1
|
Tsareva A, Shelyakin PV, Shagina IA, Myshkin MY, Merzlyak EM, Kriukova VV, Apt AS, Linge IA, Chudakov DM, Britanova OV. Aberrant adaptive immune response underlies genetic susceptibility to tuberculosis. Front Immunol 2024; 15:1380971. [PMID: 38799462 PMCID: PMC11116662 DOI: 10.3389/fimmu.2024.1380971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) remains a major threat worldwide, although only a fraction of infected individuals develops tuberculosis (TB). TB susceptibility is shaped by multiple genetic factors, and we performed comparative immunological analysis of two mouse strains to uncover relevant mechanisms underlying susceptibility and resistance. C57BL/6 mice are relatively TB-resistant, whereas I/St mice are prone to develop severe TB, partly due to the MHC-II allelic variant that shapes suboptimal CD4+ T cell receptor repertoire. We investigated the repertoires of lung-infiltrating helper T cells and B cells at the progressed stage in both strains. We found that lung CD4+ T cell repertoires of infected C57BL/6 but not I/St mice contained convergent TCR clusters with functionally confirmed Mtb specificity. Transcriptomic analysis revealed a more prominent Th1 signature in C57BL/6, and expression of pro-inflammatory IL-16 in I/St lung-infiltrating helper T cells. The two strains also showed distinct Th2 signatures. Furthermore, the humoral response of I/St mice was delayed, less focused, and dominated by IgG/IgM isotypes, whereas C57BL/6 mice generated more Mtb antigen-focused IgA response. We conclude that the inability of I/St mice to produce a timely and efficient anti-Mtb adaptive immune responses arises from a suboptimal helper T cell landscape that also impacts the humoral response, leading to diffuse inflammation and severe disease.
Collapse
Affiliation(s)
- Anastasiia Tsareva
- Precision Oncology Division, Boston Gene Laboratory, Waltham, MA, United States
| | - Pavel V. Shelyakin
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
| | - Irina A. Shagina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Mikhail Yu. Myshkin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ekaterina M. Merzlyak
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Valeriia V. Kriukova
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexander S. Apt
- Laboratory for Immunogenetics, Central Tuberculosis Research Institute, Moscow, Russia
| | - Irina A. Linge
- Laboratory for Immunogenetics, Central Tuberculosis Research Institute, Moscow, Russia
| | - Dmitriy M. Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Olga V. Britanova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| |
Collapse
|
2
|
Chow L, Wheat W, Ramirez D, Impastato R, Dow S. Direct comparison of canine and human immune responses using transcriptomic and functional analyses. Sci Rep 2024; 14:2207. [PMID: 38272935 PMCID: PMC10811214 DOI: 10.1038/s41598-023-50340-9] [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: 09/28/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
The canine spontaneous cancer model is increasingly utilized to evaluate new combined cancer immunotherapy approaches. While the major leukocyte subsets and phenotypes are closely related in dogs and humans, the functionality of T cells and antigen presenting cells in the two species has not been previously compared in detail. Such information would be important in interpreting immune response data and evaluating the potential toxicities of new cancer immunotherapies in dogs. To address this question, we used in vitro assays to compare the transcriptomic, cytokine, and proliferative responses of activated canine and human T cells, and also compared responses in activated macrophages. Transcriptomic analysis following T cell activation revealed shared expression of 515 significantly upregulated genes and 360 significantly downregulated immune genes. Pathway analysis identified 33 immune pathways shared between canine and human activated T cells, along with 34 immune pathways that were unique to each species. Activated human T cells exhibited a marked Th1 bias, whereas canine T cells were transcriptionally less active overall. Despite similar proliferative responses to activation, canine T cells produced significantly less IFN-γ than human T cells. Moreover, canine macrophages were significantly more responsive to activation by IFN-γ than human macrophages, as reflected by co-stimulatory molecule expression and TNF-α production. Thus, these studies revealed overall broad similarity in responses to immune activation between dogs and humans, but also uncovered important key quantitative and qualitative differences, particularly with respect to T cell responses, that should be considered in designing and evaluating cancer immunotherapy studies in dogs.
