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Rogers GL, Huang C, Mathur A, Huang X, Chen HY, Stanten K, Morales H, Chang CH, Kezirian EJ, Cannon PM. Reprogramming human B cells with custom heavy chain antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546944. [PMID: 37425794 PMCID: PMC10327003 DOI: 10.1101/2023.06.28.546944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
We describe a genome editing strategy to reprogram the immunoglobulin heavy chain (IgH) locus of human B cells to express custom molecules that respond to immunization. These heavy chain antibodies (HCAbs) comprise a custom antigen-recognition domain linked to an Fc domain derived from the IgH locus and can be differentially spliced to express either B cell receptor (BCR) or secreted antibody isoforms. The HCAb editing platform is highly flexible, supporting antigen-binding domains based on both antibody and non-antibody components, and also allowing alterations in the Fc domain. Using HIV Env protein as a model antigen, we show that B cells edited to express anti-Env HCAbs support the regulated expression of both BCRs and antibodies, and respond to Env antigen in a tonsil organoid model of immunization. In this way, human B cells can be reprogrammed to produce customized therapeutic molecules with the potential for in vivo amplification.
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Affiliation(s)
- Geoffrey L. Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Chun Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Atishay Mathur
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Xiaoli Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Hsu-Yu Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Kalya Stanten
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Heidy Morales
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Chan-Hua Chang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Eric J. Kezirian
- Department of Otolaryngology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Paula M. Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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2
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Marasco LE, Kornblihtt AR. The physiology of alternative splicing. Nat Rev Mol Cell Biol 2023; 24:242-254. [PMID: 36229538 DOI: 10.1038/s41580-022-00545-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Alternative splicing is a substantial contributor to the high complexity of transcriptomes of multicellular eukaryotes. In this Review, we discuss the accumulated evidence that most of this complexity is reflected at the protein level and fundamentally shapes the physiology and pathology of organisms. This notion is supported not only by genome-wide analyses but, mainly, by detailed studies showing that global and gene-specific modulations of alternative splicing regulate highly diverse processes such as tissue-specific and species-specific cell differentiation, thermal regulation, neuron self-avoidance, infrared sensing, the Warburg effect, maintenance of telomere length, cancer and autism spectrum disorders (ASD). We also discuss how mastering the control of alternative splicing paved the way to clinically approved therapies for hereditary diseases.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
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3
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Mukherjee S, Graber JH, Moore CL. Macrophage differentiation is marked by increased abundance of the mRNA 3' end processing machinery, altered poly(A) site usage, and sensitivity to the level of CstF64. Front Immunol 2023; 14:1091403. [PMID: 36761770 PMCID: PMC9905730 DOI: 10.3389/fimmu.2023.1091403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Regulation of mRNA polyadenylation is important for response to external signals and differentiation in several cell types, and results in mRNA isoforms that vary in the amount of coding sequence or 3' UTR regulatory elements. However, its role in differentiation of monocytes to macrophages has not been investigated. Macrophages are key effectors of the innate immune system that help control infection and promote tissue-repair. However, overactivity of macrophages contributes to pathogenesis of many diseases. In this study, we show that macrophage differentiation is characterized by shortening and lengthening of mRNAs in relevant cellular pathways. The cleavage/polyadenylation (C/P) proteins increase during differentiation, suggesting a possible mechanism for the observed changes in poly(A) site usage. This was surprising since higher C/P protein levels correlate with higher proliferation rates in other systems, but monocytes stop dividing after induction of differentiation. Depletion of CstF64, a C/P protein and known regulator of polyadenylation efficiency, delayed macrophage marker expression, cell cycle exit, attachment, and acquisition of structural complexity, and impeded shortening of mRNAs with functions relevant to macrophage biology. Conversely, CstF64 overexpression increased use of promoter-proximal poly(A) sites and caused the appearance of differentiated phenotypes in the absence of induction. Our findings indicate that regulation of polyadenylation plays an important role in macrophage differentiation.
