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Groeneveld CS, Sanchez-Quiles V, Dufour F, Shi M, Dingli F, Nicolle R, Chapeaublanc E, Poullet P, Jeffery D, Krucker C, Maillé P, Vacherot F, Vordos D, Benhamou S, Lebret T, Micheau O, Zinovyev A, Loew D, Allory Y, de Reyniès A, Bernard-Pierrot I, Radvanyi F. Proteogenomic Characterization of Bladder Cancer Reveals Sensitivity to Apoptosis Induced by Tumor Necrosis Factor-related Apoptosis-inducing Ligand in FGFR3-mutated Tumors. Eur Urol 2024; 85:483-494. [PMID: 37380559 DOI: 10.1016/j.eururo.2023.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/26/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Molecular understanding of muscle-invasive (MIBC) and non-muscle-invasive (NMIBC) bladder cancer is currently based primarily on transcriptomic and genomic analyses. OBJECTIVE To conduct proteogenomic analyses to gain insights into bladder cancer (BC) heterogeneity and identify underlying processes specific to tumor subgroups and therapeutic outcomes. DESIGN, SETTING, AND PARTICIPANTS Proteomic data were obtained for 40 MIBC and 23 NMIBC cases for which transcriptomic and genomic data were already available. Four BC-derived cell lines harboring FGFR3 alterations were tested with interventions. INTERVENTION Recombinant tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), second mitochondrial-derived activator of caspases mimetic (birinapant), pan-FGFR inhibitor (erdafitinib), and FGFR3 knockdown. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Proteomic groups from unsupervised analyses (uPGs) were characterized using clinicopathological, proteomic, genomic, transcriptomic, and pathway enrichment analyses. Additional enrichment analyses were performed for FGFR3-mutated tumors. Treatment effects on cell viability for FGFR3-altered cell lines were evaluated. Synergistic treatment effects were evaluated using the zero interaction potency model. RESULTS AND LIMITATIONS Five uPGs, covering both NMIBC and MIBC, were identified and bore coarse-grained similarity to transcriptomic subtypes underlying common features of these different entities; uPG-E was associated with the Ta pathway and enriched in FGFR3 mutations. Our analyses also highlighted enrichment of proteins involved in apoptosis in FGFR3-mutated tumors, not captured through transcriptomics. Genetic and pharmacological inhibition demonstrated that FGFR3 activation regulates TRAIL receptor expression and sensitizes cells to TRAIL-mediated apoptosis, further increased by combination with birinapant. CONCLUSIONS This proteogenomic study provides a comprehensive resource for investigating NMIBC and MIBC heterogeneity and highlights the potential of TRAIL-induced apoptosis as a treatment option for FGFR3-mutated bladder tumors, warranting a clinical investigation. PATIENT SUMMARY We integrated proteomics, genomics, and transcriptomics to refine molecular classification of bladder cancer, which, combined with clinical and pathological classification, should lead to more appropriate management of patients. Moreover, we identified new biological processes altered in FGFR3-mutated tumors and showed that inducing apoptosis represents a new potential therapeutic option.
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Affiliation(s)
- Clarice S Groeneveld
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France; Centre de Recherche des Cordeliers, AP-HP, Université Paris Cité, Paris, France
| | - Virginia Sanchez-Quiles
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - Florent Dufour
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France; Inovarion, Paris, France
| | - Mingjun Shi
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France; Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Florent Dingli
- Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Rémy Nicolle
- Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, Université Paris Cité, Paris, France
| | - Elodie Chapeaublanc
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - Patrick Poullet
- INSERM U900, MINES ParisTech, Institut Curie, PSL Research University, Paris, France
| | - Daniel Jeffery
- Urology Medico-Scientific Program, Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Clémentine Krucker
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - Pascale Maillé
- Département de Pathologie, Hôpital Henri Mondor, APHP, Créteil, France
| | | | - Dimitri Vordos
- Service d'Urologie, Hôpital Henri Mondor, APHP, Créteil, France
| | | | - Thierry Lebret
- Service d'Urologie, Hôpital Foch, UVSQ, Université Paris-Saclay, Suresnes, France
| | - Olivier Micheau
- INSERM, LNC UMR1231, Université Bourgogne Franche-Comté, Dijon, France
| | - Andrei Zinovyev
- INSERM U900, MINES ParisTech, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Yves Allory
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France; Department of Pathology, Institut Curie, UVSQ, Université Paris-Saclay, Saint-Cloud, France
| | - Aurélien de Reyniès
- Centre de Recherche des Cordeliers, AP-HP, Université Paris Cité, Paris, France
| | - Isabelle Bernard-Pierrot
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France
| | - François Radvanyi
- Equipe labellisée Ligue Contre le Cancer, CNRS, UMR144, Institut Curie, PSL Research University, Paris, France.
