GWAS Identifies Pharmacogenetic Markers Associated with Premedication-Related Pegaspargase Hypersensitivity and Toxicities in Pediatric and Adolescent Young Adults (AYAs) with Acute Lymphoblastic Leukemia or Lymphoma

Background: Pediatric acute lymphoblastic leukemia (ALL) patients have significantly improved outcomes over the last few decades with overall survival (OS) rates exceeding 90%. Several factors, including incorporation of asparaginase therapy in chemotherapy regimens of pediatric and adolescent and young adult (AYA) patients with ALL have played a critical role in improving outcomes. Asparaginase is a bacterial enzyme which depletes non-essential amino acid asparagine leading to apoptosis in lymphoblastic leukemia cells. Limitations of frontline pegaspargase (PEG) chemotherapy include hypersensitivity reactions and other asparaginase associated toxicity. A prospective multi-institutional study initiated by Children's Hospital of Orange County (CHOC) and conducted at 6 pediatric cancer centers: 1) evaluated the efficacy of premedicating pediatric and AYA patients with B or T-ALL or lymphoblastic lymphoma (Lly) receiving PEG with antihistamines (H1 and H2 blockers), and 2) performed therapeutic drug monitoring to better identify patients with true hypersensitivity reactions versus those with non-antibody mediated infusion reactions. Here, we report findings from a genome-wide association study (GWAS) in these patients to identify pharmacogenomic markers associated with premedication-related PEG hypersensitivity or grade >3 toxicities and determine whether certain populations are more at risk for hypersensitivity and PEG-associated toxicities.

Patients and Methods: GWAS was performed on 87 patients with ALL/Lly. Median age was 8.3 years, 64.4% were male, and 55.2% identified as Hispanic. Overall, 17 (19.5%) patients had hypersensitive reaction to PEG and 44 (50.6%) had an incidence of CTCAE V5 Grade > 3 toxicity (hyperbilirubinemia, hyper/hypoglycemia, hypertriglyceridemia, pancreatitis, or thrombosis) with onset ≤30 days from PEG infusion. Infinium GSA-24 v3.0 was used to genotype 650k single nucleotide polymorphisms (SNPs) and post standard QC, 233,798 SNPs were tested for association with hypersensitivity and grade >3 toxicities by logistic regression analysis using PLINK. Principal component analysis (PCA) was performed for ethnicity and 2 components explaining 67% variance within ethnicity (Hispanic or non-Hispanic) were used to perform ethnicity-adjusted association analyses with 74,198 SNPs post- Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) pruning.

Results: 72 SNPs in 59 genes were associated with incidence of premedication-related PEG hypersensitivity and 75 SNPs in 64 genes were associated with any grade >3 toxicity (p < 0.001). Top genes included PRKCE, ALX4, STAG1, DAB1, MPK10 for hypersensitivity and SPRY4, PALM2-AKAP2 fusion gene, and ALK (toxicities) in addition to genes reported in GWAS data available in literature such as GRIA1, NFATC2, CNOT3, SOD2, and ATF5. Adjusted for Hispanic ethnicity, 34 SNPs in 30 genes were associated with hypersensitivity (p< 0.001). In addition to hits from unadjusted analysis, these included ITPR2, ABHD6, ST6GAL2, RORA, and PAPSS1 and showed significant enrichment of hypersensitivity-related pathways such as NFAT activation, immune signal transduction, hemostasis, and protein metabolism. 25 SNPs in 24 genes were associated with any grade >3 toxicity (p< 0.001) when adjusted for ethnicity. In addition to hits from unadjusted analysis, these included KCNN2, KCNH5, CLASP1, PON2, WWOX, STIM1, IQCE, and FUT10 with significant enrichment in pathways such as calcium and potassium channels, activation of SMO signaling, hemostasis, and ERBB4 signaling which could be involved in mediating hepato-toxicities.

Conclusion: Our GWAS analyses have identified previously unreported SNPs associated with PEG hypersensitivity and grade >3 toxicities. And our analyses adjusted for Hispanic ethnicity has uncovered a novel, unique subset of markers associated with either PEG-hypersensitivity or grade >3 toxicities within this population. Given their fundamental importance, ongoing work is focused on imputing HLA alleles for further association analyses in our dataset. Future work will entail validating these results in an independent cohort of patients as well as planned functional studies that will focus on defining the underlying molecular mechanisms.

Funding for this study was provided by CHOC PSF Tithe Grant, CHOC Hyundai Cancer Institute Research Grant, and Servier Pharmaceuticals.