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Pathway-Based Analysis of Genome-Wide Association Data fphar-09-00158 March 9, 2018 Time: 17:6 # 1 ORIGINAL RESEARCH published: 13 March 2018 doi: 10.3389/fphar.2018.00158 Pathway-Based Analysis of Genome-Wide Association Data Identified SNPs in HMMR as Biomarker for Chemotherapy- Induced Neutropenia in Breast Cancer Patients Edited by: Rick Kittles, Behzad Bidadi1†, Duan Liu1, Krishna R. Kalari2, Matthias Rubner3, Alexander Hein3, Irell and Manella Graduate School Matthias W. Beckmann3, Brigitte Rack4, Wolfgang Janni5, Peter A. Fasching3, of Biological Sciences, United States Richard M. Weinshilboum1 and Liewei Wang1* Reviewed by: Ming Ta Michael Lee, 1 Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Geisinger Health System, Rochester, MN, United States, 2 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, United States Mayo Clinic, Rochester, MN, United States, 3 Department of Gynecology and Obstetrics, University Hospital Erlangen, Ken Batai, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany, 4 Department of Gynecology and Obstetrics, University of Arizona, United States Ludwig-Maximilians-Universität München, Munich, Germany, 5 Department of Gynecology and Obstetrics, University Hospital Ulm, Ulm, Germany *Correspondence: Liewei Wang [email protected] Neutropenia secondary to chemotherapy in breast cancer patients can be life- † Present address: threatening and there are no biomarkers available to predict the risk of drug-induced Behzad Bidadi, Merck & Co., Inc., North Wales, PA, neutropenia in those patients. We previously performed a genome-wide association United States study (GWAS) for neutropenia events in women with breast cancer who were treated with 5-fluorouracil, epirubicin and cyclophosphamide and recruited to the SUCCESS- Specialty section: This article was submitted to A trial. A genome-wide significant single-nucleotide polymorphism (SNP) signal in Pharmacogenetics the tumor necrosis factor superfamily member 13B (TNFSF13B) gene, encoding the and Pharmacogenomics, a section of the journal cytokine B-cell activating factor (BAFF), was identified in that GWAS. Taking advantage Frontiers in Pharmacology of these existing GWAS data, in the present study we utilized a pathway-based analysis Received: 23 October 2017 approach by leveraging knowledge of the pharmacokinetics and pharmacodynamics of Accepted: 13 February 2018 drugs and breast cancer pathophysiology to identify additional SNPs/genes associated Published: 13 March 2018 with the underlying etiology of chemotherapy-induced neutropenia. We identified Citation: Bidadi B, Liu D, Kalari KR, three SNPs in the hyaluronan mediated motility receptor (HMMR) gene that were Rubner M, Hein A, Beckmann MW, significantly associated with neutropenia (p < 1.0E-04). Those three SNPs were trans- Rack B, Janni W, Fasching PA, Weinshilboum RM and Wang L expression quantitative trait loci for the expression of TNFSF13B (p < 1.0E-04). The (2018) Pathway-Based Analysis minor allele of these HMMR SNPs was associated with a decreased TNFSF13B of Genome-Wide Association Data mRNA level. Additional functional studies performed with lymphoblastoid cell lines Identified SNPs in HMMR as Biomarker for Chemotherapy- (LCLs) demonstrated that LCLs possessing the minor allele for the HMMR SNPs Induced Neutropenia in Breast were more sensitive to drug treatment. Knock-down of TNFSF13B in LCLs and Cancer Patients. Front. Pharmacol. 9:158. HL-60 promyelocytic cells and treatment of those cells with BAFF modulated the doi: 10.3389/fphar.2018.00158 cell sensitivity to chemotherapy treatment. These results demonstrate that HMMR Frontiers in Pharmacology| www.frontiersin.org 1 March 2018| Volume 9| Article 158 fphar-09-00158 March 9, 2018 Time: 17:6 # 2 Bidadi et al. HMMR SNP and Chemotherapy-Induced Neutropenia SNP-dependent cytotoxicity of these chemotherapeutic agents might be related to TNFSF13B expression level. In summary, utilizing a pathway-based approach for the analysis of GWAS data, we identified additional SNPs in the HMMR gene that were associated with neutropenia and also were correlated with TNFSF13B expression. Keywords: breast cancer, neutropenia, HMMR, TNFSF13B, GWAS INTRODUCTION contradictory results among these studies — e.g., no SNPs/genes were replicated from one study to another even though the Breast cancer is the most common invasive cancer in women same chemotherapy regimens were administrated to those breast worldwide and approximately 1.3 million cases are diagnosed cancer patients. To our knowledge, no genome-wide association worldwide annually (Ferlay et al., 2015). Those patients study (GWAS) for CIN has been reported. Compared to the with high-risk features require chemotherapy following candidate gene approach, GWAS