: squamous cell carcinoma (SCC) and adenocarcinoma (ADC). The current study aims at identifying novel potential candidate mRNA and miRNA biomarkers for SCC based on a protein-protein interaction (PPI) and miRNA-mRNA network analysis. The current project utilized a transcriptome profile for normal and SCC samples. First, the PPI network was constructed for the 1335 DEGs, and then, a significant gene module was extracted from the PPI network. Next, a list of miRNAs targeting module's genes was collected from the experimentally validated databases, and a miRNA-mRNA regulatory network was formed. After network analysis, four driver genes were selected from the module's genes including MCM2, MCM10, POLA1, and TONSL and introduced as potential candidate biomarkers for SCC. In addition, two hub miRNAs, including miR-193b-3p and miR-615-3p, were selected from the miRNA-mRNA regulatory network and reported as possible candidate biomarkers. In summary, six potential candidate RNA-based biomarkers consist of four genes containing MCM2, MCM10, POLA1, and TONSL, and two miRNAs containing miR-193b-3p and miR-615-3p are opposed as potential candidate biomarkers for CC.
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Affiliation(s)
| | - Habib MotieGhader
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
- Department of Health Ecosystem, Medical Faculty, Nisantasi University, Istanbul, Turkey
| | - Masoud Maleki
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Soner Sahin
- Department of Health Ecosystem, Medical Faculty, Nisantasi University, Istanbul, Turkey
| | - Sajjad Nematzadeh
- Software Engineering Department, Engineering Faculty, Topkapi University, Istanbul, Turkey
| | - Mahsa Torkamanian-Afshar
- Department of Computer Engineering, Faculty of Engineering and Architecture, Nisantasi University, Istanbul, Turkey
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10
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Armstrong L, Willoughby CE, McKenna DJ. Targeting of AKT1 by miR-143-3p Suppresses Epithelial-to-Mesenchymal Transition in Prostate Cancer. Cells 2023; 12:2207. [PMID: 37759434 PMCID: PMC10526992 DOI: 10.3390/cells12182207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
An altered expression of miR-143-3p has been previously reported in prostate cancer where it is purported to play a tumor suppressor role. Evidence from other cancers suggests miR-143-3p acts as an inhibitor of epithelial-to-mesenchymal transition (EMT), a key biological process required for metastasis. However, in prostate cancer the interaction between miR-143-3p and EMT-associated mechanisms remains unclear. Therefore, this paper investigated the link between miR-143-3p and EMT in prostate cancer using in vitro and in silico analyses. PCR detected that miR-143-3p expression was significantly decreased in prostate cancer cell lines compared to normal prostate cells. Bioinformatic analysis of The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA PRAD) data showed a significant downregulation of miR-143-3p in prostate cancer, correlating with pathological markers of advanced disease. Functional enrichment analysis confirmed the significant association of miR-143-3p and its target genes with EMT. The EMT-linked gene AKT1 was subsequently shown to be a novel target of miR-143-3p in prostate cancer cells. The in vitro manipulation of miR-143-3p levels significantly altered the cell proliferation, clonogenicity, migration and expression of EMT-associated markers. Further TCGA PRAD analysis suggested miR-143-3p tumor expression may be a useful predictor of disease recurrence. In summary, this is the first study to report that miR-143-3p overexpression in prostate cancer may inhibit EMT by targeting AKT1. The findings suggest miR-143-3p could be a useful diagnostic and prognostic biomarker for prostate cancer.
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Affiliation(s)
| | | | - Declan J. McKenna
- Genomic Medicine Research Group, Ulster University, Cromore Road, Coleraine BT52 1SA, UK; (L.A.); (C.E.W.)
