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Soldatos TG, Kim S, Schmidt S, Lesko LJ, Jackson DB. Advancing drug safety science by integrating molecular knowledge with post-marketing adverse event reports. CPT Pharmacometrics Syst Pharmacol 2022; 11:540-555. [PMID: 35143713 PMCID: PMC9124355 DOI: 10.1002/psp4.12765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 12/15/2022] Open
Abstract
Promising drug development efforts may frequently fail due to unintended adverse reactions. Several methods have been developed to analyze such data, aiming to improve pharmacovigilance and drug safety. In this work, we provide a brief review of key directions to quantitatively analyzing adverse events and explore the potential of augmenting these methods using additional molecular data descriptors. We argue that molecular expansion of adverse event data may provide a path to improving the insights gained through more traditional pharmacovigilance approaches. Examples include the ability to assess statistical relevance with respect to underlying biomolecular mechanisms, the ability to generate plausible causative hypotheses and/or confirmation where possible, the ability to computationally study potential clinical trial designs and/or results, as well as the further provision of advanced features incorporated in innovative methods, such as machine learning. In summary, molecular data expansion provides an elegant way to extend mechanistic modeling, systems pharmacology, and patient‐centered approaches for the assessment of drug safety. We anticipate that such advances in real‐world data informatics and outcome analytics will help to better inform public health, via the improved ability to prospectively understand and predict various types of drug‐induced molecular perturbations and adverse events.
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Affiliation(s)
| | - Sarah Kim
- Department of PharmaceuticsCenter for Pharmacometrics and Systems PharmacologyUniversity of FloridaOrlandoFloridaUSA
| | - Stephan Schmidt
- Department of PharmaceuticsCenter for Pharmacometrics and Systems PharmacologyUniversity of FloridaOrlandoFloridaUSA
| | - Lawrence J. Lesko
- Department of PharmaceuticsCenter for Pharmacometrics and Systems PharmacologyUniversity of FloridaOrlandoFloridaUSA
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Prouteau A, Mottier S, Primot A, Cadieu E, Bachelot L, Botherel N, Cabillic F, Houel A, Cornevin L, Kergal C, Corre S, Abadie J, Hitte C, Gilot D, Lindblad-Toh K, André C, Derrien T, Hedan B. Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets. Cancers (Basel) 2022; 14:cancers14020276. [PMID: 35053440 PMCID: PMC8774001 DOI: 10.3390/cancers14020276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary In humans, mucosal melanoma (MM) is a rare and aggressive cancer. The canine model is frequently and spontaneously affected by MM, thus facilitating the collection of samples and the study of its genetic bases. Thanks to an integrative genomic and transcriptomic analysis of 32 canine MM samples, we identified two molecular subgroups of MM with a different microenvironment and structural variant (SV) content. We demonstrated that SVs are associated with recurrently amplified regions, and identified new candidate oncogenes (TRPM7, GABPB1, and SPPL2A) for MM. Our findings suggest the existence of two MM molecular subgroups that could benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine. Abstract Mucosal melanoma (MM) is a rare, aggressive clinical cancer. Despite recent advances in genetics and treatment, the prognosis of MM remains poor. Canine MM offers a relevant spontaneous and immunocompetent model to decipher the genetic bases and explore treatments for MM. We performed an integrative genomic and transcriptomic analysis of 32 canine MM samples, which identified two molecular subgroups with a different microenvironment and structural variant (SV) content. The overexpression of genes related to the microenvironment and T-cell response was associated with tumors harboring a lower content of SVs, whereas the overexpression of pigmentation-related pathways and oncogenes, such as TERT, was associated with a high SV burden. Using whole-genome sequencing, we showed that focal amplifications characterized complex chromosomal rearrangements targeting oncogenes, such as MDM2 or CDK4, and a recurrently amplified region on canine chromosome 30. We also demonstrated that the genes TRPM7, GABPB1, and SPPL2A, located in this CFA30 region, play a role in cell proliferation, and thus, may be considered as new candidate oncogenes for human MM. Our findings suggest the existence of two MM molecular subgroups that may benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine.
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Affiliation(s)
- Anais Prouteau
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Stephanie Mottier
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Aline Primot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Edouard Cadieu
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Laura Bachelot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Nadine Botherel
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Florian Cabillic
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU de Rennes, INSERM, INRA, University of Rennes 1, Nutrition Metabolisms and Cancer, 35000 Rennes, France; (F.C.); (L.C.)
| | - Armel Houel
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Laurence Cornevin
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU de Rennes, INSERM, INRA, University of Rennes 1, Nutrition Metabolisms and Cancer, 35000 Rennes, France; (F.C.); (L.C.)
| | - Camille Kergal
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Sébastien Corre
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Jérôme Abadie
- Laboniris, Department of Biology, Pathology and Food Sciences, Oniris, 44300 Nantes, France;
| | - Christophe Hitte
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - David Gilot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Catherine André
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Thomas Derrien
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
- Correspondence: (T.D.); (B.H.); Tel.: +33-2-23-23-43-19 (B.H.)
| | - Benoit Hedan
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
- Correspondence: (T.D.); (B.H.); Tel.: +33-2-23-23-43-19 (B.H.)
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