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Affiliation(s)
- Srimoyee Mukherjee
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
| | - Joel H. Graber
- Computational Biology and Bioinformatics Core, Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Claire L. Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
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4
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Gallicchio L, Olivares GH, Berry CW, Fuller MT. Regulation and function of alternative polyadenylation in development and differentiation. RNA Biol 2023; 20:908-925. [PMID: 37906624 PMCID: PMC10730144 DOI: 10.1080/15476286.2023.2275109] [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] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Alternative processing of nascent mRNAs is widespread in eukaryotic organisms and greatly impacts the output of gene expression. Specifically, alternative cleavage and polyadenylation (APA) is a co-transcriptional molecular process that switches the polyadenylation site (PAS) at which a nascent mRNA is cleaved, resulting in mRNA isoforms with different 3'UTR length and content. APA can potentially affect mRNA translation efficiency, localization, stability, and mRNA seeded protein-protein interactions. APA naturally occurs during development and cellular differentiation, with around 70% of human genes displaying APA in particular tissues and cell types. For example, neurons tend to express mRNAs with long 3'UTRs due to preferential processing at PASs more distal than other PASs used in other cell types. In addition, changes in APA mark a variety of pathological states, including many types of cancer, in which mRNAs are preferentially cleaved at more proximal PASs, causing expression of mRNA isoforms with short 3'UTRs. Although APA has been widely reported, both the function of APA in development and the mechanisms that regulate the choice of 3'end cut sites in normal and pathogenic conditions are still poorly understood. In this review, we summarize current understanding of how APA is regulated during development and cellular differentiation and how the resulting change in 3'UTR content affects multiple aspects of gene expression. With APA being a widespread phenomenon, the advent of cutting-edge scientific techniques and the pressing need for in-vivo studies, there has never been a better time to delve into the intricate mechanisms of alternative cleavage and polyadenylation.
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Affiliation(s)
- Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
| | - Gonzalo H. Olivares
- Escuela de Kinesiología, Facultad de Medicina y Ciencias de la Salud, Center for Integrative Biology (CIB), Universidad Mayor, Chile and Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | | | - Margaret T. Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
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5
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Trezise S, Nutt SL. The gene regulatory network controlling plasma cell function. Immunol Rev 2021; 303:23-34. [PMID: 34109653 DOI: 10.1111/imr.12988] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/16/2022]
Abstract
Antibodies are an essential element of the immune response to infection, and in long-term protection upon re-exposure to the same micro-organism. Antibodies are produced by plasmablasts and plasma cells, the terminally differentiated cells of the B lymphocyte lineage. These relatively rare populations, collectively termed antibody secreting cells (ASCs), have developed highly specialized transcriptional and metabolic pathways to facilitate their extraordinarily high rates of antibody synthesis and secretion. In this review, we discuss the gene regulatory network that controls ASC identity and function, with a particular focus on the processes that influence the transcription, translation, folding, modification and secretion of antibodies. We will address how ASCs have adapted their transcriptional, metabolic and protein homeostasis pathways to sustain such high rates of antibody production, and the roles that the major ASC regulators, the transcription factors, Irf4, Blimp-1 and Xbp1, play in co-ordinating these processes.
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Affiliation(s)
- Stephanie Trezise
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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6
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Page A, Fusil F, Cosset FL. Towards Physiologically and Tightly Regulated Vectored Antibody Therapies. Cancers (Basel) 2020; 12:E962. [PMID: 32295072 PMCID: PMC7226531 DOI: 10.3390/cancers12040962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/20/2022] Open
Abstract
Cancers represent highly significant health issues and the options for their treatment are often not efficient to cure the disease. Immunotherapy strategies have been developed to modulate the patient's immune system in order to eradicate cancerous cells. For instance, passive immunization consists in the administration at high doses of exogenously produced monoclonal antibodies directed either against tumor antigen or against immune checkpoint inhibitors. Its main advantage is that it provides immediate immunity, though during a relatively short period, which consequently requires frequent injections. To circumvent this limitation, several approaches, reviewed here, have emerged to induce in vivo antibody secretion at physiological doses. Gene delivery vectors, such as adenoviral vectors or adeno-associated vectors, have been designed to induce antibody secretion in vivo after in situ cell modification, and have driven significant improvements in several cancer models. However, anti-idiotypic antibodies and escape mutants have been detected, probably because of both the continuous expression of antibodies and their expression by unspecialized cell types. To overcome these hurdles, adoptive transfer of genetically modified B cells that secrete antibodies either constitutively or in a regulated manner have been developed by ex vivo transgene insertion with viral vectors. Recently, with the emergence of gene editing technologies, the endogenous B cell receptor loci of B cells have been modified with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonuclease (Cas-9) system to change their specificity in order to target a given antigen. The expression of the modified BCR gene hence follows the endogenous regulation mechanisms, which may prevent or at least reduce side effects. Although these approaches seem promising for cancer treatments, major questions, such as the persistence and the re-activation potential of these engineered cells, remain to be addressed in clinically relevant animal models before translation to humans.