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11
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Yuan T, Edelmann D, Fan Z, Alwers E, Kather JN, Brenner H, Hoffmeister M. Machine learning in the identification of prognostic DNA methylation biomarkers among patients with cancer: A systematic review of epigenome-wide studies. Artif Intell Med 2023; 143:102589. [PMID: 37673571 DOI: 10.1016/j.artmed.2023.102589] [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: 07/21/2022] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND DNA methylation biomarkers have great potential in improving prognostic classification systems for patients with cancer. Machine learning (ML)-based analytic techniques might help overcome the challenges of analyzing high-dimensional data in relatively small sample sizes. This systematic review summarizes the current use of ML-based methods in epigenome-wide studies for the identification of DNA methylation signatures associated with cancer prognosis. METHODS We searched three electronic databases including PubMed, EMBASE, and Web of Science for articles published until 2 January 2023. ML-based methods and workflows used to identify DNA methylation signatures associated with cancer prognosis were extracted and summarized. Two authors independently assessed the methodological quality of included studies by a seven-item checklist adapted from 'A Tool to Assess Risk of Bias and Applicability of Prediction Model Studies (PROBAST)' and from the 'Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK). Different ML methods and workflows used in included studies were summarized and visualized by a sunburst chart, a bubble chart, and Sankey diagrams, respectively. RESULTS Eighty-three studies were included in this review. Three major types of ML-based workflows were identified. 1) unsupervised clustering, 2) supervised feature selection, and 3) deep learning-based feature transformation. For the three workflows, the most frequently used ML techniques were consensus clustering, least absolute shrinkage and selection operator (LASSO), and autoencoder, respectively. The systematic review revealed that the performance of these approaches has not been adequately evaluated yet and that methodological and reporting flaws were common in the identified studies using ML techniques. CONCLUSIONS There is great heterogeneity in ML-based methodological strategies used by epigenome-wide studies to identify DNA methylation markers associated with cancer prognosis. In theory, most existing workflows could not handle the high multi-collinearity and potentially non-linearity interactions in epigenome-wide DNA methylation data. Benchmarking studies are needed to compare the relative performance of various approaches for specific cancer types. Adherence to relevant methodological and reporting guidelines are urgently needed.
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Affiliation(s)
- Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ziwen Fan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elizabeth Alwers
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany; Medical Oncology, National Center of Tumour Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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12
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Khalili-Tanha G, Mohit R, Asadnia A, Khazaei M, Dashtiahangar M, Maftooh M, Nassiri M, Hassanian SM, Ghayour-Mobarhan M, Kiani MA, Ferns GA, Batra J, Nazari E, Avan A. Identification of ZMYND19 as a novel biomarker of colorectal cancer: RNA-sequencing and machine learning analysis. J Cell Commun Signal 2023:10.1007/s12079-023-00779-2. [PMID: 37428302 DOI: 10.1007/s12079-023-00779-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 05/29/2023] [Indexed: 07/11/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cause of cancer-related deaths. The five-year relative survival rate for CRC is estimated to be approximately 90% for patients diagnosed with early stages and 14% for those diagnosed at an advanced stages of disease, respectively. Hence, the development of accurate prognostic markers is required. Bioinformatics enables the identification of dysregulated pathways and novel biomarkers. RNA expression profiling was performed in CRC patients from the TCGA database using a Machine Learning approach to identify differential expression genes (DEGs). Survival curves were assessed using Kaplan-Meier analysis to identify prognostic biomarkers. Furthermore, the molecular pathways, protein-protein interaction, the co-expression of DEGs, and the correlation between DEGs and clinical data have been evaluated. The diagnostic markers were then determined based on machine learning analysis. The results indicated that key upregulated genes are associated with the RNA processing and heterocycle metabolic process, including C10orf2, NOP2, DKC1, BYSL, RRP12, PUS7, MTHFD1L, and PPAT. Furthermore, the survival analysis identified NOP58, OSBPL3, DNAJC2, and ZMYND19 as prognostic markers. The combineROC curve analysis indicated that the combination of C10orf2 -PPAT- ZMYND19 can be considered as diagnostic markers with sensitivity, specificity, and AUC values of 0.98, 1.00, and 0.99, respectively. Eventually, ZMYND19 gene was validated in CRC patients. In conclusion, novel biomarkers of CRC have been identified that may be a promising strategy for early diagnosis, potential treatment, and better prognosis.
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Affiliation(s)
- Ghazaleh Khalili-Tanha
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Mohit
- Department of Anesthesia, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Alireza Asadnia
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mina Maftooh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Ghayour-Mobarhan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ali Kiani
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pediatrics, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex, BN1 9PH, UK
| | - Jyotsna Batra
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Elham Nazari
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- College of Medicine, University of Warith Al-Anbiyaa, Karbala, Iraq.
