Article

Detection and Surveillance of Bladder Cancer Using Urine Tumor DNA

Authors:
  • Anesthesia Care Associates Medical Group (ACAMG)
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Abstract

Current regimens for the detection and surveillance of bladder cancer are invasive and have suboptimal sensitivity. Here, we present a novel high-throughput sequencing (HTS) method for detection of urine tumor DNA (utDNA) called utDNA CAPP-Seq (uCAPP-Seq) and apply it to 67 healthy adults and 118 patients with early-stage bladder cancer who had urine collected either prior to treatment or during surveillance. Using this targeted sequencing approach, we detected a median of 6 mutations per patient with bladder cancer and observed surprisingly frequent mutations of the PLEKHS1 promoter (46%), suggesting these mutations represent a useful biomarker for detection of bladder cancer. We detected utDNA pretreatment in 93% of cases using a tumor mutation–informed approach and in 84% when blinded to tumor mutation status, with 96% to 100% specificity. In the surveillance setting, we detected utDNA in 91% of patients who ultimately recurred, with utDNA detection preceding clinical progression in 92% of cases. uCAPP-Seq outperformed a commonly used ancillary test (UroVysion, P = 0.02) and cytology and cystoscopy combined (P ≤ 0.006), detecting 100% of bladder cancer cases detected by cytology and 82% that cytology missed. Our results indicate that uCAPP-Seq is a promising approach for early detection and surveillance of bladder cancer. Significance This study shows that utDNA can be detected using HTS with high sensitivity and specificity in patients with early-stage bladder cancer and during post-treatment surveillance, significantly outperforming standard diagnostic modalities and facilitating noninvasive detection, genotyping, and monitoring. This article is highlighted in the In This Issue feature, p. 453

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... Several published studies have also shown that targeted sequencing of utDNA can be a reliable alternative method for diagnosis and perioperative monitoring BUC, showing higher sensitivity and specificity than cytology [6][7][8]. However, utDNA as a noninvasive detection method for tumour monitoring has not been fully studied in the UTUC cohort. ...
... In the past few years, it has been demonstrated that genomic, transcriptomic, epigenomic and macrogenomic studies for utDNA have shown high diagnostic efficacy and recurrence monitoring capabilities in UC [7][8][9][10]. However, utDNA as a noninvasive detection method for tumour monitoring has not been fully studied in the UTUC cohort. ...
... However, studies detecting MRD based on utDNA are still lacking. In addition, utDNA methylation assessment tools have also shown that utDNA shares a strong correlation with tumour malignancy and burden [7,9]. Our study demonstrated that postoperative utLIFE MRD scores decreased after surgery, regardless of stages and grades, indicating that utLIFE was associated with tumour burden in real-time. ...
Article
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Background For early detection and postoperative monitoring of upper tract urothelial carcinoma (UTUC), the traditional detection method was limited to its invasiveness and insufficient sensitivity. We aim to use urine tumour DNA (utDNA) for detecting minimal residual disease (MRD), early diagnosis and perioperative monitoring in UTUC. Method We previously established a utDNA multidimensional bioinformatic valuation model, named utLIFE, using low‐coverage whole‐genome sequencing and targeted deep sequencing. This prospective cohort enrolled 93 patients diagnosed with UTUC without metastasis. We collected morning urine samples on the day of surgery and the discharge day after the operation for utLIFE testing. In addition, we also enrolled 80 healthy controls to further validate the specificity of the utLIFE model in the study. Results The utLIFE of preoperative samples could discriminate UTUC with high specificity (96.25%, 77/80), and high sensitivity (96.77%, 90/93) regardless of stage and grade. The sensitivity of utLIFE was significantly higher than urine cytology (p < 0.001) and fluorescence in situ hybridisation (FISH) (p < 0.001) (N = 19), especially in early‐stage and low‐grade UTUC. Postoperative utLIFE scores were significantly decreased compared with those of preoperative samples (79 vs. 36, p < 0.001), indicating its association with tumour burden. For special pathology types, utLIFE performed less well in sensitivity and perioperative alteration. Conclusion In conclusion, we established a bioinformatic utDNA valuation model, utLIFE, which was validated to be a rapid and noninvasive approach with high sensitivity for early detection and MRD monitoring for UTUC.
... Cell-free circulating tumor DNA in the plasma (ctDNA) and urine (utDNA) are emerging as promising biomarkers for identifying the presence of bladder cancer, predicting pathologic complete response (pCR), detecting disease recurrence following RC, and assessing response to adjuvant immunotherapy [4][5][6][7][8][9]. Though significant inroads have been made to maximize clinical utility, neither ctDNA nor utDNA has been shown to predict pathologic T-stage following RC. ...
... various bladder cancer settings [5,6,8,9,19]. Significant advances in next-generation sequencing technologies and the integration of genome-wide tumor DNA metrics have improved the ability to predict pathologic complete response to neoadjuvant chemotherapy and estimate survival after RC [6]. However, the accurate prediction of pathologic T-stage using quantitative cfDNA metrics has not yet been demonstrated. ...
Article
Objective To assess the ability of cell-free urinary and plasma tumor DNA (cfDNA) to predict pathologic stage at radical cystectomy for patients with clinical muscle-invasive bladder cancer. MethodsA total of 25 patients with clinical muscle-invasive bladder cancer were enrolled before undergoing radical cystectomy. Blood and urine were collected before surgery. The 600-gene PredicineATLAS panel was used to sequence blood buffy-coat germline DNA, plasma cfDNA, and urine cfDNA samples. Low-pass whole genome sequencing was performed on plasma- and urine-derived cfDNA. CfDNA tumor fraction (TF), genome-wide copy number burden (CNB), and estimated tumor mutational burden (TMB) were measured in both plasma and urine samples and their correlation with pathologic T-stage was examined. ResultsThree of 25 plasma samples had insufficient cfDNA. In 22 of 22 plasma samples and 24 of 25 urine samples, at least one nonsynonymous somatic variant was detected. Across the cohort, 44% of plasma variants were concordant with paired urine variants. The mean number of variants did not differ between noninvasive (< pT1/pN0) and invasive disease (≥ pT1 or N+) for both plasma (8 vs. 9.5 variants; P = 0.85) and urine (33.7 vs. 30 variants; P = 0.45). A strong correlation was observed between urine TF and urine CNB score within patients (rv = 0.92). Plasma TF (r = 0.38), urine TF (r = 0.21), and urine CNB score (r = 0.16) exhibited positive correlations with pT stage. Patients with carcinoma in situ (CIS) had higher mean urine TF and CNB scores ( P = 0.07 and P = 0.05, respectively). Plasma TF and CNB score did not correlate with the presence of CIS.Conclusions Combining plasma- and urine-based cfDNA analysis may help identify patients with residual disease at radical, although we were unable to predict pathologic T-stage based on these metrics.The presence of CIS may contribute to greater urinary CNB and TF levels. Considering CIS in the analysis may improve the ability to correlate tumor metrics with pathologic stage. Low-pass whole genome sequencing–derived urinary CNB correlates strongly with urinary TF and may provide a less resource-intensive method for future longitudinal disease monitoring.
... To harness 5hmC's potential in cancer detection and monitoring, many studies have aimed to identify cancer-specific 5hmC changes in cfDNA by comparing 5hmC profiles between large groups of patient and control cohorts. Such large population of sample sizes often lead to limitations in the scope of genomic analyses to only focus on a subset of the genomic regions [23,28,29,34,36] or selective sites enriched for high 5hmC levels [17,33,37,38]. Little is known about the regulatory roles of 5hmC, its genome-wide changes and their impacts on the molecular phenotypes in tumors. ...
Preprint
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Characterization of tumor epigenetic aberrations is integral to understanding the mechanisms of tumorigenesis and provide diagnostic, prognostic, and predictive information of high clinical relevance. Among the different tumor-associated epigenetic signatures, 5 methyl-cytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the two most well-characterized DNA methylation alterations linked to cancer pathogenesis. 5hmC has a tissue-specific distribution and its abundance is subjected to changes in tumor DNA, making it a promising biomarker. Detecting tumor-related DNA methylation alterations in tissues is highly invasive, while the analysis of the cell-free DNA (cfDNA) is poised to supplement, if not replace, surgical biopsies. Despite many studies attempted to identify new epigenetic targets for liquid biopsy assays, little is known about the regulatory roles of 5hmC, its impacts on the molecular phenotypes in tumors. Most importantly, whether the oncogenic-associated 5hmC signatures found in tumor tissues can be recapitulated in patient cfDNA. In this study, we performed the unbiased and simultaneous detection of 5mC and 5hmC whole-genome DNA modifications at base-resolution from two distinct cancer cohorts, from patients with bladder cancer or B-Cell lymphoma, their corresponding normal tissues, and cfDNAs from plasma. We analyzed tissue-specific methylation patters and searched for signatures in gene coding and regulatory regions linked to cancerous states. We then looked for methylation signatures in patients cfDNA to determine if they were consistent with the tumor-specific patterns. We determined the functional significance of 5hmC in tissue specific transcription and uncovered hundreds of tumor-associated 5hmC signatures. These tumor-associated 5hmC changes, particularly in genes and enhancers, were functionally significant in tumorigenesis pathways and correlated with tumor specific gene expression. To investigate if cfDNA is a faithful surrogate for tumor-associated 5hmC, we devised a targeted capture strategy to examine the alterations of 5hmC in cfDNA from patients with bladder cancer and lymphoma with sufficient sensitivity and specificity and confirmed that they recapitulated the patterns we observed in tumor tissues. Our results provide analytic validation of 5hmC as a cancer-specific biomarker. The methods described here for systematic characterization of 5hmC at functional elements open new avenues to discover epigenetic markers for non-invasive diagnosis, monitoring, and stratifying cancer.
... The rate of concordance was higher for clonal mutations than subclonal mutations. 31,32 Hence, if the ctDNA-identified mutations were not found in the tissue analysis, it can be considered either as a subclonal variant not found in the collected sample or as a technical error or a CHIP, which can be identified by WBC DNA cross-analysis. However, crossreferencing the results of single nucleotide variants from 1,397 ctDNA samples of metastatic CRC patients with tissue analysis results from three online databases showed a high concordance rate between the two for the top 20 genes. ...
Article
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Narmadha Rathnasamy Evidence is mounting that circulating tumor deoxyribonucleic acid can be tested accurately, frequently, and in a noninvasive form. Its role in monitoring patients with cancer, particularly colorectal cancer, is increasing. In this brief review, we discuss its current role when measured using next-generation sequencing-based methods.
