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Li D, Thomas C, Shrivastava N, Gersten A, Gadsden N, Schlecht N, Kawachi N, Schiff BA, Smith RV, Rosenblatt G, Augustine S, Gavathiotis E, Burk R, Prystowsky MB, Guha C, Mehta V, Ow TJ. Establishment of a diverse head and neck squamous cancer cell bank using conditional reprogramming culture methods. J Med Virol 2023; 95:e28388. [PMID: 36477880 PMCID: PMC10168123 DOI: 10.1002/jmv.28388] [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: 07/31/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022]
Abstract
Most laboratory models of head and neck squamous cell cancer (HNSCC) rely on established immortalized cell lines, which carry inherent bias due to selection and clonality. We established a robust panel of HNSCC tumor cultures using a "conditional reprogramming" (CR) method, which utilizes a rho kinase inhibitor (Y-27632) and co-culture with irradiated fibroblast (J2 strain) feeder cells to support indefinite tumor cell survival. Sixteen CR cultures were successfully generated from 19 consecutively enrolled ethnically and racially diverse patients with HNSCC at a tertiary care center in the Bronx, NY. Of the 16 CR cultures, 9/16 were derived from the oral cavity, 4/16 were derived from the oropharynx, and 3/16 were from laryngeal carcinomas. Short tandem repeat (STR) profiling was used to validate culture against patient tumor tissue DNA. All CR cultures expressed ΔNp63 and cytokeratin 5/6, which are markers of squamous identity. Human papillomavirus (HPV) testing was assessed utilizing clinical p16 staining on primary tumors, reverse transcription polymerase chain reaction (RT-PCR) of HPV16/18-specific viral oncogenes E6 and E7 in RNA extracted from tumor samples, and HPV DNA sequencing. Three of four oropharyngeal tumors were p16 and HPV-positive and maintained HPV in culture. CR cultures were able to establish three-dimensional spheroid and murine flank and orthotopic tongue models. CR methods can be readily applied to all HNSCC tumors regardless of patient characteristics, disease site, and molecular background, providing a translational research model that properly includes patient and tumor diversity.
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Affiliation(s)
- Daniel Li
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Carlos Thomas
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nitisha Shrivastava
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Adam Gersten
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicholas Gadsden
- Department of Anesthesiology, Columbia University, New York, NY, USA
| | - Nicolas Schlecht
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Nicole Kawachi
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bradley A. Schiff
- Department of Otorhinolaryngology - Head and Neck Surgery, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Richard V. Smith
- Department of Otorhinolaryngology - Head and Neck Surgery, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Surgery, Montefiore Medical Center/ Albert Einstein College of Medicine, Bronx, NY USA
| | - Gregory Rosenblatt
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Stelby Augustine
- Department of Otorhinolaryngology - Head and Neck Surgery, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Robert Burk
- Department of Pediatrics, Montefiore Medical Center/ Albert Einstein College of Medicine, Bronx, NY USA
| | - Michael B. Prystowsky
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Chandan Guha
- Department of Radiation Oncology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vikas Mehta
- Department of Otorhinolaryngology - Head and Neck Surgery, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
| | - Thomas J Ow
- Department of Pathology, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Otorhinolaryngology - Head and Neck Surgery, Montefiore Medical Center / Albert Einstein College of Medicine, Bronx, NY, USA
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2
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Meng W, Zhang W, Yang S, Dou X, Liu Y, Li H, Liu J, Jin T, Li B. Analysis of pharmacogenomic very important pharmacogenomic variants: CYP3A5, ACE, PTGS2 and NAT2 genes in Chinese Bai population. Per Med 2022; 19:403-410. [PMID: 35801384 DOI: 10.2217/pme-2021-0157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Our study aimed to screen the genotype frequencies of very important pharmacogenomic (VIP) mutations and identify their differences between Bai and other populations. Materials & methods: We selected 66 VIP variants from PharmGKB (www.pharmgkb.org/) for genotyping. χ2 test was used to identify differences in loci between these populations and Fst values of Bai and the other 26 populations were analyzed. Results: Our study showed that the frequencies of SNPs of CYP3A5, ACE, PTGS2 and NAT2 differed significantly from those of the other 26 populations. At the same time, we found that some VIP variants may affect the metabolism of drugs and the genetic relationship between the Bai population and East Asian populations was found to be the closest. Conclusion: By comparing the genotype frequencies of different populations, the loci with significant differences were identified and discussed, providing a theoretical basis for individualized drug use in the Bai ethnic population.