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Fontugne J, Xylinas E, Krucker C, Dixon V, Groeneveld CS, Pinar U, Califano G, Bucau M, Verine J, Desgrandchamps F, Hermieu JF, Radvanyi F, Allory Y, Masson-Lecomte A. Transcriptomic Profiling of Upper Tract Urothelial Carcinoma: Bladder Cancer Consensus Classification Relevance, Molecular Heterogeneity, and Differential Immune Signatures. Mod Pathol 2023; 36:100300. [PMID: 37558130 DOI: 10.1016/j.modpat.2023.100300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/25/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023]
Abstract
Analyses of large transcriptomics data sets of muscle-invasive bladder cancer (MIBC) have led to a consensus classification. Molecular subtypes of upper tract urothelial carcinomas (UTUCs) are less known. Our objective was to determine the relevance of the consensus classification in UTUCs by characterizing a novel cohort of surgically treated ≥pT1 tumors. Using immunohistochemistry (IHC), subtype markers GATA3-CK5/6-TUBB2B in multiplex, CK20, p16, Ki67, mismatch repair system proteins, and PD-L1 were evaluated. Heterogeneity was assessed morphologically and/or with subtype IHC. FGFR3 mutations were identified by pyrosequencing. We performed 3'RNA sequencing of each tumor, with multisampling in heterogeneous cases. Consensus classes, unsupervised groups, and microenvironment cell abundance were determined using gene expression. Most of the 66 patients were men (77.3%), with pT1 (n = 23, 34.8%) or pT2-4 stage UTUC (n = 43, 65.2%). FGFR3 mutations and mismatch repair-deficient status were identified in 40% and 4.7% of cases, respectively. Consensus subtypes robustly classified UTUCs and reflected intrinsic subgroups. All pT1 tumors were classified as luminal papillary (LumP). Combining our consensus classification results with those of previously published UTUC cohorts, LumP tumors represented 57.2% of ≥pT2 UTUCs, which was significantly higher than MIBCs. Ten patients (15.2%) harbored areas of distinct subtypes. Consensus classes were associated with FGFR3 mutations, stage, morphology, and IHC. The majority of LumP tumors were characterized by low immune infiltration and PD-L1 expression, in particular, if FGFR3 mutated. Our study shows that MIBC consensus classification robustly classified UTUCs and highlighted intratumoral molecular heterogeneity. The proportion of LumP was significantly higher in UTUCs than in MIBCs. Most LumP tumors showed low immune infiltration and PD-L1 expression and high proportion of FGFR3 mutations. These findings suggest differential response to novel therapies between patients with UTUC and those with MIBC.
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Affiliation(s)
- Jacqueline Fontugne
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, Paris Sciences et Lettres Research University, Paris, France; Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France.
| | - Evanguelos Xylinas
- Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Department of Urology, Bichat-Claude Bernard Hospital, Paris, France; Université de Paris, INSERM U976, Human Immunology, Pathophysiology, Immunotherapy, Paris, France
| | - Clémentine Krucker
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, Paris Sciences et Lettres Research University, Paris, France
| | - Victoria Dixon
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, Paris Sciences et Lettres Research University, Paris, France
| | - Clarice S Groeneveld
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, Paris Sciences et Lettres Research University, Paris, France; Ligue Nationale Contre le Cancer, Cartes d'Identité des Tumeurs Program, Paris, France
| | - Ugo Pinar
- Assistance Publique-Hôpitaux de Paris, Department of Urology, Saint-Louis Hospital, Paris, France
| | - Gianluigi Califano
- Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Department of Urology, Bichat-Claude Bernard Hospital, Paris, France
| | - Margot Bucau
- Assistance Publique-Hôpitaux de Paris, Department of Pathology, Bichat-Claude Bernard Hospital, Paris, France
| | - Jérôme Verine
- Assistance Publique-Hôpitaux de Paris, Department of Pathology, Saint-Louis Hospital, Paris, France
| | - François Desgrandchamps
- Assistance Publique-Hôpitaux de Paris, Department of Urology, Saint-Louis Hospital, Paris, France; Université Paris Cité, Service de Recherche en Hémato-Immunologie, CEA, INSERM U976, Human Immunology, Pathophysiology, Immunotherapy, Paris, France
| | - Jean-François Hermieu
- Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Department of Urology, Bichat-Claude Bernard Hospital, Paris, France
| | - François Radvanyi
- Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, Paris Sciences et Lettres Research University, Paris, France
| | - Yves Allory
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, CNRS, UMR144, Equipe labellisée Ligue Contre le Cancer, Paris Sciences et Lettres Research University, Paris, France; Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France
| | - Alexandra Masson-Lecomte
- Assistance Publique-Hôpitaux de Paris, Department of Urology, Saint-Louis Hospital, Paris, France; Université Paris Cité, Service de Recherche en Hémato-Immunologie, CEA, INSERM U976, Human Immunology, Pathophysiology, Immunotherapy, Paris, France
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3
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Robertson AG, Meghani K, Cooley LF, McLaughlin KA, Fall LA, Yu Y, Castro MAA, Groeneveld CS, de Reyniès A, Nazarov VI, Tsvetkov VO, Choy B, Raggi D, Marandino L, Montorsi F, Powles T, Necchi A, Meeks JJ. Expression-based subtypes define pathologic response to neoadjuvant immune-checkpoint inhibitors in muscle-invasive bladder cancer. Nat Commun 2023; 14:2126. [PMID: 37105962 PMCID: PMC10140274 DOI: 10.1038/s41467-023-37568-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Checkpoint immunotherapy (CPI) has increased survival for some patients with advanced-stage bladder cancer (BCa). However, most patients do not respond. Here, we characterized the tumor and immune microenvironment in pre- and post-treatment tumors from the PURE01 neoadjuvant pembrolizumab immunotherapy trial, using a consolidative approach that combined transcriptional and genetic profiling with digital spatial profiling. We identify five distinctive genetic and transcriptomic programs and validate these in an independent neoadjuvant CPI trial to identify the features of response or resistance to CPI. By modeling the regulatory network, we identify the histone demethylase KDM5B as a repressor of tumor immune signaling pathways in one resistant subtype (S1, Luminal-excluded) and demonstrate that inhibition of KDM5B enhances immunogenicity in FGFR3-mutated BCa cells. Our study identifies signatures associated with response to CPI that can be used to molecularly stratify patients and suggests therapeutic alternatives for subtypes with poor response to neoadjuvant immunotherapy.