... 16 PLEKHS1 promoter mutations were frequently identified in bladder cancer and could serve as a potential biomarker for diagnosis and monitor the posttreatment surveillance of the disease. 17 Although increased PLEKHS1 expression was associated with aggressive characteristics and adverse outcomes of PTC, PLEKHS1 promoter hotspot mutations were only commonly identified in radioiodine refractory DTC, but relatively uncommon in sporadic PTC, ATC, and thyroid cancer cell lines. [18][19][20] According to the results in the current study, all these noncoding mutations in GPR126, SDHD, and PLEKHS1 genes were identified in ATC, indicating the complexity of the genetic basis of ATC, although the prevalence of these mutations was not very high. ...
Article
Background: Anaplastic thyroid cancer (ATC) is a rare but one of the most lethal types of human cancer. Although increasing evidence demonstrated that ATC tumors had a high mutation burden, little is known about the aberrancy of the noncoding genome of ATC except the well-investigated telomerase reverse transcriptase (TERT) promoter mutations. Methods: The mutational statuses of TBC1D12 5' untranslated region (5'UTR), GPR126 intron 6, SDHD and PLEKHS1 promoters, as well as the TERT promoter and BRAFV600E mutations were determined using Sanger sequencing in 28 patients with ATC (19 women and 9 men) with a median (interquartile range) age of 64 (55-71) years, 14 thyroid cancer cell lines and a normal thyroid cell line. The prevalence of TBC1D12 5'UTR mutations in papillary thyroid cancer (PTC) and their association with clinicopathologic characteristics were explored by analyzing The Cancer Genome Atlas thyroid cancer dataset. Results: The noncoding mutations in TERT, SDHD and PLEKHS1 promoters, TBC1D12 5'UTR, and GPR126 intron 6 were collectively found in 82.1% (23/28) of ATC samples. Specifically, TERT promoter mutations were detected in 22 (78.6%) samples; GPR126 intron mutations were detected in 2 (7.1%) samples; and both SDHD and PLEKHS1 promoter mutations were detected in 1 (3.6%) ATC sample. Two hotspot mutations in TBC1D12 5'UTR were observed in 14 of 28 (50%) ATCs, 7 of 492 (1.4%) PTCs, and 1 cell line derived from ATC. TBC1D12 5'UTR mutations were significantly associated with older age at diagnosis (60 vs. 46 for wild type, p = 0.003), pathological T3/T4 stage (85.7% vs. 37.7%, p = 0.010), and advanced tumor stages (85.7% vs. 32.5%, p = 0.006) in PTC. Conclusions: This preliminary study for the first time showed a high prevalence of TBC1D12 5'UTR mutations in ATC and indicated an association between TBC1D12 mutation and aggressive characteristics of PTC, which needs to be confirmed in large cohort studies.
... UroSEEk demonstrated up to 80% and 68% sensitivity in detecting either the presence or recurrence of bladder cancer, respectively. However, the utility of utDNA sequencing in assessing CCR after NAC in MIBC remains unclear (62,65,66). ...
Article
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Background and Objective A standard of care for muscle-invasive bladder cancer (MIBC) is cisplatin-based neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC). Given recent improvements in NAC and the morbidity associated with RC, bladder-sparing therapy has been investigated as a promising treatment for patients with MIBC who experience a complete clinical response (CCR) to systemic therapy. However, clinical staging is unreliable, making it challenging to determine ideal candidates for bladder-sparing therapy. Our primary objective is to review the efficacy of NAC, strategies for determining a CCR as a surrogate for a complete pathologic response, and the emerging role of imaging, tumor genomics, and biomarkers in selecting candidates for bladder-sparing therapy. Methods We surveyed the literature for studies investigating the outcomes of current treatment modalities for MIBC and methods for determining a CCR following systemic therapy as well as the impact this has on pathologic staging. Studies employing imaging, tumor biomarkers, and genomics were included. Key Content and Findings Clinical staging with cystoscopy or transurethral resection shows significant discordance with final pathology, with high rates of understaging. Multiparametric magnetic resonance imaging (mpMRI) has shown strong utility in determining the presence of MIBC, but it has yet to reliably identify CCR. Meanwhile, somatic DNA damage repair mutations and biomarkers such as circulating and urinary tumor DNA are strong predictors of recurrence, showing promise in predicting and monitoring a CCR to systemic therapy. Multiple ongoing trials are currently assessing the use of biomarkers and genomic analyses in determining eligibility for bladder-sparing therapy. Conclusions While no one method has reliably demonstrated the ability to detect a true CCR, a multimodal approach involving imaging, biomarkers, and genomic analyses holds promise. We eagerly await the results of clinical trials investigating these tools, which may allow for the safe recommendation of bladder-sparing therapy.
... . 许多新型尿液诊断技术, 如基于DNA甲 基化的UriFind和Bladder EpiCheck等展现出良好的临 图 1 膀胱癌尿液检测技术 Figure 1 Urine assays for detection of bladder cancer 床性能, 已经获批上市并进入临床应用 [16] . [26] . 另一项分析了42例局限性 膀胱癌患者的研究中 [27] , uCAPP-Seq判断肿瘤MDR的 [28] . ...
... In a clinical study of 118 patients with NMIBC, utDNA was detected in 91% of patients who developed recurrent disease and the detection of utDNA preceded clinical disease recurrence in 92% of patients by a median of 2.7 months. The performance of this utDNA assay exceeded that of commonly used tests including UroVysion, cytology and cystoscopy [96]. It detected 100% of cases found by cytology and detected 82% of cases missed by cytology. ...
Article
Full-text available
Urothelial carcinoma (UC) is the fourth most prevalent cancer amongst males worldwide. While patients with non-muscle-invasive disease have a favorable prognosis, 25% of UC patients present with locally advanced disease which is associated with a 10–15% 5-year survival rate and poor overall prognosis. Muscle-invasive bladder cancer (MIBC) is associated with about 50% 5 year survival when treated by radical cystectomy or trimodality therapy; stage IV disease is associated with 10–15% 5 year survival. Current therapeutic modalities for MIBC include neoadjuvant chemotherapy, surgery and/or chemoradiation, although patients with relapsed or refractory disease have a poor prognosis. However, the rapid success of immuno-oncology in various hematologic and solid malignancies offers new targets with tremendous therapeutic potential in UC. Historically, there were no predictive biomarkers to guide the clinical management and treatment of UC, and biomarker development was an unmet need. However, recent and ongoing clinical trials have identified several promising tumor biomarkers that have the potential to serve as predictive or prognostic tools in UC. This review provides a comprehensive summary of emerging biomarkers and molecular tumor targets including programmed death ligand 1 (PD-L1), epidermal growth factor receptor (EGFR), human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor (FGFR), DNA damage response and repair (DDR) mutations, poly (ADP-ribose) polymerase (PARP) expression and circulating tumor DNA (ctDNA), as well as their clinical utility in UC. We also evaluate recent advancements in precision oncology in UC, while illustrating limiting factors and challenges related to the clinical application of these biomarkers in clinical practice.
... Several studies also focused on the utility of utDNA in the detection and surveillance of bladder cancer. In patients with early-stage bladder cancer, utDNA can be facilitating noninvasive detection, genotyping, and monitoring during post-treatment surveillance, significantly outperforming standard diagnostic modalities [61] . In patients with muscle-invasive bladder cancer, the detection of utDNA minimal residual disease prior to RC showed a significant correlation with pathologic response and PFS [62] . ...
Article
Full-text available
Background Circulating tumor DNA (ctDNA) has emerged as a non-invasive technique that provides valuable insights into molecular profiles and tumor disease management. This study aimed to evaluate the prognostic significance of circulating tumor DNA (ctDNA) in urothelial carcinoma (UC) through a systematic review and meta-analysis. Methods A comprehensive search was conducted in MEDLINE, EMBASE, and the Cochrane Library from the inception to December 2023. Studies investigating the prognostic value of ctDNA in UC were included. Hazard ratios (HRs) of disease-free survival (DFS) and overall survival (OS) were extracted. Overall meta-analysis and subgroup exploration stratified by metastatic status, ctDNA sampling time, treatment type, and detection method was performed using the R software (version 4.2.2). Results A total of sixteen studies with 1725 patients were included. Fourteen studies assessed the association between baseline ctDNA status and patient outcomes. Patients with elevated ctDNA levels exhibited significantly worse DFS (HR=6.26; 95% CI, 3.71-10.58, P <0.001) and OS (HR=4.23; 95% CI, 2.72-6.57, P <0.001) regardless of metastatic status, ctDNA sampling time, treatment type and detection methods. Six studies evaluated the prognostic value of ctDNA dynamics in UC. Patients who showed a decrease or clearance in ctDNA levels during treatment or observation demonstrated more favorable DFS (HR=0.26, 95% CI, 0.17–0.41, P <0.001) and OS (HR=0.21, 95% CI, 0.11–0.38, P <0.001) compared to those who did not. The association remained consistent across the subgroup analysis based on metastatic status and detection methods. In the immune checkpoint inhibitor-treated setting, both lower baseline ctDNA level and ctDNA decrease during the treatment were significantly associated with more favorable oncologic outcomes. Furthermore, specific gene mutations such as FGFR3 identified in ctDNA also demonstrated predictive value in UC patients. Conclusion This meta-analysis demonstrates a strong association of ctDNA status and its dynamic change with survival outcomes in UC, suggesting substantial clinical utility of ctDNA testing in prognosis prediction and decision making in this setting.
... cfDNA are fragments of extracellular nucleic acids, which are released into biological fluids through multiple mechanisms, such as cellular apoptosis, necrosis, phagocytosis and possibly active secretion (14,15) ( Fig. 1). cfDNA exists in various bodily fluids, including blood plasma (16), saliva (17), urine (18), cerebrospinal fluid (19) and pleural fluid (20), but mostly in blood plasma. cfDNA is typically double-stranded, highly fragmented and ~150-200 base pairs (bp) in length. ...
... However, the long-term effectiveness of these treatments is significantly compromised due to tumor recurrence and resistance to chemotherapy (6,7). Previous studies have shown that early diagnosis and continuous monitoring can improve the survival rates of bladder cancer patients (8,9). ...