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Affiliation(s)
| | | | - François-Loïc Cosset
- CIRICentre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 allée d’Italie, F-69007 Lyon, France; (A.P.); (F.F.)
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7
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Herrero AB, Quwaider D, Corchete LA, Mateos MV, García-Sanz R, Gutiérrez NC. FAM46C controls antibody production by the polyadenylation of immunoglobulin mRNAs and inhibits cell migration in multiple myeloma. J Cell Mol Med 2020; 24:4171-4182. [PMID: 32141701 PMCID: PMC7171423 DOI: 10.1111/jcmm.15078] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/22/2020] [Accepted: 01/29/2020] [Indexed: 12/30/2022] Open
Abstract
FAM46C, frequently mutated in multiple myeloma (MM), has recently been shown to encode a non‐canonical poly(A) polymerase (ncPAP). However, its target mRNAs and its role in MM pathogenesis remain mostly unknown. Using CRISPR‐Cas9 technology and gene expression analysis, we found that the inactivation of FAM46C in MM down‐regulates immunoglobulins (Igs) and several mRNAs encoding ER‐resident proteins, including some involved in unfolded protein response and others that affect glycosylation. Interestingly, we show that FAM46C expression is induced during plasma cell (PC) differentiation and that Ig mRNAs encoding heavy and light chains are substrates of the ncPAP, as revealed by poly(A) tail‐length determination assays. The absence of the ncPAP results in Ig mRNA poly(A) tail‐shortening, leading to a reduction in mRNA and protein abundance. On the other hand, loss of FAM46C up‐regulates metastasis‐associated lncRNA MALAT1 and results in a sharp increase in the migration ability. This phenotype depends mainly on the activation of PI3K/Rac1 signalling, which might have significant therapeutic implications. In conclusion, our results identify Ig mRNAs as targets of FAM46C, reveal an important function of this protein during PC maturation to increase antibody production and suggest that its role as a tumour suppressor might be related to the inhibition of myeloma cell migration.
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Affiliation(s)
- Ana Belén Herrero
- Haematology Department, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Dalia Quwaider
- Haematology Department, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Luis Antonio Corchete
- Haematology Department, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Maria Victoria Mateos
- Haematology Department, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Ramón García-Sanz
- Haematology Department, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain.,Center for Biomedical Research in Network of Cancer (CIBERONC), Salamanca, Spain
| | - Norma C Gutiérrez
- Haematology Department, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, Salamanca, Spain.,Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain.,Center for Biomedical Research in Network of Cancer (CIBERONC), Salamanca, Spain
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8
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Maiolo E, Alma E, Napodano C, Gulli F, Bellesi S, Cuccaro A, Pocino K, D’Alo’ F, Iachini M, Martini M, Larocca LM, De Stefano V, Basile U, Hohaus S. The prognostic impact of monoclonal immune globulin and free light chain secretion in diffuse large B cell lymphoma (DLBCL). Leuk Lymphoma 2019; 61:1133-1139. [DOI: 10.1080/10428194.2019.1706731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Elena Maiolo
- Area di Ematologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Eleonora Alma
- Area di Ematologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Cecilia Napodano
- Dipartimento di Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Francesca Gulli
- Dipartimento di Medicina di Laboratorio, Ospedale Madre Giuseppina Vannini, Rome, Italy
| | - Silvia Bellesi
- Area di Ematologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Annarosa Cuccaro
- Area di Ematologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Krizia Pocino
- Dipartimento di Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Francesco D’Alo’
- Area di Ematologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
- Istituto di Ematologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marco Iachini
- Istituto di Ematologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Martini
- Istituto di Anatomia Patologica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Luigi Maria Larocca
- Istituto di Anatomia Patologica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Valerio De Stefano
- Area di Ematologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
- Istituto di Ematologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Umberto Basile
- Area di Diagnostica di Laboratorio, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Stefan Hohaus
- Area di Ematologia, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
- Istituto di Ematologia, Università Cattolica del Sacro Cuore, Rome, Italy
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9
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Aresta-Branco F, Erben E, Papavasiliou FN, Stebbins CE. Mechanistic Similarities between Antigenic Variation and Antibody Diversification during Trypanosoma brucei Infection. Trends Parasitol 2019; 35:302-315. [PMID: 30826207 DOI: 10.1016/j.pt.2019.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/19/2019] [Accepted: 01/23/2019] [Indexed: 02/06/2023]
Abstract
Trypanosoma brucei, which causes African trypanosomiasis, avoids immunity by periodically switching its surface composition. The parasite is coated by 10 million identical, monoallelically expressed variant surface glycoprotein (VSG) molecules. Multiple distinct parasites (with respect to their VSG coat) coexist simultaneously during each wave of parasitemia. This substantial antigenic load is countered by B cells whose antigen receptors (antibodies or immunoglobulins) are also monoallelically expressed, and that diversify dynamically to counter each variant antigen. Here we examine parallels between the processes that generate VSGs and antibodies. We also discuss current insights into VSG mRNA regulation that may inform the emerging field of Ig mRNA biology. We conclude by extending the parallels between VSG and Ig to the protein level.
