51
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Schaible P. Modifying enzyme replacement therapy - A perspective. J Cell Mol Med 2022; 27:165-173. [PMID: 36566487 PMCID: PMC9843529 DOI: 10.1111/jcmm.17653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/26/2022] Open
Abstract
Several diseases are caused by the lack of functional proteins, including lysosomal storage diseases or haemophilia A and B. Patients suffering from one of these diseases are treated via enzyme replacement therapies to restore the missing protein. Although this treatment strategy prevents some disease symptoms, enzyme replacement therapies are very expensive and require very frequent infusions, which can cause infusion adverse reactions and massively impair the quality of life of the patients. This review proposes a technology to sustainably produce proteins within the patient to potentially make frequent protein-infusions redundant. This technology is based on blood circulating immune cells as producers of the needed therapeutic protein. To ensure a stable protein concentration over time the cells are equipped with a system, which induces cell proliferation when low therapeutic protein levels are detected and a system inhibiting cell proliferation when high therapeutic protein levels are detected.
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52
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Tan TCJ, Kelly V, Zou X, Wright D, Ly T, Zamoyska R. Translation factor eIF5a is essential for IFNγ production and cell cycle regulation in primary CD8 + T lymphocytes. Nat Commun 2022; 13:7796. [PMID: 36528626 PMCID: PMC9759561 DOI: 10.1038/s41467-022-35252-y] [Citation(s) in RCA: 6] [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: 11/19/2021] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Control of mRNA translation adjusts protein production rapidly and facilitates local cellular responses to environmental conditions. Traditionally initiation of translation is considered to be a major translational control point, however, control of peptide elongation is also important. Here we show that the function of the elongation factor, eIF5a, is regulated dynamically in naïve CD8+ T cells upon activation by post-translational modification, whereupon it facilitates translation of specific subsets of proteins. eIF5a is essential for long-term survival of effector CD8+ T cells and sequencing of nascent polypeptides indicates that the production of proteins which regulate proliferation and key effector functions, particularly the production of IFNγ and less acutely TNF production and cytotoxicity, is dependent on the presence of functional eIF5a. Control of translation in multiple immune cell lineages is required to co-ordinate immune responses and these data illustrate that translational elongation contributes to post-transcriptional regulons important for the control of inflammation.
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Affiliation(s)
- Thomas C J Tan
- Institute of Immunology and Infection Research, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Van Kelly
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Xiaoyan Zou
- Institute of Immunology and Infection Research, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - David Wright
- Institute of Immunology and Infection Research, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Tony Ly
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
- Centre for Gene Regulation and Expression, Life Sciences Research Complex, University of Dundee, Dundee, DD1 5EH, UK
| | - Rose Zamoyska
- Institute of Immunology and Infection Research, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.
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53
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Riesenberg BP, Hunt EG, Tennant MD, Hurst KE, Andrews AM, Leddy LR, Neskey DM, Hill EG, Rivera GOR, Paulos CM, Gao P, Thaxton JE. Stress-Mediated Attenuation of Translation Undermines T-cell Activity in Cancer. Cancer Res 2022; 82:4386-4399. [PMID: 36126165 PMCID: PMC9722626 DOI: 10.1158/0008-5472.can-22-1744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/06/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023]
Abstract
Protein synthesis supports robust immune responses. Nutrient competition and global cell stressors in the tumor microenvironment (TME) may impact protein translation in T cells and antitumor immunity. Using human and mouse tumors, we demonstrated here that protein translation in T cells is repressed in solid tumors. Reduced glucose availability to T cells in the TME led to activation of the unfolded protein response (UPR) element eIF2α (eukaryotic translation initiation factor 2 alpha). Genetic mouse models revealed that translation attenuation mediated by activated p-eIF2α undermines the ability of T cells to suppress tumor growth. Reprograming T-cell metabolism was able to alleviate p-eIF2α accumulation and translational attenuation in the TME, allowing for sustained protein translation. Metabolic and pharmacological approaches showed that proteasome activity mitigates induction of p-eIF2α to support optimal antitumor T-cell function, protecting from translation attenuation and enabling prolonged cytokine synthesis in solid tumors. Together, these data identify a new therapeutic avenue to fuel the efficacy of tumor immunotherapy. SIGNIFICANCE Proteasome function is a necessary cellular component for endowing T cells with tumor killing capacity by mitigating translation attenuation resulting from the unfolded protein response induced by stress in the tumor microenvironment.
