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Aristolochic acid mutational signature defines the low-risk subtype in upper tract urothelial carcinoma.

ABSTRACT: Rationale: Dietary exposure to aristolochic acids and similar compounds (collectively, AA) is a significant risk factor for nephropathy and subsequent upper tract urothelial carcinoma (UTUC). East Asian populations, who have a high prevalence of UTUC, have an unusual genome-wide AA-induced mutational pattern (COSMIC signature 22). Integrating mutational signature analysis with clinicopathological information may demonstrate great potential for risk ranking this UTUC subtype. Methods: We performed whole-genome sequencing (WGS) on 90 UTUC Chinese patients to extract mutational signatures. Genome sequencing data for urinary cell-free DNA from 26 UTUC patients were utilized to noninvasively identify the mutational signatures. Genome sequencing for primary tumors on 8 out of 26 patients was also performed. Metastasis-free survival (MFS) and cancer-specific survival (CSS) were measured using Kaplan-Meier methods. Results: Data analysis showed that a substantial proportion of patients harbored the AA mutational signature and were associated with AA-containing herbal drug intake, female gender, poor renal function, and multifocality. Field cancerization was found to partially contribute to multifocality. Nevertheless, AA Sig subtype UTUC patients exhibited favorable outcomes of CSS and MFS compared to the No-AA Sig subtype. Additionally, AA Sig subtype patients showed a higher tumor mutation burden, higher numbers of predicted neoantigens, and infiltrating lymphocytes, suggesting the potential for immunotherapy. We also confirmed the AA signature in AA-treated human renal tubular HK-2 cells. Notably, the AA subtype could be ascertained using a clinically applicable sequencing strategy (low coverage) in both primary tumors and urinary cell-free DNA as a basis for therapy selection. Conclusion: The AA mutational signature as a screening tool defines low-risk UTUC with therapeutic relevance. The AA mutational signature, as a molecular prognostic marker using either ureteroscopy and/or urinary cell-free DNA, is especially useful for diagnostic uncertainty when kidney-sparing treatment and/or immune checkpoint inhibitor therapy were considered.

SUBMITTER: Lu H

PROVIDER: S-EPMC7150494 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Aristolochic acid mutational signature defines the low-risk subtype in upper tract urothelial carcinoma.

Lu Huan H Liang Yuan Y Guan Bao B Shi Yue Y Gong Yanqing Y Li Juan J Kong Wenwen W Liu Jin J Fang Dong D Liu Libo L He Qun Q Shakeel Muhammad M Li Xuesong X Zhou Liqun L Ci Weimin W

Theranostics 20200304 10

<b>Rationale</b>: Dietary exposure to aristolochic acids and similar compounds (collectively, AA) is a significant risk factor for nephropathy and subsequent upper tract urothelial carcinoma (UTUC). East Asian populations, who have a high prevalence of UTUC, have an unusual genome-wide AA-induced mutational pattern (COSMIC signature 22). Integrating mutational signature analysis with clinicopathological information may demonstrate great potential for risk ranking this UTUC subtype. <b>Methods</b ...[more]

PMID: 32292497

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Project description:Despite a similar histologic appearance, upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) tumors have distinct epidemiologic and clinicopathologic differences.To investigate whether the differences between UTUC and UCB result from intrinsic biological diversity.Tumor and germline DNA from patients with UTUC (n=83) and UCB (n=102) were analyzed using a custom next-generation sequencing assay to identify somatic mutations and copy number alterations in 300 cancer-associated genes.We described co-mutation patterns and copy number alterations in UTUC. We also compared mutation frequencies in high-grade UTUC (n=59) and high-grade UCB (n=102).Comparison of high-grade UTUC and UCB revealed significant differences in the prevalence of somatic alterations. Genes altered more commonly in high-grade UTUC included FGFR3 (35.6% vs 21.6%; p=0.065), HRAS (13.6% vs 1.0%; p=0.001), and CDKN2B (15.3% vs 3.9%; p=0.016). Genes less frequently mutated in high-grade UTUC included TP53 (25.4% vs 57.8%; p<0.001), RB1 (0.0% vs 18.6%; p<0.001), and ARID1A (13.6% vs 27.5%; p=0.050). Because our assay was restricted to genomic alterations in a targeted panel, rare mutations and epigenetic changes were not analyzed.High-grade UTUC tumors display a spectrum of genetic alterations similar to high-grade UCB. However, there were significant differences in the prevalence of several recurrently mutated genes including HRAS, TP53, and RB1. As relevant targeted inhibitors are being developed and tested, these results may have important implications for the site-specific management of patients with urothelial carcinoma.Comparison of next-generation sequencing of upper tract urothelial carcinoma (UTUC) with urothelial bladder cancer identified that similar mutations were present in both cancer types but at different frequencies, indicating a potential need for unique management strategies. UTUC tumors were found to have a high rate of mutations that could be targeted with novel therapies.