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Affiliation(s)
- Francisco Aresta-Branco
- Division of Immune Diversity, German Cancer Research Center, Heidelberg, Germany; Division of Structural Biology of Infection and Immunity, German Cancer Research Center, Heidelberg, Germany; These authors contributed equally to this work
| | - Esteban Erben
- Division of Immune Diversity, German Cancer Research Center, Heidelberg, Germany; These authors contributed equally to this work
| | - F Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center, Heidelberg, Germany.
| | - C Erec Stebbins
- Division of Structural Biology of Infection and Immunity, German Cancer Research Center, Heidelberg, Germany.
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10
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Lee HN, Mitra M, Bosompra O, Corney DC, Johnson EL, Rashed N, Ho LD, Coller HA. RECK isoforms have opposing effects on cell migration. Mol Biol Cell 2018; 29:1825-1838. [PMID: 29874120 PMCID: PMC6085827 DOI: 10.1091/mbc.e17-12-0708] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cell migration is a highly conserved process involving cytoskeletal reorganization and restructuring of the surrounding extracellular matrix. Although there are many studies describing mechanisms underlying cell motility, little has been reported about the contribution of alternative isoform use toward cell migration. Here, we investigated whether alternative isoform use can affect cell migration focusing on reversion-inducing-cysteine-rich protein with Kazal motifs (RECK), an established inhibitor of cell migration. We found that a shorter isoform of RECK is more highly expressed in proliferating fibroblasts, in TGF-β-treated fibroblasts, and in tumors compared with differentiated tissue. Knockdown of this short RECK isoform reduces fibroblast migration through Matrigel. Thus, this short isoform of RECK generated by a combination of alternative splicing and alternative polyadenylation plays an opposing role to the canonical RECK isoform, as knockdown of canonical RECK results in faster cell migration through Matrigel. We show that the short RECK protein competes with matrix metalloprotease 9 (MMP9) for binding to the Kazal motifs of canonical RECK, thus liberating MMP9 from an inactivating interaction with canonical RECK. Our studies provide a new paradigm and a detailed mechanism for how alternative isoform use can regulate cell migration by producing two proteins with opposing effects from the same genetic locus.
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Affiliation(s)
- Ha Neul Lee
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - Mithun Mitra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
| | - Oye Bosompra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095
| | - David C Corney
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Nadine Rashed
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095
| | - Linda D Ho
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095
| | - Hilary A Coller
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095
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11
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IgH isotype-specific B cell receptor expression influences B cell fate. Proc Natl Acad Sci U S A 2017; 114:E8411-E8420. [PMID: 28923960 DOI: 10.1073/pnas.1704962114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Ig heavy chain (IgH) isotypes (e.g., IgM, IgG, and IgE) are generated as secreted/soluble antibodies (sIg) or as membrane-bound (mIg) B cell receptors (BCRs) through alternative RNA splicing. IgH isotype dictates soluble antibody function, but how mIg isotype influences B cell behavior is not well defined. We examined IgH isotype-specific BCR function by analyzing naturally switched B cells from wild-type mice, as well as by engineering polyclonal Ighγ1/γ1 and Ighε/ε mice, which initially produce IgG1 or IgE from their respective native genomic configurations. We found that B cells from wild-type mice, as well as Ighγ1/γ1 and Ighε/ε mice, produce transcripts that generate IgM, IgG1, and IgE in an alternative splice form bias hierarchy, regardless of cell stage. In this regard, we found that mIgμ > mIgγ1 > mIgε, and that these BCR expression differences influence respective developmental fitness. Restrained B cell development from Ighγ1/γ1 and Ighε/ε mice was proportional to sIg/mIg ratios and was rescued by enforced expression of the respective mIgs. In addition, artificially enhancing BCR signal strength permitted IgE+ memory B cells-which essentially do not exist under normal conditions-to provide long-lived memory function, suggesting that quantitative BCR signal weakness contributes to restraint of IgE B cell responses. Our results indicate that IgH isotype-specific mIg/BCR dosage may play a larger role in B cell fate than previously anticipated.