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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13
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Al-Tashi Q, Saad MB, Muneer A, Qureshi R, Mirjalili S, Sheshadri A, Le X, Vokes NI, Zhang J, Wu J. Machine Learning Models for the Identification of Prognostic and Predictive Cancer Biomarkers: A Systematic Review. Int J Mol Sci 2023; 24:7781. [PMID: 37175487 PMCID: PMC10178491 DOI: 10.3390/ijms24097781] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
The identification of biomarkers plays a crucial role in personalized medicine, both in the clinical and research settings. However, the contrast between predictive and prognostic biomarkers can be challenging due to the overlap between the two. A prognostic biomarker predicts the future outcome of cancer, regardless of treatment, and a predictive biomarker predicts the effectiveness of a therapeutic intervention. Misclassifying a prognostic biomarker as predictive (or vice versa) can have serious financial and personal consequences for patients. To address this issue, various statistical and machine learning approaches have been developed. The aim of this study is to present an in-depth analysis of recent advancements, trends, challenges, and future prospects in biomarker identification. A systematic search was conducted using PubMed to identify relevant studies published between 2017 and 2023. The selected studies were analyzed to better understand the concept of biomarker identification, evaluate machine learning methods, assess the level of research activity, and highlight the application of these methods in cancer research and treatment. Furthermore, existing obstacles and concerns are discussed to identify prospective research areas. We believe that this review will serve as a valuable resource for researchers, providing insights into the methods and approaches used in biomarker discovery and identifying future research opportunities.
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Affiliation(s)
- Qasem Al-Tashi
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maliazurina B. Saad
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amgad Muneer
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rizwan Qureshi
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Seyedali Mirjalili
- Centre for Artificial Intelligence Research and Optimization, Torrens University Australia, Fortitude Valley, Brisbane, QLD 4006, Australia
- Yonsei Frontier Lab, Yonsei University, Seoul 03722, Republic of Korea
- University Research and Innovation Center, Obuda University, 1034 Budapest, Hungary
| | - Ajay Sheshadri
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Natalie I. Vokes
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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14
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Grypari IM, Pappa I, Papastergiou T, Zolota V, Bravou V, Melachrinou M, Megalooikonomou V, Tzelepi V. Elucidating the role of PRMTs in prostate cancer using open access databases and a patient cohort dataset. Histol Histopathol 2023; 38:287-302. [PMID: 36082942 DOI: 10.14670/hh-18-513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Protein arginine methylation is an understudied epigenetic mechanism catalyzed by enzymes known as Protein Methyltransferases of Arginine (PRMTs), while the opposite reaction is performed by Jumonji domain- containing protein 6 (JMJD6). There is increasing evidence that PRMTs are deregulated in prostate cancer (PCa). In this study, the expression of two PRMT members, PRMT2 and PRMT7 as well as JMJD6, a demethylase, was analyzed in PCa. Initially, we retrieved data from The Cancer Genome Atlas (TCGA) project and the Gene Expression Omnibus (GEO) database to explore the differential expression of various PRMT family members in patients with PCa and then applied immunohistochemistry in a patient cohort across the spectrum of PCa, including non-neoplastic prostate tissue and lymph node metastatic foci. The results from the TCGA analysis revealed that PRMT7, PRMT6 and PRMT3 expression increased while PRMT2, PRMT9 and JMJD6 levels decreased in the tumor compared to non-neoplastic prostate. Results from the GEO datasets were similar, albeit not identical with the TCGA results, with PRMT7 and PRMT3 being upregulated and PRMT2 and JMJD6 being downregulated in the tumor compared to non-neoplastic tissue in some of them. In addition, PRMT7 levels decreased with stage and grade progression in the TCGA analysis. In the patient cohort, both PRMTs and JMJD6 were overexpressed in PCa compared to non-neoplastic tissue, and nuclear PRMT2 and JMJD6 were upregulated in lymph node metastasis, too. PRMT7 and JMJD6 expression were upregulated with the progression of stage and JMJD6 was also increased with the elevation of grade. After androgen ablation therapy, nuclear expression of PRMT7 and JMJD6 were elevated compared to untreated tumors. PRMT2, PRMT7 and JMD6 were also correlated with markers of EMT and cell cycle regulators. Finally, our findings indicate that PRMTs and JMJD6 are involved in prostate cancer progression and revealed a potential interplay of PRMTs with EMT mediators, underscoring the need for therapeutic targeting of arginine methylation in prostate cancer.