Collapse
Affiliation(s)
- Lyndah Chow
- Flint Animal Cancer Center, Department of Clinical Sciences and Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Campus Delivery 1678, Fort Collins, CO, USA.
| | - William Wheat
- Flint Animal Cancer Center, Department of Clinical Sciences and Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Campus Delivery 1678, Fort Collins, CO, USA
| | - Dominique Ramirez
- Flint Animal Cancer Center, Department of Clinical Sciences and Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Campus Delivery 1678, Fort Collins, CO, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Renata Impastato
- Flint Animal Cancer Center, Department of Clinical Sciences and Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Campus Delivery 1678, Fort Collins, CO, USA
| | - Steven Dow
- Flint Animal Cancer Center, Department of Clinical Sciences and Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Campus Delivery 1678, Fort Collins, CO, USA.
| |
Collapse
|
3
|
Ben Abdallah H, Bregnhøj A, Iversen L, Johansen C. Transcriptomic Analysis of Hidradenitis Suppurativa: A Unique Molecular Signature with Broad Immune Activation. Int J Mol Sci 2023; 24:17014. [PMID: 38069342 PMCID: PMC10707244 DOI: 10.3390/ijms242317014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Hidradenitis suppurativa is a chronic inflammatory skin disease with limited treatment options. The poorly understood pathogenesis hinders the development of effective treatments; therefore, a pressing need exists to further elucidate the molecular mechanisms in hidradenitis suppurativa. This study investigated the underlying inflammatory pathways and cell types in hidradenitis suppurativa using transcriptomic approaches with RNA sequencing of lesional and non-lesional skin biopsies from hidradenitis suppurativa, which was jointly analyzed with previously published transcriptomic data from atopic dermatitis and psoriasis patients. The differential expression and pathway enrichment analyses demonstrated the activation of multiple inflammatory processes, including the innate and adaptive immune systems, implicated in the hidradenitis suppurativa pathogenesis. In agreement, hidradenitis suppurativa exhibited a unique and heterogeneous cell type signature involving lymphoid and myeloid cells such as B cells and macrophages. Furthermore, hidradenitis suppurativa displayed increased expression of TH1/2/17 signatures with no predominant TH signatures unlike psoriasis (TH1/17) and atopic dermatitis (TH2). In summary, our study provides molecular insights into the pathomechanisms in hidradenitis suppurativa, revealing a strong and widespread immune activation, which may benefit from treatment strategies offering a broad immunomodulation of various key inflammatory pathways. Our data not only corroborate previously reported findings but also enhance our understanding of the immune dysregulation in hidradenitis suppurativa, uncovering novel and potential therapeutic targets.
Collapse
Affiliation(s)
- Hakim Ben Abdallah
- Department of Dermatology and Venereology, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.B.); (L.I.); (C.J.)
| | | | | | | |
Collapse
|
4
|
Dooley NL, Chabikwa TG, Pava Z, Loughland JR, Hamelink J, Berry K, Andrew D, Soon MSF, SheelaNair A, Piera KA, William T, Barber BE, Grigg MJ, Engwerda CR, Lopez JA, Anstey NM, Boyle MJ. Single cell transcriptomics shows that malaria promotes unique regulatory responses across multiple immune cell subsets. Nat Commun 2023; 14:7387. [PMID: 37968278 PMCID: PMC10651914 DOI: 10.1038/s41467-023-43181-7] [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: 11/23/2022] [Accepted: 11/02/2023] [Indexed: 11/17/2023] Open
Abstract
Plasmodium falciparum malaria drives immunoregulatory responses across multiple cell subsets, which protects from immunopathogenesis, but also hampers the development of effective anti-parasitic immunity. Understanding malaria induced tolerogenic responses in specific cell subsets may inform development of strategies to boost protective immunity during drug treatment and vaccination. Here, we analyse the immune landscape with single cell RNA sequencing during P. falciparum malaria. We identify cell type specific responses in sub-clustered major immune cell types. Malaria is associated with an increase in immunosuppressive monocytes, alongside NK and γδ T cells which up-regulate tolerogenic markers. IL-10-producing Tr1 CD4 T cells and IL-10-producing regulatory B cells are also induced. Type I interferon responses are identified across all cell types, suggesting Type I interferon signalling may be linked to induction of immunoregulatory networks during malaria. These findings provide insights into cell-specific and shared immunoregulatory changes during malaria and provide a data resource for further analysis.
Collapse
Affiliation(s)
- Nicholas L Dooley
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia
| | | | - Zuleima Pava
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Julianne Hamelink
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | - Kiana Berry
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Queensland University of Technology, Brisbane, QLD, Australia
| | - Dean Andrew
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Megan S F Soon
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Arya SheelaNair
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kim A Piera
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Timothy William
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
- Subang Jaya Medical Centre, Selangor, Malaysia
| | - Bridget E Barber
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | - Matthew J Grigg
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | | | - J Alejandro Lopez
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia
| | - Nicholas M Anstey
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | - Michelle J Boyle
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia.
