Author:
Miranda Adam X.,Kemp Justin,Davidson Brad A.,Bellomo Sara Erika,Miranda Verda E.,Manoni Alexandra,Marchiò Caterina,Croessmann Sarah,Park Ben H.,Hodges Emily
Abstract
Abstract
Background
Recent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype.
Results
In this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspot PIK3CA mutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with each PIK3CA hotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated through in vitro analysis and publicly available patient databases.
Conclusions
Using our multi-modal genomics framework, we discover distinct differences in genomic regulation between PIK3CA hotspot mutations, suggesting the PIK3CA mutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.
Funder
Vanderbilt-Ingram Cancer Center
Breast Cancer Research Foundation
Susan G. Komen Foundation
National Institutes of Health
The Canney Foundation
Sage Patient Advocates
Marcie and Ellen Foundation
The Eddie and Sandy Garcia Foundation
Amy and Barry Baker
John and Donna Hall
Breast Cancer SPORE
U.S. Department of Defense
American Cancer Society
Vanderbilt Stanley Cohen Innovation Fund
Publisher
Springer Science and Business Media LLC
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