Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities

Purpose: Chemotherapies are associated with significant interindividual variability in therapeutic effect and adverse drug reactions. In lung cancer, the use of gemcitabine and carboplatin induces grade 3 or 4 myelosuppression in about a quarter of the patients, while an equal fraction of patients is basically unaffected in terms of myelosuppressive side effects. We therefore set out to identify genetic markers for gemcitabine/carboplatin-induced myelosuppression. Experimental Design: We exome sequenced 32 patients that suffered extremely high neutropenia and thrombocytopenia (grade 3 or 4 after first chemotherapy cycle) or were virtually unaffected (grade 0 or 1). The genetic differences/polymorphism between the groups were compared using six different bioinformatics strategies: (i) whole-exome nonsynonymous single-nucleotide variants association analysis, (ii) deviation from Hardy–Weinberg equilibrium, (iii) analysis of genes selected by a priori biologic knowledge, (iv) analysis of genes selected from gene expression meta-analysis of toxicity datasets, (v) Ingenuity Pathway Analysis, and (vi) FunCoup network enrichment analysis. Results: A total of 53 genetic variants that differed among these groups were validated in an additional 291 patients and were correlated to the patients' myelosuppression. In the validation, we identified rs1453542 in OR4D6 (P = 0.0008; OR, 5.2; 95% CI, 1.8–18) as a marker for gemcitabine/carboplatin-induced neutropenia and rs5925720 in DDX53 (P = 0.0015; OR, 0.36; 95% CI, 0.17–0.71) as a marker for thrombocytopenia. Patients homozygous for the minor allele of rs1453542 had a higher risk of neutropenia, and for rs5925720 the minor allele was associated with a lower risk for thrombocytopenia. Conclusions: We have identified two new genetic markers with the potential to predict myelosuppression induced by gemcitabine/carboplatin chemotherapy. Clin Cancer Res; 22(2); 366–73. ©2015 AACR.

[1]  J. Roh,et al.  An association between RRM1 haplotype and gemcitabine-induced neutropenia in breast cancer patients. , 2007, The oncologist.

[2]  R. Rosell,et al.  Chemotherapy-induced neutropenia does not correlate with DNA repair gene polymorphisms and treatment efficacy in advanced non-small-cell lung cancer patients. , 2011, Clinical lung cancer.

[3]  H. Ueno,et al.  Pharmacokinetics of gemcitabine in Japanese cancer patients: the impact of a cytidine deaminase polymorphism. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[4]  Michel Eichelbaum,et al.  Pharmacogenomics and individualized drug therapy. , 2006, Annual review of medicine.

[5]  J. Knights,et al.  Genetic factors associated with gemcitabine pharmacokinetics, disposition, and toxicity , 2014, Pharmacogenetics and genomics.

[6]  Y. Bang,et al.  Identification and characterization of a novel cancer/testis antigen gene CAGE. , 2002, Biochemical and biophysical research communications.

[7]  Jeffrey A. Riffell,et al.  Identification of a Testicular Odorant Receptor Mediating Human Sperm Chemotaxis , 2003, Science.

[8]  Yun‐Sil Lee,et al.  Cancer/Testis Antigen CAGE Exerts Negative Regulation on p53 Expression through HDAC2 and Confers Resistance to Anti-cancer Drugs* , 2010, The Journal of Biological Chemistry.

[9]  Hong-yan Cheng,et al.  XPC Lys939Gln polymorphism is associated with the decreased response to platinum based chemotherapy in advanced non-small-cell lung cancer. , 2010, Chinese medical journal.

[10]  J. Doroshow,et al.  Phase II studies of gemcitabine and cisplatin in heavily and minimally pretreated metastatic breast cancer. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[11]  F. Innocenti,et al.  Clinical pharmacology and pharmacogenetics of gemcitabine , 2009, Drug metabolism reviews.

