1
|
Gounou C, Rouyer L, Siegfried G, Harté E, Bouvet F, d'Agata L, Darbo E, Lefeuvre M, Derieppe MA, Bouton L, Mélane M, Chapeau D, Martineau J, Prouzet-Mauleon V, Tan S, Souleyreau W, Saltel F, Argoul F, Khatib AM, Brisson AR, Iggo R, Bouter A. Inhibition of the membrane repair protein annexin-A2 prevents tumor invasion and metastasis. Cell Mol Life Sci 2023; 81:7. [PMID: 38092984 PMCID: PMC10719157 DOI: 10.1007/s00018-023-05049-3] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 12/17/2023]
Abstract
Cancer cells are exposed to major compressive and shearing forces during invasion and metastasis, leading to extensive plasma membrane damage. To survive this mechanical stress, they need to repair membrane injury efficiently. Targeting the membrane repair machinery is thus potentially a new way to prevent invasion and metastasis. We show here that annexin-A2 (ANXA2) is required for membrane repair in invasive breast and pancreatic cancer cells. Mechanistically, we show by fluorescence and electron microscopy that cells fail to reseal shear-stress damaged membrane when ANXA2 is silenced or the protein is inhibited with neutralizing antibody. Silencing of ANXA2 has no effect on proliferation in vitro, and may even accelerate migration in wound healing assays, but reduces tumor cell dissemination in both mice and zebrafish. We expect that inhibiting membrane repair will be particularly effective in aggressive, poor prognosis tumors because they rely on the membrane repair machinery to survive membrane damage during tumor invasion and metastasis. This could be achieved either with anti-ANXA2 antibodies, which have been shown to inhibit metastasis of breast and pancreatic cancer cells, or with small molecule drugs.
Collapse
Affiliation(s)
- C Gounou
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bât. B14, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
| | - L Rouyer
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
| | - G Siegfried
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
- XenoFish, B2 Ouest, Allée Geoffroy St Hilaire CS50023, 33615, Pessac, France
| | - E Harté
- CNRS, LOMA, UMR 5798, University of Bordeaux, 33400, Talence, France
| | - F Bouvet
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bât. B14, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
| | - L d'Agata
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bât. B14, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
| | - E Darbo
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
| | - M Lefeuvre
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bât. B14, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
| | - M A Derieppe
- Animalerie Mutualisée, Service Commun des Animaleries, University of Bordeaux, 33000, Bordeaux, France
| | - L Bouton
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
| | - M Mélane
- CNRS, LOMA, UMR 5798, University of Bordeaux, 33400, Talence, France
| | - D Chapeau
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bât. B14, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
| | - J Martineau
- Animalerie Mutualisée, Service Commun des Animaleries, University of Bordeaux, 33000, Bordeaux, France
| | - V Prouzet-Mauleon
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
- CRISPRedit, TBMcore, UAR CNRS 3427, Inserm US 005, University of Bordeaux, Bordeaux, France
| | - S Tan
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bât. B14, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
| | - W Souleyreau
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
| | - F Saltel
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
| | - F Argoul
- CNRS, LOMA, UMR 5798, University of Bordeaux, 33400, Talence, France
| | - A M Khatib
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
- XenoFish, B2 Ouest, Allée Geoffroy St Hilaire CS50023, 33615, Pessac, France
- Bergonié Institute, Bordeaux, France
| | - A R Brisson
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bât. B14, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
| | - R Iggo
- INSERM, BRIC, U 1312, University of Bordeaux, 33000, Bordeaux, France
| | - A Bouter
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bât. B14, Allée Geoffroy Saint Hilaire, 33600, Pessac, France.
| |
Collapse
|
2
|
Feng X, Tonon L, Li H, Darbo E, Pleasance E, Macagno N, Dufresne A, Brahmi M, Bollard J, Ducimetière F, Karanian M, Meurgey A, Pérot G, Valentin T, Chibon F, Blay JY. Comprehensive Immune Profiling Unveils a Subset of Leiomyosarcoma with "Hot" Tumor Immune Microenvironment. Cancers (Basel) 2023; 15:3705. [PMID: 37509366 PMCID: PMC10378143 DOI: 10.3390/cancers15143705] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Purpose: To investigate the immune biomarker in Leiomyosarcoma (LMS), which is rare and recognized as an immune cold cancer showing a poor response rate (<10%) to immune checkpoint inhibitors (ICIs). However, durable response and clinical benefit to ICIs has been observed in a few cases of LMS, including, but not only, LMS with tertiary lymphoid structure (TLS) structures. Patients and methods: We used comprehensive transcriptomic profiling and a deconvolution method extracted from RNA-sequencing gene expression data in two independent LMS cohorts, the International Cancer Genome Consortium (ICGC, N = 146) and The Cancer Genome Atlas (TCGA, N = 75), to explore tumor immune microenvironment (TIME) in LMS. Results: Unsupervised clustering analysis using the previously validated two methods, 90-gene signature and Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT), identified immune hot (I-H) and immune high (I-Hi) LMS, respectively, in the ICGC cohort. Similarly, immune active groups (T-H, T-Hi) were identified in the TCGA cohort using these two methods. These immune active ("hot") clusters were significantly associated, but not completely overlapping, with several validated immune signatures such as sarcoma immune class (SIC) classification and TLS score, T cell inflamed signature (TIS) score, immune infiltration score (IIS), and macrophage score (M1/M2), with more patients identified by our clustering as potentially immune hot. Conclusions: Comprehensive immune profiling revealed a subset of LMS with a distinct active ("hot") TIME, consistently associated with several validated immune signatures in other cancers. This suggests that the methodologies that we used in this study warrant further validation and development, which can potentially help refine our current immune biomarkers to select the right LMS patients for ICIs in clinical trials.
Collapse
Affiliation(s)
- Xiaolan Feng
- Tom Baker Cancer Center, Department of Medical Oncology, University of Calgary, Calgary, AB T2N 4N2, Canada
| | - Laurie Tonon
- Synergie Lyon Cancer, Gille Thomas Bioinformatice Platform, Centre Léon Bérard, 69008 Lyon, France
| | - Haocheng Li
- Department of Mathematics and Statistics, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Elodie Darbo
- BRIC, INSERM U1312, Université de Bordeaux, 33600 Bordeaux, France
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Nicolas Macagno
- Department of Pathology, Aix Marseille University, INSERM, APHM MMG, UMR1251, Marmara Institute, La Timone Hospital, 13005 Marseille, France
| | - Armelle Dufresne
- Department of Medical Oncology, Centre Leon Bérard, 69008 Lyon, France
| | - Mehdi Brahmi
- Department of Medical Oncology, Centre Leon Bérard, 69008 Lyon, France
| | - Julien Bollard
- Department of Medical Oncology, Centre Leon Bérard, 69008 Lyon, France
| | | | - Marie Karanian
- Centre Léon Bérard, Department of Pathology, 69008 Lyon, France
| | | | - Gaëlle Pérot
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Thibaud Valentin
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Frédéric Chibon
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Jean-Yves Blay
- Department of Medical Oncology, Centre Léon Bérard, University Claude Bernard Lyon, 69008 Lyon, France
| |
Collapse
|
3
|
Michot A, Lagarde P, Lesluyes T, Darbo E, Neuville A, Baud J, Perot G, Bonomo I, Maire M, Michot M, Coindre JM, Le Loarer F, Chibon F. Analysis of the Peritumoral Tissue Unveils Cellular Changes Associated with a High Risk of Recurrence. Cancers (Basel) 2023; 15:3450. [PMID: 37444560 DOI: 10.3390/cancers15133450] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The management of soft-tissue sarcoma (STS) relies on a multidisciplinary approach involving specialized oncological surgery combined with other adjuvant therapies to achieve optimal local disease control. Purpose and Results: Genomic and transcriptomic pseudocapsules of 20 prospective sarcomas were analyzed and revealed to be correlated with a higher risk of recurrence after surgery. CONCLUSIONS A peritumoral environment that has been remodeled and infiltrated by M2 macrophages, and is less expressive of healthy tissue, would pose a significant risk of relapse and require more aggressive treatment strategies.
