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Published on: July 25, 2020
Evolution and Co-occurrence of PI3K Pathway Gene Mutations in Endometrial Carcinoma Molecular Subtypes at the
Arnaud Da Cruz Paula1, Yingjie Zhu2, David N Brown2
1Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
Purpose:
The PI3K pathway is altered in >85% of endometrioid endometrial carcinomas (EEC), with multiple mutations commonly co-occurring. Yet, the therapeutic effects of single-agent PI3K pathway inhibitors have been limited. We used single-cell sequencing to determine whether co-occurring PTEN, PIK3CA, and/or PIK3R1 somatic mutations in EECs stratified by molecular subtype originated through convergent or linear evolution.
Experimental Design:
Banked frozen EECs with co-occurring PI3K pathway mutations of no specific molecular profile (NSMP; n = 5), mismatch repair-deficient (MMRd; n = 3), and POLE (n = 3) subtypes were selected for single-nucleus DNA sequencing targeting hotspot variants of 64 cancer-related genes and the PTEN, PIK3R1, and PIK3CA coding sequences. EEC cell lines and nonmalignant samples were used to define error rates and filter false-positive calls.
Results:
Single-nucleus analyses (n = 50,009 cells) revealed that in NSMP EECs, the co-occurring PIK3CA, PIK3R1, and/or PTEN mutations affected nearly all cells through linear evolution. MMRd EECs displayed higher levels of genetic heterogeneity, harboring PI3K pathway gene mutations in subsets of cells ranging from 3.9% to 96%. POLE EECs had the highest level of clonal diversity and harbored multiple, minor subclonal structures in all cases, through convergent evolution. We found a clear distinction between nearly clonal PI3K pathway gene alterations (>95%) and multiple, minor mutually exclusive subclones only affecting 1.4% to 27% of the tumor cells sequenced.
Conclusions:
Our exploratory, hypothesis-generating analysis suggests that PI3K pathway alterations evolve distinctly in MMRd/POLE compared with NSMP EECs, which may have therapeutic consequences. Further studies on the signaling output and PI3K pathway inhibitor response in EECs with subclonal PI3K pathway alterations are warranted.
Insights
Endometrioid endometrial carcinomas (EECs) show distinct PI3K pathway mutation evolution. NSMP EECs evolve linearly, while MMRd/POLE EECs exhibit convergent evolution, impacting potential therapies.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- The PI3K pathway is frequently altered in endometrioid endometrial carcinomas (EECs), often with multiple co-occurring mutations.
- Limited therapeutic success with single-agent PI3K inhibitors suggests complex evolutionary mechanisms.
Purpose of the Study:
- To investigate the evolutionary trajectories of co-occurring PTEN, PIK3CA, and PIK3R1 mutations in different molecular subtypes of EECs.
- To determine if these mutations arise through linear or convergent evolution using single-cell sequencing.
Main Methods:
- Single-nucleus DNA sequencing of 50,009 cells from banked EECs across no specific molecular profile (NSMP), mismatch repair-deficient (MMRd), and POLE subtypes.
- Targeted sequencing of 64 cancer-related genes, including PTEN, PIK3CA, and PIK3R1 hotspot variants.
- Utilized EEC cell lines and non-malignant samples to establish error rates and filter false positives.
Main Results:
- NSMP EECs showed linear evolution, with PI3K pathway mutations affecting nearly all cells.
- MMRd EECs displayed significant genetic heterogeneity, with mutations present in 3.9%-96% of cells.
- POLE EECs exhibited the highest clonal diversity, with multiple minor subclones evolving convergently.
Conclusions:
- PI3K pathway alterations evolve distinctly in MMRd/POLE EECs compared to NSMP EECs.
- These distinct evolutionary patterns may have significant therapeutic implications.
- Further research is needed on PI3K pathway signaling and inhibitor response in EECs with subclonal alterations.
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