[12]  C. Martín,et al.  Safety profile of gemcitabine, a novel anticancer agent, in non-small cell lung cancer , 1997, Anti-cancer drugs.

[13]  Andrey Alexeyenko,et al.  Network enrichment analysis: extension of gene-set enrichment analysis to gene networks , 2012, BMC Bioinformatics.

[14]  A. Khrunin,et al.  Genetic polymorphisms and the efficacy and toxicity of cisplatin-based chemotherapy in ovarian cancer patients , 2010, The Pharmacogenomics Journal.

[15]  Vadim J. Gurvich,et al.  SLC28A3 genotype and gemcitabine rate of infusion affect dFdCTP metabolite disposition in patients with solid tumours , 2013, British Journal of Cancer.

[16]  D. Jeoung,et al.  The Cancer/Testis Antigen CAGE with Oncogenic Potential Stimulates Cell Proliferation by Up-regulating Cyclins D1 and E in an AP-1- and E2F-dependent Manner* , 2010, The Journal of Biological Chemistry.

[17]  Howard L McLeod,et al.  Pharmacogenomics--drug disposition, drug targets, and side effects. , 2003, The New England journal of medicine.

[18]  E. Sonnhammer,et al.  Global networks of functional coupling in eukaryotes from comprehensive data integration. , 2009, Genome research.

[19]  Cheng Cheng,et al.  The expression of 70 apoptosis genes in relation to lineage, genetic subtype, cellular drug resistance, and outcome in childhood acute lymphoblastic leukemia. , 2006, Blood.

[20]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[21]  S. Ng,et al.  Bexarotene (LGD1069, Targretin), a selective retinoid X receptor agonist, prevents and reverses gemcitabine resistance in NSCLC cells by modulating gene amplification. , 2007, Cancer research.

[22]  J. Lundeberg,et al.  Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues. , 2012, Gene.

[23]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[24]  Yusuke Nakamura,et al.  A Genome-Wide Association Study of Overall Survival in Pancreatic Cancer Patients Treated with Gemcitabine in CALGB 80303 , 2011, Clinical Cancer Research.

[25]  S. Ren,et al.  Association between polymorphisms of DNA repair genes and survival of advanced NSCLC patients treated with platinum-based chemotherapy. , 2012, Lung Cancer.

[26]  Y. Gilad,et al.  Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray , 2007, Genome biology.

[27]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[28]  Yusuke Nakamura,et al.  A genome-wide association study identifies four genetic markers for hematological toxicities in cancer patients receiving gemcitabine therapy , 2012, Pharmacogenetics and genomics.

[29]  M. Yashiro,et al.  Establishment and characterization of multidrug-resistant gastric cancer cell lines. , 2010, Anticancer research.

[30]  J. Robert,et al.  Predicting drug response and toxicity based on gene polymorphisms. , 2005, Critical reviews in oncology/hematology.

[31]  Donghui Li,et al.  Gemcitabine metabolic and transporter gene polymorphisms are associated with drug toxicity and efficacy in patients with locally advanced pancreatic cancer , 2010, Cancer.

[32]  M. Baiget,et al.  Pharmacogenetics of the DNA repair pathways in advanced non-small cell lung cancer patients treated with platinum-based chemotherapy. , 2014, Cancer letters.

[33]  Yi Shi,et al.  Predictive value of ERCC1 and XPD polymorphism in patients with advanced non-small cell lung cancer receiving platinum-based chemotherapy: a systematic review and meta-analysis , 2011, Medical oncology.

[34]  J. Brockmöller,et al.  Pharmacogenetic analyses of cisplatin-induced nephrotoxicity indicate a renoprotective effect of ERCC1 polymorphisms. , 2011, Pharmacogenomics.

[35]  Xiuwen Wang,et al.  The Impact of CDA A79C Gene Polymorphisms on the Response and Hematologic Toxicity in Gemcitabine-Treated Patients: A Meta-Analysis , 2014, The International journal of biological markers.