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Affiliation(s)
| | - Khyati Meghani
- Departments of Urology, and Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Lauren Folgosa Cooley
- Departments of Urology, and Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Kimberly A McLaughlin
- Departments of Urology, and Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Leigh Ann Fall
- Departments of Urology, and Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Yanni Yu
- Departments of Urology, and Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, Brazil
| | - Clarice S Groeneveld
- Université Paris Cité, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, F-75018, Paris, France
- Oncologie Moleculaire, Institut Curie, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Aurélien de Reyniès
- Université Paris Cité, INSERM U1138 Centre de Recherches des Cordeliers, APHP, SeQOIA-IT, Paris, France
| | | | | | - Bonnie Choy
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Daniele Raggi
- Department of Medical Oncology, IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy
| | - Laura Marandino
- Department of Medical Oncology, IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy
| | - Francesco Montorsi
- Department of Urology, IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Thomas Powles
- Barts Experimental Cancer Medicine Centre, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andrea Necchi
- Department of Medical Oncology, IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Joshua J Meeks
- Departments of Urology, and Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Jesse Brown VA Medical Center, Chicago, IL, 60611, USA.
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4
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Neyret-Kahn H, Fontugne J, Meng XY, Groeneveld CS, Cabel L, Ye T, Guyon E, Krucker C, Dufour F, Chapeaublanc E, Rapinat A, Jeffery D, Tanguy L, Dixon V, Neuzillet Y, Lebret T, Gentien D, Davidson I, Allory Y, Bernard-Pierrot I, Radvanyi F. Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks. Oncogene 2023; 42:1524-1542. [PMID: 36944729 PMCID: PMC10162941 DOI: 10.1038/s41388-023-02662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
Muscle-invasive bladder cancer (BLCA) is an aggressive disease. Consensus BLCA transcriptomic subtypes have been proposed, with two major Luminal and Basal subgroups, presenting distinct molecular and clinical characteristics. However, how these distinct subtypes are regulated remains unclear. We hypothesized that epigenetic activation of distinct super-enhancers could drive the transcriptional programs of BLCA subtypes. Through integrated RNA-sequencing and epigenomic profiling of histone marks in primary tumours, cancer cell lines, and normal human urothelia, we established the first integrated epigenetic map of BLCA and demonstrated the link between subtype and epigenetic control. We identified the repertoire of activated super-enhancers and highlighted Basal, Luminal and Normal-associated SEs. We revealed super-enhancer-regulated networks of candidate master transcription factors for Luminal and Basal subgroups including FOXA1 and ZBED2, respectively. FOXA1 CRISPR-Cas9 mutation triggered a shift from Luminal to Basal phenotype, confirming its role in Luminal identity regulation and induced ZBED2 overexpression. In parallel, we showed that both FOXA1 and ZBED2 play concordant roles in preventing inflammatory response in cancer cells through STAT2 inhibition. Our study furthers the understanding of epigenetic regulation of muscle-invasive BLCA and identifies a co-regulated network of super-enhancers and associated transcription factors providing potential targets for the treatment of this aggressive disease.
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Affiliation(s)
- Hélène Neyret-Kahn
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France.
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France.
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France.
| | - Jacqueline Fontugne
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
| | - Xiang Yu Meng
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- College of Basic Medical Sciences, Medical School, Hubei Minzu University, Enshi, 445000, China
| | - Clarice S Groeneveld
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Université de Paris, Centre de Recherche des Cordeliers, Paris, France
| | - Luc Cabel
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Centre National de Recherche Scientifique (CNRS) UMR7104, Université de Strasbourg,1 rue Laurent Fries, 67404, Illkirch, France
| | - Elodie Guyon
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Paris, France
| | - Clémentine Krucker
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Florent Dufour
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Elodie Chapeaublanc
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Audrey Rapinat
- Department of Translational Research, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Daniel Jeffery
- Urology Medico-Scientific Program, Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Laura Tanguy
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - Victoria Dixon
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Yann Neuzillet
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
- Department of Urology, Hôpital Foch, Suresnes, France
| | - Thierry Lebret
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
- Department of Urology, Hôpital Foch, Suresnes, France
| | - David Gentien
- Department of Translational Research, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Genétique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/UDS, 67404, Illkirch Cedex, France
| | - Yves Allory
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université Versailles St-Quentin, Université Paris-Saclay, F-78180, Montigny-le-Bretonneux, France
| | - Isabelle Bernard-Pierrot
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
| | - François Radvanyi
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France
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5
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Lang H, Béraud C, Cabel L, Fontugne J, Lassalle M, Krucker C, Dufour F, Groeneveld CS, Dixon V, Meng X, Kamoun A, Chapeaublanc E, De Reynies A, Gamé X, Rischmann P, Bieche I, Masliah-Planchon J, Beaurepere R, Allory Y, Lindner V, Misseri Y, Radvanyi F, Lluel P, Bernard-Pierrot I, Massfelder T. Integrated molecular and pharmacological characterization of patient-derived xenografts from bladder and ureteral cancers identifies new potential therapies. Front Oncol 2022; 12:930731. [PMID: 36033544 PMCID: PMC9405192 DOI: 10.3389/fonc.2022.930731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
Background Muscle-invasive bladder cancer (MIBC) and upper urinary tract urothelial carcinoma (UTUC) are molecularly heterogeneous. Despite chemotherapies, immunotherapies, or anti-fibroblast growth factor receptor (FGFR) treatments, these tumors are still of a poor outcome. Our objective was to develop a bank of patient-derived xenografts (PDXs) recapitulating the molecular heterogeneity of MIBC and UTUC, to facilitate the preclinical identification of therapies. Methods Fresh tumors were obtained from patients and subcutaneously engrafted into immune-compromised mice. Patient tumors and matched PDXs were compared regarding histopathology, transcriptomic (microarrays), and genomic profiles [targeted Next-Generation Sequencing (NGS)]. Several PDXs were treated with chemotherapy (cisplatin/gemcitabine) or targeted therapies [FGFR and epidermal growth factor (EGFR) inhibitors]. Results A total of 31 PDXs were established from 1 non-MIBC, 25 MIBC, and 5 upper urinary tract tumors, including 28 urothelial (UC) and 3 squamous cell carcinomas (SCCs). Integrated genomic and transcriptomic profiling identified the PDXs of three different consensus molecular subtypes [basal/squamous (Ba/Sq), luminal papillary, and luminal unstable] and included FGFR3-mutated PDXs. High histological and genomic concordance was found between matched patient tumor/PDX. Discordance in molecular subtypes, such as a Ba/Sq patient tumor giving rise to a luminal papillary PDX, was observed (n=5) at molecular and histological levels. Ten models were treated with cisplatin-based chemotherapy, and we did not observe any association between subtypes and the response. Of the three Ba/Sq models treated with anti-EGFR therapy, two models were sensitive, and one model, of the sarcomatoid variant, was resistant. The treatment of three FGFR3-mutant PDXs with combined FGFR/EGFR inhibitors was more efficient than anti-FGFR3 treatment alone. Conclusions We developed preclinical PDX models that recapitulate the molecular heterogeneity of MIBCs and UTUC, including actionable mutations, which will represent an essential tool in therapy development. The pharmacological characterization of the PDXs suggested that the upper urinary tract and MIBCs, not only UC but also SCC, with similar molecular characteristics could benefit from the same treatments including anti-FGFR for FGFR3-mutated tumors and anti-EGFR for basal ones and showed a benefit for combined FGFR/EGFR inhibition in FGFR3-mutant PDXs, compared to FGFR inhibition alone.