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Affiliation(s)
- Brian P. Riesenberg
- Immunotherapy Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill; Chapel Hill, NC 27514; USA
| | - Elizabeth G. Hunt
- Immunotherapy Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill; Chapel Hill, NC 27514; USA,Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27514; USA
| | - Megan D. Tennant
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC 29425; USA
| | - Katie E. Hurst
- Immunotherapy Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill; Chapel Hill, NC 27514; USA
| | - Alex M. Andrews
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425; USA
| | - Lee R. Leddy
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425; USA
| | - David M. Neskey
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425; USA
| | - Elizabeth G. Hill
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425; USA,Department of Public Health Sciences, Hollings Cancer Center Biostatistics Shared Resource; Director, Medical University of South Carolina, Charleston, SC 29425; USA
| | - Guillermo O. Rangel Rivera
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC 29425; USA,Department of Surgery and Microbiology & Immunology, Winship Cancer Institute, Emory University, Atlanta, GA, 30322; USA
| | - Chrystal M. Paulos
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC 29425; USA,Department of Surgery and Microbiology & Immunology, Winship Cancer Institute, Emory University, Atlanta, GA, 30322; USA
| | - Peng Gao
- Department of Medicine, Metabolomics Core Facility; Director, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611; USA
| | - Jessica E. Thaxton
- Immunotherapy Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill; Chapel Hill, NC 27514; USA,Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27514; USA,Correspondence: Dr. Jessica Thaxton, Department of Cell Biology & Physiology, Immunotherapy Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC 27514, 919-966-4913,
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54
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Matheson LS, Petkau G, Sáenz-Narciso B, D'Angeli V, McHugh J, Newman R, Munford H, West J, Chakraborty K, Roberts J, Łukasiak S, Díaz-Muñoz MD, Bell SE, Dimeloe S, Turner M. Multiomics analysis couples mRNA turnover and translational control of glutamine metabolism to the differentiation of the activated CD4 + T cell. Sci Rep 2022; 12:19657. [PMID: 36385275 PMCID: PMC9669047 DOI: 10.1038/s41598-022-24132-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
The ZFP36 family of RNA-binding proteins acts post-transcriptionally to repress translation and promote RNA decay. Studies of genes and pathways regulated by the ZFP36 family in CD4+ T cells have focussed largely on cytokines, but their impact on metabolic reprogramming and differentiation is unclear. Using CD4+ T cells lacking Zfp36 and Zfp36l1, we combined the quantification of mRNA transcription, stability, abundance and translation with crosslinking immunoprecipitation and metabolic profiling to determine how they regulate T cell metabolism and differentiation. Our results suggest that ZFP36 and ZFP36L1 act directly to limit the expression of genes driving anabolic processes by two distinct routes: by targeting transcription factors and by targeting transcripts encoding rate-limiting enzymes. These enzymes span numerous metabolic pathways including glycolysis, one-carbon metabolism and glutaminolysis. Direct binding and repression of transcripts encoding glutamine transporter SLC38A2 correlated with increased cellular glutamine content in ZFP36/ZFP36L1-deficient T cells. Increased conversion of glutamine to α-ketoglutarate in these cells was consistent with direct binding of ZFP36/ZFP36L1 to Gls (encoding glutaminase) and Glud1 (encoding glutamate dehydrogenase). We propose that ZFP36 and ZFP36L1 as well as glutamine and α-ketoglutarate are limiting factors for the acquisition of the cytotoxic CD4+ T cell fate. Our data implicate ZFP36 and ZFP36L1 in limiting glutamine anaplerosis and differentiation of activated CD4+ T cells, likely mediated by direct binding to transcripts of critical genes that drive these processes.