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Affiliation(s)
- Wenting Meng
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Wenjie Zhang
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Shuangyu Yang
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Xia Dou
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Yuanwei Liu
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Haiyue Li
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Jianfeng Liu
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Bin Li
- Key Laboratory of Resource Biology & Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, 229 TaiBai North Road, Xi'an, 710069, China.,Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
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3
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Magavern EF, Gurdasani D, Ng FL, Lee SSJ. Health equality, race and pharmacogenomics. Br J Clin Pharmacol 2022; 88:27-33. [PMID: 34251046 PMCID: PMC8752640 DOI: 10.1111/bcp.14983] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/23/2021] [Accepted: 07/02/2021] [Indexed: 12/15/2022] Open
Abstract
Pharmacogenomics is increasingly moving into mainstream clinical practice. Careful consideration must be paid to inclusion of diverse populations in research, translation and implementation, in the historical and social context of population stratification, to ensure that this leads to improvements in healthcare for all rather than increased health disparities. This review takes a broad and critical approach to the current role of diversity in pharmacogenomics and addresses potential pitfalls in order to raise awareness for prescribers. It also emphasizes evidence gaps and suggests approaches that may minimize negative consequences and promote health equality.
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Affiliation(s)
- Emma F. Magavern
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Deepti Gurdasani
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Fu L. Ng
- Department of Clinical Pharmacology, St Georges University of London, London, UK
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department Medical Humanities and Ethics, Columbia University, New York, N.Y., USA
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4
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Sonis S, Patel J, Ashbury FD. The application of "Omics" to accelerate precision medicine in Supportive Care in Cancer. Support Care Cancer 2021; 29:7143-7144. [PMID: 34546453 DOI: 10.1007/s00520-021-06519-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 08/24/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen Sonis
- Division of Oral Medicine, Brigham and Women's Hospital and the Dana-Farber Cancer Institute, Boston, MA, USA. .,Primary Endpoint Solutions, 360 Second Avenue, Waltham, MA, 02451, USA.
| | - Jai Patel
- Department of Cancer Pharmacology & Pharmacogenomics, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Fredrick D Ashbury
- VieCure, Denver, CO, USA.,Department of Oncology, University of Calgary, Calgary, Alberta, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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5
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Varela NM, Guevara-Ramírez P, Acevedo C, Zambrano T, Armendáriz-Castillo I, Guerrero S, Quiñones LA, López-Cortés A. A New Insight for the Identification of Oncogenic Variants in Breast and Prostate Cancers in Diverse Human Populations, With a Focus on Latinos. Front Pharmacol 2021; 12:630658. [PMID: 33912047 PMCID: PMC8072346 DOI: 10.3389/fphar.2021.630658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Breast cancer (BRCA) and prostate cancer (PRCA) are the most commonly diagnosed cancer types in Latin American women and men, respectively. Although in recent years large-scale efforts from international consortia have focused on improving precision oncology, a better understanding of genomic features of BRCA and PRCA in developing regions and racial/ethnic minority populations is still required. Methods: To fill in this gap, we performed integrated in silico analyses to elucidate oncogenic variants from BRCA and PRCA driver genes; to calculate their deleteriousness scores and allele frequencies from seven human populations worldwide, including Latinos; and to propose the most effective therapeutic strategies based on precision oncology. Results: We analyzed 339,100 variants belonging to 99 BRCA and 82 PRCA driver genes and identified 18,512 and 15,648 known/predicted oncogenic variants, respectively. Regarding known oncogenic variants, we prioritized the most frequent and deleterious variants of BRCA (n = 230) and PRCA (n = 167) from Latino, African, Ashkenazi Jewish, East Asian, South Asian, European Finnish, and European non-Finnish populations, to incorporate them into pharmacogenomics testing. Lastly, we identified which oncogenic variants may shape the response to anti-cancer therapies, detailing the current status of pharmacogenomics guidelines and clinical trials involved in BRCA and PRCA cancer driver proteins. Conclusion: It is imperative to unify efforts where developing countries might invest in obtaining databases of genomic profiles of their populations, and developed countries might incorporate racial/ethnic minority populations in future clinical trials and cancer researches with the overall objective of fomenting pharmacogenomics in clinical practice and public health policies.
