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Bejarano L, Kauzlaric A, Lamprou E, Lourenco J, Fournier N, Ballabio M, Colotti R, Maas R, Galland S, Massara M, Soukup K, Lilja J, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms. Cancer Cell 2024; 42:378-395.e10. [PMID: 38242126 DOI: 10.1016/j.ccell.2023.12.018] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/11/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Brain metastasis (BrM) is a common malignancy, predominantly originating from lung, melanoma, and breast cancers. The vasculature is a key component of the BrM tumor microenvironment with critical roles in regulating metastatic seeding and progression. However, the heterogeneity of the major BrM vascular components, namely endothelial and mural cells, is still poorly understood. We perform single-cell and bulk RNA-sequencing of sorted vascular cell types and detect multiple subtypes enriched specifically in BrM compared to non-tumor brain, including previously unrecognized immune regulatory subtypes. We integrate the human data with mouse models, creating a platform to interrogate vascular targets for the treatment of BrM. We find that the CD276 immune checkpoint molecule is significantly upregulated in the BrM vasculature, and anti-CD276 blocking antibodies prolonged survival in preclinical trials. This study provides important insights into the complex interactions between the vasculature, immune cells, and cancer cells, with translational relevance for designing therapeutic interventions.
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Affiliation(s)
- Leire Bejarano
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Annamaria Kauzlaric
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eleni Lamprou
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Joao Lourenco
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nadine Fournier
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Translational Data Science Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michelle Ballabio
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Roberto Colotti
- In Vivo Imaging Facility (IVIF), University of Lausanne, Lausanne, Switzerland
| | - Roeltje Maas
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Sabine Galland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Matteo Massara
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Klara Soukup
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Johanna Lilja
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Jean-Philippe Brouland
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Andreas F Hottinger
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Roy T Daniel
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Monika E Hegi
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Johanna A Joyce
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre Lausanne, Lausanne, Switzerland; Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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2
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Peyvandi S, Bulliard M, Yilmaz A, Kauzlaric A, Marcone R, Haerri L, Coquoz O, Huang YT, Duffey N, Gafner L, Lorusso G, Fournier N, Lan Q, Rüegg C. Tumor-educated Gr1+CD11b+ cells drive breast cancer metastasis via OSM/IL-6/JAK-induced cancer cell plasticity. J Clin Invest 2024; 134:e166847. [PMID: 38236642 PMCID: PMC10940099 DOI: 10.1172/jci166847] [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: 11/07/2022] [Accepted: 01/17/2024] [Indexed: 03/16/2024] Open
Abstract
Cancer cell plasticity contributes to therapy resistance and metastasis, which represent the main causes of cancer-related death, including in breast cancer. The tumor microenvironment drives cancer cell plasticity and metastasis, and unraveling the underlying cues may provide novel strategies for managing metastatic disease. Using breast cancer experimental models and transcriptomic analyses, we show that stem cell antigen-1 positive (SCA1+) murine breast cancer cells enriched during tumor progression and metastasis had higher in vitro cancer stem cell-like properties, enhanced in vivo metastatic ability, and generated tumors rich in Gr1hiLy6G+CD11b+ cells. In turn, tumor-educated Gr1+CD11b+ (Tu-Gr1+CD11b+) cells rapidly and transiently converted low metastatic SCA1- cells into highly metastatic SCA1+ cells via secreted oncostatin M (OSM) and IL-6. JAK inhibition prevented OSM/IL-6-induced SCA1+ population enrichment, while OSM/IL-6 depletion suppressed Tu-Gr1+CD11b+-induced SCA1+ population enrichment in vitro and metastasis in vivo. Moreover, chemotherapy-selected highly metastatic 4T1 cells maintained high SCA1+ positivity through autocrine IL-6 production, and in vitro JAK inhibition blunted SCA1 positivity and metastatic capacity. Importantly, Tu-Gr1+CD11b+ cells invoked a gene signature in tumor cells predicting shorter overall survival (OS), relapse-free survival (RFS), and lung metastasis in breast cancer patients. Collectively, our data identified OSM/IL-6/JAK as a clinically relevant paracrine/autocrine axis instigating breast cancer cell plasticity and triggering metastasis.
