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Lamba JK, Marrero R, Wu H, Cao X, Parcha PK, Karol SE, Inaba H, Kuo DJ, Degar BA, Heym K, Taub JW, Lacayo NJ, Pui CH, Ribeiro RC, Pounds SB, Rubnitz JE. Pharmacogenomics, Race, and Treatment Outcome in Pediatric Acute Myeloid Leukemia. JAMA Netw Open 2024; 7:e2411726. [PMID: 38753328 PMCID: PMC11099689 DOI: 10.1001/jamanetworkopen.2024.11726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/15/2024] [Indexed: 05/19/2024] Open
Abstract
Importance Disparities in outcomes exist between Black and White patients with acute myeloid leukemia (AML), with Black patients experiencing poorer prognosis compared with their White counterparts. Objective To assess whether varying intensity of induction therapy to treat pediatric AML is associated with reduced disparities in treatment outcome by race. Design, Setting, and Participants A comparative effectiveness analysis was conducted of 86 Black and 359 White patients with newly diagnosed AML who were enrolled in the AML02 trial from 2002 to 2008 or the AML08 trial from 2008 to 2017. Statistical analysis was conducted from July 2023 through January 2024. Interventions Patients in AML02 were randomly assigned to receive standard low-dose cytarabine-based induction therapy or augmented high-dose cytarabine-based induction therapy, whereas patients in AML08 received high-dose cytarabine-based therapy. Main Outcomes and Measures Cytarabine pharmacogenomic 10-single-nucleotide variant (ACS10) scores were evaluated for association with outcome according to race and treatment arm. Results This analysis included 86 Black patients (mean [SD] age, 8.8 [6.5] years; 54 boys [62.8%]; mean [SD] leukocyte count, 52 600 [74 000] cells/µL) and 359 White patients (mean [SD] age, 9.1 [6.2] years; 189 boys [52.6%]; mean [SD] leukocyte count, 54 500 [91 800] cells/µL); 70 individuals with other or unknown racial and ethnic backgrounds were not included. Among all patients without core binding factor AML who received standard induction therapy, Black patients had significantly worse outcomes compared with White patients (5-year event-free survival rate, 25% [95% CI, 9%-67%] compared with 56% [95% CI, 46%-70%]; P = .03). By contrast, among all patients who received augmented induction therapy, there were no differences in outcome according to race (5-year event-free survival rate, Black patients, 50% [95% CI, 38%-67%]; White patients, 48% [95% CI, 42%-55%]; P = .78). Among patients who received standard induction therapy, those with low ACS10 scores had a significantly worse 5-year event-free survival rate compared with those with high scores (42.4% [95% CI, 25.6%-59.3%] and 70.0% [95% CI, 56.6%-83.1%]; P = .004); however, among patients who received augmented induction therapy, there were no differences in 5-year event-free survival rates according to ACS10 score (low score, 60.6% [95% CI, 50.9%-70.2%] and high score, 54.8% [95% CI, 47.1%-62.5%]; P = .43). Conclusions and Relevance In this comparative effectiveness study of pediatric patients with AML treated in 2 consecutive clinical trials, Black patients had worse outcomes compared with White patients after treatment with standard induction therapy, but this disparity was eliminated by treatment with augmented induction therapy. When accounting for ACS10 scores, no outcome disparities were seen between Black and White patients. Our results suggest that using pharmacogenomics parameters to tailor induction regimens for both Black and White patients may narrow the racial disparity gap in patients with AML.
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Affiliation(s)
- Jatinder K. Lamba
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville
- University of Florida Health Cancer Center, University of Florida, Gainesville
- Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville
| | - Richard Marrero
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville
| | - Huiyun Wu
- Department of Biostatistics, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Xueyuan Cao
- Department of Health Promotion and Disease Prevention, University of Tennessee Health Science Center, Memphis
| | - Phani Krisha Parcha
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville
| | - Seth E. Karol
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Hiroto Inaba
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Dennis John Kuo
- Division of Pediatric Hematology-Oncology, Rady Children’s Hospital San Diego/University of California, San Diego
| | - Barbara A. Degar
- Hematology/Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
| | - Kenneth Heym
- Hematology/Oncology, Cook Children’s Medical Center, Fort Worth, Texas
| | - Jeffrey W. Taub
- Hematology/Oncology, Children’s Hospital of Michigan, Detroit
| | - Norman J. Lacayo
- Hematology/Oncology, Lucile Packard Children’s Hospital, Palo Alto, California
- Hematology/Oncology, Stanford Cancer Institute, Palo Alto, California
| | - Ching-Hon Pui
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Raul C. Ribeiro
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Stanley B. Pounds
- Department of Biostatistics, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Jeffrey E. Rubnitz
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
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2
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Liu M, Khasiyev F, Sariya S, Spagnolo‐Allende A, Sanchez DL, Andrews H, Yang Q, Beiser A, Qiao Y, Thomas EA, Romero JR, Rundek T, Brickman AM, Manly JJ, Elkind MSV, Seshadri S, Chen C, Hilal S, Wasserman BA, Tosto G, Fornage M, Gutierrez J. Chromosome 10q24.32 Variants Associate With Brain Arterial Diameters in Diverse Populations: A Genome-Wide Association Study. J Am Heart Assoc 2023; 12:e030935. [PMID: 38038215 PMCID: PMC10727334 DOI: 10.1161/jaha.123.030935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Brain arterial diameters (BADs) are novel imaging biomarkers of cerebrovascular disease, cognitive decline, and dementia. Traditional vascular risk factors have been associated with BADs, but whether there may be genetic determinants of BADs is unknown. METHODS AND RESULTS The authors studied 4150 participants from 6 geographically diverse population-based cohorts (40% European, 14% African, 22% Hispanic, 24% Asian ancestries). Brain arterial diameters for 13 segments were measured and averaged to obtain a global measure of BADs as well as the posterior and anterior circulations. A genome-wide association study revealed 14 variants at one locus associated with global BAD at genome-wide significance (P<5×10-8) (top single-nucleotide polymorphism, rs7921574; β=0.06 [P=1.54×10-8]). This locus mapped to an intron of CNNM2. A trans-ancestry genome-wide association study meta-analysis identified 2 more loci at NT5C2 (rs10748839; P=2.54×10-8) and AS3MT (rs10786721; P=4.97×10-8), associated with global BAD. In addition, 2 single-nucleotide polymorphisms colocalized with expression of CNNM2 (rs7897654; β=0.12 [P=6.17×10-7]) and AL356608.1 (rs10786719; β=-0.17 [P=6.60×10-6]) in brain tissue. For the posterior BAD, 2 variants at one locus mapped to an intron of TCF25 were identified (top single-nucleotide polymorphism, rs35994878; β=0.11 [P=2.94×10-8]). For the anterior BAD, one locus at ADAP1 was identified in trans-ancestry genome-wide association analysis (rs34217249; P=3.11×10-8). CONCLUSIONS The current study reveals 3 novel risk loci (CNNM2, NT5C2, and AS3MT) associated with BADs. These findings may help elucidate the mechanism by which BADs may influence cerebrovascular health.
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Affiliation(s)
- Minghua Liu
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Farid Khasiyev
- Department of NeurologySaint Louis University School of MedicineSt. LouisMOUSA
| | - Sanjeev Sariya
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Antonio Spagnolo‐Allende
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Danurys L Sanchez
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Howard Andrews
- Biostatistics Department, Mailman School of Public HealthColumbia UniversityNew YorkNYUSA
| | - Qiong Yang
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Alexa Beiser
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Ye Qiao
- Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Emy A Thomas
- Brown Foundation Institute of Molecular Medicine, McGovern Medical SchoolThe University of Texas Health Science Center at HoustonHoustonTXUSA
| | | | - Tatjana Rundek
- Department of NeurologyUniversity of Miami Miller School of MedicineMiamiFLUSA
- Department of Public Health SciencesUniversity of Miami Miller School of MedicineMiamiFLUSA
- Evelyn F. McKnight Brain InstituteUniversity of Miami Miller School of MedicineMiamiFLUSA
| | - Adam M Brickman
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Jennifer J Manly
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Mitchell SV Elkind
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Department of Epidemiology, Mailman School of Public HealthColumbia UniversityNew YorkNYUSA
| | - Sudha Seshadri
- Department of NeurologyBoston University School of MedicineBostonMAUSA
- The Glenn Biggs Institute for Alzheimer’s and Neurodegenerative DiseasesUniversity of Texas Health Sciences CenterSan AntonioTXUSA
| | - Christopher Chen
- Memory Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Saima Hilal
- Memory Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Bruce A Wasserman
- Johns Hopkins University School of MedicineBaltimoreMDUSA
- University of Maryland School of MedicineBaltimoreMDUSA
| | - Giuseppe Tosto
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical SchoolThe University of Texas Health Science Center at HoustonHoustonTXUSA
- Human Genetics Center, School of Public HealthThe University of Texas Health Science Center at HoustonHoustonTXUSA
| | - Jose Gutierrez
- Department of Neurology, Vagelos College of Physicians and SurgeonsColumbia UniversityNew YorkNYUSA
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Hruba L, Das V, Hajduch M, Dzubak P. Nucleoside-based anticancer drugs: Mechanism of action and drug resistance. Biochem Pharmacol 2023; 215:115741. [PMID: 37567317 DOI: 10.1016/j.bcp.2023.115741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Nucleoside-based drugs, recognized as purine or pyrimidine analogs, have been potent therapeutic agents since their introduction in 1950, deployed widely in the treatment of diverse diseases such as cancers, myelodysplastic syndromes, multiple sclerosis, and viral infections. These antimetabolites establish complex interactions with cellular molecular constituents, primarily via activation of phosphorylation cascades leading to consequential interactions with nucleic acids. However, the therapeutic efficacy of these agents is frequently compromised by the development of drug resistance, a continually emerging challenge in their clinical application. This comprehensive review explores the mechanisms of resistance to nucleoside-based drugs, encompassing a wide spectrum of phenomena from alterations in membrane transporters and activating kinases to changes in drug elimination strategies and DNA damage repair mechanisms. The critical analysis in this review underlines complex interactions of drug and cell and also guides towards novel therapeutic strategies to counteract resistance. The development of targeted therapies, novel nucleoside analogs, and synergistic drug combinations are promising approaches to restore tumor sensitivity and improve patient outcomes.
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Affiliation(s)
- Lenka Hruba
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Olomouc, Czech Republic
| | - Viswanath Das
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Olomouc, Czech Republic; Laboratory of Experimental Medicine, University Hospital, Olomouc 779 00, Czech Republic
| | - Petr Dzubak
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Olomouc, Czech Republic; Laboratory of Experimental Medicine, University Hospital, Olomouc 779 00, Czech Republic.
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4
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Marrero RJ, Cao X, Wu H, Elsayed AH, Klco JM, Ribeiro RC, Rubnitz JE, Ma X, Meshinchi S, Aplenc R, Kolb EA, Ries RE, Alonzo TA, Pounds SB, Lamba JK. SAMHD1 single nucleotide polymorphisms impact outcome in children with newly diagnosed acute myeloid leukemia. Blood Adv 2023; 7:2538-2550. [PMID: 36689724 PMCID: PMC10242642 DOI: 10.1182/bloodadvances.2022009088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/08/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Cytarabine arabinoside (Ara-C) has been the cornerstone of acute myeloid leukemia (AML) chemotherapy for decades. After cellular uptake, it is phosphorylated into its active triphosphate form (Ara-CTP), which primarily exerts its cytotoxic effects by inhibiting DNA synthesis in proliferating cells. Interpatient variation in the enzymes involved in the Ara-C metabolic pathway has been shown to affect intracellular abundance of Ara-CTP and, thus, its therapeutic benefit. Recently, SAMHD1 (SAM and HD domain-containing deoxynucleoside triphosphate triphosphohydrolase 1) has emerged to play a role in Ara-CTP inactivation, development of drug resistance, and, consequently, clinical response in AML. Despite this, the impact of genetic variations in SAMHD1 on outcome in AML has not been investigated in depth. In this study, we evaluated 25 single nucleotide polymorphisms (SNPs) within the SAMHD1 gene for association with clinical outcome in 400 pediatric patients with newly diagnosed AML from 2 clinical trials, AML02 and AML08. Three SNPs, rs1291128, rs1291141, and rs7265241 located in the 3' region of SAMHD1 were significantly associated with at least 1 clinical outcome: minimal residual disease after induction I, event-free survival (EFS), or overall survival (OS) in the 2 cohorts. In an independent cohort of patients from the COG-AAML1031 trial (n = 854), rs7265241 A>G remained significantly associated with EFS and OS. In multivariable analysis, all the SNPs remained independent predictors of clinical outcome. These results highlight the relevance of the SAMHD1 pharmacogenomics in context of response to Ara-C in AML and warrants the need for further validation in expanded patient cohorts.
