1
|
Jopek MA, Pastuszak K, Sieczczyński M, Cygert S, Żaczek AJ, Rondina MT, Supernat A. Improving platelet-RNA-based diagnostics: a comparative analysis of machine learning models for cancer detection and multiclass classification. Mol Oncol 2024. [PMID: 38887841 DOI: 10.1002/1878-0261.13689] [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: 12/29/2023] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Liquid biopsy demonstrates excellent potential in patient management by providing a minimally invasive and cost-effective approach to detecting and monitoring cancer, even at its early stages. Due to the complexity of liquid biopsy data, machine-learning techniques are increasingly gaining attention in sample analysis, especially for multidimensional data such as RNA expression profiles. Yet, there is no agreement in the community on which methods are the most effective or how to process the data. To circumvent this, we performed a large-scale study using various machine-learning techniques. First, we took a closer look at existing datasets and filtered out some patients to assert data collection quality. The final data collection included platelet RNA samples acquired from 1397 cancer patients (17 types of cancer) and 354 asymptomatic, presumed healthy, donors. Then, we assessed an array of different machine-learning models and techniques (e.g., feature selection of RNA transcripts) in pan-cancer detection and multiclass classification. Our results show that simple logistic regression performs the best, reaching a 68% cancer detection rate at a 99% specificity level, and multiclass classification accuracy of 79.38% when distinguishing between five cancer types. In summary, by revisiting classical machine-learning models, we have exceeded the previously used method by 5% and 9.65% in cancer detection and multiclass classification, respectively. To ease further research, we open-source our code and data processing pipelines (https://gitlab.com/jopekmaksym/improving-platelet-rna-based-diagnostics), which we hope will serve the community as a strong baseline.
Collapse
Affiliation(s)
- Maksym A Jopek
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Poland
- Centre of Biostatistics and Bioinformatics, Medical University of Gdańsk, Poland
| | - Krzysztof Pastuszak
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Poland
- Centre of Biostatistics and Bioinformatics, Medical University of Gdańsk, Poland
- Department of Algorithms and Systems Modelling, Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Poland
| | - Michał Sieczczyński
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Poland
- Centre of Biostatistics and Bioinformatics, Medical University of Gdańsk, Poland
| | - Sebastian Cygert
- Department of Multimedia Systems, Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Poland
- Ideas, NCBR, Warsaw, Poland
| | - Anna J Żaczek
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Poland
| | - Matthew T Rondina
- Molecular Medicine Program, University of Utah, Salt Lake City, UT, USA
- George E. Wahlen Veterans Affairs Medical Center Department of Internal Medicine and the Geriatric Research Education and Clinical Center (GRECC), Salt Lake City, UT, USA
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- Division of General Internal Medicine, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Anna Supernat
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Poland
- Centre of Biostatistics and Bioinformatics, Medical University of Gdańsk, Poland
| |
Collapse
|
2
|
Urabe F, Tamura T, Sakamoto S, Kimura T, Ochiya T. Extracellular vesicles as novel uro-oncology biomarkers: insights toward clinical applications. Curr Opin Urol 2024:00042307-990000000-00162. [PMID: 38835180 DOI: 10.1097/mou.0000000000001194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
PURPOSE OF REVIEW We discussed the challenges associated with the clinical application of extracellular vesicles and summarized their potential impact on oncological clinical practice in urology. RECENT FINDINGS Despite extensive research on extracellular vesicles, their clinical applications remain limited; this is likely to be because of small study cohorts, a lack of large-scale analyses, and the impact of variable extraction and storage methods on analysis outcomes. However, promising results have emerged from clinical trials targeting urinary extracellular vesicles in prostate cancer using ExoDx Prostate Test. The ExoDx Prostate Test has demonstrated its efficacy in diagnosing prostate cancer in previous studies and is the only FDA-approved kit for this purpose. Moreover, recent trials have investigated the use of the ExoDx Prostate Test to determine the optimal timing for biopsies in prostate cancer patients undergoing active surveillance. SUMMARY We summarized recent studies on the potential of extracellular vesicles in the management of urological cancers. Particularly, the diagnosis of prostate cancer using the ExoDx Prostate Test has yielded positive results in several clinical trials. Additionally, while there are other studies suggesting its efficacy, most of these are based on retrospective analyses. These findings warrant further large-scale studies to optimize extracellular vesicle-based diagnostic and monitoring strategies. Although further research is required, extracellular vesicles would be attractive for early detection and surveillance.