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Affiliation(s)
- Sanam Peyvandi
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Manon Bulliard
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Alev Yilmaz
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Annamaria Kauzlaric
- Translational Data Science Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Rachel Marcone
- Translational Data Science Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lisa Haerri
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Oriana Coquoz
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Yu-Ting Huang
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Nathalie Duffey
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Laetitia Gafner
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Girieca Lorusso
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Nadine Fournier
- Translational Data Science Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Qiang Lan
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Curzio Rüegg
- Pathology Unit, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
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3
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Banga R, Procopio FA, Lana E, Gladkov GT, Roseto I, Parsons EM, Lian X, Armani-Tourret M, Bellefroid M, Gao C, Kauzlaric A, Foglierini M, Alfageme-Abello O, Sluka SHM, Munoz O, Mastrangelo A, Fenwick C, Muller Y, Mkindi CG, Daubenberger C, Cavassini M, Trunfio R, Déglise S, Corpataux JM, Delorenzi M, Lichterfeld M, Pantaleo G, Perreau M. Lymph node dendritic cells harbor inducible replication-competent HIV despite years of suppressive ART. Cell Host Microbe 2023; 31:1714-1731.e9. [PMID: 37751747 PMCID: PMC11068440 DOI: 10.1016/j.chom.2023.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 02/13/2023] [Revised: 06/02/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Although gut and lymph node (LN) memory CD4 T cells represent major HIV and simian immunodeficiency virus (SIV) tissue reservoirs, the study of the role of dendritic cells (DCs) in HIV persistence has long been limited to the blood due to difficulties to access lymphoid tissue samples. In this study, we show that LN migratory and resident DC subpopulations harbor distinct phenotypic and transcriptomic profiles. Interestingly, both LN DC subpopulations contain HIV intact provirus and inducible replication-competent HIV despite the expression of the antiviral restriction factor SAMHD1. Notably, LN DC subpopulations isolated from HIV-infected individuals treated for up to 14 years are transcriptionally silent but harbor replication-competent virus that can be induced upon TLR7/8 stimulation. Taken together, these results uncover a potential important contribution of LN DCs to HIV infection in the presence of ART.
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Affiliation(s)
- Riddhima Banga
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Francesco Andrea Procopio
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Erica Lana
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | | | | | - Elizabeth M Parsons
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Annamaria Kauzlaric
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathilde Foglierini
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Oscar Alfageme-Abello
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Susanna H M Sluka
- Newborn Screening Switzerland, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Olivia Munoz
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Andrea Mastrangelo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Craig Fenwick
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Yannick Muller
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Catherine Gerald Mkindi
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania; Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Matthias Cavassini
- Services of Infectious Diseases, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rafael Trunfio
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Sébastien Déglise
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jean-Marc Corpataux
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Giuseppe Pantaleo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Matthieu Perreau
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
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4
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Tichet M, Wullschleger S, Chryplewicz A, Fournier N, Marcone R, Kauzlaric A, Homicsko K, Deak LC, Umaña P, Klein C, Hanahan D. Bispecific PD1-IL2v and anti-PD-L1 break tumor immunity resistance by enhancing stem-like tumor-reactive CD8 + T cells and reprogramming macrophages. Immunity 2023; 56:162-179.e6. [PMID: 36630914 DOI: 10.1016/j.immuni.2022.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [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: 03/04/2022] [Revised: 09/29/2022] [Accepted: 12/06/2022] [Indexed: 01/11/2023]
Abstract
Immunotherapies have shown remarkable, albeit tumor-selective, therapeutic benefits in the clinic. Most patients respond transiently at best, highlighting the importance of understanding mechanisms underlying resistance. Herein, we evaluated the effects of the engineered immunocytokine PD1-IL2v in a mouse model of de novo pancreatic neuroendocrine cancer that is resistant to checkpoint and other immunotherapies. PD1-IL2v utilizes anti-PD-1 as a targeting moiety fused to an immuno-stimulatory IL-2 cytokine variant (IL2v) to precisely deliver IL2v to PD-1+ T cells in the tumor microenvironment. PD1-IL2v elicited substantial infiltration by stem-like CD8+ T cells, resulting in tumor regression and enhanced survival in mice. Combining anti-PD-L1 with PD1-IL2v sustained the response phase, improving therapeutic efficacy both by reprogramming immunosuppressive tumor-associated macrophages and enhancing T cell receptor (TCR) immune repertoire diversity. These data provide a rationale for clinical trials to evaluate the combination therapy of PD1-IL2v and anti-PD-L1, particularly in immunotherapy-resistant tumors infiltrated with PD-1+ stem-like T cells.