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Affiliation(s)
- Louise S Matheson
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Georg Petkau
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Beatriz Sáenz-Narciso
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Vanessa D'Angeli
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: IONTAS, The Works, Unity Campus, Cambridge, CB22 3EF, UK
| | - Jessica McHugh
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Nature Reviews Rheumatology, The Campus, 4 Crinan Street, London, N1 9XW, UK
| | - Rebecca Newman
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Immunology Research Unit, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, Herts, UK
| | - Haydn Munford
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, IBR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James West
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Krishnendu Chakraborty
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Bioanalysis, Immunogenicity and Biomarkers (BIB), IVIVT, GSK, Stevenage, SG1 2NY, UK
| | - Jennie Roberts
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Sebastian Łukasiak
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Manuel D Díaz-Muñoz
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, BP3028, 31024, Toulouse, France
| | - Sarah E Bell
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Sarah Dimeloe
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, IBR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Martin Turner
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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55
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Ndinyanka Fabrice T, Bianda C, Zhang H, Jayachandran R, Ruer-Laventie J, Mori M, Moshous D, Fucile G, Schmidt A, Pieters J. An evolutionarily conserved coronin-dependent pathway defines cell population size. Sci Signal 2022; 15:eabo5363. [DOI: 10.1126/scisignal.abo5363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Maintenance of cell population size is fundamental to the proper functioning of multicellular organisms. Here, we describe a cell-intrinsic cell density–sensing pathway that enabled T cells to reach and maintain an appropriate population size. This pathway operated “kin-to-kin” or between identical or similar T cell populations occupying a niche within a tissue or organ, such as the lymph nodes, spleen, and blood. We showed that this pathway depended on the cell density–dependent abundance of the evolutionarily conserved protein coronin 1, which coordinated prosurvival signaling with the inhibition of cell death until the cell population reached threshold densities. At or above threshold densities, coronin 1 expression peaked and remained stable, thereby resulting in the initiation of apoptosis through kin-to-kin intercellular signaling to return the cell population to the appropriate cell density. This cell population size-controlling pathway was conserved from amoeba to humans, thus providing evidence for the existence of a coronin-regulated, evolutionarily conserved mechanism by which cells are informed of and coordinate their relative population size.
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Affiliation(s)
| | | | - Haiyan Zhang
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | | | - Mayumi Mori
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Despina Moshous
- Pediatric Immunology, Hematology and Rheumatology Unit, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris and Imagine Institute, INSERM UMR1163, Université de Paris, 75015 Paris, France
| | - Geoffrey Fucile
- SIB Swiss Institute of Bioinformatics, sciCORE Computing Center, University of Basel, 4056 Basel, Switzerland
| | | | - Jean Pieters
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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56
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Nicolet BP, Wolkers MC. The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristics. PLoS One 2022; 17:e0276294. [PMID: 36260607 PMCID: PMC9581405 DOI: 10.1371/journal.pone.0276294] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022] Open
Abstract
T cells are key players in our defence against infections and malignancies. When T cells differentiate or become activated, they undergo substantial alterations in gene expression. Even though RNA expression levels are now well documented throughout different stages of T cells, it is not well understood how mRNA expression translates into the protein landscape. By combining paired RNA sequencing and mass spectrometry data of primary human CD8+ T cells, we report that mRNA expression is a poor proxy for the overall protein output, irrespective of the differentiation or activation status. Yet, gene class stratification revealed a function-specific correlation of mRNA with protein expression. This gene class-specific expression pattern associated with differences in gene characteristics such as sequence conservation and untranslated region (UTR) lengths. In addition, the presence of AU-rich elements in the 3'UTR associated with alterations in mRNA and protein abundance T cell activation dependent, gene class-specific manner. In conclusion, our study highlights the role of gene characteristics as a determinant for gene expression in T cells.
