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    Comprehensive Analysis of the Expression and Prognosis for E2Fs in Human Breast Cancer. Sun Cheng-Cao,Li Shu-Jun,Hu Wei,Zhang Jian,Zhou Qun,Liu Cong,Li Lin-Lin,Songyang Yi-Yan,Zhang Feng,Chen Zhen-Long,Li Guang,Bi Zhuo-Yue,Bi Yong-Yi,Gong Feng-Yun,Bo Tao,Yuan Zhan-Peng,Hu Wei-Dong,Zhan Bo-Tao,Zhang Qian,He Qi-Qiang,Li De-Jia Molecular therapy : the journal of the American Society of Gene Therapy E2F transcription factors (E2Fs), a group of genes that encode a family of transcription factors, have been identified as being involved in the tumor progression of various cancer types. Increasing experimental evidence indicates that E2Fs are implicated in breast cancer tumorigenesis. However, the diverse expression patterns and prognostic values of eight E2Fs have yet to be analyzed. Herein we investigated the transcriptional and survival data of E2Fs in patients with breast cancer from the Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier Plotter, and cBioPortal databases. We found that the expression levels of E2F1-3 and 5-8 were higher in breast cancer tissues than in normal breast tissues, whereas the expression level of E2F4 was lower in the former than in the latter. The expression levels of E2F2, 5, 7, and 8 were correlated with advanced tumor stage. Survival analysis using the Kaplan-Meier Plotter database revealed that the high transcription levels of E2F1-3, 5, 7, and 8 were associated with low relapse-free survival in all of the patients with breast cancer. Conversely, high E2F4 and E2F6 levels predicted high relapse-free survival in these patients. This study implied that E2F1-3, 5, 7, and 8 are potential targets of precision therapy for patients with breast cancer and that E2F4 and 6 are new biomarkers for the prognosis of breast cancer. 10.1016/j.ymthe.2019.03.019
    METTL3 promote tumor proliferation of bladder cancer by accelerating pri-miR221/222 maturation in m6A-dependent manner. Han Jie,Wang Jing-Zi,Yang Xiao,Yu Hao,Zhou Rui,Lu Hong-Cheng,Yuan Wen-Bo,Lu Jian-Chen,Zhou Zi-Jian,Lu Qiang,Wei Ji-Fu,Yang Haiwei Molecular cancer BACKGROUND:METTL3 is known to be involved in all stages in the life cycle of RNA. It affects the tumor formation by the regulation the m6A modification in the mRNAs of critical oncogenes or tumor suppressors. In bladder cancer, METTL3 could promote the bladder cancer progression via AFF4/NF-κB/MYC signaling network by an m6A dependent manner. Recently, METTL3 was also found to affect the m6A modification in non-coding RNAs including miRNAs, lincRNAs and circRNAs. However, whether this mechanism is related to the proliferation of tumors induced by METTL3 is not reported yet. METHODS:Quantitative real-time PCR, western blot and immunohistochemistry were used to detect the expression of METTL3 in bladder cancer. The survival analysis was adopted to explore the association between METTL3 expression and the prognosis of bladder cancer. Bladder cancer cells were stably transfected with lentivirus and cell proliferation and cell cycle, as well as tumorigenesis in nude mice were performed to assess the effect of METTL3 in bladder cancer. RNA immunoprecipitation (RIP), co-immunoprecipitations and RNA m6A dot blot assays were conducted to confirm that METTL3 interacted with the microprocessor protein DGCR8 and modulated the pri-miR221/222 process in an m6A-dependent manner. Luciferase reporter assay was employed to identify the direct binding sites of miR221/222 with PTEN. Colony formation assay and CCK8 assays were conducted to confirm the function of miR-221/222 in METTL3-induced cell growth in bladder cancer. RESULTS:We confirmed the oncogenic role of METTL3 in bladder cancer by accelerating the maturation of pri-miR221/222, resulting in the reduction of PTEN, which ultimately leads to the proliferation of bladder cancer. Moreover, we found that METTL3 was significantly increased in bladder cancer and correlated with poor prognosis of bladder cancer patients. CONCLUSIONS:Our findings suggested that METTL3 may have an oncogenic role in bladder cancer through interacting with the microprocessor protein DGCR8 and positively modulating the pri-miR221/222 process in an m6A-dependent manner. To our knowledge, this is the first comprehensive study that METTL3 affected the tumor formation by the regulation the m6A modification in non-coding RNAs, which might provide fresh insights into bladder cancer therapy. 10.1186/s12943-019-1036-9
