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Caputo V, Ciardiello F, Corte CMD, Martini G, Troiani T, Napolitano S. Diagnostic value of liquid biopsy in the era of precision medicine: 10 years of clinical evidence in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:102-138. [PMID: 36937316 PMCID: PMC10017193 DOI: 10.37349/etat.2023.00125] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/13/2022] [Indexed: 03/06/2023] Open
Abstract
Liquid biopsy is a diagnostic repeatable test, which in last years has emerged as a powerful tool for profiling cancer genomes in real-time with minimal invasiveness and tailoring oncological decision-making. It analyzes different blood-circulating biomarkers and circulating tumor DNA (ctDNA) is the preferred one. Nevertheless, tissue biopsy remains the gold standard for molecular evaluation of solid tumors whereas liquid biopsy is a complementary tool in many different clinical settings, such as treatment selection, monitoring treatment response, cancer clonal evolution, prognostic evaluation, as well as the detection of early disease and minimal residual disease (MRD). A wide number of technologies have been developed with the aim of increasing their sensitivity and specificity with acceptable costs. Moreover, several preclinical and clinical studies have been conducted to better understand liquid biopsy clinical utility. Anyway, several issues are still a limitation of its use such as false positive and negative results, results interpretation, and standardization of the panel tests. Although there has been rapid development of the research in these fields and recent advances in the clinical setting, many clinical trials and studies are still needed to make liquid biopsy an instrument of clinical routine. This review provides an overview of the current and future clinical applications and opening questions of liquid biopsy in different oncological settings, with particular attention to ctDNA liquid biopsy.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
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Samimi H, Tavakoli R, Fallah P, Naderi Sohi A, Amini Shirkouhi M, Naderi M, Haghpanah V. BI-847325, a selective dual MEK and Aurora kinases inhibitor, reduces aggressive behavior of anaplastic thyroid carcinoma on an in vitro three-dimensional culture. Cancer Cell Int 2022; 22:388. [PMID: 36482411 PMCID: PMC9730667 DOI: 10.1186/s12935-022-02813-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Anaplastic thyroid carcinoma (ATC) is the most aggressive subtype of thyroid cancer. In this study, we used a three-dimensional in vitro system to evaluate the effect of a dual MEK/Aurora kinase inhibitor, BI-847325 anticancer drug, on several cellular and molecular processes involved in cancer progression. METHODS Human ATC cell lines, C643 and SW1736, were grown in alginate hydrogel and treated with IC50 values of BI-847325. The effect of BI-847325 on inhibition of kinases function of MEK1/2 and Aurora kinase B (AURKB) was evaluated via Western blot analysis of phospho-ERK1/2 and phospho-Histone H3 levels. Sodium/iodide symporter (NIS) and thyroglobulin (Tg), as two thyroid-specific differentiation markers, were measured by qRT-PCR as well as flow cytometry and immunoradiometric assay. Apoptosis was assessed by Annexin V/PI flow cytometry and BIM, NFκB1, and NFκB2 expressions. Cell cycle distribution and proliferation were determined via P16, AURKA, and AURKB expressions as well as PI and CFSE flow cytometry assays. Multidrug resistance was evaluated by examining the expression of MDR1 and MRP1. Angiogenesis and invasion were investigated by VEGF expression and F-actin labeling with Alexa Fluor 549 Phalloidin. RESULTS Western blot results showed that BI-847325 inhibits MEK1/2 and AURKB functions by decreasing phospho-ERK1/2 and phospho-Histone H3 levels. BI-847325 induced thyroid differentiation markers and apoptosis in ATC cell lines. Inversely, BI-847325 intervention decreased multidrug resistance, cell cycle progression, proliferation, angiogenesis, and invasion at the molecular and/or cellular levels. CONCLUSION The results of the present study suggest that BI-857,325 might be an effective multi-targeted anticancer drug for ATC treatment.
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Affiliation(s)
- Hilda Samimi
- grid.411705.60000 0001 0166 0922Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran ,grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rezvan Tavakoli
- grid.420169.80000 0000 9562 2611Hepatitis and HIV Department, Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Fallah
- grid.411705.60000 0001 0166 0922Department of Laboratory Science, Faculty of Allied Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Alireza Naderi Sohi
- grid.411705.60000 0001 0166 0922Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Amini Shirkouhi
- grid.411705.60000 0001 0166 0922Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Naderi
- grid.411705.60000 0001 0166 0922Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Haghpanah
- grid.411705.60000 0001 0166 0922Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran ,grid.411705.60000 0001 0166 0922Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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Chen M, Hou L, Hu L, Tan C, Wang X, Bao P, Ran Q, Chen L, Li Z. Platelet detection as a new liquid biopsy tool for human cancers. Front Oncol 2022; 12:983724. [PMID: 36185270 PMCID: PMC9515491 DOI: 10.3389/fonc.2022.983724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/09/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is still a leading cause of death worldwide and liquid biopsy is a powerful tool that can be applied to different stages of cancer screening and treatment. However, as the second most abundant cell type in the bloodstream, platelets are isolated through well-established and fast methods in clinic but their value as a BioSource of cancer biomarkers is relatively recent. Many studies demonstrated the bidirectional interaction between cancer cells and platelets. Platelets transfer various proteins (e.g., growth factors, cytokine, chemokines) and RNAs (e.g., mRNA, lncRNA, miRNA, circRNA) into the tumor cells and microenvironment, leading the stimulation of tumor growth and metastasis. In turn, the platelet clinical characteristics (e.g., count and volume) and contents (e.g., RNA and protein) are altered by the interactions with cancer cells and this enables the early cancer detection using these features of platelets. In addition, platelet-derived microparticles also demonstrate the prediction power of being cancer biomarkers. In this review, we focus on the clinical applications of platelet detection using the platelet count, mean platelet volume, platelet RNA and protein profiles for human cancers and discuss the gap in bringing these implementations into the clinic.