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Affiliation(s)
- Ioanna Maria Grypari
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece
| | - Ioanna Pappa
- Multidimensional Data Analysis and Knowledge Management Laboratory, Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Thomas Papastergiou
- Multidimensional Data Analysis and Knowledge Management Laboratory, Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Vasiliki Zolota
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece
| | - Vasiliki Bravou
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, Patras, Greece
| | - Maria Melachrinou
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece
| | - Vasileios Megalooikonomou
- Multidimensional Data Analysis and Knowledge Management Laboratory, Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Vasiliki Tzelepi
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece.
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15
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Mikaeloff F, Gelpi M, Benfeitas R, Knudsen AD, Vestad B, Høgh J, Hov JR, Benfield T, Murray D, Giske CG, Mardinoglu A, Trøseid M, Nielsen SD, Neogi U. Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection. eLife 2023; 12:82785. [PMID: 36794912 PMCID: PMC10017104 DOI: 10.7554/elife.82785] [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: 08/17/2022] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
Multiomics technologies improve the biological understanding of health status in people living with HIV on antiretroviral therapy (PWH). Still, a systematic and in-depth characterization of metabolic risk profile during successful long-term treatment is lacking. Here, we used multi-omics (plasma lipidomic, metabolomic, and fecal 16 S microbiome) data-driven stratification and characterization to identify the metabolic at-risk profile within PWH. Through network analysis and similarity network fusion (SNF), we identified three groups of PWH (SNF-1-3): healthy (HC)-like (SNF-1), mild at-risk (SNF-3), and severe at-risk (SNF-2). The PWH in the SNF-2 (45%) had a severe at-risk metabolic profile with increased visceral adipose tissue, BMI, higher incidence of metabolic syndrome (MetS), and increased di- and triglycerides despite having higher CD4+ T-cell counts than the other two clusters. However, the HC-like and the severe at-risk group had a similar metabolic profile differing from HIV-negative controls (HNC), with dysregulation of amino acid metabolism. At the microbiome profile, the HC-like group had a lower α-diversity, a lower proportion of men having sex with men (MSM) and was enriched in Bacteroides. In contrast, in at-risk groups, there was an increase in Prevotella, with a high proportion of MSM, which could potentially lead to higher systemic inflammation and increased cardiometabolic risk profile. The multi-omics integrative analysis also revealed a complex microbial interplay of the microbiome-associated metabolites in PWH. Those severely at-risk clusters may benefit from personalized medicine and lifestyle intervention to improve their dysregulated metabolic traits, aiming to achieve healthier aging.
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Affiliation(s)
- Flora Mikaeloff
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstituteStockholmSweden
| | - Marco Gelpi
- Copenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | | | - Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Norwegian PSC Research Center, Oslo University Hospital RikshospitaletOsloNorway
| | - Julie Høgh
- Copenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - Johannes R Hov
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Norwegian PSC Research Center, Oslo University Hospital RikshospitaletOsloNorway
- Institute of Clinical Medicine, University of OsloOsloNorway
| | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital – Amager and HvidovreHvidovreDenmark
| | - Daniel Murray
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of CopenhagenCopenhagenDenmark
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstitutetStockholmSweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of TechnologyStockholmSweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College LondonLondonUnited Kingdom
| | - Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital RikshospitaletOsloNorway
- Institute of Clinical MedicineOsloNorway
| | | | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska InstituteStockholmSweden
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16
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Liu C, Duan Y, Zhou Q, Wang Y, Gao Y, Kan H, Hu J. A classification method of gastric cancer subtype based on residual graph convolution network. Front Genet 2023; 13:1090394. [PMID: 36685956 PMCID: PMC9845413 DOI: 10.3389/fgene.2022.1090394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Clinical diagnosis and treatment of tumors are greatly complicated by their heterogeneity, and the subtype classification of cancer frequently plays a significant role in the subsequent treatment of tumors. Presently, the majority of studies rely far too heavily on gene expression data, omitting the enormous power of multi-omics fusion data and the potential for patient similarities. Method: In this study, we created a gastric cancer subtype classification model called RRGCN based on residual graph convolutional network (GCN) using multi-omics fusion data and patient similarity network. Given the multi-omics data's high dimensionality, we built an artificial neural network Autoencoder (AE) to reduce the dimensionality of the data and extract hidden layer features. The model is then built using the feature data. In addition, we computed the correlation between patients using the Pearson correlation coefficient, and this relationship between patients forms the edge of the graph structure. Four graph convolutional network layers and two residual networks with skip connections make up RRGCN, which reduces the amount of information lost during transmission between layers and prevents model degradation. Results: The results show that RRGCN significantly outperforms other classification methods with an accuracy as high as 0.87 when compared to four other traditional machine learning methods and deep learning models. Conclusion: In terms of subtype classification, RRGCN excels in all areas and has the potential to offer fresh perspectives on disease mechanisms and disease progression. It has the potential to be used for a broader range of disorders and to aid in clinical diagnosis.