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Affiliation(s)
- Richard J. Marrero
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL
| | - Xueyuan Cao
- Department of Health Promotion and Disease Prevention, University of Tennessee Health Science Center, Memphis, TN
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Abdelrahman H. Elsayed
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Raul C. Ribeiro
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Richard Aplenc
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - E. Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Todd A. Alonzo
- Children's Oncology Group Statistics and Data Center, Monrovia, CA
- Biostatistics Division, University of Southern California, Los Angeles, CA
| | - Stanley B. Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jatinder K. Lamba
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL
- University of Florida Health Cancer Center, University of Florida, Gainesville, FL
- Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL
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5
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Liu M, Khasiyev F, Sariya S, Spagnolo-Allende A, Sanchez DL, Andrews H, Yang Q, Beiser A, Qiao Y, Thomas EA, Romero JR, Rundek T, Brickman AM, Manly JJ, Elkind MSV, Seshadri S, Chen C, Sacco RL, Hilal S, Wasserman BA, Tosto G, Fornage M, Gutierrez J. Chromosome 10q24.32 Variants Associate with Brain Arterial Diameters in Diverse Populations: A Genome-Wide Association Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.31.23285251. [PMID: 36778463 PMCID: PMC9915818 DOI: 10.1101/2023.01.31.23285251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background Brain arterial diameters are novel imaging biomarkers of cerebrovascular disease, cognitive decline and dementia. Traditional vascular risk factors have been associated with brain arterial diameters but whether there may be genetic determinants of brain arterial diameters is unknown. Results We studied 4150 participants from six geographically diverse population-based cohorts (40% European, 14% African, 22% Hispanic, 24% Asian ancestries). We measured brain arterial diameters for 13 segments and averaged them to obtain a global measure of brain arterial diameters as well as the posterior and anterior circulations. A genome-wide association study (GWAS) revealed 14 variants at one locus associated with global brain arterial diameter at genome-wide significance (P<5×10-8) (top SNP, rs7921574; β =0.06, P=1.54×10-8). This locus mapped to an intron of CNNM2. A trans-ancestry GWAS meta-analysis identified two more loci at NT5C2 (rs10748839; P=2.54×10-8) and at AS3MT (rs10786721; P=4.97×10-8), associated with global brain arterial diameter. In addition, two SNPs co-localized with expression of CNNM2 (rs7897654, β=0.12, P=6.17×10-7) and AL356608.1 (rs10786719, β =-0.17, P=6.60×10-6) in brain tissue. For the posterior brain arterial diameter, two variants at one locus mapped to an intron of TCF25 were identified (top SNP, rs35994878; β =0.11, P=2.94×10-8). For the anterior brain arterial diameter, one locus at ADAP1 was identified in trans-ancestry genome-wide association analysis (rs34217249; P=3.11×10-8). Conclusion Our study reveals three novel risk loci (CNNM2, NT5C2 and AS3MT) associated with brain arterial diameters. Our finding may elucidate the mechanisms by which brain arterial diameters influence the risk of stroke and dementia.
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Affiliation(s)
- Minghua Liu
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Farid Khasiyev
- Department of Neurology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Sanjeev Sariya
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Antonio Spagnolo-Allende
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Danurys L Sanchez
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Howard Andrews
- Biostatistics Department, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Qiong Yang
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Alexa Beiser
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Ye Qiao
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emy A Thomas
- Brown Foundation Institute of Molecular Medicine, Mc Govern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jose Rafael Romero
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Tatjana Rundek
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Adam M Brickman
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jennifer J Manly
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mitchell SV Elkind
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- The Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Christopher Chen
- Memory Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ralph L Sacco
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
- Evelyn F. McKnight Brain Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Saima Hilal
- Memory Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bruce A Wasserman
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Giuseppe Tosto
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, Mc Govern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jose Gutierrez
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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Díaz-Santa J, Rodríguez-Romanos R, Coll R, Osca G, Pratcorona M, González-Bartulos M, Garrido A, Angona A, Talarn C, Tormo M, Arnan M, Vives S, Salamero O, Tuset E, Lloveras N, Díez I, Zamora L, Bargay J, Sampol A, Cruz D, Vila J, Sitges M, Garcia A, Vall-Llovera F, Esteve J, Sierra J, Gallardo D. 5'-nucleotidase, cytosolic ii genotype and clinical outcome in patients with acute myeloid leukemia with intermediate-risk cytogenetics. Eur J Haematol Suppl 2022; 109:755-764. [PMID: 36063368 DOI: 10.1111/ejh.13862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 11/26/2022]
Abstract
Acute myeloid leukemia (AML) is a complex disease, and its treatment needs to be adjusted to the risk, which is conferred by cytogenetics and molecular markers. Cytarabine is the main drug to treat AML, and it has been suggested that the genotype of cytarabine metabolizing enzymes may have a prognostic relevance in AML. Here we report the association between the 5'-nucleotidase, cytosolic II (NT5C2) rs10883841, cytidine deaminase (CDA) rs2072671 and rs532545 genotypes and the clinical outcome of 477 intermediate-risk cytogenetic AML patients receiving cytarabine-based chemotherapy. Patients younger than 50 years old with the NT5C2 rs10883841 AA genotype had lower overall survival (OS) (p: 0.003; HR 2.16, 95%CI 1.29 - 3.61) and lower disease-free survival (DFS) (p: 0.002; HR 2.45, 95%CI 1.41 - 4.27), associated to a higher relapse incidence (p: 0.010; HR 2.23, 95%CI 1.21 - 4.12). Interestingly, subgroup analysis showed that the negative effect of the NT5C2 rs10883841 AA genotype was detected in all subgroups except in patients with nucleophosmin mutation without high ratio FLT-3 internal tandem duplication. CDA polymorphisms were associated with the complete remission rate after induction chemotherapy, without influencing OS. Further studies are warranted to determine whether this pharmacogenomic approach may be helpful to individualize AML treatment.
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Affiliation(s)
- Johana Díaz-Santa
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Rocío Rodríguez-Romanos
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Rosa Coll
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Gemma Osca
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Marta Pratcorona
- Hematology Department, Hospital de la Santa Creu i Sant Pau; Institut d'Investigació Biomèdica Sant Pau; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta González-Bartulos
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Ana Garrido
- Hematology Department, Hospital de la Santa Creu i Sant Pau; Institut d'Investigació Biomèdica Sant Pau; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Angona
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Carme Talarn
- Hematology Department, Institut Català d'Oncologia - Hospital Joan XXIII, Tarragona, Spain
| | - Mar Tormo
- Hematology Department, Hospital Clínico Universitario, Valencia, Spain
| | - Montserrat Arnan
- Hematology Department, Institut Català d'Oncologia - Hospital Duran I Reynals; Institut d'Investigació Biomèdica de Bellvitge (IDIBELL); Universitat de Barcelona, L'Hospitalet, Barcelona, Spain
| | - Susanna Vives
- Institut Català d'Oncologia - Hospital Germans Trias i Pujol; Josep Carreras Research Institute, Badalona; Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
| | - Olga Salamero
- Hematology Department, Hospital Universitari Vall d'Hebró. Barcelona, Spain
| | - Esperanza Tuset
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Natàlia Lloveras
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Isabel Díez
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Lurdes Zamora
- Institut Català d'Oncologia - Hospital Germans Trias i Pujol; Josep Carreras Research Institute, Badalona; Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
| | - Joan Bargay
- Hematology Department, Hospital de Son Llàtzer, Palma de Mallorca, Spain
| | - Antonia Sampol
- Hematology Department, Hospital Son Espases. Palma de Mallorca, Spain
| | - David Cruz
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Jordi Vila
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Marta Sitges
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
| | - Antoni Garcia
- Hematology Department, Hospital Arnau de Vilanova. Lleida, Spain
| | | | - Jordi Esteve
- Hematology Department, Hospital Clínic de Barcelona, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Jorge Sierra
- Hematology Department, Hospital de la Santa Creu i Sant Pau; Institut d'Investigació Biomèdica Sant Pau; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - David Gallardo
- Hematology Department, Institut Català d'Oncologia - Hospital Dr. Josep Trueta; Institut d'Investigació Biomèdica de Girona (IDIBGI); Josep Carreras Research Institute, Girona; Universitat de Girona, Girona, Spain
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Pinto-Merino Á, Labrador J, Zubiaur P, Alcaraz R, Herrero MJ, Montesinos P, Abad-Santos F, Saiz-Rodríguez M. Role of Pharmacogenetics in the Treatment of Acute Myeloid Leukemia: Systematic Review and Future Perspectives. Pharmaceutics 2022; 14:pharmaceutics14030559. [PMID: 35335935 PMCID: PMC8954545 DOI: 10.3390/pharmaceutics14030559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by remarkable toxicity and great variability in response to treatment. Plenteous pharmacogenetic studies have already been published for classical therapies, such as cytarabine or anthracyclines, but such studies remain scarce for newer drugs. There is evidence of the relevance of polymorphisms in response to treatment, although most studies have limitations in terms of cohort size or standardization of results. The different responses associated with genetic variability include both increased drug efficacy and toxicity and decreased response or resistance to treatment. A broad pharmacogenetic understanding may be useful in the design of dosing strategies and treatment guidelines. The aim of this study is to perform a review of the available publications and evidence related to the pharmacogenetics of AML, compiling those studies that may be useful in optimizing drug administration.
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Affiliation(s)
| | - Jorge Labrador
- Research Unit, Fundación Burgos por la Investigación de la Salud (FBIS), Hospital Universitario de Burgos, 09006 Burgos, Spain; (J.L.); (R.A.)
- Haematology Department, Hospital Universitario de Burgos, 09006 Burgos, Spain
- Facultad de Ciencias de la Salud, Universidad Isabel I, 09003 Burgos, Spain
| | - Pablo Zubiaur
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; (P.Z.); (F.A.-S.)
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), 28006 Madrid, Spain
| | - Raquel Alcaraz
- Research Unit, Fundación Burgos por la Investigación de la Salud (FBIS), Hospital Universitario de Burgos, 09006 Burgos, Spain; (J.L.); (R.A.)
| | - María José Herrero
- Pharmacogenetics Department, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain;
| | - Pau Montesinos
- Haematology Department, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain;
| | - Francisco Abad-Santos
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; (P.Z.); (F.A.-S.)
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), 28006 Madrid, Spain
| | - Miriam Saiz-Rodríguez
- Department of Health Sciences, University of Burgos, 09001 Burgos, Spain;
- Research Unit, Fundación Burgos por la Investigación de la Salud (FBIS), Hospital Universitario de Burgos, 09006 Burgos, Spain; (J.L.); (R.A.)