- University of Queensland, Brisbane, QLD, Australia.
- Queensland University of Technology, Brisbane, QLD, Australia.
- Burnet Institute, Melbourne, VIC, Australia.
| |
Collapse
|
5
|
Khantakova JN, Sennikov SV. T-helper cells flexibility: the possibility of reprogramming T cells fate. Front Immunol 2023; 14:1284178. [PMID: 38022605 PMCID: PMC10646684 DOI: 10.3389/fimmu.2023.1284178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Various disciplines cooperate to find novel approaches to cure impaired body functions by repairing, replacing, or regenerating cells, tissues, or organs. The possibility that a stable differentiated cell can reprogram itself opens the door to new therapeutic strategies against a multitude of diseases caused by the loss or dysfunction of essential, irreparable, and specific cells. One approach to cell therapy is to induce reprogramming of adult cells into other functionally active cells. Understanding the factors that cause or contribute to T cell plasticity is not only of clinical importance but also expands the knowledge of the factors that induce cells to differentiate and improves the understanding of normal developmental biology. The present review focuses on the advances in the conversion of peripheral CD4+ T cells, the conditions of their reprogramming, and the methods proposed to control such cell differentiation.
Collapse
Affiliation(s)
- Julia N. Khantakova
- Department of Molecular Immunology, Federal State Budgetary Scientific Institution “Research Institute of Fundamental and Clinical Immunology” (RIFCI), Novosibirsk, Russia
| | | |
Collapse
|
6
|
Banerjee S, Galarza-Muñoz G, Garcia-Blanco MA. Role of RNA Alternative Splicing in T Cell Function and Disease. Genes (Basel) 2023; 14:1896. [PMID: 37895245 PMCID: PMC10606310 DOI: 10.3390/genes14101896] [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: 09/12/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative RNA splicing, a ubiquitous mechanism of gene regulation in eukaryotes, expands genome coding capacity and proteomic diversity. It has essential roles in all aspects of human physiology, including immunity. This review highlights the importance of RNA alternative splicing in regulating immune T cell function. We discuss how mutations that affect the alternative splicing of T cell factors can contribute to abnormal T cell function and ultimately lead to autoimmune diseases. We also explore the potential applications of strategies that target the alternative splicing changes of T cell factors. These strategies could help design therapeutic approaches to treat autoimmune disorders and improve immunotherapy.
Collapse
Affiliation(s)
- Shefali Banerjee
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA;
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | | | - Mariano A. Garcia-Blanco
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA;
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| |
Collapse
|
7
|
Garner LC, Amini A, FitzPatrick MEB, Lett MJ, Hess GF, Filipowicz Sinnreich M, Provine NM, Klenerman P. Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity. Nat Immunol 2023; 24:1565-1578. [PMID: 37580605 PMCID: PMC10457204 DOI: 10.1038/s41590-023-01575-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/26/2023] [Indexed: 08/16/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells that recognize microbial metabolites through a semi-invariant T cell receptor (TCR). Major questions remain regarding the extent of human MAIT cell functional and clonal diversity. To address these, we analyzed the single-cell transcriptome and TCR repertoire of blood and liver MAIT cells and developed functional RNA-sequencing, a method to integrate function and TCR clonotype at single-cell resolution. MAIT cell clonal diversity was comparable to conventional memory T cells, with private TCR repertoires shared across matched tissues. Baseline functional diversity was low and largely related to tissue site. MAIT cells showed stimulus-specific transcriptional responses in vitro, with cells positioned along gradients of activation. Clonal identity influenced resting and activated transcriptional profiles but intriguingly was not associated with the capacity to produce IL-17. Overall, MAIT cells show phenotypic and functional diversity according to tissue localization, stimulation environment and clonotype.
Collapse
Affiliation(s)
- Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Ali Amini
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michael E B FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Martin J Lett
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Gabriel F Hess
- Division of Visceral Surgery, Clarunis University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Magdalena Filipowicz Sinnreich
- Department of Biomedicine, Liver Immunology, University Hospital Basel and University of Basel, Basel, Switzerland
- Gastroenterology and Hepatology, University Department of Medicine, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.
