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Miglierina E, Ordanoska D, Le Noir S, Laffleur B. RNA processing mechanisms contribute to genome organization and stability in B cells. Oncogene 2024; 43:615-623. [PMID: 38287115 PMCID: PMC10890934 DOI: 10.1038/s41388-024-02952-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
RNA processing includes post-transcriptional mechanisms controlling RNA quality and quantity to ensure cellular homeostasis. Noncoding (nc) RNAs that are regulated by these dynamic processes may themselves fulfill effector and/or regulatory functions, and recent studies demonstrated the critical role of RNAs in organizing both chromatin and genome architectures. Furthermore, RNAs can threaten genome integrity when accumulating as DNA:RNA hybrids, but could also facilitate DNA repair depending on the molecular context. Therefore, by qualitatively and quantitatively fine-tuning RNAs, RNA processing contributes directly or indirectly to chromatin states, genome organization, and genome stability. B lymphocytes represent a unique model to study these interconnected mechanisms as they express ncRNAs transcribed from key specific sequences before undergoing physiological genetic remodeling processes, including V(D)J recombination, somatic hypermutation, and class switch recombination. RNA processing actors ensure the regulation and degradation of these ncRNAs for efficient DNA repair and immunoglobulin gene remodeling while failure leads to B cell development alterations, aberrant DNA repair, and pathological translocations. This review highlights how RNA processing mechanisms contribute to genome architecture and stability, with emphasis on their critical roles during B cell development, enabling physiological DNA remodeling while preventing lymphomagenesis.
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Affiliation(s)
- Emma Miglierina
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Delfina Ordanoska
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Sandrine Le Noir
- UMR CNRS 7276, Inserm 1262, Université de Limoges: Contrôle de la Réponse Immune B et des Lymphoproliférations, Team 2, B-NATION: B cell Nuclear Architecture, Immunoglobulin genes and Oncogenes, Limoges, France
| | - Brice Laffleur
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France.
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2
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van Anken E, Bakunts A, Hu CCA, Janssens S, Sitia R. Molecular Evaluation of Endoplasmic Reticulum Homeostasis Meets Humoral Immunity. Trends Cell Biol 2021; 31:529-541. [PMID: 33685797 DOI: 10.1016/j.tcb.2021.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022]
Abstract
The biosynthesis of about one third of the human proteome, including membrane receptors and secreted proteins, occurs in the endoplasmic reticulum (ER). Conditions that perturb ER homeostasis activate the unfolded protein response (UPR). An 'optimistic' UPR output aims at restoring homeostasis by reinforcement of machineries that guarantee efficiency and fidelity of protein biogenesis in the ER. Yet, once the UPR 'deems' that ER homeostatic readjustment fails, it transitions to a 'pessimistic' output, which, depending on the cell type, will result in apoptosis. In this article, we discuss emerging concepts on how the UPR 'evaluates' ER stress, how the UPR is repurposed, in particular in B cells, and how UPR-driven counter-selection of cells undergoing homeostatic failure serves organismal homeostasis and humoral immunity.
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Affiliation(s)
- Eelco van Anken
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy.
| | - Anush Bakunts
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | | | - Sophie Janssens
- Laboratory for Endoplasmic Reticulum (ER) Stress and Inflammation, VIB Center for Inflammation Research, and Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Roberto Sitia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
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Mechanisms and Regulation of Nonsense-Mediated mRNA Decay and Nonsense-Associated Altered Splicing in Lymphocytes. Int J Mol Sci 2020; 21:ijms21041335. [PMID: 32079193 PMCID: PMC7072976 DOI: 10.3390/ijms21041335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
The presence of premature termination codons (PTCs) in transcripts is dangerous for the cell as they encode potentially deleterious truncated proteins that can act with dominant-negative or gain-of-function effects. To avoid the synthesis of these shortened polypeptides, several RNA surveillance systems can be activated to decrease the level of PTC-containing mRNAs. Nonsense-mediated mRNA decay (NMD) ensures an accelerated degradation of mRNAs harboring PTCs by using several key NMD factors such as up-frameshift (UPF) proteins. Another pathway called nonsense-associated altered splicing (NAS) upregulates transcripts that have skipped disturbing PTCs by alternative splicing. Thus, these RNA quality control processes eliminate abnormal PTC-containing mRNAs from the cells by using positive and negative responses. In this review, we describe the general mechanisms of NMD and NAS and their respective involvement in the decay of aberrant immunoglobulin and TCR transcripts in lymphocytes.
