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Mondello A, Dal Bo M, Toffoli G, Polano M. Machine learning in onco-pharmacogenomics: a path to precision medicine with many challenges. Front Pharmacol 2024; 14:1260276. [PMID: 38264526 PMCID: PMC10803549 DOI: 10.3389/fphar.2023.1260276] [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: 07/17/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Over the past two decades, Next-Generation Sequencing (NGS) has revolutionized the approach to cancer research. Applications of NGS include the identification of tumor specific alterations that can influence tumor pathobiology and also impact diagnosis, prognosis and therapeutic options. Pharmacogenomics (PGx) studies the role of inheritance of individual genetic patterns in drug response and has taken advantage of NGS technology as it provides access to high-throughput data that can, however, be difficult to manage. Machine learning (ML) has recently been used in the life sciences to discover hidden patterns from complex NGS data and to solve various PGx problems. In this review, we provide a comprehensive overview of the NGS approaches that can be employed and the different PGx studies implicating the use of NGS data. We also provide an excursus of the ML algorithms that can exert a role as fundamental strategies in the PGx field to improve personalized medicine in cancer.
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Affiliation(s)
| | | | | | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
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Emde-Rajaratnam M, Beck S, Benes V, Salwender H, Bertsch U, Scheid C, Hänel M, Weisel K, Hielscher T, Raab MS, Goldschmidt H, Jauch A, Maes K, De Bruyne E, Menu E, De Veirman K, Moreaux J, Vanderkerken K, Seckinger A, Hose D. RNA-sequencing based first choice of treatment and determination of risk in multiple myeloma. Front Immunol 2023; 14:1286700. [PMID: 38035078 PMCID: PMC10684778 DOI: 10.3389/fimmu.2023.1286700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Background Immunotherapeutic targets in multiple myeloma (MM) have variable expression height and are partly expressed in subfractions of patients only. With increasing numbers of available compounds, strategies for appropriate choice of targets (combinations) are warranted. Simultaneously, risk assessment is advisable as patient's life expectancy varies between months and decades. Methods We first assess feasibility of RNA-sequencing in a multicenter trial (GMMG-MM5, n=604 patients). Next, we use a clinical routine cohort of untreated symptomatic myeloma patients undergoing autologous stem cell transplantation (n=535, median follow-up (FU) 64 months) to perform RNA-sequencing, gene expression profiling (GEP), and iFISH by ten-probe panel on CD138-purified malignant plasma cells. We subsequently compare target expression to plasma cell precursors, MGUS (n=59), asymptomatic (n=142) and relapsed (n=69) myeloma patients, myeloma cell lines (n=26), and between longitudinal samples (MM vs. relapsed MM). Data are validated using the independent MMRF CoMMpass-cohort (n=767, FU 31 months). Results RNA-sequencing is feasible in 90.8% of patients (GMMG-MM5). Actionable immune-oncological targets (n=19) can be divided in those expressed in all normal and >99% of MM-patients (CD38, SLAMF7, BCMA, GPRC5D, FCRH5, TACI, CD74, CD44, CD37, CD79B), those with expression loss in subfractions of MM-patients (BAFF-R [81.3%], CD19 [57.9%], CD20 [82.8%], CD22 [28.4%]), aberrantly expressed in MM (NY-ESO1/2 [12%], MUC1 [12.7%], CD30 [4.9%], mutated BRAF V600E/K [2.1%]), and resistance-conveying target-mutations e.g., against part but not all BCMA-directed treatments. Risk is assessable regarding proliferation, translated GEP- (UAMS70-, SKY92-, RS-score) and de novo (LfM-HRS) defined risk scores. LfM-HRS delineates three groups of 40%, 38%, and 22% of patients with 5-year and 12-year survival rates of 84% (49%), 67% (18%), and 32% (0%). R-ISS and RNA-sequencing identify partially overlapping patient populations, with R-ISS missing, e.g., 30% (22/72) of highly proliferative myeloma. Conclusion RNA-sequencing based assessment of risk and targets for first choice treatment is possible in clinical routine.
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Affiliation(s)
- Martina Emde-Rajaratnam
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
| | - Susanne Beck
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
- Universitätsklinikum Heidelberg, Molekularpathologisches Zentrum, Heidelberg, Germany
| | - Vladimir Benes
- Europäisches Laboratorium für Molekularbiologie, GeneCore, Heidelberg, Germany
| | - Hans Salwender
- Asklepios Tumorzentrum Hamburg, AK Altona and St. Georg, Hamburg, Germany
| | - Uta Bertsch
- Universitätsklinikum Heidelberg, Medizinische Klinik V, Heidelberg, Germany
| | - Christoph Scheid
- Department I of Internal Medicine, University of Cologne, Cologne, Germany
| | - Mathias Hänel
- Department of Internal Medicine III, Klinikum Chemnitz GmbH, Chemnitz, Germany
| | - Katja Weisel
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Hielscher
- Deutsches Krebsforschungszentrum, Abteilung für Biostatistik, Heidelberg, Germany
| | - Marc S. Raab
- Universitätsklinikum Heidelberg, Medizinische Klinik V, Heidelberg, Germany
| | - Hartmut Goldschmidt
- Universitätsklinikum Heidelberg, Medizinische Klinik V, Heidelberg, Germany
- Nationales Centrum für Tumorerkrankungen, Heidelberg, Germany
| | - Anna Jauch
- Universität Heidelberg, Institut für Humangenetik, Heidelberg, Germany
| | - Ken Maes
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
| | - Elke De Bruyne
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
| | - Eline Menu
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
| | - Kim De Veirman
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
| | - Jérôme Moreaux
- Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Karin Vanderkerken
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
| | - Anja Seckinger
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
| | - Dirk Hose
- Department of Hematology and Immunology, Myeloma Center Brussels & Labor für Myelomforschung, Vrije Universiteit Brussel (VUB), Jette, Belgium
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