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Affiliation(s)
- Maoshan Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
- *Correspondence: Maoshan Chen, ; Li Chen, ; Zhongjun Li,
| | - Lijia Hou
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Lanyue Hu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Chengning Tan
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Xiaojie Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Peipei Bao
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Qian Ran
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Li Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
- *Correspondence: Maoshan Chen, ; Li Chen, ; Zhongjun Li,
| | - Zhongjun Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
- State Key Laboratory of Trauma, Burns and Combined Injuries, The Second Affiliated Hospital, Army Medical University, Chongqing, China
- *Correspondence: Maoshan Chen, ; Li Chen, ; Zhongjun Li,
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High-Risk Polymorphisms Associated with the Molecular Function of Human HMGCR Gene Infer the Inhibition of Cholesterol Biosynthesis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4558867. [PMID: 35707384 PMCID: PMC9192228 DOI: 10.1155/2022/4558867] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/13/2022] [Indexed: 11/17/2022]
Abstract
HMG-CoA reductase or HMGCR (3-hydroxy-3-methylglutaryl-CoA reductase) is a rate-limiting enzyme involved in cholesterol biosynthesis. HMGCR plays an important role in the possible occurrence of hypercholesterolemia leading to atherosclerosis and coronary heart disease. This enzyme is a major target for cholesterol-lowering drugs such as "statin" which blocks the synthesis of mevalonate, a precursor for cholesterol biosynthesis. This study is aimed at characterizing deleterious mutations and classifying functional single nucleotide polymorphisms (SNPs) of the HMGCR gene through analysis of functional and structural evaluation, domain association, solvent accessibility, and energy minimization studies. The functional and characterization tools such as SIFT, PolyPhen, SNPs and GO, Panther, I-Mutant, and Pfam along with programming were employed to explore all the available SNPs in the HMGCR gene in the database. Among 6815 SNP entries from different databases, approximately 388 SNPs were found to be missense. Analysis showed that seven missense SNPs are more likely to have deleterious effects. A tertiary model of the mutant protein was constructed to determine the functional and structural effects of the HMGCR mutation. In addition, the location of the mutations suggests that they may have deleterious effects because most of the mutations are residing in the functional domain of the protein. The findings from the analysis predicted that rs147043821 and rs193026499 missense SNPs could cause significant structural and functional instability in the mutated proteins of the HMGCR gene. The findings of the current study will likely be useful in future efforts to uncover the mechanism and cause of hypercholesterolemia. In addition, the identified SNPs of HMGCR gene could set up a strong foundation for further therapeutic discovery.
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Hirahata T, ul Quraish R, Quraish AU, ul Quraish S, Naz M, Razzaq MA. Liquid Biopsy: A Distinctive Approach to the Diagnosis and Prognosis of Cancer. Cancer Inform 2022; 21:11769351221076062. [PMID: 35153470 PMCID: PMC8832574 DOI: 10.1177/11769351221076062] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. Over the past decades, the concept of precision cancer medicine has emerged as a novel approach in the field of oncology that aims to tailor the most effective treatment options to each individual cancer patient based on the genetic profile of the tumor of each individual patient. Recently, tissue biopsy has become an essential part of cancer care and is widely used to characterize the tumor. However, tissue biopsy techniques face different challenges due to their invasiveness, cost, time, and adversity in potential sampling due to tissue heterogeneity. To overcome these issues, a non-invasive approach has developed, which is known as liquid biopsy. It is a simple, fast, and worthwhile technique based on the analysis of circulating tumor DNA (which is a fraction of cfDNA), circulating tumor cells (CTCs), and other tumor-derived material in blood plasma. This review provides an overview of the concept of liquid biopsy and briefly discusses the role of ctDNA and CTC analysis as tools for early diagnosis and prognosis of cancer. In this review, we also speculate on the advantages of liquid biopsy as opposed to tissue biopsy and postulate that liquid biopsy may be a comprehensive approach to overcome the current limitations associated with costly, invasive, and time-consuming tissue biopsy.
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Affiliation(s)
| | | | | | | | - Munazzah Naz
- Hirahata Gene Therapy Laboratory, HIC Clinic, Tokyo, Japan
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Abstract
Most commonly described as sporadic, pulmonary adenocarcinoma with enteric differentiation (PAED) is a rare variant of invasive lung cancer recently established and recognised by the World Health Organization. This tumour is highly heterogeneous and shares several morphological features with pulmonary and colorectal adenocarcinomas. Our objective is to summarise current research on PAED, focusing on its immunohistochemical and molecular features as potential tools for differential diagnosis from colorectal cancer, as well as prognosis definition and therapeutic choice. PAED exhibits an 'entero-like' pathological morphology in more than half cases, expressing at least one of the typical immunohistochemical markers of enteric differentiation, namely CDX2, CK20 or MUC2. For this reason, this malignancy appears often indistinguishable from a colorectal cancer metastasis, making the differential diagnosis laborious. Although standard diagnostic criteria have not been established yet, in the past few years, a number of approaches have been addressed, aimed at defining specific immunohistochemical and molecular signatures. Based on previously published literature, we have collected and analysed molecular and immunohistochemical data on this rare neoplasm, and have described the state of the art on diagnostic criteria as well as major clinical and therapeutic implications.The analysis of data from 295 patients from 58 published articles allowed us to identify the most represented immunohistochemical and molecular markers, as well as major differences between Asian PAEDs and those diagnosed in European/North American countries. The innovative molecular approaches, exploring driver mutations or new gene alterations, could help to identify rare prognostic factors and guide future tailored therapeutic approaches to this rare neoplasm.
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Pastore D, Pacifici F, Dave KR, Palmirotta R, Bellia A, Pasquantonio G, Guadagni F, Donadel G, Di Daniele N, Abete P, Lauro D, Rundek T, Perez-Pinzon MA, Della-Morte D. Age-Dependent Levels of Protein Kinase Cs in Brain: Reduction of Endogenous Mechanisms of Neuroprotection. Int J Mol Sci 2019; 20:E3544. [PMID: 31331067 PMCID: PMC6678180 DOI: 10.3390/ijms20143544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases are among the leading causes of mortality and disability worldwide. However, current therapeutic approaches have failed to reach significant results in their prevention and cure. Protein Kinase Cs (PKCs) are kinases involved in the pathophysiology of neurodegenerative diseases, such as Alzheimer's Disease (AD) and cerebral ischemia. Specifically ε, δ, and γPKC are associated with the endogenous mechanism of protection referred to as ischemic preconditioning (IPC). Existing modulators of PKCs, in particular of εPKC, such as ψεReceptor for Activated C-Kinase (ψεRACK) and Resveratrol, have been proposed as a potential therapeutic strategy for cerebrovascular and cognitive diseases. PKCs change in expression during aging, which likely suggests their association with IPC-induced reduction against ischemia and increase of neuronal loss occurring in senescent brain. This review describes the link between PKCs and cerebrovascular and cognitive disorders, and proposes PKCs modulators as innovative candidates for their treatment. We report original data showing εPKC reduction in levels and activity in the hippocampus of old compared to young rats and a reduction in the levels of δPKC and γPKC in old hippocampus, without a change in their activity. These data, integrated with other findings discussed in this review, demonstrate that PKCs modulators may have potential to restore age-related reduction of endogenous mechanisms of protection against neurodegeneration.