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Lambert JM, Srour N, Delpy L. The Yin and Yang of RNA surveillance in B lymphocytes and antibody-secreting plasma cells. BMB Rep 2019. [PMID: 31619318 PMCID: PMC6941761 DOI: 10.5483/bmbrep.2019.52.12.232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The random V(D)J recombination process ensures the diversity of the primary immunoglobulin (Ig) repertoire. In two thirds of cases, imprecise recombination between variable (V), diversity (D), and joining (J) segments induces a frameshift in the open reading frame that leads to the appearance of premature termination codons (PTCs). Thus, many B lineage cells harbour biallelic V(D)J-rearrangements of Ig heavy or light chain genes, with a productively-recombined allele encoding the functional Ig chain and a nonproductive allele potentially encoding truncated Ig polypeptides. Since the pattern of Ig gene expression is mostly biallelic, transcription initiated from nonproductive Ig alleles generates considerable amounts of primary transcripts with out-of-frame V(D)J junctions. How RNA surveillance pathways cooperate to control the noise from nonproductive Ig genes will be discussed in this review, focusing on the benefits of nonsense-mediated mRNA decay (NMD) activation during B-cell development and detrimental effects of nonsense-associated altered splicing (NAS) in terminally differentiated plasma cells.
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Affiliation(s)
- Jean-Marie Lambert
- UMR CNRS 7276 - INSERM 1268 - Université de Limoges, Centre de Biologie et de Recherche en Santé, 2 rue du Dr Marcland, Limoges F-87025, France
| | - Nivine Srour
- UMR CNRS 7276 - INSERM 1268 - Université de Limoges, Centre de Biologie et de Recherche en Santé, 2 rue du Dr Marcland, Limoges F-87025, France
| | - Laurent Delpy
- UMR CNRS 7276 - INSERM 1268 - Université de Limoges, Centre de Biologie et de Recherche en Santé, 2 rue du Dr Marcland, Limoges F-87025, France
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Ashi MO, Srour N, Lambert JM, Marchalot A, Martin O, Le Noir S, Pinaud E, Ayala MV, Sirac C, Saulière J, Moreaux J, Cogné M, Delpy L. Physiological and druggable skipping of immunoglobulin variable exons in plasma cells. Cell Mol Immunol 2018; 16:810-819. [PMID: 30127381 DOI: 10.1038/s41423-018-0160-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/07/2018] [Indexed: 11/09/2022] Open
Abstract
The error-prone V(D)J recombination process generates considerable amounts of nonproductive immunoglobulin (Ig) pre-mRNAs. We recently demonstrated that aberrant Ig chains lacking variable (V) domains can be produced after nonsense-associated altered splicing (NAS) events. Remarkably, the expression of these truncated Ig polypeptides heightens endoplasmic reticulum stress and shortens plasma cell (PC) lifespan. Many questions remain regarding the molecular mechanisms underlying this new truncated Ig exclusion (TIE-) checkpoint and its restriction to the ultimate stage of B-cell differentiation. To address these issues, we evaluated the extent of NAS of Ig pre-mRNAs using an Ig heavy chain (IgH) knock-in model that allows for uncoupling of V exon skipping from TIE-induced apoptosis. We found high levels of V exon skipping in PCs compared with B cells, and this skipping was correlated with a biallelic boost in IgH transcription during PC differentiation. Chromatin analysis further revealed that the skipped V exon turned into a pseudo-intron. Finally, we showed that hypertranscription of Ig genes facilitated V exon skipping upon passive administration of splice-switching antisense oligonucleotides (ASOs). Thus, V exon skipping is coupled to transcription and increases as PC differentiation proceeds, likely explaining the late occurrence of the TIE-checkpoint and opening new avenues for ASO-mediated strategies in PC disorders.
