A genome-wide association study using HapMap cell lines reveals modulators of cellular response to cyclophosphamide

This study identifies single-nucleotide polymorphisms (SNPs) associated with cellular response to cyclophosphamide (CTX) using phosphoramide mustard (PM), its primary cytotoxic metabolite, and explores the downstream consequences for breast cancer (BC) patients. We analyzed 1,978,545 SNPs from EBV-transformed lymphoblastic cell lines (LCLs) derived from 53 unrelated European individuals, in a genome-wide association study using cellular PM sensitivity data. We filtered SNPs associated with PM sensitivity (<i>p</i> &lt; 5 × 10⁻⁵) predicted to overlap with regulatory elements in breast tissue using a chromatin state prediction model. We then assessed the consequences using LCL transcriptomic data and data from BC patients treated with (ACT-BC; <i>N</i> = 155) and without CTX. Twenty SNPs were filtered out including rs12408401, which was associated with PM resistance (<i>p</i> = 3.89 × 10⁻⁵), potentially disrupted a CTCF-loop, and was associated with increased <i>RFX5</i> expression (<i>p</i> = 0.036), which was associated with poor disease-free interval in ACT-BC patients (HR = 5.32; <i>p</i> = 0.028); and rs784562, which was associated with improved PM sensitivity (<i>p</i> = 6.41 × 10⁻⁶), potentially altered nearby enhancer functionality, and reduced expression of <i>KRT72</i> which was associated with poor progression-free survival in ACT-BC patients (HR = 3.61; <i>p</i> = 0.040). Our study identifies SNPs significantly associated with cellular CTX response with potential mechanistic and clinical relevance, thereby providing insights toward optimized CTX treatment strategies.