- Correspondence: ; Tel.: +34-947-281-800 (ext. 36078)
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8
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Elsayed AH, Cao X, Mitra AK, Wu H, Raimondi S, Cogle C, Al-Mansour Z, Ribeiro RC, Gamis A, Kolb EA, Aplenc R, Alonzo TA, Meshinchi S, Rubnitz J, Pounds S, Lamba JK. Polygenic Ara-C Response Score Identifies Pediatric Patients With Acute Myeloid Leukemia in Need of Chemotherapy Augmentation. J Clin Oncol 2022; 40:772-783. [PMID: 34990262 PMCID: PMC8887949 DOI: 10.1200/jco.21.01422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
PURPOSE To establish a patient-specific polygenic score derived from cytarabine (ara-C) pathway pharmacogenomic evaluation to personalize acute myeloid leukemia (AML) treatment. MATERIALS AND METHODS Single nucleotide polymorphisms (SNPs) in the ara-C-pathway genes were analyzed with outcome in patients from the multicenter-AML02 trial (N = 166). Multi-SNP predictor modeling was used to develop 10-SNP Ara-C_SNP score (ACS10) using top SNPs predictive of minimal residual disease and event-free survival (EFS) from the AML02-cohort and four SNPs previously associated with ara-C triphosphate levels in the AML97 trial. ACS10 was evaluated for association with outcomes in each clinical trial arms: the standard low-dose ara-C (LDAC, n = 91) and augmented high-dose ara-C (HDAC, n = 75) arms of AML02 and the standard Ara-C, daunorubicin and etoposide (ADE) (n = 465) and the augmented ADE + gemtuzumab ozogamicin (GO; n = 466) arms of AAML0531 trial. RESULTS In the standard LDAC-arm of AML02 cohort, the low-ACS10 score group (≤ 0) had significantly worse EFS (ACS10 low v high hazard ratio [HR] = 2.81; 95% CI, 1.45 to 5.43; P = .002) and overall survival (OS; HR = 2.98; 95% CI, 1.32 to 6.75; P = .009) compared with the high-ACS10 group (score > 0). These results were validated in the standard-ADE arm of AAML0531, with poor outcome in the low-ASC10 group compared with the high-ACS10 group (EFS: HR = 1.35, 95% CI, 1.04 to 1.75, P = .026; OS: HR = 1.64, 95% CI, 1.2 to 2.22, P = .002). Within the augmented arms (AML02-HDAC and AAML0531-ADE + GO), EFS and OS did not differ between low- and high-ACS10 score groups. In both cohorts, patients with low-ACS10 consistently showed a 10-percentage point improvement in 5-year EFS with augmented therapy (AML02-HDAC or AAML0531-ADE + GO arms) than with standard therapy (AML02-LDAC or AAML0531-ADE arms). CONCLUSION Patients with low-ACS10 score experienced significantly poor outcome when treated on standard regimen. Augmentation with either high-dose ara-C or GO addition improved outcome in low-ACS10 group. A polygenic ACS10 score can identify patients with unfavorable pharmacogenetic characteristics and offers a potential for an elective augmented therapy option.
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Affiliation(s)
- Abdelrahman H. Elsayed
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL
| | - Xueyuan Cao
- Department of Acute and Tertiary Care, University of Tennessee Health Science Center, Memphis, TN
| | - Amit K. Mitra
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL
| | - Huiyun Wu
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN
| | - Susana Raimondi
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | | | | | - Raul C. Ribeiro
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Alan Gamis
- Department of Hematology-Oncology, Children's Mercy Hospitals and Clinics, Kansas City, MO
| | | | - Richard Aplenc
- Division of Pediatric Oncology/Stem Cell Transplant, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Todd A. Alonzo
- COG Statistics and Data Center, Monrovia, CA,Biostatistics Division, University of Southern California, Los Angeles, CA
| | | | - Jeffrey Rubnitz
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Stanley Pounds
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN
| | - Jatinder K. Lamba
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL,University of Florida Health Cancer Center, University of Florida, Gainesville, FL,Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL,Jatinder K. Lamba, PhD, Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, 1345 Center Drive, Gainesville, FL 32608; e-mail:
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9
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Stockard B, Bhise N, Shin M, Guingab-Cagmat J, Garrett TJ, Pounds S, Lamba JK. Cellular Metabolomics Profiles Associated With Drug Chemosensitivity in AML. Front Oncol 2021; 11:678008. [PMID: 34178663 PMCID: PMC8222790 DOI: 10.3389/fonc.2021.678008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/04/2021] [Indexed: 01/03/2023] Open
Abstract
Background Acute myeloid leukemia (AML) is a hematological malignancy with a dismal prognosis. For over four decades, AML has primarily been treated by cytarabine combined with an anthracycline. Although a significant proportion of patients achieve remission with this regimen, roughly 40% of children and 70% of adults relapse. Over 90% of patients with resistant or relapsed AML die within 3 years. Thus, relapsed and resistant disease following treatment with standard therapy are the most common clinical failures that occur in treating this disease. In this study, we evaluated the relationship between AML cell line global metabolomes and variation in chemosensitivity. Methods We performed global metabolomics on seven AML cell lines with varying chemosensitivity to cytarabine and the anthracycline doxorubicin (MV4.11, KG-1, HL-60, Kasumi-1, AML-193, ME1, THP-1) using ultra-high performance liquid chromatography - mass spectrometry (UHPLC-MS). Univariate and multivariate analyses were performed on the metabolite peak intensity values from UHPLC-MS using MetaboAnalyst to identify cellular metabolites associated with drug chemosensitivity. Results A total of 1,624 metabolic features were detected across the leukemic cell lines. Of these, 187 were annotated to known metabolites. With respect to doxorubicin, we observed significantly greater abundance of a carboxylic acid (1-aminocyclopropane-1-carboxylate) and several amino acids in resistant cell lines. Pathway analysis found enrichment of several amino acid biosynthesis and metabolic pathways. For cytarabine resistance, nine annotated metabolites were significantly different in resistance vs. sensitive cell lines, including D-raffinose, guanosine, inosine, guanine, aldopentose, two xenobiotics (allopurinol and 4-hydroxy-L-phenylglycine) and glucosamine/mannosamine. Pathway analysis associated these metabolites with the purine metabolic pathway. Conclusion Overall, our results demonstrate that metabolomics differences contribute toward drug resistance. In addition, it could potentially identify predictive biomarkers for chemosensitivity to various anti-leukemic drugs. Our results provide opportunity to further explore these metabolites in patient samples for association with clinical response.
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Affiliation(s)
- Bradley Stockard
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Neha Bhise
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Miyoung Shin
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Joy Guingab-Cagmat
- Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL, United States
| | - Timothy J Garrett
- Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL, United States
| | - Stanley Pounds
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Jatinder K Lamba
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, United States.,University of Florida Health Cancer Center, Gainesville, FL, United States.,Center for Pharmacogenetics, University of Florida, Gainesville, FL, United States
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10
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Lai SH, Li YC, Zhang S, Deng R, Deng Y, Fan FY. Whole genome, exon mutation and transcriptomic profiling of acute myeloid leukemia: A case report. Oncol Lett 2021; 22:559. [PMID: 34084226 PMCID: PMC8161460 DOI: 10.3892/ol.2021.12820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
The present study aimed to observe previously unidentified gene mutation and expression profiles associated with acute myeloid leukemia (AML) at the individual level, based on the blood samples of a father-son pair. Genomic DNA and RNA samples from blood serum were collected. Whole-genome sequencing (WGS) and whole-exome sequencing (WES), as well as mRNA sequencing of the son, were performed. For the father's sample, a total of 3,897,164 single nucleotide polymorphisms (SNPs) and 780,834 insertion and deletions (indels) were identified. Regarding amino acid translation, there were 11,316 non-synonymous, 12 stop-loss, 12,033 synonymous, 92 stop-gain SNPs, 63 frameshift insertions, 73 frameshift deletions, 242 non-frameshift insertions, 248 non-frameshift deletions, four stop-gains and two stop-loss for indel variants. Among the AML-related genes that had been previously identified, 14 genes were found in the father's exon region. For WES of the son's DNA, 96,639 SNPs were identified, including 10,504 non-synonymous SNPs. Seven mutant genes were found in sons' exon region compared with 121 AML-related genes. Based on the transcriptomic sequencing, there were 54 differentially expressed mRNAs, including 31 upregulated and 23 downregulated mRNAs. In the exon region, 10,072 SNPs were detected, and different types of alternative splicing in the son's sample were observed. Overall, whole genome, exon mutation and transcriptomic profiling of the present two patients with AML may provide a new insight into the molecular events governing the development of AML.
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Affiliation(s)
- Si-Han Lai
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Ye-Cheng Li
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Shan Zhang
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Rui Deng
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Yan Deng
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Fang-Yi Fan
- Hematology Department and Hematopoietic Stem Cell Transplantation Center, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
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Di Francia R, Crisci S, De Monaco A, Cafiero C, Re A, Iaccarino G, De Filippi R, Frigeri F, Corazzelli G, Micera A, Pinto A. Response and Toxicity to Cytarabine Therapy in Leukemia and Lymphoma: From Dose Puzzle to Pharmacogenomic Biomarkers. Cancers (Basel) 2021; 13:cancers13050966. [PMID: 33669053 PMCID: PMC7956511 DOI: 10.3390/cancers13050966] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary In this review, the authors propose a crosswise examination of cytarabine-related issues ranging from the spectrum of clinical activity and severe toxicities, through updated cellular pharmacology and drug formulations, to the genetic variants associated with drug-induced phenotypes. Cytarabine (cytosine arabinoside; Ara-C) in multiagent chemotherapy regimens is often used for leukemia or lymphoma treatments, as well as neoplastic meningitis. Chemotherapy regimens can induce a suboptimal clinical outcome in a fraction of patients. The individual variability in clinical response to Leukemia & Lymphoma treatments among patients appears to be associated with intracellular accumulation of Ara-CTP due to genetic variants related to metabolic enzymes. The review provides exhaustive information on the effects of Ara-C-based therapies, the adverse drug reaction will also be provided including bone pain, ocular toxicity (corneal pain, keratoconjunctivitis, and blurred vision), maculopapular rash, and occasional chest pain. Evidence for predicting the response to cytarabine-based treatments will be highlighted, pointing at their significant impact on the routine management of blood cancers. Abstract Cytarabine is a pyrimidine nucleoside analog, commonly used in multiagent chemotherapy regimens for the treatment of leukemia and lymphoma, as well as for neoplastic meningitis. Ara-C-based chemotherapy regimens can induce a suboptimal clinical outcome in a fraction of patients. Several studies suggest that the individual variability in clinical response to Leukemia & Lymphoma treatments among patients, underlying either Ara-C mechanism resistance or toxicity, appears to be associated with the intracellular accumulation and retention of Ara-CTP due to genetic variants related to metabolic enzymes. Herein, we reported (a) the latest Pharmacogenomics biomarkers associated with the response to cytarabine and (b) the new drug formulations with optimized pharmacokinetics. The purpose of this review is to provide readers with detailed and comprehensive information on the effects of Ara-C-based therapies, from biological to clinical practice, maintaining high the interest of both researcher and clinical hematologist. This review could help clinicians in predicting the response to cytarabine-based treatments.
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Affiliation(s)
- Raffaele Di Francia
- Italian Association of Pharmacogenomics and Molecular Diagnostics, 60126 Ancona, Italy;
| | - Stefania Crisci
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Angela De Monaco
- Clinical Patology, ASL Napoli 2 Nord, “S.M. delle Grazie Hospital”, 80078 Pozzuoli, Italy;
| | - Concetta Cafiero
- Medical Oncology, S.G. Moscati, Statte, 74010 Taranto, Italy
- Correspondence: or (C.C.); (A.M.); Tel.:+39-34-0101-2002 (C.C.); +39-06-4554-1191 (A.M.)
| | - Agnese Re
- Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Giancarla Iaccarino
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Rosaria De Filippi
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
- Department of Clinical Medicine and Surgery, Federico II University, 80131 Naples, Italy
| | | | - Gaetano Corazzelli
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
| | - Alessandra Micera
- Research and Development Laboratory for Biochemical, Molecular and Cellular Applications in Ophthalmological Sciences, IRCCS—Fondazione Bietti, 00184 Rome, Italy
- Correspondence: or (C.C.); (A.M.); Tel.:+39-34-0101-2002 (C.C.); +39-06-4554-1191 (A.M.)
| | - Antonio Pinto
- Hematology-Oncology and Stem Cell transplantation Unit, National Cancer Institute, Fondazione “G. Pascale” IRCCS, 80131 Naples, Italy; (S.C.); (G.I.); (R.D.F.); (G.C.); (A.P.)
