An essential role for decorin in bladder cancer invasiveness

Muscle-invasive forms of urothelial carcinomas are responsible for most mortality in bladder cancer. Finding new treatments for invasive bladder tumours requires adequate animal models to decipher the mechanisms of progression, in particular the way tumours interact with their microenvironment. Herein, using the murine bladder tumour cell line MB49 and its more aggressive variant MB49-I, we demonstrate that the adaptive immune system efficiently limits progression of MB49, whereas MB49-I has lost tumour antigens and is insensitive to adaptive immune responses. Furthermore, we unravel a parallel mechanism developed by MB49-I to subvert its environment: de novo secretion of the proteoglycan decorin. We show that decorin overexpression in the MB49/MB49-I model is required for efficient progression, by promoting angiogenesis and tumour cell invasiveness. Finally, we show that these results are relevant to muscle-invasive human bladder carcinomas, which overexpress decorin together with angiogenesis- and adhesion/migration-related genes, and that decorin overexpression in the human bladder carcinoma cell line TCCSUP is required for efficient invasiveness in vitro. We thus propose decorin as a new therapeutic target for these aggressive tumours.Fil: El Behi, Mohamed. Institute Curie; Francia. Centre de Recherche de I; Francia. Inserm; FranciaFil: Krumeich, Sophie. Institute Curie; Francia. Inserm; FranciaFil: Lodillinsky, Catalina. Institute Curie; Francia. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Oncología "Ángel H. Roffo"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kamoun, Aurélie. Institute Curie; FranciaFil: Tibaldi, Lorenzo. Institute Curie; Francia. Inserm; FranciaFil: Sugano, Gaël. Institute Curie; Francia. Inserm; FranciaFil: de Reynies, Aurélien. Ligue Nationale Contre le Cancer; FranciaFil: Chapeaublanc, Elodie. Institute Curie; Francia. Centre National de la Recherche Scientifique; FranciaFil: Laplanche, Agnès. Centre National de la Recherche Scientifique; Francia. Institut de Cancérologie Gustave Roussy; FranciaFil: Lebret, Thierry. Hôpital Foch. Service d; Francia. Université de Versailles; FranciaFil: Allory, Yves. Inserm; FranciaFil: Radvanyi, François. Institute Curie; Francia. Centre National de la Recherche Scientifique; FranciaFil: Lantz, Olivier. Institute Curie; Francia. Inserm; FranciaFil: Eijan, Ana Maria. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Oncología "Ángel H. Roffo"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bernard Pierrot, Isabelle. Institute Curie; Francia. Centre National de la Recherche Scientifique; FranciaFil: Théery, Clotilde. Institute Curie; Francia. Inserm; Franci

A Consensus Molecular Classification of Muscle-invasive Bladder Cancer

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. An international consortium of bladder cancer expert teams establishes a consensus reconciling the diverse molecular classifications of muscle-invasive bladder cancer. This work offers a robust framework that will enable testing and validating predictive biomarkers in future prospective clinical trials