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Affiliation(s)
- Nelson M Varela
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile.,Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Patricia Guevara-Ramírez
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Cristian Acevedo
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Basic and Clinical Oncology, Clinical Hospital University of Chile, Santiago, Chile
| | - Tomás Zambrano
- Department of Medical Technology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Isaac Armendáriz-Castillo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Santiago Guerrero
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Luis A Quiñones
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile.,Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Andrés López-Cortés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain.,Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador.,Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruna, A Coruña, Spain
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6
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Towards precision medicine: interrogating the human genome to identify drug pathways associated with potentially functional, population-differentiated polymorphisms. THE PHARMACOGENOMICS JOURNAL 2019; 19:516-527. [PMID: 31578463 PMCID: PMC6867962 DOI: 10.1038/s41397-019-0096-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/10/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022]
Abstract
Drug response variations amongst different individuals/populations are influenced by several factors including allele frequency differences of single nucleotide polymorphisms (SNPs) that functionally affect drug-response genes. Here, we aim to identify drugs that potentially exhibit population differences in response using SNP data mining and analytics. Ninety-one pairwise-comparisons of >22,000,000 SNPs from the 1000 Genomes Project, across 14 different populations, were performed to identify ‘population-differentiated’ SNPs (pdSNPs). Potentially-functional pdSNPs (pf-pdSNPs) were then selected, mapped into genes, and integrated with drug–gene databases to identify ‘population-differentiated’ drugs enriched with genes carrying pf-pdSNPs. 1191 clinically-approved drugs were found to be significantly enriched (Z > 2.58) with genes carrying SNPs that were differentiated in one or more population-pair comparisons. Thirteen drugs were found to be enriched with such differentiated genes across all 91 population-pairs. Notably, 82% of drugs, which were previously reported in the literature to exhibit population differences in response were also found by this method to contain a significant enrichment of population specific differentiated SNPs. Furthermore, drugs with genetic testing labels, or those suspected to cause adverse reactions, contained a significantly larger number (P < 0.01) of population-pairs with enriched pf-pdSNPs compared with those without these labels. This pioneering effort at harnessing big-data pharmacogenomics to identify ‘population differentiated’ drugs could help to facilitate data-driven decision-making for a more personalized medicine.
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7
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Miscio G, Paroni G, Bisceglia P, Gravina C, Urbano M, Lozupone M, Piccininni C, Prisciandaro M, Ciavarella G, Daniele A, Bellomo A, Panza F, Di Mauro L, Greco A, Seripa D. Pharmacogenetics in the clinical analysis laboratory: clinical practice, research, and drug development pipeline. Expert Opin Drug Metab Toxicol 2019; 15:751-765. [PMID: 31512953 DOI: 10.1080/17425255.2019.1658742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: Over the last decade, the spread of next-generation sequencing technology along with the rising cost in health management in national health systems has led to widespread use/abuse of pharmacogenetic tests (PGx) in the practice of many clinical disciplines. However, given their clinical significance, it is important to standardize these tests for having an interaction with the clinical analysis laboratory (CAL), in which a PGx service can meet these requirements. Areas covered: A diagnostic test must meet the criteria of reproducibility and validity for its utility in the clinical routine. This present review mainly describes the utility of introducing PGx tests in the CAL routine to produce correct results useful for setting up personalized drug treatments. Expert opinion: With a PGx service, CALs can provide the right tool to help clinicians to make better choices about different categories of drugs and their dosage and to manage the economic impact both in hospital-based settings and in National Health Services, throughout electronic health records. Advances in PGx also allow a new approach for pharmaceutical companies in order to improve drug development and clinical trials. As a result, CALs can achieve a powerful source of epidemiological, clinical, and research findings from PGx tests.
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Affiliation(s)
- Giuseppe Miscio
- Clinical Laboratory Analysis and Transfusional Medicine, Laboratory and Transfusional Diagnostics, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Giulia Paroni
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Paola Bisceglia
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Carolina Gravina
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Maria Urbano
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medical Sciences, Neuroscience, and Sense Organs, University of Bari Aldo Moro , Bari , Italy
| | - Carla Piccininni
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia , Foggia , Italy
| | - Michele Prisciandaro
- Clinical Laboratory Analysis and Transfusional Medicine, Laboratory and Transfusional Diagnostics, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Grazia Ciavarella
- Clinical Laboratory Analysis and Transfusional Medicine, Laboratory and Transfusional Diagnostics, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Antonio Daniele
- Institute of Neurology, Catholic University of Sacred Heart , Rome , Italy.,Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS , Rome , Italy
| | - Antonello Bellomo