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Affiliation(s)
- Hervé Lang
- Department of Urology, New Civil Hospital and Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | | | - Luc Cabel
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
| | - Jacqueline Fontugne
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université de Versailles-Saint-Quentin-en-Yvelines (UVSQ), Paris-Saclay University, Versailles, France
| | | | - Clémentine Krucker
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Florent Dufour
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
- Inovarion, Paris, France
| | - Clarice S. Groeneveld
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
- La Ligue Contre Le Cancer, Paris, France
| | - Victoria Dixon
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Xiangyu Meng
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | | | - Elodie Chapeaublanc
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
| | | | - Xavier Gamé
- Department of Urology, Rangueil Hospital, Toulouse, France
| | | | - Ivan Bieche
- Department of Genetics, Institut Curie, Paris, France
| | | | | | - Yves Allory
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Department of Pathology, Institut Curie, Saint-Cloud, France
- Université de Versailles-Saint-Quentin-en-Yvelines (UVSQ), Paris-Saclay University, Versailles, France
| | | | | | - François Radvanyi
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
| | - Philippe Lluel
- Urosphere, Toulouse, France
- *Correspondence: Isabelle Bernard-Pierrot, ; Philippe Lluel,
| | - Isabelle Bernard-Pierrot
- Institut Curie, Centre National de la Recherche Scientifique (CNRS), UMR144, Molecular Oncology team, PSL Research University, Paris, France
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC), Univ Paris, Paris, France
- *Correspondence: Isabelle Bernard-Pierrot, ; Philippe Lluel,
| | - Thierry Massfelder
- INSERM (French National Institute of Health and Medical Research) UMR_S1260, Université de Strasbourg, Regenerative Nanomedicine, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
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6
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Cardoso MA, Rizzardi LEA, Kume LW, Groeneveld CS, Trefflich S, Morais DAA, Dalmolin RJS, Ponder BAJ, Meyer KB, Castro MAA. TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves. Bioinformatics 2022; 38:1463-1464. [PMID: 34864914 DOI: 10.1093/bioinformatics/btab819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/15/2021] [Accepted: 11/30/2021] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION Dendrogram is a classical diagram for visualizing binary trees. Although efficient to represent hierarchical relations, it provides limited space for displaying information on the leaf elements, especially for large trees. RESULTS Here, we present TreeAndLeaf, an R/Bioconductor package that implements a hybrid layout strategy to represent tree diagrams with focus on the leaves. The TreeAndLeaf package combines force-directed graph and tree layout algorithms using a single visualization system, allowing projection of multiple layers of information onto a graph-tree diagram. The Supplementary Information provides two case studies that use breast cancer data from epidemiological and experimental studies. AVAILABILITY AND IMPLEMENTATION TreeAndLeaf is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/TreeAndLeaf/ (version≥1.4.2). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Milena A Cardoso
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Luis E A Rizzardi
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Leonardo W Kume
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Clarice S Groeneveld
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Sheyla Trefflich
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
- Bioinformatics Department, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Diego A A Morais
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Bruce A J Ponder
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
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7
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Zinovyev A, Sadovsky M, Calzone L, Fouché A, Groeneveld CS, Chervov A, Barillot E, Gorban AN. Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches. Front Mol Biosci 2022; 8:793912. [PMID: 35178429 PMCID: PMC8846220 DOI: 10.3389/fmolb.2021.793912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Cell cycle is a biological process underlying the existence and propagation of life in time and space. It has been an object for mathematical modeling for long, with several alternative mechanistic modeling principles suggested, describing in more or less details the known molecular mechanisms. Recently, cell cycle has been investigated at single cell level in snapshots of unsynchronized cell populations, exploiting the new methods for transcriptomic and proteomic molecular profiling. This raises a need for simplified semi-phenomenological cell cycle models, in order to formalize the processes underlying the cell cycle, at a higher abstracted level. Here we suggest a modeling framework, recapitulating the most important properties of the cell cycle as a limit trajectory of a dynamical process characterized by several internal states with switches between them. In the simplest form, this leads to a limit cycle trajectory, composed by linear segments in logarithmic coordinates describing some extensive (depending on system size) cell properties. We prove a theorem connecting the effective embedding dimensionality of the cell cycle trajectory with the number of its linear segments. We also develop a simplified kinetic model with piecewise-constant kinetic rates describing the dynamics of lumps of genes involved in S-phase and G2/M phases. We show how the developed cell cycle models can be applied to analyze the available single cell datasets and simulate certain properties of the observed cell cycle trajectories. Based on our model, we can predict with good accuracy the cell line doubling time from the length of cell cycle trajectory.
