Abstract A27: Microsatellite instability and tumor mutation burden as factors in ovarian clear-cell carcinoma therapy selection
Authors: Shiro Takamatsu, Noriomi Matsumura, J.B. Brown, Hiroaki Itamochi, Junzo Hamanishi, Ken Yamaguchi, Toru Sugiyama, Tsukasa Baba, Masaki Mandai
Journal: Clinical Cancer Research (2020)

Abstract Background: Microsatellite instability (MSI) and tumor mutation burden (TMB) are being considered as predictive biomarkers for PD-1 and PD-L1 blockade immunotherapy. However, in ovarian clear-cell carcinoma (OCC), which demonstrates characteristic resistance to standard chemotherapy, the extent of MSI and TMB and their subsequent prognostic capability are unresolved. The aim of this study is to investigate TMB and MSI in OCC for improved therapy decision making. Methods: Tumor-normal paired whole-exome data of 55 OCC patients (Itamochi et al., Br J Cancer 2017) were analyzed. Sequence data preprocessing was performed in accordance with GATK best practice workflows using BWA, Picard, the GATK toolkit, and SAMtools. Somatic SNVs and indels were detected by using Mutect and VarScan. Resulting variants were annotated by ANNOVAR, and exonic or splicing variants were extracted. SNVs with allele frequency &amp;gt;= 2.0% were kept and further processed by the combination of the pathogenicity prediction values obtained from SIFT, PolyPhen-2, and PROVEAN; SNVs annotated as deleterious or damaging by at least one of the tools were retained. The TMB of each sample was evaluated by the total number of nonsynonymous SNVs called by the preannotation pipeline. A threshold defining high TMB was derived from the inflection point on the right tail of the TMB distribution; the resulting value was positioned at the 85th percentile of TMB values. MSI was calculated using MSIsensor, with the MSI-high classification threshold set as per the software’s documentation. Results: Among the 55 OCC cases, 11 (20%) had at least one or a combination of either MSI-high status, mismatch repair (MMR) mutations, or TMB-high status. Specifically, three had MSI-high status, five had MMR gene mutations, and eight had TMB-high status. MSI-high samples showed elevated TMB (p= 0.052 Fisher-T). TMB was also elevated in MMR-mutated samples (p=0.018 Fisher-T). Among the three samples with MSI-high status, only one contained a deleterious mutation in MMR gene MSH6. One TMB-high sample had a POLE1 mutation. Critically, discrete- and continuous-valued survival analyses using MSI and TMB as independent variables did not suggest correlation with patient prognosis. Conclusion: Within gynecologic oncology, MSI and TMB are correlated with prognosis in uterine endometrial cancer subtypes, though here they have demonstrated relatively reduced prognostic ability in OCC so far as examined by the samples available for this study. Thus, OCC patients are warranted the consideration of immune checkpoint inhibitor therapy at an earlier stage of treatment, and further studies to improve the resolution between MSI/TMB/MMR and phenotypical aspects should be encouraged. Citation Format: Shiro Takamatsu, Noriomi Matsumura, J.B. Brown, Hiroaki Itamochi, Junzo Hamanishi, Ken Yamaguchi, Toru Sugiyama, Tsukasa Baba, Masaki Mandai. Microsatellite instability and tumor mutation burden as factors in ovarian clear-cell carcinoma therapy selection [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A27.