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Illangeswaran RSS, Das S, Paul DZ, Mathews V, Balasubramanian P. A personalized approach to acute myeloid leukemia therapy: current options. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2019; 12:167-179. [PMID: 31447578 PMCID: PMC6684879 DOI: 10.2147/pgpm.s168267] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022]
Abstract
Therapeutic options for acute myeloid leukemia (AML) have remained unchanged for nearly the past 5 decades, with cytarabine and anthracyclines and use of hypomethylating agents for less intensive therapy. Implementation of large-scale genomic studies in the past decade has unraveled the genetic landscape and molecular etiology of AML. The approval of several novel drugs for targeted therapy, including midostaurin, enasidenib, ivosidenib, gemtuzumab–ozogamicin, and CPX351 by the US Food and Drug Administration has widened the treatment options for clinicians treating AML. This review focuses on some of these novel therapies and other promising agents under development, along with key clinical trial findings in AML.
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Affiliation(s)
| | - Saswati Das
- Department of Haematology, Christian Medical College, Vellore, India
| | | | - Vikram Mathews
- Department of Haematology, Christian Medical College, Vellore, India
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13
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Bargal SA, Rafiee R, Crews KR, Wu H, Cao X, Rubnitz JE, Ribeiro RC, Downing JR, Pounds SB, Lamba JK. Genome-wide association analysis identifies SNPs predictive of in vitro leukemic cell sensitivity to cytarabine in pediatric AML. Oncotarget 2018; 9:34859-34875. [PMID: 30405880 PMCID: PMC6201857 DOI: 10.18632/oncotarget.26163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/08/2018] [Indexed: 12/02/2022] Open
Abstract
Cytarabine has been an integral part of acute myeloid leukemia (AML) chemotherapy for over four decades. However, development of resistance and high rates of relapse is a significant impediment in successfully treating AML. We performed a genome-wide association analysis (GWAS) and identified 113 (83 after adjusting for Linkage Disequilibrium) SNPs associated with in vitro cytarabine chemosensitivity of diagnostic leukemic cells from a cohort of 50 pediatric AML patients (p<10-4). Further evaluation of diagnostic leukemic cell gene-expression identified 19 SNP-gene pairs with a concordant triad of associations: i)SNP genotype with cytarabine sensitivity (p<0.0001), ii) gene-expression with cytarabine sensitivity (p<0.05), and iii) genotype with gene-expression (p<0.1). Two genes from SNP-gene pairs, rs1376041-GPR56 and rs75400242-IGF1R, were functionally validated by siRNA knockdown in AML cell lines. Consistent with association of rs1376041 and gene-expression in AML patients siRNA mediated knock-down of GPR56 increased cytarabine sensitivity of AML cell lines. Similarly for IGF1R, knockdown increased the cytarabine sensitivity of AML cell lines consistent with results in AML patients. Given both IGF1R and GPR56 are promising drug-targets in AML, our results on SNPs driving the expression/function of these genes will not only enhance our understanding of cytarabine resistance but also hold promise in personalizing AML for targeted therapies.
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Affiliation(s)
- Salma A Bargal
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Roya Rafiee
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Kristine R Crews
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Huiyun Wu
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Xueyuan Cao
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA.,Department of Acute and Tertiary Care, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Raul C Ribeiro
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - James R Downing
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley B Pounds
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jatinder K Lamba
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA
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14
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Tulstrup M, Grosjean M, Nielsen SN, Grell K, Wolthers BO, Wegener PS, Jonsson OG, Lund B, Harila-Saari A, Abrahamsson J, Vaitkeviciene G, Pruunsild K, Toft N, Holm M, Hulegårdh E, Liestøl S, Griskevicius L, Punab M, Wang J, Carroll WL, Zhang Z, Dalgaard MD, Gupta R, Nersting J, Schmiegelow K. NT5C2 germline variants alter thiopurine metabolism and are associated with acquired NT5C2 relapse mutations in childhood acute lymphoblastic leukaemia. Leukemia 2018; 32:2527-2535. [PMID: 30201983 DOI: 10.1038/s41375-018-0245-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/12/2018] [Accepted: 07/19/2018] [Indexed: 12/18/2022]
Abstract
The antileukaemic drug 6-mercaptopurine is converted into thioguanine nucleotides (TGN) and incorporated into DNA (DNA-TG), the active end metabolite. In a series of genome-wide association studies, we analysed time-weighted means (wm) of erythrocyte concentrations of TGN (Ery-TGN) and DNA-TG in 1009 patients undergoing maintenance therapy for acute lymphoblastic leukaemia (ALL). In discovery analyses (454 patients), the propensity for DNA-TG incorporation (wmDNA-TG/wmEry-TGN ratio) was significantly associated with three intronic SNPs in NT5C2 (top hit: rs72846714; P = 2.09 × 10-10, minor allele frequency 15%). In validation analyses (555 patients), this association remained significant during both early and late maintenance therapy (P = 8.4 × 10-6 and 1.3 × 10-3, respectively). The association was mostly driven by differences in wmEry-TGN, but in regression analyses adjusted for wmEry-TGN (P < 0.0001), rs72846714-A genotype was also associated with a higher wmDNA-TG (P = 0.029). Targeted sequencing of NT5C2 did not identify any missense variants associated with rs72846714 or wmEry-TGN/wmDNA-TG. rs72846714 was not associated with relapse risk, but in a separate cohort of 180 children with relapsed ALL, rs72846714-A genotype was associated with increased occurrence of relapse-specific NT5C2 gain-of-function mutations that reduce cytosol TGN levels (P = 0.03). These observations highlight the impact of both germline and acquired mutations in drug metabolism and disease trajectory.
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Affiliation(s)
- Morten Tulstrup
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Marie Grosjean
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stine Nygaard Nielsen
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kathrine Grell
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark.,Section of Biostatistics, Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin Ole Wolthers
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Peder Skov Wegener
- Department of Pediatric Hematology and Oncology, H. C. Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | | | - Bendik Lund
- Department of Pediatrics, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Laboratory Medicine, Faculty of Medicine and Health sciences, Children's and Women's Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arja Harila-Saari
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, Institution for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Goda Vaitkeviciene
- Clinic of Children's Diseases, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Kaie Pruunsild
- Department of Onco-haematology, Talinn Children's Hospital, Talinn, Estonia
| | - Nina Toft
- Department of Hematology, University Hospital Rishospitalet, Copenhagen, Denmark
| | - Mette Holm
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - Erik Hulegårdh
- Department of Hematology and Coagulation, Sahlgrenska University Hospital, Göteborg, Sweden
| | - Sigurd Liestøl
- Department of Hematology, Ullevål University Hospital, Faculty Division Ullevål University Hospital, University of Oslo, Oslo, Norway
| | - Laimonas Griskevicius
- Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Mari Punab
- Clinic of Hematology and Oncology, Tartu University Clinic, Tartu, Estonia
| | - Jinhua Wang
- Masonic Cancer Center, Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
| | - William L Carroll
- Department of Pediatrics, New York University Medical Center, Perlmutter Cancer Center, New York, NY, USA
| | - Zeyu Zhang
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.,Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Marlene D Dalgaard
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ramneek Gupta
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jacob Nersting
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark. .,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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15
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Elsayed AH, Cao X, Crews KR, Gandhi V, Plunkett W, Rubnitz JE, Ribeiro RC, Pounds SB, Lamba JK. Comprehensive Ara-C SNP score predicts leukemic cell intracellular ara-CTP levels in pediatric acute myeloid leukemia patients. Pharmacogenomics 2018; 19:1101-1110. [PMID: 30088438 DOI: 10.2217/pgs-2018-0086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIM Cytarabine (Ara-C), a mainstay of acute myeloid leukemia (AML) treatment, is a prodrug requiring activation to ara-CTP for its antileukemic activity. Aim of this study was to evaluate impact of genetic variants in the key genes involved in ara-C metabolism on the leukemic cell intracellular levels of ara-CTP. METHOD We investigated SNPs in 14 ara-C metabolic-pathway genes, for association with intracellular ara-CTP levels, in leukemic cells obtained post-initiation of cytarabine infusion in pediatric AML patients (n = 68). RESULTS Nine SNPs were significantly associated with leukemic cell intracellular concentration of ara-CTP. A comprehensive ara-CTP-SNP-score (ACSS) was further developed from top four SNPs identified in regression model. Patients were classified into three groups based on ACSS: high-ACSS (score >0), intermediate-ACSS (score = 0) and low-ACSS (score <0). ACSS designation was significant predictor of intracellular ara-CTP levels (p = 0.00012), suggesting a cumulative or synergistic effect of the significant SNPs. CONCLUSION ACSS score designation holds promise in definfing ara-C dose. Validation of the clinical utility of ACSS score in other independent cohorts will help identification of patients with potentially lower or higher levels of the ara-CTP in leukemic cells, thereby opening up opportunities for dose management to reduce toxicity and enhance efficacy.
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Affiliation(s)
- Abdelrahman H Elsayed
- Department of Pharmacotherapy & Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Xueyuan Cao
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Acute & Tertiary Care, University of Tennessee Health Science Center, Memphis 38163, TN, USA
| | - Kristine R Crews
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Varsha Gandhi
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX 77054, USA
| | - William Plunkett
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Raul C Ribeiro
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stanley B Pounds
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jatinder K Lamba
- Department of Pharmacotherapy & Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
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16
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Tsesmetzis N, Paulin CBJ, Rudd SG, Herold N. Nucleobase and Nucleoside Analogues: Resistance and Re-Sensitisation at the Level of Pharmacokinetics, Pharmacodynamics and Metabolism. Cancers (Basel) 2018; 10:cancers10070240. [PMID: 30041457 PMCID: PMC6071274 DOI: 10.3390/cancers10070240] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
Antimetabolites, in particular nucleobase and nucleoside analogues, are cytotoxic drugs that, starting from the small field of paediatric oncology, in combination with other chemotherapeutics, have revolutionised clinical oncology and transformed cancer into a curable disease. However, even though combination chemotherapy, together with radiation, surgery and immunotherapy, can nowadays cure almost all types of cancer, we still fail to achieve this for a substantial proportion of patients. The understanding of differences in metabolism, pharmacokinetics, pharmacodynamics, and tumour biology between patients that can be cured and patients that cannot, builds the scientific basis for rational therapy improvements. Here, we summarise current knowledge of how tumour-specific and patient-specific factors can dictate resistance to nucleobase/nucleoside analogues, and which strategies of re-sensitisation exist. We revisit well-established hurdles to treatment efficacy, like the blood-brain barrier and reduced deoxycytidine kinase activity, but will also discuss the role of novel resistance factors, such as SAMHD1. A comprehensive appreciation of the complex mechanisms that underpin the failure of chemotherapy will hopefully inform future strategies of personalised medicine.
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Affiliation(s)
- Nikolaos Tsesmetzis
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Cynthia B J Paulin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Sean G Rudd
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Nikolas Herold
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
- Paediatric Oncology, Theme of Children's and Women's Health, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden.
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17
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Toffalorio F, Santarpia M, Radice D, Jaramillo CA, Spitaleri G, Manzotti M, Catania C, Jordheim LP, Pelosi G, Peters GJ, Tibaldi C, Funel N, Spaggiari L, de Braud F, De Pas T, Giovannetti E. 5'-nucleotidase cN-II emerges as a new predictive biomarker of response to gemcitabine/platinum combination chemotherapy in non-small cell lung cancer. Oncotarget 2018; 9:16437-16450. [PMID: 29662657 PMCID: PMC5893252 DOI: 10.18632/oncotarget.24505] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 02/02/2018] [Indexed: 02/04/2023] Open
Abstract
A number of pharmacogenetic studies have been carried out in non-small-cell lung cancer (NSCLC) to identify and characterize genes involved in chemotherapy activity. However, the results obtained so far are controversial and no reliable biomarker is currently used to predict clinical benefit from platinum-based chemotherapy, which represents the cornerstone of treatment of advanced NSCLC. This study investigated the expression levels of ERCC1 and of six genes (RRM1, RRM2, hENT1, dCK, cN-II and CDA) involved in gemcitabine metabolism in locally/advanced NSCLC patients treated with gemcitabine/platinum combination. Gene expression was assessed by quantitative-PCR in laser-microdissected specimens and correlated with tumor response. Frequency distribution of responses above and below the median expression level of biomarkers was compared using a two-sided Fisher’s test. 5′-nucleotidase (cN-II) was the only gene differently expressed (p = 0.016) in the responders (complete/partial-response) compared to non-responders (stable/progressive disease). In the multivariate analysis, overexpression of this catabolic enzyme of gemcitabine remained a significant negative predictive factor. Patients with low cN-II had a modest trend toward increased survival, while both survival and progression-free survival were significantly longer in a more homogenous validation cohort of 40 advanced NSCLC (8.0 vs. 5.1 months, p = 0.026). Moreover, in vitro studies showed that silencing or pharmacological inhibition of cN-II increased the cytotoxicity of gemcitabine. This is the first study demonstrating the role of cN-II as a predictor of response to gemcitabine/platinum combinations in NSCLC. Its validation in prospective studies may improve clinical outcome of selected patients.