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Affiliation(s)
- Benoît P. Nicolet
- Department of Hematopoiesis, Sanquin Research, Amsterdam, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Monika C. Wolkers
- Department of Hematopoiesis, Sanquin Research, Amsterdam, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- * E-mail:
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57
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Choi JO, Ham JH, Hwang SS. RNA Metabolism in T Lymphocytes. Immune Netw 2022; 22:e39. [PMID: 36381959 PMCID: PMC9634142 DOI: 10.4110/in.2022.22.e39] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023] Open
Abstract
RNA metabolism plays a central role in regulating of T cell-mediated immunity. RNA processing, modifications, and regulations of RNA decay influence the tight and rapid regulation of gene expression during T cell phase transition. Thymic selection, quiescence maintenance, activation, differentiation, and effector functions of T cells are dependent on selective RNA modulations. Recent technical improvements have unveiled the complex crosstalk between RNAs and T cells. Moreover, resting T cells contain large amounts of untranslated mRNAs, implying that the regulation of RNA metabolism might be a key step in controlling gene expression. Considering the immunological significance of T cells for disease treatment, an understanding of RNA metabolism in T cells could provide new directions in harnessing T cells for therapeutic implications.
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Affiliation(s)
- Jin Ouk Choi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeong Hyeon Ham
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Soo Seok Hwang
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea.,Chronic Intractable Disease Systems Medicine Research Center, Institute of Genetic Science, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
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58
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59
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Salloum D, Singh K, Davidson NR, Cao L, Kuo D, Sanghvi VR, Jiang M, Lafoz MT, Viale A, Ratsch G, Wendel HG. A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1189-1199. [PMID: 36002234 PMCID: PMC9492650 DOI: 10.4049/jimmunol.2100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 05/25/2022] [Indexed: 01/04/2023]
Abstract
The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes in CD8 memory T cells following initial activation events. We find that initial translation enables subsequent events of human and mouse T cell activation and expansion. Briefly, early events in the activation of Ag-experienced CD8 T cells are insensitive to transcriptional blockade with actinomycin D, and instead depend on the translation of pre-existing mRNAs and are blocked by cycloheximide. Ribosome profiling identifies ∼92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine-rich 5' untranslated regions and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, and serine metabolism enzymes Psat1 and Shmt2 (serine hydroxymethyltransferase 2), as well as translation factors eEF1a1 (eukaryotic elongation factor α1) and eEF2 (eukaryotic elongation factor 2). The increased production of receptors of IL-2 and IFN-γ precedes the activation of gene expression and augments cellular signals and T cell activation. Taken together, we identify an early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 memory T cell expansion and activation.
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Affiliation(s)
- Darin Salloum
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Bronx, NY
| | - Natalie R Davidson
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Linlin Cao
- Swiss Institute for Experimental Cancer Research, EPFL, Lausanne, Switzerland
| | - David Kuo
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Viraj R Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami FL
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Tello Lafoz
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Agnes Viale
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunnar Ratsch
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY;
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60
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Mechanical coupling of supracellular stress amplification and tissue fluidization during exit from quiescence. Proc Natl Acad Sci U S A 2022; 119:e2201328119. [PMID: 35914175 PMCID: PMC9371707 DOI: 10.1073/pnas.2201328119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Most cells in the human body reside in a dormant state characterized by slow growth and minimal motility. During episodes such as wound healing, stem cell activation, and cancer growth, cells adapt to a more dynamic behavior characterized by proliferation and migration. However, little is known about the mechanical forces controlling the transition from static to motile following exit from dormancy. We demonstrate that keratinocyte monolayers install a mechanical system during dormancy that produces a coordinated burst of intercellular mechanical tension only minutes after dormancy exit. The activated forces are essential for large-scale displacements of otherwise motility-restricted cell sheets. Thus, cells sustain a mechanical system during dormancy that idles in anticipation of cell cycle entry and prompt activation of motion. Cellular quiescence is a state of reversible cell cycle arrest that is associated with tissue dormancy. Timely regulated entry into and exit from quiescence is important for processes such as tissue homeostasis, tissue repair, stem cell maintenance, developmental processes, and immunity. However, little is known about processes that control the mechanical adaption to cell behavior changes during the transition from quiescence to proliferation. Here, we show that quiescent human keratinocyte monolayers sustain an actinomyosin-based system that facilitates global cell sheet displacements upon serum-stimulated exit from quiescence. Mechanistically, exposure of quiescent cells to serum-borne mitogens leads to rapid amplification of preexisting contractile sites, leading to a burst in monolayer tension that subsequently drives large-scale displacements of otherwise motility-restricted monolayers. The stress level after quiescence exit correlates with the level of quiescence depth at the time of activation, and a critical stress magnitude must be reached to overcome the cell sheet displacement barrier. The study shows that static quiescent cell monolayers are mechanically poised for motility, and it identifies global stress amplification as a mechanism for overcoming motility restrictions in confined confluent cell monolayers.