Article
Full-text available
Objective The primary objective of this study was to examine the levels of serum EZH2 in patients diagnosed with bladder cancer, and subsequently evaluate its potential as a biomarker for both the diagnosis and prognosis of bladder cancer. Methods Blood samples were obtained from 115 bladder cancer patients and 115 healthy persons. We measured the EZH2 concentrations in the serum of these subjects via enzyme-linked immunosorbent assay (ELISA). To assess the diagnostic performance of serum EZH2 in detecting bladder cancer, we plotted receiver operating characteristic (ROC) curves and calculated their corresponding area under the curve (AUC). We also used the Cox regression model and log-rank test to investigate the correlation between EZH2 levels and clinicopathological characteristics, and survival rates of bladder cancer patients. Results Serum EZH2 levels were significantly higher in bladder cancer patients when compared to those in healthy persons. Serum EZH2 levels exhibited a significant correlation with TNM stage, lymph node metastasis, muscle invasion, and tumor size. At a cutoff value of 8.23 ng/mL, EZH2 was able to differentiate bladder cancer patients from healthy persons, with an AUC of 0.87, a sensitivity of 81.31%, and a specificity of 78.42%. High EZH2 levels correlated with poor overall survival rates and progression-free survival rates of bladder cancer patients. Conclusions Serum EZH2 levels were elevated in bladder cancer patients, and patients with higher serum EZH2 levels exhibited a poorer prognosis. This indicates that serum EZH2 could be a novel biomarker for bladder cancer diagnosis and prognosis. Such findings could improve the prognosis of bladder cancer patients by facilitating early detection and continuous monitoring.
... Finally, as ctDNA is present in different biofluids, sampling strategies that exploit the spatial relationship between tumor site and biofluid type can further increase the sensitivity of ctDNA detection. Especially important in the case of low disease burden settings, biofluids sampled proximal to a tumor site (e.g., urine for urothelial carcinoma) [142] can be more enriched for ctDNA than plasma [64]. Combining these approaches creates opportunities for establishing highly sensitive ctDNA-based MCED and MRD tests for use in the clinic. ...
Article
Full-text available
DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.
... Dudley et al. used a 311 kb custom panel (460 gene regions) sequencing method (uCAPP-Seq) to analyze urine tumor DNA in 118 patients with NMIBC. They detected urine tumor DNA in 91% of patients who experienced recurrence in the surveillance setting, with a positive lead time in 92% of cases [3]. In another study, Ward et al. applied deep-targeted sequencing of mutations in 23 genes and demonstrated a sensitivity of 87% and specificity of 85% in 165 hematuria patients diagnosed with bladder cancer. ...
... sequencing-based hybrid capture assay [14]. uCAPP-Seq captures single nucleotide variants (SNVs), insertions and deletions, and copy number alterations in genomic regions known to harbor common driver mutations for bladder cancer. ...
Article
Bladder cancer has a significant impact on patients, in terms of both morbidity and financial burden. This is especially true for patients with nonmuscle-invasive bladder cancer, who undergo long-term surveillance via cystoscopy and imaging, resulting in significant costs and risks. To address this issue, urinary tumor DNA analysis, or “urinary liquid biopsy,” has emerged as a potential solution to reduce the testing burden and mitigate many of the costs and risks. Over time, urinary tumor DNA analysis has undergone several refinements. However, existing FDA-approved urinary biomarker assays currently lack the sensitivity and specificity to significantly impact clinical decision-making. Subsequent iterations of these technologies have attempted to bridge this gap by improving their diagnostic accuracy, and ultimately, clinical utility. Here, we discuss the current role as well as future directions of urinary tumor DNA analysis for the detection and long-term surveillance of nonmuscle-invasive bladder cancer.
... Urine has been shown by us and others to be a reliable source for cell-free DNA (cfDNA) for cancer screening and monitoring [11][12][13][14][15][16][17][18] . Epigenetic alterations such as increased DNA methylation levels in critical genes can signify early tumorigenesis events presenting an opportunity for early cancer detection 19 . ...
Article
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An optimized hepatocellular carcinoma (HCC)-targeted methylation next generation sequencing assay was developed to discover HCC-associated methylation markers directly from urine for HCC screening. Urine cell-free DNA (ucfDNA) isolated from a discovery cohort of 31 non-HCC and 30 HCC was used for biomarker discovery, identifying 29 genes with differentially methylated regions (DMRs). Methylation-specific qPCR (MSqPCR) assays were developed to verify the selected DMRs corresponding to 8 genes (GRASP, CCND2, HOXA9, BMP4, VIM, EMX1, SFRP1, and ECE). Using archived ucfDNA, methylation of GRASP, HOXA9, BMP4, and ECE1, were found to be significantly different (p < 0.05) between HCC and non-HCC patients. The four markers together with previously reported GSTP1 and RASSF1A markers were assessed as a 6-marker panel in an independent training cohort of 87 non-HCC and 78 HCC using logistic regression modeling. AUROC of 0.908 (95% CI, 0.8656–0.9252) was identified for the 6-marker panel with AFP, which was significantly higher than AFP-alone (AUROC 0.841 (95% CI, 0.778–0.904), p = 0.0026). Applying backward selection method, a 4-marker panel was found to exhibit similar performance to the 6-marker panel with AFP having 80% sensitivity compared to 29.5% by AFP-alone at a specificity of 85%. This study supports the potential use of methylated transrenal ucfDNA for HCC screening.
... There have been multiple techniques that have been utilized to evaluate the liquid biopsy in bladder cancer, including droplet digital polymerase chain reaction (ddPCR), beads, emulsion, amplification, and magnetics (BEAMing), tagged-amplicon deep sequencing (TAm-Seq), urine cancer personalized profiling by deep sequencing (uCAPP-Seq), whole genome bisulfite sequencing (WGBS-Seq), whole exome sequencing (WES), and shallow whole genome sequencing (sWGS) [16][17][18][19][20][21]. ...
Article
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Up to 430,000 cases of bladder cancer are diagnosed each year worldwide. A proposed method for non-invasive monitoring has been to utilize a "liquid biopsy." Liquid biopsy has been proposed as a non-invasive method of testing biomarkers in bodily fluids in order to detect and survey cancer. The liquid biopsy could be utilized to obtain information regarding circulating tumor cells, circulating cell-free tumor DNA, circulating cell-free tumor RNA, and more. It is currently being investigated to help guide adjuvant therapy and improve oncological outcomes. We highlight an array of exciting past and ongoing clinical trials regarding ctDNA and adjuvant therapy in regard to urothelial carcinoma which we believe to be amongst the leaders in the field.
... In many cancers, the persistence of ctDNA following resection or treatment can indicate a higher risk of recurrence, and detection of ctDNA may indicate a more aggressive therapy to optimize survival outcomes [18,26,36,[44][45][46][47][48][49][50][51][52][53][54][55][56]. In addition, ctDNA provides real-time data for monitoring treatment efficacy and detecting drug resistance early, which can be used to establish personalized treatment plans [57][58][59][60][61][62][63][64][65][66]. Recurrence may be less likely if ctDNA is not detected, allowing for consideration of treatment de-escalation, which can help patients avoid unnecessary treatment if they are measurably disease free and unlikely to relapse [28,67]. ...
Article
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Background: Highly sensitive molecular assays have been developed to detect plasma-based circulating tumor DNA (ctDNA), and emerging evidence suggests their clinical utility for monitoring minimal residual disease and recurrent disease, providing prognostic information, and monitoring therapy responses in patients with solid tumors. The Invitae Personalized Cancer Monitoring™ assay uses a patient-specific, tumor-informed variant signature identified through whole exome sequencing to detect ctDNA in peripheral blood of patients with solid tumors. Methods: The assay's tumor whole exome sequencing and ctDNA detection components were analytically validated using 250 unique human specimens and nine commercial reference samples that generated 1349 whole exome sequencing and cell-free DNA (cfDNA)-derived libraries. A comparison of tumor and germline whole exome sequencing was used to identify patient-specific tumor variant signatures and generate patient-specific panels, followed by targeted next-generation sequencing of plasma-derived cfDNA using the patient-specific panels with anchored multiplex polymerase chain reaction chemistry leveraging unique molecular identifiers. Results: Whole exome sequencing resulted in overall sensitivity of 99.8% and specificity of > 99.9%. Patient-specific panels were successfully designed for all 63 samples (100%) with ≥ 20% tumor content and 24 (80%) of 30 samples with ≥ 10% tumor content. Limit of blank studies using 30 histologically normal, formalin-fixed paraffin-embedded specimens resulted in 100% expected panel design failure. The ctDNA detection component demonstrated specificity of > 99.9% and sensitivity of 96.3% for a combination of 10 ng of cfDNA input, 0.008% allele frequency, 50 variants on the patient-specific panels, and a baseline threshold. Limit of detection ranged from 0.008% allele frequency when utilizing 60 ng of cfDNA input with 18-50 variants in the patient-specific panels (> 99.9% sensitivity) with a baseline threshold, to 0.05% allele frequency when using 10 ng of cfDNA input with an 18-variant panel with a monitoring threshold (> 99.9% sensitivity). Conclusions: The Invitae Personalized Cancer Monitoring assay, featuring a flexible patient-specific panel design with 18-50 variants, demonstrated high sensitivity and specificity for detecting ctDNA at variant allele frequencies as low as 0.008%. This assay may support patient prognostic stratification, provide real-time data on therapy responses, and enable early detection of residual/recurrent disease.
... In 570 patients at risk for bladder cancer, UroSEEK alone identified 83% of patients who went on to be diagnosed with bladder cancer, this sensitivity increasing to 95% when combined with urinary cytology [317]. Another recent high-throughput sequencing method for detection of urine tumor, called CAPP-Seq, proved to be not only a promising method of early cancer detection but also for monitoring disease progression or recurrence in patients with urothelial carcinomas [318]. Studies in RCC patients found less ctDNA than other tumour types and limited overlap between the plasma and urine ctDNA content [330]. ...
Article
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Tissue-based biopsy is the present main tool to explore the molecular landscape of cancer, but it also has many limits to be frequently executed, being too invasive with the risk of side effects. These limits and the ability of cancer to constantly evolve its genomic profile, have recently led to the need of a less invasive and more accurate alternative, such as liquid biopsy. By searching Circulating Tumor Cells and residues of their nucleic acids or other tumor products in body fluids, especially in blood, but also in urine, stools and saliva, liquid biopsy is becoming the future of clinical oncology. Despite the current lack of a standardization for its workflows, that makes it hard to be reproduced, liquid biopsy has already obtained promising results for cancer screening, diagnosis, prognosis, and risk of recurrence. Through a more accessible molecular profiling of tumors, it could become easier to identify biomarkers predictive of response to treatment, such as EGFR mutations in non-small cell lung cancer and KRAS mutations in colorectal cancer, or Microsatellite Instability and Mismatch Repair as predictive markers of pembrolizumab response. By monitoring circulating tumor DNA in longitudinal repeated sampling of blood we could also predict Minimal Residual Disease and the risk of recurrence in already radically resected patients. In this review we will discuss about the current knowledge of limitations and strengths of the different forms of liquid biopsies for its inclusion in normal cancer management, with a brief nod to their newest biomarkers and its future implications.
... It can aid in post-treatment surveillance by predicting clinical progression in 92% of the cases. This significantly outperforms the standard diagnostic modalities [73]. ...