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Affiliation(s)
- Donatella Pastore
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Francesca Pacifici
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Kunjan R Dave
- Department of Neurology, The Evelyn McKnight Brain Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Raffaele Palmirotta
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Alfonso Bellia
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Policlinico Tor Vergata Foundation, University Hospital, 00133 Rome, Italy
| | - Guido Pasquantonio
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Fiorella Guadagni
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Roma Open University, 00166 Rome, Italy
| | - Giulia Donadel
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Nicola Di Daniele
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Policlinico Tor Vergata Foundation, University Hospital, 00133 Rome, Italy
| | - Pasquale Abete
- Department of Translational Medical Sciences, University of Naples, Federico II, 80138 Naples, Italy
| | - Davide Lauro
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Policlinico Tor Vergata Foundation, University Hospital, 00133 Rome, Italy
| | - Tatjana Rundek
- Department of Neurology, The Evelyn McKnight Brain Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Miguel A Perez-Pinzon
- Department of Neurology, The Evelyn McKnight Brain Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - David Della-Morte
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy.
- Department of Neurology, The Evelyn McKnight Brain Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Roma Open University, 00166 Rome, Italy.
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8
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Palmirotta R, Lovero D, Delacour H, Le Roy A, Cremades S, Silvestris F. Rare Dihydropyrimidine Dehydrogenase Variants and Toxicity by Floropyrimidines: A Case Report. Front Oncol 2019; 9:139. [PMID: 30915274 PMCID: PMC6421267 DOI: 10.3389/fonc.2019.00139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 02/18/2019] [Indexed: 12/11/2022] Open
Abstract
Variations in the activity, up to absolute deficiency, of the enzyme dihydropyrimidine dehydrogenase (DPD), result in the occurrence of adverse reactions to chemotherapy, and have been included among the pharmacogenetic factors underlying inter-individual variability in response to fluoropyrimidines. The study of single-nucleotide polymorphisms of the DPYD gene, which encodes the DPD enzyme, is one of the main parameters capable of predicting reduced enzymatic activity and the consequent influence on fluoropyrimidine treatment, in terms of reduction of both adverse reactions and therapeutic efficacy in disease control. In this paper, we describe a patient with metastatic breast cancer showing signs of increased toxicity following capecitabine therapy. The DPD enzyme activity analysis revealed a partial deficiency. The study of the most frequent polymorphisms of the DPYD gene suggested a wild-type genotype but indicated a novel variant c.1903A>G (p.Asn635Asp), not previously described, proximal to the splice donor site of exon 14. After excluding the potential pathogenic feature of the newly-identified variant, we performed cDNA sequencing of the entire DPYD coding sequence. This analysis identified the variants c.85T>C and c.496A>G, which were previously described as pivotal components of the haplotype associated with decreased enzyme activity and suggested that both variant alleles are related to DPD deficiency. The clinical case findings described in this study emphasize the importance of performing complete genetic analysis of the DPYD gene in order to identify rare and low frequency variants potentially responsible for toxic reactions to fluoropyrimidine treatment.
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Affiliation(s)
- Raffaele Palmirotta
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, Università degli Studi di Bari, Bari, Italy
| | - Domenica Lovero
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, Università degli Studi di Bari, Bari, Italy
| | - Hervé Delacour
- Department of Biology, Military Training Hospital Begin, Saint Mandé, France.,Val-de-Grâce Military School, Paris, France
| | - Audrey Le Roy
- Department of Oncology, Military Training Hospital Begin, Saint Mandé, France
| | - Serge Cremades
- Val-de-Grâce Military School, Paris, France.,Department of Oncology, Military Training Hospital Begin, Saint Mandé, France
| | - Franco Silvestris
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, Università degli Studi di Bari, Bari, Italy
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Assadollahi V, Rashidieh B, Alasvand M, Abdolahi A, Lopez JA. Interaction and molecular dynamics simulation study of Osimertinib (AstraZeneca 9291) anticancer drug with the EGFR kinase domain in native protein and mutated L844V and C797S. J Cell Biochem 2019; 120:13046-13055. [PMID: 30916819 DOI: 10.1002/jcb.28575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/20/2019] [Accepted: 01/24/2019] [Indexed: 01/14/2023]
Abstract
BACKGROUND Targeted therapy is a novel, promising approach to anticancer treatment that endeavors to overcome drug resistance to traditional chemotherapies. Patients with the L858R mutation in epidermal growth factor receptor (EGFR) respond to the first generation tyrosine kinase inhibitors (TKIs); however, after one year of treatment, they may become resistant. The T790M mutation is the most probable cause for drug resistance. Third generation drugs, including Osimertinib (AZD9291), are more effective against T790M and other sensitive mutations. Osimertinib is effective against the L844V mutation, has conditional effectiveness for the L718Q mutation, and is ineffective for the Cys797Ser (C797S) mutation. Cells that have both the T790M and C797 mutations are more resistant to third generation drugs. Although research has shown that Osimertinib is an effective treatment for EGFR L844V cells, this has not been shown for cells that have the C797S mutation. This molecular mechanism has not been well-studied. METHODS In the present study, we used the GROMACS software for molecular dynamics simulation to identify interactions between Osimertinib and the kinase part of EGFR in L844V and C797S mutants. RESULTS We evaluated native EGFR protein and the L844V and C797S mutations' docking and binding energy, kI, intermolecular, internal, and torsional energy parameters. Osimertinib was effective for the EGFR L844V mutation, but not for EGFR C797S. All simulations were validated by root-mean-square deviation (RMSD), root-mean square fluctuation (RMSF), and radius of gyration (ROG). CONCLUSION According to our computational simulation, the results supported the experimental models and, therefore, could confirm and predict the molecular mechanism of drug efficacy.
