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Benitez-Cantos MS, Cano C, Cuadros M, Medina PP. Activation-induced cytidine deaminase causes recurrent splicing mutations in diffuse large B-cell lymphoma. Mol Cancer 2024; 23:42. [PMID: 38402205 PMCID: PMC10893679 DOI: 10.1186/s12943-024-01960-w] [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: 12/04/2023] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma. A major mutagenic process in DLBCL is aberrant somatic hypermutation (aSHM) by activation-induced cytidine deaminase (AID), which occurs preferentially at RCH/TW sequence motifs proximal to transcription start sites. Splice sequences are highly conserved, rich in RCH/TW motifs, and recurrently mutated in DLBCL. Therefore, we hypothesized that aSHM may cause recurrent splicing mutations in DLBCL. In a meta-cohort of > 1,800 DLBCLs, we found that 77.5% of splicing mutations in 29 recurrently mutated genes followed aSHM patterns. In addition, in whole-genome sequencing (WGS) data from 153 DLBCLs, proximal mutations in splice sequences, especially in donors, were significantly enriched in RCH/TW motifs (p < 0.01). We validated this enrichment in two additional DLBCL cohorts (N > 2,000; p < 0.0001) and confirmed its absence in 12 cancer types without aSHM (N > 6,300). Comparing sequencing data from mouse models with and without AID activity showed that the splice donor sequences were the top genomic feature enriched in AID-induced mutations (p < 0.0001). Finally, we observed that most AID-related splice site mutations are clonal within a sample, indicating that aSHM may cause early loss-of-function events in lymphomagenesis. Overall, these findings support that AID causes an overrepresentation of clonal splicing mutations in DLBCL.
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Affiliation(s)
- Maria S Benitez-Cantos
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, Granada, 18016, Spain
| | - Carlos Cano
- Department of Computer Science and Artificial Intelligence, School of Computer and Telecommunication Engineering, University of Granada, Calle Periodista Daniel Saucedo Aranda s/n, Granada, 18014, Spain
| | - Marta Cuadros
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, Granada, 18016, Spain
| | - Pedro P Medina
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain.
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain.
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Avenida de Fuentenueva s/n, Granada, 18071, Spain.
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2
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Tkachenko A, Kupcova K, Havranek O. B-Cell Receptor Signaling and Beyond: The Role of Igα (CD79a)/Igβ (CD79b) in Normal and Malignant B Cells. Int J Mol Sci 2023; 25:10. [PMID: 38203179 PMCID: PMC10779339 DOI: 10.3390/ijms25010010] [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: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
B-cell receptor (BCR) is a B cell hallmark surface complex regulating multiple cellular processes in normal as well as malignant B cells. Igα (CD79a)/Igβ (CD79b) are essential components of BCR that are indispensable for its functionality, signal initiation, and signal transduction. CD79a/CD79b-mediated BCR signaling is required for the survival of normal as well as malignant B cells via a wide signaling network. Recent studies identified the great complexity of this signaling network and revealed the emerging role of CD79a/CD79b in signal integration. In this review, we have focused on functional features of CD79a/CD79b, summarized signaling consequences of CD79a/CD79b post-translational modifications, and highlighted specifics of CD79a/CD79b interactions within BCR and related signaling cascades. We have reviewed the complex role of CD79a/CD79b in multiple aspects of normal B cell biology and how is the normal BCR signaling affected by lymphoid neoplasms associated CD79A/CD79B mutations. We have also summarized important unresolved questions and highlighted issues that remain to be explored for better understanding of CD79a/CD79b-mediated signal transduction and the eventual identification of additional therapeutically targetable BCR signaling vulnerabilities.
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Affiliation(s)
- Anton Tkachenko
- BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Kristyna Kupcova
- BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic
- First Department of Internal Medicine–Hematology, General University Hospital and First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Ondrej Havranek
- BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic
- First Department of Internal Medicine–Hematology, General University Hospital and First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
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3
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Berta D, Girma M, Melku M, Adane T, Birke B, Yalew A. Role of RNA Splicing Mutations in Diffuse Large B Cell Lymphoma. Int J Gen Med 2023; 16:2469-2480. [PMID: 37342407 PMCID: PMC10278864 DOI: 10.2147/ijgm.s414106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Ribonucleic acid splicing is a crucial process to create a mature mRNA molecule by removing introns and ligating exons. This is a highly regulated process, but any alteration in splicing factors, splicing sites, or auxiliary components affects the final products of the gene. In diffuse large B-cell lymphoma, splicing mutations such as mutant splice sites, aberrant alternative splicing, exon skipping, and intron retention are detected. The alteration affects tumor suppression, DNA repair, cell cycle, cell differentiation, cell proliferation, and apoptosis. As a result, malignant transformation, cancer progression, and metastasis occurred in B cells at the germinal center. B-cell lymphoma 7 protein family member A (BCL7A), cluster of differentiation 79B (CD79B), myeloid differentiation primary response gene 88 (MYD88), tumor protein P53 (TP53), signal transducer and activator of transcription (STAT), serum- and glucose-regulated kinase 1 (SGK1), Pou class 2 associating factor 1 (POU2AF1), and neurogenic locus notch homolog protein 1 (NOTCH) are the most common genes affected by splicing mutations in diffuse large B cell lymphoma.