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Affiliation(s)
- Andrei Zinovyev
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
- *Correspondence: Andrei Zinovyev,
| | - Michail Sadovsky
- Institute of Computational Modeling (RAS), Krasnoyarsk, Russia
- Laboratory of Medical Cybernetics, V.F.Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Federal Research and Clinic Center of FMBA of Russia, Krasnoyarsk, Russia
- Laboratory of Advanced Methods for High-Dimensional Data Analysis, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Laurence Calzone
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Aziz Fouché
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Clarice S. Groeneveld
- Cartes d’Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
- Oncologie Moleculaire, UMR144, Institut Curie, Paris, France
| | - Alexander Chervov
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Alexander N. Gorban
- Laboratory of Advanced Methods for High-Dimensional Data Analysis, Lobachevsky University, Nizhniy Novgorod, Russia
- Department of Mathematics, University of Leicester, Leicester, United Kingdom
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8
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Robertson AG, Groeneveld CS, Jordan B, Lin X, McLaughlin KA, Das A, Fall LA, Fantini D, Taxter TJ, Mogil LS, Lindskrog SV, Dyrskjøt L, McConkey DJ, Svatek RS, de Reyniès A, Castro MAA, Meeks JJ. Corrigendum to "Identification of Differential Tumor Subtypes of T1 Bladder Cancer" [Eur. Urol. 78 (2020) 533-537]. Eur Urol 2021; 81:e53. [PMID: 34801336 DOI: 10.1016/j.eururo.2021.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Clarice S Groeneveld
- Cartes d'Identité des Tumeurs Program, Ligue Nationale Contre le Cancer, Paris, France; Oncologie Moleculaire, Institut Curie, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Brian Jordan
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Xiaoqi Lin
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Kimberly A McLaughlin
- Departments of Urology, Biochemistry, and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arighno Das
- Departments of Urology, Biochemistry, and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Leigh Ann Fall
- Departments of Urology, Biochemistry, and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Damiano Fantini
- Departments of Urology, Biochemistry, and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Lauren S Mogil
- Center for Translational Data Science, University of Chicago, Chicago, IL, USA
| | | | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Robert S Svatek
- Experimental Developmental Therapeutics Program, UT Health MD Anderson, San Antonio, TX, USA; Department of Urology, UT Health San Antonio, San Antonio, TX, USA
| | - Aurélien de Reyniès
- Cartes d'Identité des Tumeurs Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, Brazil
| | - Joshua J Meeks
- Departments of Urology, Biochemistry, and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Jesse Brown VA Medical Center, Chicago, IL, USA.
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9
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Lindskrog SV, Prip F, Lamy P, Taber A, Groeneveld CS, Birkenkamp-Demtröder K, Jensen JB, Strandgaard T, Nordentoft I, Christensen E, Sokac M, Birkbak NJ, Maretty L, Hermann GG, Petersen AC, Weyerer V, Grimm MO, Horstmann M, Sjödahl G, Höglund M, Steiniche T, Mogensen K, de Reyniès A, Nawroth R, Jordan B, Lin X, Dragicevic D, Ward DG, Goel A, Hurst CD, Raman JD, Warrick JI, Segersten U, Sikic D, van Kessel KEM, Maurer T, Meeks JJ, DeGraff DJ, Bryan RT, Knowles MA, Simic T, Hartmann A, Zwarthoff EC, Malmström PU, Malats N, Real FX, Dyrskjøt L. An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer. Nat Commun 2021; 12:2301. [PMID: 33863885 PMCID: PMC8052448 DOI: 10.1038/s41467-021-22465-w] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
The molecular landscape in non-muscle-invasive bladder cancer (NMIBC) is characterized by large biological heterogeneity with variable clinical outcomes. Here, we perform an integrative multi-omics analysis of patients diagnosed with NMIBC (n = 834). Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness. Both transcriptome-based subtyping and the level of chromosomal instability provide independent prognostic value beyond established prognostic clinicopathological parameters. High chromosomal instability, p53-pathway disruption and APOBEC-related mutations are significantly associated with transcriptomic class 2a and poor outcome. RNA-derived immune cell infiltration is associated with chromosomally unstable tumors and enriched in class 2b. Spatial proteomics analysis confirms the higher infiltration of class 2b tumors and demonstrates an association between higher immune cell infiltration and lower recurrence rates. Finally, the independent prognostic value of the transcriptomic classes is documented in 1228 validation samples using a single sample classification tool. The classifier provides a framework for biomarker discovery and for optimizing treatment and surveillance in next-generation clinical trials.
