Introduction:

Upper tract urothelial carcinoma (UTUC) is a relatively rare but lethal form of urothelial carcinoma with its own genetic distinctions and unique biology.  Accurate genomic profiling of UTUC may improve risk-stratification and future targeted therapies.  Urine cytology specimens represent a non-invasive source of cellular material, but their utility in characterizing the genomic landscape of UTUC has yet to be evaluated.  We aimed to determine the feasibility of next-generation sequencing (NGS) of urine cytology specimens of UTUC and its concordance with the genetic profiles of matched tissue specimens.

Methods:

14 patients with urine cytology specimens from UTUC tumors with available paired tissue specimens, either from ureteroscopic biopsy or radical nephroureterectomy, were selected for this study.  The cytology and tissue specimens were then subjected to NGS with a hybridization-based exon capture assay comprised of 505 cancer-related genes.

Results:

Of 14 total urine cytology specimens from UTUC tumors with available paired tissue specimens, 12 (86%) had adequate material for sequencing.  Paired tissue specimens included 8 ureteroscopic biopsies and 4 radical nephroureterectomies.  The most frequently altered genes in the UTUC cytology cohort are displayed in Figure 1.  Consistent with prior studies, TERT (50%), KMT2D (50%), FGFR3 (42%), STAG2 (33%), and PIK3CA (25%) were commonly mutated.  The urine cytology molecular landscape was highly concordant with that of the paired tissue.  There were no statistically significant differences in the frequencies of the 20 most commonly altered genes in the cytology cohort compared to paired tissue, including the TERT promoter (50% vs 67%, p=0.34), hotspot activating mutations in FGFR3 (42% vs 58%, p=0.34), and chromatin remodeling genes KMT2D (50% vs 67%, p=0.34), KDM6A (17% vs 17%, p=0.71), KMT2C (17% vs 25%, p=0.50), ARID1A (17% vs 17%, p=0.71), and CREBBP (17% vs 33%, p=0.32).

Conclusion:

In the first study of its kind, we demonstrate that urine cytology specimens obtained from UTUC tumors can be used for genomic profiling in the vast majority of patients (86%), with high concordance with tissue specimens.  These findings lay the foundation for future work to establish non-invasive methodologies to accurately stage and risk stratify UTUC, as well as monitor treatment response.

Funding: This work was supported by funding from the Thompson Foundation and U.S. Department of Defense Award Number W81XWH-20-1-0722.