Collapse
Affiliation(s)
- Audrey Michot
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, 33000 Bordeaux, France
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - Pauline Lagarde
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - Tom Lesluyes
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Elodie Darbo
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, 33000 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - Agnès Neuville
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Jessica Baud
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, 33000 Bordeaux, France
| | - Gaëlle Perot
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Iris Bonomo
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Mathilde Maire
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Maxime Michot
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
| | - Jean-Michel Coindre
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - François Le Loarer
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, 33000 Bordeaux, France
- Institut Bergonié, Centre de Lutte Contre le Cancer de Bordeaux, 33076 Bordeaux, France
- Department of Biopathology, Bergonié Institute, Université Victor Segalen Site Carreire, Bordeaux 2, 33076 Bordeaux, France
| | - Frédéric Chibon
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| |
Collapse
|
4
|
Entrialgo-Cadierno R, Cueto-Ureña C, Welch C, Feliu I, Macaya I, Vera L, Morales X, Michelina SV, Scaparone P, Lopez I, Darbo E, Erice O, Vallejo A, Moreno H, Goñi-Salaverri A, Lara-Astiaso D, Halberg N, Cortes-Dominguez I, Guruceaga E, Ambrogio C, Lecanda F, Vicent S. Correction: The phospholipid transporter PITPNC1 links KRAS to MYC to prevent autophagy in lung and pancreatic cancer. Mol Cancer 2023; 22:97. [PMID: 37328838 DOI: 10.1186/s12943-023-01795-x] [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: 06/18/2023] Open
Affiliation(s)
- Rodrigo Entrialgo-Cadierno
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | - Cristina Cueto-Ureña
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | - Connor Welch
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Iker Feliu
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | - Irati Macaya
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | - Laura Vera
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | - Xabier Morales
- Imaging Unit and Cancer Imaging Laboratory, University of Navarra, CIMA, Pamplona, Spain
| | - Sandra Vietti Michelina
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Pietro Scaparone
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Ines Lopez
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | - Elodie Darbo
- University of Bordeaux, INSERM, BRIC, Bordeaux, 1312, F‑33000, France
| | - Oihane Erice
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | - Adrian Vallejo
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | - Haritz Moreno
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
| | | | - David Lara-Astiaso
- Molecular Therapies Program, University of Navarra, CIMA, Pamplona, Spain
- Wellcome - MRC Cambridge Stem Cell Institute (CSCI), Cambridge, UK
| | - Nils Halberg
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ivan Cortes-Dominguez
- Imaging Unit and Cancer Imaging Laboratory, University of Navarra, CIMA, Pamplona, Spain
- Bioinformatics Platform, University of Navarra, CIMA, Pamplona, Spain
| | - Elizabeth Guruceaga
- Bioinformatics Platform, University of Navarra, CIMA, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Fernando Lecanda
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Department of Pathology, Anatomy and Physiology, University of Navarra, Pamplona, Spain
| | - Silve Vicent
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, Pamplona, 31008, Spain.
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
- Department of Pathology, Anatomy and Physiology, University of Navarra, Pamplona, Spain.
| |
Collapse
|
5
|
Entrialgo-Cadierno R, Cueto-Ureña C, Welch C, Feliu I, Macaya I, Vera L, Morales X, Michelina SV, Scaparone P, Lopez I, Darbo E, Erice O, Vallejo A, Moreno H, Goñi-Salaverri A, Lara-Astiaso D, Halberg N, Cortes-Dominguez I, Guruceaga E, Ambrogio C, Lecanda F, Vicent S. The phospholipid transporter PITPNC1 links KRAS to MYC to prevent autophagy in lung and pancreatic cancer. Mol Cancer 2023; 22:86. [PMID: 37210549 DOI: 10.1186/s12943-023-01788-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND The discovery of functionally relevant KRAS effectors in lung and pancreatic ductal adenocarcinoma (LUAD and PDAC) may yield novel molecular targets or mechanisms amenable to inhibition strategies. Phospholipids availability has been appreciated as a mechanism to modulate KRAS oncogenic potential. Thus, phospholipid transporters may play a functional role in KRAS-driven oncogenesis. Here, we identified and systematically studied the phospholipid transporter PITPNC1 and its controlled network in LUAD and PDAC. METHODS Genetic modulation of KRAS expression as well as pharmacological inhibition of canonical effectors was completed. PITPNC1 genetic depletion was performed in in vitro and in vivo LUAD and PDAC models. PITPNC1-deficient cells were RNA sequenced, and Gene Ontology and enrichment analyses were applied to the output data. Protein-based biochemical and subcellular localization assays were run to investigate PITPNC1-regulated pathways. A drug repurposing approach was used to predict surrogate PITPNC1 inhibitors that were tested in combination with KRASG12C inhibitors in 2D, 3D, and in vivo models. RESULTS PITPNC1 was increased in human LUAD and PDAC, and associated with poor patients' survival. PITPNC1 was regulated by KRAS through MEK1/2 and JNK1/2. Functional experiments showed PITPNC1 requirement for cell proliferation, cell cycle progression and tumour growth. Furthermore, PITPNC1 overexpression enhanced lung colonization and liver metastasis. PITPNC1 regulated a transcriptional signature which highly overlapped with that of KRAS, and controlled mTOR localization via enhanced MYC protein stability to prevent autophagy. JAK2 inhibitors were predicted as putative PITPNC1 inhibitors with antiproliferative effect and their combination with KRASG12C inhibitors elicited a substantial anti-tumour effect in LUAD and PDAC. CONCLUSIONS Our data highlight the functional and clinical relevance of PITPNC1 in LUAD and PDAC. Moreover, PITPNC1 constitutes a new mechanism linking KRAS to MYC, and controls a druggable transcriptional network for combinatorial treatments.