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Affiliation(s)
- Mélanie Tichet
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Ludwig Institute for Cancer Research, Lausanne Branch, 1011 Lausanne, Switzerland; Agora Translational Cancer Research Center, Rue du Bugnon 25A, 1011 Lausanne, Switzerland
| | - Stephan Wullschleger
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
| | - Agnieszka Chryplewicz
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Agora Translational Cancer Research Center, Rue du Bugnon 25A, 1011 Lausanne, Switzerland
| | - Nadine Fournier
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Rachel Marcone
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Annamaria Kauzlaric
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Krisztian Homicsko
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Agora Translational Cancer Research Center, Rue du Bugnon 25A, 1011 Lausanne, Switzerland; Department of Oncology, CHUV, 46 Rue Bugnon, 1011 Lausanne, Switzerland; Center for Personalized Oncology, CHUV, 46 Rue Bugnon, 1011 Lausanne, Switzerland
| | | | - Pablo Umaña
- Roche-Innovation Center Zurich, 8952 Schlieren, Switzerland
| | | | - Douglas Hanahan
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Ludwig Institute for Cancer Research, Lausanne Branch, 1011 Lausanne, Switzerland; Agora Translational Cancer Research Center, Rue du Bugnon 25A, 1011 Lausanne, Switzerland.
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5
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Marcaida MJ, Kauzlaric A, Duperrex A, Sülzle J, Moncrieffe MC, Adebajo D, Manley S, Trono D, Dal Peraro M. The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity. iScience 2020; 23:101811. [PMID: 33313488 PMCID: PMC7721647 DOI: 10.1016/j.isci.2020.101811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Received: 05/25/2020] [Revised: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Members of the DEAD-box helicase family are involved in all fundamental processes of RNA metabolism, and as such, their malfunction is associated with various diseases. Currently, whether and how oligomerization impacts their biochemical and biological functions is not well understood. In this work, we show that DDX21, a human DEAD-box helicase with RNA G-quadruplex resolving activity, is dimeric and that its oligomerization state influences its helicase activity. Solution small-angle X-ray scattering (SAXS) analysis uncovers a flexible multi-domain protein with a central dimerization domain. While the Arg/Gly rich C termini, rather than dimerization, are key to maintaining high affinity for RNA substrates, in vitro helicase assays indicate that an intact dimer is essential for both DDX21 ATP-dependent double-stranded RNA unwinding and ATP-independent G-quadruplex remodeling activities. Our results suggest that oligomerization plays a key role in regulating RNA DEAD-box helicase activity. The human RNA DEAD-box helicase DDX21 is dimeric DDX21 dimerization is mediated by a hydrophobic central core domain SAXS-based modeling reveals that DDX21 is intrinsically flexible Dimerization and C-terminal domains mediate G-quadruplex and dsRNA unwinding
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Affiliation(s)
- Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Annamaria Kauzlaric
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Alice Duperrex
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Jenny Sülzle
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Martin C Moncrieffe
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Damilola Adebajo
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Suliana Manley
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
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6
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Kauzlaric A, Jang SM, Morchikh M, Cassano M, Planet E, Benkirane M, Trono D. KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190334. [PMID: 32068487 PMCID: PMC7061982 DOI: 10.1098/rstb.2019.0334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 12/28/2022] Open
Abstract
KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation, notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
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Affiliation(s)
- Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Suk Min Jang
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Mehdi Morchikh
- Laboratory of Molecular Virology, Institute of Human Genetics, CNRS UPR1142, MGX-Montpellier GenomiX, 141 rue de la Cardonille, 34396 Montpellier, France.,Institute of Molecular Genetics of Montpellier, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Marco Cassano