Article
Introduction: Liquid biopsies are used for the detection of tumor-specific elements in body fluid. Their application in prognosis and diagnosis of muscle/non-muscle invasive bladder cancer (MIBC/NMIBC) or upper tract urothelial cancer (UTUC) remains poorly known and rarely mentioned in clinical guidelines. Areas covered: Herein, we provide an overview of current data regarding the use of liquid biopsies in urothelial tumors. Expert opinion: Studies that were included analyzed liquid biopsies using the detection of circulating tumor cells (CTCs), deoxyribonucleic acid (DNA), ribonucleic acid (RNA), exosomes or metabolomics. The sensitivity of blood CTC detection in patients with localized cancer was 35% and raised to 50% in patients with metastatic cancer. In NMIBC patients, blood CTC was associated with poor prognosis (time to recurrence and progression), whereas discrepancies were seen in MIBC patients. Circulating plasma DNA presented a superior sensitivity to urine. Moreover, it was a good indicator for diagnosis, follow-up, and oncological outcome. In urine, specific bladder cancer (BC) microRNA had an overall sensitivity of 85% and a specificity of 86% in the diagnosis of urothelial cancer. These results support the growing evidence for the use of liquid biopsies to provide biomarkers for the diagnosis, follow-up or prognosis of urothelial cancer. Further development and understanding on the use of liquid biopsies are needed in order to include it as part of urothelial cancer management.
... Urinary cfDNA was extracted from 15-50 mL of urine after thawing at room temperature (RT) either with the Quick-DNA Urine Kit (Zymo Research, Irvine, CA, USA) as previously described [17] or using a quaternary ammonium anion exchange resin-based Q Sepharose method based on the method published by Dudley et al. [18]. ...
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Methylation sequencing is a promising approach to infer the tissue of origin of cell-free DNA (cfDNA). In this study, a single- and a double-stranded library preparation approach were evaluated with respect to their technical biases when applied on cfDNA from plasma and urine. Additionally, tissue of origin (TOO) proportions were evaluated using two deconvolution methods. Sequencing cfDNA from urine using the double-stranded method resulted in a substantial within-read methylation bias and a lower global methylation (56.0% vs. 75.8%, p ≤ 0.0001) compared to plasma cfDNA, both of which were not observed with the single-stranded approach. Individual CpG site-based TOO deconvolution resulted in a significantly increased proportion of undetermined TOO with the double-stranded method (urine: 32.3% vs. 1.9%; plasma: 5.9% vs. 0.04%; p ≤ 0.0001), but no major differences in proportions of individual cell types. In contrast, fragment-level deconvolution led to multiple cell types, with significantly different TOO proportions between the two methods. This study thus outlines potential limitations of double-stranded library preparation for methylation analysis of cfDNA especially for urinary cfDNA. While the double-stranded method allows jagged end analysis in addition to TOO analysis, it leads to significant methylation bias in urinary cfDNA, which single-stranded methods can overcome.
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Purposes This study aimed to clarify the clinical outcomes of Bacillus Calmette-Guérin (BCG) treatment in patients with urothelial carcinoma (UC) of the prostatic urethra. Methods Between August 2003 and January 2023, 428 patients with non-muscle-invasive UC received BCG treatment (Tokyo strain, 80 mg, ≥ 5 times) in our hospital; 39 had UC of the prostatic urethra. We evaluated the cumulative incidence of intravesical recurrence, progression (muscle-invasive bladder cancer [MIBC] or metastasis), and subsequent radical cystectomy after BCG treatment in patients with UC of the prostatic urethra. Results The median follow-up period was 57 months (interquartile range, 30–85 months). The exact T stage of the patients with UC of the prostatic urethra was carcinoma in situ (CIS) in 29 (27 in the prostatic urethral mucosa and two in the ductal spread), Ta in 7, Ta + CIS in 2, and T1 in 1. All 39 patients had previous or concurrent bladder cancer. Patients with UC of the prostatic urethra experienced significantly higher rates of intravesical recurrence, progression (MIBC or metastasis), and subsequent radical cystectomy than those without UC of the prostatic urethra. In the multivariate analysis, UC of the prostatic urethra was a significant risk factor for progression (hazard ratio 4.06, 95% confidence interval 1.86–8.86, p < 0.001). Conclusions This study reported the largest number of clinical outcomes after BCG treatment in patients with UC of the prostatic urethra. Concomitant UC of the prostatic urethra is a strong predictor of subsequent progression; therefore, early timing of radical cystectomy should be discussed.
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Flexible cystoscopy is the mainstay of bladder cancer detection but is an imperfect test which is resource-intensive and invasive for patients. A focus of bladder cancer research has been to develop non-invasive tests to reliably detect urothelial cancers without the need for cystoscopy. Bladder cancer is unique in that tumor cells are in prolonged contact with a plentiful and easily-collected liquid biopsy, urine; hence, non-invasive alternatives to cystoscopy have been sought for over 30 years. Despite considerable progress in recent years in identifying and commercializing diagnostic urinary biomarkers (some of which rival the sensitivity and specificity of cystoscopy), none are yet being used routinely at the clinical front line as a replacement for cystoscopy, nor are any recommended for this purpose by international guideline committees. It is recognized that there are challenges to overcome, such as false-negative tests due to low rates of shedding by some tumors, false positives caused by hematuria, urothelial field changes or inflammatory conditions, and clinical study design. In this chapter, we outline the relevant clinical settings, the molecular changes associated with bladder cancer that can be detected in urine, the mechanisms of release of these biomolecules into urine, and important considerations for their detection, measurement, and validity. Furthermore, we provide an overview of all classes of diagnostic urinary biomarkers, highlighting a new generation of urine tests that have been enabled by the expansion of our understanding of bladder cancer genomics during the course of the last 10 years. Finally, in order to realize the full potential and clinical impact of these biomarkers and to progress beyond simple descriptions of test accuracy, we encourage investigators to conduct randomized interventional studies to assess how such tests can change clinical pathways for the better. Consequently, there is a realistic expectation that the latest nucleic acid-based tests will be in routine clinical use within 5 years.
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Bladder cancer (BC) is the most common neoplasm of the urinary system and ranks tenth in global cancer incidence. Due to its high recurrence rate and the need for continuous monitoring, it is the cancer with the highest cost per patient. Cystoscopy is the traditional method for its detection and surveillance; however, this is an invasive technique, while non-invasive methods, such as cytology, have a limited sensitivity. For this reason, new non-invasive strategies have emerged, analyzing useful markers for BC detection from urine samples. The identification of tumor markers is essential for early cancer detection and treatment. Urine analysis offers a non-invasive method to identify these markers. Microsatellite instability (MSI) has been proposed as a promising marker for tumor cell detection and guided targeted therapies. Therefore, this review aims to explore the evidence supporting the identification of MSI in exfoliated bladder tumor cells (EBTCs) in the urine, emphasizing its potential as a non-invasive and clinically effective alternative for tumor identification. Furthermore, establishing clinical guidelines is crucial for standardizing its application in oncological screening and validating its clinical utility.
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Until recently, the main diagnostic methods for bladder cancer (BC) are still voided urine cytology and cystoscopy, and many drawbacks persist. In this retrospective study, we evaluated the sensitivity and specificity of the CellDetect assay in the detection of BC with comparison to standard diagnostic methods. Between August 2020 and July 2022, B-ultrasonography or computed tomography (CT) scan was performed for patients with hematuria or irritative voiding symptoms. If no bladder mass was detected, the patient was excluded. A total of 148 patients with bladder mass formed the final study cohort. The patients’ urine samples were measured with CellDetect assay, followed by cystoscopy or diagnostic transurethral resection of bladder tumor. The patients were divided into two groups based on previous history of BC: group P and group R. The analysis included descriptive statistics and percentages. Finally, 115 cases had a positive CellDetect result, with 68 cases in group P and 47 in group R, respectively. And 134 cases revealed malignant tumor pathologically. The overall sensitivity and specificity for all patients were 82.1% and 64.2%, respectively. Concerning the subgroups, the respective sensitivity and specificity were: in group P- 81.0% and 50.0%; and in group R- 85.2% and 83.3%, respectively. In conclusion, CellDetect assay demonstrated significant performance for diagnosis of BC: it can identify BC patients at early stage with significant diagnostic performance and good reliability. This assay might develop novel methods and ideas for future clinical practice.
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Background cfDNA fragmentomics-based liquid biopsy is a potential option for noninvasive bladder cancer (BLCA) detection that remains an unmet clinical need. Methods We assessed the diagnostic performance of cfDNA hotspot-driven machine-learning models in a cohort of 55 BLCA patients, 51 subjects with benign conditions, and 11 healthy volunteers. We further performed functional bioinformatics analysis for biological understanding and interpretation of the tool’s diagnostic capability. Results Urinary cfDNA hotspots-based machine-learning model enabled effective BLCA detection, achieving high performance (area under curve 0.96) and an 87% sensitivity at 100% specificity. It outperformed models using other cfDNA-derived features. In stage-stratified analysis, the sensitivity at 100% specificity of the urine hotspots-based model was 71% and 92% for early (low-grade Ta and T1) and advanced (high-grade T1 and muscle-invasive) disease, respectively. Biologically, cfDNA hotspots effectively retrieved regulatory elements and were correlated with the cell of origin. Urine cfDNA hotspots specifically captured BLCA-related molecular features, including key functional pathways, chromosome loci associated with BLCA risk as identified in genome-wide association studies, or presenting frequent somatic alterations in BLCA tumors, and the transcription factor regulatory landscape. Conclusions Our findings support the applicability of urine cfDNA fragmentation hotspots for noninvasive BLCA diagnosis, as well as for future translational study regarding its molecular pathology and heterogeneity.
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Simple Summary Circulating tumor DNA (ctDNA) is a non-invasive method of identifying and monitoring genitourinary cancers, including prostate, bladder, and renal cell carcinoma, via blood or urine samples. CtDNA introduces a potential method for cancer screening. If detected, ctDNA may reveal genetic alterations that have prognostic value. As treatment options for genitourinary cancers progress towards accounting for tumor genetic profiles, ctDNA may predict which patients have improved responses to therapeutic targets. CtDNA may play an important role in surveillance after tumor resection and may be used to reveal mechanisms of treatment resistance. The clinical utility of ctDNA has yet to be established. Significantly more research is needed to understand the utility ctDNA has in clinical practice. Abstract CtDNA is emerging as a non-invasive clinical detection method for several cancers, including genitourinary (GU) cancers such as prostate cancer, bladder cancer, and renal cell carcinoma (RCC). CtDNA assays have shown promise in early detection of GU cancers, providing prognostic information, assessing real-time treatment response, and detecting residual disease and relapse. The ease of obtaining a “liquid biopsy” from blood or urine in GU cancers enhances its potential to be used as a biomarker. Interrogating these “liquid biopsies” for ctDNA can then be used to detect common cancer mutations, novel genomic alterations, or epigenetic modifications. CtDNA has undergone investigation in numerous clinical trials, which could address clinical needs in GU cancers, for instance, earlier detection in RCC, therapeutic response prediction in castration-resistant prostate cancer, and monitoring for recurrence in bladder cancers. The utilization of liquid biopsy for ctDNA analysis provides a promising method of advancing precision medicine within the field of GU cancers.