    m6A RNA methylation regulators can contribute to malignant progression and impact the prognosis of bladder cancer. Chen Mei,Nie Zhen-Yu,Wen Xiao-Hong,Gao Yuan-Hui,Cao Hui,Zhang Shu-Fang Bioscience reports N6-methyladenosine (m6A) is the most common form of messenger RNA (mRNA) modification. An increasing number of studies have proven that m6A RNA methylation regulators are overexpressed in many cancers and participate in the development of cancer through the dynamic regulation of m6A RNA methylation regulators. However, the prognostic role of m6A RNA methylation regulators in bladder cancer (BC) is poorly understood. In the present study, we downloaded the mRNA expression data from The Cancer Genome Atlas (TCGA) database and the corresponding clinical and prognostic information. The relationship between m6A RNA methylation regulators and clinicopathological variables of BC patients was assessed by the Kolmogorov-Smirnov test. The expression of the m6A RNA methylation regulators was differentially associated with different clinicopathological variables of BC patients. The least absolute shrinkage and selection operator (LASSO) Cox regression model was then applied to identify three m6A RNA methylation regulators. The risk signature was constructed as follows: 0.164FTO - (0.081YTHDC1+0.032WTAP). Based on the risk signature, the risk score of each patient was calculated, and the patients were divided into a high-risk group and a low-risk group. The overall survival (OS) rate of the high-risk group was significantly lower than that of the low-risk group. The risk signature was not only an independent prognostic marker for BC patients but also a predictor of clinicopathological variables. In conclusion, m6A RNA methylation regulators can participate in the malignant progression of BC, and a risk signature with three selected m6A RNA methylation regulators may be a promising prognostic biomarker to guide personalized treatment for BC patients. 10.1042/BSR20192892
    The mA methyltransferase METTL3 promotes bladder cancer progression via AFF4/NF-κB/MYC signaling network. Cheng Maosheng,Sheng Lu,Gao Qian,Xiong Qiuchan,Zhang Haojie,Wu Mingqing,Liang Yu,Zhu Fengyu,Zhang Yingyin,Zhang Xiuhong,Yuan Quan,Li Yang Oncogene N-methyladenosine (m6A) is the most abundant modification in eukaryotic messenger RNAs (mRNAs), and plays important roles in many bioprocesses. However, its functions in bladder cancer (BCa) remain elusive. Here, we discovered that methyltransferase-like 3 (METTL3), a major RNA N-adenosine methyltransferase, was significantly up-regulated in human BCa. Knockdown of METTL3 drastically reduced BCa cell proliferation, invasion, and survival in vitro and tumorigenicity in vivo. On the other hand, overexpression of METTL3 significantly promoted BCa cell growth and invasion. Through transcriptome sequencing, mA sequencing and mA methylated RNA immuno-precipitation quantitative reverse-transcription polymerase chain reaction, we revealed the profile of METTL3-mediated mA modification in BCa cells for the first time. AF4/FMR2 family member 4 (AFF4), two key regulators of NF-κB pathway (IKBKB and RELA) and MYC were further identified as direct targets of METTL3-mediated mA modification. In addition, we showed that besides NF-κB, AFF4 binds to the promoter of MYC and promotes its expression, implying a novel multilevel regulatory network downstream of METTL3. Our results uncovered an AFF4/NF-κB/MYC signaling network operated by METTL3-mediated m6A modification and provided insight into the mechanisms of BCa progression. 10.1038/s41388-019-0683-z
    The mA Methylation-Regulated AFF4 Promotes Self-Renewal of Bladder Cancer Stem Cells. Gao Qian,Zheng Jin,Ni Zegui,Sun Pengli,Yang Congcong,Cheng Maosheng,Wu Mingqing,Zhang Xiuhong,Yuan Lin,Zhang Yingyin,Li Yang Stem cells international The dynamic N-methyladenosine (mA) modification of mRNA plays a role in regulating gene expression and determining cell fate. However, the functions of mA mRNA modification in bladder cancer stem cells (BCSCs) have not been described. Here, we show that global RNA mA abundance and the expression of mA-forming enzyme METTL3 are higher in BCSCs than those in non-CSCs of bladder cancer (BCa) cells. The depletion of the inhibited the self-renewal of BCSCs, as evidenced by decreased ALDH activity and sphere-forming ability. Mechanistically, METTL3 regulates the mA modification and thereby the expression of AF4/FMR2 family member 4 (AFF4), knockdown of which phenocopies the ablation and diminishes the tumor-initiating capability of BCSCs . AFF4 binds to the promoter regions and sustains the transcription of and which have critical biological functions in BCSCs. Collectively, our results demonstrate the critical roles of mA modification in self-renewal and tumorigenicity of BCSCs through a novel signaling axis of METTL3-AFF4-SOX2/MYC. 10.1155/2020/8849218