| |
Collapse
|
8
|
Wilkens AB, Fulton EC, Pont MJ, Cole GO, Leung I, Stull SM, Hart MR, Bernstein ID, Furlan SN, Riddell SR. NOTCH1 signaling during CD4+ T-cell activation alters transcription factor networks and enhances antigen responsiveness. Blood 2022; 140:2261-2275. [PMID: 35605191 PMCID: PMC9837446 DOI: 10.1182/blood.2021015144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/09/2022] [Indexed: 01/21/2023] Open
Abstract
Adoptive transfer of T cells expressing chimeric antigen receptors (CAR-T) effectively treats refractory hematologic malignancies in a subset of patients but can be limited by poor T-cell expansion and persistence in vivo. Less differentiated T-cell states correlate with the capacity of CAR-T to proliferate and mediate antitumor responses, and interventions that limit tumor-specific T-cell differentiation during ex vivo manufacturing enhance efficacy. NOTCH signaling is involved in fate decisions across diverse cell lineages and in memory CD8+ T cells was reported to upregulate the transcription factor FOXM1, attenuate differentiation, and enhance proliferation and antitumor efficacy in vivo. Here, we used a cell-free culture system to provide an agonistic NOTCH1 signal during naïve CD4+ T-cell activation and CAR-T production and studied the effects on differentiation, transcription factor expression, cytokine production, and responses to tumor. NOTCH1 agonism efficiently induced a stem cell memory phenotype in CAR-T derived from naïve but not memory CD4+ T cells and upregulated expression of AhR and c-MAF, driving heightened production of interleukin-22, interleukin-10, and granzyme B. NOTCH1-agonized CD4+ CAR-T demonstrated enhanced antigen responsiveness and proliferated to strikingly higher frequencies in mice bearing human lymphoma xenografts. NOTCH1-agonized CD4+ CAR-T also provided superior help to cotransferred CD8+ CAR-T, driving improved expansion and curative antitumor responses in vivo at low CAR-T doses. Our data expand the mechanisms by which NOTCH can shape CD4+ T-cell behavior and demonstrate that activating NOTCH1 signaling during genetic modification ex vivo is a potential strategy for enhancing the function of T cells engineered with tumor-targeting receptors.
Collapse
Affiliation(s)
- Alec B. Wilkens
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Molecular and Cellular Biology, University of Washington, Seattle, WA
| | - Elena C. Fulton
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Margot J. Pont
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Gabriel O. Cole
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Isabel Leung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sylvia M. Stull
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Matthew R. Hart
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Irwin D. Bernstein
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Scott N. Furlan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Stanley R. Riddell
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Molecular and Cellular Biology, University of Washington, Seattle, WA
| |
Collapse
|
9
|
Crum RJ, Johnson SA, Jiang P, Jui JH, Zamora R, Cortes D, Kulkarni M, Prabahar A, Bolin J, Gann E, Elster E, Schobel SA, Larie D, Cockrell C, An G, Brown B, Hauskrecht M, Vodovotz Y, Badylak SF. Transcriptomic, Proteomic, and Morphologic Characterization of Healing in Volumetric Muscle Loss. Tissue Eng Part A 2022; 28:941-957. [PMID: 36039923 DOI: 10.1089/ten.tea.2022.0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Skeletal muscle has a robust, inherent ability to regenerate in response to injury from acute to chronic. In severe trauma, however, complete regeneration is not possible, resulting in a permanent loss of skeletal muscle tissue referred to as volumetric muscle loss (VML). There are few consistently reliable therapeutic or surgical options to address VML. A major limitation in investigation of possible therapies is the absence of a well-characterized large animal model. Here, we present results of a comprehensive transcriptomic, proteomic, and morphologic characterization of wound healing following volumetric muscle loss in a novel canine model of VML which we compare to a nine-patient cohort of combat-associated VML. The canine model is translationally relevant as it provides both a regional (spatial) and temporal map of the wound healing processes that occur in human VML. Collectively, these data show the spatiotemporal transcriptomic, proteomic, and morphologic properties of canine VML healing as a framework and model system applicable to future studies investigating novel therapies for human VML.