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Affiliation(s)
- Can Liu
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China,Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, Anhui, China
| | - Yuchen Duan
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Qingqing Zhou
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yongkang Wang
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China,Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, Anhui, China
| | - Yong Gao
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China,Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, Anhui, China
| | - Hongxing Kan
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China,Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, Anhui, China
| | - Jili Hu
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui, China,Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, Anhui, China,*Correspondence: Jili Hu,
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17
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The Potential of MicroRNAs as Non-Invasive Prostate Cancer Biomarkers: A Systematic Literature Review Based on a Machine Learning Approach. Cancers (Basel) 2022; 14:cancers14215418. [PMID: 36358836 PMCID: PMC9657574 DOI: 10.3390/cancers14215418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is the most common cancer in men worldwide. Screening and diagnosis are based on prostate-specific antigen (PSA) blood testing and digital rectal examination. Nevertheless, these methods are not specific and have a high risk of mistaken results. This has led to overtreatment and unnecessary radical therapy; thus, better prognostic tools are urgently needed. In this view, microRNAs (miRs) appear as potential non-invasive biomarkers for PCa diagnosis, prognosis, and therapy. As the scientific literature available in this field is huge and very often controversial, we identified and discussed three topics that characterize the investigated research area by combining the big data from the literature together with a novel machine learning approach. By analyzing the papers clustered into these topics we have offered a deeper understanding of the current research, which helps to contribute to the advancement of this research field. Abstract Background: Prostate cancer (PCa) is the second leading cause of cancer-related deaths in men. Although the prostate-specific antigen (PSA) test is used in clinical practice for screening and/or early detection of PCa, it is not specific, thus resulting in high false-positive rates. MicroRNAs (miRs) provide an opportunity as biomarkers for diagnosis, prognosis, and recurrence of PCa. Because the size of the literature on it is increasing and often controversial, this study aims to consolidate the state-of-art of relevant published research. Methods: A Systematic Literature Review (SLR) approach was applied to analyze a set of 213 scientific publications through a text mining method that makes use of the Latent Dirichlet Allocation (LDA) algorithm. Results and Conclusions: The result of this activity, performed through the MySLR digital platform, allowed us to identify a set of three relevant topics characterizing the investigated research area. We analyzed and discussed all the papers clustered into them. We highlighted that several miRs are associated with PCa progression, and that their detection in patients’ urine seems to be the more reliable and promising non-invasive tool for PCa diagnosis. Finally, we proposed some future research directions to help future scientists advance the field further.