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61
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Freimer JW, Shaked O, Naqvi S, Sinnott-Armstrong N, Kathiria A, Garrido CM, Chen AF, Cortez JT, Greenleaf WJ, Pritchard JK, Marson A. Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks. Nat Genet 2022; 54:1133-1144. [PMID: 35817986 PMCID: PMC10035359 DOI: 10.1038/s41588-022-01106-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 05/26/2022] [Indexed: 12/14/2022]
Abstract
Gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed, it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map connections between regulatory genes and their downstream targets. However, we lack comprehensive knowledge of the upstream regulators of most genes. Here, we developed an approach for systematic discovery of upstream regulators of critical immune factors-IL2RA, IL-2 and CTLA4-in primary human T cells. Then, we mapped the network of the target genes of these regulators and putative cis-regulatory elements using CRISPR perturbations, RNA-seq and ATAC-seq. These regulators form densely interconnected networks with extensive feedback loops. Furthermore, this network is enriched for immune-associated disease variants and genes. These results provide insight into how immune-associated disease genes are regulated in T cells and broader principles about the structure of human gene regulatory networks.
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Affiliation(s)
- Jacob W Freimer
- Department of Genetics, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Oren Shaked
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, CA, USA
| | - Sahin Naqvi
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, USA
| | | | - Arwa Kathiria
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Amy F Chen
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jessica T Cortez
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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62
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Pfenninger P, Yerly L, Abe J. Naïve Primary Mouse CD8+ T Cells Retain In Vivo Immune Responsiveness After Electroporation-Based CRISPR/Cas9 Genetic Engineering. Front Immunol 2022; 13:777113. [PMID: 35844563 PMCID: PMC9280190 DOI: 10.3389/fimmu.2022.777113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
CRISPR/Cas9 technology has revolutionized genetic engineering of primary cells. Although its use is gaining momentum in studies on CD8+ T cell biology, it remains elusive to what extent CRISPR/Cas9 affects in vivo function of CD8+ T cells. Here, we optimized nucleofection-based CRISPR/Cas9 genetic engineering of naïve and in vitro-activated primary mouse CD8+ T cells and tested their in vivo immune responses. Nucleofection of naïve CD8+ T cells preserved their in vivo antiviral immune responsiveness to an extent that is indistinguishable from non-nucleofected cells, whereas nucleofection of in vitro-activated CD8+ T cells led to slightly impaired expansion/survival at early time point after adoptive transfer and more pronounced contraction. Of note, different target proteins displayed distinct decay rates after gene editing. This is in stark contrast to a comparable period of time required to complete gene inactivation. Thus, for optimal experimental design, it is crucial to determine the kinetics of the loss of target gene product to adapt incubation period after gene editing. In sum, nucleofection-based CRISPR/Cas9 genome editing achieves efficient and rapid generation of mutant CD8+ T cells without imposing detrimental constraints on their in vivo functions.