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Bladder cancer (BC) is a prevalent urological tumor with high recurrence rates, requiring long‐term monitoring. Although cystoscopy is the primary diagnostic method, its invasiveness and cost hinder routine screening and follow‐up. This study aimed to develop a novel diagnostic tool utilizing newly developed on‐chip heating dPCR platform, which features integrated and rapid temperature control capabilities, for non‐invasive BC detection. The dPCR platform is improved by integrating a multi‐color detection system, enabling precise quantification of mutant allelic fraction (MAF) of TERT promoter mutations with a limit of detection (LOD) of 0.29%. Diagnostic performance is enhanced by integrating the NRN1 methylation biomarker and employing machine learning to optimize biomarker weighting. Testing the model on urine samples from controls (n = 35) and BC patients (n = 41) yielded a sensitivity of 0.92, specificity of 0.94, and an AUC of 0.98, surpassing conventional cytology in sensitivity while maintaining comparable specificity. Furthermore, the model effectively differentiated between normal controls and different stages, achieving accuracies of 0.92, 0.71, and 0.79 for NC, stage I, and stage II+ respectively. These findings suggest the proposed dPCR assays could serve as a sensitive and non‐invasive approach for BC detection in clinical practice.
Article
PURPOSE There is significant interest in identifying complete responders to neoadjuvant chemotherapy (NAC) before radical cystectomy (RC) to potentially avoid removal of a pathologically benign bladder. However, clinical restaging after NAC is highly inaccurate. The objective of this study was to develop a next-generation sequencing–based molecular assay using urine to enhance clinical staging of patients with bladder cancer. METHODS Urine samples from 20 and 44 patients with bladder cancer undergoing RC were prospectively collected for retrospective analysis for molecular correlate analysis from two clinical trials, respectively. The first cohort was used to benchmark the assay, and the second was used to determine the performance characteristics of the test as it correlates to responder status as measured by pathologic examination. RESULTS First, to benchmark the assay, known mutations identified in the tissue (M T ) of patients from the Accelerated Methotrexate, Vinblastine, Doxorubicin, Cisplatin trial (ClinicalTrials.gov identifier: NCT01611662 , n = 16) and a cohort from University of California-San Francisco (n = 4) were cross referenced against mutation profiles from urine (M U ). We then determined the correlation between M U persistence and residual disease in pre-RC urine samples from a second prospective clinical trial (The pT0 trial; ClinicalTrials.gov identifier: NCT02968732 ). Residual M U status correlated strongly with residual disease status (pT0 trial; n = 44; P = .0092) when M U from urine supernatant and urine pellet were assessed separately and analyzed in tandem. The sensitivity, specificity, PPV, and NPV were 91%, 50%, 86%, and 63% respectively, with an overall accuracy of 82% for this second cohort. CONCLUSION M U are representative of M T and thus can be used to enhance clinical staging of urothelial carcinoma. Urine biopsy may be used as a reliable tool that can be further developed to identify complete response to NAC in anticipation of safe RC avoidance.
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Purpose of review This review sought to define the emerging roles of urinary tumor DNA (utDNA) for diagnosis, monitoring, and treatment of bladder cancer. Building from early landmark studies the focus is on recent studies, highlighting how utDNA could aid personalized care. Recent findings Recent research underscores the potential for utDNA to be the premiere biomarker in bladder cancer due to the constant interface between urine and tumor. Many studies find utDNA to be more informative than other biomarkers in bladder cancer, especially in early stages of disease. Points of emphasis include superior sensitivity over traditional urine cytology, broad genomic and epigenetic insights, and the potential for non-invasive, real-time analysis of tumor biology. Summary utDNA shows promise for improving all phases of bladder cancer care, paving the way for personalized treatment strategies. Building from current research, future comprehensive clinical trials will validate utDNA's clinical utility, potentially revolutionizing bladder cancer management.
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The standard treatment paradigm for muscle invasive bladder cancer has been neoadjuvant cisplatin-based chemotherapy followed by radical cystectomy. However, efforts are ongoing to personalize treatment by incorporating biomarkers to better guide treatment selection. In addition, bladder preservation strategies are aimed at avoiding cystectomy in well-selected patients. Similarly, in the metastatic urothelial cancer space, the standard frontline treatment option of platinum-based chemotherapy has changed with the availability of data from EV-302 trial, making the combination of enfortumab vedotin (EV) and pembrolizumab the preferred first-line treatment option. Here, we examine the optimization of treatment intensity and sequencing, focusing on the challenges and opportunities associated with EV/pembrolizumab therapy, including managing toxicities and exploring alternative dosing approaches. Together, these articles provide a comprehensive overview of contemporary strategies in bladder cancer management, highlighting the importance of individualized treatment approaches, ongoing research, and multidisciplinary collaboration to improve patient outcomes in this complex disease landscape.
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Bladder cancer (BC) represents a significant global health challenge, contributing to high mortality rates. The progression of non-muscle invasive bladder cancer to muscle-invasive bladder cancer is the critical turning point in the disease trajectory, necessitating effective early detection methods. While practical, conventional diagnostic tools, cystoscopy, and cytology, are costly and painful, emerging molecular markers offer promise in enhancing diagnostic precision by bolstering sensitivity and specificity. This review explores the potential of molecular biomarkers, specifically on cell-free DNA (cfDNA) alterations, to detect, prognosticate, predict, and monitor BC. We examined the specificity and sensitivity of different biomarkers, emphasizing mutations and epigenetic changes in cfDNA as an important indicator. A comprehensive literature search was conducted to identify relevant studies on bladder cancer detection. The selected biomarkers encompass cfDNA, diverse RNA species (mRNA, miRNA, lncRNA), exosomal biomarkers, and proteins in bodily fluids. The review highlights the potential utility of cfDNA and other molecular markers in revolutionizing BC diagnostics. It explores their diagnostic accuracy, the extent of specificity and sensitivity, and their role in predicting disease progression. Novel and refined biomarker offers promising routes for early detection, prognosis, and monitoring of BC. Integration in clinical practice can subsequently reduce the disease burden and enhance patient outcomes. Further research is needed to fully harness the diagnostic potential for the future.
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T-cell lymphoma is a highly invasive tumor with significant heterogeneity. Invasive tissue biopsy is the gold standard for acquiring molecular data and categorizing lymphoma patients into genetic subtypes. However, surgical intervention is unfeasible for patients who are critically ill, have unresectable tumors, or demonstrate low compliance, making tissue biopsies inaccessible to these patients. A critical need for a minimally invasive approach in T-cell lymphoma is evident, particularly in the areas of early diagnosis, prognostic monitoring, treatment response, and drug resistance. Therefore, the clinical application of liquid biopsy techniques has gained significant attention in T-cell lymphoma. Moreover, liquid biopsy requires fewer samples, exhibits good reproducibility, and enables real-time monitoring at molecular levels, thereby facilitating personalized health care. In this review, we provide a comprehensive overview of the current liquid biopsy biomarkers used for T-cell lymphoma, focusing on circulating cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), Epstein-Barr virus (EBV) DNA, antibodies, and cytokines. Additionally, we discuss their clinical application, detection methodologies, ongoing clinical trials, and the challenges faced in the field of liquid biopsy.
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This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 26 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Circulating tumor DNA (ctDNA) has been widely used as a minimally invasive biomarker in clinical routine. However, a number of factors such as panel design, sample quality, patients' disease stages are known to influence ctDNA detection sensitivity. In this study, we systematically evaluated common factors associated with the variability of ctDNA detection in plasma and investigated ctDNA abundance in bronchoalveolar lavage (BAL). Whole exome profiling was conducted on 61 tumor tissue samples to identify tumor‐specific variants, which were then used to design personalized assay MarRyDa® for ctDNA detection. DNA extracted from BAL fluid and plasma were genotyped using MarRyDa® platform. Our analysis showed that histological subtypes and disease stages had significant differences in ctDNA detection rate. Furthermore, we found that DNA purified from BAL supernatants contains the highest levels of ctDNA compared with BAL precipitates and plasma; therefore, utilizing BAL supernatants for tumor detection might provide additional benefits. Finally, we demonstrated that tumor cellularity played significant roles in the design of personalized ctDNA panel which eventually impacts ctDNA detection sensitivity. We suggest setting a flexible criteria for sample quality control and utilization of BAL might benefit more patients in clinics.
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Bladder cancer is a common urological cancer with a high recurrence rate that requires long‐term follow‐up, and early detection positively affects prognosis. To date, the initial diagnosis and follow‐up for bladder cancer rely on cystoscopy, which is an invasive and expensive procedure. Therefore, urinary markers for the detection of bladder cancer have attracted research attention for decades to reduce unnecessary cystoscopies. Urine, which is in continuous contact with bladder cancer, is considered a suitable fluid for providing tumor information. Urinary cytology is the only widely used urinary marker in clinical practice; however, it has poor sensitivity for low‐grade tumors; indicating the need for novel urinary markers. Considerable research has been conducted on this topic over the years, resulting in a complex landscape with a wide range of urinary markers, including protein‐, exfoliated cell‐, RNA‐, DNA‐, and extracellular vesicle‐based markers. Although some of these markers have been approved by the U.S. Food and Drug Administration and are commercially available, their use in clinical practice is limited. To facilitate clinical application, potential urinary markers must withstand prospective clinical trials and be easy for patients and clinicians to understand and utilize in a clinical context. This review provides a comprehensive overview of currently available and recently reported promising urinary markers for bladder cancer. Additionally, the challenges and the prospects of these urinary markers for clinical implementation in bladder cancer treatment were discussed.
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Molecular residual disease (MRD), detected by circulating tumor DNA (ctDNA) can be involved in the entire process of solid tumor management, including recurrence prediction, efficacy evaluation, and risk stratification. Currently, the detection technologies are divided into two main categories, as follows: tumor-agnostic and tumor informed. Tumor-informed assay obtains mutation information by sequencing tumor tissue samples before blood MRD monitoring, followed by formulation of a personalized MRD panel. Tumor-agnostic assays are carried out using a fixed panel without the mutation information from primary tumor tissue. The choice of testing strategy may depend on the level of evidence from ongoing randomized clinical trials, investigator preference, cost-effectiveness, patient economics, and availability of tumor tissue. The review describes the difference between tumor informed and tumor agnostic detection. In addition, the clinical application of ctDNA MRD in solid tumors was introduced, with emphasis on lung cancer, colorectal cancer, Urinary system cancer, and breast cancer.