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia , Foggia , Italy
| | - Francesco Panza
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy.,Neurodegenerative Disease Unit, Department of Basic Medical Sciences, Neuroscience, and Sense Organs, University of Bari Aldo Moro , Bari , Italy
| | - Lazzaro Di Mauro
- Clinical Laboratory Analysis and Transfusional Medicine, Laboratory and Transfusional Diagnostics, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Antonio Greco
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
| | - Davide Seripa
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza , Foggia , Italy
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8
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Castro-Rojas CA, Esparza-Mota AR, Hernandez-Cabrera F, Romero-Diaz VJ, Gonzalez-Guerrero JF, Maldonado-Garza H, Garcia-Gonzalez IS, Buenaventura-Cisneros S, Sanchez-Lopez JY, Ortiz-Lopez R, Camacho-Morales A, Barboza-Quintana O, Rojas-Martinez A. Thymidylate synthase gene variants as predictors of clinical response and toxicity to fluoropyrimidine-based chemotherapy for colorectal cancer. Drug Metab Pers Ther 2018; 32:209-218. [PMID: 29257755 DOI: 10.1515/dmpt-2017-0028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/15/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND Fluoropyrimidines form the chemotherapy backbone of advanced and metastatic colorectal cancer (CRC). These drugs are frequently associated with toxicity events that result in dose adjustments and even suspension of the treatment. The thymidylate synthase (TYMS) gene is a potential marker of response and toxicity to fluoropyirimidines as this enzyme is the molecular target of these drugs. Our aim was to assess the association between variants of TYMS with response and toxicity to fluoropyrimidines in patients with CRC in independent retrospective and prospective studies. METHODS Variants namely rs45445694, rs183205964, rs2853542 and rs151264360 of TYMS were genotyped in 105 CRC patients and were evaluated to define their association with clinical response and toxicity to fluoropyrimidines. Additionally, the relationship between genotypes and tumor gene expression was analyzed by quantitative polymerase chain reaction. RESULTS The 2R/2R (rs45445694) was associated with clinical response (p=0.05, odds ratio (OR)=3.45) and severe toxicity (p=0.0014, OR=5.21, from pooled data). Expression analysis in tumor tissues suggested a correlation between the 2R/2R genotype and low TYMS expression. CONCLUSIONS The allele 2R (rs45445694) predicts severe toxicity and objective response in advanced CRC patients. In addition, the alleles G(rs2853542) and 6bp-(rs151264360) are independent predictors of response failure to chemotherapy. This is the first study made on a Latin American population that points out TYMS gene variants have predictive values for response and toxicity in patients with CRC treated with fluoropyrimidine-based chemotherapy.
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Affiliation(s)
- Carlos A Castro-Rojas
- Universidad Autonoma de Nuevo Leon, Center for Research and Development in Health Sciences, Monterrey, Mexico
| | - Antonio R Esparza-Mota
- Universidad Autonoma de Nuevo Leon, Center for Research and Development in Health Sciences, Monterrey, Mexico
| | | | - Viktor J Romero-Diaz
- Universidad Autonoma de Nuevo Leon, Center for Research and Development in Health Sciences, Monterrey, Mexico
| | | | - Hector Maldonado-Garza
- Universidad Autonoma de Nuevo Leon, Service of Gastroenterology, University Hospital, Monterrey, Mexico
| | - Irma S Garcia-Gonzalez
- Mexican Institute for Social Security (IMSS), High Specialties Unit No. 25, Monterrey, Mexico
| | | | - Josefina Y Sanchez-Lopez
- Mexican Institute for Social Security (IMSS), Western Center for Biomedical Research, Guadalajara, Mexico
| | - Rocio Ortiz-Lopez
- Universidad Autonoma de Nuevo Leon, Center for Research and Development in Health Sciences, Monterrey, Mexico
| | | | | | - Augusto Rojas-Martinez
- Universidad Autonoma de Nuevo Leon, Center for Research and Development in Health Sciences, Monterrey, Mexico
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9
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Guerrero S, López-Cortés A, Indacochea A, García-Cárdenas JM, Zambrano AK, Cabrera-Andrade A, Guevara-Ramírez P, González DA, Leone PE, Paz-Y-Miño C. Analysis of Racial/Ethnic Representation in Select Basic and Applied Cancer Research Studies. Sci Rep 2018; 8:13978. [PMID: 30228363 PMCID: PMC6143551 DOI: 10.1038/s41598-018-32264-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
Over the past decades, consistent studies have shown that race/ethnicity have a great impact on cancer incidence, survival, drug response, molecular pathways and epigenetics. Despite the influence of race/ethnicity in cancer outcomes and its impact in health care quality, a comprehensive understanding of racial/ethnic inclusion in oncological research has never been addressed. We therefore explored the racial/ethnic composition of samples/individuals included in fundamental (patient-derived oncological models, biobanks and genomics) and applied cancer research studies (clinical trials). Regarding patient-derived oncological models (n = 794), 48.3% have no records on their donor's race/ethnicity, the rest were isolated from White (37.5%), Asian (10%), African American (3.8%) and Hispanic (0.4%) donors. Biobanks (n = 8,293) hold specimens from unknown (24.56%), White (59.03%), African American (11.05%), Asian (4.12%) and other individuals (1.24%). Genomic projects (n = 6,765,447) include samples from unknown (0.6%), White (91.1%), Asian (5.6%), African American (1.7%), Hispanic (0.5%) and other populations (0.5%). Concerning clinical trials (n = 89,212), no racial/ethnic registries were found in 66.95% of participants, and records were mainly obtained from Whites (25.94%), Asians (4.97%), African Americans (1.08%), Hispanics (0.16%) and other minorities (0.9%). Thus, two tendencies were observed across oncological studies: lack of racial/ethnic information and overrepresentation of Caucasian/White samples/individuals. These results clearly indicate a need to diversify oncological studies to other populations along with novel strategies to enhanced race/ethnicity data recording and reporting.
