Harnessing EHR-linked Genomics Data to Study Clonal Hematopoiesis and its Evolution to Inflammatory Phenotypes

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Project Summary Clonal hematopoiesis (CH), a genetic mosaicism which occurs after hematopoietic stem/progenitor cells acquire one or more mutations, is a common phenomenon associated with aging, affecting between 10-30% of individuals aged 70 and older. Although there is substantial overlap between the mutations seen in CH and those seen in hematologic cancers, individuals with CH often have normal blood counts. However, harboring a clone is not harmless – a growing body of research has demonstrated that CH is associated with 1) increased all- cause mortality, 2) a ten-fold higher rate of leukemic transformation, and 3) a doubling of the risk of ischemic cardiovascular events, which independent mouse models have shown to be linked to a CH-mediated increase in inflammation. That only a subset of individuals with CH go on to have a myocardial infarction or develop leukemia raises the question of how germline and environmental factors shape clonal outgrowth and phenotypic consequences. This proposal seeks to investigate a specific germline-somatic-phenotype interaction through identification of CH within a unique Vanderbilt University Medical Center resource: a large genetic database (BioVU) linked to a complete, de-identified version of patients’ electronic health records (EHR). The basis for this work rests on the more than 90,000 individuals within BioVU who have been genotyped on the same single nucleotide polymorphism (SNP) array. In preliminary data presented in this proposal, it is shown that this germline genotyping array can be used to detect the somatic variant JAK2V617F, a mutation common in both CH and myeloproliferative neoplasia (MPN), with a high degree of accuracy for variant allele fractions (VAFs) > 5%. Aim 1 of the proposed studies will expand this computational approach to identify somatic mutations to other common CH lesion sites and validate its effectiveness. Existing array data will be used to define SNP-specific and generalized cutoff values to differentiate putative somatic mutants from germline variants. Digital PCR will then be used to determine the accuracy of this approach and to define its limit of detection for JAK2V617F and other CH mutations. Aim 2 of these studies will seek to demonstrate the utility of these methods by investigating a possible mechanism by which germline SNPs associated with higher rates of somatic JAK2V617F mutations influence the progression to JAK2V617F-positive MPN. Data presented in the proposal identify an immune- associated protein predicted to be highly expressed in cells with these JAK2V617F-associated germline SNPs. These studies will elucidate the target’s contribution to inflammation via in vitro overexpression studies utilizing human cell lines and primary hematopoietic cells and will correlate target protein expression with MPN diagnosis and progression through chart review. Together, these studies will characterize the contribution of a germline- induced proinflammatory state to JAK2V617F clonal outgrowth and will establish a tool for studying the influence of germline and environmental exposures on CH acquisition, progression, associated comorbidities, and mortality.