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Mavromatis LA, Rosoff DB, Bell AS, Jung J, Wagner J, Lohoff FW. Multi-omic underpinnings of epigenetic aging and human longevity. Nat Commun 2023; 14:2236. [PMID: 37076473 PMCID: PMC10115892 DOI: 10.1038/s41467-023-37729-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 03/28/2023] [Indexed: 04/21/2023] Open
Abstract
Biological aging is accompanied by increasing morbidity, mortality, and healthcare costs; however, its molecular mechanisms are poorly understood. Here, we use multi-omic methods to integrate genomic, transcriptomic, and metabolomic data and identify biological associations with four measures of epigenetic age acceleration and a human longevity phenotype comprising healthspan, lifespan, and exceptional longevity (multivariate longevity). Using transcriptomic imputation, fine-mapping, and conditional analysis, we identify 22 high confidence associations with epigenetic age acceleration and seven with multivariate longevity. FLOT1, KPNA4, and TMX2 are novel, high confidence genes associated with epigenetic age acceleration. In parallel, cis-instrument Mendelian randomization of the druggable genome associates TPMT and NHLRC1 with epigenetic aging, supporting transcriptomic imputation findings. Metabolomics Mendelian randomization identifies a negative effect of non-high-density lipoprotein cholesterol and associated lipoproteins on multivariate longevity, but not epigenetic age acceleration. Finally, cell-type enrichment analysis implicates immune cells and precursors in epigenetic age acceleration and, more modestly, multivariate longevity. Follow-up Mendelian randomization of immune cell traits suggests lymphocyte subpopulations and lymphocytic surface molecules affect multivariate longevity and epigenetic age acceleration. Our results highlight druggable targets and biological pathways involved in aging and facilitate multi-omic comparisons of epigenetic clocks and human longevity.
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Affiliation(s)
- Lucas A Mavromatis
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Daniel B Rosoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program, University of Oxford, Oxford, UK
| | - Andrew S Bell
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Josephin Wagner
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Falk W Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA.
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Cacabelos R, Naidoo V, Corzo L, Cacabelos N, Carril JC. Genophenotypic Factors and Pharmacogenomics in Adverse Drug Reactions. Int J Mol Sci 2021; 22:ijms222413302. [PMID: 34948113 PMCID: PMC8704264 DOI: 10.3390/ijms222413302] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
Adverse drug reactions (ADRs) rank as one of the top 10 leading causes of death and illness in developed countries. ADRs show differential features depending upon genotype, age, sex, race, pathology, drug category, route of administration, and drug–drug interactions. Pharmacogenomics (PGx) provides the physician effective clues for optimizing drug efficacy and safety in major problems of health such as cardiovascular disease and associated disorders, cancer and brain disorders. Important aspects to be considered are also the impact of immunopharmacogenomics in cutaneous ADRs as well as the influence of genomic factors associated with COVID-19 and vaccination strategies. Major limitations for the routine use of PGx procedures for ADRs prevention are the lack of education and training in physicians and pharmacists, poor characterization of drug-related PGx, unspecific biomarkers of drug efficacy and toxicity, cost-effectiveness, administrative problems in health organizations, and insufficient regulation for the generalized use of PGx in the clinical setting. The implementation of PGx requires: (i) education of physicians and all other parties involved in the use and benefits of PGx; (ii) prospective studies to demonstrate the benefits of PGx genotyping; (iii) standardization of PGx procedures and development of clinical guidelines; (iv) NGS and microarrays to cover genes with high PGx potential; and (v) new regulations for PGx-related drug development and PGx drug labelling.