Collapse
Affiliation(s)
- Rodrigo Entrialgo-Cadierno
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Cristina Cueto-Ureña
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Connor Welch
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Iker Feliu
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Irati Macaya
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Laura Vera
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Xabier Morales
- Imaging Unit and Cancer Imaging Laboratory, University of Navarra, CIMA, Pamplona, Spain
| | - Sandra Vietti Michelina
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Pietro Scaparone
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Ines Lopez
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Elodie Darbo
- University of Bordeaux, INSERM, BRIC, U 1312, F-33000, Bordeaux, France
| | - Oihane Erice
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Adrian Vallejo
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | - Haritz Moreno
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
| | | | - David Lara-Astiaso
- Molecular Therapies Program, University of Navarra, CIMA, Pamplona, Spain
- Wellcome - MRC Cambridge Stem Cell Institute (CSCI), Cambridge, UK
| | - Nils Halberg
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ivan Cortes-Dominguez
- Imaging Unit and Cancer Imaging Laboratory, University of Navarra, CIMA, Pamplona, Spain
- Bioinformatics Platform, University of Navarra, CIMA, Pamplona, Spain
| | - Elizabeth Guruceaga
- Bioinformatics Platform, University of Navarra, CIMA, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Centre, University of Torino, Turin, Italy
| | - Fernando Lecanda
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- Department of Pathology, Anatomy and Physiology, University of Navarra, Pamplona, Spain
| | - Silve Vicent
- Program in Solid Tumours, University of Navarra, Centre of Applied Medical Research (CIMA), 55 Pio XII Avenue, 31008, Pamplona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
- Department of Pathology, Anatomy and Physiology, University of Navarra, Pamplona, Spain.
| |
Collapse
|
6
|
Darbo E, Pérot G, Darmusey L, Le Guellec S, Leroy L, Gaston L, Desplat N, Thébault N, Merle C, Rochaix P, Valentin T, Ferron G, Chevreau C, Bui B, Stoeckle E, Ranchere-Vince D, Méeus P, Terrier P, Piperno-Neumann S, Collin F, De Pinieux G, Duffaud F, Coindre JM, Blay JY, Chibon F. Distinct Cellular Origins and Differentiation Process Account for Distinct Oncogenic and Clinical Behaviors of Leiomyosarcomas. Cancers (Basel) 2023; 15:cancers15020534. [PMID: 36672483 PMCID: PMC9856933 DOI: 10.3390/cancers15020534] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
In leiomyosarcoma (LMS), a very aggressive disease, a relatively transcriptionally uniform subgroup of well-differentiated tumors has been described and is associated with poor survival. The question raised how differentiation and tumor progression, two apparently antagonist processes, coexist and allow tumor malignancy. We first identified the most transcriptionally homogeneous LMS subgroup in three independent cohorts, which we named 'hLMS'. The integration of multi-omics data and functional analysis suggests that hLMS originate from vascular smooth muscle cells and show that hLMS transcriptional program reflects both modulations of smooth muscle contraction activity controlled by MYOCD/SRF regulatory network and activation of the cell cycle activity controlled by E2F/RB1 pathway. We propose that the phenotypic plasticity of vascular smooth muscle cells coupled with MYOCD/SRF pathway amplification, essential for hLMS survival, concomitant with PTEN absence and RB1 alteration, could explain how hLMS balance this uncommon interplay between differentiation and aggressiveness.
Collapse
Affiliation(s)
- Elodie Darbo
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
- CNRS UMR5800, LaBRI, 33400 Talence, France
- Department of Medical and Biological Sciences, Université de Bordeaux, 33000 Bordeaux, France
| | - Gaëlle Pérot
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Centre Hospitalier Universitaire (CHU) de Toulouse, IUCT-Oncopole, 31000 Toulouse, France
| | - Lucie Darmusey
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Department of Medical and Biological Sciences, University of Toulouse 3, 31000 Toulouse, France
| | - Sophie Le Guellec
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Laura Leroy
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Laëtitia Gaston
- Department of Medical Genetics, CHU de Bordeaux, 33000 Bordeaux, France
| | - Nelly Desplat
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
| | - Noémie Thébault
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Candice Merle
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Department of Medical and Biological Sciences, University of Toulouse 3, 31000 Toulouse, France
| | - Philippe Rochaix
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Thibaud Valentin
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Gwenaël Ferron
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Surgical Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Christine Chevreau
- Department of Oncology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
| | - Binh Bui
- Department of Oncology, Institut Bergonié, 33000 Bordeaux, France
| | | | | | - Pierre Méeus
- Department of Surgery, Centre Léon Bérard, 69000 Lyon, France
| | - Philippe Terrier
- Department of Pathology, Institut Gustave Roussy, 94800 Villejuif, France
| | | | - Françoise Collin
- Department of Pathology, Centre Georges-François Leclerc, 21000 Dijon, France
| | - Gonzague De Pinieux
- Department of Pathology, Hôpital Universitaire Trousseau, 37170 Tours, France
| | - Florence Duffaud
- Medical Oncology Unit, APHM Hôpital La Timone, Aix Marseille University, 13000 Marseille, France
| | - Jean-Michel Coindre
- INSERM U1218 ACTION, Institut Bergonié, 33000 Bordeaux, France
- Department of Pathology, Institut Bergonié, 33000 Bordeaux, France
| | - Jean-Yves Blay
- Department of Medical Oncology, Centre Léon Bérard, 69000 Lyon, France
- INSERM U1052, CNRS 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, 69000 Lyon, France
| | - Frédéric Chibon
- OncoSarc, INSERM U1037, Cancer Research Center in Toulouse (CRCT), 31000 Toulouse, France
- Department of Pathology, Institut Claudius Régaud, IUCT-Oncopole, 31000 Toulouse, France
- Correspondence: ; Tel.: +33-0582741765
| |
Collapse
|
7
|
Blaye C, Darbo E, Debled M, Brouste V, Vélasco V, Pinard C, Pellegrin I, Tarricone A, Arnedos M, Commeny J, Bonnefoi H, Larmonier C, Macgrogan G. 8P An immunological signature to predict outcome in patients with triple-negative breast cancer with residual disease after neoadjuvant chemotherapy. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
8
|
Darmusey L, Pérot G, Thébault N, Le Guellec S, Desplat N, Gaston L, Delespaul L, Lesluyes T, Darbo E, Gomez-Brouchet A, Richard E, Baud J, Leroy L, Coindre JM, Blay JY, Chibon F. ATRX Alteration Contributes to Tumor Growth and Immune Escape in Pleomorphic Sarcomas. Cancers (Basel) 2021; 13:2151. [PMID: 33946962 PMCID: PMC8124877 DOI: 10.3390/cancers13092151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 12/17/2022] Open
Abstract
Whole genome and transcriptome sequencing of a cohort of 67 leiomyosarcomas has been revealed ATRX to be one of the most frequently mutated genes in leiomyosarcomas after TP53 and RB1. While its function is well described in the alternative lengthening of telomeres mechanism, we wondered whether its alteration could have complementary effects on sarcoma oncogenesis. ATRX alteration is associated with the down-expression of genes linked to differentiation in leiomyosarcomas, and to immunity in an additional cohort of 60 poorly differentiated pleomorphic sarcomas. In vitro and in vivo models showed that ATRX down-expression increases tumor growth rate and immune escape by decreasing the immunity load of active mast cells in sarcoma tumors. These data indicate that an alternative to unsuccessful targeting of the adaptive immune system in sarcoma could target the innate system. This might lead to a better outcome for sarcoma patients in terms of ATRX status.
