Cell cycle checkpoint proficiency of endometrial cancer cells [WES]
Endometrial cancers (EC) are the most common gynecologic malignancy in the US. Most ECs harbor limited targetable somatic alterations, and are often grouped by histology (endometrioid, serous, or clear cell), mismatch repair, or TP53 status, none of which perfectly predict therapeutic response. A better mechanistic understanding of the key functional defects in ECs and more therapies with which to engage those targets in advanced stage EC are needed. Here we utilize functional, transcriptomic and genomic assays on a panel of EC cell lines and patient-derived organoids across EC histologic and genomic subtypes to characterize the TP53 and RB1 cell cycle regulatory proficiency and therapeutic vulnerabilities in this disease. We were surprised to find that TP53 genomic and functional status has little predictive capacity for EC therapeutic response. Rather, RB regulatory status correlated better with response to G1/S targeted therapies. Overall design: For both cell lines and organoids, the cells were grown to 80% confluence in regular growth medium. Cell lines were trypsinized and organoids were scraped, and the pellets were stored at -80°C until DNA was prepared. DNA was prepared using Qiagen's DNA Mini kit (Qiagen Cat. # 51304) according to the manufacturer's protocol. DNA was snap frozen and sent to Novogene (Sacramento, CA) for standard whole exome sequencing according to their protocol. Specifically, at Novogene, Agilent SureSelect Human All Exon V6 was utilized for library preparation. Sequencing occurred on the NovaSeq 6000 with a PE150 sequencing strategy.