is an “unbiased” approach that surgical resection of the tumor. However, administration of has the capability of revealing novel genetic variants associated chemotherapy regimens such as cytotoxic agents potentially with drug response (Weinshilboum and Wang, 2004; Wang et al., leads to life-threatening adverse drug effects, of which the most 2011; Motsinger-Reif et al., 2013). We have previously performed common adverse event is chemotherapy-induced neutropenia GWASs for adverse events in breast cancer patients treated (CIN) (Fontanella et al., 2014). This adverse event is common with aromatase inhibitors and identified novel genetic variants in breast cancer patients receiving adjuvant chemotherapy and associated with musculoskeletal pain (Ingle et al., 2010) and bone affects more than 50% of patients (Holmes et al., 2002; Therasse fractures (Liu et al., 2014). Recently, we performed a GWAS for et al., 2003). More than 20% of patients with breast cancer CIN in 3,252 women with early stage breast cancer who received receiving adjuvant chemotherapy developed febrile neutropenia, adjuvant chemotherapy. Novel SNP signals that were genome- which is a more severe, life-threatening adverse event (Do et al., wide significantly associated with CIN were identified in that 2015). CIN may lead to infection and hospitalization, which GWAS. That GWAS will be reported in detail elsewhere. potentially results in compromised treatment because of the Although GWAS has been very successful for identifying requirement for reduction in dose intensity of the chemotherapy novel and statistically significant SNPs that were associated with regimen (Link et al., 2001; Fontanella et al., 2014; Agiro et al., phenotypes, many SNPs/genes that have biological significance 2016). To prevent CIN, co-administration of white blood cell could be overlooked in GWAS since those SNPs do not growth factor such as the granulocyte colony-stimulating growth meet the threshold to reach genome-wide significance (Wang factor (G-CSF) is recommend with chemotherapy (Smith et al., et al., 2007, 2010). To overcome this problem, pathway-based 2015), and has shown benefit in patients with breast cancer approaches, which consider prior knowledge of genes and who received chemotherapy (Holmes et al., 2002; Vogel et al., pathways contributing to the phenotype of interest has been 2005; Agiro et al., 2016). However, considerable inter-individual developed to provide additional insight into the interpretation variabilities in both risk and severity of CIN, and in the beneficial of GWAS data on complex phenotypes (Wang et al., 2007; effect of G-CSF prophylaxis were found among breast cancer Ramanan et al., 2012). This approach has been successfully used patients (Agiro et al., 2016). Sub-classification of patients to analyze and interpret GWAS data for many clinical phenotypes at increased risk of CIN may allow for improved treatment (Torkamani et al., 2008; Baranzini et al., 2009; Holmans et al., modifications, such as G-CSF support, dose reduction, or use of 2009; Ballard et al., 2010; Jia et al., 2010) chemotherapy regimens with a lower risk of myelosuppression. In the present study, we took advantage of the GWAS data Clinical risk factors such as older age, poor nutrition and prior we generated for CIN in breast cancer patients, and performed chemotherapy have been associated with increased risk of febrile pathway-based analysis to identify SNPs/genes that might be neutropenia (Aapro et al., 2006). However, predictive models associated with CIN. The SNPs identified by this pathway-based using these factors for risk of CIN have shown limited utility analysis were pursued by functional characterization to help us (Lyman et al., 2015). Other predictors for CIN risk are urgently understand underlying mechanisms. needed which may help to improve the individualized care of breast cancer patients during adjuvant chemotherapy. Germline genetic polymorphisms in patients with cancer MATERIALS AND METHODS have been associated with risk for chemotherapy-related toxicity, including CIN (Ulrich et al., 2003; Pinto et al., 2012). Using a Patients and the Clinic Trial candidate gene approach, previous studies have demonstrated Patients in this study were recruited to the SUCCESS-A that single-nucleotide polymorphisms (SNPs) in genes encoding trial (ClinicalTrials.gov Identifier: NCT02181101), a randomized drug-metabolizing enzymes and transporters were associated Phase III study of response to the treatment of early primary with the risk for CIN in breast cancer patients (Low et al., breast cancer with adjuvant therapy after surgical resection 2009; Yao et al., 2010; Okishiro et al., 2012; Tang et al., 2013). (Rack et al., 2014; Widschwendter et al., 2015). All
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