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Marin LE, Zavaleta-Guzman DI, Gutierrez-Garcia JI, Racoceanu D, Casado FL. Prediction of biochemical prostate cancer recurrence from any Gleason score using robust tissue structure and clinically available information. Discov Oncol 2025; 16:128. [PMID: 39918772 PMCID: PMC11805747 DOI: 10.1007/s12672-025-01896-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 02/03/2025] [Indexed: 02/09/2025] Open
Abstract
Biopsy information and protein Prostate-Specific Antigen (PSA) levels are the most robust information available to oncologists worldwide to diagnose and decide therapies for prostate cancer patients. However, prostate cancer presents a high risk of recurrence, and the technologies used to evaluate it demand more complex resources. This paper aims to predict Biochemical Recurrence (BCR) based on Whole Slide Images (WSI) of biopsies, Gleason scores, and PSA levels. A U-net model was used to segment phenotypic features and trained on images from the Prostate Cancer Grade Assessment (PANDA) database to segment tumorous regions from pre-processed and scored WSI of biopsies. Then, the model was tested on data from publicly available repositories achieving an Intersection over Union of 87%. Tissue features, Gleason scores, and PSA levels provided high accuracy and precision in classifying patients according to their risk of presenting recurrence, for any Gleason score sampled. The trained classifier model demonstrated a 79.2% relative accuracy, and a precision of 69.7% for patients experiencing recurrences before 24 months. Our results provide a robust, cost-efficient approach using already available information to predict the risk of BCR.
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Affiliation(s)
- Laura E Marin
- Institute of Omics Sciences and Applied Biotechnology, Pontificia Universidad Catolica del Peru, Lima, Peru
| | - Daniel I Zavaleta-Guzman
- Institute of Omics Sciences and Applied Biotechnology, Pontificia Universidad Catolica del Peru, Lima, Peru
| | - Jessyca I Gutierrez-Garcia
- Institute of Omics Sciences and Applied Biotechnology, Pontificia Universidad Catolica del Peru, Lima, Peru
| | - Daniel Racoceanu
- Sorbonne University, Paris Brain Institute, CNRS, Inria, Inserm, AP-HP, Paris, France
| | - Fanny L Casado
- Institute of Omics Sciences and Applied Biotechnology, Pontificia Universidad Catolica del Peru, Lima, Peru.
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Hachem S, Yehya A, El Masri J, Mavingire N, Johnson JR, Dwead AM, Kattour N, Bouchi Y, Kobeissy F, Rais-Bahrami S, Mechref Y, Abou-Kheir W, Woods-Burnham L. Contemporary Update on Clinical and Experimental Prostate Cancer Biomarkers: A Multi-Omics-Focused Approach to Detection and Risk Stratification. BIOLOGY 2024; 13:762. [PMID: 39452071 PMCID: PMC11504278 DOI: 10.3390/biology13100762] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/11/2024] [Accepted: 09/20/2024] [Indexed: 10/26/2024]
Abstract
Prostate cancer remains a significant health challenge, being the most prevalent non-cutaneous cancer in men worldwide. This review discusses the critical advancements in biomarker discovery using single-omics and multi-omics approaches. Multi-omics, integrating genomic, transcriptomic, proteomic, metabolomic, and epigenomic data, offers a comprehensive understanding of the molecular heterogeneity of prostate cancer, leading to the identification of novel biomarkers and therapeutic targets. This holistic approach not only enhances the specificity and sensitivity of prostate cancer detection but also supports the development of personalized treatment strategies. Key studies highlighted include the identification of novel genes, genetic mutations, peptides, metabolites, and potential biomarkers through multi-omics analyses, which have shown promise in improving prostate cancer management. The integration of multi-omics in clinical practice can potentially revolutionize prostate cancer prognosis and treatment, paving the way for precision medicine. This review underscores the importance of continued research and the application of multi-omics to overcome current challenges in prostate cancer diagnosis and therapy.
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Affiliation(s)
- Sana Hachem
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Amani Yehya
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Jad El Masri
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Nicole Mavingire
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA 30310, USA; (N.M.)
| | - Jabril R. Johnson
- Department of Microbiology, Biochemistry, & Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA;
| | - Abdulrahman M. Dwead
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA 30310, USA; (N.M.)
| | - Naim Kattour
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Yazan Bouchi
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Firas Kobeissy
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Soroush Rais-Bahrami
- Department of Urology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Radiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- O’Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology, and Physiological Sciences, American University of Beirut, Beirut 1107-2020, Lebanon (A.Y.)
| | - Leanne Woods-Burnham
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA 30310, USA; (N.M.)
