Clinical Targeted Next-Generation Sequencing Shows Increased Mutational Load in Endometrioid-type Endometrial Adenocarcinoma With Deficient DNA Mismatch Repair

Abstract

A subset of endometrial adenocarcinomas (EACs) exhibit microsatellite instability and have deficient DNA mismatch repair (dMMR). The overall aim of the study was to compare the spectrum of mutations in endometrioid-type EAC with and without dMMR by using a clinically validated next-generation sequencing assay. We retrospectively identified 19 EACs with known mismatch repair status that had undergone targeted sequencing of a panel of cancer-related genes. The mismatch repair status was ascertained by immunohistochemistry against MLH1, PMS2, MSH2, and MSH6 mismatch proteins. Somatic mutations in EAC with dMMR were compared against those in cases with proficient MMR (pMMR). The dMMR EAC showed a normalized mean of 66.6 mutations/Mb per case compared with pMMR EAC with a mean of 26.2 (P<0.05). The most commonly mutated genes were PTEN (89% of dMMR, 50% of pMMR), PIK3CA (67% vs. 40%), ATM (89% vs. 40%), and FLT3 (67% vs. 50%). The transition/transversion ratio was 4.7 versus 2.8 for the dMMR and pMMR cohorts, respectively (P<0.05). Copy number variant analysis did not demonstrate significant differences between the dMMR and pMMR cohorts and was not correlated with histologic grade of EAC. In conclusion, tumorigenesis of EAC in the context of dMMR demonstrated heavier mutational burdens and higher transition/transversion ratio. The spectrum of genetic alterations can potentially help identify cases with microsatellite instability phenotype using next-generation sequencing data from a targeted cancer gene panel.

Detection of driver mutations and genomic signatures in endometrial cancers using artificial intelligence algorithms

“…All comparisons produced significant p-values suggesting that ECs have unique mutation signatures than other cancers ( S1C Table ). As expected, G>A and C>T mutations occur at a higher frequency than the other mutations [ 33 ]. However, five mutation types (C>G, G>C, G>T, T>A, T>C) show a statistically significant higher frequency compared to other cancers.…”

“…We next examined the type of point mutations arising in ECs ( Fig 1D , S1B Table ). A previous report has investigated mutation signatures in endometrial adenocarcinoma and found that A:T>T:A and G:C>C:G are increased in proficient MMR cancers compared with deficient MMR [ 33 ]. Here, we analyzed each transversion and transition independently and compared the frequency of each nucleotide change in ECs to the frequency in other cancers (independent samples t-test).…”

“…The significance of this is not immediately obvious but the high levels of both changes suggests that they are replication rather than transcription driven (e.g., they occur on both DNA strands). Additionally, this cannot be due to MMR status because 1) previous findings showed that deficient MMR ECs have fewer G:C>C:G mutations [ 33 ] and 2) most cancers used for this comparison are not MMR unstable. Thus, the increase in the G:C>C:G signature is unique to ECs.…”

FDA-Approved and Emerging Next Generation Predictive Biomarkers for Immune Checkpoint Inhibitors in Cancer Patients

“…Although MSI-H can be present in almost all solid tumor types, its prevalence is widely variable across the different tumor types. MSI testing should be performed using IHC, PCR, or NGS method for the tumor types with high frequency of MSI, generally belonging to the spectrum of Lynch syndrome, including colorectal cancer ( 31 ), endometrial cancer ( 32 ), gastric cancer ( 33 ), ovarian cancer ( 34 ), and small Intestinal cancer ( 35 ). For other tumor types that do not belong to the spectrum of Lynch syndrome with low prevalence of MSI or no MSI data available on the reliability of IHC and the PCR method, such as NSCLC, breast cancer, melanoma, and kidney cancer, NGS-MSI should be considered because the NGS method can scan all types of MSI and also couple analyses of MSI with TMB.…”

Identification of long non‑coding RNA expression patterns useful for molecular‑based classification of type�I endometrial cancers

“…Indeed, it is currently established that a classification only based on morphologic features is inconsistent and that molecular-based classification is desirable for optimal treatment and prognosis of such cancers. Nevertheless, although several genetic alterations have been associated with increased risk of EC (8)(9)(10) and mutations in genes such as ATR have been established to be associated with poor clinical outcomes in EEC (11), new molecular markers need to be identified for early diagnosis and treatment purposes.…”