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In conjunction with our understanding of the disease, the role of pathologists has evolved from a pure morphologic assessment to a more active participation in triaging specimens for a host of ancillary studies and incorporating these results into the pathology report in order to refine diagnoses and/or guide therapeutic decisions. As molecular characterization of different types of cancer becomes standard of care, pathologists will continue to play a pivotal role in early diagnosis, monitoring of tumor response, and disease progression of cancer patients. The powerful combination of advanced molecular diagnostics and the minimally invasive nature of cytology specimens that define molecular cytopathology, amplifies our ability to do more with less and propels this new field to the forefront of personalized medicine. Given that many patients present with advanced-stage cancers in whom the diagnosis is made only based on cytology, optimizing and validating cytology specimens for molecular testing is critical. We review in this chapter, the range of cytology specimens and the different ways in which they can be utilized for various molecular tests.
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Minimal residual disease (MRD) is termed as the small numbers of remnant tumor cells in a subset of patients with tumors. Liquid biopsy is increasingly used for the detection of MRD, illustrating the potential of MRD detection to provide more accurate management for cancer patients. As new techniques and algorithms have enhanced the performance of MRD detection, the approach is becoming more widely and routinely used to predict the prognosis and monitor the relapse of cancer patients. In fact, MRD detection has been shown to achieve better performance than imaging methods. On this basis, rigorous investigation of MRD detection as an integral method for guiding clinical treatment has made important advances. This review summarizes the development of MRD biomarkers, techniques, and strategies for the detection of cancer, and emphasizes the application of MRD detection in solid tumors, particularly for the guidance of clinical treatment.
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Background: There is limited ability to accurately diagnose and clinically stage patients with upper tract urothelial carcinoma (UTUC). The most easily available and widely used urinary biomarker is urine cytology, which evaluates cellular material yet lacks sensitivity. We sought to assess the feasibility of performing next-generation sequencing (NGS) on urine cytology specimens from patients with UTUC and evaluate the genomic concordance with tissue from primary tumor. Methods: In this retrospective study, we identified 48 patients with a diagnosis of UTUC treated at Memorial Sloan Kettering Cancer Center (MSK) between 2019 and 2022 who had banked or fresh urine samples. A convenience cohort of matching, previously sequenced tumor tissue was used when available. Urine specimens were processed and the residual material, including precipitated cell-free DNA, was sequenced using our tumor-naïve, targeted exome sequencing platform that evaluates 505 cancer-related genes (MSK-IMPACT). The primary outcome was at least 1 detectable mutation in urinary cytology specimens. The secondary outcome was concordance to matched tissue (using ANOVA or Chi-Square, as indicated). Results: Genomic sequencing was successful for 45 (94%) of the 48 urinary cytology patient samples. The most common mutations identified were TERT (62.2%), KMT2D (46.7%), and FGFR3 (35.6%). All patients with negative urine cytology and low-grade tissue had successful cytology sequencing. Thirty-six of the 45 patients had matching tumor tissue available; concordance to matched tissue was 55% overall (131 of the total 238 oncogenic or likely oncogenic somatic mutations identified). However, in 94.4% (n = 34/36) of patients, the cytology had at least 1 shared mutation with tissue. Eleven (30.6%) patients had 100% concordance between cytology and tissue. Conclusions: Sequencing urinary specimens from selective UTUC cytology is feasible in nearly all patients with UTUC. Prospective studies are underway to investigate a clinical role for this promising technology.
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Current non-invasive approaches for detection of urothelial cancers are suboptimal. We developed a test to detect urothelial neoplasms using DNA recovered from cells shed into urine. UroSEEK incorporates massive parallel sequencing assays for mutations in 11 genes and copy number changes on 39 chromosome arms. In 570 patients at risk for bladder cancer (BC), UroSEEK was positive in 83% of those who developed BC. Combined with cytology, UroSEEK detected 95% of patients who developed BC. Of 56 patients with upper tract urothelial cancer, 75% tested positive by UroSEEK, including 79% of those with non-invasive tumors. UroSEEK detected genetic abnormalities in 68% of urines obtained from BC patients under surveillance who demonstrated clinical evidence of recurrence. The advantages of UroSEEK over cytology were evident in low-grade BCs; UroSEEK detected 67% of cases whereas cytology detected none. These results establish the foundation for a new non-invasive approach for detection of urothelial cancer.
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This selection from the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Bladder Cancer focuses on systemic therapy for muscle-invasive urothelial bladder cancer, as substantial revisions were made in the 2017 updates, such as new recommendations for nivolumab, pembrolizumab, at-ezolizumab, durvalumab, and avelumab. The complete version of the NCCN Guidelines for Bladder Cancer addresses additional aspects of the management of bladder cancer, including non-muscle-invasive urothelial bladder cancer and nonurothelial histologies, as well as staging, evaluation, and follow-up. © JNCCN - Journal of the National Comprehensive Cancer Network.
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Muscle Invasive Bladder Cancer (MIBC) has a poor prognosis. Whilst patients can achieve a 6% improvement in overall survival with Neo-Adjuvant Chemotherapy (NAC), many do not respond. Body fluid mutant DNA (mutDNA) may allow non-invasive identification of treatment failure. We collected 248 liquid biopsy samples including plasma, cell pellet (UCP) and supernatant (USN) from spun urine, from 17 patients undergoing NAC. We assessed single nucleotide variants and copy number alterations in mutDNA using Tagged-Amplicon- and shallow Whole Genome- Sequencing. MutDNA was detected in 35.3%, 47.1% and 52.9% of pre-NAC plasma, UCP and USN samples respectively, and urine samples contained higher levels of mutDNA (p = <0.001). Longitudinal mutDNA demonstrated tumour evolution under the selective pressure of NAC e.g. in one case, urine analysis tracked two distinct clones with contrasting treatment sensitivity. Of note, persistence of mutDNA detection during NAC predicted disease recurrence (p = 0.003), emphasising its potential as an early biomarker for chemotherapy response.
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Background Some applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed to profile the sequencing quality, but few of them can quantify or correct the sequencing errors. This unmet requirement motivated us to develop AfterQC, a tool with functions to profile sequencing errors and correct most of them, plus highly automated quality control and data filtering features. Different from most tools, AfterQC analyses the overlapping of paired sequences for pair-end sequencing data. Based on overlapping analysis, AfterQC can detect and cut adapters, and furthermore it gives a novel function to correct wrong bases in the overlapping regions. Another new feature is to detect and visualise sequencing bubbles, which can be commonly found on the flowcell lanes and may raise sequencing errors. Besides normal per cycle quality and base content plotting, AfterQC also provides features like polyX (a long sub-sequence of a same base X) filtering, automatic trimming and K-MER based strand bias profiling. ResultsFor each single or pair of FastQ files, AfterQC filters out bad reads, detects and eliminates sequencer’s bubble effects, trims reads at front and tail, detects the sequencing errors and corrects part of them, and finally outputs clean data and generates HTML reports with interactive figures. AfterQC can run in batch mode with multiprocess support, it can run with a single FastQ file, a single pair of FastQ files (for pair-end sequencing), or a folder for all included FastQ files to be processed automatically. Based on overlapping analysis, AfterQC can estimate the sequencing error rate and profile the error transform distribution. The results of our error profiling tests show that the error distribution is highly platform dependent. Conclusion Much more than just another new quality control (QC) tool, AfterQC is able to perform quality control, data filtering, error profiling and base correction automatically. Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations. While providing rich configurable options, AfterQC can detect and set all the options automatically and require no argument in most cases.
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Background: Highly sensitive and specific urine-based tests to detect either primary or recurrent bladder cancer have proved elusive to date. Our ever increasing knowledge of the genomic aberrations in bladder cancer should enable the development of such tests based on urinary DNA. Methods: DNA was extracted from urine cell pellets and PCR used to amplify the regions of the TERT promoter and coding regions of FGFR3, PIK3CA, TP53, HRAS, KDM6A and RXRA which are frequently mutated in bladder cancer. The PCR products were barcoded, pooled and paired-end 2 x 250 bp sequencing performed on an Illumina MiSeq. Urinary DNA was analysed from 20 non-cancer controls, 120 primary bladder cancer patients (41 pTa, 40 pT1, 39 pT2+) and 91 bladder cancer patients post-TURBT (89 cancer-free). Results: Despite the small quantities of DNA extracted from some urine cell pellets, 96% of the samples yielded mean read depths >500. Analysing only previously reported point mutations, TERT mutations were found in 55% of patients with bladder cancer (independent of stage), FGFR3 mutations in 30% of patients with bladder cancer, PIK3CA in 14% and TP53 mutations in 12% of patients with bladder cancer. Overall, these previously reported bladder cancer mutations were detected in 86 out of 122 bladder cancer patients (70% sensitivity) and in only 3 out of 109 patients with no detectable bladder cancer (97% specificity). Conclusion: This simple, cost-effective approach could be used for the non-invasive surveillance of patients with non-muscle-invasive bladder cancers harbouring these mutations. The method has a low DNA input requirement and can detect low levels of mutant DNA in a large excess of normal DNA. These genes represent a minimal biomarker panel to which extra markers could be added to develop a highly sensitive diagnostic test for bladder cancer.
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Urothelial bladder cancers (UBCs) have heterogeneous clinical characteristics that are mirrored in their diverse genomic profiles. Genomic profiling of UBCs has the potential to benefit routine clinical practice by providing prognostic utility above and beyond conventional clinicopathological factors, and allowing for prediction and surveillance of treatment responses. Urinary DNAs representative of the tumour genome provide a promising resource as a liquid biopsy for non-invasive genomic profiling of UBCs. We compared the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine with matched diagnostic formalin-fixed paraffin-embedded tumour DNAs for 23 well-characterised UBC patients. Our data show urinary DNAs to be highly representative of patient tumours, allowing for detection of recurrent clinically actionable genomic aberrations. Furthermore, a greater aberrant load (indicative of tumour genome) was observed in cfDNA over cellular DNA (P<0.001), resulting in a higher analytical sensitivity for detection of clinically actionable genomic aberrations (P<0.04) when using cfDNA. Thus, cfDNA extracted from the urine of UBC patients has a higher tumour genome burden and allows greater detection of key genomic biomarkers (90%) than cellular DNA from urine (61%) and provides a promising resource for robust whole-genome tumour profiling of UBC with potential to influence clinical decisions without invasive patient interventions.European Journal of Human Genetics advance online publication, 13 January 2016; doi:10.1038/ejhg.2015.281.