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12
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Verbeeren J, Verma B, Niemelä EH, Yap K, Makeyev EV, Frilander MJ. Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA. PLoS Genet 2017; 13:e1006824. [PMID: 28549066 PMCID: PMC5473595 DOI: 10.1371/journal.pgen.1006824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/16/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3′ untranslated region (3′UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3′UTR to non-productive isoforms with a long 3′UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12- and U2-type 5′ splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3′UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm. The cellular homeostasis of many components of the eukaryotic RNA processing machinery is regulated via negative feed-back pathways that result in the formation of both productive and non-productive mRNA species. Typically, the formation of non-productive mRNAs species results from changes in alternative splicing that disrupt the reading frame of the protein coding region and leads to destabilization of the mRNA. Here, we have investigated the homeostasis regulation of the U11/U12-65K mRNA that encodes an essential protein component of the minor (U12-dependent) spliceosome intron recognition complex. We show that homeostasis is regulated at the level of nuclear mRNA export and mRNA 3′-end formation, and that it can be further regulated during neuronal differentiation. We describe a multilayered regulatory system utilizing alternative exon definition interactions that use the input from both spliceosomes and the polyadenylation machinery to decide between productive and non-productive mRNA formation. Because the 65K protein is an essential component of the minor spliceosome, this regulatory pathway can potentially affect the expression of ~700 genes containing U12-type introns.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Bhupendra Verma
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Elina H. Niemelä
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Karen Yap
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Eugene V. Makeyev
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Mikko J. Frilander
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
- * E-mail:
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DeMicco A, Naradikian MS, Sindhava VJ, Yoon JH, Gorospe M, Wertheim GB, Cancro MP, Bassing CH. B Cell-Intrinsic Expression of the HuR RNA-Binding Protein Is Required for the T Cell-Dependent Immune Response In Vivo. THE JOURNAL OF IMMUNOLOGY 2015; 195:3449-62. [PMID: 26320247 DOI: 10.4049/jimmunol.1500512] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/03/2015] [Indexed: 11/19/2022]
Abstract
The HuR RNA-binding protein posttranscriptionally controls expression of genes involved in cellular survival, proliferation, and differentiation. To determine roles of HuR in B cell development and function, we analyzed mice with B lineage-specific deletion of the HuR gene. These HuRΔ/Δ mice have reduced numbers of immature bone marrow and mature splenic B cells, with only the former rescued by p53 inactivation, indicating that HuR supports B lineage cells through developmental stage-specific mechanisms. Upon in vitro activation, HuRΔ/Δ B cells have a mild proliferation defect and impaired ability to produce mRNAs that encode IgH chains of secreted Abs, but no deficiencies in survival, isotype switching, or expression of germinal center (GC) markers. In contrast, HuRΔ/Δ mice have minimal serum titers of all Ab isotypes, decreased numbers of GC and plasma B cells, and few peritoneal B-1 B cells. Moreover, HuRΔ/Δ mice have severely decreased GCs, T follicular helper cells, and high-affinity Abs after immunization with a T cell-dependent Ag. This failure of HuRΔ/Δ mice to mount a T cell-dependent Ab response contrasts with the ability of HuRΔ/Δ B cells to become GC-like in vitro, indicating that HuR is essential for aspects of B cell activation unique to the in vivo environment. Consistent with this notion, we find in vitro stimulated HuRΔ/Δ B cells exhibit modestly reduced surface expression of costimulatory molecules whose expression is similarly decreased in humans with common variable immunodeficiency. HuRΔ/Δ mice provide a model to identify B cell-intrinsic factors that promote T cell-dependent immune responses in vivo.