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Affiliation(s)
- Vahideh Assadollahi
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Behnam Rashidieh
- School of Environment and Sciences, Griffith University, Nathan, Queensland, Australia.,Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Masoud Alasvand
- Department of Medical Physiology and Pharmacology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Alina Abdolahi
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - J Alejandro Lopez
- School of Environment and Sciences, Griffith University, Nathan, Queensland, Australia.,Tumour Immunology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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Palmirotta R, Lovero D, Cafforio P, Felici C, Mannavola F, Pellè E, Quaresmini D, Tucci M, Silvestris F. Liquid biopsy of cancer: a multimodal diagnostic tool in clinical oncology. Ther Adv Med Oncol 2018; 10:1758835918794630. [PMID: 30181785 PMCID: PMC6116068 DOI: 10.1177/1758835918794630] [Citation(s) in RCA: 266] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/28/2018] [Indexed: 12/17/2022] Open
Abstract
Over the last decades, the concept of precision medicine has dramatically renewed
the field of medical oncology; the introduction of patient-tailored therapies
has significantly improved all measurable outcomes. Liquid biopsy is a
revolutionary technique that is opening previously unexpected perspectives. It
consists of the detection and isolation of circulating tumor cells, circulating
tumor DNA and exosomes, as a source of genomic and proteomic information in
patients with cancer. Many technical hurdles have been resolved thanks to newly
developed techniques and next-generation sequencing analyses, allowing a broad
application of liquid biopsy in a wide range of settings. Initially correlated
to prognosis, liquid biopsy data are now being studied for cancer diagnosis,
hopefully including screenings, and most importantly for the prediction of
response or resistance to given treatments. In particular, the identification of
specific mutations in target genes can aid in therapeutic decisions, both in the
appropriateness of treatment and in the advanced identification of secondary
resistance, aiming to early diagnose disease progression. Still application is
far from reality but ongoing research is leading the way to a new era in
oncology. This review summarizes the main techniques and applications of liquid
biopsy in cancer.
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Affiliation(s)
- Raffaele Palmirotta
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Domenica Lovero
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Paola Cafforio
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Felici
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Mannavola
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Eleonora Pellè
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Davide Quaresmini
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Tucci
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Franco Silvestris
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, 70124, Italy
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11
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Wellmann R, Borden BA, Danahey K, Nanda R, Polite BN, Stadler WM, Ratain MJ, O'Donnell PH. Analyzing the clinical actionability of germline pharmacogenomic findings in oncology. Cancer 2018; 124:3052-3065. [PMID: 29742281 DOI: 10.1002/cncr.31382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Germline and tumor pharmacogenomics impact drug responses, but germline markers less commonly guide oncology prescribing. The authors hypothesized that a critical number of clinically actionable germline pharmacogenomic associations exist, representing clinical implementation opportunities. METHODS In total, 125 oncology drugs were analyzed for positive germline pharmacogenomic associations in journals with impact factors ≥5. Studies were assessed for design and genotyping quality, clinically relevant outcomes, statistical rigor, and evidence of drug-gene effects. Associations from studies of high methodologic quality were deemed potentially clinically actionable, and translational summaries were written as point-of-care clinical decision support (CDS) tools and formally evaluated using the Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument. RESULTS The authors identified germline pharmacogenomic results for 56 of 125 oncology drugs (45%) across 173 publications. Actionable associations were detected for 12 drugs, including 6 that had germline pharmacogenomic information within US Food and Drug Administration labels or published guidelines (capecitabine/fluorouracil/dihydropyrimidine dehydrogenase [DPYD], irinotecan/uridine diphosphate glucuronosyltransferase family 1 member A1 [UGT1A1], mercaptopurine/thioguanine/thiopurine S-methyltransferase [TPMT], tamoxifen/cytochrome P450 [CYP] family 2 subfamily D member 6 [CYP2D6]), and 6 others were novel (asparaginase/nuclear factor of activated T-cells 2 [NFATC2]/human leukocyte antigen D-related β1 [HLA-DRB1], cisplatin/acylphosphatase 2 [ACYP2], doxorubicin/adenosine triphosphate-binding cassette subfamily C member 2/Rac family small guanosine triphosphatase 2/neutrophil cytosolic factor 4 [ABCC2/RAC2/NCF4], lapatinib/human leukocyte antigen DQ α1 [HLA-DQA1], sunitinib/cytochrome P450 family 3 subfamily A member 5 [CYP3A5], vincristine/centrosomal protein 72 [CEP72]). By using AGREE II, the developed CDS summaries had high mean ± standard deviation scores (maximum score, 100) for scope and purpose (92.7 ± 5.1) and rigour of development (87.6 ± 7.4) and moderate yet robust scores for clarity of presentation (58.6 ± 25.1) and applicability (55.9 ± 24.6). The overall mean guideline quality score was 5.2 ± 1.0 (maximum score, 7). Germline pharmacogenomic CDS summaries for these 12 drugs were recommended for implementation. CONCLUSIONS Several oncology drugs have actionable germline pharmacogenomic information, justifying their delivery through institutional pharmacogenomic implementations to determine clinical utility. Cancer 2018;124:3052-65. © 2018 American Cancer Society.
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Affiliation(s)
- Rebecca Wellmann
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois
| | - Brittany A Borden
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois
| | - Keith Danahey
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Center for Research Informatics, The University of Chicago, Chicago, Illinois
| | - Rita Nanda
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Blase N Polite
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Walter M Stadler
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Mark J Ratain
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois.,Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois
| | - Peter H O'Donnell
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois.,Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois
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12
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Palmirotta R, Lovero D, Silvestris E, Felici C, Quaresmini D, Cafforio P, Silvestris F. Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA). Cancer Genomics Proteomics 2018; 14:173-179. [PMID: 28446532 DOI: 10.21873/cgp.20029] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS). However, the sequence of these molecular techniques is time-consuming and may also favor operator-dependent errors, related to the procedures themselves that, as in the case of the WGA technique, might affect downstream molecular analyses. MATERIALS AND METHODS A preliminary approach of molecular analysis by NGS on a model of CTCs without previous WGA procedural step was performed. We set-up an artificial sample obtained by spiking the SK-MEL-28 melanoma cell line in normal donor peripheral whole blood. Melanoma cells were first enriched using an AutoMACS® (Miltenyi) cell separator and then isolated as single and pooled CTCs by DEPArray™ System (Silicon Biosystems). NGS analysis, using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies) with the Ion Torrent PGM™ system (Life Technologies), was performed on the SK-MEL-28 cell pellet, a single CTC previously processed with WGA and on 1, 2, 4 and 8 recovered CTCs without WGA pre-amplification. RESULTS NGS directly carried out on CTCs without WGA showed the same mutations identified in SK-MEL-28 cell line pellet, with a considerable efficiency and avoiding the errors induced by the WGA procedure. CONCLUSION We identified a cost-effective, time-saving and reliable methodological approach that could improve the analytical accuracy of the liquid biopsy and appears promising in studying CTCs from cancer patients for both research and clinical purposes.