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Affiliation(s)
- Santiago Guerrero
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador.
| | - Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador
| | - Alberto Indacochea
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Oncology and Molecular Pathology Research Group-VHIR- Vall d' Hebron Institut de Recerca-Vall d' Hebron Hospital, P/de la Vall d'Hebron, Barcelona, Spain
| | - Jennyfer M García-Cárdenas
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador
| | - Ana Karina Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador
| | - Alejandro Cabrera-Andrade
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador
- Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de las Américas, Avenue de los Granados, Quito, 170125, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de las Américas, Avenue de los Granados, Quito, 170125, Ecuador
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador
| | - Diana Abigail González
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador
| | - Paola E Leone
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador
| | - César Paz-Y-Miño
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Av. Mariscal Sucre and Mariana de Jesús, Block I, 2nd floor, 170129, Quito, Ecuador.
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Li B, Wang L, Lei L, Zhang M, Niu F, Chen P, Jin T. Genetic polymorphisms of pharmacogenomic VIP variants in the Lisu population of southwestern China: A cohort study. Medicine (Baltimore) 2018; 97:e12231. [PMID: 30235667 PMCID: PMC6160020 DOI: 10.1097/md.0000000000012231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/14/2018] [Indexed: 11/26/2022] Open
Abstract
Pharmacogenomic studies of different ethnic or racial groups have been used to develop personalized therapies specific to subjects. This study aimed to identify the distribution differences of very important pharmacogenetic (VIP) variants between the Lisu population from southwestern China and other ethnic groups.Eighty VIP variants in 37 genes were selected from the pharmacogenomic knowledge base (PharmGKB), and compared with genotype data of the Lisu population then compared with other 11 populations from the HapMap dataset and previously published data including Miao, Li, Deng, Sherpa, Lhoba, Tibetan, Kirghiz, Tajik, Mongol, Shaanxi Han ethnic, and Uygur populations.VDR rs1540339, MTHFR rs1801131, P2RY1 rs701265, and PTGS2 rs689466 were significantly different between Lisu and 11 HapMap populations. ANKK1 rs1800497 was the least statistical significant locus among selected single nucleotide polymorphisms. In addition, genetic background of Lisu was strongly closest to Shaanxi Han ethnic cohort, and followed by Chinese in metropolitan Denver population based on population structure and F-statistics analyses.Our results showed significant interethnic differences between Lisu and other populations, which will give useful information for prospective studies and better individualized treatments.
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Affiliation(s)
- Bin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Li Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Lingyu Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Mingxiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Fanglin Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
| | - Peng Chen
- Institution of Basic Medical Science, Xi’an Medical University, Xi’an
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region
- Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China
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Hertz DL, Glatz A, Pasternak AL, Lonigro RJ, Vats P, Wu YM, Anderson B, Rabban E, Mora E, Frank K, Robinson DR, Mody RJ, Chinnaiyan A. Integration of Germline Pharmacogenetics Into a Tumor Sequencing Program. JCO Precis Oncol 2018; 2:PO.18.00011. [PMID: 32832831 PMCID: PMC7434089 DOI: 10.1200/po.18.00011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Evidence-based guidelines inform treatment decisions for patients for whom germline genetic information is available. Our real-time tumor sequencing program, which makes precision treatment decisions for patients with cancer, produces matched germline information, providing a unique opportunity to efficiently implement pharmacogenetics and benefit patients. METHODS The germline genetic database from the Michigan Oncology Sequencing (MI-Oncoseq) program was searched for 21 clinically actionable polymorphisms in five cancer-relevant genes: TPMT, DPYD, CYP2C19, CYP3A5, and UGT1A1. Residual germ line DNA was sent to an external Clinical Laboratory Improvement Amendments-approved laboratory for confirmatory genotyping. The medical records of MI-Oncoseq patients with actionable phenotypes were searched for receipt of relevant drugs and to determine whether having genetic information at the time of treatment would have led to a treatment recommendation. RESULTS All nine variants in TPMT, DPYD, and CYP2C19 that were detected in MI-Oncoseq were confirmed by external genotyping. Genotype determinations could not be made for CYP3A5*3, UGT1A1*28, or UGT1A1*80. On the basis of retrospective assessment of 115 adult and pediatric patient records, 4.3% (n = 5) had a potentially clinically actionable phenotype for TPMT, DPYD, or CYP2C19 and received a relevant medication. After accounting for differences in adult and pediatric recommendations, three of these patients could have received a treatment recommendation at the time of prescribing. CONCLUSION Germline genotype determinations for TPMT, DPYD, and CYP2C19 can be used to make evidence-based treatment recommendations in MI-Oncoseq patients. Although the proportion of patients for whom recommendations can be made is small, this added value to MI-Oncoseq and patient care comes at no additional genotyping cost. Pharmacogenetic assessment should be integrated into tumor sequencing programs that genotype matched germline DNA; however, the complexity and additional cost of implementing pharmacogenetics remain challenging.