Bladder cancer characterisation by an integrative exon array data analysis

Les rapides progrès technologiques en matière de techniques de biologie à grande échelle, comprenant notamment les microarrays, conduisent en 2006 au développement d’une nouvelle génération de puces à très haute résolution, capables de cibler à la fois tous les gènes du transcriptome humain, mais également tous les exons de ces gènes pris individuellement. L’avènement de cette puce, communément appelée puce exon, permit d’obtenir une mesure précise des changements transcriptomiques affectant les cellules cancéreuses, en offrant la possibilité de prendre en compte l’expression relative de différents exons d’un même gène.L’épissage alternatif et la transcription alternative sont les deux principaux mécanismes biologiques à l’origine de l’existence de plusieurs transcrits pour un même gène. Ces processus biologiques ont été mis en évidence depuis longtemps mais leur régulation dans les cellules normales ainsi que leurs dérégulations dans les cancers sont encore mal caractérisées de par la complexité des mécanismes impliqués. Par leur design, les puces exons permettent de mettre en évidence la présence de variations d’expression entre plusieurs transcrits potentiels d’un même gène, ouvrant ainsi la voie à une meilleure compréhension de ces processus biologiques.A partir d’un important jeu de données d’échantillons de cancers de la vessie dont le profil transcriptomique fut obtenu par puces exons, nous nous sommes intéressés à l’étude des changements d’épissage alternatif et à l’utilisation de promoteurs alternatifs dans les tumeurs de vessie. L’utilisation d’outils statistiques et mathématiques dédiés à l’analyse de ces puces nous a permis dans un premier temps d’identifier de nombreux gènes dont l’expression relative des différents transcrits est spécifiquement dérégulée dans les tumeurs de vessie. Ces transcrits constituent une nouvelle source pour l’identification de cibles thérapeutiques spécifiques des tumeurs. Nous avons pu montrer qu’avec une approche ciblée sur les changements d’expression relative de transcrits alternatifs d’un même gène, il était possible de constituer un panel de potentiels marqueurs tumoraux permettant le développement de nouveaux tests urinaires utiles à la détection des cancers de vessie et à la surveillance des patients.Par une analyse non supervisée des profils d’exons potentiellement dérégulés, nous avons pu observer une stratification des tumeurs similaire à celle observée par l’étude des profils géniques issus de puces classiques, confirmant alors l’existence d’un sous groupe de tumeurs de vessie présentant des caractéristiques transcriptomiques propres. Nous avons pu associer à ce sous-groupe de mauvais pronostic, une signature d’inclusion différentielle de certains exons. Cette signature impliquant 19 gènes permet d’identifier précisément ces tumeurs de manière très spécifique et constitue par conséquent un outil puissant utilisable en clinique.L’étude ciblée d’une voie de signalisation fréquemment dérégulée dans les cancers nous a permis de mettre en évidence une dérégulation globale de l’expression relative des transcrits alternatifs de gènes impliqués dans la prolifération cellulaire, et d’en identifier de probables régulateurs. Enfin, L’analyse des données de puces exons à la lumière des données de méthylation de l’ADN nous a permis d’identifier un mécanisme épigénétique régulant l’utilisation de promoteurs alternatifs dans un sous-groupe de tumeurs de vessie.L’ensemble des résultats obtenus par l’analyse de ces puces exons a par conséquent permis de caractériser à l’échelle du transcrit les dérégulations spécifiques des tumeurs de vessie, et d’en identifier certains mécanismes. Ces dérégulations permettent non seulement d’identifier spécifiquement plusieurs sous-groupe de tumeurs dont un de mauvais pronostic, mais offrent également de nouvelles possibilités quant-à la recherche de marqueurs urinaires