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Affiliation(s)
- Ramón Cacabelos
- Department of Genomic Medicine, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, 15165 Corunna, Spain
- Correspondence: ; Tel.: +34-981-780-505
| | - Vinogran Naidoo
- Department of Neuroscience, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, 15165 Corunna, Spain;
| | - Lola Corzo
- Department of Medical Biochemistry, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, 15165 Corunna, Spain;
| | - Natalia Cacabelos
- Department of Medical Documentation, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, 15165 Corunna, Spain;
| | - Juan C. Carril
- Departments of Genomics and Pharmacogenomics, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, 15165 Corunna, Spain;
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Maillard M, Louveau B, Vilquin P, Goldwirt L, Thomas F, Mourah S. Pharmacogenomics in solid cancers and hematologic malignancies: Improving personalized drug prescription. Therapie 2021; 77:171-183. [PMID: 34922740 DOI: 10.1016/j.therap.2021.11.003] [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: 09/11/2021] [Accepted: 09/29/2021] [Indexed: 11/30/2022]
Abstract
The discovery of molecular alterations involved in oncogenesis is evolving rapidly and has led to the development of new innovative targeted therapies in oncology. High-throughput sequencing techniques help to identify genomic targets and to provide predictive molecular biomarkers of response to guide alternative therapeutic strategies. Besides the emergence of these theranostic markers for the new targeted treatments, pharmacogenetic markers (corresponding to genetic variants existing in the constitutional DNA, i.e., the host genome) can help to optimize the use of chemotherapy. In this review, we present the current clinical applications of constitutional PG and the recent concepts and advances in pharmacogenomics, a rapidly evolving field that focuses on various molecular alterations identified on constitutional or somatic (tumor) genome.
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Affiliation(s)
- Maud Maillard
- Institut Claudius-Regaud, Institut universitaire du cancer de Toulouse, IUCT-Oncopole, 31059 Toulouse, France; Centre de recherches en cancérologie de Toulouse CRCT, 31037 Toulouse, France; Université Paul-Sabatier Toulouse III, 31062 Toulouse, France
| | - Baptiste Louveau
- Inserm, UMR_S976, 75475 Paris, France; Université de Paris, 75010 Paris, France; Pharmacogenomics department, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
| | - Paul Vilquin
- Inserm, UMR_S976, 75475 Paris, France; Université de Paris, 75010 Paris, France; Pharmacogenomics department, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
| | - Lauriane Goldwirt
- Inserm, UMR_S976, 75475 Paris, France; Université de Paris, 75010 Paris, France; Pharmacogenomics department, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
| | - Fabienne Thomas
- Institut Claudius-Regaud, Institut universitaire du cancer de Toulouse, IUCT-Oncopole, 31059 Toulouse, France; Centre de recherches en cancérologie de Toulouse CRCT, 31037 Toulouse, France; Université Paul-Sabatier Toulouse III, 31062 Toulouse, France
| | - Samia Mourah
- Inserm, UMR_S976, 75475 Paris, France; Université de Paris, 75010 Paris, France; Pharmacogenomics department, Hôpital Saint-Louis, AP-HP, 75010 Paris, France.
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Al-Mahayri ZN, Patrinos GP, Ali BR. Pharmacogenomics in pediatric acute lymphoblastic leukemia: promises and limitations. Pharmacogenomics 2017; 18:687-699. [PMID: 28468529 DOI: 10.2217/pgs-2017-0005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the significant advances achieved in pediatric acute lymphocytic leukemia (ALL) treatment, adverse side effects of drugs remain a challenging issue. Numerous ALL pharmacogenomic studies have been conducted to elucidate the predisposing genetic factors for their development. Plausible pharmacogenomic data are available for the osteonecrosis associated with glucocorticoids, the neurotoxicity associated with vincristine and the cardiotoxicity related to anthracyclines. However, these data have not been fully translated into the clinic due to several limitations, most importantly the lack of reliable evidence. The most robust pharmacogenomics data are those for thiopurines and methotrexate use, with evidence-based preemptive testing recommendations for the former. Pharmacogenomics has a significant potential utility in pediatric ALL treatment regimens. In this review, gaps and limitations in this field are emphasized, which may provide a useful guide for future research design.