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Affiliation(s)
- Daniel L. Hertz
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Andrew Glatz
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Amy L. Pasternak
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Robert J. Lonigro
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Pankaj Vats
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Yi-Mi Wu
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Bailey Anderson
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Erica Rabban
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Erika Mora
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Kevin Frank
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Dan R. Robinson
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Rajen J. Mody
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Arul Chinnaiyan
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
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12
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Kranzler HR, Smith RV, Schnoll R, Moustafa A, Greenstreet-Akman E. Precision medicine and pharmacogenetics: what does oncology have that addiction medicine does not? Addiction 2017; 112:2086-2094. [PMID: 28431457 PMCID: PMC5650957 DOI: 10.1111/add.13818] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/08/2017] [Accepted: 03/08/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Precision, personalized or stratified medicine, which promises to deliver the right treatment to the right patient, is a topic of international interest in both the lay press and the scientific literature. A key aspect of precision medicine is the identification of biomarkers that predict the response to medications (i.e. pharmacogenetics). We examined why, despite the great strides that have been made in biomarker identification in many areas of medicine, only in oncology has there been substantial progress in their clinical implementation. We also considered why progress in this effort has lagged in addiction medicine. METHODS We compared the development of pharmacogenetic biomarkers in oncology, cardiovascular medicine (where developments are also promising) and addictive disorders. RESULTS The first major reason for the success of oncologic pharmacogenetics is ready access to tumor tissue, which allows in-vitro testing and insights into cancer biology. The second major reason is funding, with cancer research receiving, by far, the largest allocation by the National Institutes of Health (NIH) during the past two decades. The second largest allocation of research funding has gone to cardiovascular disease research. Addictions research received a much smaller NIH funding allocation, despite the major impact that tobacco use, alcohol consumption and illicit drug use have on the public health and healthcare costs. CONCLUSIONS Greater support for research on the personalized treatment of addictive disorders can be expected to yield disproportionately large benefits to the public health and substantial reductions in healthcare costs.
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Affiliation(s)
- Henry R. Kranzler
- Center for Studies of Addiction, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA 19104
| | - Rachel V. Smith
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA 19104
| | - Robert Schnoll
- Center for Interdisciplinary Research on Nicotine Addiction, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Afaf Moustafa
- Center for Studies of Addiction, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Emma Greenstreet-Akman
- Center for Studies of Addiction, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
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13
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Pan ST, Li ZL, He ZX, Qiu JX, Zhou SF. Molecular mechanisms for tumour resistance to chemotherapy. Clin Exp Pharmacol Physiol 2017; 43:723-37. [PMID: 27097837 DOI: 10.1111/1440-1681.12581] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 04/13/2016] [Accepted: 04/18/2016] [Indexed: 12/25/2022]
Abstract
Chemotherapy is one of the prevailing methods used to treat malignant tumours, but the outcome and prognosis of tumour patients are not optimistic. Cancer cells gradually generate resistance to almost all chemotherapeutic drugs via a variety of distinct mechanisms and pathways. Chemotherapeutic resistance, either intrinsic or acquired, is caused and sustained by reduced drug accumulation and increased drug export, alterations in drug targets and signalling transduction molecules, increased repair of drug-induced DNA damage, and evasion of apoptosis. In order to better understand the mechanisms of chemoresistance, this review highlights our current knowledge of the role of altered drug metabolism and transport and deregulation of apoptosis and autophagy in the development of tumour chemoresistance. Reduced intracellular activation of prodrugs (e.g. thiotepa and tegafur) or enhanced drug inactivation by Phase I and II enzymes contributes to the development of chemoresistance. Both primary and acquired resistance can be caused by alterations in the transport of anticancer drugs which is mediated by a variety of drug transporters such as P-glycoprotein (P-gp), multidrug resistance associated proteins, and breast cancer resistance protein. Presently there is a line of evidence indicating that deregulation of programmed cell death including apoptosis and autophagy is also an important mechanism for tumour resistance to anticancer drugs. Reversal of chemoresistance is likely via pharmacological and biological approaches. Further studies are warranted to grasp the full picture of how each type of cancer cells develop resistance to anticancer drugs and to identify novel strategies to overcome it.