pour la surveillance des patients.The development of microarray technology in the late 1990’s served as an essential tool to comprehend the scope of transcriptomic deregulations occurring in cancer cells. Signals generated from the first generation of transcriptomic microarrays gave simultaneous measures of expression from a large number of genes, therefore enabling to identify candidate genes involved in cancer progression and putative therapeutic targets. In 2006, through a fast de- velopment of high-throughput technologies, the available large scale analysis tools became enriched with a new generation of high resolution microarrays measuring expression signals both at the gene-level and at the exon-level of each gene. The advent of this high-resolution microarray, commonly called exon array, provided the opportunity to get a more accurate meas- ure of transcriptomic changes affecting cancer cells by enabling to consider relative expression changes of the exons from a same gene.Alternative splicing and alternative transcription are the two main biological mechanisms accounting for the production of several transcripts from a same gene. Although these bio- logical processes have been known for a long time, their regulation in normal cells and their deregulation in cancer still remain challenging to well-characterize, mainly due to the complex- ity of the involved mechanisms. Through their design, exon arrays enable to identify variable expression patterns within several potential transcripts of a same gene, therefore bringing new insight into these biological processes.Based on a large dataset of bladder cancer samples that were profiled on exon arrays, we focused on the study of alternative splicing changes and alternative promoter usage in bladder tumours. Analysis of these exon arrays through the use of adapted statistical and mathemat- ical tools initially resulted in the identification of numerous genes showing differential relative expression patterns of their transcripts between cancer and normal samples. These transcripts represent a new opportunity to define tumour-specific therapeutic targets. We demonstrated that using an approach targeted on relative expression changes of transcripts from a same gene, it was possible to build up a panel of potential tumour-specific markers enabling the development of new urinary test to detect bladder cancer and monitor its evolution.Through an unsupervised analysis of putatively deregulated exon profiles, we observed that the partitioning of bladder tumours was similar to the classification resulting from the study of classical gene microarray expression profiles, consequently confirming the existence of a bladder subgroup with peculiar transcriptomic properties. For this subgroup of bad prognosis, we established a signature based on the differential alternative inclusion of several exons. This signature relates to 19 genes and enables to accurately identify tumours from this subgroup, therefore providing a powerful tool to be used in clinical practice.By studying a specific pathway often deregulated in cancer, we highlighted an overall dereg- ulation of the relative expression of alternative transcripts from genes involved in cell prolifer- ation, and identified potential actors involved in the underlying regulatory process. Eventually, the analysis of exon arrays in the light of DNA methylation array data enabled us to identify an epigenetic mechanism regulating the use of alternative promoters in a subgroup of bladder tumours.Together, the results obtained from exon array analysis consequently provided a character- ization at the transcript level of bladder tumour specific deregulations and brought insight into the underlying mechanisms. The highlighted deregulations not only allow to accurately identify two subgroups of tumours, of which one has a bad prognosis, but also offer new possibilities regarding the definition of urinary markers for patient monitoring