Collapse
Affiliation(s)
- Raphael John Crum
- University of Pittsburgh, McGowan Institute for Regenerative Medicine, 450 Technology Dr., Suite 300, Pittsburgh, Pennsylvania, United States, 15219;
| | - Scott A Johnson
- University of Pittsburgh, McGowan Institute for Regenerative Medicine, 450 Technology Dr, Suite 300, Pittsburgh, Pennsylvania, United States, 15219;
| | - Peng Jiang
- Cleveland State University, Center for Gene Regulation in Health and Disease, Cleveland, Ohio, United States.,Cleveland State University, Center for Applied Data Analysis and Modeling (ADAM), Cleveland, Ohio, United States.,Cleveland State University, Department of Biological, Geological, and Environmental Sciences (BGES), Cleveland, Ohio, United States;
| | - Jayati H Jui
- University of Pittsburgh, Department of Computer Science, Pittsburgh, Pennsylvania, United States;
| | - Ruben Zamora
- University of Pittsburgh, McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Surgery, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Center for Inflammation and Regeneration Modeling, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Center for Systems Immunology, Pittsburgh, Pennsylvania, United States;
| | - Devin Cortes
- University of Pittsburgh, McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Bioengineering, Pittsburgh, Pennsylvania, United States;
| | - Mangesh Kulkarni
- University of Pittsburgh, McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Bioengineering, Pittsburgh, Pennsylvania, United States;
| | - Archana Prabahar
- Cleveland State University, Center for Gene Regulation in Health and Disease, Cleveland, Ohio, United States;
| | - Jennifer Bolin
- Morgridge Institute for Research, Madison, Wisconsin, United States;
| | - Eric Gann
- Uniformed Services University of the Health Sciences, Surgery, Bethesda, Maryland, United States.,Uniformed Services University of the Health Sciences, Surgical Critical Care Initiative, Department of Surgery, Bethesda, Maryland, United States.,Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, United States;
| | - Eric Elster
- Uniformed Services University of the Health Sciences, Surgery, Bethesda, Maryland, United States.,Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, United States.,Uniformed Services University of the Health Sciences, Surgical Critical Care Initiative, Department of Surgery, Bethesda, Maryland, United States.,Walter Reed Army Medical Center, Bethesda, Maryland, United States;
| | - Seth A Schobel
- Uniformed Services University of the Health Sciences, Surgery, Bethesda, Maryland, United States.,Henry M Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, Maryland, United States.,Uniformed Services University of the Health Sciences, Surgical Critical Care Initiative, Department of Surgery, Bethesda, Maryland, United States;
| | - Dale Larie
- University of Vermont, Department of Surgery, Burlington, Vermont, United States;
| | - Chase Cockrell
- University of Vermont, Department of Surgery, Burlington, Vermont, United States;
| | - Gary An
- University of Vermont, Department of Surgery, Burlington, Vermont, United States;
| | - Bryan Brown
- University of Pittsburgh, McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Bioengineering, Pittsburgh, Pennsylvania, United States;
| | - Milos Hauskrecht
- University of Pittsburgh, Department of Computer Science, Pittsburgh, Pennsylvania, United States;
| | - Yoram Vodovotz
- University of Pittsburgh, Surgery, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Surgery, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Center for Inflammation and Regeneration Modeling, Pittsburgh, Pennsylvania, United States.,University of Pittsburgh, Center for Systems Immunology, Pittsburgh, Pennsylvania, United States;
| | - Stephen F Badylak
- University of Pittsburgh, McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania, United States;
| |
Collapse
|
10
|
Álvarez-Sierra D, Marín-Sánchez A, Gómez-Brey A, Bello I, Caubet E, Moreno-Llorente P, Petit A, Zafón C, Iglesias C, González Ó, Pujol-Borrell R. Lymphocytic Thyroiditis Transcriptomic Profiles Support the Role of Checkpoint Pathways and B Cells in Pathogenesis. Thyroid 2022; 32:682-693. [PMID: 35403441 PMCID: PMC9360182 DOI: 10.1089/thy.2021.0694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background: Autoimmune thyroid diseases are the most common types of autoimmune diseases, but their physiopathology is still relatively unexplored. Genotype-tissue expression (GTEx) is a publicly available repository containing RNAseq data, including profiles from thyroid. Approximately 14.8% of these glands were affected by focal lymphocytic thyroiditis and 6.3% were annotated as Hashimoto. We interrogated these data to improve the characterization of infiltrating cells and to identify new molecular pathways active in autoimmune thyroiditis. Materials and Methods: Histological GTEx images of 336 thyroid samples were classified into three categories, that is, non-infiltrated thyroid, small focal infiltrated thyroid, and extensive lymphoid infiltrated thyroid. Differentially expressed genes among these categories were identified and subjected to in silico pathway enrichment analysis accordingly. CIBERSORTx deconvolution was used to characterize infiltrating cells. Results: As expected, most of the transcriptional changes were dependent on tissue infiltration. Upregulated genes in tissues include-in addition to lineage-specific B and T cell genes-a broad representation of inhibitory immune checkpoint receptors expressed by B and T lymphocytes. CIBERSORTx analysis identified 22 types of infiltrating cells showed that T cells predominate 3:1 over B cells in glands with small infiltrates, only by 1.7:1 in those with large infiltrates. Follicular helper and memory CD4 T cells were significantly more abundant in glands with large infiltrates (p < 0.0001), but the most prominent finding in these glands was an almost sixfold increase in the number of naive B cells (p < 0.0001). A predominance of M2 macrophages over M1 and M0 macrophages was observed in the three gland categories (p < 0.001). Conclusions: Analysis of transcriptomic RNA-seq profiles constitutes a rich source of information for the analysis of autoimmune tissues. High-resolution transcriptomic data analysis of thyroid glands indicates the following: (a) in all infiltrated glands, active autoimmune response coexists with suppressor counteracting mechanisms involving several inhibitory checkpoint receptor pairs, (b) glands with small infiltrates contain an unexpected relatively high proportion of B lymphocytes, and (c) in highly infiltrated glands, there is a distinct transcriptomic signature of active tertiary lymphoid organs. These results support the concept that the autoimmune response is amplified in the thyroid tissue.