    The Emerging Role of Epitranscriptomics in Cancer: Focus on Urological Tumors. Lobo João,Barros-Silva Daniela,Henrique Rui,Jerónimo Carmen Genes Epitranscriptomics has gained ground in recent years, especially after the advent of techniques for accurately studying these mechanisms. Among all modifications occurring in RNA molecules, N6-methyladenosine (m⁶A) is the most frequent, especially among mRNAs. m⁶A has been demonstrated to play important roles in many physiological processes and several disease states, including various cancer models (from solid to liquid tumors). Tumor cells' epitranscriptome is indeed disrupted in a way to promote cancer-prone features, by means of up/downregulating m⁶A-related players: the so-called writers, readers and erasers. These proteins modulate m⁶A establishment, removal and determine mRNAs fate, acting in a context-dependent manner, so that a single player may act as an oncogenic signal in one tumor model (methyltransferase like 3 (METTL3) in lung cancer) and as a tumor suppressor in another context (METTL3 in glioblastoma). Despite recent advances, however, little attention has been directed towards urological cancer. By means of a thorough analysis of the publicly available TCGA (The Cancer Genome Atlas) database, we disclosed the most relevant players in four major urogenital neoplasms-kidney, bladder, prostate and testicular cancer-for prognostic, subtype discrimination and survival purposes. In all tumor models assessed, the most promising player was shown to be Vir like m⁶A methyltransferase associated (VIRMA), which could constitute a potential target for personalized therapies. 10.3390/genes9110552
    Role of methyltransferase-like enzyme 3 and methyltransferase-like enzyme 14 in urological cancers. Tao Zijia,Zhao Yiqiao,Chen Xiaonan PeerJ N6-methyladenosine (m6A) modifications can be found in eukaryotic messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA). Several studies have demonstrated a close relationship between m6A modifications and cancer cells. Methyltransferase-like enzyme 3 (METTL3) and methyltransferase-like enzyme 14 (METTL14) are two major enzymes involved in m6A modifications that play vital roles in various cancers. However, the roles and regulatory mechanisms of METTL3 and METTL14 in urological cancers are largely unknown. In this review, we summarize the current research results for METTL3 and METTL14 and identify potential pathways involving these enzymes in kidney, bladder, prostate, and testicular cancer. We found that METTL3 and METTL14 have different expression patterns in four types of urological cancers. METTL3 is highly expressed in bladder and prostate cancer and plays an oncogenic role on cancer cells; however, its expression and role are opposite in kidney cancer. METTL14 is expressed at low levels in kidney and bladder cancer, where it has a tumor suppressive role. Low METTL3 or METTL14 expression in cancer cells negatively regulates cell growth-related pathways (e.g., mTOR, EMT, and P2XR6) but positively regulates cell death-related pathways (e.g., P53, PTEN, and Notch1). When METTL3 is highly expressed, it positively regulates the NF-kB and SHH-GL1pathways but negatively regulates PTEN. These results suggest that although METTL3 and METTL14 have different expression levels and regulatory mechanisms in urological cancers, they control cancer cell fate via cell growth- and cell death-related pathways. These findings suggest that m6A modification may be a potential new therapeutic target in urological cancer. 10.7717/peerj.9589
    METTL3/YTHDF2 m A axis promotes tumorigenesis by degrading SETD7 and KLF4 mRNAs in bladder cancer. Xie Haiyun,Li Jiangfeng,Ying Yufan,Yan Huaqing,Jin Ke,Ma Xueyou,He Liujia,Xu Xin,Liu Ben,Wang Xiao,Zheng Xiangyi,Xie Liping Journal of cellular and molecular medicine N6-Methyladenosine (m A) modification, the most prevalent modification of eukaryotic messenger RNA (mRNA), is involved in the progression of various tumours. However, the specific role of m A in bladder cancer (BCa) is still poorly understood. In this study, we demonstrated the tumour-promoting function and specific regulatory mechanism of m A axis, consisting of the core 'writer' protein METTL3 and the major reader protein YTHDF2. Depletion of METTL3 impaired cancer proliferation and cancer metastasis in vitro and in vivo. Through transcriptome sequencing, m A methylated RNA immunoprecipitation (MeRIP) and RIP, we determined that the METTL3/YTHDF2 m A axis directly degraded the mRNAs of the tumour suppressors SETD7 and KLF4, contributing to the progression of BCa. In addition, overexpression of SETD7 and KLF4 revealed a phenotype consistent with that induced by depletion of the m A axis. Thus, our findings on the METTL3/YTHDF2/SETD7/KLF4 m A axis provide the insight into the underlying mechanism of carcinogenesis and highlight potential therapeutic targets for BCa. 10.1111/jcmm.15063
    Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis. de Jong Joep J,Liu Yang,Robertson A Gordon,Seiler Roland,Groeneveld Clarice S,van der Heijden Michiel S,Wright Jonathan L,Douglas James,Dall'Era Marc,Crabb Simon J,van Rhijn Bas W G,van Kessel Kim E M,Davicioni Elai,Castro Mauro A A,Lotan Yair,Zwarthoff Ellen C,Black Peter C,Boormans Joost L,Gibb Ewan A Genome medicine BACKGROUND:Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease, and gene expression profiling has identified several molecular subtypes with distinct biological and clinicopathological characteristics. While MIBC subtyping has primarily been based on messenger RNA (mRNA), long non-coding RNAs (lncRNAs) may provide additional resolution. METHODS:LncRNA expression was quantified from microarray data of a MIBC cohort treated with neoadjuvant chemotherapy (NAC) and radical cystectomy (RC) (n = 223). Unsupervised consensus clustering of highly variant lncRNAs identified a four-cluster solution, which was characterized using a panel of MIBC biomarkers, regulon activity profiles, gene signatures, and survival analysis. The four-cluster solution was confirmed in The Cancer Genome Atlas (TCGA) cohort (n = 405). A single-sample genomic classifier (GC) was trained using ridge-penalized logistic regression and validated in two independent cohorts (n = 255 and n = 94). RESULTS:NAC and TCGA cohorts both contained an lncRNA cluster (LC3) with favorable prognosis that was enriched with tumors of the luminal-papillary (LP) subtype. In both cohorts, patients with LP tumors in LC3 (LPL-C3) were younger and had organ-confined, node-negative disease. The LPL-C3 tumors had enhanced FGFR3, SHH, and wild-type p53 pathway activity. In the TCGA cohort, LPL-C3 tumors were enriched for FGFR3 mutations and depleted for TP53 and RB1 mutations. A GC trained to identify these LPL-C3 patients showed robust performance in two validation cohorts. CONCLUSIONS:Using lncRNA expression profiles, we identified a biologically distinct subgroup of luminal-papillary MIBC with a favorable prognosis. These data suggest that lncRNAs provide additional information for higher-resolution subtyping, potentially improving precision patient management. 10.1186/s13073-019-0669-z
    Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer. Guo Charles C,Majewski Tadeusz,Zhang Li,Yao Hui,Bondaruk Jolanta,Wang Yan,Zhang Shizhen,Wang Ziqiao,Lee June Goo,Lee Sangkyou,Cogdell David,Zhang Miao,Wei Peng,Grossman H Barton,Kamat Ashish,Duplisea Jonathan James,Ferguson James Edward,Huang He,Dadhania Vipulkumar,Gao Jianjun,Dinney Colin,Weinstein John N,Baggerly Keith,McConkey David,Czerniak Bogdan Cell reports Sarcomatoid urothelial bladder cancer (SARC) displays a high propensity for distant metastasis and is associated with short survival. We report a comprehensive genomic analysis of 28 cases of SARC and 84 cases of conventional urothelial carcinoma (UC), with the TCGA cohort of 408 muscle-invasive bladder cancers serving as the reference. SARCs show a distinct mutational landscape, with enrichment of TP53, RB1, and PIK3CA mutations. They are related to the basal molecular subtype of conventional UCs and could be divided into epithelial-basal and more clinically aggressive mesenchymal subsets on the basis of TP63 and its target gene expression levels. Other analyses reveal that SARCs are driven by downregulation of homotypic adherence genes and dysregulation of the EMT network, and nearly half exhibit a heavily infiltrated immune phenotype. Our observations have important implications for prognostication and the development of more effective therapies for this highly lethal variant of bladder cancer. 10.1016/j.celrep.2019.04.048
    Inhibition of EZH2 induces NK cell-mediated differentiation and death in muscle-invasive bladder cancer. Ramakrishnan Swathi,Granger Victoria,Rak Monika,Hu Qiang,Attwood Kristopher,Aquila Lanni,Krishnan Nithya,Osiecki Rafal,Azabdaftari Gissou,Guru Khurshid,Chatta Gurkamal,Gueron Geraldine,McNally Lacey,Ohm Joyce,Wang Jianmin,Woloszynska Anna Cell death and differentiation Lysine-specific demethylase 6A (KDM6A) and members of the Switch/Sucrose Non-Fermentable (SWI/SNF) family are known to counteract the activity of Enhancer of Zeste Homolog 2 (EZH2), which is often overexpressed and is associated with poor prognosis in muscle-invasive bladder cancer. Here we provide evidence that alterations in chromatin modifying enzymes, including KDM6A and members of the SWI/SNF complex, are frequent in muscle-invasive bladder cancer. We exploit the loss of function mutations in KDM6A and SWI/SNF complex to make bladder cancer cells susceptible to EZH2-based epigenetic therapy that activates an immune response to drive tumor cell differentiation and death. We reveal a novel mechanism of action of EZH2 inhibition, alone and in combination with cisplatin, which induces immune signaling with the largest changes observed in interferon gamma (IFN-γ). This upregulation is a result of activated natural killer (NK) signaling as demonstrated by the increase in NK cell-associated genes MIP-1α, ICAM1, ICAM2, and CD86 in xenografts treated with EZH2 inhibitors. Conversely, EZH2 inhibition results in decreased expression of pluripotency markers, ALDH2 and CK5, and increased cell death. Our results reveal a novel sensitivity of muscle-invasive bladder cancer cells with KMD6A and SWI/SNF mutations to EZH2 inhibition alone and in combination with cisplatin. This sensitivity is mediated through increased NK cell-related signaling resulting in tumor cell differentiation and cell death. 10.1038/s41418-019-0278-9