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Cancer primarily develops because of somatic alterations in the genome. Advances in sequencing have enabled large-scale sequencing studies across many tumor types, emphasizing the discovery of alterations in protein-coding genes. However, the protein-coding exome comprises less than 2% of the human genome. Here we analyze the complete genome sequences of 863 human tumors from The Cancer Genome Atlas and other sources to systematically identify noncoding regions that are recurrently mutated in cancer. We use new frequency- and sequence-based approaches to comprehensively scan the genome for noncoding mutations with potential regulatory impact. These methods identify recurrent mutations in regulatory elements upstream of PLEKHS1, WDR74 and SDHD, as well as previously identified mutations in the TERT promoter. SDHD promoter mutations are frequent in melanoma and are associated with reduced gene expression and poor prognosis. The non-protein-coding cancer genome remains widely unexplored, and our findings represent a step toward targeting the entire genome for clinical purposes.
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Unlabelled: Cisplatin-based chemotherapy is the standard of care for patients with muscle-invasive urothelial carcinoma. Pathologic downstaging to pT0/pTis after neoadjuvant cisplatin-based chemotherapy is associated with improved survival, although molecular determinants of cisplatin response are incompletely understood. We performed whole-exome sequencing on pretreatment tumor and germline DNA from 50 patients with muscle-invasive urothelial carcinoma who received neoadjuvant cisplatin-based chemotherapy followed by cystectomy (25 pT0/pTis "responders," 25 pT2+ "nonresponders") to identify somatic mutations that occurred preferentially in responders. ERCC2, a nucleotide excision repair gene, was the only significantly mutated gene enriched in the cisplatin responders compared with nonresponders (q < 0.01). Expression of representative ERCC2 mutants in an ERCC2-deficient cell line failed to rescue cisplatin and UV sensitivity compared with wild-type ERCC2. The lack of normal ERCC2 function may contribute to cisplatin sensitivity in urothelial cancer, and somatic ERCC2 mutation status may inform cisplatin-containing regimen usage in muscle-invasive urothelial carcinoma. Significance: Somatic ERCC2 mutations correlate with complete response to cisplatin-based chemosensitivity in muscle-invasive urothelial carcinoma, and clinically identified mutations lead to cisplatin sensitivity in vitro. Nucleotide excision repair pathway defects may drive exceptional response to conventional chemotherapy.
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Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents have been approved for treatment of the disease. As part of The Cancer Genome Atlas project, we report here an integrated analysis of 131 urothelial carcinomas to provide a comprehensive landscape of molecular alterations. There were statistically significant recurrent mutations in 32 genes, including multiple genes involved in cell-cycle regulation, chromatin regulation, and kinase signalling pathways, as well as 9 genes not previously reported as significantly mutated in any cancer. RNA sequencing revealed four expression subtypes, two of which (papillary-like and basal/squamous-like) were also evident in microRNA sequencing and protein data. Whole-genome and RNA sequencing identified recurrent in-frame activating FGFR3-TACC3 fusions and expression or integration of several viruses (including HPV16) that are associated with gene inactivation. Our analyses identified potential therapeutic targets in 69% of the tumours, including 42% with targets in the phosphatidylinositol-3-OH kinase/AKT/mTOR pathway and 45% with targets (including ERBB2) in the RTK/MAPK pathway. Chromatin regulatory genes were more frequently mutated in urothelial carcinoma than in any other common cancer studied so far, indicating the future possibility of targeted therapy for chromatin abnormalities.
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Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive assessment of cancer burden, but existing ctDNA detection methods have insufficient sensitivity or patient coverage for broad clinical applicability. Here we introduce cancer personalized profiling by deep sequencing (CAPP-Seq), an economical and ultrasensitive method for quantifying ctDNA. We implemented CAPP-Seq for non-small-cell lung cancer (NSCLC) with a design covering multiple classes of somatic alterations that identified mutations in >95% of tumors. We detected ctDNA in 100% of patients with stage II-IV NSCLC and in 50% of patients with stage I, with 96% specificity for mutant allele fractions down to ∼0.02%. Levels of ctDNA were highly correlated with tumor volume and distinguished between residual disease and treatment-related imaging changes, and measurement of ctDNA levels allowed for earlier response assessment than radiographic approaches. Finally, we evaluated biopsy-free tumor screening and genotyping with CAPP-Seq. We envision that CAPP-Seq could be routinely applied clinically to detect and monitor diverse malignancies, thus facilitating personalized cancer therapy.
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PURPOSEWe sought to define the prevalence and co-occurrence of actionable genomic alterations in patients with high-grade bladder cancer to serve as a platform for therapeutic drug discovery. PATIENTS AND METHODS An integrative analysis of 97 high-grade bladder tumors was conducted to identify actionable drug targets, which are defined as genomic alterations that have been clinically validated in another cancer type (eg, BRAF mutation) or alterations for which a selective inhibitor of the target or pathway is under clinical investigation. DNA copy number alterations (CNAs) were defined by using array comparative genomic hybridization. Mutation profiling was performed by using both mass spectroscopy-based genotyping and Sanger sequencing.ResultsSixty-one percent of tumors harbored potentially actionable genomic alterations. A core pathway analysis of the integrated data set revealed a nonoverlapping pattern of mutations in the RTK-RAS-RAF and phosphoinositide 3-kinase/AKT/mammalian target of rapamycin pathways and regulators of G1-S cell cycle progression. Unsupervised clustering of CNAs defined two distinct classes of bladder tumors that differed in the degree of their CNA burden. Integration of mutation and copy number analyses revealed that mutations in TP53 and RB1 were significantly more common in tumors with a high CNA burden (P < .001 and P < .003, respectively). CONCLUSION High-grade bladder cancer possesses substantial genomic heterogeneity. The majority of tumors harbor potentially tractable genomic alterations that may predict for response to target-selective agents. Given the genomic diversity of bladder cancers, optimal development of target-specific agents will require pretreatment genomic characterization.
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Fragments of DNA from cells dying throughout the body are detectable in urine (transrenal DNA, or Tr-DNA). Our goal was the optimization of Tr-DNA isolation and detection techniques, using as a model the analysis of fetal DNA in maternal urine. We isolated urinary DNA using a traditional silica-based method and using a new technique based on adsorption of cell-free nucleic acids on Q-Sepharose resin. The presence of Y chromosome-specific SRY (sex-determining region Y) sequences in urine of pregnant women was detected by conventional and real-time PCR using primers/probe sets designed for 25-, 39-, 65-, and 88-bp PCR targets. Method of DNA isolation and PCR target size affected fetal Tr-DNA detection. Assay diagnostic sensitivity increases as the PCR target is shortened. Shorter DNA fragments (50-150 bp) could be isolated by Q-resin-based technique, which also facilitated fetal Tr-DNA analysis. Using DNA isolated by Q-resin-based method and an "ultrashort" DNA target, we successfully detected SRY sequences in 78 of 82 urine samples from women pregnant with male fetuses (positive predictive value 87.6%). Eleven of 91 urine samples from women pregnant with female fetuses produced SRY false-positive results (negative predictive value 95.2%). Single-copy fetal DNA sequences can be successfully detected in the urine of pregnant women when adequate methods for DNA isolation and analysis are applied. Strong precautions against sample contamination with male cells and DNA are necessary to avoid false-positive results.
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We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.
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Identifying molecular residual disease (MRD) after treatment of localized lung cancer could facilitate early intervention and personalization of adjuvant therapies. Here, we apply cancer personalized profiling by deep sequencing (CAPP-seq) circulating tumor DNA (ctDNA) analysis to 255 samples from 40 patients treated with curative intent for stage I–III lung cancer and 54 healthy adults. In 94% of evaluable patients experiencing recurrence, ctDNA was detectable in the first posttreatment blood sample, indicating reliable identification of MRD. Posttreatment ctDNA detection preceded radiographic progression in 72% of patients by a median of 5.2 months, and 53% of patients harbored ctDNA mutation profiles associated with favorable responses to tyrosine kinase inhibitors or immune checkpoint blockade. Collectively, these results indicate that ctDNA MRD in patients with lung cancer can be accurately detected using CAPP-seq and may allow personalized adjuvant treatment while disease burden is lowest. Significance: This study shows that ctDNA analysis can robustly identify posttreatment MRD in patients with localized lung cancer, identifying residual/recurrent disease earlier than standard-of-care radiologic imaging, and thus could facilitate personalized adjuvant treatment at early time points when disease burden is lowest. Cancer Discov; 7(12); 1394–403. ©2017 AACR. See related commentary by Comino-Mendez and Turner, p. 1368. This article is highlighted in the In This Issue feature, p. 1355
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Detection of circulating tumor DNA (ctDNA) after resection of stage II colon cancer may identify patients at the highest risk of recurrence and help inform adjuvant treatment decisions. We used massively parallel sequencing-based assays to evaluate the ability of ctDNA to detect minimal residual disease in 1046 plasma samples from a prospective cohort of 230 patients with resected stage II colon cancer. In patients not treated with adjuvant chemotherapy, ctDNA was detected postoperatively in 14 of 178 (7.9%) patients, 11 (79%) of whom had recurred at a median follow-up of 27 months; recurrence occurred in only 16 (9.8 %) of 164 patients with negative ctDNA [hazard ratio (HR), 18; 95% confidence interval (CI), 7.9 to 40; P < 0.001]. In patients treated with chemotherapy, the presence of ctDNA after completion of chemotherapy was also associated with an inferior recurrence-free survival (HR, 11; 95% CI, 1.8 to 68; P = 0.001). ctDNA detection after stage II colon cancer resection provides direct evidence of residual disease and identifies patients at very high risk of recurrence.
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High-throughput sequencing of circulating tumor DNA (ctDNA) promises to facilitate personalized cancer therapy. However, low quantities of cell-free DNA (cfDNA) in the blood and sequencing artifacts currently limit analytical sensitivity. To overcome these limitations, we introduce an approach for integrated digital error suppression (iDES). Our method combines in silico elimination of highly stereotypical background artifacts with a molecular barcoding strategy for the efficient recovery of cfDNA molecules. Individually, these two methods each improve the sensitivity of cancer personalized profiling by deep sequencing (CAPP-Seq) by about threefold, and synergize when combined to yield ∼15-fold improvements. As a result, iDES-enhanced CAPP-Seq facilitates noninvasive variant detection across hundreds of kilobases. Applied to non-small cell lung cancer (NSCLC) patients, our method enabled biopsy-free profiling of EGFR kinase domain mutations with 92% sensitivity and >99.99% specificity at the variant level, and with 90% sensitivity and 96% specificity at the patient level. In addition, our approach allowed monitoring of NSCLC ctDNA down to 4 in 10(5) cfDNA molecules. We anticipate that iDES will aid the noninvasive genotyping and detection of ctDNA in research and clinical settings.