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Affiliation(s)
- Shu-Ting Pan
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Zhi-Ling Li
- Department of Pharmacy, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Xu He
- Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Centre & Sino-US Joint Laboratory for Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jia-Xuan Qiu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
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14
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Chandrani P, Prabhash K, Prasad R, Sethunath V, Ranjan M, Iyer P, Aich J, Dhamne H, Iyer DN, Upadhyay P, Mohanty B, Chandna P, Kumar R, Joshi A, Noronha V, Patil V, Ramaswamy A, Karpe A, Thorat R, Chaudhari P, Ingle A, Choughule A, Dutt A. Drug-sensitive FGFR3 mutations in lung adenocarcinoma. Ann Oncol 2017; 28:597-603. [PMID: 27998968 PMCID: PMC5391708 DOI: 10.1093/annonc/mdw636] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related deaths across the world. In this study, we present therapeutically relevant genetic alterations in lung adenocarcinoma of Indian origin. MATERIALS AND METHODS Forty-five primary lung adenocarcinoma tumors were sequenced for 676 amplicons using RainDance cancer panel at an average coverage of 1500 × (reads per million mapped reads). To validate the findings, 49 mutations across 23 genes were genotyped in an additional set of 363 primary lung adenocarcinoma tumors using mass spectrometry. NIH/3T3 cells over expressing mutant and wild-type FGFR3 constructs were characterized for anchorage independent growth, constitutive activation, tumor formation and sensitivity to FGFR inhibitors using in vitro and xenograft mouse models. RESULTS We present the first spectrum of actionable alterations in lung adenocarcinoma tumors of Indian origin, and shows that mutations of FGFR3 are present in 20 of 363 (5.5%) patients. These FGFR3 mutations are constitutively active and oncogenic when ectopically expressed in NIH/3T3 cells and using a xenograft model in NOD/SCID mice. Inhibition of FGFR3 kinase activity inhibits transformation of NIH/3T3 overexpressing FGFR3 constructs and growth of tumors driven by FGFR3 in the xenograft models. The reduction in tumor size in the mouse is paralleled by a reduction in the amounts of phospho-ERK, validating the in vitro findings. Interestingly, the FGFR3 mutations are significantly higher in a proportion of younger patients and show a trend toward better overall survival, compared with patients lacking actionable alterations or those harboring KRAS mutations. CONCLUSION We present the first actionable mutation spectrum in Indian lung cancer genome. These findings implicate FGFR3 as a novel therapeutic in lung adenocarcinoma.
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Affiliation(s)
- P. Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - K. Prabhash
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
- Department of Medical Oncology, Tata Memorial Hospital
| | - R. Prasad
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - V. Sethunath
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - M. Ranjan
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - J. Aich
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - H. Dhamne
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - D. N. Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Upadhyay
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - B. Mohanty
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Chandna
- AceProbe Technologies Pvt. Ltd, New Delhi, India
| | - R. Kumar
- Department of Pathology, Tata Memorial Hospital
| | - A. Joshi
- Department of Medical Oncology, Tata Memorial Hospital
| | - V. Noronha
- Department of Medical Oncology, Tata Memorial Hospital
| | - V. Patil
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Ramaswamy
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Karpe
- Department of Medical Oncology, Tata Memorial Hospital
| | - R. Thorat
- Department of Pathology, Tata Memorial Hospital
| | - P. Chaudhari
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - A. Ingle
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - A. Choughule
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
- Correspondence to: Dr Amit Dutt, Wellcome Trust/DBT India Alliance Intermediate Fellow, Tata Memorial Centre, ACTREC, Navi Mumbai 410 210, India. Tel: +91-22-27405056; E-mail:
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15
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The impact of DNA damage response gene polymorphisms on therapeutic outcomes in late stage ovarian cancer. Sci Rep 2016; 6:38142. [PMID: 27905519 PMCID: PMC5131275 DOI: 10.1038/srep38142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/04/2016] [Indexed: 02/06/2023] Open
Abstract
Late stage epithelial ovarian cancer has a dismal prognosis. Identification of pharmacogenomic markers (i.e. polymorphisms) to stratify patients to optimize individual therapy is of paramount importance. We here report the retrospective analysis of polymorphisms in 5 genes (ATM, ATR, Chk1, Chk2 and CDK12) involved in the cellular response to platinum in a cohort of 240 cancer patients with late stage ovarian cancer. The aim of the present study was to evaluate associations between the above mentioned SNPs and patients’ clinical outcomes: overall survival (OS) and progression free survival (PFS). None of the ATM, ATR, Chk1 and Chk2 polymorphisms was found to significantly affect OS nor PFS in this cohort of patients. Genotype G/G of CDK12 polymorphism (rs1054488) predicted worse OS and PFS than the genotype A/A-A/G in univariate analysis. The predictive value was lost in the multivariate analysis. The positive correlation observed between this polymorphism and age, grade and residual tumor may explain why the CDK12 variant was not confirmed as an independent prognostic factor in multivariate analysis.The importance of CDK12 polymorphism as possible prognostic biomarker need to be confirmed in larger ovarian cancer cohorts, and possibly in other cancer population responsive to platinum agents.