    The Splicing Factor PTBP1 Promotes Expression of Oncogenic Splice Variants and Predicts Poor Prognosis in Patients with Non-muscle-Invasive Bladder Cancer. Bielli Pamela,Panzeri Valentina,Lattanzio Rossano,Mutascio Simona,Pieraccioli Marco,Volpe Elisabetta,Pagliarulo Vincenzo,Piantelli Mauro,Giannantoni Antonella,Di Stasi Savino M,Sette Claudio Clinical cancer research : an official journal of the American Association for Cancer Research Non-muscle-invasive bladder cancer (NMIBC) is a malignant disease characterized by high heterogeneity, which corresponds to dysregulated gene expression and alternative splicing (AS) profiles. Bioinformatics analyses of splicing factors potentially linked to bladder cancer progression identified the heterogeneous nuclear ribonucleoprotein I (i.e., PTBP1) as candidate. This study aimed at investigating whether PTBP1 expression associates with clinical outcome in patients with NMIBC. A cohort of 152 patients presenting with primary NMIBC (pTa-pT1) was enrolled. Primary NMIBCs were assessed for PTBP1 expression by IHC, and the results were correlated with clinical data using Kaplan-Meier curves and Cox regression analyses. Cell proliferation and survival assays were performed to assess the function of PTBP1. Furthermore, the impact of PTBP1 on the AS pattern of specific bladder cancer-related genes was investigated in cancer cell lines and in patients' specimens. Public datasets querying highlighted a positive correlation between PTBP1 expression and NMIBC progression, which was then confirmed by IHC analysis. High PTBP1 expression was associated with worse clinical outcome in terms of incidence of tumor relapse and survival in patients with NMIBC. Interestingly, downregulation of PTBP1 in bladder cancer cell lines affected prosurvival features. Accordingly, PTBP1 modulated AS of bladder cancer-related genes in cell lines and patient's specimens. PTBP1 expression correlates with disease progression, poor prognosis, and worse survival in patients with NMIBC. Downregulation of PTBP1 expression affects prosurvival features of bladder cancer cells and modulates AS of genes with relevance for bladder cancer, suggesting its role as an outcome-predictor in this disease. . 10.1158/1078-0432.CCR-17-3850
    Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications. Hovelson Daniel H,Udager Aaron M,McDaniel Andrew S,Grivas Petros,Palmbos Phillip,Tamura Shuzo,Lazo de la Vega Lorena,Palapattu Ganesh,Veeneman Brendan,El-Sawy Layla,Sadis Seth E,Morgan Todd M,Montgomery Jeffrey S,Weizer Alon Z,Day Kathleen C,Neamati Nouri,Liebert Monica,Keller Evan T,Day Mark L,Mehra Rohit,Tomlins Scott A European urology BACKGROUND:Integrated molecular profiling has identified intrinsic expression-based bladder cancer molecular subtypes. Despite frequent histological diversity, robustness of subtypes in paired conventional (urothelial) and squamous components of the same bladder tumor has not been reported. OBJECTIVE:To assess the impact of histological heterogeneity on expression-based bladder cancer subtypes. DESIGN, SETTING, AND PARTICIPANTS:We performed clinically applicable, targeted DNA and/or RNA sequencing (multiplexed DNA and RNA sequencing [mxDNAseq and mxRNAseq, respectively]) on 112 formalin-fixed paraffin-embedded (FFPE) bladder cancer samples, including 12 cases with paired urothelial/squamous components and 21 bladder cancer cell lines. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS:Unsupervised hierarchical and consensus clustering of target gene expression enabled derivation of basal/luminal molecular subtyping. RESULTS AND LIMITATION:Across 21 bladder cancer cell lines, our custom mxRNAseq panel was highly concordant with whole transcriptome sequencing, and assessed targets robustly determined expression-based basal/luminal subtypes from The Cancer Genome Atlas data (in silico) and internally sequenced FFPE tissues. Frequent deleterious TP53 (56%) and activating hotspot PIK3CA (30%) somatic mutations were seen across 69 high-quality tissue samples. Potentially targetable focal ERBB2 (6%) or EGFR (6%) amplifications were also identified, and a novel subgene copy-number detection approach is described. Combined DNA/RNA analysis showed that focally amplified samples exhibit outlier EGFR and ERBB2 expression distinct from subtype-intrinsic profiles. Critically, paired