Article
Background: At least half of the patients diagnosed with non-muscle-invasive bladder cancer (NMIBC) experience recurrence and approximately 15% will develop progression to muscle invasive or metastatic disease. Biomarkers for disease surveillance are urgently needed. Objective: Development of assays for surveillance using genomic variants in cell-free tumour DNA from plasma and urine. Design, setting, and participants: Retrospective pilot study of 377 samples from 12 patients with recurrent or progressive/metastatic disease. Three next-generation sequencing methods were applied and somatic variants in DNA from tumour, plasma, and urine were subsequently monitored by personalised assays using droplet digital polymerase chain reaction (ddPCR). Samples were collected from 1994 to 2015, with up to 20 yr of follow-up. Outcome measurements and statistical analysis: Progression to muscle-invasive or metastatic bladder cancer; t test for ddPCR data. Results and limitations: We developed from one to six personalised assays per patient. Patients with progressive disease showed significantly higher levels of tumour DNA in plasma and urine before disease progression, compared with patients with recurrent disease (p=0.032 and 1.3×10(-6), respectively). Interestingly, tumour DNA was detected in plasma and urine in patients with noninvasive disease, being no longer detectable in disease-free patients. A significant level of heterogeneity was observed for each patient; this could be due to tumour heterogeneity or assay performance. Conclusions: Cell-free tumour DNA can be detected in plasma and urine, even in patients with noninvasive disease, with high levels of tumour DNA detectable before progression, especially in urine samples. Personalised assays of genomic variants may be useful for disease monitoring. Patient summary: Tumour DNA can be detected in blood and urine in early and advanced stages of bladder cancer. Measurement of these highly tumour-specific biomarkers may represent a novel diagnostic tool to indicate the presence of residual disease or to discover aggressive forms of bladder cancer early in the disease course.
Article
Background: Urinary biomarkers may be a useful alternative or adjunct to cystoscopy for diagnosis of bladder cancer. Purpose: To systematically review the evidence on the accuracy of urinary biomarkers for diagnosis of bladder cancer in adults who have signs or symptoms of the disease or are undergoing surveillance for recurrent disease. Data sources: Ovid MEDLINE (January 1990 through June 2015), Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and reference lists. Study selection: 57 studies that evaluated the diagnostic accuracy of quantitative or qualitative nuclear matrix protein 22 (NMP22), qualitative or quantitative bladder tumor antigen (BTA), fluorescent in situ hybridization (FISH), fluorescent immunohistochemistry (ImmunoCyt [Scimedx]), and Cxbladder (Pacific Edge Diagnostics USA) using cystoscopy and histopathology as the reference standard met inclusion criteria. Case-control studies were excluded. Data extraction: Dual extraction and quality assessment of individual studies. Overall strength of evidence (SOE) was also assessed. Data synthesis: Across biomarkers, sensitivities ranged from 0.57 to 0.82 and specificities ranged from 0.74 to 0.88. Positive likelihood ratios ranged from 2.52 to 5.53, and negative likelihood ratios ranged from 0.21 to 0.48 (moderate SOE for quantitative NMP22, qualitative BTA, FISH, and ImmunoCyt; low SOE for others). For some biomarkers, sensitivity was higher for initial diagnosis of bladder cancer than for diagnosis of recurrence. Sensitivity increased with higher tumor stage or grade. Studies that directly compared the accuracy of quantitative NMP22 and qualitative BTA found no differences in diagnostic accuracy (moderate SOE); head-to-head studies of other biomarkers were limited. Urinary biomarkers plus cytologic evaluation were more sensitive than biomarkers alone but missed about 10% of bladder cancer cases. Limitation: Restricted to English-language studies; no search for studies published only as abstracts; statistical heterogeneity present in most analyses; few studies for qualitative NMP22, quantitative BTA, and Cxbladder; and methodological shortcomings in almost all studies. Conclusion: Urinary biomarkers miss a substantial proportion of patients with bladder cancer and are subject to false-positive results in others. Accuracy is poor for low-stage and low-grade tumors. Primary funding source: Agency for Healthcare Research and Quality. (PROSPERO registration number: CRD42014013284).
Article
The identification of early-stage breast cancer patients at high risk of relapse would allow tailoring of adjuvant therapy approaches. We assessed whether analysis of circulating tumor DNA (ctDNA) in plasma can be used to monitor for minimal residual disease (MRD) in breast cancer. In a prospective cohort of 55 early breast cancer patients receiving neoadjuvant chemotherapy, detection of ctDNA in plasma after completion of apparently curative treatment-either at a single postsurgical time point or with serial follow-up plasma samples-predicted metastatic relapse with high accuracy [hazard ratio, 25.1 (confidence interval, 4.08 to 130.5; log-rank P < 0.0001) or 12.0 (confidence interval, 3.36 to 43.07; log-rank P < 0.0001), respectively]. Mutation tracking in serial samples increased sensitivity for the prediction of relapse, with a median lead time of 7.9 months over clinical relapse. We further demonstrated that targeted capture sequencing analysis of ctDNA could define the genetic events of MRD, and that MRD sequencing predicted the genetic events of the subsequent metastatic relapse more accurately than sequencing of the primary cancer. Mutation tracking can therefore identify early breast cancer patients at high risk of relapse. Subsequent adjuvant therapeutic interventions could be tailored to the genetic events present in the MRD, a therapeutic approach that could in part combat the challenge posed by intratumor genetic heterogeneity. Copyright © 2015, American Association for the Advancement of Science.
Article
Urothelial carcinoma of the bladder comprises two long-recognized disease entities with distinct molecular features and clinical outcome. Low-grade non-muscle-invasive tumours recur frequently but rarely progress to muscle invasion, whereas muscle-invasive tumours are usually diagnosed de novo and frequently metastasize. Recent genome-wide expression and sequencing studies identify genes and pathways that are key drivers of urothelial cancer and reveal a more complex picture with multiple molecular subclasses that traverse conventional grade and stage groupings. This improved understanding of molecular features, disease pathogenesis and heterogeneity provides new opportunities for prognostic application, disease monitoring and personalized therapy.
Article
The "atypical urothelial cell" cytologic category is nonstandardized. We subclassify atypical cases to "atypical, favor a reactive process" or "atypical, unclear if reactive or neoplastic." We evaluated the predictive significance of atypical cases by looking at their histologic follow-up. Among the 1,114 patients and 3,261 specimens included, 282 specimens had histologic follow-up. An atypical diagnosis did not carry a significant increased risk of urothelial neoplasia compared with the benign category. Although an "atypical unclear" diagnosis carried a higher rate of detection of high-grade cancer on follow-up biopsy in comparison with "atypical reactive" or "negative" diagnoses (26/58 [45%] vs 15/52 [29%] and 16/103 [15.5%], respectively), this difference was not statistically significant. These results suggest that dividing atypical cases into 2 categories based on the level of cytologic suspicion of cancer does not add clinically relevant information within the atypical category. They also raise the question of the significance of the atypical category altogether.
Article
To determine the clinical utility of urine-based bladder tumor markers (UBBTMs) and cytology in the treatment of patients with transitional cell carcinoma on the basis of their statistical performance. A comprehensive literature review was performed using Medline (1966 to current) and other search engines. Data regarding the statistical performance of UBBTMs were double extracted and rectified. Studies addressing comparable patient populations were combined and hierarchical Bayesian meta-analyses performed to calculate the sensitivity and specificity of commonly used UBBTMs, as well as urinary cytology. Patient populations were stratified by tumor stage and grade when data were presented in an extractable fashion. The literature review yielded 54 publications, 338 distinct patient groups (controls, screening population, patients with cancer, strata based on grade and stage) and more than 10,000 patients. The number of groups varied from 1 to 18, and the number of patients ranged from less than 100 to more than 1500 for the various markers. All UBBTMs have better sensitivity compared with cytology, especially for low-grade/stage disease, but do not match cytology regarding specificity. In patients with grade 1 and 2 tumors, several UBBTMs are significantly superior statistically in terms of sensitivity compared with cytology. The sensitivity for transitional cell carcinoma in situ (Tis) is surprisingly poor for all UBBTMs. UBBTMs can be used for follow-up of low-grade/stage tumors but should not replace cystoscopy. All UBBTMs have better sensitivity than cytology and could potentially replace routine cytology during patient follow-up.
Article
To estimate the lifetime cost of bladder cancer and the contribution of complications to the total costs. We reviewed the medical records of a retrospective cohort of 208 patients with bladder cancer who registered at our comprehensive cancer center from 1991 to 1999. We multiplied the number of resources used during management of bladder cancer by their unit charges. We converted charges into costs using the Medicare cost-to-charge ratio and inflated these to 2005 U.S. dollars. We estimated future costs by creating two extreme hypothetical scenarios. In the best-case scenario, we assumed patients with superficial disease developed recurrences at the cohort's mean rate and that patients with muscle-invasive disease were disease free after definitive therapy. Survival was based on the U.S. life expectancy in both cases. In the worst-case scenario, we assumed patients with superficial disease developed muscle-invasive disease and that all patients subsequently died of bladder cancer. The average cost of bladder cancer was 65,158 dollars among the cohort patients. Sixty percent of this cost (39,393 dollars) was associated with surveillance and treatment of recurrences, and 30% (19,811 dollars) was attributable to complications. The lifetime cost of bladder cancer was lower for the worst-case scenario (99,270 dollars) than for the best-case scenario (120,684 dollars). However, a greater proportion of the costs were attributable to complications with the worst-case scenario (43%, 42,290 dollars) compared with the best (28%, 34,169 dollars). The management of bladder cancer and its associated complications results in a major economic burden. More cost-effective surveillance strategies and approaches for preventing complications are crucial to minimizing the disease's clinical and economic consequences.
Cancer Genome Atlas Research N. Comprehensive molecular characterization of urothelial bladder carcinoma
Cancer Genome Atlas Research N. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 2014;507: 315-22.
Clinical model of lifetime cost of treating bladder cancer and associated complications
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Urinary Biomarkers for Diagnosis of Bladder Cancer: A Systematic Review and Meta-analysis
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Early detection of molecular residual disease in localized lung cancer by circulating tumor DNA profiling
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An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage
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Integrated digital error suppression for improved detection of circulating tumor DNA
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Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy
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Genomic Alterations in Liquid Biopsies from Patients with Bladder Cancer
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Optimization of transrenal DNA analysis: detection of fetal DNA in maternal urine
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Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer
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Comprehensive molecular characterization of urothelial bladder carcinoma
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MRD, minimal residual disease; utDNA, urinary tumor DNA. Research. on February 11, 2019. © 2018 American Association for Cancer cancerdiscovery.aacrjournals.org Downloaded from Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
Author Manuscript Published OnlineFirst on
Author Manuscript Published OnlineFirst on December 21, 2018; DOI: 10.1158/2159-8290.CD-18-0825