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Komiyama T, Ogura A, Kajiwara T, Okada Y, Kobayashi H. Analysis of Candidate Idarubicin Drug Resistance Genes in MOLT-3 Cells Using Exome Nuclear DNA. Genes (Basel) 2018; 9:genes9080390. [PMID: 30071629 PMCID: PMC6116115 DOI: 10.3390/genes9080390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 02/05/2023] Open
Abstract
Various gene alterations related to acute leukemia are reported to be involved in drug resistance. We investigated idarubicin (IDR) resistance using exome nuclear DNA analyses of the human acute leukemia cell line MOLT-3 and the derived IDR-resistant cell line MOLT-3/IDR. We detected mutations in MOLT-3/IDR and MOLT-3 using both Genome Analysis Toolkit (GATK) and SnpEff program. We found 8839 genes with specific mutations in MOLT-3/IDR and 1162 genes with accompanying amino acid mutations. The 1162 genes were identified by exome analysis of polymerase-related genes using Kyoto Encyclopedia of Genes and Genomes (KEGG) and, among these, we identified genes with amino acid changes. In resistant strains, LIG and helicase plurality genes showed amino-acid-related changes. An amino acid mutation was also confirmed in polymerase-associated genes. Gene ontology (GO) enrichment testing was performed, and lipid-related genes were selected from the results. Fluorescent activated cell sorting (FACS) was used to determine whether IDR permeability was significantly different in MOLT-3/IDR and MOLT-3. The results showed that an IDR concentration of 0.5 μg/mL resulted in slow permeability in MOLT-3/IDR. This slow IDR permeability may be due to the effects of amino acid changes in polymerase- and lipid-associated genes.
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Affiliation(s)
- Tomoyoshi Komiyama
- Department of Clinical Pharmacology, Tokai University School of Medicine, Kanagawa 259-1193, Japan.
| | - Atsushi Ogura
- Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan.
| | - Takehito Kajiwara
- Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan.
| | - Yoshinori Okada
- Support Center for Medical Research and Education, Tokai University, Kanagawa 259-1193, Japan.
| | - Hiroyuki Kobayashi
- Department of Clinical Pharmacology, Tokai University School of Medicine, Kanagawa 259-1193, Japan.
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Tu HC, Lee GH, Hsiao TH, Kao TT, Wang TY, Tsai JN, Fu TF. One crisis, diverse impacts-Tissue-specificity of folate deficiency-induced circulation defects in zebrafish larvae. PLoS One 2017; 12:e0188585. [PMID: 29176804 PMCID: PMC5703520 DOI: 10.1371/journal.pone.0188585] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/09/2017] [Indexed: 12/17/2022] Open
Abstract
Folate (vitamin B9) is an essential nutrient required for cell survival, proliferation, differentiation and therefore embryogenesis. Folate deficiency has been associated with many diseases, including congenital heart diseases and megaloblastic anemia, yet the mechanisms underlying these remains elusive. Here, we examine the impact of folate deficiency on the development of the circulation system using a zebrafish transgenic line which displays inducible folate deficiency. Impaired hematopoiesis includes decreased hemoglobin levels, decreased erythrocyte number, increased erythrocyte size and aberrant c-myb expression pattern were observed in folate deficient embryos. Cardiac defects, including smaller chamber size, aberrant cardiac function and cmlc2 expression pattern, were also apparent in folate deficient embryos. Characterization of intracellular folate content in folate deficiency revealed a differential fluctuation among the different folate derivatives that carry a single carbon group at different oxidation levels. Rescue attempts by folic acid and nucleotides resulted in differential responses among affected tissues, suggesting that different pathomechanisms are involved in folate deficiency-induced anomalies in a tissue-specific manner. The results of the current study provide an explanation for the inconsistent outcome observed clinically in patients suffering from folate deficiency and/or receiving folate supplementation. This study also supports the use of this model for further research on the defective cardiogenesis and hematopoiesis caused by folate deficiency.
