Unique somatic variants in DNA from urine exosomes of individuals with bladder cancer

Abstract

Bladder cancer (BC), a heterogeneous disease characterized by high recurrence rates, is diagnosed and monitored by cystoscopy. Accurate clinical staging based on biopsy remains a challenge, and additional, objective diagnostic tools are needed urgently. We used exosomal DNA (exoDNA) as an analyte to examine cancer-associated mutations and compared the diagnostic utility of exoDNA from urine and serum of individuals with BC. In contrast to urine exosomes from healthy individuals, urine exosomes from individuals with BC contained significant amounts of DNA. Whole-exome sequencing of DNA from matched urine and serum exosomes, bladder tumors, and normal tissue (peripheral blood mononuclear cells) identified exonic and 3 0 UTR variants in frequently mutated genes in BC, detectable in urine exoDNA and matched tumor samples. Further analyses identified somatic variants in driver genes, unique to urine exoDNA, possibly because of the inherent intra-tumoral heterogeneity of BC, which is not fully represented in random small biopsies. Multiple variants were also found in untranslated portions of the genome, such as micro-RNA (miRNA)-binding regions of the KRAS gene. Gene network analyses revealed that exoDNA is associated with cancer, inflammation, and immunity in BC exosomes. Our findings show utility of exoDNA as an objective, non-invasive strategy to identify novel biomarkers and targets for BC.

CASC1 Expression in Bladder Cancer Is Regulated by Exosomal miRNA-150: A Comprehensive Pan-Cancer and Bioinformatics Study

“…Moreover, miRNAs may be released by cells and loaded into exosomes, acting as messengers for transmitting information between cells and participating in tumor development [ 21 , 22 ]. A number of studies have shown that exosomal miRNAs play a crucial role in the development of bladder cancer [ 23 ]. Researchers have found that miRNA-150 affects bladder cancer prognosis, and we speculate that CASC1 may be associated with miRNA-150 [ 24 ].…”

EV‐ADD, a database for EV‐associated DNA in human liquid biopsy samples

“…EV-DNA size distribution profile is reported in 24 of the 76 studies in the EV-ADD with high fragment size variance between studies (Supplementary Table 4). For example, a study demonstrated that the length of urine EV-DNA (1593-16,295 bp) and serum EV-DNA (1508-29,640 bp) are significantly larger than that reported for cfDNA (Zhou et al, 2021). Similar studies have indicated the presence of larger DNA fragments within EVs (Mao et al, 2019;Nguyen et al, 2020;Ruhen et al, 2021).…”

Recent development of urinary biomarkers for bladder cancer diagnosis and monitoring

“…Recently, a few studies reported that BC‐specific genes in exosomes are involved in immune activities 136 . Based on these findings, urinary exosomes can act as a novel non‐invasive biomarker of BC, including detecting somatic variants, mRNA or miRNAs 137,138 . By performing 168 BC urine samples and 90 controls with RT‐PCR, the high expression level of CA9 mRNA in urinary exosomes was highly correlated with BC patients (85.28% sensitivity and 83.15% specificity) 139 .…”

“…137,138 By performing 168 BC urine samples and 90 controls with RT-PCR, the high expression level of CA9 mRNA in urinary exosomes was highly correlated with BC patients (85.28% sensitivity and 83.15% specificity). 139 Zhou et al 137 also found that multiple somatic variants (e.g., miRNA-binding regions of the KRAS gene) were found in DNA from urinary exosomes of BC patients. Lin et al 138 utilised urinary exosomes-miRNAs as biomarkers for BC, and they also conducted experimental verification of the mechanism of miR-93-5p in BC.…”