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Monsef Benkirane
- Laboratory of Molecular Virology, Institute of Human Genetics, CNRS UPR1142, MGX-Montpellier GenomiX, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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7
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Jang SM, Kauzlaric A, Quivy JP, Pontis J, Rauwel B, Coluccio A, Offner S, Duc J, Turelli P, Almouzni G, Trono D. KAP1 facilitates reinstatement of heterochromatin after DNA replication. Nucleic Acids Res 2019; 46:8788-8802. [PMID: 29955894 PMCID: PMC6158507 DOI: 10.1093/nar/gky580] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 01/11/2018] [Accepted: 06/25/2018] [Indexed: 12/30/2022] Open
Abstract
During cell division, maintenance of chromatin features from the parental genome requires their proper establishment on its newly synthetized copy. The loss of epigenetic marks within heterochromatin, typically enriched in repetitive elements, endangers genome stability and permits chromosomal rearrangements via recombination. However, how histone modifications associated with heterochromatin are maintained across mitosis remains poorly understood. KAP1 is known to act as a scaffold for a repressor complex that mediates local heterochromatin formation, and was previously demonstrated to play an important role during DNA repair. Accordingly, we investigated a putative role for this protein in the replication of heterochromatic regions. We first found that KAP1 associates with several DNA replication factors including PCNA, MCM3 and MCM6. We then observed that these interactions are promoted by KAP1 phosphorylation on serine 473 during S phase. Finally, we could demonstrate that KAP1 forms a complex with PCNA and the histone-lysine methyltransferase Suv39h1 to reinstate heterochromatin after DNA replication.
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Affiliation(s)
- Suk Min Jang
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Jean-Pierre Quivy
- Institut Curie, Centre de Recherche, Paris 75248, France.,Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France.,Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France.,Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France.,Sorbonne University, PSL, Paris 75005, France
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Benjamin Rauwel
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Andrea Coluccio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris 75248, France.,Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France.,Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France.,Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France.,Sorbonne University, PSL, Paris 75005, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
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Kauzlaric A, Ecco G, Cassano M, Duc J, Imbeault M, Trono D. The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units. PLoS One 2017; 12:e0173746. [PMID: 28334004 PMCID: PMC5363842 DOI: 10.1371/journal.pone.0173746] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [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: 11/29/2016] [Accepted: 02/24/2017] [Indexed: 12/13/2022] Open
Abstract
KRAB-containing poly-zinc finger proteins (KZFPs) constitute the largest family of transcription factors encoded by mammalian genomes, and growing evidence indicates that they fulfill functions critical to both embryonic development and maintenance of adult homeostasis. KZFP genes underwent broad and independent waves of expansion in many higher vertebrates lineages, yet comprehensive studies of members harbored by a given species are scarce. Here we present a thorough analysis of KZFP genes and related units in the murine genome. We first identified about twice as many elements than previously annotated as either KZFP genes or pseudogenes, notably by assigning to this family an entity formerly considered as a large group of Satellite repeats. We then could delineate an organization in clusters distributed throughout the genome, with signs of recombination, translocation, duplication and seeding of new sites by retrotransposition of KZFP genes and related genetic units (KZFP/rGUs). Moreover, we harvested evidence indicating that closely related paralogs had evolved through both drifting and shifting of sequences encoding for zinc finger arrays. Finally, we could demonstrate that the KAP1-SETDB1 repressor complex tames the expression of KZFP/rGUs within clusters, yet that the primary targets of this regulation are not the KZFP/rGUs themselves but enhancers contained in neighboring endogenous retroelements and that, underneath, KZFPs conserve highly individualized patterns of expression.