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Affiliation(s)
- Hung-Chi Tu
- The Institute of Basic Medical Sciences, National Cheng Kung University, College of Medicine, Tainan, Taiwan
| | - Gang-Hui Lee
- The Institute of Basic Medical Sciences, National Cheng Kung University, College of Medicine, Tainan, Taiwan
| | - Tsun-Hsien Hsiao
- The Institute of Basic Medical Sciences, National Cheng Kung University, College of Medicine, Tainan, Taiwan
| | - Tseng-Ting Kao
- The Institute of Basic Medical Sciences, National Cheng Kung University, College of Medicine, Tainan, Taiwan
| | - Tzu-Ya Wang
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, College of Medicine, Tainan, Taiwan
| | - Jen-Ning Tsai
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, Taichung, Taiwan
- Department of Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Tzu-Fun Fu
- The Institute of Basic Medical Sciences, National Cheng Kung University, College of Medicine, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, College of Medicine, Tainan, Taiwan
- * E-mail:
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Raz S, Stark M, Assaraf YG. Folylpoly-γ-glutamate synthetase: A key determinant of folate homeostasis and antifolate resistance in cancer. Drug Resist Updat 2016; 28:43-64. [PMID: 27620954 DOI: 10.1016/j.drup.2016.06.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 06/10/2016] [Accepted: 06/16/2016] [Indexed: 01/26/2023]
Abstract
Mammalians are devoid of autonomous biosynthesis of folates and hence must obtain them from the diet. Reduced folate cofactors are B9-vitamins which play a key role as donors of one-carbon units in the biosynthesis of purine nucleotides, thymidylate and amino acids as well as in a multitude of methylation reactions including DNA, RNA, histone and non-histone proteins, phospholipids, as well as intermediate metabolites. The products of these S-adenosylmethionine (SAM)-dependent methylations are involved in the regulation of key biological processes including transcription, translation and intracellular signaling. Folate-dependent one-carbon metabolism occurs in several subcellular compartments including the cytoplasm, mitochondria, and nucleus. Since folates are essential for DNA replication, intracellular folate cofactors play a central role in cancer biology and inflammatory autoimmune disorders. In this respect, various folate-dependent enzymes catalyzing nucleotide biosynthesis have been targeted by specific folate antagonists known as antifolates. Currently, antifolates are used in drug treatment of multiple human cancers, non-malignant chronic inflammatory disorders as well as bacterial and parasitic infections. An obligatory key component of intracellular folate retention and intracellular homeostasis is (anti)folate polyglutamylation, mediated by the unique enzyme folylpoly-γ-glutamate synthetase (FPGS), which resides in both the cytoplasm and mitochondria. Consistently, knockout of the FPGS gene in mice results in embryonic lethality. FPGS catalyzes the addition of a long polyglutamate chain to folates and antifolates, hence rendering them polyanions which are efficiently retained in the cell and are now bound with enhanced affinity by various folate-dependent enzymes. The current review highlights the crucial role that FPGS plays in maintenance of folate homeostasis under physiological conditions and delineates the plethora of the molecular mechanisms underlying loss of FPGS function and consequent antifolate resistance in cancer.
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Affiliation(s)
- Shachar Raz
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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Gonen N, Assaraf YG. Antifolates in cancer therapy: Structure, activity and mechanisms of drug resistance. Drug Resist Updat 2012; 15:183-210. [DOI: 10.1016/j.drup.2012.07.002] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 06/25/2012] [Accepted: 07/11/2012] [Indexed: 01/19/2023]
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Volpato JP, Yachnin BJ, Blanchet J, Guerrero V, Poulin L, Fossati E, Berghuis AM, Pelletier JN. Multiple conformers in active site of human dihydrofolate reductase F31R/Q35E double mutant suggest structural basis for methotrexate resistance. J Biol Chem 2009; 284:20079-89. [PMID: 19478082 PMCID: PMC2740434 DOI: 10.1074/jbc.m109.018010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 05/06/2009] [Indexed: 11/06/2022] Open
Abstract
Methotrexate is a slow, tight-binding, competitive inhibitor of human dihydrofolate reductase (hDHFR), an enzyme that provides key metabolites for nucleotide biosynthesis. In an effort to better characterize ligand binding in drug resistance, we have previously engineered hDHFR variant F31R/Q35E. This variant displays a >650-fold decrease in methotrexate affinity, while maintaining catalytic activity comparable to the native enzyme. To elucidate the molecular basis of decreased methotrexate affinity in the doubly substituted variant, we determined kinetic and inhibitory parameters for the simple variants F31R and Q35E. This demonstrated that the important decrease of methotrexate affinity in variant F31R/Q35E is a result of synergistic effects of the combined substitutions. To better understand the structural cause of this synergy, we obtained the crystal structure of hDHFR variant F31R/Q35E complexed with methotrexate at 1.7-A resolution. The mutated residue Arg-31 was observed in multiple conformers. In addition, seven native active-site residues were observed in more than one conformation, which is not characteristic of the wild-type enzyme. This suggests that increased residue disorder underlies the observed methotrexate resistance. We observe a considerable loss of van der Waals and polar contacts with the p-aminobenzoic acid and glutamate moieties. The multiple conformers of Arg-31 further suggest that the amino acid substitutions may decrease the isomerization step required for tight binding of methotrexate. Molecular docking with folate corroborates this hypothesis.
