Application of a Combination of a Knowledge-Based Algorithm and 2-Stage Screening to Hypothesis-Free Genomic Data on Irinotecan-Treated Patients for Identification of a Candidate Single Nucleotide Polymorphism Related to an Adverse Effect

et al. (2014) Application of a Combination of a Knowledge-Based Algorithm and 2-Stage Screening to Hypothesis-Free Genomic Data on Irinotecan-Treated Patients for Identification of a Candidate Single Nucleotide Polymorphism Related to an Adverse Effect. PLoS ONE 9(8): e105160. doi:10.1371/journal.pone.0105160 Application of a Combination of a Knowledge-Based Algorithm and 2-Stage Screening to Hypothesis-Free Genomic Data on Irinotecan-Treated Patients for Identification of a Candidate Single Nucleotide Polymorphism Related to an Adverse Effect Nagahiro Saijo 0 Jun-ichi Sawada 0 Hiromi Sakamoto 0 Teruhiko Yoshida 0 Olga Y. Gorlova, Geisel School of Medicine at Dartmouth College, United States of America 0 a Current address: Japanese Society of Medical Oncology, Tokyo, Japan b Current address: Pharmaceutical and Medical Devices Agency , Tokyo , Japan Interindividual variation in a drug response among patients is known to cause serious problems in medicine. Genomic information has been proposed as the basis for ''personalized'' health care. The genome-wide association study (GWAS) is a powerful technique for examining single nucleotide polymorphisms (SNPs) and their relationship with drug response variation; however, when using only GWAS, it often happens that no useful SNPs are identified due to multiple testing problems. Therefore, in a previous study, we proposed a combined method consisting of a knowledge-based algorithm, 2 stages of screening, and a permutation test for identifying SNPs. In the present study, we applied this method to a pharmacogenomics study where 109,365 SNPs were genotyped using Illumina Human-1 BeadChip in 168 cancer patients treated with irinotecan chemotherapy. We identified the SNP rs9351963 in potassium voltage-gated channel subfamily KQT member 5 (KCNQ5) as a candidate factor related to incidence of irinotecan-induced diarrhea. The p value for rs9351963 was 3.3161025 in Fisher's exact test and 0.0289 in the permutation test (when multiple testing problems were corrected). Additionally, rs9351963 was clearly superior to the clinical parameters and the model involving rs9351963 showed sensitivity of 77.8% and specificity of 57.6% in the evaluation by means of logistic regression. Recent studies showed that KCNQ4 and KCNQ5 genes encode members of the M channel expressed in gastrointestinal smooth muscle and suggested that these genes are associated with irritable bowel syndrome and similar peristalsis diseases. These results suggest that rs9351963 in KCNQ5 is a possible predictive factor of incidence of diarrhea in cancer patients treated with irinotecan chemotherapy and for selecting chemotherapy regimens, such as irinotecan alone or a combination of irinotecan with a KCNQ5 opener. Nonetheless, clinical importance of rs9351963 should be further elucidated. - Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files. Competing Interests: The authors have declared that no competing interests exist. Introduction Genomic information has been proposed to be utilized as the basis for personalized health care. Interindividual variation in a drug response among patients has been well documented to cause serious problems in pharmacotherapy. This variation may be due to multiple factors such as disease phenotypes, genetic and clinical parameters (or environmental factors), and variability in the drug target or allergic response; all of these factors may affect both main and side effects [1,2]. Although some biomarkers [39] have been proposed, it is still difficult to determine which group of patients will respond positively, which patients are nonresponders, and which may experience adverse reactions in cases where patients are administered the same medication dose. For effectiveness of personalized medicine in cancer chemotherapy, it is critically important to observe interindividual differences in a drug response and the role of genetic polymorphisms relevant to the drug metabolic pathways and drug response biology in pharmacogenomics [10]. Irinotecan (CPT-11), an anticancer prodrug, is widely used for the treatment of a broad range of carcinomas, such as colorectal, lung, ovarian, and cervical cancers. Unexpected severe diarrhea and neutropenia are prominent adverse effects of irinotecan treatment. The active metabolite SN-38 (7-ethyl-10-hydroxycamptothecin), a topoisomerase I inhibitor, is generated via hydrolysis of the parent compound by carboxylesterases [11], and is subsequently glucuronidated by uridine diphosphate glucuronosyltransferases (UGTs), such as UGT1A1, UGT1A7, or UGT1A9, to form an inactive metabolite, SN-38 glucuronide (SN-38G) [12 14]. Irinotecan is also inactivated by CYP3A4 to produce 7-ethyl10- [4-N-(5-aminopentanoic acid)-1-piperidino] carbonyloxycamptothecin (APC; a major CYP3A4 product) and 7-ethyl-10(4-amino-1-piperidino) carbonyloxycamptothecin (NPC; a minor product) [15,16]. Irinotecan and its metabolites are excreted into the bile and urine via the action of ATP-binding cassette (ABC) transporters, such as P-glycoprotein (P-gp/ABCB1), multiple resistance-associated protein 2 (MRP2/ABCC2), and breast cancer resistance protein (BCRP/ABCG2) [17]. Transport of SN-38 from the plasma into the liver is mediated by the organic anion transporting polypeptide C (OATP-C/SLCO1B1) [18]. Most of the previous pharmacogenetic studies of irinotecan have been focused on UGT1A1 polymorphisms and have shown clinical relevance of UGT1A1*28, a repeat polymorphism in the TATA box [-54_-39A(TA)6TAA.A(TA)7TAA or -40_-39ins TA], to severe adverse effects [3,19,20]. Based on these findings, in 2005, the Food and Drug Administration (FDA) of the United States approved an amendment for the formulation called Camptosar (irinotecan-HCl) (NDA 20-571/S-024/S-027/S-028) and for clinical use of a genetic diagnostic kit for the *28 allele. In parallel with this advance in the USA, clinical relevance to severe neutropenia of UGT1A1*6 [211G.A(G71R)], another lowactivity allele detected specifically in East Asians, as well as *28, was demonstrated in several studies on Asian patients [5,2123]. Accordingly, in June 2008, the Ministry of Health, Labor, and Welfare of Japan approved changes to irinotecan formulations (Campto and Topotecin) by adding a warning about the risk of severe adverse effects in patients either homozygous or compoundheterozygous for UGT1A1*28 and *6 (*28/*28, *6/*6, *28/*6) and also approved clinical use of a diagnostic kit for UGT1A1*28 and *6. Severe adverse effects, however, are reported in patients without the genetic variations *6/*6, *28/*28, and *28/*6; therefore, several clinical studies have suggested that polymorphisms of the drug transporter genes, such as ABCB1, ABCC2, ABCG2, and SLCO1B1, might affect irinotecan pharmacokinetics (PK)/pharmacodynamics (PD) in Caucasian and Asian patient (...truncated)