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Affiliation(s)
- Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gabriela Ecco
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marco Cassano
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael Imbeault
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- * E-mail:
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Ecco G, Cassano M, Kauzlaric A, Duc J, Coluccio A, Offner S, Imbeault M, Rowe HM, Turelli P, Trono D. Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues. Dev Cell 2016; 36:611-23. [PMID: 27003935 DOI: 10.1016/j.devcel.2016.02.024] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 02/10/2016] [Accepted: 02/24/2016] [Indexed: 12/21/2022]
Abstract
KRAB-containing zinc finger proteins (KRAB-ZFPs) are early embryonic controllers of transposable elements (TEs), which they repress with their cofactor KAP1 through histone and DNA methylation, a process thought to result in irreversible silencing. Using a target-centered functional screen, we matched murine TEs with their cognate KRAB-ZFP. We found the paralogs ZFP932 and Gm15446 to bind overlapping but distinguishable subsets of ERVK (endogenous retrovirus K), repress these elements in embryonic stem cells, and regulate secondarily the expression of neighboring genes. Most importantly, we uncovered that these KRAB-ZFPs and KAP1 control TEs in adult tissues, in cell culture and in vivo, where they partner up to modulate cellular genes. Therefore, TEs and KRAB-ZFPs establish transcriptional networks that likely regulate not only development but also many physiological events. Given the high degree of species specificity of TEs and KRAB-ZFPs, these results have important implications for understanding the biology of higher vertebrates, including humans.
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Affiliation(s)
- Gabriela Ecco
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Marco Cassano
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Annamaria Kauzlaric
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Andrea Coluccio
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Michaël Imbeault
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Helen M Rowe
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland.
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Meylan S, Groner AC, Ambrosini G, Malani N, Quenneville S, Zangger N, Kapopoulou A, Kauzlaric A, Rougemont J, Ciuffi A, Bushman FD, Bucher P, Trono D. A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics 2011; 12:378. [PMID: 21791101 PMCID: PMC3199781 DOI: 10.1186/1471-2164-12-378] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [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: 04/12/2011] [Accepted: 07/26/2011] [Indexed: 01/20/2023] Open
Abstract
Background KRAB-ZFPs (Krüppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors responsible for the formation of facultative heterochromatin. We have recently shown that KRAB/KAP1 can mediate long-range transcriptional repression through heterochromatin spreading, but also demonstrated that this process is at times countered by endogenous influences. Method To investigate this issue further we used an ectopic KRAB-based repressor. This system allowed us to tether KRAB/KAP1 to hundreds of euchromatic sites within genes, and to record its impact on gene expression. We then correlated this KRAB/KAP1-mediated transcriptional effect to pre-existing genomic and chromatin structures to identify specific characteristics making a gene susceptible to repression. Results We found that genes that were susceptible to KRAB/KAP1-mediated silencing carried higher levels of repressive histone marks both at the promoter and over the transcribed region than genes that were insensitive. In parallel, we found a high enrichment in euchromatic marks within both the close and more distant environment of these genes. Conclusion Together, these data indicate that high levels of gene activity in the genomic environment and the pre-deposition of repressive histone marks within a gene increase its susceptibility to KRAB/KAP1-mediated repression.
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Affiliation(s)
- Sylvain Meylan
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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