Collapse
Affiliation(s)
- Lucie Darmusey
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- IUCT-Oncopole, Institut Claudius Régaud, Department of Pathology, 31000 Toulouse, France
- University of Toulouse 3, Paul Sabatier, 31000 Toulouse, France
| | - Gaëlle Pérot
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- Centre Hospitalier Universitaire (CHU) de Toulouse, IUCT-Oncopole, 31000 Toulouse, France
| | - Noémie Thébault
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- IUCT-Oncopole, Institut Claudius Régaud, Department of Pathology, 31000 Toulouse, France
| | - Sophie Le Guellec
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- IUCT-Oncopole, Institut Claudius Régaud, Department of Pathology, 31000 Toulouse, France
| | - Nelly Desplat
- Inserm UMR1218, Action, Institut Bergonié, 33000 Bordeaux, France; (N.D.); (E.D.); (E.R.); (J.B.); (J.-M.C.)
| | - Laëtitia Gaston
- CHU de Bordeaux, Department of Medical Genetics, 33000 Bordeaux, France;
| | - Lucile Delespaul
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- University of Bordeaux, 33000 Bordeaux, France
| | - Tom Lesluyes
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- University of Bordeaux, 33000 Bordeaux, France
| | - Elodie Darbo
- Inserm UMR1218, Action, Institut Bergonié, 33000 Bordeaux, France; (N.D.); (E.D.); (E.R.); (J.B.); (J.-M.C.)
- University of Bordeaux, 33000 Bordeaux, France
- CNRS UMR5800, LaBRI, 33400 Talence, France
| | - Anne Gomez-Brouchet
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- IUCT-Oncopole, Institut Claudius Régaud, Department of Pathology, 31000 Toulouse, France
- Centre Hospitalier Universitaire (CHU) de Toulouse, IUCT-Oncopole, 31000 Toulouse, France
| | - Elodie Richard
- Inserm UMR1218, Action, Institut Bergonié, 33000 Bordeaux, France; (N.D.); (E.D.); (E.R.); (J.B.); (J.-M.C.)
| | - Jessica Baud
- Inserm UMR1218, Action, Institut Bergonié, 33000 Bordeaux, France; (N.D.); (E.D.); (E.R.); (J.B.); (J.-M.C.)
| | - Laura Leroy
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- IUCT-Oncopole, Institut Claudius Régaud, Department of Pathology, 31000 Toulouse, France
| | - Jean-Michel Coindre
- Inserm UMR1218, Action, Institut Bergonié, 33000 Bordeaux, France; (N.D.); (E.D.); (E.R.); (J.B.); (J.-M.C.)
- Institut Bergonie, Department of Pathology, 33000 Bordeaux, France
| | - Jean-Yves Blay
- Centre Léon Bérard, Department of Medical Oncology, 69000 Lyon, France;
- Inserm U1052, CNRS 5286, Cancer Research Center of Lyon, University Claude Bernard Lyon 1, 69000 Lyon, France
| | - Frédéric Chibon
- INSERM U1037, Cancer Research Center in Toulouse (CRCT), OncoSarc, 31000 Toulouse, France; (L.D.); (G.P.); (N.T.); (S.L.G.); (L.D.); (T.L.); (A.G.-B.); (L.L.)
- IUCT-Oncopole, Institut Claudius Régaud, Department of Pathology, 31000 Toulouse, France
- Inserm UMR1218, Action, Institut Bergonié, 33000 Bordeaux, France; (N.D.); (E.D.); (E.R.); (J.B.); (J.-M.C.)
| |
Collapse
|
9
|
Nokin MJ, Darbo E, Travert C, Drogat B, Lacouture A, San José S, Cabrera N, Turcq B, Prouzet-Mauleon V, Falcone M, Villanueva A, Wang H, Herfs M, Mosteiro M, Jänne PA, Pujol JL, Maraver A, Barbacid M, Nadal E, Santamaría D, Ambrogio C. Inhibition of DDR1 enhances in vivo chemosensitivity in KRAS-mutant lung adenocarcinoma. JCI Insight 2020; 5:137869. [PMID: 32759499 DOI: 10.1172/jci.insight.137869] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 03/05/2020] [Accepted: 06/18/2020] [Indexed: 12/30/2022] Open
Abstract
Platinum-based chemotherapy in combination with immune-checkpoint inhibitors is the current standard of care for patients with advanced lung adenocarcinoma (LUAD). However, tumor progression evolves in most cases. Therefore, predictive biomarkers are needed for better patient stratification and for the identification of new therapeutic strategies, including enhancing the efficacy of chemotoxic agents. Here, we hypothesized that discoidin domain receptor 1 (DDR1) may be both a predictive factor for chemoresistance in patients with LUAD and a potential target positively selected in resistant cells. By using biopsies from patients with LUAD, KRAS-mutant LUAD cell lines, and in vivo genetically engineered KRAS-driven mouse models, we evaluated the role of DDR1 in the context of chemotherapy treatment. We found that DDR1 is upregulated during chemotherapy both in vitro and in vivo. Moreover, analysis of a cohort of patients with LUAD suggested that high DDR1 levels in pretreatment biopsies correlated with poor response to chemotherapy. Additionally, we showed that combining DDR1 inhibition with chemotherapy prompted a synergistic therapeutic effect and enhanced cell death of KRAS-mutant tumors in vivo. Collectively, this study suggests a potential role for DDR1 as both a predictive and prognostic biomarker, potentially improving the chemotherapy response of patients with LUAD.