urothelial and squamous components showed divergent basal/luminal status in three of 12 cases (25%), despite identical putatively clonal prioritized somatic genomic alterations. Limitations include lack of profiled paired normal tissues for formal somatic alteration determination, and the need for formal analytical and clinical validation. CONCLUSIONS:Our results support the feasibility of clinically relevant integrative bladder cancer profiling and challenge the intrinsic nature of expression subtypes in histologically diverse bladder cancers. PATIENT SUMMARY:A targeted RNA sequencing assay is capable of assessing gene expression-based subtypes in individual components of clinical bladder cancer tissue specimens. Different histological components of the same tumor may yield divergent expression profiles, suggesting that expression-based subtypes should be interpreted with caution in heterogeneous cancers. 10.1016/j.eururo.2018.06.047
    Re: Ming-Jun Shi, Xiang-Yu Meng, Philippe Lamy, et al. APOBEC-mediated Mutagenesis as a Likely Cause of FGFR3 S249C Mutation Over-representation in Bladder Cancer. Eur Urol 2019;76:9-13. Yang Alexander,Cannataro Vincent L,Townsend Jeffrey P European urology 10.1016/j.eururo.2019.08.018
    Consensus Genomic Subtypes of Muscle-invasive Bladder Cancer: A Step in the Right Direction but Still a Long Way To Go. Yatai Kenneth B,Dunning Mark J,Wang Dennis European urology 10.1016/j.eururo.2019.09.032
    Gene Expression Profile of the Clinically Aggressive Micropapillary Variant of Bladder Cancer. Guo Charles Chuanhai,Dadhania Vipulkumar,Zhang Li,Majewski Tadeusz,Bondaruk Jolanta,Sykulski Maciej,Wronowska Weronika,Gambin Anna,Wang Yan,Zhang Shizhen,Fuentes-Mattei Enrique,Kamat Ashish Madhav,Dinney Colin,Siefker-Radtke Arlene,Choi Woonyoung,Baggerly Keith A,McConkey David,Weinstein John N,Czerniak Bogdan European urology BACKGROUND:Progression of conventional urothelial carcinoma of the bladder to a tumor with unique microscopic features referred to as micropapillary carcinoma is coupled with aggressive clinical behavior signified by a high propensity for metastasis to regional lymph nodes and distant organs resulting in shorter survival. OBJECTIVE:To analyze the expression profile of micropapillary cancer and define its molecular features relevant to clinical behavior. DESIGN, SETTING, AND PARTICIPANTS:We retrospectively identified 43 patients with micropapillary bladder cancers and a reference set of 89 patients with conventional urothelial carcinomas and performed whole-genome expression messenger RNA profiling. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS:The tumors were segregated into distinct groups according to hierarchical clustering analyses. They were also classified according to luminal, p53-like, and basal categories using a previously described algorithm. We applied Ingenuity Pathway Analysis software (Qiagen, Redwood City, CA, USA) and gene set enrichment analysis for pathway analyses. Cox proportional hazards models and Kaplan-Meier methods were used to assess the relationship between survival and molecular subtypes. The expression profile of micropapillary cancer was validated for selected markers by immunohistochemistry on parallel tissue microarrays. RESULTS AND LIMITATIONS:We show that the striking features of micropapillary cancer are downregulation of miR-296 and activation of chromatin-remodeling complex RUVBL1. In contrast to conventional urothelial carcinomas that based on their expression can be equally divided into luminal and basal subtypes, micropapillary cancer is almost exclusively luminal, displaying enrichment of active peroxisome proliferator-activated receptor γ and suppression of p63 target genes. As with conventional luminal urothelial carcinomas, a subset of micropapillary cancers exhibit activation of wild-type p53 downstream genes and represent the most aggressive molecular subtype of the disease with the shortest survival. The involvement of miR-296 and RUVBL1 in the development of micropapillary bladder cancer was identified by the analyses of correlative associations of genome expression profiles and requires mechanistic validation. CONCLUSIONS:Micropapillary cancer evolves through the luminal pathway and is characterized by the activation of miR-296 and RUVBL1 target genes. PATIENT SUMMARY:Our observations have important implications for prognosis and for possible future development of more effective therapies for micropapillary bladder cancer. 10.1016/j.eururo.2016.02.056