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Affiliation(s)
- Francesca Toffalorio
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Medical Affairs, Roche Spa, Monza, Italy
| | - Mariacarmela Santarpia
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Medical Oncology Unit, Department of Human Pathology, University of Messina, Messina, Italy
| | - Davide Radice
- Epidemiology and Biostatistics Division, European Institute of Oncology, Milan, Italy
| | | | - Gianluca Spitaleri
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Thoracic Oncology Division, European Institute of Oncology, Milan, Italy
| | - Michela Manzotti
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Chiara Catania
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy.,Thoracic Oncology Division, European Institute of Oncology, Milan, Italy
| | - Lars Petter Jordheim
- Centre de Recherche en Cancérologie de Lyon, INSERM 1052/CNRS UMR 5286, Lyon, France
| | - Giuseppe Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Inter-Hospital Pathology Division, Science and Technology Park, IRCCS MultiMedica, Milan, Italy
| | - Godefridus J Peters
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Carmelo Tibaldi
- Division of Oncology, Department of Oncology, S. Luca Hospital, Lucca, Italy
| | - Niccola Funel
- CNR-Nano, Institute of Nanoscience and Nanotechnology, Pisa, Italy.,Cancer Pharmacology Laboratory, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
| | - Lorenzo Spaggiari
- Thoracic Surgery Division, European Institute of Oncology, Milan, Italy
| | - Filippo de Braud
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Inter-Hospital Pathology Division, Science and Technology Park, IRCCS MultiMedica, Milan, Italy
| | - Tommaso De Pas
- Medical Oncology Unit of Respiratory Tract and Sarcomas, New Drugs Development Division, European Institute of Oncology, Milan, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.,CNR-Nano, Institute of Nanoscience and Nanotechnology, Pisa, Italy.,Cancer Pharmacology Laboratory, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
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18
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Wang Y, Lamba JK. Retracted: Influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in different populations. J Clin Pharm Ther 2017. [PMID: 29164635 DOI: 10.1111/jcpt.12653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/28/2017] [Indexed: 12/24/2022]
Abstract
'Influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in different populations' by Y. Wang & J. K. Lamba1 The above article from the Journal of Clinical Pharmacy and Therapeutics, published online on 21 November 2017 in Wiley Online Library (wileyonlinelibrary.com), has been retracted following discussions with the authors, the Journal Editors and John Wiley & Sons Ltd. The Retraction has been agreed as this paper was submitted under the joint names of Yan Wang, Jatinder K. Lamba and a third co-author. After acceptance of the paper, Dr Wang wrote to the EiC asking for the name of the third co-author to be dropped because of insufficient contribution. The EiC asked that the request be signed by all three authors. When this arrived, the paper was published online with only Dr Wang and Dr Lamba. However, Dr Lamba wrote to the EiC after publication indicating that she had not previously seen the manuscript and that there were co-authors missing. As it is clear that Dr Lamba's signature was forged, we cannot rely on the integrity of the report. The retraction is with the agreement of Dr Lamba but not of Dr Wang. REFERENCE 1. Wang Y, Lamba JK. Influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in different populations. J Clin Pharm Ther. 2017;00:1-9. https://doi.org/10.1111/jcpt.12653.
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Affiliation(s)
- Y Wang
- Department of Pharmacy, Affiliated Hospital of Xuzhou Medical University, Jiangsu, China
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - J K Lamba
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
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19
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Cao HX, Miao CF, Yan L, Tang P, Zhang LR, Sun L. Polymorphisms at microRNA binding sites of Ara-C and anthracyclines-metabolic pathway genes are associated with outcome of acute myeloid leukemia patients. J Transl Med 2017; 15:235. [PMID: 29141648 PMCID: PMC5688732 DOI: 10.1186/s12967-017-1339-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/04/2017] [Indexed: 12/11/2022] Open
Abstract
Background Gene polymorphisms at microRNA-binding sites (poly-miRTS) may affect gene transcription and expression through miRNA regulation, which is associated with cancer susceptibility, sensitivity to chemotherapy and prognosis. This study investigated the association between poly-miRTS of Ara-C/anthracycline metabolic pathways genes and the outcome of acute myeloid leukemia (AML) in Chinese patients after Ara-C-based chemotherapy. Methods A total of 17 poly-miRTS were selected from the SNPinfo Web Server and genotyped in 206 Chinese Han non-FAB-M3 AML patients using the SEQUENOM Mass-ARRAY system. Results Among these 17 poly-miRTS, five Ara-C metabolic gene single nucleotide polymorphisms (SNPs, NT5C2 rs10786736 and rs8139, SLC29A1 rs3734703, DCTD rs7278, and RRM1 rs1042919) were identified to significantly associate with complete AML remission and/or overall and relapse-free survival (OS and RFS, respectively), and four anthracycline-metabolic gene SNPs (ABCC1 rs3743527, rs212091, and rs212090 and CBR1 rs9024) were significantly associated with chemotherapy-related toxicities. Moreover, SLC29A1 rs3734703 was shown to associate with both chemotherapy response and survival (adjusted OR 2.561 in the overdominant model; adjusted HR 2.876 for OS and 2.357 for RFS in the dominant model). Conclusions The data from the current study demonstrated that the poly-miRTS of Ara-C/anthracyclines metabolic genes predicted the sensitivity and side effects of AML to Ara-C-based chemotherapy and patient survival. Further study will confirm them as biomarkers for AML patients after Ara-C-based chemotherapy. Electronic supplementary material The online version of this article (10.1186/s12967-017-1339-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hai-Xia Cao
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Zhengzhou, 450052, Henan, China
| | - Chao-Feng Miao
- Department of Vascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Liang Yan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ping Tang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Li-Rong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Ling Sun
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshedong Road, Zhengzhou, 450052, Henan, China.
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20
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Genetic Variants Contributing to Colistin Cytotoxicity: Identification of TGIF1 and HOXD10 Using a Population Genomics Approach. Int J Mol Sci 2017; 18:ijms18030661. [PMID: 28335481 PMCID: PMC5372673 DOI: 10.3390/ijms18030661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/27/2022] Open
Abstract
Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines. To this end, we employed International HapMap lymphoblastoid cell lines (LCLs) of Yoruban ancestry with known genetic information to perform a genome-wide association study (GWAS) with cellular sensitivity to colistin. Further association studies revealed that single nucleotide polymorphisms (SNPs) associated with gene expression and protein expression were significantly enriched in SNPs associated with cytotoxicity (p ≤ 0.001 for gene and p = 0.015 for protein expression). The most highly associated SNP, chr18:3417240 (p = 6.49 × 10−8), was nominally a cis-expression quantitative trait locus (eQTL) of the gene TGIF1 (transforming growth factor β (TGFβ)-induced factor-1; p = 0.021) and was associated with expression of the protein HOXD10 (homeobox protein D10; p = 7.17 × 10−5). To demonstrate functional relevance in a murine colistin nephrotoxicity model, HOXD10 immunohistochemistry revealed upregulated protein expression independent of mRNA expression in response to colistin administration. Knockdown of TGIF1 resulted in decreased protein expression of HOXD10 and increased resistance to colistin cytotoxicity. Furthermore, knockdown of HOXD10 in renal cells also resulted in increased resistance to colistin cytotoxicity, supporting the physiological relevance of the initial genomic associations.
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21
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Megías-Vericat JE, Montesinos P, Herrero MJ, Bosó V, Martínez-Cuadrón D, Poveda JL, Sanz MÁ, Aliño SF. Pharmacogenomics and the treatment of acute myeloid leukemia. Pharmacogenomics 2016; 17:1245-1272. [DOI: 10.2217/pgs-2016-0055] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clinically and biologically heterogeneous malignancy that is primarily treated with combinations of cytarabine and anthracyclines. Although this scheme remains effective in most of the patients, variability of outcomes in patients has been partly related with their genetic variability. Several pharmacogenetic studies have analyzed the impact of polymorphisms in genes encoding transporters, metabolizers or molecular targets of chemotherapy agents. A systematic review on all eligible studies was carried out in order to estimate the effect of polymorphisms of anthracyclines and cytarabine pathways on efficacy and toxicity of AML treatment. Other emerging genes recently studied in AML, such as DNA repair genes, genes potentially related to chemotherapy response or AML prognosis, have also been included.
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Affiliation(s)
- Juan Eduardo Megías-Vericat
- Unidad de Farmacogenética, Instituto Investigación Sanitaria La Fe and Área del Medicamento, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
- Servicio de Farmacia, Área del Medicamento, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
| | - Pau Montesinos
- Servicio de Hematología y Hemoterapia, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
| | - María José Herrero
- Unidad de Farmacogenética, Instituto Investigación Sanitaria La Fe and Área del Medicamento, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
- Departamento Farmacología, Facultad de Medicina, Universidad de Valencia, Avda, Blasco Ibáñez 15, 46010 – Valencia, Spain
| | - Virginia Bosó
- Unidad de Farmacogenética, Instituto Investigación Sanitaria La Fe and Área del Medicamento, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
- Servicio de Farmacia, Área del Medicamento, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
| | - David Martínez-Cuadrón
- Servicio de Hematología y Hemoterapia, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
| | - José Luis Poveda
- Servicio de Farmacia, Área del Medicamento, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
| | - Miguel Ángel Sanz
- Servicio de Hematología y Hemoterapia, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
| | - Salvador F Aliño
- Unidad de Farmacogenética, Instituto Investigación Sanitaria La Fe and Área del Medicamento, Hospital Universitario y Politécnico La Fe Avda, Fernando Abril Martorell 106, 46026 – Valencia, Spain
- Departamento Farmacología, Facultad de Medicina, Universidad de Valencia, Avda, Blasco Ibáñez 15, 46010 – Valencia, Spain
- Unidad de Farmacología Clínica, Área del Medicamento, Hospital Universitario y Politécnico La Fe. Avda. Fernando Abril Martorell 106, 46026 – Valencia, Spain
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22
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Saliba J, Zabriskie R, Ghosh R, Powell BC, Hicks S, Kimmel M, Meng Q, Ritter DI, Wheeler DA, Gibbs RA, Tsai FTF, Plon SE. Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs. Pharmacogenet Genomics 2016; 26:271-9. [PMID: 26906009 PMCID: PMC4853247 DOI: 10.1097/fpc.0000000000000208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Mutations or alterations in expression of the 5' nucleotidase gene family can lead to altered responses to treatment with nucleoside analogs. While investigating leukemia susceptibility genes, we discovered a very rare p.L254P NT5C1A missense variant in the substrate recognition motif. Given the paucity of cellular drug response data from the NT5C1A germline variation, we characterized p.L254P and eight rare variants of NT5C1A from genomic databases. MATERIALS AND METHODS Through lentiviral infection, we created HEK293 cell lines that stably overexpress wild-type NT5C1A, p.L254P, or eight NT5C1A variants reported in the National Heart Lung and Blood Institute Exome Variant Server (one truncating and seven missense). IC50 values were determined by cytotoxicity assays after exposure to chemotherapeutic nucleoside analogs (cladribine, gemcitabine, 5-fluorouracil). In addition, we used structure-based homology modeling to generate a three-dimensional model for the C-terminal region of NT5C1A. RESULTS The p.R180X (truncating), p.A214T, and p.L254P missense changes were the only variants that significantly impaired protein function across all nucleotide analogs tested (>5-fold difference vs. wild-type; P<0.05). Several of the remaining variants individually showed differential effects (both more and less resistant) across the analogs tested. The homology model provided a structural framework to understand the impact of NT5C1A mutants on catalysis and drug processing. The model predicted active site residues within NT5C1A motif III and we experimentally confirmed that p.K314 (not p.K320) is required for NT5C1A activity. CONCLUSION We characterized germline variation and predicted protein structures of NT5C1A. Individual missense changes showed considerable variation in response to the different nucleoside analogs tested, which may impact patients' responses to treatment.