Collapse
Affiliation(s)
- Daniel Álvarez-Sierra
- Translational Immunology Research Group, Vall d'Hebron Institute of Research (VHIR), Campus Vall d'Hebron, Barcelona, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Ana Marín-Sánchez
- Translational Immunology Research Group, Vall d'Hebron Institute of Research (VHIR), Campus Vall d'Hebron, Barcelona, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Aroa Gómez-Brey
- Department of Transplant Coordination, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Irene Bello
- Department of Thoracic Surgery and Lung Transplantation, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Enric Caubet
- Department of Endocrine Surgery Division, Department of General Surgery, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | | | - Anna Petit
- Department of Histopathology, Hospital Universitari de Bellvitge (HUB), Barcelona, Spain
| | - Carles Zafón
- Department of Endocrinology and Nutrition, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Carmela Iglesias
- Department of Histopathology, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Campus Vall d'Hebron, Barcelona, Spain
| | - Óscar González
- Department of Endocrine Surgery Division, Department of General Surgery, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
- Address correspondence to: Óscar Gónzalez, MD, PhD, Endocrine Surgery Division, Department of General Surgery, Hospital Universitari Vall d'Hebron (HUVH), Passeig de la Vall d'Hebron 119-129, Barcelona 08035, Spain
| | - Ricardo Pujol-Borrell
- Translational Immunology Research Group, Vall d'Hebron Institute of Research (VHIR), Campus Vall d'Hebron, Barcelona, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Campus Vall d'Hebron, Barcelona, Spain
- Address correspondence to: Ricardo Pujol-Borrell, MD, PhD, Translational Immunology Research Group, Vall d'Hebron Institute of Oncology (VHIO), Campus Vall d'Hebron, Natzaret 115-117, Barcelona 08035, Spain
| |
Collapse
|
11
|
Duddu AS, Majumdar SS, Sahoo S, Jhunjhunwala S, Jolly MK. Emergent dynamics of a three-node regulatory network explain phenotypic switching and heterogeneity: a case study of Th1/Th2/Th17 cell differentiation. Mol Biol Cell 2022; 33:ar46. [PMID: 35353012 PMCID: PMC9265159 DOI: 10.1091/mbc.e21-10-0521] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Naïve helper (CD4+) T-cells can differentiate into distinct functional subsets including Th1, Th2, and Th17 phenotypes. Each of these phenotypes has a 'master regulator' - T-bet (Th1), GATA3 (Th2) and RORγT (Th17) - that inhibits the other two master regulators. Such mutual repression among them at a transcriptional level can enable multistability, giving rise to six experimentally observed phenotypes - Th1, Th2, Th17, hybrid Th/Th2, hybrid Th2/Th17 and hybrid Th1/Th17. However, the dynamics of switching among these phenotypes, particularly in the case of epigenetic influence, remains unclear. Here, through mathematical modeling, we investigated the coupled transcription-epigenetic dynamics in a three-node mutually repressing network to elucidate how epigenetic changes mediated by any 'master regulator' can influence the transition rates among different cellular phenotypes. We show that the degree of plasticity exhibited by one phenotype depends on relative strength and duration of mutual epigenetic repression mediated among the master regulators in a three-node network. Further, our model predictions can offer putative mechanisms underlying relatively higher plasticity of Th17 phenotype as observed in vitro and in vivo. Together, our modeling framework characterizes phenotypic plasticity and heterogeneity as an outcome of emergent dynamics of a three-node regulatory network, such as the one mediated by T-bet/GATA3/RORγT.