    ILC2-modulated T cell-to-MDSC balance is associated with bladder cancer recurrence. Chevalier Mathieu F,Trabanelli Sara,Racle Julien,Salomé Bérengère,Cesson Valérie,Gharbi Dalila,Bohner Perrine,Domingos-Pereira Sonia,Dartiguenave Florence,Fritschi Anne-Sophie,Speiser Daniel E,Rentsch Cyrill A,Gfeller David,Jichlinski Patrice,Nardelli-Haefliger Denise,Jandus Camilla,Derré Laurent The Journal of clinical investigation Non-muscle-invasive bladder cancer (NMIBC) is a highly recurrent tumor despite intravesical immunotherapy instillation with the bacillus Calmette-Guérin (BCG) vaccine. In a prospective longitudinal study, we took advantage of BCG instillations, which increase local immune infiltration, to characterize immune cell populations in the urine of patients with NMIBC as a surrogate for the bladder tumor microenvironment. We observed an infiltration of neutrophils, T cells, monocytic myeloid-derived suppressor cells (M-MDSCs), and group 2 innate lymphoid cells (ILC2). Notably, patients with a T cell-to-MDSC ratio of less than 1 showed dramatically lower recurrence-free survival than did patients with a ratio of greater than 1. Analysis of early and later time points indicated that this patient dichotomy existed prior to BCG treatment. ILC2 frequency was associated with detectable IL-13 in the urine and correlated with the level of recruited M-MDSCs, which highly expressed IL-13 receptor α1. In vitro, ILC2 were increased and potently expressed IL-13 in the presence of BCG or tumor cells. IL-13 induced the preferential recruitment and suppressive function of monocytes. Thus, the T cell-to-MDSC balance, associated with a skewing toward type 2 immunity, may predict bladder tumor recurrence and influence the mortality of patients with muscle-invasive cancer. Moreover, these results underline the ILC2/IL-13 axis as a targetable pathway to curtail the M-MDSC compartment and improve bladder cancer treatment. 10.1172/JCI89717
    Targeted Exome Sequencing of the Cancer Genome in Patients with Very High-risk Bladder Cancer. Longo Thomas,McGinley Kathleen F,Freedman Jennifer A,Etienne Wiguins,Wu Yuan,Sibley Alexander,Owzar Kouros,Gresham Jeremy,Moy Christopher,Szabo Stephen,Greshock Joel,Zhou Hui,Bai Yuchen,Inman Brant A European urology We completed targeted exome sequencing of the tumors of 50 patients with pTis-pT4b bladder cancer. Mutations were categorized by type, stratified against previously identified cancer loci in the Catalogue of Somatic Mutations in Cancer and The Cancer Genome Atlas databases, and evaluated in pathway analysis and comutation plots. We analyzed mutation associations with receipt of neoadjuvant chemotherapy, nodal involvement, metastatic disease development, and survival. Compared with The Cancer Genome Atlas, we found higher mutation rates in genes encoding products involved in epigenetic regulation and cell cycle regulation. Of the pathways examined, PI3K/mTOR and Cell Cycle/DNA Repair exhibited the greatest frequencies of mutation. RB1 and TP53, as well as NF1 and PIK3CA were frequently comutated. We identified no association between mutations in specific genes and key clinical outcomes of interest when corrected for multiple testing. Discovery phase analysis of the somatic mutations in 50 high-risk bladder cancer patients revealed novel mutations and mutational patterns, which may be useful for developing targeted therapy regimens or new biomarkers for patients at very high risk of disease metastasis and death. PATIENT SUMMARY:In this report we found known, as well as previously unreported, genetic mutations in the tumors of patients with high-risk bladder cancer. These mutations, if validated, may serve as actionable targets for new trials. 10.1016/j.eururo.2016.07.049
    Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Robertson A Gordon,Kim Jaegil,Al-Ahmadie Hikmat,Bellmunt Joaquim,Guo Guangwu,Cherniack Andrew D,Hinoue Toshinori,Laird Peter W,Hoadley Katherine A,Akbani Rehan,Castro Mauro A A,Gibb Ewan A,Kanchi Rupa S,Gordenin Dmitry A,Shukla Sachet A,Sanchez-Vega Francisco,Hansel Donna E,Czerniak Bogdan A,Reuter Victor E,Su Xiaoping,de Sa Carvalho Benilton,Chagas Vinicius S,Mungall Karen L,Sadeghi Sara,Pedamallu Chandra Sekhar,Lu Yiling,Klimczak Leszek J,Zhang Jiexin,Choo Caleb,Ojesina Akinyemi I,Bullman Susan,Leraas Kristen M,Lichtenberg Tara M,Wu Catherine J,Schultz Nicholaus,Getz Gad,Meyerson Matthew,Mills Gordon B,McConkey David J, ,Weinstein John N,Kwiatkowski David J,Lerner Seth P Cell 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. 10.1016/j.cell.2017.09.007
