Deep phenotyping and pan-omics of acute lymphoblastic leukemia in Down syndrome

Baylor College Of Medicine, Houston TX

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Abstract

ABSTRACT This application is being submitted to PA-18-591 in accordance with NOT-OD-18-194.. The focus of this supplement is on acute lymphoblastic leukemia (ALL). We have developed this supplement application to fully characterize a cohort of >400 children diagnosed with DS-ALL, with the goal of addressing both Components 2 and 1 of the INCLUDE Project. For Component 2 (providing a molecular snapshot of DS through a cohort study), we propose to add a DS cohort to the existing cohort of COG childhood ALL subjects which has undergone comprehensive omic profiling through the NCI TARGET initiative. In combination with extensive clinical and outcome data, TARGET investigations have yielded remarkable insights into key pathways driving biological subsets of childhood ALL, and in some cases identified novel therapeutic approaches which have been integrated into current clinical trials. However, patients with DS-ALL have been largely excluded from these prior and ongoing genomic studies. Here, we propose to add a DS-ALL cohort to this COG childhood ALL cohort. We will conduct deep phenotyping on this cohort?obtaining information both on co-occurring conditions and outcomes? and develop linkage to include these data in the DS-Connect patient registry. Additionally, this application is aligned with Component 1 through (1) development of a novel patient-derived xenograft (PDX) model system; and (2) epigenetic and transcriptomic profiling of the primary DS-ALL and PDX models. These studies will address a critical unmet need, since no systematic molecular profiling of DS-ALL has been undertaken at this scale and nor have any tractable preclinical laboratory models been developed for DS-ALL (e.g., mouse models or cell lines). To address these Components, the Aims of this application are to: (1) conduct deep phenotyping of children with DS-ALL, utilizing a variety of sources to develop a data warehouse which will be an unparalleled resource to facilitate research on ALL susceptibility and outcomes in DS children, and (2) conduct comprehensive ?omic studies of leukemic samples from children with DS-ALL, leveraging our COG cohort of 390 DS-ALL cases for which we already have germline genotyping and basic clinical data. These analyses will include transcriptome profiling of all ALL samples to define gene fusion events and expression profiles and correlate these molecular features with key clinical characteristics and treatment outcomes; establishing a library of PDX of DS-ALL; and utilizing PDX-expanded cells for epigenetic profiling by ATAC-seq and histone H3K27 CHiP-seq. Overall, our proposed studies will illuminate the unique ALL susceptibility pattern in the background of trisomy 21 that contributes to disease risk in this population, and may have implications for improved genetic counseling, surveillance, clinical management, and treatment strategies for these children.