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Affiliation(s)
- Sia Viborg Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Ann Taber
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Clarice S Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
- Oncologie Moleculaire, UMR144, Institut Curie, Paris, France
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus N, Denmark
| | - Trine Strandgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mateo Sokac
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Nicolai J Birkbak
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lasse Maretty
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Gregers G Hermann
- Department of Urology, Herlev hospital, Copenhagen University, Copenhagen, Denmark
| | - Astrid C Petersen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Veronika Weyerer
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Marcus Horstmann
- Department of Urology, Jena University Hospital, Jena, Germany
- Department of Urology, Malteser Hospital St. Josephshospital, Krefeld Uerdingen, Krefeld, Germany
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Aarhus N, Denmark
| | - Karin Mogensen
- Department of Urology, Herlev hospital, Copenhagen University, Copenhagen, Denmark
| | - Aurélien de Reyniès
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Roman Nawroth
- Department of Urology, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Brian Jordan
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Xiaoqi Lin
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Dejan Dragicevic
- Clinic of Urology, Clinical Centre of Serbia, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Douglas G Ward
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Anshita Goel
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Carolyn D Hurst
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jay D Raman
- Department of Surgery, Division of Urology, Pennsylvania State University, Hershey, PA, USA
| | - Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Division of Urology, Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA, USA
| | - Ulrika Segersten
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Danijel Sikic
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Kim E M van Kessel
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tobias Maurer
- Department of Urology, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
- Department of Urology and Martini-Clinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joshua J Meeks
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Division of Urology, Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA, USA
| | - Richard T Bryan
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Margaret A Knowles
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Tatjana Simic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Per-Uno Malmström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), CIBERONC, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, CIBERONC, Barcelona, Spain
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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10
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Groeneveld CS, Fontugne J, Cabel L, Bernard-Pierrot I, Radvanyi F, Allory Y, de Reyniès A. Tertiary lymphoid structures marker CXCL13 is associated with better survival for patients with advanced-stage bladder cancer treated with immunotherapy. Eur J Cancer 2021; 148:181-189. [PMID: 33743486 DOI: 10.1016/j.ejca.2021.01.036] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/22/2020] [Accepted: 01/29/2021] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Immune checkpoint inhibitors (ICIs) have proved to be an effective treatment for up to 40% of muscle-invasive bladder cancer (MIBC), but there is still a need for better performing biomarkers allowing to improve prediction of response to ICI. Response to immunotherapy in soft-tissue sarcoma, melanoma and renal cell carcinoma have been recently linked to the presence of tertiary lymphoid structures (TLS) in the tumour. TLS are organised aggregates of T, B and dendritic cells, participating in adaptive antitumor immune response. The chemokine CXCL13 is involved in the formation of TLS, and is reported as a reliable transcriptomic marker of TLS. OBJECTIVES In this study, we sought to assess whether CXCL13 transcript expression can be a prognostic biomarker for ICI-treated MIBC patients and also investigated whether it can serve a biomarker of TLS in MIBC. METHODS We analysed transcriptomic data from three publicly available MIBC cohorts and evaluated pathological slides from the TCGA-BLCA cohort for TLS presence and stage of maturation. RESULTS We showed that CXCL13 was independently associated with both prolonged survival (HR = 0.8, 95% CI [0.68-0.94]) and objective response (p < 0.0001) in patients treated with ICI, at the difference of others immunological signatures. However, it was not a predictor for non-ICI-treated MIBC, suggesting a predictive effect of ICI efficacy. Finally, we validated that CXCL13 expression was correlated with tumour TLS in TCGA data set (p < 0.001), and can serve as a marker of TLS in bladder cancer. CONCLUSION These results support that CXCL13 expression, as a surrogate for tumour TLS, is a relevant candidate predictive biomarker of response to ICI for patients with advanced-stage bladder cancer.
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Affiliation(s)
- Clarice S Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France; Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Jacqueline Fontugne
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France; Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Luc Cabel
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Isabelle Bernard-Pierrot
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - François Radvanyi
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Yves Allory
- Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France; Department of Pathology, Institut Curie, Saint-Cloud, France
| | - Aurélien de Reyniès
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France.
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11
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Mathias C, Groeneveld CS, Trefflich S, Zambalde EP, Lima RS, Urban CA, Prado KB, Ribeiro EMSF, Castro MAA, Gradia DF, de Oliveira JC. Novel lncRNAs Co-Expression Networks Identifies LINC00504 with Oncogenic Role in Luminal A Breast Cancer Cells. Int J Mol Sci 2021; 22:ijms22052420. [PMID: 33670895 PMCID: PMC7957645 DOI: 10.3390/ijms22052420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are functional transcripts with more than 200 nucleotides. These molecules exhibit great regulatory capacity and may act at different levels of gene expression regulation. Despite this regulatory versatility, the biology of these molecules is still poorly understood. Computational approaches are being increasingly used to elucidate biological mechanisms in which these lncRNAs may be involved. Co-expression networks can serve as great allies in elucidating the possible regulatory contexts in which these molecules are involved. Herein, we propose the use of the pipeline deposited in the RTN package to build lncRNAs co-expression networks using TCGA breast cancer (BC) cohort data. Worldwide, BC is the most common cancer in women and has great molecular heterogeneity. We identified an enriched co-expression network for the validation of relevant cell processes in the context of BC, including LINC00504. This lncRNA has increased expression in luminal subtype A samples, and is associated with prognosis in basal-like subtype. Silencing this lncRNA in luminal A cell lines resulted in decreased cell viability and colony formation. These results highlight the relevance of the proposed method for the identification of lncRNAs in specific biological contexts.
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Affiliation(s)
- Carolina Mathias
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-900, PR, Brazil; (C.M.); (E.P.Z.); (K.B.P.); (E.M.S.F.R.); (D.F.G.)
| | - Clarice S. Groeneveld
- Cartes d’Identité des Tumeurs Program, Ligue Nationale Contre le Cancer, 75013 Paris, France;
- Oncologie Moleculaire, Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France
| | - Sheyla Trefflich
- Bioinformatics and Systems Biology Laboratory, Polytechnic Center, Federal University of Parana (UFPR), Curitiba 81520-260, PR, Brazil; (S.T.); (M.A.A.C.)
| | - Erika P. Zambalde
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-900, PR, Brazil; (C.M.); (E.P.Z.); (K.B.P.); (E.M.S.F.R.); (D.F.G.)
| | - Rubens S. Lima
- Breast Disease Center, Hospital Nossa Senhora das Graças, Curitiba 80810040, PR, Brazil; (R.S.L.); (C.A.U.)