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Affiliation(s)
- Raffaele Palmirotta
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Domenica Lovero
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Erica Silvestris
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Claudia Felici
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Davide Quaresmini
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Paola Cafforio
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Franco Silvestris
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
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13
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Palmirotta R, Quaresmini D, Lovero D, Silvestris F. ALK gene alterations in cancer: biological aspects and therapeutic implications. Pharmacogenomics 2017; 18:277-292. [DOI: 10.2217/pgs-2016-0166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
ALK was first reported in 1994 as a translocation in anaplastic large cell lymphoma and then described with different abnormalities in a number of tumors. Recently, a shortly accumulated biomedical research clarified the numerous biological processes underlying its ability to support cancer development, growth and progression. Advent of precision medicine has finally provided unexpected advances, leading to the development of ALK-targeting inhibitors with superior efficacy as compared with standard chemotherapy regimens, as well as the identification of resistance mechanisms and the creation of ‘next-generation’ treatments. This review summarizes the current understanding of ALK-driven cancers from the oncogenesis and mutation frequency by The Cancer Genome Atlas database through the diagnostic approach, to an updated portrait of available tyrosine kinase inhibitors, considering their effectiveness in cancer treatment, the molecular reasons of therapeutic failure, and the actual and future ways to overcome resistances.
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Affiliation(s)
- Raffaele Palmirotta
- Department of Biomedical Sciences & Human Oncology, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Davide Quaresmini
- Department of Biomedical Sciences & Human Oncology, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Domenica Lovero
- Department of Biomedical Sciences & Human Oncology, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Franco Silvestris
- Department of Biomedical Sciences & Human Oncology, University of Bari ‘Aldo Moro’, Bari, Italy
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14
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Chen S, Sutiman N, Zhang CZ, Yu Y, Lam S, Khor CC, Chowbay B. Pharmacogenetics of irinotecan, doxorubicin and docetaxel transporters in Asian and Caucasian cancer patients: a comparative review. Drug Metab Rev 2016; 48:502-540. [DOI: 10.1080/03602532.2016.1226896] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Serra M, Hattinger CM. The pharmacogenomics of osteosarcoma. THE PHARMACOGENOMICS JOURNAL 2016; 17:11-20. [PMID: 27241064 DOI: 10.1038/tpj.2016.45] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/15/2016] [Accepted: 05/04/2016] [Indexed: 12/30/2022]
Abstract
Osteosarcoma (OS), the most common malignant tumor of bone, is presently treated with multidrug neoadjuvant chemotherapy protocols, which allow to cure 60-65% of patients but also induce toxicity events that cannot be predicted or efficiently prevented. The identification and validation of pharmacogenomic biomarkers is, therefore, absolutely warranted to provide the bases for planning personalized treatments with the aim to increase the therapeutic benefits and to avoid or limit unnecessary toxicities. As several targeted therapies against molecular and immunological markers in OS are presently under clinical investigation, it may be speculated that some new agents for innovative treatments may emerge in the next years. However, the real improvement of therapeutic perspectives for OS is strictly connected to the identification of pharmacogenomic biomarkers that may stratify patients in responders or non-responders and identify those individuals with higher susceptibility to treatment-associated toxicity. This review provides an overview of the pharmacogenomic biomarkers identified so far in OS, which appear to be promising candidates for a translation to clinical practice, after further investigation and/or prospective validation.
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Affiliation(s)
- M Serra
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - C M Hattinger
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
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16
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Association of ABCB1 and ABCG2 single nucleotide polymorphisms with clinical findings and response to chemotherapy treatments in Kurdish patients with breast cancer. Tumour Biol 2015; 37:7901-6. [DOI: 10.1007/s13277-015-4679-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 12/16/2015] [Indexed: 12/22/2022] Open
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17
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Zeron-Medina J, Ochoa de Olza M, Braña I, Rodon J. The Personalization of Therapy: Molecular Profiling Technologies and Their Application. Semin Oncol 2015; 42:775-87. [DOI: 10.1053/j.seminoncol.2015.09.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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Morales-Espinosa D, García-Román S, Karachaliou N, Rosell R. Pharmacogenomics in the treatment of lung cancer: an update. Pharmacogenomics 2015; 16:1751-60. [DOI: 10.2217/pgs.15.99] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Significant advances have been made in the analysis of the human genome in the first decades of the 21st century and understanding of tumor biology has matured greatly. The identification of tumor-associated mutations and the pathways involved has led to the development of targeted anticancer therapies. However, the challenge now in using chemotherapy to treat nonsmall-cell lung cancer is to identify more molecular markers predictive of drug sensitivity and determine the optimal drug sequences in order to tailor treatment to each patient. This approach could permit selection of patients who could benefit most from a specific type of chemotherapy by matching their tumor and individual genetic profile. Nevertheless, this potential has been limited so far by reliance on the single biomarker approach, though this is now on the way to being overcome through whole genome studies.