Collapse
Affiliation(s)
- Atchuta Srinivas Duddu
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sauma Suvra Majumdar
- epartment of Biotechnology, National Institute of Technology, Durgapur 713216, India
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Siddharth Jhunjhunwala
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
12
|
Blake D, Radens CM, Ferretti MB, Gazzara MR, Lynch KW. Alternative splicing of apoptosis genes promotes human T cell survival. eLife 2022; 11:80953. [PMID: 36264057 PMCID: PMC9625086 DOI: 10.7554/elife.80953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing occurs in the vast majority of human genes, giving rise to distinct mRNA and protein isoforms. We, and others, have previously identified hundreds of genes that change their isoform expression upon T cell activation via alternative splicing; however, how these changes link activation input with functional output remains largely unknown. Here, we investigate how costimulation of T cells through the CD28 receptor impacts alternative splicing in T cells activated through the T cell receptor (TCR, CD3) and find that while CD28 signaling alone has minimal impact on splicing, it enhances the extent of change for up to 20% of TCR-induced alternative splicing events. Interestingly, a set of CD28-enhanced splicing events occur within genes encoding key components of the apoptotic signaling pathway; namely caspase-9, Bax, and Bim. Using both CRISPR-edited cells and antisense oligos to force expression of specific isoforms, we show for all three of these genes that the isoform induced by CD3/CD28 costimulation promotes resistance to apoptosis, and that changes in all three genes together function combinatorially to further promote cell viability. Finally, we show that the JNK signaling pathway, induced downstream of CD3/CD28 costimulation, is required for each of these splicing events, further highlighting their co-regulation. Together, these findings demonstrate that alternative splicing is a key mechanism by which costimulation of CD28 promotes viability of activated T cells.
Collapse
Affiliation(s)
- Davia Blake
- Immunology Graduate Group, University of PennsylvaniaPhiladelphiaUnited States,Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States
| | - Caleb M Radens
- Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States
| | - Max B Ferretti
- Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States,Department of Genetics, University of PennsylvaniaPhildelphiaUnited States
| | - Kristen W Lynch
- Immunology Graduate Group, University of PennsylvaniaPhiladelphiaUnited States,Department of Biochemistry and Biophysics, University of PennsylvaniaPhiladelphiaUnited States
| |
Collapse
|
13
|
Alhamdan F, Marsh LM, Pedersen F, Alhamwe BA, Thölken C, Pfefferle PI, Bahmer T, Greulich T, Potaczek DP, Garn H. Differential Regulation of Interferon Signaling Pathways in CD4 + T Cells of the Low Type-2 Obesity-Associated Asthma Phenotype. Int J Mol Sci 2021; 22:ijms221810144. [PMID: 34576307 PMCID: PMC8469911 DOI: 10.3390/ijms221810144] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/14/2022] Open
Abstract
In the era of personalized medicine, insights into the molecular mechanisms that differentially contribute to disease phenotypes, such as asthma phenotypes including obesity-associated asthma, are urgently needed. Peripheral blood was drawn from 10 obese, non-atopic asthmatic adults with a high body mass index (BMI; 36.67 ± 6.90); 10 non-obese, non-atopic asthmatic adults with normal BMI (23.88 ± 2.73); and 10 healthy controls with normal BMI (23.62 ± 3.74). All asthmatic patients were considered to represent a low type-2 asthma phenotype according to selective clinical parameters. RNA sequencing (RNA-Seq) was conducted on peripheral blood CD4+ T cells. Thousands of differentially expressed genes were identified in both asthma groups compared with heathy controls. The expression of interferon (IFN)-stimulated genes associated with IFN-related signaling pathways was specifically affected in obese asthmatics, while the gap junction and G protein-coupled receptor (GPCR) ligand binding pathways were enriched in both asthma groups. Furthermore, obesity gene markers were also upregulated in CD4+ T cells from obese asthmatics compared with the two other groups. Additionally, the enriched genes of the three abovementioned pathways showed a unique correlation pattern with various laboratory and clinical parameters. The specific activation of IFN-related signaling and viral infection pathways might provide a novel view of the molecular mechanisms associated with the development of the low type-2 obesity-associated asthma phenotype, which is a step ahead in the development of new stratified therapeutic approaches.