    c-Met activation leads to the establishment of a TGFβ-receptor regulatory network in bladder cancer progression. Sim Wen Jing,Iyengar Prasanna Vasudevan,Lama Dilraj,Lui Sarah Kit Leng,Ng Hsien Chun,Haviv-Shapira Lior,Domany Eytan,Kappei Dennis,Tan Tuan Zea,Saei Azad,Jaynes Patrick William,Verma Chandra Shekhar,Kumar Alan Prem,Rouanne Mathieu,Ha Hong Koo,Radulescu Camelia,Ten Dijke Peter,Eichhorn Pieter Johan Adam,Thiery Jean Paul Nature communications Treatment of muscle-invasive bladder cancer remains a major clinical challenge. Aberrant HGF/c-MET upregulation and activation is frequently observed in bladder cancer correlating with cancer progression and invasion. However, the mechanisms underlying HGF/c-MET-mediated invasion in bladder cancer remains unknown. As part of a negative feedback loop SMAD7 binds to SMURF2 targeting the TGFβ receptor for degradation. Under these conditions, SMAD7 acts as a SMURF2 agonist by disrupting the intramolecular interactions within SMURF2. We demonstrate that HGF stimulates TGFβ signalling through c-SRC-mediated phosphorylation of SMURF2 resulting in loss of SMAD7 binding and enhanced SMURF2 C2-HECT interaction, inhibiting SMURF2 and enhancing TGFβ receptor stabilisation. This upregulation of the TGFβ pathway by HGF leads to TGFβ-mediated EMT and invasion. In vivo we show that TGFβ receptor inhibition prevents bladder cancer invasion. Furthermore, we make a rationale for the use of combinatorial TGFβ and MEK inhibitors for treatment of high-grade non-muscle-invasive bladder cancers. 10.1038/s41467-019-12241-2
    A Consensus Molecular Classification of Muscle-invasive Bladder Cancer. Kamoun Aurélie,de Reyniès Aurélien,Allory Yves,Sjödahl Gottfrid,Robertson A Gordon,Seiler Roland,Hoadley Katherine A,Groeneveld Clarice S,Al-Ahmadie Hikmat,Choi Woonyoung,Castro Mauro A A,Fontugne Jacqueline,Eriksson Pontus,Mo Qianxing,Kardos Jordan,Zlotta Alexandre,Hartmann Arndt,Dinney Colin P,Bellmunt Joaquim,Powles Thomas,Malats Núria,Chan Keith S,Kim William Y,McConkey David J,Black Peter C,Dyrskjøt Lars,Höglund Mattias,Lerner Seth P,Real Francisco X,Radvanyi François, European urology BACKGROUND:Muscle-invasive bladder cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, but the diversity of their subtype sets impedes their clinical application. OBJECTIVE:To achieve an international consensus on MIBC molecular subtypes that reconciles the published classification schemes. DESIGN, SETTING, AND PARTICIPANTS:We used 1750 MIBC transcriptomic profiles from 16 published datasets and two additional cohorts. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS:We performed a network-based analysis of six independent MIBC classification systems to identify a consensus set of molecular classes. Association with survival was assessed using multivariable Cox models. RESULTS AND LIMITATIONS:We report the results of an international effort to reach a consensus on MIBC molecular subtypes. We identified a consensus set of six molecular classes: luminal papillary (24%), luminal nonspecified (8%), luminal unstable (15%), stroma-rich (15%), basal/squamous (35%), and neuroendocrine-like (3%). These consensus classes differ regarding underlying oncogenic mechanisms, infiltration by immune and stromal cells, and histological and clinical characteristics, including outcomes. We provide a single-sample classifier that assigns a consensus class label to a tumor sample's transcriptome. Limitations of the work are retrospective clinical data collection and a lack of complete information regarding patient treatment. CONCLUSIONS:This consensus system offers a robust framework that will enable testing and validation of predictive biomarkers in future prospective clinical trials. PATIENT SUMMARY:Bladder cancers are heterogeneous at the molecular level, and scientists have proposed several classifications into sets of molecular classes. While these classifications may be useful to stratify patients for prognosis or response to treatment, a consensus classification would facilitate the clinical use of molecular classes. Conducted by multidisciplinary expert teams in the field, this study proposes such a consensus and provides a tool for applying the consensus classification in the clinical setting. 10.1016/j.eururo.2019.09.006
    Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency. Hurst Carolyn D,Alder Olivia,Platt Fiona M,Droop Alastair,Stead Lucy F,Burns Julie E,Burghel George J,Jain Sunjay,Klimczak Leszek J,Lindsay Helen,Roulson Jo-An,Taylor Claire F,Thygesen Helene,Cameron Angus J,Ridley Anne J,Mott Helen R,Gordenin Dmitry A,Knowles Margaret A Cancer cell Bladder cancer incurs a higher lifetime treatment cost than other cancers due to frequent recurrence of non-invasive disease. Improved prognostic biomarkers and localized therapy are needed for this large patient group. We defined two major genomic subtypes of primary stage Ta tumors. One of these was characterized by loss of 9q including TSC1, increased KI67 labeling index, upregulated glycolysis, DNA repair, mTORC1 signaling, features of the unfolded protein response, and altered cholesterol homeostasis. Comparison with muscle-invasive bladder cancer mutation profiles revealed lower overall mutation rates and more frequent mutations in RHOB and chromatin modifier genes. More mutations in the histone lysine demethylase KDM6A were present in non-invasive tumors from females than males. 10.1016/j.ccell.2017.08.005