Collapse
Affiliation(s)
- Marie-Julie Nokin
- University of Bordeaux, INSERM U1218, ACTION Laboratory, IECB, Pessac, France
| | - Elodie Darbo
- University of Bordeaux, INSERM U1218, ACTION Laboratory, Bordeaux INP, CNRS, LaBRI, UMR5800, Talence, France
| | - Camille Travert
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Benjamin Drogat
- University of Bordeaux, INSERM U1218, ACTION Laboratory, IECB, Pessac, France
| | - Aurélie Lacouture
- University of Bordeaux, INSERM U1218, ACTION Laboratory, IECB, Pessac, France
| | - Sonia San José
- University of Bordeaux, INSERM U1218, ACTION Laboratory, IECB, Pessac, France
| | - Nuria Cabrera
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Béatrice Turcq
- University of Bordeaux, INSERM U1218, ACTION Laboratory, Laboratory of Mammary and Leukaemic Oncogenesis, Bordeaux, France
| | - Valérie Prouzet-Mauleon
- University of Bordeaux, INSERM U1218, ACTION Laboratory, Laboratory of Mammary and Leukaemic Oncogenesis, Bordeaux, France
| | - Mattia Falcone
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Alberto Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Barcelona, Spain
| | - Haiyun Wang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Michael Herfs
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Miguel Mosteiro
- Department of Medical Oncology, Catalan Institute of Oncology, Clinical Research in Solid Tumors (CReST) Group, Oncobell Program, IDIBELL, L'Hospitalet, Barcelona, Spain
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jean-Louis Pujol
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France.,Montpellier Academic Hospital, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Antonio Maraver
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Mariano Barbacid
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Ernest Nadal
- Department of Medical Oncology, Catalan Institute of Oncology, Clinical Research in Solid Tumors (CReST) Group, Oncobell Program, IDIBELL, L'Hospitalet, Barcelona, Spain
| | - David Santamaría
- University of Bordeaux, INSERM U1218, ACTION Laboratory, IECB, Pessac, France
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
| |
Collapse
|
10
|
Dufresne A, Lesluyes T, Ménétrier-Caux C, Brahmi M, Darbo E, Toulmonde M, Italiano A, Mir O, Le Cesne A, Le Guellec S, Valentin T, Chevreau C, Bonvalot S, Robin YM, Coindre JM, Caux C, Blay JY, Chibon F. Specific immune landscapes and immune checkpoint expressions in histotypes and molecular subtypes of sarcoma. Oncoimmunology 2020; 9:1792036. [PMID: 32923153 PMCID: PMC7458655 DOI: 10.1080/2162402x.2020.1792036] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Soft tissue sarcomas are a group of rare and aggressive connective tissue neoplasms for which curative therapeutic opportunities are limited in advanced phase. Clinical trials assessing immunotherapy in these tumors have so far reported limited efficacy. The objective of this study is to provide a description of the immunologic landscape of sarcomas to guide the next clinical trials of immunotherapy in these diseases. The gene expression profile of 93 immune checkpoint (ICP) and membrane markers (MM) of immune cells was analyzed in a series of 253 soft tissue sarcoma (synovial sarcoma, myxoid liposarcoma, sarcoma with complex genomic and GIST) using Agilent Whole Human Genome Microarrays. The unsupervised hierarchical clustering of gene expression level was found able to properly group patients according to the histological subgroup of sarcoma, indicating that each sarcoma subgroup is associated with a specific immune signature defined by its gene expression pattern. Using the prognostic impact of CIBERSORT signature on metastatic-free survival in each subgroup, specific target could be proposed for each of the four groups: Treg through ICOS and GITR in GIST, M0 macrophages in all four sarcoma subtypes, OX40 in SS, CD40 in GIST and SS. The immune landscape of sarcoma was found to be as heterogeneous as the histotypes and molecular subtypes, but strongly correlated to the histotype. Histotype adapted immunotherapeutic approaches in each sarcoma subtypes must be considered in view of these results, consistently with the already reported specific response of histotypes of ICPs.
Collapse
Affiliation(s)
- A Dufresne
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - T Lesluyes
- University of Bordeaux, Bordeaux, France.,Inserm U1218, Institut Bergonié, Bordeaux, France.,Inserm UMR1037, Cancer Research Center of Toulouse, Toulouse, France.,Department of Medical Oncology, Institut Claudius Regaud, Toulouse, France
| | - C Ménétrier-Caux
- Inserm U1052, CNRS 5286, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, Bordeaux, France
| | - M Brahmi
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - E Darbo
- University of Bordeaux, Bordeaux, France.,Inserm U1218, Institut Bergonié, Bordeaux, France.,Bordeaux Bioinformatics Center (BCIB), Bordeaux, France
| | - M Toulmonde
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France
| | - A Italiano
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France
| | - O Mir
- Department of Ambulatory Care, Institut Gustave Roussy, Villejuif, France
| | - A Le Cesne
- Department of Cancer Medicine, Institut Gustave Roussy, Villejuif, France
| | - S Le Guellec
- Inserm UMR1037, Cancer Research Center of Toulouse, Toulouse, France.,Department of Pathology, Institut Claudius Regaud, Toulouse, France
| | - T Valentin
- Inserm UMR1037, Cancer Research Center of Toulouse, Toulouse, France.,Department of Medical Oncology, Institut Claudius Regaud, Toulouse, France
| | - C Chevreau
- Department of Medical Oncology, Institut Claudius Regaud, Toulouse, France
| | - S Bonvalot
- Department of Surgery, Institut Curie, Bordeaux, France
| | - Y M Robin
- Department of Pathology, Centre Oscar Lambret, Lille, France
| | - J-M Coindre
- University of Bordeaux, Bordeaux, France.,Department of Pathology, Institut Bergonié, Bordeaux, France
| | - C Caux
- Inserm U1052, CNRS 5286, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, Bordeaux, France
| | - J Y Blay
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France.,Inserm U1052, CNRS 5286, Cancer Research Center of Lyon, Université Claude Bernard Lyon 1, Bordeaux, France
| | - F Chibon
- Inserm UMR1037, Cancer Research Center of Toulouse, Toulouse, France.,Department of Medical Oncology, Institut Claudius Regaud, Toulouse, France
| |
Collapse
|
11
|
Beauvarlet J, Nath Das R, Alvarez-Valadez K, Martins I, Muller A, Darbo E, Richard E, Soubeyran P, Kroemer G, Guillon J, Mergny JL, Djavaheri-Mergny M. Triarylpyridine Compounds and Chloroquine Act in Concert to Trigger Lysosomal Membrane Permeabilization and Cell Death in Cancer Cells. Cancers (Basel) 2020; 12:cancers12061621. [PMID: 32570977 PMCID: PMC7352983 DOI: 10.3390/cancers12061621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/08/2020] [Accepted: 06/12/2020] [Indexed: 01/07/2023] Open
Abstract
Lysosomes play a key role in regulating cell death in response to cancer therapies, yet little is known on the possible role of lysosomes in the therapeutic efficacy of G-quadruplex DNA ligands (G4L) in cancer cells. Here, we investigate the relationship between the modulation of lysosomal membrane damage and the degree to which cancer cells respond to the cytotoxic effects of G-quadruplex ligands belonging to the triarylpyridine family. Our results reveal that the lead compound of this family, 20A promotes the enlargement of the lysosome compartment as well as the induction of lysosome-relevant mRNAs. Interestingly, the combination of 20A and chloroquine (an inhibitor of lysosomal functions) led to a significant induction of lysosomal membrane permeabilization coupled to massive cell death. Similar effects were observed when chloroquine was added to three new triarylpyridine derivatives. Our findings thus uncover the lysosomal effects of triarylpyridines compounds and delineate a rationale for combining these compounds with chloroquine to increase their anticancer effects.
Collapse
Affiliation(s)
- Jennifer Beauvarlet
- Institut Bergonié, INSERM U1218, Université de Bordeaux, 33000 Bordeaux, France; (J.B.); (E.D.); (E.R.); (P.S.)
| | - Rabindra Nath Das
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, 33000 Bordeaux, France; (R.N.D.); (J.G.); (J.-L.M.)
| | - Karla Alvarez-Valadez
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France; (K.A.-V.); (A.M.); (G.K.)
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université de Paris, Equipe 11 labellisée par la Ligue contre le Cancer, 75006 Paris, France
| | - Isabelle Martins
- Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France;
| | - Alexandra Muller
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France; (K.A.-V.); (A.M.); (G.K.)