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Affiliation(s)
- Jason Saliba
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ryan Zabriskie
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Rajarshi Ghosh
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Bradford C Powell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | | | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX
| | - Qingchang Meng
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Deborah I Ritter
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Francis T F Tsai
- Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Sharon E Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
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Ciccolini J, Serdjebi C, Le Thi Thu H, Lacarelle B, Milano G, Fanciullino R. Nucleoside analogs: ready to enter the era of precision medicine? Expert Opin Drug Metab Toxicol 2016; 12:865-77. [DOI: 10.1080/17425255.2016.1192128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Joseph Ciccolini
- SMARTc Unit, Inserm S_911 CRO2 Aix-Marseille University, Marseille, France
| | - Cindy Serdjebi
- Assistance Publique Hôpitaux de Marseille. Multidisciplinary Oncology & Therapeutic Innovations dpt, Aix Marseille University, Marseille, France
| | - Hau Le Thi Thu
- SMARTc Unit, Inserm S_911 CRO2 Aix-Marseille University, Marseille, France
| | - Bruno Lacarelle
- SMARTc Unit, Inserm S_911 CRO2 Aix-Marseille University, Marseille, France
| | - Gerard Milano
- Oncopharmacology Unit, Centre Antoine Lacassagne, Nice, France
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Drenberg CD, Paugh SW, Pounds SB, Shi L, Orwick SJ, Li L, Hu S, Gibson AA, Ribeiro RC, Rubnitz JE, Evans WE, Sparreboom A, Baker SD. Inherited variation in OATP1B1 is associated with treatment outcome in acute myeloid leukemia. Clin Pharmacol Ther 2016; 99:651-60. [PMID: 26663398 DOI: 10.1002/cpt.315] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/21/2015] [Indexed: 12/20/2022]
Abstract
Using broad interrogation of clinically relevant drug absorption, distribution, metabolism, and excretion (ADME) genes on the DMET platform, we identified a genetic variant in SLCO1B1 (rs2291075; c.597C>T), encoding the transporter OATP1B1, associated with event-free (P = 0.006, hazard ratio = 1.74) and overall survival (P = 0.012, hazard ratio = 1.85) in children with de novo acute myeloid leukemia (AML). Lack of SLCO1B1 expression in leukemic blasts suggested the association might be due to an inherited rather than a somatic effect. rs2291075 was in strong linkage with known functional variants rs2306283 (c.388A>G) and rs4149056 (c.521T>C). Functional studies in vitro determined that four AML-directed chemotherapeutics (cytarabine, daunorubicin, etoposide, and mitoxantrone) are substrates for OATP1B1 and the mouse ortholog Oatp1b2. In vivo pharmacokinetic studies using Oatp1b2-deficient mice further confirmed our results. Collectively, these findings demonstrate an important role for OATP1B1 in the systemic pharmacokinetics of multiple drugs used in the treatment of AML and suggest that inherited variability in host transporter function influences the effectiveness of therapy.
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Affiliation(s)
- C D Drenberg
- College of Pharmacy Division of Pharmaceutics and Pharmaceutical Chemistry, Ohio State University, Columbus, Ohio, USA.,Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - S W Paugh
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - S B Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - L Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - S J Orwick
- Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - L Li
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - S Hu
- College of Pharmacy Division of Pharmaceutics and Pharmaceutical Chemistry, Ohio State University, Columbus, Ohio, USA.,Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - A A Gibson
- College of Pharmacy Division of Pharmaceutics and Pharmaceutical Chemistry, Ohio State University, Columbus, Ohio, USA.,Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - R C Ribeiro
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - J E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - W E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - A Sparreboom
- College of Pharmacy Division of Pharmaceutics and Pharmaceutical Chemistry, Ohio State University, Columbus, Ohio, USA.,Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
| | - S D Baker
- College of Pharmacy Division of Pharmaceutics and Pharmaceutical Chemistry, Ohio State University, Columbus, Ohio, USA.,Comprehensive Cancer Center, Ohio State University, Columbus, Ohio, USA
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25
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Bhise NS, Chauhan L, Shin M, Cao X, Pounds S, Lamba V, Lamba JK. MicroRNA-mRNA Pairs Associated with Outcome in AML: From In Vitro Cell-Based Studies to AML Patients. Front Pharmacol 2016; 6:324. [PMID: 26858643 PMCID: PMC4729948 DOI: 10.3389/fphar.2015.00324] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/30/2015] [Indexed: 12/22/2022] Open
Abstract
Cytarabine is the primary chemotherapeutic agent used for treatment of acute myeloid leukemia (AML). Disease relapse after initial remission remains one of the most pressing therapeutic challenges in the treatment of AML. Relapsed disease is often resistant to cytarabine and subsequent salvage therapy is ineffective. Recent studies have shown that some microRNAs (miRNAs) are associated with prognosis, but have not yet explored the role of miRNAs in cellular response to cytarabine. We identified 20 miRNAs that associate with the in vitro cytarabine chemo-sensitivity or apoptotic response of eight AML cell lines. Out of the 20 miRNAs, data on 18 miRNAs was available in AML patients from The Cancer Genome Atlas database. Our stepwise-integrated analyses (step 1 - miRNA-target mRNA that were significantly correlated in AML patients; step 2 - mRNAs from step 1 with significant association with overall survival (OS)) identified 23 unique miRNA-mRNA pairs predictive of OS in AML patients. As expected HOX genes (HOXA9, HOXB7, and HOXA10) were identified to be regulated by miRs as well as predictive of worse OS. Additionally, miR107-Myb, miR-378-granzyme B involved in granzyme signaling and miR10a-MAP4K4 were identified to be predictive of outcome through integrated analysis. Although additional functional validations to establish clinical/pharmacologic importance of miRNA-mRNA pairs are needed, our results from RNA electrophoretic mobility shift assay confirmed binding of miR-10a, miR-378, and miR-107 with their target genes GALNT1, GZMB, and MYB, respectively. Integration of pathogenic and pharmacologically significant miRNAs and miRNA-mRNA relationships identified in our study opens up opportunities for development of targeted/miRNA-directed therapies.
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Affiliation(s)
- Neha S Bhise
- Department of Pharmacotherapy and Translational Research, University of FloridaGainesville, FL, USA; Department of Experimental and Clinical Pharmacology, University of MinnesotaMinneapolis, MN, USA
| | - Lata Chauhan
- Department of Pharmacotherapy and Translational Research, University of Florida Gainesville, FL, USA
| | - Miyoung Shin
- Department of Pharmacotherapy and Translational Research, University of Florida Gainesville, FL, USA
| | - Xueyuan Cao
- Department of Biostatistics, St. Jude Children's Research Hospital Memphis, TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital Memphis, TN, USA
| | - Vishal Lamba
- Department of Pharmacotherapy and Translational Research, University of Florida Gainesville, FL, USA
| | - Jatinder K Lamba
- Department of Pharmacotherapy and Translational Research, University of Florida Gainesville, FL, USA
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26
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Mitra AK, Mukherjee UK, Harding T, Jang JS, Stessman H, Li Y, Abyzov A, Jen J, Kumar S, Rajkumar V, Van Ness B. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors. Leukemia 2015; 30:1094-102. [DOI: 10.1038/leu.2015.361] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/30/2015] [Accepted: 12/15/2015] [Indexed: 12/14/2022]
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Cividini F, Filoni DN, Pesi R, Allegrini S, Camici M, Tozzi MG. IMP-GMP specific cytosolic 5'-nucleotidase regulates nucleotide pool and prodrug metabolism. Biochim Biophys Acta Gen Subj 2015; 1850:1354-61. [PMID: 25857773 DOI: 10.1016/j.bbagen.2015.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/26/2015] [Accepted: 03/31/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Type II cytosolic 5'-nucleotidase (cN-II) catalyzes the hydrolysis of purine and, to some extent, of pyrimidine monophosphates. Recently, a number of papers demonstrated the involvement of cN-II in the mechanisms of resistance to antitumor drugs such as cytarabine, gemcitabine and fludarabine. Furthermore, cN-II is involved in drug resistance in patients affected by hematological malignancies influencing the clinical outcome. Although the implication of cN-II expression and/or activity appears to be correlated with drug resistance and poor prognosis, the molecular mechanism by which cN-II mediates drug resistance is still unknown. METHODS HEK 293 cells carrying an expression vector coding for cN-II linked to green fluorescent protein (GFP) and a control vector without cN-II were utilized. A highly sensitive capillary electrophoresis method was applied for nucleotide pool determination and cytotoxicity exerted by drugs was determined with 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. RESULTS Over-expression of cN-II causes a drop of nucleoside triphosphate concentration and a general disturbance of nucleotide pool. Over-expressing cells were resistant to fludarabine, gemcitabine and cytarabine independently of cN-II ability to hydrolyze their monophosphates. CONCLUSIONS An increase of cN-II expression is sufficient to cause both a general disturbance of nucleotide pool and an increase of half maximal inhibitory concentration (IC50) of the drugs. Since the monophosphates of cytarabine and gemcitabine are not substrates of cN-II, the protection observed cannot be directly ascribed to drug inactivation. GENERAL SIGNIFICANCE Our results indicate that cN-II exerts a relevant role in nucleotide and drug metabolism through not only enzyme activity but also a mechanism involving a protein-protein interaction, thus playing a general regulatory role in cell survival. SENTENCE Resistance to fludarabine, gemcitabine and cytarabine can be determined by an increase of cN-II both through dephosphorylation of active drugs and perturbation of nucleotide pool.
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Affiliation(s)
- Federico Cividini
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Via San Zeno 51, 56127, Pisa, Italy
| | - Daniela Nicole Filoni
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Via San Zeno 51, 56127, Pisa, Italy; Dipartimento di Chimica e Farmacia, Università di Sassari, Via Muroni 23A, 07100, Sassari, Italy
| | - Rossana Pesi
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Via San Zeno 51, 56127, Pisa, Italy
| | - Simone Allegrini
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Muroni 23A, 07100, Sassari, Italy.