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Affiliation(s)
| | | | - Jonathan Blanchet
- the Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7 and
| | - Vanessa Guerrero
- the Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7 and
| | - Lucie Poulin
- the Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7 and
| | | | - Albert M. Berghuis
- the Departments of Biochemistry and
- Microbiology and Immunology, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Joelle N. Pelletier
- From the Département de Biochimie and
- the Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7 and
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Rader JS, Clarke-Pearson D, Moore M, Carson L, Holloway R, Kao MS, Wiznitzer I, Douglass EC. A phase II study to determine the efficacy and tolerability of intravenous ZD9331 in heavily pretreated patients with ovarian cancer. Gynecol Oncol 2003; 91:318-25. [PMID: 14599861 DOI: 10.1016/s0090-8258(03)00491-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVES This Phase II, multicenter, open-label study was conducted to assess the efficacy and tolerability of ZD9331, a novel direct-acting thymidylate synthase inhibitor, in heavily pretreated patients with ovarian cancer. METHODS The study recruited 44 women with ovarian cancer or primary peritoneal cancer previously treated with platinum therapy and paclitaxel and with progressive disease after, or intolerance to, topotecan administered as the most recent therapy. ZD9331 was administered as an intravenous infusion at 130 mg/m(2) on Days 1 and 8 of 3-week cycles, until objective evidence of disease progression. A cutoff date of 3 months after the last patient received the first dose was set for data collection. RESULTS Patients received a mean of 3.3 cycles of ZD9331 and a total of 143 cycles were administered. Among the 42 patients evaluated for best overall tumor response, one achieved a complete response and two achieved a partial response, giving an objective tumor response rate of 7%. The complete response occurred at Day 15 of Cycle 2 in a patient receiving ZD9331 as her eighth-line therapy. Seven patients had stable disease, giving a disease control rate of 23%. Thirty-one patients (71%) had disease progression and the median time to progression was 53 days. Most patients (89%) experienced drug-related adverse events, most commonly nausea (73%), vomiting (48%), and neutropenia (50%). Six patients (14%) were withdrawn from treatment due to adverse events. CONCLUSIONS The preliminary evidence of efficacy and acceptable tolerability of ZD9331 in this heavily pretreated population with ovarian cancer warrants further investigation, especially in a less heavily pretreated patient population.
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Affiliation(s)
- J S Rader
- Washington University School of Medicine, St. Louis, MO 63110, USA.
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Snijders AM, Fridlyand J, Mans DA, Segraves R, Jain AN, Pinkel D, Albertson DG. Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene 2003; 22:4370-9. [PMID: 12853973 DOI: 10.1038/sj.onc.1206482] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tumors with defects in mismatch repair (MMR) show fewer chromosomal changes by cytogenetic analyses than most solid tumors, suggesting that a greater proportion of the alterations required for malignancy occur in genes with nucleotide sequences susceptible to errors normally corrected by MMR. Here, we used genome-wide microarray comparative genomic hybridization to carry out a higher resolution evaluation of the effect of MMR competence on genomic alterations occurring in 20 cell lines and to determine if characteristic aberrations arise in MMR-proficient and -deficient HCT116 cells undergoing selection for methotrexate resistance. We observed different spectra of aberrations in MMR-proficient compared to -deficient cell lines, as well as among cell lines with different types of MMR-deficiency. We also observed different genetic routes to drug resistance. Resistant MMR-deficient cells most frequently displayed no copy number alterations (16/29 cell pools), whereas all MMR-proficient cells had unique abnormalities involving chromosome 5, including amplicons centered on the target gene, DHFR and/or a neighboring novel locus (7/13 pools). These observations support the concept that tumor genomes are shaped by selection for alterations that promote survival and growth advantage, as well as by the particular dysfunctions in genes responsible for maintenance of genetic integrity.
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Affiliation(s)
- Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
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