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Affiliation(s)
- Daniela Morales-Espinosa
- Translational Research Laboratory, Catalan Institute of Oncology, Hospital Universitari Germans Trias I Pujol, Ctra Canyet s/n, Badalona, 08916 Barcelona, Spain
- Fundación Clínica, Médica Sur, Mexico City, Mexico
- Carcinogenesis Laboratory, National Cancer Institute, Mexico City, México
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | - Niki Karachaliou
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Rafael Rosell
- Translational Research Laboratory, Catalan Institute of Oncology, Hospital Universitari Germans Trias I Pujol, Ctra Canyet s/n, Badalona, 08916 Barcelona, Spain
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
- Pangaea Biotech S.L., Barcelona, Spain
- Molecular Oncology Research (MORe) Foundation, Barcelona, Spain
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19
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Simhadri VL, Banerjee AS, Simon J, Kimchi-Sarfaty C, Sauna ZE. Personalized approaches to the treatment of hemophilia A and B. Per Med 2015; 12:403-415. [PMID: 29771661 DOI: 10.2217/pme.15.6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The recognition that individuals respond differently to the same medication is not new and dates almost to the founding of western medicine. In the last century it came to be recognized that genetic factors influence the heterogeneity of individual responses to medications with respect to both toxicity and effectiveness. Nonetheless, it has been challenging to integrate pharmacogenetic approaches in the routine practice of medicine as the identification of biomarkers is difficult due to the inherent complexity of biological systems. Here, we present potential applications of pharmacogenetics in managing hemophilia A and B. We discuss how predicting and circumventing immunogenicity, an important impediment to treating hemophilia patients, particularly lends itself to a pharmacogenetic approach. In addition, we discuss new trends toward personalizing the management of hemophilia in clinical settings.
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Affiliation(s)
- Vijaya L Simhadri
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Aditi Sengupta Banerjee
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Jonathan Simon
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Chava Kimchi-Sarfaty
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
| | - Zuben E Sauna
- Laboratory of Hemostasis, Division of Hematology Research & Review, Center for Biologics Evaluation & Research, Food & Drug Administration, New Hampshire Ave, Silver Spring, MD 20993, USA
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20
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Jaiswal AS, Panda H, Law BK, Sharma J, Jani J, Hromas R, Narayan S. NSC666715 and Its Analogs Inhibit Strand-Displacement Activity of DNA Polymerase β and Potentiate Temozolomide-Induced DNA Damage, Senescence and Apoptosis in Colorectal Cancer Cells. PLoS One 2015; 10:e0123808. [PMID: 25933036 PMCID: PMC4416822 DOI: 10.1371/journal.pone.0123808] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 03/07/2015] [Indexed: 01/29/2023] Open
Abstract
Recently approved chemotherapeutic agents to treat colorectal cancer (CRC) have made some impact; however, there is an urgent need for newer targeted agents and strategies to circumvent CRC growth and metastasis. CRC frequently exhibits natural resistance to chemotherapy and those who do respond initially later acquire drug resistance. A mechanism to potentially sensitize CRC cells is by blocking the DNA polymerase β (Pol-β) activity. Temozolomide (TMZ), an alkylating agent, and other DNA-interacting agents exert DNA damage primarily repaired by a Pol-β-directed base excision repair (BER) pathway. In previous studies, we used structure-based molecular docking of Pol-β and identified a potent small molecule inhibitor (NSC666715). In the present study, we have determined the mechanism by which NSC666715 and its analogs block Fen1-induced strand-displacement activity of Pol-β-directed LP-BER, cause apurinic/apyrimidinic (AP) site accumulation and induce S-phase cell cycle arrest. Induction of S-phase cell cycle arrest leads to senescence and apoptosis of CRC cells through the p53/p21 pathway. Our initial findings also show a 10-fold reduction of the IC50 of TMZ when combined with NSC666715. These results provide a guide for the development of a target-defined strategy for CRC chemotherapy that will be based on the mechanisms of action of NSC666715 and TMZ. This combination strategy can be used as a framework to further reduce the TMZ dosages and resistance in CRC patients.
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Affiliation(s)
- Aruna S. Jaiswal
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Harekrushna Panda
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Brian K. Law
- Department of Pharmacology and Experimental Therapeutics, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Jay Sharma
- Celprogen Inc., Torrance, California, 90503, United States of America
| | - Jitesh Jani
- Celprogen Inc., Torrance, California, 90503, United States of America
| | - Robert Hromas
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, 32610, United States of America
- * E-mail:
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22
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Haghgoo SM, Allameh A, Mortaz E, Garssen J, Folkerts G, Barnes PJ, Adcock IM. Pharmacogenomics and targeted therapy of cancer: Focusing on non-small cell lung cancer. Eur J Pharmacol 2015; 754:82-91. [PMID: 25725115 DOI: 10.1016/j.ejphar.2015.02.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/11/2015] [Accepted: 02/17/2015] [Indexed: 12/20/2022]
Abstract
Recent studies have been established high degree of genetic diversity in solid organ tumors among individuals and even between individual tumor cells. This intratumor and intertumor genetic diversity results in a heterogeneous tumor with unique characteristics which potentially allows effective drug therapy. The goal of pharmacogenomics is to elucidate the genetic network(s) that underlie drug efficacy and drug resistance. Advances in targeted and personalized therapy play an increasingly important role in many common cancers, notably lung cancer, due to the high incidence, prevalence, mortality and the greater tendency towards drug resistance seen in these patients. Non-small cell lung cancer (NSCLC) is characterized by mutations in the epidermal growth factor receptor (EGFR) and or downstream kinase pathways. This has led to the development of highly selective monoclonal antibodies and EGFR tyrosine kinase inhibitors (EGFR-TKIs) to prevent cancer initiation, proliferation, differentiation, angiogenesis, survival, and invasion. However, resistance to many of these new treatments is induced and further pharmacogenomic analysis has revealed mutations associated with increased or reduced drug efficacy. Combinations of kinase inhibitors or potentially the targeting of cancer stem cells may further increase the success of pharmacogenomics in treating patients with lung cancer.