| | - Marcella Camici
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Via San Zeno 51, 56127, Pisa, Italy
| | - Maria Grazia Tozzi
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Via San Zeno 51, 56127, Pisa, Italy
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Cividini F, Pesi R, Chaloin L, Allegrini S, Camici M, Cros-Perrial E, Dumontet C, Jordheim L, Tozzi M. The purine analog fludarabine acts as a cytosolic 5′-nucleotidase II inhibitor. Biochem Pharmacol 2015; 94:63-8. [DOI: 10.1016/j.bcp.2015.01.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/26/2015] [Accepted: 01/26/2015] [Indexed: 11/29/2022]
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30
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Wan H, Zhu J, Chen F, Xiao F, Huang H, Han X, Zhong L, Zhong H, Xu L, Ni B, Zhong J. SLC29A1 single nucleotide polymorphisms as independent prognostic predictors for survival of patients with acute myeloid leukemia: an in vitro study. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014; 33:90. [PMID: 25398670 PMCID: PMC4234887 DOI: 10.1186/s13046-014-0090-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/20/2014] [Indexed: 12/12/2022]
Abstract
Background The mechanism behind poor survival of acute myeloid leukemia (AML) patients with 1-barabinofuranosylcytosine (Ara-C) based treatment remains unclear. This study aimed to assess the pharmacogenomic effects of Ara-C metabolic pathway in patients with AML. Methods The genotypes of 19 single nucleotide polymorphisms (SNPs) of DCK, CDA and SLC29A1from 100 AML patients treated with Ara-C were examined. All the SNPs were screened with ligase detection reaction assay. The transcription analysis of genes was examined by quantitative real time polymerase chain reaction. The association between clinical outcome and gene variants was evaluated by Kaplan-Meier method. Results Genotypes of rs9394992 and rs324148 for SLC29A1 in remission patients were significantly different from those in relapsed ones. Post-induction overall survival (OS) significantly decreased in patients with the CC genotype of rs324148 compared with CT and TT genotypes (hazard ratio [HR] = 2.997 [95% confidence interval (CI): 1.71-5.27]). As compared with CT and TT genotype, patients with the CC genotype of rs9394992 had longer survival time (HR = 0.25 [95% CI: 0.075-0.81]; HR = 0.43 [95% CI: 0.24-0.78]) and longer disease-free survival (DFS) (HR = 0.52 [95% CI: 0.29-0.93]; HR = 0.15 [95% CI: 0.05-0.47]) as well As compared with CT and TT genotype, patients with the CC genotype of rs324148 had shorter DFS (HR = 3.18 [95% CI: 1.76-5.76]). Additionally, patients with adverse karyotypes had shorter DFS (HR = 0.17 [95% CI: 0.05-0.54]) and OS (HR = 0.18 [95% CI: 0.05-0.68]). Conclusions AML patients with low activity of SLC29A1 genotype have shorter DFS and OS in Ara-C based therapy. Genotypes of rs9394992 and rs324148 may be independent prognostic predictors for the survival of AML patients. Electronic supplementary material The online version of this article (doi:10.1186/s13046-014-0090-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haixia Wan
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Jianyi Zhu
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Fangyuan Chen
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Fei Xiao
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Honghui Huang
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Xiaofeng Han
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Lu Zhong
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Hua Zhong
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Lan Xu
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Beiwen Ni
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Jihua Zhong
- Department of Hematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
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Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/471836] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Advances in several biology-oriented initiatives such as genome sequencing and structural genomics, along with the progress made through traditional biological and biochemical research, have opened up a unique opportunity to better understand the molecular effects of human diseases. Human DNA can vary significantly from person to person and determines an individual’s physical characteristics and their susceptibility to diseases. Armed with an individual’s DNA sequence, researchers and physicians can check for defects known to be associated with certain diseases by utilizing various databases. However, for unclassified DNA mutations or in order to reveal molecular mechanism behind the effects, the mutations have to be mapped onto the corresponding networks and macromolecular structures and then analyzed to reveal their effect on the wild type properties of biological processes involved. Predicting the effect of DNA mutations on individual’s health is typically referred to as personalized or companion diagnostics. Furthermore, once the molecular mechanism of the mutations is revealed, the patient should be given drugs which are the most appropriate for the individual genome, referred to as pharmacogenomics. Altogether, the shift in focus in medicine towards more genomic-oriented practices is the foundation of personalized medicine. The progress made in these rapidly developing fields is outlined.
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Cao X, Mitra AK, Pounds S, Crews KR, Gandhi V, Plunkett W, Dolan ME, Hartford C, Raimondi S, Campana D, Downing J, Rubnitz JE, Ribeiro RC, Lamba JK. RRM1 and RRM2 pharmacogenetics: association with phenotypes in HapMap cell lines and acute myeloid leukemia patients. Pharmacogenomics 2014; 14:1449-66. [PMID: 24024897 DOI: 10.2217/pgs.13.131] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Ribonucleotide reductase catalyzes an essential step in the cellular production of deoxyribonucleotide triphosphates and has been associated with clinical outcome in cancer patients receiving nucleoside analog-based chemotherapy. MATERIALS & METHODS In the current study, we sequenced the genes RRM1 and RRM2 in genomic DNA from HapMap cell lines with European (Utah residents with northern and western European ancestry [CEU]; n = 90) or African (Yoruba people in Ibadan, Nigeria [YRI]; n = 90) ancestry. RESULTS We identified 44 genetic variants including eight coding SNPs in RRM1 and 15 SNPs including one coding SNP in RRM2. RRM1 and RRM2 mRNA expression levels were significantly correlated with each other in both CEU and YRI lymphoblast cell lines, and in leukemic blasts from acute myeloid leukemia (AML) patients (AML97, n = 89; AML02, n = 187). Additionally, RRM1 expression was higher among patient features indicative of a high relapse hazard. We evaluated SNPs within the RRM1 and RRM2 genes in the HapMap lymphoblast cell lines from CEU and YRI panels for association with expression and cytarabine chemosensitivity. SNPs of potential significance were further evaluated in AML patients. RRM1 SNPs rs1042919 (which occurs in linkage disequilbrium with multiple other SNPs) and promoter SNP rs1561876 were associated with intracellular 1-β-D-arabinofuranosyl-CTP levels, response after remission induction therapy, risk of relapse and overall survival in AML patients receiving cytarabine and cladribine. CONCLUSION These results suggest that SNPs within ribonucleotide reductase might be helpful predictive markers of response to nucleoside analogs and should be further validated in larger cohorts.
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Affiliation(s)
- Xueyuan Cao
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
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Stark AL, Hause RJ, Gorsic LK, Antao NN, Wong SS, Chung SH, Gill DF, Im HK, Myers JL, White KP, Jones RB, Dolan ME. Protein quantitative trait loci identify novel candidates modulating cellular response to chemotherapy. PLoS Genet 2014; 10:e1004192. [PMID: 24699359 PMCID: PMC3974641 DOI: 10.1371/journal.pgen.1004192] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 01/07/2014] [Indexed: 11/24/2022] Open
Abstract
Annotating and interpreting the results of genome-wide association studies (GWAS) remains challenging. Assigning function to genetic variants as expression quantitative trait loci is an expanding and useful approach, but focuses exclusively on mRNA rather than protein levels. Many variants remain without annotation. To address this problem, we measured the steady state abundance of 441 human signaling and transcription factor proteins from 68 Yoruba HapMap lymphoblastoid cell lines to identify novel relationships between inter-individual protein levels, genetic variants, and sensitivity to chemotherapeutic agents. Proteins were measured using micro-western and reverse phase protein arrays from three independent cell line thaws to permit mixed effect modeling of protein biological replicates. We observed enrichment of protein quantitative trait loci (pQTLs) for cellular sensitivity to two commonly used chemotherapeutics: cisplatin and paclitaxel. We functionally validated the target protein of a genome-wide significant trans-pQTL for its relevance in paclitaxel-induced apoptosis. GWAS overlap results of drug-induced apoptosis and cytotoxicity for paclitaxel and cisplatin revealed unique SNPs associated with the pharmacologic traits (at p<0.001). Interestingly, GWAS SNPs from various regions of the genome implicated the same target protein (p<0.0001) that correlated with drug induced cytotoxicity or apoptosis (p≤0.05). Two genes were functionally validated for association with drug response using siRNA: SMC1A with cisplatin response and ZNF569 with paclitaxel response. This work allows pharmacogenomic discovery to progress from the transcriptome to the proteome and offers potential for identification of new therapeutic targets. This approach, linking targeted proteomic data to variation in pharmacologic response, can be generalized to other studies evaluating genotype-phenotype relationships and provide insight into chemotherapeutic mechanisms. The central dogma of biology explains that DNA is transcribed to mRNA that is further translated into protein. Many genome-wide studies have implicated genetic variation that influences gene expression and that ultimately affect downstream complex traits including response to drugs. However, because of technical limitations, few studies have evaluated the contribution of genetic variation on protein expression and ensuing effects on downstream phenotypes. To overcome this challenge, we used a novel technology to simultaneously measure the baseline expression of 441 proteins in lymphoblastoid cell lines and compared them with publicly available genetic data. To further illustrate the utility of this approach, we compared protein-level measurements with chemotherapeutic induced apoptosis and cell-growth inhibition data. This study demonstrates the importance of using protein information to understand the functional consequences of genetic variants identified in genome-wide association studies. This protein data set will also have broad utility for understanding the relationship between other genome-wide studies of complex traits.
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Affiliation(s)
- Amy L. Stark
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Ronald J. Hause
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Lidija K. Gorsic
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Nirav N. Antao
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Shan S. Wong
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Sophie H. Chung
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Daniel F. Gill
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Hae K. Im
- Department of Health Studies, The University of Chicago, Chicago, Illinois, United States of America
| | - Jamie L. Myers
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Kevin P. White
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Richard Baker Jones
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (RBJ); (MED)
| | - M. Eileen Dolan
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (RBJ); (MED)
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Keane N, Freeman C, Swords R, Giles FJ. Elacytarabine: lipid vector technology under investigation in acute myeloid leukemia. Expert Rev Hematol 2014; 6:9-24. [DOI: 10.1586/ehm.12.68] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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35
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Eadon MT, Wheeler HE, Stark AL, Zhang X, Moen EL, Delaney SM, Im HK, Cunningham PN, Zhang W, Dolan ME. Genetic and epigenetic variants contributing to clofarabine cytotoxicity. Hum Mol Genet 2013; 22:4007-20. [PMID: 23720496 DOI: 10.1093/hmg/ddt240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine (Clofarabine), a purine nucleoside analog, is used in the treatment of hematologic malignancies and as induction therapy for stem cell transplantation. The discovery of pharmacogenomic markers associated with chemotherapeutic efficacy and toxicity would greatly benefit the utility of this drug. Our objective was to identify genetic and epigenetic variants associated with clofarabine toxicity using an unbiased, whole genome approach. To this end, we employed International HapMap lymphoblastoid cell lines (190 LCLs) of European (CEU) or African (YRI) ancestry with known genetic information to evaluate cellular sensitivity to clofarabine. We measured modified cytosine levels to ascertain the contribution of genetic and epigenetic factors influencing clofarabine-mediated cytotoxicity. Association studies revealed 182 single nucleotide polymorphisms (SNPs) and 143 modified cytosines associated with cytotoxicity in both populations at the threshold P ≤ 0.0001. Correlation between cytotoxicity and baseline gene expression revealed 234 genes at P ≤ 3.98 × 10(-6). Six genes were implicated as: (i) their expression was directly correlated to cytotoxicity, (ii) they had a targeting SNP associated with cytotoxicity, and (iii) they had local modified cytosines associated with gene expression and cytotoxicity. We identified a set of three SNPs and three CpG sites targeting these six genes explaining 43.1% of the observed variation in phenotype. siRNA knockdown of the top three genes (SETBP1, BAG3, KLHL6) in LCLs revealed altered susceptibility to clofarabine, confirming relevance. As clofarabine's toxicity profile includes acute kidney injury, we examined the effect of siRNA knockdown in HEK293 cells. siSETBP1 led to a significant change in HEK293 cell susceptibility to clofarabine.
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Impact of polymorphisms in drug pathway genes on disease-free survival in adults with acute myeloid leukemia. J Hum Genet 2013; 58:353-61. [PMID: 23677058 PMCID: PMC4068832 DOI: 10.1038/jhg.2013.38] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia (AML) is a clinically heterogeneous disease, with 5-year disease-free survival (DFS) ranging from under 10% to over 70% for distinct groups of patients. At our institution, cytarabine, etoposide and busulfan are used in first or second remission patients treated with a 2-step approach to autologous stem cell transplantation (ASCT). In this study, we tested the hypothesis that polymorphisms in the pharmacokinetic and pharmacodynamic pathway genes of these drugs are associated with DFS in AML patients. A total of 1659 variants in 42 genes were analyzed for their association with DFS using a Cox proportional hazards model. 154 genetically European patients were used for the primary analysis. An intronic SNP in ABCC3 (rs4148405) was associated with a significantly shorter DFS (HR=3.2, p=5.6 x 10(-6)) in our primary cohort. In addition a SNP in the GSTM1-GSTM5 locus, rs3754446, was significantly associated with a shorter DFS in all patients (HR=1.8, p=0.001 for 154 European ancestry; HR=1.7, p=0.028 for 125 non-European patients). Thus for the first time, genetic variants in drug pathway genes are shown to be associated with DFS in AML patients treated with chemotherapy-based autologous ASCT.