Project description:Recurrent upper tract urothelial carcinomas (UTUCs) arise in the context of nephropathy linked to exposure to the herbal carcinogen aristolochic acid (AA). Here we delineated the molecular programs underlying UTUC tumorigenesis in patients from endemic aristolochic acid nephropathy (AAN) regions in Southern Europe. We applied an integrative multiomics analysis of UTUCs, corresponding unaffected tissues and of patient urines. Quantitative microRNA (miRNA) and messenger ribonucleic acid (mRNA) expression profiling, immunohistochemical analysis by tissue microarrays and exome and transcriptome sequencing were performed in UTUC and nontumor tissues. Urinary miRNAs of cases undergoing surgery were profiled before and after tumor resection. Ribonucleic acid (RNA) and protein levels were analyzed using appropriate statistical tests and trend assessment. Dedicated bioinformatic tools were used for analysis of pathways, mutational signatures and result visualization. The results delineate UTUC-specific miRNA:mRNA networks comprising 89 miRNAs associated with 1,862 target mRNAs, involving deregulation of cell cycle, deoxyribonucleic acid (DNA) damage response, DNA repair, bladder cancer, oncogenes, tumor suppressors, chromatin structure regulators and developmental signaling pathways. Key UTUC-specific transcripts were confirmed at the protein level. Exome and transcriptome sequencing of UTUCs revealed AA-specific mutational signature SBS22, with 68% to 76% AA-specific, deleterious mutations propagated at the transcript level, a possible basis for neoantigen formation and immunotherapy targeting. We next identified a signature of UTUC-specific miRNAs consistently more abundant in the patients' urine prior to tumor resection, thereby defining biomarkers of tumor presence. The complex gene regulation programs of AAN-associated UTUC tumors involve regulatory miRNAs prospectively applicable to noninvasive urine-based screening of AAN patients for cancer presence and recurrence.

Project description:ObjectivesTo develop a CT-based radiomics model and a combined model for preoperatively discriminating infiltrative renal cell carcinoma (RCC) and pyelocaliceal upper urinary tract urothelial carcinoma (UTUC), which invades the renal parenchyma.Materials and methodsEighty patients (37 pathologically proven infiltrative RCCs and 43 pathologically proven pyelocaliceal UTUCs) were retrospectively enrolled and randomly divided into a training set (n = 56) and a testing set (n = 24) at a ratio of 7:3. Traditional CT imaging characteristics in the portal venous phase were collected by two radiologists (SPH and ZXL, who have 4 and 30 years of experience in abdominal radiology, respectively). Patient demographics and traditional CT imaging characteristics were used to construct the clinical model. The radiomics score was calculated based on the radiomics features extracted from the portal venous CT images and the random forest (RF) algorithm to construct the radiomics model. The combined model was constructed using the radiomics score and significant clinical factors according to the multivariate logistic regression. The diagnostic efficacy of the models was evaluated using receiver operating characteristic (ROC) curve analysis and the area under the curve (AUC).ResultsThe RF score based on the eight validated features extracted from the portal venous CT images was used to build the radiomics model. Painless hematuria as an independent risk factor was used to build the clinical model. The combined model was constructed using the RF score and the selected clinical factor. Both the radiomics model and combined model showed higher efficacy in differentiating infiltrative RCC and pyelocaliceal UTUC in the training and testing cohorts with AUC values of 0.95 and 0.90, respectively, for the radiomics model and 0.99 and 0.90, respectively, for the combined model. The decision curves of the combined model as well as the radiomics model indicated an overall net benefit over the clinical model. Both the radiomics model and the combined model achieved a notable reduction in false-positive and false-negativerates, resulting in significantly higher accuracy compared to the visual assessments in both the training and testing cohorts.ConclusionThe radiomics model and combined model had the potential to accurately differentiate infiltrative RCC and pyelocaliceal UTUC, which invades the renal parenchyma, and provide a new potentially non-invasive method to guide surgery strategies.

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Aristolochic acid mutational signature defines the low-risk subtype in upper tract urothelial carcinoma.

Publications

Aristolochic acid mutational signature defines the low-risk subtype in upper tract urothelial carcinoma.

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