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Affiliation(s)
- Seyyed Mortaza Haghgoo
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abdolamir Allameh
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Esmaeil Mortaz
- Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, UK; Department of Immunology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Chronic Respiratory Diseases Research Center and National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands; Nutricia Research, Immunology, Utrecht, The Netherlands
| | - Gert Folkerts
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Peter J Barnes
- Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Ian M Adcock
- Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
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Palmirotta R, De Marchis ML, Ludovici G, Ferroni P, Abete P, Guadagni F, Della-Morte D. Diagnostic procedures for paraffin-embedded tissues analysis in pharmacogenomic studies. Methods Mol Biol 2014; 1175:45-65. [PMID: 25150866 DOI: 10.1007/978-1-4939-0956-8_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this book chapter we report our own experience of mutational analysis in selecting tailored anticancer treatments for solid tumors. Our Department of Advanced Biotechnologies and Bioimaging, IRCCS San Raffaele Pisana, Rome, Italy, routinely performs pharmacogenetic screenings for different genes such as K-ras, BRAF, KIT, PDGFRα, and EGFR on paraffin-embedded cancer sections. Therefore, the chapter describes the mutational analysis procedures on paraffin-embedded tumors aimed to predict individual response to anticancer therapy. These molecular diagnostic methodologies may help us in improving the translational impact of genetic information on clinical practice.
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Affiliation(s)
- Raffaele Palmirotta
- Department of Advanced Biotechnologies and Bioimaging, IRCCS San Raffaele Pisana, Rome, Italy
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A reliable and reproducible technique for DNA fingerprinting in biorepositories: a pilot study from BioBIM. Int J Biol Markers 2013; 28:e398-404. [PMID: 23873620 DOI: 10.5301/jbm.5000044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2013] [Indexed: 02/04/2023]
Abstract
Standard operating procedures (SOPs) optimization for nucleic acid extraction from stored samples is of crucial importance in a biological repository, considering the large number of collected samples and their future downstream molecular and biological applications. However, the validity of molecular studies using stored specimens depends not only on the integrity of the biological samples, but also on the procedures that ensure the traceability of the same sample, certifying its uniqueness, and ensuring the identification of potential sample contaminations. With this aim, we have developed a rapid, reliable, low-cost, and simple DNA fingerprinting tool for a routine use in quality control of biorepositories samples. The method consists of a double ALU insertion/deletion genotyping panel suitable for uniqueness, identification of sample contaminations, and gender validation. Preliminary data suggest that this easy-to-use DNA fingerprinting protocol could routinely provide assurances of DNA identity and quality in a biorepository setting.
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Lee JS, Cheong HS, Kim LH, Kim JO, Seo DW, Kim YH, Chung MW, Han SY, Shin HD. Screening of Genetic Polymorphisms of CYP3A4 and CYP3A5 Genes. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2013; 17:479-84. [PMID: 24381495 PMCID: PMC3874433 DOI: 10.4196/kjpp.2013.17.6.479] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 05/16/2013] [Accepted: 11/10/2013] [Indexed: 11/15/2022]
Abstract
Given the CYP3A4 and CYP3A5's impact on the efficacy of drugs, the genetic backgrounds of individuals and populations are regarded as an important factor to be considered in the prescription of personalized medicine. However, genetic studies with Korean population are relatively scarce compared to those with other populations. In this study, we aimed to identify CYP3A4/5 polymorphisms and compare the genotype distributions among five ethnicities. To identify CYP3A4/5 SNPs, we first performed direct sequencing with 288 DNA samples which consisted of 96 Koreans, 48 European-Americans, 48 African-Americans, 48 Han Chinese, and 48 Japanese. The direct sequencing identified 15 novel SNPs, as well as 42 known polymorphisms. We defined the genotype distributions, and compared the allele frequencies among five ethnicities. The results showed that minor allele frequencies of Korean population were similar with those of the Japanese and Han Chinese populations, whereas there were distinct differences from European-Americans or African-Americans. Among the pharmacogenetic markers, frequencies of CYP3A4*1B (rs2740574) and CYP3A5*3C (rs776742) in Asian groups were different from those in other populations. In addition, minor allele frequency of CYP3A4*18 (rs28371759) was the highest in Korean population. Additional in silico analysis predicted that two novel non-synonymous SNPs in CYP3A5 (+27256C>T, P389S and +31546T>G, I488S) could alter protein structure. The frequency distributions of the identified polymorphisms in the present study may contribute to the expansion of pharmacogenetic knowledge.
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Affiliation(s)
- Jin Sol Lee
- Department of Life Science, Sogang University, Seoul 121-742, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Korea
| | - Doo Won Seo
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong 363-700, Korea
| | - Young Hoon Kim
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong 363-700, Korea
| | - Myeon Woo Chung
- Clinical Research Division, Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong 363-700, Korea
| | - Soon Young Han
- Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong 363-700, Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul 121-742, Korea. ; Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Korea
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Shin JG, Cheong HS, Kim JY, Kim LH, Han CS, Kim JO, Kim HD, Kim YH, Chung MW, Han SY, Shin HD. Screening of dihydropyrimidine dehydrogenase genetic variants by direct sequencing in different ethnic groups. J Korean Med Sci 2013; 28:1129-33. [PMID: 23960437 PMCID: PMC3744698 DOI: 10.3346/jkms.2013.28.8.1129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 06/07/2013] [Indexed: 12/15/2022] Open
Abstract
Dihydropyrimidine dehydrogenase (DPYD) is an enzyme that regulates the rate-limiting step in pyrimidine metabolism, especially catabolism of fluorouracil, a chemotherapeutic agent for cancer. In order to determine the genetic distribution of DPYD, we directly sequenced 288 subjects from five ethnic groups (96 Koreans, 48 Japanese, 48 Han Chinese, 48 African Americans, and 48 European Americans). As a result, 56 polymorphisms were observed, including 6 core polymorphisms and 18 novel polymorphisms. Allele frequencies were nearly the same across the Asian populations, Korean, Han Chinese and Japanese, whereas several SNPs showed different genetic distributions between Asians and other ethnic populations (African American and European American). Additional in silico analysis was performed to predict the function of novel SNPs. One nonsynonymous SNP (+199381A > G, Asn151Asp) was predicted to change its polarity of amino acid (Asn, neutral to Asp, negative). These findings would be valuable for further research, including pharmacogenetic and drug responses studies.