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Affiliation(s)
- Dereje Berta
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mekonnen Girma
- Department of Quality Assurance and Laboratory Management, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mulugeta Melku
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tiruneh Adane
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Bisrat Birke
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Aregawi Yalew
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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4
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Armand M, Degaud M, Tesson B, Laurent C, Vavasseur M, Parisot M, Hoareau-Coudert B, Canioni D, Michot JM, Charlotte F, Meignin V, Laurent C, Traverse-Gléhen A, Damotte D, Bachy E, Besson C, Hermine O, Davi F, Couronné L. Exploring the genetic landscape of HCV-related B-cell lymphomas using whole exome sequencing. Leukemia 2023:10.1038/s41375-023-01868-2. [PMID: 36914771 DOI: 10.1038/s41375-023-01868-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Affiliation(s)
- Marine Armand
- Hematology Laboratory, Hôpital Pitié-Salpêtrière, Assistance-Publique-Hôpitaux de Paris and Sorbonne University, Paris, France.,Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, F-75006, Paris, France
| | - Michaël Degaud
- Hematology Laboratory, Hôpital Pitié-Salpêtrière, Assistance-Publique-Hôpitaux de Paris and Sorbonne University, Paris, France.,Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, F-75006, Paris, France
| | - Bruno Tesson
- Bioinformatics Department, LYSARC, Paris, France
| | | | - Manon Vavasseur
- Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, INSERM UMR_S 1163, Imagine Institute, Université Paris Cité, Paris, France
| | - Mélanie Parisot
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UAR3633, Paris Descartes Sorbonne Paris Cité University, Paris, France
| | | | - Danielle Canioni
- Department of Pathology, Hôpital Necker-Enfants Malades, Assistance-Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Jean Marie Michot
- Gustave Roussy Institute, Département des Innovations Thérapeutiques et Essais Précoces, Université Paris-Saclay, Villejuif, France.,Unité mixte de recherche Inserm 1170, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Frédéric Charlotte
- Department of Pathology, Hôpital Pitié-Salpêtrière, Assistance-Publique-Hôpitaux de Paris, Sorbonne University, Paris, France
| | - Véronique Meignin
- Department of Pathology, Hôpital Saint-Louis, Assistance-Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Camille Laurent
- Department of Pathology, CHU de Toulouse, Institut Universitaire du Cancer, Toulouse, France.,INSERM U1037, Centre de Recherche en Cancérologie de Toulouse, Toulouse, France
| | - Alexandra Traverse-Gléhen
- Université Lyon 1, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS, UMR5308, ENS Lyon, France.,Hospices Civils de Lyon, Institut de Pathologie Multisite, Hôpital Lyon Sud, Lyon, France
| | - Diane Damotte
- Department of Pathology, Hôpitaux Universitaire Paris Centre, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Emmanuel Bachy
- Department of Hematology, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, Lyon, France.,INSERM U1111, Lymphoma-Immunobiology Biology (LIB) Team, International Center for Research in Infectious Diseases (CIRI), Lyon, France
| | - Caroline Besson
- Department of Hematology and Oncology, Centre Hospitalier de Versailles, Le Chesnay, France.,Université Paris-Saclay, UVSQ, Inserm, Équipe "Exposome et Hérédité", CESP, Villejuif, France
| | - Olivier Hermine
- Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, INSERM UMR_S 1163, Imagine Institute, Université Paris Cité, Paris, France.,Department of Hematology, Hôpital Necker-Enfants Malades, Assistance-Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Frédéric Davi
- Hematology Laboratory, Hôpital Pitié-Salpêtrière, Assistance-Publique-Hôpitaux de Paris and Sorbonne University, Paris, France.,Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, F-75006, Paris, France
| | - Lucile Couronné
- Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutical Implications, INSERM UMR_S 1163, Imagine Institute, Université Paris Cité, Paris, France. .,Laboratory of Onco-Hematology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France.
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5
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Andrades A, Peinado P, Alvarez-Perez JC, Sanjuan-Hidalgo J, García DJ, Arenas AM, Matia-González AM, Medina PP. SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities. Mol Cancer 2023; 22:39. [PMID: 36810086 PMCID: PMC9942420 DOI: 10.1186/s12943-023-01736-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.
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Affiliation(s)
- Alvaro Andrades
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Paola Peinado
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain ,grid.451388.30000 0004 1795 1830Present Address: The Francis Crick Institute, London, UK
| | - Juan Carlos Alvarez-Perez
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Juan Sanjuan-Hidalgo
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Daniel J. García
- grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.4489.10000000121678994Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Alberto M. Arenas
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Ana M. Matia-González
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Pedro P. Medina
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
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