| | - Cícero A. Urban
- Breast Disease Center, Hospital Nossa Senhora das Graças, Curitiba 80810040, PR, Brazil; (R.S.L.); (C.A.U.)
| | - Karin B. Prado
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-900, PR, Brazil; (C.M.); (E.P.Z.); (K.B.P.); (E.M.S.F.R.); (D.F.G.)
| | - Enilze M. S. F. Ribeiro
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-900, PR, Brazil; (C.M.); (E.P.Z.); (K.B.P.); (E.M.S.F.R.); (D.F.G.)
| | - Mauro A. A. Castro
- Bioinformatics and Systems Biology Laboratory, Polytechnic Center, Federal University of Parana (UFPR), Curitiba 81520-260, PR, Brazil; (S.T.); (M.A.A.C.)
| | - Daniela F. Gradia
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-900, PR, Brazil; (C.M.); (E.P.Z.); (K.B.P.); (E.M.S.F.R.); (D.F.G.)
| | - Jaqueline C. de Oliveira
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-900, PR, Brazil; (C.M.); (E.P.Z.); (K.B.P.); (E.M.S.F.R.); (D.F.G.)
- Correspondence:
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Kamoun A, de Reyniès A, Allory Y, Sjödahl G, Robertson AG, Seiler R, Hoadley KA, Groeneveld CS, Al-Ahmadie H, Choi W, Castro MAA, Fontugne J, Eriksson P, Mo Q, Kardos J, Zlotta A, Hartmann A, Dinney CP, Bellmunt J, Powles T, Malats N, Chan KS, Kim WY, McConkey DJ, Black PC, Dyrskjøt L, Höglund M, Lerner SP, Real FX, Radvanyi F, Aine M, Bernard-Pierrot I, Czerniak B, Gibb EA, Kim J, Kwiatkowski DJ, Lebret T, Liedberg F, Siefker-Radtke AA, Sirab N, Taber A, Weinstein JN. Reply To Kenneth B. Yatai, Mark J. Dunning, Dennis Wang. Consensus Genomic Subtypes of Muscle-invasive Bladder Cancer: A Step in the Right Direction but Still a Long Way To Go. Eur Urol 2020;77:434-5. Eur Urol 2020; 77:436-438. [PMID: 32037144 DOI: 10.1016/j.eururo.2019.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 12/17/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Aurélie Kamoun
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France.
| | - Aurélien de Reyniès
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Yves Allory
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC, Canada
| | - Roland Seiler
- Department of Urology, Bern University Hospital, Bern, Switzerland
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Clarice S Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute and Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | - Jacqueline Fontugne
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Pontus Eriksson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Qianxing Mo
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jordan Kardos
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandre Zlotta
- Division of Urology, Department of Surgery, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, ON, Canada
| | - Arndt Hartmann
- Institute of Pathology, University Erlangen-Nürnberg, Erlangen, Germany
| | - Colin P Dinney
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joaquim Bellmunt
- Bladder Cancer Center, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Thomas Powles
- Barts Cancer Institute ECMC, Barts Health and the Royal Free NHS Trust, Queen Mary University of London, London, UK
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), CIBERONC, Madrid, Spain
| | - Keith S Chan
- Cedars-Sinai Samuel Oschin Cancer Institute, Los Angeles, CA, USA
| | - William Y Kim
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute and Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Seth P Lerner
- Scott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), CIBERONC, Madrid, Spain
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mattias Aine
- Division of Molecular Hematology, Department of Laboratory Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Isabelle Bernard-Pierrot
- Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ewan A Gibb
- GenomeDx Biosciences Inc., Vancouver, BC, Canada
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Thierry Lebret
- Department of Urology, University of Versailles-Saint-Quentin-en-Yvelines, Foch Hospital, Suresnes, France
| | - Fredrik Liedberg
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - A Arlene Siefker-Radtke
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nanor Sirab
- Department of Pathology, Institut Curie Hospital Group, Paris, France
| | - Ann Taber
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Chagas VS, Groeneveld CS, Oliveira KG, Trefflich S, de Almeida RC, Ponder BAJ, Meyer KB, Jones SJM, Robertson AG, Castro MAA. RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons. Bioinformatics 2019; 35:5357-5358. [PMID: 31250887 DOI: 10.1093/bioinformatics/btz534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 04/01/2019] [Accepted: 06/26/2019] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Transcription factors (TFs) are key regulators of gene expression, and can activate or repress multiple target genes, forming regulatory units, or regulons. Understanding downstream effects of these regulators includes evaluating how TFs cooperate or compete within regulatory networks. Here we present RTNduals, an R/Bioconductor package that implements a general method for analyzing pairs of regulons. RESULTS RTNduals identifies a dual regulon when the number of targets shared between a pair of regulators is statistically significant. The package extends the RTN (Reconstruction of Transcriptional Networks) package, and uses RTN transcriptional networks to identify significant co-regulatory associations between regulons. The Supplementary Information reports two case studies for TFs using the METABRIC and TCGA breast cancer cohorts. AVAILABILITY AND IMPLEMENTATION RTNduals is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNduals/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vinicius S Chagas
- Bioinformatics and Systems Biology Lab, Federal University of Paraná, Curitiba, Brazil
| | - Clarice S Groeneveld
- Bioinformatics and Systems Biology Lab, Federal University of Paraná, Curitiba, Brazil
| | - Kelin G Oliveira
- Bioinformatics and Systems Biology Lab, Federal University of Paraná, Curitiba, Brazil.,Department of Clinical Sciences, Section of Oncology and Pathology, Lund University, Lund 221 85, Sweden
| | - Sheyla Trefflich
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo C de Almeida
- Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Bruce A J Ponder
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 ORE, UK
| | - Kerstin B Meyer
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 ORE, UK.,Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver V5Z 4S6, Canada
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver V5Z 4S6, Canada
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Lab, Federal University of Paraná, Curitiba, Brazil