Collapse
Affiliation(s)
- Fahd Alhamdan
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, Medical Faculty, Philipps University of Marburg, D-35043 Marburg, Germany; (F.A.); (D.P.P.)
| | - Leigh M. Marsh
- Ludwig Boltzmann Institute for Lung Vascular Research, A-8010 Graz, Austria;
| | - Frauke Pedersen
- Lungen Clinic Grosshansdorf GmbH, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), D-22927 Großhansdorf, Germany; (F.P.); (T.B.)
| | - Bilal Alashkar Alhamwe
- Clinic for Hematology, Oncology and Immunology, Center for Tumor Biology and Immunology, Institute of Tumor Immunology, Medical Faculty, Philipps University of Marburg, D-35043 Marburg, Germany;
- College of Pharmacy, International University for Science and Technology (IUST), Daraa 15, Syria
| | - Clemens Thölken
- Institute of Medical Bioinformatics and Biostatistics, Medical Faculty, Philipps University of Marburg, D-35037 Marburg, Germany;
| | - Petra Ina Pfefferle
- Comprehensive Biobank Marburg (CBBMR), Member of the German Biobank Alliance (GBA) and the German Center for Lung Research (DZL), Medical Faculty, Philipps University of Marburg, D-35043 Marburg, Germany;
| | - Thomas Bahmer
- Lungen Clinic Grosshansdorf GmbH, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), D-22927 Großhansdorf, Germany; (F.P.); (T.B.)
- Department for Internal Medicine I, Campus Kiel, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Timm Greulich
- Pulmonary and Critical Care Medicine, Member of the German Center for Lung Research, University Medical Center Giessen and Marburg, Department of Medicine, D-35043 Marburg, Germany;
| | - Daniel P. Potaczek
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, Medical Faculty, Philipps University of Marburg, D-35043 Marburg, Germany; (F.A.); (D.P.P.)
| | - Holger Garn
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, Medical Faculty, Philipps University of Marburg, D-35043 Marburg, Germany; (F.A.); (D.P.P.)
- Correspondence: ; Tel.: +49-6421-2866040
| |
Collapse
|
14
|
Chromatin Modifications in 22q11.2 Deletion Syndrome. J Clin Immunol 2021; 41:1853-1864. [PMID: 34435264 DOI: 10.1007/s10875-021-01123-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/11/2021] [Indexed: 12/31/2022]
Abstract
PURPOSE Chromosome 22q11.2 deletion syndrome is a common inborn error of immunity. The early consequences of thymic hypoplasia are low T cell numbers. Later in life, atopy, autoimmunity, inflammation, and evolving hypogammaglobulinemia can occur and the causes of these features are not understood. This study utilized an unbiased discovery approach to define alterations in histone modifications. Our goal was to identify durable chromatin changes that could influence cell behavior. METHODS CD4 T cells and CD19 B cells underwent ChIP-seq analysis using antibodies to H3K4me3, H3K27ac, and H4ac. RNA effects were defined in CD4 T cells by RNA-seq. Serum cytokines were examined by Luminex. RESULTS Histone marks of transcriptional activation at CD4 T cell promoters and enhancers were globally increased. The promoter activation signature had elements related to T cell activation and inflammation, concordant with effects seen in the transcriptome. B cells, in contrast, had a minimally altered epigenetic landscape in 22q11.2. Both cell types had an "edge" effect with markedly altered chromatin adjacent to the deletion. CONCLUSIONS People with 22q11.2 deletion have altered CD4 T cell chromatin and a transcriptome concordant with the changes in the epigenome. These effects support a disease model where qualitative changes to T cells occur in addition to quantitative defects that have been well characterized. This study offers unique insight into qualitative differences in the T cells in 22q11.2 deletion, an aspect that has received limited attention.
Collapse
|
15
|
Blake D, Lynch KW. The three as: Alternative splicing, alternative polyadenylation and their impact on apoptosis in immune function. Immunol Rev 2021; 304:30-50. [PMID: 34368964 DOI: 10.1111/imr.13018] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The latest advances in next-generation sequencing studies and transcriptomic profiling over the past decade have highlighted a surprising frequency of genes regulated by RNA processing mechanisms in the immune system. In particular, two control steps in mRNA maturation, namely alternative splicing and alternative polyadenylation, are now recognized to occur in the vast majority of human genes. Both have the potential to alter the identity of the encoded protein, as well as control protein abundance or even protein localization or association with other factors. In this review, we will provide a summary of the general mechanisms by which alternative splicing (AS) and alternative polyadenylation (APA) occur, their regulation within cells of the immune system, and their impact on immunobiology. In particular, we will focus on how control of apoptosis by AS and APA is used to tune cell fate during an immune response.
Collapse
Affiliation(s)
- Davia Blake
- Immunology Graduate Group and the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen W Lynch
- Immunology Graduate Group and the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|