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Affiliation(s)
- Mohamad Omar Ashi
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Nivine Srour
- Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Jean-Marie Lambert
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Anne Marchalot
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Ophélie Martin
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Sandrine Le Noir
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Eric Pinaud
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Maria Victoria Ayala
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Christophe Sirac
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Jérôme Saulière
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France
| | - Jérôme Moreaux
- Institute of Human Genetics, CNRS-UM UMR9002, Department of Biological Haematology, CHU Montpellier, University of Montpellier, UFR Medecine, Montpellier, France
| | - Michel Cogné
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France.,Institut Universitaire de France, Université de Limoges, Limoges, France
| | - Laurent Delpy
- Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262-Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France.
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Bender S, Ayala MV, Javaugue V, Bonaud A, Cogné M, Touchard G, Jaccard A, Bridoux F, Sirac C. Comprehensive molecular characterization of a heavy chain deposition disease case. Haematologica 2018; 103:e557-e560. [PMID: 30026336 DOI: 10.3324/haematol.2018.196113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sébastien Bender
- Centre National de la recherche Scientifique UMR CNRS 7276/INSERM U1262, Université de Limoges.,Centre National de l'Amylose AL et Autres Maladies par Dépôt d'Immunoglobulines Monoclonales, Centre Hospitalier Universitaire de Limoges
| | - Maria Victoria Ayala
- Centre National de la recherche Scientifique UMR CNRS 7276/INSERM U1262, Université de Limoges
| | - Vincent Javaugue
- Centre National de la recherche Scientifique UMR CNRS 7276/INSERM U1262, Université de Limoges.,Centre National de l'Amylose AL et Autres Maladies par Dépôt d'Immunoglobulines Monoclonales, Centre Hospitalier Universitaire de Limoges.,Service de Néphrologie et Transplantation, Centre Hospitalier Universitaire de Poitiers
| | - Amélie Bonaud
- Institut national de la santé et de la recherche médicale INSERM UMR996 - Cytokines, Chimiokines, Immunopathologie, Université Paris-Sud et Université Paris-Saclay
| | - Michel Cogné
- Centre National de la recherche Scientifique UMR CNRS 7276/INSERM U1262, Université de Limoges.,Centre National de l'Amylose AL et Autres Maladies par Dépôt d'Immunoglobulines Monoclonales, Centre Hospitalier Universitaire de Limoges
| | - Guy Touchard
- Service de Néphrologie et Transplantation, Centre Hospitalier Universitaire de Poitiers
| | - Arnaud Jaccard
- Centre National de la recherche Scientifique UMR CNRS 7276/INSERM U1262, Université de Limoges.,Centre National de l'Amylose AL et Autres Maladies par Dépôt d'Immunoglobulines Monoclonales, Centre Hospitalier Universitaire de Limoges.,Service d'Hématologie Clinique, Centre Hospitalier Universitaire de Limoges, France
| | - Frank Bridoux
- Centre National de la recherche Scientifique UMR CNRS 7276/INSERM U1262, Université de Limoges.,Centre National de l'Amylose AL et Autres Maladies par Dépôt d'Immunoglobulines Monoclonales, Centre Hospitalier Universitaire de Limoges.,Service de Néphrologie et Transplantation, Centre Hospitalier Universitaire de Poitiers
| | - Christophe Sirac
- Centre National de la recherche Scientifique UMR CNRS 7276/INSERM U1262, Université de Limoges .,Centre National de l'Amylose AL et Autres Maladies par Dépôt d'Immunoglobulines Monoclonales, Centre Hospitalier Universitaire de Limoges
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Sirac C, Herrera GA, Sanders PW, Batuman V, Bender S, Ayala MV, Javaugue V, Teng J, Turbat-Herrera EA, Cogné M, Touchard G, Leung N, Bridoux F. Animal models of monoclonal immunoglobulin-related renal diseases. Nat Rev Nephrol 2018; 14:246-264. [DOI: 10.1038/nrneph.2018.8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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8
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Plasma cell checkpoint. Nat Immunol 2016. [DOI: 10.1038/ni.3401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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