Genome-Wide Association Study Identifies Variants Predictive of Febrile Neutropenia during Induction I in Newly Diagnosed Pediatric Acute Myeloid Leukemia Patients
Authors: Nittu Satyavardhan Rao , Marrero Richard J , Cao Xueyuan , Wu Huiyun , Ribeiro Raul C. , Rubnitz Jeffrey E. , Pounds Stanley , Lamba Jatinder K. 
Published: December 2024

Background: Febrile neutropenia (FN) is common in acute myeloid leukemia (AML) patients and can significantly impact their morbidity and mortality. The incidence of infectious complications in patients with severe FN is notably high, with a significant proportion of patients experiencing grade 3 or more toxicity (PMID: 38961525). One of the most severe complications is bloodstream infections (), which can lead to severe sepsis and significantly contribute to treatment-related mortality (TRM) specifically in patients with severe FN (≥ grade 3). Following induction chemotherapy, which often includes cytarabine and daunorubicin, TRM occurs in approximately 5% of AML patients, with BSI being a major cause of these fatal outcomes (PMID: 35583829). While other factors affecting FN have been investigated, the impact of genetic variants on infection complications and severity of with FN are not well studied. To address this gap, the objective of this study was to identify single nucleotide polymorphisms (SNPs) associated with grade 3 and higher FN during induction I in newly diagnosed pediatric AML patients.
Methods: Patients treated on AML02 [NCT00136084, N=134] and AML08 [NCT00703820, N=176] trials with toxicity and genotype data generated using Illumina 2.5 Omni supplemented with exome chip were included in the current investigation. The grades for febrile neutropenia were defined using the Common Terminology Criteria for Adverse Events (CTCAE) in use during the respective trials. Specifically, CTCAE version 2 was used for the AML02 trial and version 3 was used for AML08 trial. Patients were divided into two groups: with or without grade 3 or higher FN as defined by CTCAE criteria used. After standard GWAS (Genome Wide Association Studies) quality control steps and using a minor allele frequency cutoff of 10%, a total of 1,132,935 variants were evaluated for association with incidence of ≥ grade 3 FN. PLINK software was used to perform robust logistic regression analysis to identify SNPs associated with greater incidence of grade 3 or more FN. The genome-wide significance threshold was set at P &lt; 5 x 10^-8, with a suggestive threshold of P &lt; 1 x 10^-4.
Results: Among the 311 patients analyzed, 234 experienced ≥ grade 3 FN during Induction 1 and 77 did not. A total of 93 SNPs were associated with incidence of ≥ grade 3 FN at P &lt; 1 x 10^-4, though none achieved genome-wide significance. After Linkage Disequilibrium pruning, 65 independent SNPs across 58 genes were identified. Notable SNPs and genes with association with incidence of FN included: a 5'UTR SNP in the Tissue Factor Pathway Inhibitor (TFPI) gene (OR = 0.41, p = 5.07 x 10^-5) with presence of the variant G allele conferring decreased risk of FN. TFPI has been implicated playing a role in sepsis and infection by potentially affecting coagulation and inflammatory responses (PMID: 26377606). An Intronic SNP in the Phospholipase A2 Group IVE (PLA2G4E) gene (OR = 2.39, p = 3.76 x 10^-5) was associated greater incidence of ≥ grade 3 FN. Phospholipases have been previously shown to promote immune response inflammation, indicating its potential to exacerbate inflammatory responses during infections. (PMID: 34491907). Finally, a SNP in the E74-Like Factor 2 (ELF2) gene (OR = 2.78, p = 9.01 x 10^-5) was associated with greater FN incidence. ELF2 has a role in immune function and hematopoiesis, contributing to increased infection susceptibility and altered immune status in AML patients. Pathway analysis of significant genes revealed involvement in hemostasis, fibrin clot formation, cytokine signaling, and adaptive immune response. The RUNX1 pathway, often dysregulated in AML, was identified as potentially relevant to infection and AML toxicity outcomes.
Conclusion: This GWAS identified several SNPs associated with FN in pediatric AML patients. Although none reached genome-wide significance, the top results indicate that genetic variation in biologically relevant genes impacts early outcomes. Despite the limited sample size, this study is the first to identify common SNPs linked to chemotherapy-induced toxicity in pediatric AML during induction I. Future research is warranted to validate these findings in larger, independent cohorts and integrate other omics. Additionally, future analyses will adjust for other known prognostic factors such as cytogenetically defined risk and clinical factors to enhance the understanding of these associations.