Low-Coverage Sequencing of Urine Sediment DNA for Detection of Copy Number Aberrations in Bladder Cancer

Abstract

Purpose Chromosomal copy number aberrations (CNAs) are a hallmark of bladder cancer and a useful target for diagnostic explorations. Here we constructed a low-coverage whole-genome sequencing method for the detection of CNAs in urine sediment DNA from patients with bladder cancer. Patients and Methods We conducted a prospective study using urine sediment samples from 65 patients with bladder tumors, including 54 patients with bladder cancer and 11 patients with benign bladder tumors. Forty-three healthy individuals were included as normal controls. DNA was extracted from urine sediments and analyzed by low-coverage whole-genome sequencing to compare differences in CNAs among these three groups. CNAs are defined by arbitrary R values (normal range ± 2). When these values exceed ± 0.2 of normal range, gain/duplication or loss/deletion are suspected. Results With this method, CNAs were detected in 39 of 51 patients with bladder cancer, 2 of 10 patients with benign bladder tumors, and 8 of 39 normal controls. The lengths of DNA deletion and duplication were significantly larger in patients with bladder cancer than in patients with benign tumors or normal controls (P < 0.05). Bladder cancer duplicate CNAs mainly occurred on chromosomes 1q, 5p, 6p, 7p, 8q, and 13q, while deletions mainly occurred on 2q, 8p, 9q, 9p, and 11p. Those regions contained bladder cancer tumor-related genes, such as STK3, COX6C, SPAG1, CDKAL1, C9orf53, CDKN2A, CDKN2B, MIR31, and IFNA1. The number of CNAs detected in urine sediment DNA during the follow-up period was significantly reduced. Conclusion Our sequencing method is highly sensitive and can detect a minimal chromosome repeat/microdeletion change of 0.15 Mb. The use of 0.1~0.3× low-coverage whole-genome sequencing can be used to detect bladder cancer CNAs in urine sediment DNA. This method provides a promising method for noninvasive diagnosis of bladder cancer, but still needs further verification in a larger sample size.

Knockdown of long non-coding RNA CDKN2B-AS1 suppresses the progression of breast cancer by miR-122-5p/STK39 axis

“…Based on our data, lncRNA CDKN2B-AS1 played an oncogenic factor in breast cancer. It is consistent with the previous other studies about its role in most cancers, which indicated that CDKN2B-AS1 exerted a pro-cancer effect [40][41][42]. For examples, in renal clear cell carcinoma, lncRNA CDKN2B-AS1 affected the malignancy through epigenetically activating NUF2 (NUF2 Component of NDC80 Kinetochore Complex) transcription [16].…”

Novel role of COX6c in the regulation of oxidative phosphorylation and diseases

“…Moreover, COX6c has been proposed as a potential participant in the chromosomal organization in a retroperitoneal lipoma instance [ 69 ]. Yun et al also found that COX6c is a key gene in bladder cancer tumors by detecting bladder cancer chromosomal copy number aberrations in urinary sediment [ 70 ].…”

Humoral cancer detection

“…The most recent study found a sensitivity of 11% for analysis in plasma 67 , which was supported by the majority of other studies describing sensitivities of less than 20% 67,[85][86][87][88] . Two studies reported specificities (96% and 100%) 67,89 , and two studies reported concordance rates (41% and 42%) 86,88 .…”

“…All six studies on helicase-like transcription factor (HLTF) hypermethylation analysis for the purpose of CRC detection used qMSP and described large cohorts of more than 100 patients 67,[85][86][87][88][89] .…”

“…To the best of our knowledge, no studies on copy number variant (CNV) analysis for detection of NSCLC of CRC in urine have been published. However, in urine of patients diagnosed with urogenital tumors such as prostate and bladder cancer, CNV analysis has shown potential for clinical use 86,87 . Furthermore, through analysis of CNV, tumors of the central nervous system (CNS) such as gliomas have been reported to be detectable in urine 88 .…”