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Groeneveld CS, Chagas VS, Jones SJM, Robertson AG, Ponder BAJ, Meyer KB, Castro MAA. RTNsurvival: an R/Bioconductor package for regulatory network survival analysis. Bioinformatics 2019; 35:4488-4489. [PMID: 30923832 PMCID: PMC6821288 DOI: 10.1093/bioinformatics/btz229] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/08/2019] [Accepted: 03/27/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Transcriptional networks are models that allow the biological state of cells or tumours to be described. Such networks consist of connected regulatory units known as regulons, each comprised of a regulator and its targets. Inferring a transcriptional network can be a helpful initial step in characterizing the different phenotypes within a cohort. While the network itself provides no information on molecular differences between samples, the per-sample state of each regulon, i.e. the regulon activity, can be used for describing subtypes in a cohort. Integrating regulon activities with clinical data and outcomes would extend this characterization of differences between subtypes. RESULTS We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles using transcriptional networks reconstructed by the RTN package, gene expression data, and a two-tailed Gene Set Enrichment Analysis. Given regulon activity profiles across a cohort, RTNsurvival can perform Kaplan-Meier analyses and Cox Proportional Hazards regressions, while also considering confounding variables. The Supplementary Information provides two case studies that use data from breast and liver cancer cohorts and features uni- and multivariate regulon survival analysis. AVAILABILITY AND IMPLEMENTATION RTNsurvival is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNsurvival/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Clarice S Groeneveld
- Bioinformatics and Systems Biology Lab, Federal University of Paraná, Curitiba, Brazil
| | - Vinicius S Chagas
- Bioinformatics and Systems Biology Lab, Federal University of Paraná, Curitiba, Brazil
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC V5Z4 S6, Canada
| | - A Gordon Robertson
- Canada’s Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC V5Z4 S6, Canada
| | - Bruce A J Ponder
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Kerstin B Meyer
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 ORE, UK Wellcome Sanger Institute, Hinxton, UK
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Lab, Federal University of Paraná, Curitiba, Brazil
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de Jong JJ, Liu Y, Robertson AG, Seiler R, Groeneveld CS, van der Heijden MS, Wright JL, Douglas J, Dall'Era M, Crabb SJ, van Rhijn BWG, van Kessel KEM, Davicioni E, Castro MAA, Lotan Y, Zwarthoff EC, Black PC, Boormans JL, Gibb EA. Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis. Genome Med 2019; 11:60. [PMID: 31619281 PMCID: PMC6796434 DOI: 10.1186/s13073-019-0669-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
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.
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Affiliation(s)
- Joep J de Jong
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Yang Liu
- Decipher Biosciences, Inc, Vancouver, British Columbia, Canada
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Roland Seiler
- Department of Urology, University of Bern, Bern, Switzerland
| | - Clarice S Groeneveld
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | | | - Jonathan L Wright
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - James Douglas
- Department of Urology, University Hospital of Southampton, Hampshire, UK
| | - Marc Dall'Era
- UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Simon J Crabb
- Department of Medical Oncology, University Hospital of Southampton, Hampshire, UK
| | - Bas W G van Rhijn
- Department of Surgical Oncology (Urology), Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Kim E M van Kessel
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Elai Davicioni
- Decipher Biosciences, Inc, Vancouver, British Columbia, Canada
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | - Yair Lotan
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ewan A Gibb
- Decipher Biosciences, Inc, Vancouver, British Columbia, Canada
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Kamoun A, de Reyniès A, Allory Y, Sjödahl G, Robertson AG, Seiler R, Hoadley KA, Groeneveld CS, Al-Ahmadie H, Choi W, Castro MAA, Fontugne J, Eriksson P, Mo Q, Kardos J, Zlotta A, Hartmann A, Dinney CP, Bellmunt J, Powles T, Malats N, Chan KS, Kim WY, McConkey DJ, Black PC, Dyrskjøt L, Höglund M, Lerner SP, Real FX, Radvanyi F. A Consensus Molecular Classification of Muscle-invasive Bladder Cancer. Eur Urol 2019; 77:420-433. [PMID: 31563503 PMCID: PMC7690647 DOI: 10.1016/j.eururo.2019.09.006] [Citation(s) in RCA: 637] [Impact Index Per Article: 127.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/02/2019] [Indexed: 01/10/2023]
Abstract
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.
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Affiliation(s)
- Aurélie Kamoun
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France.
| | - Aurélien de Reyniès
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Yves Allory
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC, Canada
| | - Roland Seiler
- Department of Urology, Bern University Hospital, Bern, Switzerland
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Clarice S Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Woonyoung Choi
- Johns Hopkins Greenberg Bladder Cancer Institute and Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Polytechnic Center, Curitiba, Brazil
| | - Jacqueline Fontugne
- Department of Pathology, Institut Curie, Saint-Cloud, France; Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Pontus Eriksson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Qianxing Mo
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jordan Kardos
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandre Zlotta
- Division of Urology, Department of Surgery, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, ON, Canada
| | - Arndt Hartmann
- Institute of Pathology, University Erlangen-Nürnberg, Erlangen, Germany
| | - Colin P Dinney
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joaquim Bellmunt
- Bladder Cancer Center, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Thomas Powles
- Barts Cancer Institute ECMC, Barts Health and the Royal Free NHS Trust, Queen Mary University of London, London, UK
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), CIBERONC, Madrid, Spain
| | - Keith S Chan
- Cedars-Sinai Samuel Oschin Cancer Institute, Los Angeles, CA, USA
| | - William Y Kim
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute and Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Seth P Lerner
- Scott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), CIBERONC, Madrid, Spain
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Paris, France
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