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
| | - Elodie Darbo
- Institut Bergonié, INSERM U1218, Université de Bordeaux, 33000 Bordeaux, France; (J.B.); (E.D.); (E.R.); (P.S.)
| | - Elodie Richard
- Institut Bergonié, INSERM U1218, Université de Bordeaux, 33000 Bordeaux, France; (J.B.); (E.D.); (E.R.); (P.S.)
| | - Pierre Soubeyran
- Institut Bergonié, INSERM U1218, Université de Bordeaux, 33000 Bordeaux, France; (J.B.); (E.D.); (E.R.); (P.S.)
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France; (K.A.-V.); (A.M.); (G.K.)
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université de Paris, Equipe 11 labellisée par la Ligue contre le Cancer, 75006 Paris, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Sciences, Suzhou 215123, China
- Department of Women’s and Children’s Health, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Jean Guillon
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, 33000 Bordeaux, France; (R.N.D.); (J.G.); (J.-L.M.)
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, 33000 Bordeaux, France; (R.N.D.); (J.G.); (J.-L.M.)
| | - Mojgan Djavaheri-Mergny
- Institut Bergonié, INSERM U1218, Université de Bordeaux, 33000 Bordeaux, France; (J.B.); (E.D.); (E.R.); (P.S.)
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France; (K.A.-V.); (A.M.); (G.K.)
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université de Paris, Equipe 11 labellisée par la Ligue contre le Cancer, 75006 Paris, France
- Correspondence:
| |
Collapse
|
12
|
Cakiroglu A, Clapier CR, Ehrensberger AH, Darbo E, Cairns BR, Luscombe NM, Svejstrup JQ. Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes. Genome Res 2019; 29:988-998. [PMID: 31097474 PMCID: PMC6581049 DOI: 10.1101/gr.243139.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 05/08/2019] [Indexed: 12/03/2022]
Abstract
Chromatin transactions are typically studied in vivo, or in vitro using artificial chromatin lacking the epigenetic complexity of the natural material. Attempting to bridge the gap between these approaches, we established a system for isolating the yeast genome as a library of mononucleosomes harboring the natural epigenetic signature, suitable for biochemical manipulation. Combined with deep sequencing, this library was used to investigate the stability of individual nucleosomes and, as proof of principle, the nucleosome preference of the chromatin remodeling complex, RSC. This approach uncovered a distinct preference of RSC for nucleosomes derived from regions with a high density of histone variant H2AZ, and this preference is indeed markedly diminished using nucleosomes from cells lacking H2AZ. The preference for H2AZ remodeling/nucleosome ejection can also be reconstituted with recombinant nucleosome arrays. Together, our data indicate that, despite being separated from their genomic context, individual nucleosomes can retain their original identity as promoter- or transcription start site (TSS)-nucleosomes. Besides shedding new light on substrate preference of the chromatin remodeler RSC, the simple experimental system outlined here should be generally applicable to the study of chromatin transactions.
Collapse
Affiliation(s)
- Aylin Cakiroglu
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Cedric R Clapier
- Department of Oncological Sciences, Huntsman Cancer Institute, and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Andreas H Ehrensberger
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Elodie Darbo
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Bradley R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute, and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| |
Collapse
|
13
|
Beauvarlet J, Bensadoun P, Darbo E, Labrunie G, Rousseau B, Richard E, Draskovic I, Londono-Vallejo A, Dupuy JW, Nath Das R, Guédin A, Robert G, Orange F, Croce S, Valesco V, Soubeyran P, Ryan KM, Mergny JL, Djavaheri-Mergny M. Modulation of the ATM/autophagy pathway by a G-quadruplex ligand tips the balance between senescence and apoptosis in cancer cells. Nucleic Acids Res 2019; 47:2739-2756. [PMID: 30759257 PMCID: PMC6451122 DOI: 10.1093/nar/gkz095] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 01/30/2019] [Accepted: 02/05/2019] [Indexed: 01/07/2023] Open
Abstract
G-quadruplex ligands exert their antiproliferative effects through telomere-dependent and telomere-independent mechanisms, but the inter-relationships among autophagy, cell growth arrest and cell death induced by these ligands remain largely unexplored. Here, we demonstrate that the G-quadruplex ligand 20A causes growth arrest of cancer cells in culture and in a HeLa cell xenografted mouse model. This response is associated with the induction of senescence and apoptosis. Transcriptomic analysis of 20A treated cells reveals a significant functional enrichment of biological pathways related to growth arrest, DNA damage response and the lysosomal pathway. 20A elicits global DNA damage but not telomeric damage and activates the ATM and autophagy pathways. Loss of ATM following 20A treatment inhibits both autophagy and senescence and sensitizes cells to death. Moreover, disruption of autophagy by deletion of two essential autophagy genes ATG5 and ATG7 leads to failure of CHK1 activation by 20A and subsequently increased cell death. Our results, therefore, identify the activation of ATM by 20A as a critical player in the balance between senescence and apoptosis and autophagy as one of the key mediators of such regulation. Thus, targeting the ATM/autophagy pathway might be a promising strategy to achieve the maximal anticancer effect of this compound.
