Abstract 4353: Integrated molecular analysis of upper urinary tract urothelial carcinoma
Authors: Fujii Yoichi , Sato Yusuke , Suzuki Hiromichi , Yoshizato Tetsuichi , Shiozawa Yusuke , Yoshida Kenichi , Shiraishi Yuichi , Nakagawa Tohru , Nishimatsu Hiroaki , Okaneya Toshikazu , Sanada Masashi , Makishima Hideki , Miyano Satoru , Kume Haruki , Ogawa Seishi 
Published: August 2018

Abstract
Backgrounds
Upper urinary tract urothelial carcinoma (UTUC) is a rare cancer accounting for 10% of all urothelial malignancies, whose molecular pathology, however, is poorly understood. To clarify diagnostic and prognostic impact of molecular profiles, we comprehensively investigated genetic alterations in UTUC.
Materials & methods
Surgical specimens of UTUC and matched normal samples were obtained from 102 patients with various stages, and were subjected to whole exome/RNA sequencing and array-based methylation analysis.
Results
UTUC cases displayed as many as 5.3 mutations per megabase (Mb). Seven cases showed hypermutation (&gt;20/Mb), 6 of which harbored biallelic defects of mismatch repair (MMR) genes, suggesting the presence of Lynch syndrome in these. Genetic alterations were most frequently observed in TERT promoter (51% of cases), followed by KMT2D (48%), FGFR3 (46%, including fusion genes), CDKN2A (homozygous deletion) (42%), TP53 (31%), and RAS family genes (HRAS/KRAS/NRAS) (21%). More than 95% of cases harbored either TP53, MDM2, FGFR3, or RAS alterations in almost mutually exclusive manner. Hierarchical clustering on the basis of commonly altered genes in 95 non-hypermutated cases identified 3 distinct subgroups. Group 1 cases were frequently affected by TP53/MDM2 alterations and complex copy number alterations (CNAs), characterized by high stage, high grade, and poor prognosis. In Group2, FGFR3 and CDKN2A alterations and simple CNAs were enriched, which were associated with low stage/grade and favorable prognosis. All cases in Group3 harbored RAS-family gene alterations, showing intermediate prognosis. In mutation signature analysis, we extracted age-related, APOBEC, Transcriptional coupled repair (TCR), and MMR associated signatures. TCR signature was more frequently found in patients with an ALDH2 polymorphism implicated in low alcohol metabolism (rs671, GG/AG). MMR signature was observed only in the hypermutated cases with MMR deficiency. Gene expression analysis using unsupervised clustering identified 3 clusters. Cluster 1 was characterized by high expression of late cell-cycle genes, basal markers, and notably, immune blockade targets, CD274 and PDCD1LG2. Cluster 1 also harbored frequent TP53 alterations. In contrast, cases in cluster 2 and 3 showed high expression of early cell cycle genes and luminal markers. Cluster 2 were associated with FGFR3 mutations (positive in 75%), while almost all (92%) of RAS-mutated cases were classified in cluster 3. Finally, hierarchical analysis of methylation data revealed that approximately 60% of examined samples showed CpG island methylator phenotype (CIMP), which was positive in all the groups defined by mutational landscape.
Conclusion
UTUC showed distinct genetic landscape, associated with various clinical features. Our findings of molecular characteristics in UTUC will contribute to the development of novel diagnostics and therapeutics.
Citation Format: Yoichi Fujii, Yusuke Sato, Hiromichi Suzuki, Tetsuichi Yoshizato, Yusuke Shiozawa, Kenichi Yoshida, Yuichi Shiraishi, Tohru Nakagawa, Hiroaki Nishimatsu, Toshikazu Okaneya, Masashi Sanada, Hideki Makishima, Satoru Miyano, Haruki Kume, Seishi Ogawa. Integrated molecular analysis of upper urinary tract urothelial carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4353.