Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia.
Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, WHO, Lyon, France.
Int J Cancer. 2022 Jan 15;150(2):374-386. doi: 10.1002/ijc.33827. Epub 2021 Oct 15.
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.
复发性上尿路尿路上皮癌（UTUC）发生在与草药致癌物马兜铃酸（AA）暴露相关的肾病背景下。在这里，我们描绘了来自欧洲南部 AA 相关肾疾病（AAN）流行地区的患者 UTUC 肿瘤发生的分子程序。我们对 UTUC 患者、相应的未受影响组织和患者尿液进行了综合多组学分析。在 UTUC 和非肿瘤组织中进行了定量 microRNA（miRNA）和信使核糖核酸（mRNA）表达谱分析、组织微阵列免疫组织化学分析以及外显子组和转录组测序。对接受手术的病例在肿瘤切除前后进行了尿液 miRNA 分析。使用适当的统计检验和趋势评估分析 RNA 和蛋白质水平。使用专用生物信息学工具分析途径、突变特征和结果可视化。结果描绘了 UTUC 特异性 miRNA:mRNA 网络，包括 89 个与 1862 个靶 mRNA 相关的 miRNA，涉及细胞周期、脱氧核糖核酸（DNA）损伤反应、DNA 修复、膀胱癌、癌基因、肿瘤抑制基因、染色质结构调节剂和发育信号通路的失调。关键的 UTUC 特异性转录本在蛋白质水平上得到了证实。UTUC 的外显子组和转录组测序揭示了 AA 特异性突变特征 SBS22，在转录水平上有 68%至 76%的 AA 特异性、有害突变，这可能是新抗原形成和免疫治疗靶点的基础。接下来，我们鉴定了一个在肿瘤切除前患者尿液中始终更丰富的 UTUC 特异性 miRNA 签名，从而定义了肿瘤存在的生物标志物。AAN 相关 UTUC 肿瘤的复杂基因调控程序涉及调节 miRNA，可前瞻性地应用于 AAN 患者非侵入性尿液筛查癌症存在和复发。