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Affiliation(s)
- Amy DeMicco
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Cell and Molecular Biology Graduate Group, Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Martin S Naradikian
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Vishal J Sindhava
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224; and
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224; and
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Michael P Cancro
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104; Cell and Molecular Biology Graduate Group, Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
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14
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Fusil F, Calattini S, Amirache F, Mancip J, Costa C, Robbins JB, Douam F, Lavillette D, Law M, Defrance T, Verhoeyen E, Cosset FL. A Lentiviral Vector Allowing Physiologically Regulated Membrane-anchored and Secreted Antibody Expression Depending on B-cell Maturation Status. Mol Ther 2015; 23:1734-1747. [PMID: 26281898 DOI: 10.1038/mt.2015.148] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/07/2015] [Indexed: 12/24/2022] Open
Abstract
The development of lentiviral vectors (LVs) for expression of a specific antibody can be achieved through the transduction of mature B-cells. This approach would provide a versatile tool for active immunotherapy strategies for infectious diseases or cancer, as well as for protein engineering. Here, we created a lentiviral expression system mimicking the natural production of these two distinct immunoglobulin isoforms. We designed a LV (FAM2-LV) expressing an anti-HCV-E2 surface glycoprotein antibody (AR3A) as a membrane-anchored Ig form or a soluble Ig form, depending on the B-cell maturation status. FAM2-LV induced high-level and functional membrane expression of the transgenic antibody in a nonsecretory B-cell line. In contrast, a plasma cell (PC) line transduced with FAM2-LV preferentially produced the secreted transgenic antibody. Similar results were obtained with primary B-cells transduced ex vivo. Most importantly, FAM2-LV transduced primary B-cells efficiently differentiated into PCs, which secreted the neutralizing anti-HCV E2 antibody upon adoptive transfer into immunodeficient NSG (NOD/SCIDγc(-/-)) recipient mice. Altogether, these results demonstrate that the conditional FAM2-LV allows preferential expression of the membrane-anchored form of an antiviral neutralizing antibody in B-cells and permits secretion of a soluble antibody following B-cell maturation into PCs in vivo.
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Affiliation(s)
- Floriane Fusil
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France
| | - Sara Calattini
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France
| | - Fouzia Amirache
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France
| | - Jimmy Mancip
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France
| | - Caroline Costa
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France
| | - Justin B Robbins
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA; Present address: Organovo Holdings, Inc., San Diego, California, USA
| | - Florian Douam
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France; Present address: Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Dimitri Lavillette
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France; Present address: Institut Pasteur Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Mansun Law
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - Thierry Defrance
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France
| | - Els Verhoeyen
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France; Inserm, U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe "contrôle métabolique des morts cellulaires", Nice, France
| | - François-Loïc Cosset
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm, U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France; CNRS, UMR5308, Lyon, France; LabEx Ecofect, Université de Lyon, Lyon, France.
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Curinha A, Oliveira Braz S, Pereira-Castro I, Cruz A, Moreira A. Implications of polyadenylation in health and disease. Nucleus 2014; 5:508-19. [PMID: 25484187 DOI: 10.4161/nucl.36360] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Polyadenylation is the RNA processing step that completes the maturation of nearly all eukaryotic mRNAs. It is a two-step nuclear process that involves an endonucleolytic cleavage of the pre-mRNA at the 3'-end and the polymerization of a polyadenosine (polyA) tail, which is fundamental for mRNA stability, nuclear export and efficient translation during development. The core molecular machinery responsible for the definition of a polyA site includes several recognition, cleavage and polyadenylation factors that identify and act on a given polyA signal present in a pre-mRNA, usually an AAUAAA hexamer or similar sequence. This mechanism is tightly regulated by other cis-acting elements and trans-acting factors, and its misregulation can cause inefficient gene expression and may ultimately lead to disease. The majority of genes generate multiple mRNAs as a result of alternative polyadenylation in the 3'-untranslated region. The variable lengths of the 3' untranslated regions created by alternative polyadenylation are a recognizable target for differential regulation and clearly affect the fate of the transcript, ultimately modulating the expression of the gene. Over the past few years, several studies have highlighted the importance of polyadenylation and alternative polyadenylation in gene expression and their impact in a variety of physiological conditions, as well as in several illnesses. Abnormalities in the 3'-end processing mechanisms thus represent a common feature among many oncological, immunological, neurological and hematological disorders, but slight imbalances can lead to the natural establishment of a specific cellular state. This review addresses the key steps of polyadenylation and alternative polyadenylation in different cellular conditions and diseases focusing on the molecular effectors that ensure a faultless pre-mRNA 3' end formation.
