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

Aims: 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.

Methods: 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 (p < 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; N = 155) and without CTX.

Results: Twenty SNPs were filtered out including rs12408401, which was associated with PM resistance (p = 3.89 × 10^-5), potentially disrupted a CTCF-loop, and was associated with increased RFX5 expression (p = 0.036), which was associated with poor disease-free interval in ACT-BC patients (HR = 5.32; p = 0.028); and rs784562, which was associated with improved PM sensitivity (p = 6.41 × 10^-6), potentially altered nearby enhancer functionality, and reduced expression of KRT72 which was associated with poor progression-free survival in ACT-BC patients (HR = 3.61; p = 0.040).

Conclusion: Our study identifies SNPs significantly associated with cellular CTX response with potential mechanistic and clinical relevance, thereby providing insights toward optimized CTX treatment strategies.