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Comparative Lesions Analysis Through a Targeted Sequencing Approach
Published on: November 5, 2019
Genomic dissection and mutation-specific target discovery for breast cancer PIK3CA hotspot mutations
Adam X Miranda1, Justin Kemp1, Brad Davidson1
1Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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.
Insights
This study identifies distinct molecular targets for specific PIK3CA mutations, revealing AREG as a preferential target for the E545K mutation. This approach enables personalized cancer therapy by uncovering mutation-specific vulnerabilities.
Area of Science:
- Genomics
- Cancer Biology
- Molecular Oncology
Background:
- Targeted cancer therapies often treat all mutations within a gene similarly, overlooking specific codon or phenotype differences.
- Advancements in genomics offer potential for precise identification and targeting of cancer-driving mutations.
Approach:
- Developed a functional genomic workflow using isogenic cell lines with distinct PIK3CA hotspot mutations (E545K, H1047R).
- Utilized RNA-seq and ATAC-seq to identify mutation-specific transcriptomic and epigenomic differences.
- Performed CRISPR knockout screens to uncover mutation-specific pathway vulnerabilities.
Key Points:
- Identified distinct transcriptomic and epigenomic profiles for E545K and H1047R PIK3CA mutations.
- Discovered AREG as a preferential target for the E545K mutation, validated in vitro and in patient data.
- Uncovered mutation-specific gene pathway vulnerabilities.
Conclusions:
- PIK3CA hotspot mutations exhibit differential genomic regulation and downstream signaling effects.
- The study demonstrates a strategy to uncover mutation-specific molecular targets like AREG for cancer therapy.
- This integrative approach can identify targets for various oncogenic mutations in isogenic systems.
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