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16
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Park YH, Kim TY, Im YH, Lee KS, Park IH, Sohn J, Lee SH, Im SA, Kim JH, Kim SH, Lee SJ, Koh SJ, Lee KH, Choi YJ, Cho EK, Lee S, Kang SY, Seo JH, Kim SB, Jung KH. Feasibility and Efficacy of Eribulin Mesilate in Korean Patients with Metastatic Breast Cancer: Korean Multi-center Phase IV Clinical Study Results. Cancer Res Treat 2016; 49:423-429. [PMID: 27488876 PMCID: PMC5398406 DOI: 10.4143/crt.2016.191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/13/2016] [Indexed: 01/26/2023] Open
Abstract
PURPOSE Eribulin mesilate was approved for the treatment of patients with locally advanced or metastatic breast cancer (MBC), who had received at least two chemotherapeutic regimens, including anthracycline and taxane. On the other hand, the efficacy and safety information of eribulin in Korean patients is limited by the lack of clinical trials. MATERIALS AND METHODS In this multicenter, open-label, single-arm, phase IV study, locally advanced or MBC patients were enrolled between June 2013 and April 2014 from 14 centers in Korea. One point four mg/m2 dose of eribulin was administered on days 1 and 8 of every 21 days. The primary endpoint was the frequency and intensity of the treatment emergent adverse event. The secondary endpoint was the disease control rate, which included the rate of complete responses, partial responses, and stable disease. RESULTS A total of 101 patients received at least one dose of eribulin and were included in the safety set. The patients received a total of 543 treatment cycles, with a median of three cycles (range, 1 to 31 cycles). The most common adverse event was neutropenia (91.1% of patients, 48.3% of cycles). The frequent non-hematological adverse events included alopecia, decrease in appetite, fatigue/asthenia, and myalgia/arthralgia. The peripheral neuropathy of any grade occurred in 27 patients (26.7%), including grade 3 in two patients. Disease control rate was 52.7% and 51.3% of patients in the full analysis set and per-protocol set, respectively. CONCLUSION This study demonstrated the feasible safety profile and activity of eribulin in Korean patients with MBC.
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Affiliation(s)
- Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Yong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Young-Hyuck Im
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keun-Seok Lee
- Division of Hematology and Medical Oncology, Department of Internal Medicine, National Cancer Center, Goyang, Korea
| | - In Hae Park
- Division of Hematology and Medical Oncology, Department of Internal Medicine, National Cancer Center, Goyang, Korea
| | - Joohyuk Sohn
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Soo-Hyeon Lee
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Se Hyun Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Soo Jung Lee
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Kyungpook National University Medical Center, Kyungpook National University School of Medicine, Daegu, Korea
| | - Su-Jin Koh
- Division of Medical Oncology, Department of Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - Ki Hyeong Lee
- Division of Hematology-Oncology, Department of Medicine, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Yoon Ji Choi
- Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Eun Kyung Cho
- Division of Hematology and Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Suee Lee
- Department of Internal Medicine, Dong-A University Medical Center, Busan, Korea
| | - Seok Yun Kang
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Jae Hong Seo
- Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Sung-Bae Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Hae Jung
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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17
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Patel JN. Cancer pharmacogenomics, challenges in implementation, and patient-focused perspectives. Pharmgenomics Pers Med 2016; 9:65-77. [PMID: 27471406 PMCID: PMC4948716 DOI: 10.2147/pgpm.s62918] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cancer pharmacogenomics is an evolving landscape and has the potential to significantly impact cancer care and precision medicine. Harnessing and understanding the genetic code of both the patient (germline) and the tumor (somatic) provides the opportunity for personalized dose and therapy selection for cancer patients. While germline DNA is useful in understanding the pharmacokinetic and pharmacodynamic disposition of a drug, somatic DNA is particularly useful in identifying drug targets and predicting drug response. Molecular profiling of somatic DNA has resulted in the current breadth of targeted therapies available, expanding the armamentarium to battle cancer. This review provides an update on cancer pharmacogenomics and genomics-based medicine, challenges in applying pharmacogenomics to the clinical setting, and patient perspectives on the use of pharmacogenomics to personalize cancer therapy.
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Affiliation(s)
- Jai N Patel
- Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
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Patel JN, Fong MK. Personalizing fluoropyrimidine administration in colorectal cancer patients. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1176860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Quiñones LA, Lee KS. Editorial: Improving cancer chemotherapy through pharmacogenomics: a research topic. Front Genet 2015; 6:195. [PMID: 26089835 PMCID: PMC4452881 DOI: 10.3389/fgene.2015.00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 05/17/2015] [Indexed: 11/21/2022] Open
Affiliation(s)
- Luis A Quiñones
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Clinical and Molecular Pharmacology Program, Faculty of Medicine, Instituto de Ciencias Biomédicas, University of Chile Santiago, Chile
| | - Kuen S Lee
- Department of Surgery, Hospital del Salvador, University of Chile Santiago, Chile
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