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18
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Chen S, Zang Y, Xu B, Lu B, Ma R, Miao P, Chen B. An Unsupervised Deep Learning-Based Model Using Multiomics Data to Predict Prognosis of Patients with Stomach Adenocarcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5844846. [PMID: 36339684 PMCID: PMC9633210 DOI: 10.1155/2022/5844846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/25/2022] [Accepted: 10/08/2022] [Indexed: 09/08/2023]
Abstract
METHODS Patients (363 in total) with stomach adenocarcinoma from The Cancer Genome Atlas (TCGA) cohort were included. An autoencoder was constructed to integrate the RNA sequencing, miRNA sequencing, and methylation data. The features of the bottleneck layer were used to perform the k-means clustering algorithm to obtain different subgroups for evaluating the prognosis-related risk of stomach adenocarcinoma. The model's robustness was verified using a 10-fold cross-validation (CV). Survival was analyzed by the Kaplan-Meier method. Univariate and multivariate Cox regression was used to estimate hazard risk. The model was validated in three independent cohorts with different endpoints. RESULTS The patients were divided into low-risk and high-risk groups according to the k-means clustering algorithm. The high-risk group had a significantly higher risk of poor survival (log-rank P value = 2.80e - 06; adjusted hazard ratio = 2.386, 95% confidence interval: 1.607~3.543), a concordance index (C-index) of 0.714, and a Brier score of 0.184. The model performed well both in the 10-fold CV procedure and three independent cohorts from the Gene Expression Omnibus (GEO) repository. CONCLUSIONS A robust and generalizable model based on the autoencoder was proposed to integrate multiomics data and predict the prognosis of patients with stomach adenocarcinoma. The model demonstrates better performance than two alternative approaches on prognosis prediction. The results might provide the grounds for further exploring the potential biomarkers to predict the prognosis of patients with stomach adenocarcinoma.
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Affiliation(s)
- Sizhen Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yiteng Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Biyun Xu
- Department of Biostatistics, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Beier Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Rongji Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Pengcheng Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Bingwei Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
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19
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Li D, Hu J, Zhang L, Li L, Yin Q, Shi J, Guo H, Zhang Y, Zhuang P. Deep learning and machine intelligence: New computational modeling techniques for discovery of the combination rules and pharmacodynamic characteristics of Traditional Chinese Medicine. Eur J Pharmacol 2022; 933:175260. [PMID: 36116517 DOI: 10.1016/j.ejphar.2022.175260] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022]
Abstract
It has been increasingly accepted that Multi-Ingredient-Based interventions provide advantages over single-target therapy for complex diseases. With the growing development of Traditional Chinese Medicine (TCM) and continually being refined of a holistic view, "multi-target" and "multi-pathway" integration characteristics of which are being accepted. However, its effector substances, efficacy targets, especially the combination rules and mechanisms remain unclear, and more powerful strategies to interpret the synergy are urgently needed. Artificial intelligence (AI) and computer vision lead to a rapidly expanding in many fields, including diagnosis and treatment of TCM. AI technology significantly improves the reliability and accuracy of diagnostics, target screening, and new drug research. While all AI techniques are capable of matching models to biological big data, the specific methods are complex and varied. Retrieves literature by the keywords such as "artificial intelligence", "machine learning", "deep learning", "traditional Chinese medicine" and "Chinese medicine". Search the application of computer algorithms of TCM between 2000 and 2021 in PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), Elsevier and Springer. This review concentrates on the application of computational in herb quality evaluation, drug target discovery, optimized compatibility and medical diagnoses of TCM. We describe the characteristics of biological data for which different AI techniques are applicable, and discuss some of the best data mining methods and the problems faced by deep learning and machine learning methods applied to Chinese medicine.
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Affiliation(s)
- Dongna Li
- State Key Laboratory of Component-based Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jing Hu
- State Key Laboratory of Component-based Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Lin Zhang
- State Key Laboratory of Component-based Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Lili Li
- State Key Laboratory of Component-based Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Qingsheng Yin
- State Key Laboratory of Component-based Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jiangwei Shi
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China; National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, China
| | - Hong Guo
- State Key Laboratory of Component-based Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yanjun Zhang
- State Key Laboratory of Component-based Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China; National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, China.
| | - Pengwei Zhuang
- State Key Laboratory of Component-based Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
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20
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Gholami N, Haghparast A, Alipourfard I, Nazari M. Prostate cancer in omics era. Cancer Cell Int 2022; 22:274. [PMID: 36064406 PMCID: PMC9442907 DOI: 10.1186/s12935-022-02691-y] [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: 05/25/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
Recent advances in omics technology have prompted extraordinary attempts to define the molecular changes underlying the onset and progression of a variety of complex human diseases, including cancer. Since the advent of sequencing technology, cancer biology has become increasingly reliant on the generation and integration of data generated at these levels. The availability of multi-omic data has transformed medicine and biology by enabling integrated systems-level approaches. Multivariate signatures are expected to play a role in cancer detection, screening, patient classification, assessment of treatment response, and biomarker identification. This review reports current findings and highlights a number of studies that are both novel and groundbreaking in their application of multi Omics to prostate cancer.
