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Boulanger M, Aqrouq M, Tempé D, Kifagi C, Ristic M, Akl D, Hallal R, Carusi A, Gabellier L, de Toledo M, Sigurdsson JO, Kaoma T, Andrieu-Soler C, Forné T, Soler E, Hicheri Y, Gueret E, Vallar L, Olsen JV, Cartron G, Piechaczyk M, Bossis G. DeSUMOylation of chromatin-bound proteins limits the rapid transcriptional reprogramming induced by daunorubicin in acute myeloid leukemias. Nucleic Acids Res 2023; 51:8413-8433. [PMID: 37462077 PMCID: PMC10484680 DOI: 10.1093/nar/gkad581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 09/09/2023] Open
Abstract
Genotoxicants have been used for decades as front-line therapies against cancer on the basis of their DNA-damaging actions. However, some of their non-DNA-damaging effects are also instrumental for killing dividing cells. We report here that the anthracycline Daunorubicin (DNR), one of the main drugs used to treat Acute Myeloid Leukemia (AML), induces rapid (3 h) and broad transcriptional changes in AML cells. The regulated genes are particularly enriched in genes controlling cell proliferation and death, as well as inflammation and immunity. These transcriptional changes are preceded by DNR-dependent deSUMOylation of chromatin proteins, in particular at active promoters and enhancers. Surprisingly, inhibition of SUMOylation with ML-792 (SUMO E1 inhibitor), dampens DNR-induced transcriptional reprogramming. Quantitative proteomics shows that the proteins deSUMOylated in response to DNR are mostly transcription factors, transcriptional co-regulators and chromatin organizers. Among them, the CCCTC-binding factor CTCF is highly enriched at SUMO-binding sites found in cis-regulatory regions. This is notably the case at the promoter of the DNR-induced NFKB2 gene. DNR leads to a reconfiguration of chromatin loops engaging CTCF- and SUMO-bound NFKB2 promoter with a distal cis-regulatory region and inhibition of SUMOylation with ML-792 prevents these changes.
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Affiliation(s)
| | - Mays Aqrouq
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Denis Tempé
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | | | - Marko Ristic
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Dana Akl
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Rawan Hallal
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Aude Carusi
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Ludovic Gabellier
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
- Service d’Hématologie Clinique, CHU de Montpellier, 80 Avenue Augustin Fliche, 34091 Montpellier, France
| | | | - Jon-Otti Sigurdsson
- Proteomics Program, Novo Nordisk Foundation Center For Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Tony Kaoma
- Genomics Research Unit, Luxembourg Institute of Health, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Charlotte Andrieu-Soler
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
- Université de Paris, Laboratory of Excellence GR-Ex, Paris, France
| | | | - Eric Soler
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
- Université de Paris, Laboratory of Excellence GR-Ex, Paris, France
| | - Yosr Hicheri
- Service d’Hématologie Clinique, CHU de Montpellier, 80 Avenue Augustin Fliche, 34091 Montpellier, France
| | - Elise Gueret
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center For Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Guillaume Cartron
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
- Service d’Hématologie Clinique, CHU de Montpellier, 80 Avenue Augustin Fliche, 34091 Montpellier, France
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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