As the initiating genetic events in tumorigenesis, germline variants in cancer predisposing genes perturb cell growth and differentiation and set the stage for malignant transformation. Accordingly, the study of cancer predisposing genes and their associated hereditary syndromes provides critical insights into normal physiology and cancer biology. By investigating families with autosomal dominant transmission of thrombocytopenia and B- acute lymphoblastic leukemia (B-ALL), we and others identified pathogenic germline variants affecting ETV6, the gene encoding the ETS variant 6 transcriptional repressor. Subsequently, we sequenced germline samples from 4,405 children with B-ALL and detected similar variants in 0.5% of patients. Further association studies revealed a significant 22.94-fold enrichment of pathogenic ETV6 variants in this ALL cohort compared to 134,187 non-ALL controls in gnomAD (P= 2.2 10-16). These data firmly support our overall premise that pathogenic germline ETV6 variants predispose to childhood ALL. To better understand how germline ETV6 variants promote leukemogenesis, we used in vitro assays to interrogate their effects on the functions of the encoded ETV6 protein. Notably, each of the pathogenic ETV6 variants examined significantly reduced ETV6 transcription repressor activity, impaired ETV6 DNA binding capacity and mis-localized ETV6 to the cytoplasm. In parallel, we generated a novel mouse model harboring a recurrent B-ALL-associated Etv6 variant (Etv6R355X). Preliminary studies of Etv6R355X/+ mice reveal significant perturbations in early B cell development, as well as hematopoietic stem and progenitor cell (HSPC) number and function. Finally, we generated isogenic induced pluripotent stem cell (iPSC) lines harboring pathogenic ETV6 variants, which generate dysplastic megakaryocytes, similar to ETV6 variant positive patients. Based on these results, we hypothesize that ETV6 variants predispose to ALL by perturbing key transcriptional programs that impair hematopoietic development. In this proposal, we will make use of our unique model systems to rigorously test this hypothesis.
In Aim 1, we will characterize the hematopoietic compartments of humans and mice that do or do not harbor pathogenic germline ETV6 variants. We will examine whether WT and ETV6 variant-positive iPSCs or mouse hematopoietic progenitors properly differentiate along various lineages. To establish how germline ETV6 variants influence gene expression in developing hematopoietic progenitors, in Aim 2 we will use RNA-sequencing and ATAC-sequencing to explore transcriptional landscapes and identify putative ETV6 target genes in mouse and iPSC-derived B progenitors and HSPC harboring WT or variant ETV6. Finally, in Aim 3 we will perform comprehensive whole genome and RNA-sequencing of B-ALL samples to elucidate the somatic genetic lesions that function in concert with germline ETV6 variants to drive B-leukemogenesis. We will use in vitro and in vivo approaches to assess the leukemia- promoting effects of these second hits. This project will provide new insights into the influence of germline genetic variation on hematopoiesis and development of B-ALL, the most common childhood cancer.
In this proposal, we will examine the mechanisms by which inherited variants in the gene ETV6 contribute to development of B-acute lymphoblastic leukemia (B-ALL), the commonest childhood cancer and leading cause of cancer-related death in children. Through these studies, we will define how ETV6 variants influence normal blood cell development and participate in progression to leukemia. This proposal has relevance to public health because it will improve our understanding of B-ALL and thereby inform the creation of new and more effective ways to classify, treat, and possibly also prevent this prevalent and at times deadly childhood cancer. .