Genomic profile of urine has high diagnostic sensitivity compared to cytology in non‐invasive urothelial bladder cancer

Abstract

Cytology is widely conducted for diagnosis of urothelial bladder cancer; however, its sensitivity is still low. Recent studies show that liquid biopsies can reflect tumor genomic profiles. We aim to investigate whether plasma or urine is more suitable for detecting tumor‐derived DNA in patients with early‐stage urothelial bladder cancer. Targeted sequencing of 71 genes was carried out using a total of 150 samples including primary tumor, urine supernatant, urine precipitation, plasma and buffy coat from 25 patients with bladder cancer and five patients with cystitis and benign tumor. We compared mutation profiles between each sample, identified tumor‐identical mutations and compared tumor diagnostic sensitivities between urine and conventional cytology. We identified a total of 168 somatic mutations in primary tumor. In liquid biopsies, tumor‐identical mutations were found at 53% (89/168) in urine supernatant, 48% (81/168) in urine precipitation and 2% (3/168) in plasma. The high variant allele fraction of urine was significantly related to worse clinical indicators such as tumor invasion and cytological examination. Although conventional cytology detected tumor cells in only 22% of non‐invasive tumor, tumor diagnostic sensitivity increased to 67% and 78% using urine supernatant and precipitation, respectively. Urine is an ideal liquid biopsy for detecting tumor‐derived DNA and more precisely reflects tumor mutational profiles than plasma. Genomic analysis of urine is clinically useful for diagnosis of superficial bladder cancer at early stage.

Urine biopsy technologies: Cancer and beyond

“…Recent studies have shown that the concentration of cfDNA in urine is even higher than that in blood. For example, Yosuke et al conducted gene detection tests on urine supernatants, urine precipitate, and blood samples from patients with BC, cystitis, and benign tumors 21 . Half of the somatic mutations present in tumors were detected in urine samples (53% in urine supernatant and 48% in urine precipitate), while 2% were detected in the blood plasma.…”

Tumor heterogeneity and the potential role of liquid biopsy in bladder cancer

“…Besides ctDNA, urothelial tumors have close contact with urine, thus, urinary biomarkers are highly promising as noninvasive tools. Somatic mutations are reliably detected in urinary cell-pellet DNA and cfDNA [75][76][77][78][79][80], and the level of cfDNA in urine supernatants was associated with pathologic features and disease progression, which makes urine tumor DNA have great potential in clinical detection, especially in the early stages of BC [81,82,80,79,83,84]. Current research on the clinical significance of UcfDNA detection for BC is increasing ( Table 2).…”

“…Increased levels of FGFR3 and Phosphatidylinositol-4,5bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutated DNA in urine and plasma are indicative of later progression and metastasis in BC. Hirotsu et al [81] compared detection rates of 71 UC commonly mutated genes in urine supernatants, urine precipitation, and plasma from 25 BC patients and 5 patients with cystitis and benign tumor. The diagnostic sensitivity of the genetic analysis was higher in urine DNA (67%-78%) compared to cfDNA or conventional cytology (22%) in NMIBC.…”

Genomic Profiling Identified ERCC2 E606Q Mutation in Helicase Domain Respond to Platinum-Based Neoadjuvant Therapy in Urothelial Bladder Cancer

“…We searched TCGA data and literature (5,(16)(17)(18)(19)(20)(21)(22) and selected 71 genes related to urological cancer (kidney cancer, prostate cancer, and BC) as described previously (23). A total of 3,652 primer pairs were designed by Ion AmpliSeq Designer contained within this panel (covering 365.34 kb) (23). Library preparation was conducted by amplicon-based multiplex PCR with Ion AmpliSeq Plus Kit (Thermo Fisher Scientific) as described previously (24)(25)(26).…”