Integration of Cell Line and Clinical Trial Genome-Wide Analyses Supports a Polygenic Architecture of Paclitaxel-Induced Sensory Peripheral Neuropathy

Abstract

Purpose We sought to demonstrate the relevance of a lymphoblastoid cell line (LCL) model in the discovery of clinically relevant genetic variants affecting chemotherapeutic response by comparing LCL genome-wide association study (GWAS) results to clinical GWAS results. Experimental Design A GWAS of paclitaxel-induced cytotoxicity was performed in 247 LCLs from the HapMap Project and compared to a GWAS of sensory peripheral neuropathy in breast cancer patients (n=855) treated with paclitaxel in the Cancer and Leukemia Group B (CALGB) 40101 trial. Significant enrichment was assessed by permutation resampling analysis. Results We observed an enrichment of LCL cytotoxicity-associated single nucleotide polymorphisms (SNPs) in the sensory peripheral neuropathy-associated SNPs from the clinical trial with concordant allelic directions of effect (empirical P = 0.007). Of the 24 SNPs that overlap between the clinical trial (P < 0.05) and the preclinical cytotoxicity study (P < 0.001), 19 of them are expression quantitative trait loci (eQTLs), which is a significant enrichment of this functional class (empirical P = 0.0447). One of these eQTLs is located in RFX2, which encodes a member of the DNA-binding regulatory factor X family. Decreased expression of this gene by siRNA resulted in increased sensitivity of NS-1 (rat pheochromocytoma) cells to paclitaxel as measured by reduced neurite outgrowth and increased cytotoxicity, functionally validating the involvement of RFX2 in nerve cell response to paclitaxel. Conclusions The enrichment results and functional example imply that cellular models of chemotherapeutic toxicity may capture components of the underlying polygenic architecture of related traits in patients.

Application of stem cell derived neuronal cells to evaluate neurotoxic chemotherapy

“…Previously, in vitro studies of CIPN were performed in rat pheochromocytoma or SK-N-SH human neuroblastoma cell lines as model systems to evaluate decreases in neurite outgrowth in response to neurotoxic chemotherapy drugs, such as paclitaxel, vincristine, oxaliplatin and cisplatin [Rovini, et al 2010, Verstappen, et al 2004, Wheeler, et al 2013, Takeshita, et al 2011, Mendonca, et al 2013]. Our knowledge of the mechanisms of CIPN has also been enhanced through studies using primary rat and mouse dorsal root ganglion neurons [Xiao, et al 2012, Xiao, et al 2011, Cavaletti, et al 1995, Zheng, et al 2012, Staff, et al 2013].…”

Replication of Genetic Polymorphisms Reported to Be Associated with Taxane-Related Sensory Neuropathy in Patients with Early Breast Cancer Treated with Paclitaxel

“…GWAS used in other clinical phenotypes have identified regions outside genes and within regulatory areas or desert regions, which the candidate gene approach would not capture. Other recent approaches used to investigate the polygenic architecture of complex pharmacogenetic traits include use of cellular models of chemotherapeutic toxicity (43).…”

Evaluation of inter-batch differences in stem-cell derived neurons

“…Notably, two protein-coding genes ( DNASE2B encoding deoxyribonuclease II beta and PALMD encoding palmdelphin) were found to be significant for the batch effect at a lenient cutoff of 20% FDR, with no detection of functional enrichment among batch effect genes. Furthermore, none of the neuropathy-associated genes [9, 21–29] was significantly (FDR < 0.2) affected by batch.…”