Collapse
Affiliation(s)
- Jennifer Beauvarlet
- Institut Bergonié, Université de Bordeaux, INSERM U1218, F-33076 Bordeaux, France
| | - Paul Bensadoun
- Institut Bergonié, Université de Bordeaux, INSERM U1218, F-33076 Bordeaux, France
| | - Elodie Darbo
- Institut Bergonié, Université de Bordeaux, INSERM U1218, F-33076 Bordeaux, France
- Centre de Bioinformatique de Bordeaux, université de Bordeaux, F-33000 Bordeaux France
| | - Gaelle Labrunie
- Institut Bergonié, Université de Bordeaux, INSERM U1218, F-33076 Bordeaux, France
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, IECB, F-33600, Pessac, France
| | - Benoît Rousseau
- Service commun des animaleries, Université de Bordeaux, F-33000 Bordeaux, France
| | - Elodie Richard
- Institut Bergonié, Université de Bordeaux, INSERM U1218, F-33076 Bordeaux, France
| | - Irena Draskovic
- Institut Curie, PSL Research University, CNRS, UMR3244, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, F-75005 Paris, France
| | - Arturo Londono-Vallejo
- Institut Curie, PSL Research University, CNRS, UMR3244, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3244, F-75005 Paris, France
| | - Jean-William Dupuy
- Université de Bordeaux, Centre de Génomique Fonctionnelle, Plateforme Protéome, F-33000, Bordeaux, France
| | - Rabindra Nath Das
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, IECB, F-33600, Pessac, France
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, IECB, F-33600, Pessac, France
| | - Guillaume Robert
- Inserm U1065, C3M, Team: Myeloid Malignancies and Multiple Myeloma, Université Côte d’Azur, F-06204 Nice, France
| | - Francois Orange
- Université Côte d’Azur, Centre Commun de Microscopie Appliquée (CCMA), 06108 Nice, France
| | - Sabrina Croce
- Department of Biopathology, Institut Bergonié, F-33076 Bordeaux, France
| | - Valerie Valesco
- Department of Biopathology, Institut Bergonié, F-33076 Bordeaux, France
| | - Pierre Soubeyran
- Institut Bergonié, Université de Bordeaux, INSERM U1218, F-33076 Bordeaux, France
| | - Kevin M Ryan
- Cancer Research UK Beatson Institute, Glasgow, G611BD, UK and Institute of Cancer Sciences, University of Glasgow,Glasgow G61 1QH, UK
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR 5320, IECB, F-33600, Pessac, France
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | | |
Collapse
|
14
|
Daubon T, Léon C, Clarke K, Andrique L, Salabert L, Darbo E, Pineau R, Guérit S, Maitre M, Dedieu S, Jeanne A, Bailly S, Feige JJ, Miletic H, Rossi M, Bello L, Falciani F, Bjerkvig R, Bikfalvi A. Deciphering the complex role of thrombospondin-1 in glioblastoma development. Nat Commun 2019; 10:1146. [PMID: 30850588 PMCID: PMC6408502 DOI: 10.1038/s41467-019-08480-y] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [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: 03/20/2017] [Accepted: 01/09/2019] [Indexed: 12/17/2022] Open
Abstract
We undertook a systematic study focused on the matricellular protein Thrombospondin-1 (THBS1) to uncover molecular mechanisms underlying the role of THBS1 in glioblastoma (GBM) development. THBS1 was found to be increased with glioma grades. Mechanistically, we show that the TGFβ canonical pathway transcriptionally regulates THBS1, through SMAD3 binding to the THBS1 gene promoter. THBS1 silencing inhibits tumour cell invasion and growth, alone and in combination with anti-angiogenic therapy. Specific inhibition of the THBS1/CD47 interaction using an antagonist peptide decreases cell invasion. This is confirmed by CD47 knock-down experiments. RNA sequencing of patient-derived xenograft tissue from laser capture micro-dissected peripheral and central tumour areas demonstrates that THBS1 is one of the gene with the highest connectivity at the tumour borders. All in all, these data show that TGFβ1 induces THBS1 expression via Smad3 which contributes to the invasive behaviour during GBM expansion. Furthermore, tumour cell-bound CD47 is implicated in this process. Thrombospondin-1 (THSB1) is a component of the ECM with a role in regulating cancer development and tumour vasculature. Here, the authors show that TGF-beta-induced THBS1 expression contributes to the invasive behaviour of GBM cells and promotes resistance to antiangiogenic therapy partially through interaction with CD47.
Collapse
Affiliation(s)
- Thomas Daubon
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France. .,University Bordeaux, 33615, Pessac, France. .,KG Jebsen Brain Tumor Research Center, University of Bergen, 5020, Bergen, Norway. .,Norlux Beuro-Oncology, Department of Biomedicine, University of Bergen, 5020, Bergen, Norway.
| | - Céline Léon
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France.,University Bordeaux, 33615, Pessac, France
| | - Kim Clarke
- Computational Biology Facility, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Laetitia Andrique
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France.,University Bordeaux, 33615, Pessac, France
| | - Laura Salabert
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France.,University Bordeaux, 33615, Pessac, France
| | - Elodie Darbo
- UMR1218 ACTION, Bioinformatic Center CBiB, University of Bordeaux, 33076, Bordeaux, France
| | - Raphael Pineau
- Animal Facility, University Bordeaux, 33615, Pessac, France
| | - Sylvaine Guérit
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France.,University Bordeaux, 33615, Pessac, France
| | - Marlène Maitre
- INSERM U1215, Neurocenter Magendie, Pathophysiology of Addiction Group, 33076, Bordeaux, France
| | | | - Albin Jeanne
- CNRS UMR 7369, MEDyC, 51687, Reims, France.,SATT Nord, 59800, Lille, France
| | | | | | - Hrvoje Miletic
- KG Jebsen Brain Tumor Research Center, University of Bergen, 5020, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, 5020, Bergen, Norway
| | - Marco Rossi
- Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Humanitas Research Hospital, Universita Degli Studi di Milano, 20089, Rozzano, Milan, Italy
| | - Lorenzo Bello
- Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Humanitas Research Hospital, Universita Degli Studi di Milano, 20089, Rozzano, Milan, Italy
| | - Francesco Falciani
- Computational Biology Facility, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rolf Bjerkvig
- KG Jebsen Brain Tumor Research Center, University of Bergen, 5020, Bergen, Norway.,Norlux Beuro-Oncology, Department of Biomedicine, University of Bergen, 5020, Bergen, Norway.,Oncology Department, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg
| | - Andréas Bikfalvi
- INSERM U1029, Institut Nationale de la Santé et de la Recherche Médicale, 33615, Pessac, France. .,University Bordeaux, 33615, Pessac, France.
| |
Collapse
|
15
|
Beauvarlet J, Sadoun PB, Labrunie G, Das R, Richard E, Rousseau B, Darbo E, Croce S, Mergny J, Djavaheri-Mergny M. PO-446 Anti-tumour efficiency of 20A, a novel G-quadruplex ligand, in in vitro and in vivocancer models: ATM and autophagy interplay. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
16
|
Abstract
The Discoidin Domain Receptor 1 (DDR1) receptor tyrosine kinase performs pleiotropic functions in the control of cell adhesion, proliferation, survival, migration, and invasion. Aberrant DDR1 function as a consequence of either mutations or increased expression has been associated with various human diseases including cancer. Pharmacological inhibition of DDR1 results in significant therapeutic benefit in several pre-clinical cancer models. Here, we discuss the potential implication of DDR1-dependent pro-survival functions in the development of cancer resistance to chemotherapeutic regimens and speculate on the molecular mechanisms that might mediate such important feature.
Collapse
Affiliation(s)
- Chiara Ambrogio
- a Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Elodie Darbo
- b University of Bordeaux , INSERM U1218, ACTION Laboratory, Centre de Bioinformatique de Bordeaux (CBiB) , Bordeaux , France
| | - Sam W Lee
- c Cutaneous Biology Research Center , Massachusetts General Hospital and Harvard Medical School , Charlestown , MA , USA
| | - David Santamaría
- d University of Bordeaux , INSERM U1218, ACTION Laboratory, IECB , Pessac , France
| |
Collapse
|
17
|
Mifsud B, Martincorena I, Darbo E, Sugar R, Schoenfelder S, Fraser P, Luscombe NM. GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. PLoS One 2017; 12:e0174744. [PMID: 28379994 PMCID: PMC5381888 DOI: 10.1371/journal.pone.0174744] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/14/2017] [Indexed: 01/16/2023] Open
Abstract
Hi-C is one of the main methods for investigating spatial co-localisation of DNA in the nucleus. However, the raw sequencing data obtained from Hi-C experiments suffer from large biases and spurious contacts, making it difficult to identify true interactions. Existing methods use complex models to account for biases and do not provide a significance threshold for detecting interactions. Here we introduce a simple binomial probabilistic model that resolves complex biases and distinguishes between true and false interactions. The model corrects biases of known and unknown origin and yields a p-value for each interaction, providing a reliable threshold based on significance. We demonstrate this experimentally by testing the method against a random ligation dataset. Our method outperforms previous methods and provides a statistical framework for further data analysis, such as comparisons of Hi-C interactions between different conditions. GOTHiC is available as a BioConductor package (http://www.bioconductor.org/packages/release/bioc/html/GOTHiC.html).