Collapse
Affiliation(s)
- Fumihiko Urabe
- Department of Urology, The Jikei University School of Medicine, Tokyo
| | - Takaaki Tamura
- Department of Urology, Chiba University, Chiba
- Department of Molecular and Cellular Medicine, Tokyo Medical University, Tokyo, Japan
| | | | - Takahiro Kimura
- Department of Urology, The Jikei University School of Medicine, Tokyo
| | - Takahiro Ochiya
- Department of Molecular and Cellular Medicine, Tokyo Medical University, Tokyo, Japan
| |
Collapse
|
3
|
Liu Q, Li S. Exosomal circRNAs: Novel biomarkers and therapeutic targets for urinary tumors. Cancer Lett 2024; 588:216759. [PMID: 38417667 DOI: 10.1016/j.canlet.2024.216759] [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: 11/06/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Exosomal circRNAs have emerged as promising biomarkers and therapeutic targets for urinary tumors. In this review, we explored the intricate role of exosomal circRNAs in urological cancers, focusing on their biological functions, dysregulation in tumors, and potential clinical applications. The review delves into the mechanisms by which exosomal circRNAs contribute to tumor progression and highlights their diagnostic and therapeutic implications. By synthesizing current research findings, we present a compelling case for the significance of exosomal circRNAs in the context of urinary tumors. Furthermore, the review discusses the challenges and opportunities associated with utilizing exosomal circRNAs as diagnostic tools and targeted therapeutic agents. There is a need for further research to elucidate the specific mechanisms of exosomal circRNA secretion and delivery, as well as to enhance the detection methods for clinical translational applications. Overall, this comprehensive review underscores the pivotal role of exosomal circRNAs in urinary tumors and underscores their potential as valuable biomarkers and therapeutic tools in the management of urological cancers.
Collapse
Affiliation(s)
- Qiang Liu
- Department of Urology, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital and Institute, Shenyang, 110042, Liaoning, China
| | - Shenglong Li
- Second Ward of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, 110042, China; The Liaoning Provincial Key Laboratory of Interdisciplinary Research on Gastrointestinal Tumor Combining Medicine with Engineering, Shenyang, Liaoning Province, 110042, China.
| |
Collapse
|
4
|
Giunta EF, Malapelle U, Russo A, De Giorgi U. Blood-based liquid biopsy in advanced prostate cancer. Crit Rev Oncol Hematol 2024; 194:104241. [PMID: 38122919 DOI: 10.1016/j.critrevonc.2023.104241] [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: 08/16/2023] [Revised: 11/25/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Prostate cancer is characterized by several genetic alterations which could impact prognosis and therapeutic decisions in the advanced disease. Tissue biopsy is still considered the gold standard approach for molecular characterization in prostate cancer, but it has several limitations, including the possibility of insufficient/inadequate tumor tissue to be analyzed. Blood-based liquid biopsy is a non-invasive method to investigate tumor cell derivatives in the bloodstream, being a valid alternative to tissue biopsy for molecular characterization but also for predictive and/or prognostic purposes. In this review, we analyze the most relevant evidence in this field, focusing on clinically relevant targets such as HRD genetic alterations and also focusing on the differences between tissue and liquid biopsy in light of the data from the latest clinical trials.
Collapse
Affiliation(s)
- Emilio Francesco Giunta
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, FC, Italy.
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Ugo De Giorgi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, FC, Italy
| |
Collapse
|
5
|
Chen TY, Mihalopoulos M, Zuluaga L, Rich J, Ganta T, Mehrazin R, Tsao CK, Tewari A, Gonzalez-Kozlova E, Badani K, Dogra N, Kyprianou N. Clinical Significance of Extracellular Vesicles in Prostate and Renal Cancer. Int J Mol Sci 2023; 24:14713. [PMID: 37834162 PMCID: PMC10573190 DOI: 10.3390/ijms241914713] [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: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 10/15/2023] Open
Abstract
Extracellular vesicles (EVs)-including apoptotic bodies, microvesicles, and exosomes-are released by almost all cell types and contain molecular footprints from their cell of origin, including lipids, proteins, metabolites, RNA, and DNA. They have been successfully isolated from blood, urine, semen, and other body fluids. In this review, we discuss the current understanding of the predictive value of EVs in prostate and renal cancer. We also describe the findings supporting the use of EVs from liquid biopsies in stratifying high-risk prostate/kidney cancer and advanced disease, such as castration-resistant (CRPC) and neuroendocrine prostate cancer (NEPC) as well as metastatic renal cell carcinoma (RCC). Assays based on EVs isolated from urine and blood have the potential to serve as highly sensitive diagnostic studies as well as predictive measures of tumor recurrence in patients with prostate and renal cancers. Overall, we discuss the biogenesis, isolation, liquid-biopsy, and therapeutic applications of EVs in CRPC, NEPC, and RCC.
Collapse
Affiliation(s)
- Tzu-Yi Chen
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Meredith Mihalopoulos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Laura Zuluaga
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Jordan Rich
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Teja Ganta
- Department of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.G.); (C.-K.T.)
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Che-Kai Tsao
- Department of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.G.); (C.-K.T.)
| | - Ash Tewari
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Ketan Badani
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Navneet Dogra
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Natasha Kyprianou
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
- The Tisch Cancer Institute, Mount Sinai Health, New York, NY 10029, USA
| |
Collapse
|
6
|
Letter to the editor re: "assessing bladder cancer prognosis through circulating tumor cell analysis and Ki-67 measurement". Int Urol Nephrol 2023:10.1007/s11255-023-03538-9. [PMID: 36869198 DOI: 10.1007/s11255-023-03538-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023]
|