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Affiliation(s)
- Nasrin Gholami
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Iraj Alipourfard
- Institutitue of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Majid Nazari
- Department of Medical Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
- , P.O. Box 14155-6117, Shiraz, Iran.
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21
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Wang K, Chen P, Feng B, Tu J, Hu Z, Zhang M, Yang J, Zhan Y, Yao J, Xu D. Machine learning prediction of prostate cancer from transrectal ultrasound video clips. Front Oncol 2022; 12:948662. [PMID: 36091110 PMCID: PMC9459141 DOI: 10.3389/fonc.2022.948662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/08/2022] [Indexed: 11/14/2022] Open
Abstract
Objective To build a machine learning (ML) prediction model for prostate cancer (PCa) from transrectal ultrasound video clips of the whole prostate gland, diagnostic performance was compared with magnetic resonance imaging (MRI). Methods We systematically collated data from 501 patients—276 with prostate cancer and 225 with benign lesions. From a final selection of 231 patients (118 with prostate cancer and 113 with benign lesions), we randomly chose 170 for the purpose of training and validating a machine learning model, while using the remaining 61 to test a derived model. We extracted 851 features from ultrasound video clips. After dimensionality reduction with the least absolute shrinkage and selection operator (LASSO) regression, 14 features were finally selected and the support vector machine (SVM) and random forest (RF) algorithms were used to establish radiomics models based on those features. In addition, we creatively proposed a machine learning models aided diagnosis algorithm (MLAD) composed of SVM, RF, and radiologists’ diagnosis based on MRI to evaluate the performance of ML models in computer-aided diagnosis (CAD). We evaluated the area under the curve (AUC) as well as the sensitivity, specificity, and precision of the ML models and radiologists’ diagnosis based on MRI by employing receiver operator characteristic curve (ROC) analysis. Results The AUC, sensitivity, specificity, and precision of the SVM in the diagnosis of PCa in the validation set and the test set were 0.78, 63%, 80%; 0.75, 65%, and 67%, respectively. Additionally, the SVM model was found to be superior to senior radiologists’ (SR, more than 10 years of experience) diagnosis based on MRI (AUC, 0.78 vs. 0.75 in the validation set and 0.75 vs. 0.72 in the test set), and the difference was statistically significant (p< 0.05). Conclusion The prediction model constructed by the ML algorithm has good diagnostic efficiency for prostate cancer. The SVM model’s diagnostic efficiency is superior to that of MRI, as it has a more focused application value. Overall, these prediction models can aid radiologists in making better diagnoses.