Collapse
Affiliation(s)
- Borbala Mifsud
- The Francis Crick Institute, London, United Kingdom
- UCL Genetics Institute, Department of Genetics Evolution and Environment, University College London, London, United Kingdom
| | | | - Elodie Darbo
- The Francis Crick Institute, London, United Kingdom
| | - Robert Sugar
- The Francis Crick Institute, London, United Kingdom
| | | | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Nicholas M. Luscombe
- The Francis Crick Institute, London, United Kingdom
- UCL Genetics Institute, Department of Genetics Evolution and Environment, University College London, London, United Kingdom
- Okinawa Institute of Science & Technology, Okinawa, Japan
| |
Collapse
|
18
|
Seyres D, Darbo E, Perrin L, Herrmann C, González A. LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines. Bioinformatics 2015; 32:1091-3. [PMID: 26628586 DOI: 10.1093/bioinformatics/btv705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/26/2015] [Indexed: 11/12/2022] Open
Affiliation(s)
- Denis Seyres
- INSERM, UMR1090 TAGC, Marseille, F-13288 France, Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288 France
| | - Elodie Darbo
- Cancer Research UK, London Research Institute, London WC2A 3LY, UK
| | - Laurent Perrin
- INSERM, UMR1090 TAGC, Marseille, F-13288 France, Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288 France, CNRS, Marseille, France and
| | - Carl Herrmann
- IPMB, Universität Heidelberg and Department of Theoretical Bioinformatics, DKFZ, Heidelberg 69120, Germany
| | - Aitor González
- INSERM, UMR1090 TAGC, Marseille, F-13288 France, Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288 France
| |
Collapse
|
19
|
Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res 2015; 25:582-97. [PMID: 25752748 PMCID: PMC4381529 DOI: 10.1101/gr.185272.114] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/11/2015] [Indexed: 12/17/2022]
Abstract
The mammalian genome harbors up to one million regulatory elements often located at great distances from their target genes. Long-range elements control genes through physical contact with promoters and can be recognized by the presence of specific histone modifications and transcription factor binding. Linking regulatory elements to specific promoters genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays. Here we apply a sequence capture approach to enrich Hi-C libraries for >22,000 annotated mouse promoters to identify statistically significant, long-range interactions at restriction fragment resolution, assigning long-range interacting elements to their target genes genome-wide in embryonic stem cells and fetal liver cells. The distal sites contacting active genes are enriched in active histone modifications and transcription factor occupancy, whereas inactive genes contact distal sites with repressive histone marks, demonstrating the regulatory potential of the distal elements identified. Furthermore, we find that coregulated genes cluster nonrandomly in spatial interaction networks correlated with their biological function and expression level. Interestingly, we find the strongest gene clustering in ES cells between transcription factor genes that control key developmental processes in embryogenesis. The results provide the first genome-wide catalog linking gene promoters to their long-range interacting elements and highlight the complex spatial regulatory circuitry controlling mammalian gene expression.
Collapse
Affiliation(s)
- Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Mayra Furlan-Magaril
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Borbala Mifsud
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Filipe Tavares-Cadete
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Robert Sugar
- Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Biola-Maria Javierre
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Takashi Nagano
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Yulia Katsman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Moorthy Sakthidevi
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Emilia Dimitrova
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Andrew Dimond
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Lucas B Edelman
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Kristina Tabbada
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Elodie Darbo
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Bram Herman
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Andy Higgs
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Emily LeProust
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Cameron S Osborne
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Nicholas M Luscombe
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; Okinawa Institute for Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom;
| |
Collapse
|
20
|
Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D’Ambrogio A, Luscombe NM, Ule J. hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature 2015; 519:491-4. [PMID: 25799984 PMCID: PMC4376666 DOI: 10.1038/nature14280] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 02/02/2015] [Indexed: 02/02/2023]
Abstract
The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans-acting factors. However, little is known about the in vivo structure of full-length mRNAs. Here we present hiCLIP, a biochemical technique for transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins (RBPs). Using this technique to investigate RNA structures bound by Staufen 1 (STAU1) in human cells, we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unexpected prevalence of long-range duplexes in 3' untranslated regions (UTRs), and a decreased incidence of single nucleotide polymorphisms in duplex-forming regions. We also discover a duplex spanning 858 nucleotides in the 3' UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes.
Collapse
Affiliation(s)
- Yoichiro Sugimoto
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Alessandra Vigilante
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Elodie Darbo
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Alexandra Zirra
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Cristina Militti
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Andrea D’Ambrogio
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK
- Okinawa Institute of Science & Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| |
Collapse
|
21
|
Darbo E, Herrmann C, Lecuit T, Thieffry D, van Helden J. Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis. BMC Genomics 2013; 14:226. [PMID: 23560912 PMCID: PMC3706223 DOI: 10.1186/1471-2164-14-226] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 06/22/2012] [Accepted: 02/28/2013] [Indexed: 01/25/2023] Open
Abstract
Background In all Metazoa, transcription is inactive during the first mitotic cycles after fertilisation. In Drosophila melanogaster, Zygotic Genome Activation (ZGA) occurs in two waves, starting respectively at mitotic cycles 8 (approximately 60 genes) and 14 (over a thousand genes). The regulatory mechanisms underlying these drastic transcriptional changes remain largely unknown. Results We developed an original gene clustering method based on discretized transition profiles, and applied it to datasets from three landmark early embryonic transcriptome studies. We identified 417 genes significantly up-regulated during ZGA. De novo motif discovery returned nine motifs over-represented in their non-coding sequences (upstream, introns, UTR), three of which correspond to previously known transcription factors: Zelda, Tramtrack and Trithorax-like (Trl). The nine discovered motifs were combined to scan ZGA-associated regions and predict about 1300 putative cis-regulatory modules. The fact that Trl is known to act as chromatin remodelling factor suggests that epigenetic regulation might play an important role in zygotic genome activation. We thus systematically compared the locations of predicted CRMs with ChIP-seq profiles for various transcription factors, 38 epigenetic marks from ModENCODE, and DNAse1 accessibility profiles. This analysis highlighted a strong and specific enrichment of predicted ZGA-associated CRMs for Zelda, CBP, Trl binding sites, as well as for histone marks associated with active enhancers (H3K4me1) and for open chromatin regions. Conclusion Based on the results of our computational analyses, we suggest a temporal model explaining the onset of zygotic genome activation by the combined action of transcription factors and epigenetic signals. Although this study is mainly based on the analysis of publicly available transcriptome and ChiP-seq datasets, the resulting model suggests novel mechanisms that underly the coordinated activation of several hundreds genes at a precise time point during embryonic development.
Collapse
Affiliation(s)
- Elodie Darbo
- Technological Advances for Genomics and Clinics (TAGC), INSERM U1090, Université de la Méditerranée, Campus de Luminy, 13288 Marseille Cedex 9, France.
| | | | | | | | | |
Collapse
|