Caractérisation des cancers de vessie par l'analyse intégrative des données de puces exons

Les rapides progrès technologiques en matière de techniques de biologie à grande échelle, comprenant notamment les microarrays, conduisent en 2006 au développement d une nouvelle génération de puces à très haute résolution, capables de cibler à la fois tous les gènes du transcriptome humain, mais également tous les exons de ces gènes pris individuellement. L avènement de cette puce, communément appelée puce exon, permit d obtenir une mesure précise des changements transcriptomiques affectant les cellules cancéreuses, en offrant la possibilité de prendre en compte l expression relative de différents exons d un même gène.L épissage alternatif et la transcription alternative sont les deux principaux mécanismes biologiques à l origine de l existence de plusieurs transcrits pour un même gène. Ces processus biologiques ont été mis en évidence depuis longtemps mais leur régulation dans les cellules normales ainsi que leurs dérégulations dans les cancers sont encore mal caractérisées de par la complexité des mécanismes impliqués. Par leur design, les puces exons permettent de mettre en évidence la présence de variations d expression entre plusieurs transcrits potentiels d un même gène, ouvrant ainsi la voie à une meilleure compréhension de ces processus biologiques.A partir d un important jeu de données d échantillons de cancers de la vessie dont le profil transcriptomique fut obtenu par puces exons, nous nous sommes intéressés à l étude des changements d épissage alternatif et à l utilisation de promoteurs alternatifs dans les tumeurs de vessie. L utilisation d outils statistiques et mathématiques dédiés à l analyse de ces puces nous a permis dans un premier temps d identifier de nombreux gènes dont l expression relative des différents transcrits est spécifiquement dérégulée dans les tumeurs de vessie. Ces transcrits constituent une nouvelle source pour l identification de cibles thérapeutiques spécifiques des tumeurs. Nous avons pu montrer qu avec une approche ciblée sur les changements d expression relative de transcrits alternatifs d un même gène, il était possible de constituer un panel de potentiels marqueurs tumoraux permettant le développement de nouveaux tests urinaires utiles à la détection des cancers de vessie et à la surveillance des patients.Par une analyse non supervisée des profils d exons potentiellement dérégulés, nous avons pu observer une stratification des tumeurs similaire à celle observée par l étude des profils géniques issus de puces classiques, confirmant alors l existence d un sous groupe de tumeurs de vessie présentant des caractéristiques transcriptomiques propres. Nous avons pu associer à ce sous-groupe de mauvais pronostic, une signature d inclusion différentielle de certains exons. Cette signature impliquant 19 gènes permet d identifier précisément ces tumeurs de manière très spécifique et constitue par conséquent un outil puissant utilisable en clinique.L étude ciblée d une voie de signalisation fréquemment dérégulée dans les cancers nous a permis de mettre en évidence une dérégulation globale de l expression relative des transcrits alternatifs de gènes impliqués dans la prolifération cellulaire, et d en identifier de probables régulateurs. Enfin, L analyse des données de puces exons à la lumière des données de méthylation de l ADN nous a permis d identifier un mécanisme épigénétique régulant l utilisation de promoteurs alternatifs dans un sous-groupe de tumeurs de vessie.L ensemble des résultats obtenus par l analyse de ces puces exons a par conséquent permis de caractériser à l échelle du transcrit les dérégulations spécifiques des tumeurs de vessie, et d en identifier certains mécanismes. Ces dérégulations permettent non seulement d identifier spécifiquement plusieurs sous-groupe de tumeurs dont un de mauvais pronostic, mais offrent également de nouvelles possibilités quant-à la recherche de marqueurs urinaires pour la surveillance des patients.The development of microarray technology in the late 1990 s served as an essential tool to comprehend the scope of transcriptomic deregulations occurring in cancer cells. Signals generated from the first generation of transcriptomic microarrays gave simultaneous measures of expression from a large number of genes, therefore enabling to identify candidate genes involved in cancer progression and putative therapeutic targets. In 2006, through a fast de- velopment of high-throughput technologies, the available large scale analysis tools became enriched with a new generation of high resolution microarrays measuring expression signals both at the gene-level and at the exon-level of each gene. The advent of this high-resolution microarray, commonly called exon array, provided the opportunity to get a more accurate meas- ure of transcriptomic changes affecting cancer cells by enabling to consider relative expression changes of the exons from a same gene.Alternative splicing and alternative transcription are the two main biological mechanisms accounting for the production of several transcripts from a same gene. Although these bio- logical processes have been known for a long time, their regulation in normal cells and their deregulation in cancer still remain challenging to well-characterize, mainly due to the complex- ity of the involved mechanisms. Through their design, exon arrays enable to identify variable expression patterns within several potential transcripts of a same gene, therefore bringing new insight into these biological processes.Based on a large dataset of bladder cancer samples that were profiled on exon arrays, we focused on the study of alternative splicing changes and alternative promoter usage in bladder tumours. Analysis of these exon arrays through the use of adapted statistical and mathemat- ical tools initially resulted in the identification of numerous genes showing differential relative expression patterns of their transcripts between cancer and normal samples. These transcripts represent a new opportunity to define tumour-specific therapeutic targets. We demonstrated that using an approach targeted on relative expression changes of transcripts from a same gene, it was possible to build up a panel of potential tumour-specific markers enabling the development of new urinary test to detect bladder cancer and monitor its evolution.Through an unsupervised analysis of putatively deregulated exon profiles, we observed that the partitioning of bladder tumours was similar to the classification resulting from the study of classical gene microarray expression profiles, consequently confirming the existence of a bladder subgroup with peculiar transcriptomic properties. For this subgroup of bad prognosis, we established a signature based on the differential alternative inclusion of several exons. This signature relates to 19 genes and enables to accurately identify tumours from this subgroup, therefore providing a powerful tool to be used in clinical practice.By studying a specific pathway often deregulated in cancer, we highlighted an overall dereg- ulation of the relative expression of alternative transcripts from genes involved in cell prolifer- ation, and identified potential actors involved in the underlying regulatory process. Eventually, the analysis of exon arrays in the light of DNA methylation array data enabled us to identify an epigenetic mechanism regulating the use of alternative promoters in a subgroup of bladder tumours.Together, the results obtained from exon array analysis consequently provided a character- ization at the transcript level of bladder tumour specific deregulations and brought insight into the underlying mechanisms. The highlighted deregulations not only allow to accurately identify two subgroups of tumours, of which one has a bad prognosis, but also offer new possibilities regarding the definition of urinary markers for patient monitoring.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF

A consensus molecular classification of muscle-invasive bladder cancer

Data de publicació electrònica: 26-09-2019Background: 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

Cystathionine as a marker for 1p/19q codeleted gliomas by in vivo magnetic resonance spectroscopy

International audienceBackground: Codeletion of chromosome arms 1p and 19q (1p/19q codeletion) highly benefits diagnosis and prognosis in gliomas. In this study, we investigated the effect of 1p/19q codeletion on cancer cell metabolism and evaluated possible metabolic targets for tailored therapies.Methods: We combined in vivo 1H (proton) magnetic resonance spectroscopy (MRS) measurements in human gliomas with the analysis of a series of standard amino acids by liquid chromatography-mass spectroscopy (LC-MS) in human glioma biopsies. Sixty-five subjects with low-grade glioma were included in the study: 31 underwent the MRI/MRS examination, 47 brain tumor tissue samples were analyzed with LC-MS, and 33 samples were analyzed for gene expression with quantitative PCR. Additionally, we performed metabolic tracer experiments in cell models with 1p deletion.Results: We report the first in vivo detection of cystathionine by MRS in 1p/19q codeleted gliomas. Selective accumulation of cystathionine was observed in codeleted gliomas in vivo, in brain tissue samples, as well as in cells harboring heterozygous deletions for serine- and cystathionine-pathway genes located on 1p: phosphoglycerate dehydrogenase (PHGDH) and cystathionine gamma-lyase (CTH). Quantitative PCR analyses showed 40-50% lower expression of both PHGDH and CTH in 1p/19q codeleted gliomas compared with their non-codeleted counterparts.Conclusions: Our results provide strong evidence of a selective vulnerability of codeleted gliomas to serine and glutathione depletion and point to cystathionine as a possible noninvasive marker of treatment response

A deep learning model to predict RNA-Seq expression of tumours from whole slide images

International audienceDeep learning methods for digital pathology analysis are an effective way to address multiple clinical questions, from diagnosis to prediction of treatment outcomes. These methods have also been used to predict gene mutations from pathology images, but no comprehensive evaluation of their potential for extracting molecular features from histology slides has yet been performed. We show that HE2RNA, a model based on the integration of multiple data modes, can be trained to systematically predict RNA-Seq profiles from whole-slide images alone, without expert annotation. Through its interpretable design, HE2RNA provides virtual spatialization of gene expression, as validated by CD3- and CD20-staining on an independent dataset. The transcriptomic representation learned by HE2RNA can also be transferred on other datasets, even of small size, to increase prediction performance for specific molecular phenotypes. We illustrate the use of this approach in clinical diagnosis purposes such as the identification of tumors with microsatellite instability

EGFR as a potential therapeutic target for a subset of muscle-invasive bladder cancers presenting a basal-like phenotype

International audienceA subtype of aggressive human muscle-invasive bladder cancer expresses basal epithelial markers and is sensitive to EGFR inhibition in preclinical models

Sensitivity of the evaluated LFAs for the antibody level subgroups (strongly and weakly positive).

Sensitivity of the evaluated LFAs for the antibody level subgroups (strongly and weakly positive).</p

Operating and storage conditions of the LFAs evaluated.

Operating and storage conditions of the LFAs evaluated.</p