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Katifelis H, Gazouli M. RNA biomarkers in cancer therapeutics: The promise of personalized oncology. Adv Clin Chem 2024; 123:179-219. [PMID: 39181622 DOI: 10.1016/bs.acc.2024.06.003] [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] [Indexed: 08/27/2024]
Abstract
Cancer therapy is a rapidly evolving and constantly expanding field. Current approaches include surgery, conventional chemotherapy and novel biologic agents as in immunotherapy, that together compose a wide armamentarium. The plethora of choices can, however, be clinically challenging in prescribing the most suitable treatment for any given patient. Fortunately, biomarkers can greatly facilitate the most appropriate selection. In recent years, RNA-based biomarkers have proven most promising. These molecules that range from small noncoding RNAs to protein coding gene transcripts can be valuable in cancer management and especially in cancer therapeutics. Compared to their DNA counterparts which are stable throughout treatment, RNA-biomarkers are dynamic. This allows prediction of success prior to treatment start and can identify alterations in expression that could reflect response. Moreover, improved nucleic acid technology allows RNA to be extracted from practically every biofluid/matrix and evaluated with exceedingly high analytic sensitivity. In addition, samples are largely obtained by minimally invasive procedures and as such can be used serially to assess treatment response real-time. This chapter provides the reader insight on currently known RNA biomarkers, the latest research employing Artificial Intelligence in the identification of such molecules and in clinical decisions driving forward the era of personalized oncology.
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Affiliation(s)
- Hector Katifelis
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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Bounoua N, Cetinkaya A, Piskin E, Kaya SI, Ozkan SA. The sensor applications for prostate and lung cancer biomarkers in terms of electrochemical analysis. Anal Bioanal Chem 2024; 416:2277-2300. [PMID: 38279011 DOI: 10.1007/s00216-024-05134-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/24/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
Prostate and lung cancers are the most common types of cancer and affect a large part of the population around the world, causing deaths. Therefore, the rapid identification of cancer can profoundly impact reducing cancer-related death rates and protecting human lives. Significant resources have been dedicated to investigating new methods for early disease detection. Cancer biomarkers encompass various biochemical entities, including nucleic acids, proteins, sugars, small metabolites, cytogenetic and cytokinetic parameters, and whole tumor cells in bodily fluids. These tools can be utilized for various purposes, such as risk assessment, diagnosis, prognosis, treatment efficacy, toxicity evaluation, and predicting a return. Due to these versatile and critical purposes, there are widespread studies on the development of new, sensitive, and selective approaches for the determination of cancer biomarkers. This review illustrates the significant lung and prostate cancer biomarkers and their determination utilizing electrochemical sensors, which have the advantage of improved sensitivity, low cost, and simple analysis. Additionally, approaches such as improving sensitivity with nanomaterials and ensuring selectivity with MIPs are used to increase the performance of the sensor. This review aims to overview the most recent electrochemical biosensor applications for determining vital biomarkers of prostate and lung cancers in terms of nanobiosensors and molecularly imprinted polymer (MIP)-based biosensors.
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Affiliation(s)
- Nadia Bounoua
- Department of Exact Sciences, Laboratory of the Innovation Sponsorship and the Emerging Institution for Graduates of Higher Education of Sustainable Development and Dealing with Emerging Conditions, Normal Higher School of Bechar, Bechar, Algeria
- Laboratory of Chemical and Environmental Science (LCSE), 8000, Bechar, Algeria
| | - Ahmet Cetinkaya
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
- Graduate School of Health Sciences, Ankara University, Ankara, Turkey
| | - Ensar Piskin
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
- Graduate School of Health Sciences, Ankara University, Ankara, Turkey
| | - S Irem Kaya
- Department of Analytical Chemistry, Gulhane Faculty of Pharmacy, University of Health Sciences, Ankara, Turkey.
| | - Sibel A Ozkan
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey.
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Berenguer CV, Pereira F, Câmara JS, Pereira JAM. Underlying Features of Prostate Cancer-Statistics, Risk Factors, and Emerging Methods for Its Diagnosis. Curr Oncol 2023; 30:2300-2321. [PMID: 36826139 PMCID: PMC9955741 DOI: 10.3390/curroncol30020178] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023] Open
Abstract
Prostate cancer (PCa) is the most frequently occurring type of malignant tumor and a leading cause of oncological death in men. PCa is very heterogeneous in terms of grade, phenotypes, and genetics, displaying complex features. This tumor often has indolent growth, not compromising the patient's quality of life, while its more aggressive forms can manifest rapid growth with progression to adjacent organs and spread to lymph nodes and bones. Nevertheless, the overtreatment of PCa patients leads to important physical, mental, and economic burdens, which can be avoided with careful monitoring. Early detection, even in the cases of locally advanced and metastatic tumors, provides a higher chance of cure, and patients can thus go through less aggressive treatments with fewer side effects. Furthermore, it is important to offer knowledge about how modifiable risk factors can be an effective method for reducing cancer risk. Innovations in PCa diagnostics and therapy are still required to overcome some of the limitations of the current screening techniques, in terms of specificity and sensitivity. In this context, this review provides a brief overview of PCa statistics, reporting its incidence and mortality rates worldwide, risk factors, and emerging screening strategies.
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Affiliation(s)
- Cristina V. Berenguer
- CQM—Centro de Química da Madeira, NPRG, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
| | - Ferdinando Pereira
- SESARAM—Serviço de Saúde da Região Autónoma da Madeira, EPERAM, Hospital Dr. Nélio Mendonça, Avenida Luís de Camões 6180, 9000-177 Funchal, Portugal
| | - José S. Câmara
- CQM—Centro de Química da Madeira, NPRG, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
- Departamento de Química, Faculdade de Ciências Exatas e Engenharia, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
| | - Jorge A. M. Pereira
- CQM—Centro de Química da Madeira, NPRG, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
- Correspondence:
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