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Key Words
- 3′ untranslated region
- 3′READS, 3′ Region Extraction and Deep Sequencing
- AD, Alzheimer disease
- APA, Alternative polyadenylation
- AREs, Au-rich elements
- BPV, bovine papilloma virus
- CAH, congenital adrenal hyperplasia
- CFIm25, Cleavage Factor Im 25 kDa
- COX-2, cyclooxygenase 2
- CPSF, Cleavage and Polyadenylation Specificity Factor
- CSTF2, cleavage stimulatory factor-64kDa
- DMKN, dermokine
- DSE, downstream sequence element
- ESC, embryonic stem cells
- FMR1, Fragil X mental retardation 1
- FOXP3, forkhead box P3
- FXPOI, fragile X-associated immature ovarian insufficiency
- FXS, Fragile X syndrome
- FXTAS, fragile X-associated tremor/ataxia syndrome
- HGRG-14, high-glucose-regulated gene
- IMP-1, Insulin-like growth factor 2 mRNA binding protein 1
- IPEX, immune dysfunction, polyendocrinopathy, enteropathy, X-linked
- LPS, lipopolysaccharide
- OPMD, oculopharyngeal muscular dystrophy
- PABPN1, poly(A) binding protein
- PAP, polyA polymerase
- PAS, polyA site
- PD, Parkinson disease
- PDXK, pyridoxal kinase
- PPIE, peptidylpropylisomerase E
- RBP, RNA-binding protein
- RNA Pol II, RNA polymerase II
- SLE, systemic lupus erythematosus
- SMA, Spinal Muscular Atrophy
- SMN, Survival Motor Neuron
- SNP, single nucleotide polymorphism
- StAR, steroigogenic acute regulatory
- TCF/LEF, T cell factor/lymphoid enhancer factor.
- TCF7L2, transcription factor 7-like 2
- TCR, T cell receptor
- TLI, tandem UTR length index
- TNF-α, tumor necrosis factor-α
- USE, upstream sequence element
- UTR, untranslated region
- WAS, Wiskott-Aldrich syndrome
- WASP, Wiskott-Aldrich syndrome protein
- aSyn, α-Synuclein
- aSynL, longest aSyn isoform
- alternative polyadenylation
- cell state
- disease
- gene expression
- miRNA, microRNA
- nuclear 1
- pA signal, polyA signal
- pA tail, polyA tail
- polyadenylation
- siRNAs, small interfering RNAs
- snRNPs, spliceosomal small nuclear ribonucleoproteins
- α-GalA, α-galactosidase A
- μ, IgM heavy-chain mRNA
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Affiliation(s)
- Ana Curinha
- a Gene Regulation Group; IBMC-Instituto de Biologia Molecular e Celular ; Universidade do Porto ; Porto , Portugal
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16
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Hollerer I, Grund K, Hentze MW, Kulozik AE. mRNA 3'end processing: A tale of the tail reaches the clinic. EMBO Mol Med 2014; 6:16-26. [PMID: 24408965 PMCID: PMC3936486 DOI: 10.1002/emmm.201303300] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent advances reveal mRNA 3′end processing as a highly regulated process that fine-tunes posttranscriptional gene expression. This process can affect the site and/or the efficiency of 3′end processing, controlling the quality and the quantity of substrate mRNAs. The regulation of 3′end processing plays a central role in fundamental physiology such as blood coagulation and innate immunity. In addition, errors in mRNA 3′end processing have been associated with a broad spectrum of human diseases, including cancer. We summarize and discuss the paradigmatic shift in the understanding of 3′end processing as a mechanism of posttranscriptional gene regulation that has reached clinical medicine.
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Affiliation(s)
- Ina Hollerer
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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Abstract
The polyadenosine (polyA) "tail" is an essential feature at the 3' end of nearly all eukaryotic mRNAs. This appendage has roles in many steps in the gene expression pathway and is subject to extensive regulation. Selection of alternative sites for polyA tail addition is a widely used mechanism to generate alternative mRNAs with distinct 3'UTRs that can be subject to distinct forms of posttranscriptional control. One such type of regulation includes cytoplasmic lengthening and shortening of the polyA tail, which is coupled to changes in mRNA translation and decay. Here we present a general overview of 3' end formation in the nucleus and regulation of the polyA tail in the cytoplasm, with an emphasis on the diverse roles of 3' end regulation in the control of gene expression in different biological systems.