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Affiliation(s)
- Joong-Gon Shin
- Department of Life Science, Sogang University, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | | | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Chang Soo Han
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Hae Deun Kim
- Clinical Research Division, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Korea
| | - Young Hoon Kim
- Clinical Research Division, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Korea
| | - Myeon Woo Chung
- Clinical Research Division, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Korea
| | - Soon Young Han
- Toxicological Evaluation and Research Department, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Korea
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
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Hohenforst-Schmidt W, Zarogoulidis P, Darwiche K, Vogl T, Goldberg EP, Huang H, Simoff M, Li Q, Browning R, Turner FJ, Le Pivert P, Spyratos D, Zarogoulidis K, Celikoglu SI, Celikoglu F, Brachmann J. Intratumoral chemotherapy for lung cancer: re-challenge current targeted therapies. DRUG DESIGN DEVELOPMENT AND THERAPY 2013; 7:571-83. [PMID: 23898222 PMCID: PMC3718837 DOI: 10.2147/dddt.s46393] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Strategies to enhance the already established doublet chemotherapy regimen for lung cancer have been investigated for more than 20 years. Initially, the concept was to administer chemotherapy drugs locally to the tumor site for efficient diffusion through passive transport within the tumor. Recent advances have enhanced the diffusion of pharmaceuticals through active transport by using pharmaceuticals designed to target the genome of tumors. In the present study, five patients with non-small cell lung cancer epidermal growth factor receptor (EGFR) negative stage IIIa–IV International Union Against Cancer 7 (UICC-7), and with Eastern Cooperative Oncology Group (ECOG) 2 scores were administered platinum-based doublet chemotherapy using combined intratumoral-regional and intravenous route of administration. Cisplatin analogues were injected at 0.5%–1% concentration within the tumor lesion and proven malignant lymph nodes according to pretreatment histological/cytological results and the concentration of systemic infusion was decreased to 70% of a standard protocol. This combined intravenous plus intratumoral-regional chemotherapy is used as a first line therapy on this short series of patients. To the best of our knowledge this is the first report of direct treatment of involved lymph nodes with cisplatin by endobronchial ultrasound drug delivery with a needle without any adverse effects. The initial overall survival and local response are suggestive of a better efficacy compared to established doublet cisplatin–based systemic chemotherapy in (higher) standard concentrations alone according to the UICC 7 database expected survival. An extensive search of the literature was performed to gather information of previously published literature of intratumoral chemo-drug administration and formulation for this treatment modality. Our study shows a favorable local response, more than a 50% reduction, for a massive tumor mass after administration of five sessions of intratumoral chemotherapy plus two cycles of low-dose intravenous chemotherapy according to our protocol. These encouraging results (even in very sick ECOG 2 patients with central obstructive non-small cell lung cancer having a worse prognosis and quality of life than a non-small cell lung cancer in ECOG 0 of the same tumor node metastasis [TNM]-stage without central obstruction) for a chemotherapy-only protocol that differs from conventional cisplatin-based doublet chemotherapy by the route, target site, and dose paves the way for broader applications of this technique. Finally, future perspectives of this treatment and pharmaceutical design for intratumoral administration are presented.
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28
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Stankov K, Sabo A, Mikov M. Pharmacogenetic Biomarkers as Tools for Pharmacoepidemiology of Severe Adverse Drug Reactions. Drug Dev Res 2012. [DOI: 10.1002/ddr.21050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Karmen Stankov
- Clinical Center of Vojvodina; Medical Faculty Novi Sad; University of Novi Sad; 21000; Novi Sad; Serbia
| | - Ana Sabo
- Department of Pharmacology, Toxicology and Clinical Pharmacology; Medical Faculty Novi Sad; University of Novi Sad; 21000; Novi Sad; Serbia
| | - Momir Mikov
- Department of Pharmacology, Toxicology and Clinical Pharmacology; Medical Faculty Novi Sad; University of Novi Sad; 21000; Novi Sad; Serbia
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29
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Ermini ML, Mariani S, Scarano S, Campa D, Barale R, Minunni M. Single nucleotide polymorphism detection by optical DNA-based sensing coupled with whole genomic amplification. Anal Bioanal Chem 2012; 405:985-93. [PMID: 22955671 DOI: 10.1007/s00216-012-6345-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/01/2012] [Accepted: 08/08/2012] [Indexed: 12/11/2022]
Abstract
The work presented here deals with the optimization of a strategy for detection of single nucleotide polymorphisms based on surface plasmon resonance imaging. First, a sandwich-like assay was designed, and oligonucleotide sequences were computationally selected in order to study optimized conditions for the detection of the rs1045642 single nucleotide polymorphism in the gene ABCB1. Then the strategy was optimized on a surface plasmon resonance imaging biosensor using synthetic DNA sequences in order to evaluate the best conditions for the detection of a single mismatching base. Finally, the assay was tested on DNA extracted from human blood which was subsequently amplified using a whole genome amplification kit. The direct detection of the polymorphism was successfully achieved. The biochip was highly regenerable and reusable for up to 20 measurements. Furthermore, coupling these promising results with the multiarray assay, we can foresee applying this biosensor in clinical research extended to concurrent analysis of different polymorphisms.
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Affiliation(s)
- M L Ermini
- Dipartimento di Chimica, Università di Firenze, Sesto Fiorentino, Italy
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30
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Wei CY, Lee MTM, Chen YT. Pharmacogenomics of adverse drug reactions: implementing personalized medicine. Hum Mol Genet 2012; 21:R58-65. [PMID: 22907657 DOI: 10.1093/hmg/dds341] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pharmacogenomics aims to investigate the genetic basis of inter-individual differences in drug responses, such as efficacy, dose requirements and adverse events. Research in pharmacogenomics has grown over the past decade, evolving from a candidate-gene approach to genome-wide association studies (GWASs). Genetic variants in genes coding for drug metabolism, drug transport and more recently human-leukocyte antigens (HLAs) have been linked to inter-individual differences in the risk of adverse drug reactions (ADRs). The tight association of specific HLA alleles with Stevens-Johnson syndrome, toxic epidermal necrolysis, drug hypersensitivity syndrome and drug-induced liver injury underscore the importance of HLA in the pathogenesis of these idiosyncratic drug hypersensitivity reactions. However, as with the search for the genetic basis for common diseases, pharmacogenomic research, including GWAS, has so far been a disappointment in discovering major gene variants responsible for the efficacy of drugs used to treat common diseases. This review focuses on the pharmacogenomics of ADRs, the underlying mechanisms and the potential use of genomic biomarkers in clinical practice for dose adjustment and the avoidance of drug toxicity. We also discuss obstacles to the implementation of pharmacogenomics and the direction of future translational research.
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Affiliation(s)
- Chun-Yu Wei
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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