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Emadi A, Karp JE. The clinically relevant pharmacogenomic changes in acute myelogenous leukemia. Pharmacogenomics 2013; 13:1257-69. [PMID: 22920396 DOI: 10.2217/pgs.12.102] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Acute myelogenous leukemia (AML) is an extremely heterogeneous neoplasm with several clinical, pathological, genetic and molecular subtypes. Combinations of various doses and schedules of cytarabine and different anthracyclines have been the mainstay of treatment for all forms of AMLs in adult patients. Although this combination, with the addition of an occasional third agent, remains effective for treatment of some young-adult patients with de novo AML, the prognosis of AML secondary to myelodysplastic syndromes or myeloproliferative neoplasms, treatment-related AML, relapsed or refractory AML, and AML that occurs in older populations remains grim. Taken into account the heterogeneity of AML, one size does not and should not be tried to fit all. In this article, the authors review currently understood, applicable and relevant findings related to cytarabine and anthracycline drug-metabolizing enzymes and drug transporters in adult patients with AML. To provide a prime-time example of clinical applicability of pharmacogenomics in distinguishing a subset of patients with AML who might be better responders to farnesyltransferase inhibitors, the authors also reviewed findings related to a two-gene transcript signature consisting of high RASGRP1 and low APTX, the ratio of which appears to positively predict clinical response in AML patients treated with farnesyltransferase inhibitors.
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Affiliation(s)
- Ashkan Emadi
- University of Maryland, School of Medicine, Marlene & Stewart Greenebaum Cancer Center, Leukemia & Hematologic Malignancies, Baltimore, MD 21201, USA
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Gamazon ER, Perera M. Genome-wide approaches in pharmacogenomics: heritability estimation and pharmacoethnicity as primary challenges. Pharmacogenomics 2013; 13:1101-4. [PMID: 22909197 DOI: 10.2217/pgs.12.88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Mitra AK, Kirstein MN, Khatri A, Skubitz KM, Dudek AZ, Greeno EW, Kratzke RA, Lamba JK. Pathway-based pharmacogenomics of gemcitabine pharmacokinetics in patients with solid tumors. Pharmacogenomics 2013; 13:1009-21. [PMID: 22838949 DOI: 10.2217/pgs.12.81] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM The aim of this study was to evaluate the association of gemcitabine pathway SNPs with detailed pharmacokinetic measures obtained from solid tumor patients receiving gemcitabine-based therapy. MATERIALS & METHODS SNPs within nine gemcitabine pathway genes, namely CDA, CMPK, DCK, DCTD, NT5C2, NT5C3, SLC28A1, SLC28A3 and SLC29A1 were analyzed for association with gemcitabine pharmacokinetics. RESULTS Significant association of gemcitabine clearance with SNPs in NT5C2 was identified. Clearance of 2´,2´-difluorodeoxyuridine, a gemcitabine metabolite was significantly predicted by CDA, SLC29A1 and NT5C2 SNPs. This study reports an association of formation clearance of 2´,2´-difluoro-2´-deoxycytidine triphosphate, an active form of gemcitabine with SNPs within uptake transporters SLC28A1, SLC28A3 and SLC29A1. CONCLUSION Genetic variation in gemcitabine pathway genes is associated with its pharmacokinetics and hence could influence gemcitabine response. Our study identified pharmacogenetic markers that could be further tested in larger patient cohorts and could open up opportunities to individualize therapy in solid tumor patients.
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Affiliation(s)
- Amit K Mitra
- Department of Experimental & Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
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Comprehensive genetic analysis of cytarabine sensitivity in a cell-based model identifies polymorphisms associated with outcome in AML patients. Blood 2013; 121:4366-76. [PMID: 23538338 DOI: 10.1182/blood-2012-10-464149] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A whole-genome approach was used to investigate the genetic determinants of cytarabine-induced cytotoxicity. We performed a meta-analysis of genome-wide association studies involving 523 lymphoblastoid cell lines (LCLs) from individuals of European, African, Asian, and African American ancestry. Several of the highest-ranked single-nucleotide polymorphisms (SNPs) were within the mutated in colorectal cancers (MCC) gene. MCC expression was induced by cytarabine treatment from 1.7- to 26.6-fold in LCLs. A total of 33 SNPs ranked at the top of the meta-analysis (P < 10(-5)) were successfully tested in a clinical trial of patients randomized to receive low-dose or high-dose cytarabine plus daunorubicin and etoposide; of these, 18 showed association (P < .05) with either cytarabine 50% inhibitory concentration in leukemia cells or clinical response parameters (minimal residual disease, overall survival (OS), and treatment-related mortality). This count (n = 18) was significantly greater than expected by chance (P = .016). For rs1203633, LCLs with AA genotype were more sensitive to cytarabine-induced cytotoxicity (P = 1.31 × 10(-6)) and AA (vs GA or GG) genotype was associated with poorer OS (P = .015), likely as a result of greater treatment-related mortality (P = .0037) in patients with acute myeloid leukemia (AML). This multicenter AML02 study trial was registered at www.clinicaltrials.gov as #NCT00136084.
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Njiaju UO, Gamazon ER, Gorsic LK, Delaney SM, Wheeler HE, Im HK, Dolan ME. Whole-genome studies identify solute carrier transporters in cellular susceptibility to paclitaxel. Pharmacogenet Genomics 2012; 22:498-507. [PMID: 22437668 DOI: 10.1097/fpc.0b013e328352f436] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The clinical use of paclitaxel is limited by variable responses and the potential for significant toxicity. To date, studies of associations between variants in candidate genes and paclitaxel effects have yielded conflicting results. We aimed to evaluate the relationships between global gene expression and paclitaxel sensitivity. METHODS We utilized well-genotyped lymphoblastoid cell lines derived from the International HapMap Project to evaluate the relationships between cellular susceptibility to paclitaxel and global gene expression. Cells were exposed to varying concentrations of paclitaxel to evaluate paclitaxel-induced cytotoxicity and apoptosis. Among the top genes, we identified solute carrier (SLC) genes associated with paclitaxel sensitivity and narrowed down the list to those that had single nucleotide polymorphisms associated with both the expression level of the SLC gene and also with paclitaxel sensitivity. We performed an independent validation in an independent set of cell lines and also conducted functional studies using RNA interference. RESULTS Of all genes associated with paclitaxel-induced cytotoxicity at P less than 0.05 (1713 genes), there was a significant enrichment in SLC genes (31 genes). A subset of SLC genes, namely SLC31A2, SLC43A1, SLC35A5, and SLC41A2, was associated with paclitaxel sensitivity and had regulating single nucleotide polymorphisms that were also associated with paclitaxel-induced cytotoxicity. Multivariate modeling demonstrated that those four SLC genes together explained 20% of the observed variability in paclitaxel susceptibility. Using RNA interference, we demonstrated increased paclitaxel susceptibility with knockdown of three SLC genes, SLC31A2, SLC35A5, and SLC41A2. CONCLUSION Our findings are novel and lend further support to the role of transporters, specifically solute carriers, in mediating cellular susceptibility to paclitaxel.
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Affiliation(s)
- Uchenna O Njiaju
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Comprehensive Cancer, Chicago, Illinois, USA
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Madian AG, Wheeler HE, Jones RB, Dolan ME. Relating human genetic variation to variation in drug responses. Trends Genet 2012; 28:487-95. [PMID: 22840197 DOI: 10.1016/j.tig.2012.06.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 06/13/2012] [Accepted: 06/22/2012] [Indexed: 02/03/2023]
Abstract
Although sequencing a single human genome was a monumental effort a decade ago, more than 1000 genomes have now been sequenced. The task ahead lies in transforming this information into personalized treatment strategies that are tailored to the unique genetics of each individual. One important aspect of personalized medicine is patient-to-patient variation in drug response. Pharmacogenomics addresses this issue by seeking to identify genetic contributors to human variation in drug efficacy and toxicity. Here, we present a summary of the current status of this field, which has evolved from studies of single candidate genes to comprehensive genome-wide analyses. Additionally, we discuss the major challenges in translating this knowledge into a systems-level understanding of drug physiology, with the ultimate goal of developing more effective personalized clinical treatment strategies.
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Affiliation(s)
- Ashraf G Madian
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, IL, USA
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Gallier F, Lallemand P, Meurillon M, Jordheim LP, Dumontet C, Périgaud C, Lionne C, Peyrottes S, Chaloin L. Structural insights into the inhibition of cytosolic 5'-nucleotidase II (cN-II) by ribonucleoside 5'-monophosphate analogues. PLoS Comput Biol 2011; 7:e1002295. [PMID: 22174667 PMCID: PMC3234209 DOI: 10.1371/journal.pcbi.1002295] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/20/2011] [Indexed: 02/04/2023] Open
Abstract
Cytosolic 5′-nucleotidase II (cN-II) regulates the intracellular nucleotide pools within the cell by catalyzing the dephosphorylation of 6-hydroxypurine nucleoside 5′-monophosphates. Beside this physiological function, high level of cN-II expression is correlated with abnormal patient outcome when treated with cytotoxic nucleoside analogues. To identify its specific role in the resistance phenomenon observed during cancer therapy, we screened a particular class of chemical compounds, namely ribonucleoside phosphonates to predict them as potential cN-II inhibitors. These compounds incorporate a chemically and enzymatically stable phosphorus-carbon linkage instead of a regular phosphoester bond. Amongst them, six compounds were predicted as better ligands than the natural substrate of cN-II, inosine 5′-monophosphate (IMP). The study of purine and pyrimidine containing analogues and the introduction of chemical modifications within the phosphonate chain has allowed us to define general rules governing the theoretical affinity of such ligands. The binding strength of these compounds was scrutinized in silico and explained by an impressive number of van der Waals contacts, highlighting the decisive role of three cN-II residues that are Phe 157, His 209 and Tyr 210. Docking predictions were confirmed by experimental measurements of the nucleotidase activity in the presence of the three best available phosphonate analogues. These compounds were shown to induce a total inhibition of the cN-II activity at 2 mM. Altogether, this study emphasizes the importance of the non-hydrolysable phosphonate bond in the design of new competitive cN-II inhibitors and the crucial hydrophobic stacking promoted by three protein residues. Nucleotidase activity is part of a biological process that allows the cell to regulate the intracellular pools of nucleotides involved in many signaling pathways. During cancer therapy with cytotoxic nucleoside analogues, the role of cN-II is unclear. Therefore, the development of specific inhibitors against this enzyme is of great interest for understanding its implication in cancer biology and drug resistance. Ribonucleoside phosphonates are of major importance because they behave as bioisosteric analogues of the natural cN-II substrates and contain a chemically and enzymatically stable phosphorus-carbon linkage. Taking the advantages of docking methods, we predicted the inhibitory potential of these compounds. Their binding strength was explained by an impressive interaction network involving mainly three residues of the enzyme (acting as hydrophobic tweezers). These new characterized inhibitors will constitute a valuable tool for elucidating the role of cN-II in cancer cells and may be used in combination with cytotoxic nucleosidic drugs in order to increase their antitumor activity. Furthermore, the strategy taking into account the hydrophobic clamp for designing new inhibitors may be applied to other nucleotidases of the HAD family as two of the three identified residues are present in the substrate binding site of cytosolic 5′-nucleotidase III and 5′-deoxynucleotidase-I.
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Affiliation(s)
- Franck Gallier
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS – Universités Montpellier 1 et 2, Université Montpellier 2, Montpellier, France
| | - Perrine Lallemand
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS – Universités Montpellier 1 et 2, Montpellier, France
| | - Maïa Meurillon
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS – Universités Montpellier 1 et 2, Université Montpellier 2, Montpellier, France
| | - Lars P. Jordheim
- Centre de Recherche de Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR 5286 – Université Claude Bernard Lyon 1, Lyon, France
| | - Charles Dumontet
- Centre de Recherche de Cancérologie de Lyon (CRCL), INSERM U1052, CNRS UMR 5286 – Université Claude Bernard Lyon 1, Lyon, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS – Universités Montpellier 1 et 2, Université Montpellier 2, Montpellier, France
| | - Corinne Lionne
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS – Universités Montpellier 1 et 2, Montpellier, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS – Universités Montpellier 1 et 2, Université Montpellier 2, Montpellier, France
| | - Laurent Chaloin
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS – Universités Montpellier 1 et 2, Montpellier, France
- * E-mail:
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