UC Berkeley

The role of genetic and environmental immune dysregulation in the etiology of childhood acute lymphoblastic leukemia and other complex diseases

Amelia Dale Wallace

Doctor of Philosophy in Epidemiology

University of California, Berkeley

Professor Lisa Barcellos, Chair

Childhood acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Epidemiologic studies suggest that of genetic and environmental factors influencing immune dysregulation play an important role in the etiology of the disease. In the following dissertation, we explore three hypotheses, one established and two nascent, wherein potential immunomodulatory risk factors are tested for association with ALL.

Allergic disease has long been suspected to play a role in the development of childhood ALL. Studies conducted over the last several decades have yielded mixed results. In the first chapter, we examine the association between allergy, a common immune-mediated disorder, and ALL in the California Childhood Leukemia Study (CCLS), a case-control study of 977 children diagnosed with ALL and 1037 matched controls (1995-2015). History of allergies in the first year of life was obtained from interviews, mainly reported by mothers. Logistic regression analyses were conducted to estimate odds ratios (ORs) and 95% confidence intervals (CIs), controlling for birth order, day care attendance, and mode of delivery. In addition, we conducted meta-analyses with data from the CCLS and 12 published studies and employed a new method to estimate between-study heterogeneity (R_b).

Overall, no associations were observed between childhood ALL risk and specific allergy phenotypes or any allergy, as a group. However, having any allergy was associated with an increased risk of ALL among the youngest study participants. In the meta-analysis random-effect models, reduced odds of ALL was associated with hay fever (metaOR=0.65, 95% CI: 0.47, 0.90); however, restricting the analysis to studies that used medical records for assessment of allergy or recently published studies led to null or attenuated results. Overall, our findings do not support a clear association between allergy and childhood ALL. We conclude that the degree to which epidemiological studies can inform the relationship between allergies and risk of childhood ALL is limited by between-study heterogeneity.

In the second chapter, we explore a putative germline genetic risk factor that could contribute to the increased incidence of ALL in Hispanics, who have the highest rate of disease (4.3 cases per 100,000 per year). Our current understanding of the complex etiology of childhood ALL has failed to explain this disproportionate burden. Recently, one predominant somatic point mutation signature (TpC>T point mutations) related to the innate immune enzyme APOBEC3B was identified in ALL tumor genomes. A common deletion polymorphism in this gene is prevalent in Hispanics and has been associated with an increased risk of other cancers that have the APOBEC3B-related point mutation signature.

We genotyped and tested for association this ~29Kb deletion polymorphism and risk of childhood ALL in 518 cases and 608 controls in the CCLS, where Hispanics account for ~45% of the study population. We found no evidence for germline risk of disease among carriers of the deletion polymorphism, or any SNP in the APOBEC3 gene megalocus in a larger set of 1,083 cases and 1,137 controls. To ensure that ethnic heterogeneity did not mask true associations, local genetic ancestry was inferred with RFMix. Adjustment for local genetic ancestry did not meaningfully alter the observed associations. Further, no specific local genetic ancestry in the APOBEC3 megalocus was independently associated with disease. While somatic mutation induced by the APOBEC3B enzyme may influence tumor progression, there is no evidence that APOBEC3 polymorphisms are associated with disease etiology.

Another leading etiologic hypothesis for ALL related to immune dysregulation states that a specific infectious agent – or mis-timing of common infection – early in life causes the disease. In an untargeted viral discovery study previously carried out in the CCLS, we observed high expression of human endogenous retroviruses (HERVs) in diagnostic bone marrow samples. Approximately 8% of the human genome is comprised of HERVs originating from historic retroviral integration into germ cells. The function of HERVs as regulators of gene expression is well established. Less well studied are insertional polymorphisms of HERVs and their contribution to the heritability of complex phenotypes like cancer. The most recent integration of HERV, HERV-K, is expressed in a range of complex human conditions from cancer to neurologic diseases. In an exploratory study to better understand potential links between HERV-K and ALL, we undertook a phenome-wide association study of HERV-K polymorphisms and present the results in the third and final chapter. Using an in-house computational pipeline and whole-genome sequencing data from the diverse 1000 Genomes Phase 3 population (n=2,504), we identified 48 polymorphic HERV-K insertions that are tagged by adjacent SNPs. To test the potential role of polymorphic HERV-K in the heritability of complex diseases, existing databases were queried for enrichment of established relationships between the HERV-K insertion-associated SNPs (hiSNPs), and tissue specific gene expression and disease phenotypes.

Overall, hiSNPs for the 48 polymorphic HERV-K sites were statistically enriched (p<1.0E-16) for eQTLs across 44 human tissues. Fifteen of the 48 HERV-K insertions had hiSNPs annotated in the EMBL-EBI GWAS Catalog and cumulatively associated with >100 phenotypes. Experimental factor ontology enrichment analysis suggests that polymorphic HERV-K specifically contribute to neurologic and immunologic disease phenotypes, including traits related to intracranial volume (FDR 2.00E-09), Parkinson’s disease (FDR 1.80E-09), and autoimmune diseases (FDR 1.80E-09). These results provide strong candidates for context-specific study of polymorphic HERV-K insertions in disease-related traits and observed enrichment in immune-related traits aw well as virally induced cancers warrant further study in ALL, despite identifying no existing associations specifically with the disease.

Overall, these studies make an important contribution to our understanding of the immune dysregulation that precedes childhood-onset ALL. Specifically, this work has lain to rest existing hypotheses while at the same time generating new ones. Future research building off this work will bring us closer to effective prevention strategies for this devastating disease.