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Affiliation(s)
- Kai Wang
- Department of Ultrasound, The Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, China
| | - Peizhe Chen
- College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Bojian Feng
- Department of Ultrasound, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Jing Tu
- Department of Ultrasound, The Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, China
| | - Zhengbiao Hu
- Department of Ultrasound, The Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, China
| | - Maoliang Zhang
- Department of Ultrasound, The Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, China
| | - Jie Yang
- Department of Ultrasound, The Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, China
| | - Ying Zhan
- Department of Ultrasound, The Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, China
| | - Jincao Yao
- Department of Ultrasound, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, China
- *Correspondence: Dong Xu, ; Jincao Yao,
| | - Dong Xu
- Department of Ultrasound, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, China
- Zhejiang Provincial Research Center for Cancer Intelligent Diagnosis and Molecular Technology, Hangzhou, China
- *Correspondence: Dong Xu, ; Jincao Yao,
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22
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Mizuno K, Beltran H. Future directions for precision oncology in prostate cancer. Prostate 2022; 82 Suppl 1:S86-S96. [PMID: 35657153 PMCID: PMC9942493 DOI: 10.1002/pros.24354] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 11/06/2022]
Abstract
Clinical genomic testing is becoming routine in prostate cancer, as biomarker-driven therapies such as poly-ADP ribose polymerase (PARP) inhibitors and anti-PD1 immunotherapy are now approved for select men with castration-resistant prostate cancer harboring alterations in DNA repair genes. Challenges for precision medicine in prostate cancer include an overall low prevalence of actionable genomic alterations and a still limited understanding of the impact of tumor heterogeneity and co-occurring alterations on treatment response and outcomes across diverse patient populations. Expanded tissue-based technologies such as whole-genome sequencing, transcriptome analysis, epigenetic analysis, and single-cell RNA sequencing have not yet entered the clinical realm and could potentially improve upon our understanding of how molecular features of tumors, intratumoral heterogeneity, and the tumor microenvironment impact therapy response and resistance. Blood-based technologies including cell-free DNA, circulating tumor cells (CTCs), and extracellular vesicles (EVs) are less invasive molecular profiling resources that could also help capture intraindividual tumor heterogeneity and track dynamic changes that occur in the context of specific therapies. Furthermore, molecular imaging is an important biomarker tool within the framework of prostate cancer precision medicine with a capability to detect heterogeneity across metastases and potential therapeutic targets less invasively. Here, we review recent technological advances that may help promote the future implementation and value of precision oncology testing for patients with advanced prostate cancer.
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Affiliation(s)
- Kei Mizuno
- Department of Medical Oncology, Dana Farber Cancer Institute
| | - Himisha Beltran
- Department of Medical Oncology, Dana Farber Cancer Institute
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23
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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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Feng Y, Cheng Z, Wei X, Chen M, Zhang J, Zhang Y, Xue L, Chen M, Li F, Shang Y, Liang T, Ding Y, Wu Q. Novel method for rapid identification of Listeria monocytogenes based on metabolomics and deep learning. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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25
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Arjmand B, Hamidpour SK, Tayanloo-Beik A, Goodarzi P, Aghayan HR, Adibi H, Larijani B. Machine Learning: A New Prospect in Multi-Omics Data Analysis of Cancer. Front Genet 2022; 13:824451. [PMID: 35154283 PMCID: PMC8829119 DOI: 10.3389/fgene.2022.824451] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer is defined as a large group of diseases that is associated with abnormal cell growth, uncontrollable cell division, and may tend to impinge on other tissues of the body by different mechanisms through metastasis. What makes cancer so important is that the cancer incidence rate is growing worldwide which can have major health, economic, and even social impacts on both patients and the governments. Thereby, the early cancer prognosis, diagnosis, and treatment can play a crucial role at the front line of combating cancer. The onset and progression of cancer can occur under the influence of complicated mechanisms and some alterations in the level of genome, proteome, transcriptome, metabolome etc. Consequently, the advent of omics science and its broad research branches (such as genomics, proteomics, transcriptomics, metabolomics, and so forth) as revolutionary biological approaches have opened new doors to the comprehensive perception of the cancer landscape. Due to the complexities of the formation and development of cancer, the study of mechanisms underlying cancer has gone beyond just one field of the omics arena. Therefore, making a connection between the resultant data from different branches of omics science and examining them in a multi-omics field can pave the way for facilitating the discovery of novel prognostic, diagnostic, and therapeutic approaches. As the volume and complexity of data from the omics studies in cancer are increasing dramatically, the use of leading-edge technologies such as machine learning can have a promising role in the assessments of cancer research resultant data. Machine learning is categorized as a subset of artificial intelligence which aims to data parsing, classification, and data pattern identification by applying statistical methods and algorithms. This acquired knowledge subsequently allows computers to learn and improve accurate predictions through experiences from data processing. In this context, the application of machine learning, as a novel computational technology offers new opportunities for achieving in-depth knowledge of cancer by analysis of resultant data from multi-omics studies. Therefore, it can be concluded that the use of artificial intelligence technologies such as machine learning can have revolutionary roles in the fight against cancer.
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Affiliation(s)
- Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Babak Arjmand, ; Bagher Larijani,
| | - Shayesteh Kokabi Hamidpour
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Goodarzi
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Aghayan
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Adibi
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Babak Arjmand, ; Bagher Larijani,
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