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Affiliation(s)
- Thomas J Sweet
- Center for RNA Molecular Biology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
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18
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Zhang C, Du Pasquier L, Hsu E. Shark IgW C region diversification through RNA processing and isotype switching. THE JOURNAL OF IMMUNOLOGY 2013; 191:3410-8. [PMID: 23935192 DOI: 10.4049/jimmunol.1301257] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Sharks and skates represent the earliest vertebrates with an adaptive immune system based on lymphocyte Ag receptors generated by V(D)J recombination. Shark B cells express two classical Igs, IgM and IgW, encoded by an early, alternative gene organization consisting of numerous autonomous miniloci, where the individual gene cluster carries a few rearranging gene segments and one C region, μ or ω. We have characterized eight distinct Ig miniloci encoding the nurse shark ω H chain. Each cluster consists of VH, D, and JH segments and six to eight C domain exons. Two interspersed secretory exons, in addition to the 3'-most C exon with tailpiece, provide the gene cluster with the ability to generate at least six secreted isoforms that differ as to polypeptide length and C domain combination. All clusters appear to be functional, as judged by the capability for rearrangement and absence of defects in the deduced amino acid sequence. We previously showed that IgW VDJ can perform isotype switching to μ C regions; in this study, we found that switching also occurs between ω clusters. Thus, C region diversification for any IgW VDJ can take place at the DNA level by switching to other ω or μ C regions, as well as by RNA processing to generate different C isoforms. The wide array of pathogens recognized by Abs requires different disposal pathways, and our findings demonstrate complex and unique pathways for C effector function diversity that evolved independently in cartilaginous fishes.
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Affiliation(s)
- Cecilia Zhang
- Department of Physiology and Pharmacology, State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
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Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proc Natl Acad Sci U S A 2012; 109:16252-7. [PMID: 22991471 DOI: 10.1073/pnas.1214414109] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
B cells and plasma cells possess distinct RNA processing environments that respectively promote the expression of membrane-associated Ig by B cells versus the secretion of Ig by plasma cells. Through a combination of transcriptional profiling and screening using a lentiviral short-hairpin RNA interference library, we show that both the splicing factor hnRNPLL and the transcription elongation factor ELL2 modulate the ratio of secreted versus membrane-encoding Ighg2b transcripts in MPC11 plasmacytoma cell lines. hnRNPLL and ELL2 are both highly expressed in primary plasma cells relative to B cells, but hnRNPLL binds Ighg2b mRNA transcripts and promotes an increase in levels of the membrane-encoding Ighg2b isoform at the expense of the secreted Ighg2b isoform, whereas ELL2 counteracts this effect and drives Ig secretion by increasing the frequency of the secreted Ighg2b isoform. As in T cells, hnRNPLL also alters the splicing pattern of mRNA encoding the adhesion receptor CD44, promoting exon inclusion, and decreasing the overall level of CD44 expression. Further characterization of ELL2-dependent transcription by RNA-Seq revealed that ∼12% of transcripts expressed by plasma cells were differentially processed because of the activities of ELL2, including B-cell maturation antigen BCMA, a receptor with a defined role in plasma cell survival. Taken together, our data identify hnRNPLL and ELL2 as regulators of pre-mRNA processing in plasma cells.
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20
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Ouna BA, Nyambega B, Manful T, Helbig C, Males M, Fadda A, Clayton C. Depletion of trypanosome CTR9 leads to gene expression defects. PLoS One 2012; 7:e34256. [PMID: 22532828 PMCID: PMC3332058 DOI: 10.1371/journal.pone.0034256] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 02/24/2012] [Indexed: 01/14/2023] Open
Abstract
The Paf complex of Opisthokonts and plants contains at least five subunits: Paf1, Cdc73, Rtf1, Ctr9, and Leo1. Mutations in, or loss of Paf complex subunits have been shown to cause defects in histone modification, mRNA polyadenylation, and transcription by RNA polymerase I and RNA polymerase II. We here investigated trypanosome CTR9, which is essential for trypanosome survival. The results of tandem affinity purification suggested that trypanosome CTR9 associates with homologues of Leo1 and Cdc73; genes encoding homologues of Rtf1 and Paf1 were not found. RNAi targeting CTR9 resulted in at least ten-fold decreases in 131 essential mRNAs: they included several that are required for gene expression and its control, such as those encoding subunits of RNA polymerases, exoribonucleases that target mRNA, RNA helicases and RNA-binding proteins. Simultaneously, some genes from regions subject to chromatin silencing were derepressed, possibly as a secondary effect of the loss of two proteins that are required for silencing, ISWI and NLP1.
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Affiliation(s)
- Benard A. Ouna
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ/ZMBH Alliance, Heidelberg, Germany
| | - Benson Nyambega
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ/ZMBH Alliance, Heidelberg, Germany
| | - Theresa Manful
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ/ZMBH Alliance, Heidelberg, Germany
| | - Claudia Helbig
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ/ZMBH Alliance, Heidelberg, Germany
| | - Matilda Males
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ/ZMBH Alliance, Heidelberg, Germany
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ/ZMBH Alliance, Heidelberg, Germany
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ/ZMBH Alliance, Heidelberg, Germany
- * E-mail:
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