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Affiliation(s)
- Zeina N Al-Mahayri
- Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, United Arab Emirates
| | - George P Patrinos
- Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, United Arab Emirates.,Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, Patras, Greece
| | - Bassam R Ali
- Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, United Arab Emirates
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Quaranta S, Thomas F. Pharmacogénétique des médicaments anticancéreux : état des connaissances et des pratiques – recommandations du Réseau national de pharmacogénétique (RNPGx). Therapie 2017; 72:193-204. [DOI: 10.1016/j.therap.2016.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/02/2016] [Indexed: 11/26/2022]
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Quaranta S, Thomas F. Pharmacogenetics of anti-cancer drugs: State of the art and implementation - recommendations of the French National Network of Pharmacogenetics. Therapie 2017; 72:205-215. [PMID: 28262261 DOI: 10.1016/j.therap.2017.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/02/2016] [Indexed: 12/27/2022]
Abstract
Individualized treatment is of special importance in oncology because the drugs used for chemotherapy have a very narrow therapeutic index. Pharmacogenetics may contribute substantially to clinical routine for optimizing cancer treatment to limit toxic effects while maintaining efficacy. This review presents the usefulness of pharmacogenetic tests for some key applications: dihydropyrimidine dehydrogenase (DPYD) genotyping for fluoropyrimidine (5-fluorouracil, capecitabine), UDP glucuronosylstransferase (UGT1A1) for irinotecan and thiopurine S-methyltransferase (TPMT) for thiopurine drugs. Depending on the level of evidence, the French National Network of Pharmacogenetics (RNPGx) has issued three levels of recommendations for these pharmacogenetic tests: essential, advisable, and potentially useful. Other applications, for which the level of evidence is still discussed, will be evoked in the final section of this review.
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Affiliation(s)
- Sylvie Quaranta
- Service de pharmacocinétique et toxicologie, laboratoire de biologie médicale, hôpital de la Timone, Assistance publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France
| | - Fabienne Thomas
- Institut Claudius-Regaud, CRCT, Université de Toulouse, Inserm, UPS, 31059 Toulouse, France; GPCO-Unicancer, 101, rue de Tolbiac, 75013 Paris, France.
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Broekman MMTJ, Wong DR, Wanten GJA, Roelofs HM, van Marrewijk CJ, Klungel OH, Verbeek ALM, Hooymans PM, Guchelaar HJ, Scheffer H, Derijks LJJ, Coenen MJH, de Jong DJ. The glutathione transferase Mu null genotype leads to lower 6-MMPR levels in patients treated with azathioprine but not with mercaptopurine. THE PHARMACOGENOMICS JOURNAL 2017; 18:160-166. [PMID: 28045129 DOI: 10.1038/tpj.2016.87] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 11/07/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022]
Abstract
The conversion of azathioprine (AZA) to mercaptopurine (MP) is mediated by glutathione transferase Mu1 (GSTM1), alpha1 (GSTA1) and alpha2 (GSTA2). We designed a case-control study with data from the TOPIC trial to explore the effects of genetic variation on steady state 6-methylmercaptopurine ribonucleotide (6-MMPR) and 6-thioguanine nucleotide (6-TGN) metabolite levels. We included 199 patients with inflammatory bowel disease (126 on AZA and 73 on MP). GSTM1-null genotype carriers on AZA had two-fold lower 6-MMPR levels than AZA users carrying one or two copies of GSTM1 (2239 (1006-4587) versus 4371 (1897-7369) pmol/8 × 108 RBCs; P<0.01). In patients on MP (control group) 6-MMPR levels were comparable (6195 (1551-10712) versus 6544 (1717-11600) pmol/8 × 108 RBCs; P=0.84). The 6-TGN levels were not affected by the GSTM1 genotype. The presence of genetic variants in GSTA1 and GSTA2 was not related to the 6-MMPR and 6-TGN levels.
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Affiliation(s)
- M M T J Broekman
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Gastroenterology, Nijmegen, The Netherlands
| | - D R Wong
- Department of Clinical Pharmacy, Pharmacology and Toxicology, Zuyderland Medical Center, Sittard-Geleen, The Netherlands
| | - G J A Wanten
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Gastroenterology, Nijmegen, The Netherlands
| | - H M Roelofs
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Gastroenterology, Nijmegen, The Netherlands
| | - C J van Marrewijk
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - O H Klungel
- Department of Pharmacoepidemiology and Pharmacotherapy, Utrecht University, Utrecht, The Netherlands
| | - A L M Verbeek
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - P M Hooymans
- Department of Clinical Pharmacy, Pharmacology and Toxicology, Zuyderland Medical Center, Sittard-Geleen, The Netherlands
| | - H-J Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - H Scheffer
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - L J J Derijks
- Department of Clinical Pharmacy, Máxima Medical Center, Veldhoven, The Netherlands
| | - M J H Coenen
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - D J de Jong
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Gastroenterology, Nijmegen, The Netherlands
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