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63
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Xie T, Chen M, Nielsen J, Xia J. Multi-omics analyses of the transition to the Crabtree effect in S. cerevisiae reveals a key role for the citric acid shuttle. FEMS Yeast Res 2022; 22:6590040. [PMID: 35595470 DOI: 10.1093/femsyr/foac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/30/2022] [Accepted: 05/18/2022] [Indexed: 11/14/2022] Open
Abstract
The Crabtree effect in the yeast, Saccharomyces cerevisiae, has been extensively studied, but only few studies have analyzed the dynamic conditions across the critical specific growth rate where the Crabtree effect sets in. Here, we carried out a multi-omics analysis of S. cerevisiae undergoing a specific growth rate transition from 0.2 h-1 to 0.35 h-1. The extracellular metabolome, the transcriptome and the proteome were analyzed in an 8-hour transition period after the specific growth rate shifted from 0.2 h-1 to 0.35 h-1. The changing trends of both the transcriptome and proteome were analyzed using principal component analysis, which showed that the transcriptome clustered together after 60 min, while the proteome reached steady-state much later. Focusing on central carbon metabolism, we analyzed both the changes in the transcriptome and proteome, and observed an interesting changing pattern in the tricarboxylic acid (TCA) pathway, which indicates an important role for citric acid shuttling across the mitochondrial membrane for α-ketoglutarate accumulation during the transition from respiratory to respiro-fermentative metabolism. This was supported by a change in the oxaloacetate and malate shuttle. Together, our findings shed new light into the onset of the Crabtree effect in S. cerevisiae.
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Affiliation(s)
- Tingting Xie
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Min Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE41296, Sweden.,BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen N, Denmark
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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64
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Gray GK, Li CMC, Rosenbluth JM, Selfors LM, Girnius N, Lin JR, Schackmann RCJ, Goh WL, Moore K, Shapiro HK, Mei S, D'Andrea K, Nathanson KL, Sorger PK, Santagata S, Regev A, Garber JE, Dillon DA, Brugge JS. A human breast atlas integrating single-cell proteomics and transcriptomics. Dev Cell 2022; 57:1400-1420.e7. [PMID: 35617956 DOI: 10.1016/j.devcel.2022.05.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/23/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022]
Abstract
The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states.
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Affiliation(s)
- G Kenneth Gray
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Carman Man-Chung Li
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Jennifer M Rosenbluth
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Nomeda Girnius
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA; The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Jia-Ren Lin
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Ron C J Schackmann
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Walter L Goh
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Kaitlin Moore
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Hana K Shapiro
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Shaolin Mei
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Kurt D'Andrea
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katherine L Nathanson
- Department of Medicine, Division of Translation Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter K Sorger
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA
| | - Sandro Santagata
- The Laboratory of Systems Pharmacology (LSP), HMS, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, MA 02115, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital (BWH), Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School (HMS), Boston, MA 02115, USA.
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65
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Reuschl AK, Mesner D, Shivkumar M, Whelan MVX, Pallett LJ, Guerra-Assunção JA, Madansein R, Dullabh KJ, Sigal A, Thornhill JP, Herrera C, Fidler S, Noursadeghi M, Maini MK, Jolly C. HIV-1 Vpr drives a tissue residency-like phenotype during selective infection of resting memory T cells. Cell Rep 2022; 39:110650. [PMID: 35417711 PMCID: PMC9350556 DOI: 10.1016/j.celrep.2022.110650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/23/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022] Open
Abstract
HIV-1 replicates in CD4+ T cells, leading to AIDS. Determining how HIV-1 shapes its niche to create a permissive environment is central to informing efforts to limit pathogenesis, disturb reservoirs, and achieve a cure. A key roadblock in understanding HIV-T cell interactions is the requirement to activate T cells in vitro to make them permissive to infection. This dramatically alters T cell biology and virus-host interactions. Here we show that HIV-1 cell-to-cell spread permits efficient, productive infection of resting memory T cells without prior activation. Strikingly, we find that HIV-1 infection primes resting T cells to gain characteristics of tissue-resident memory T cells (TRM), including upregulating key surface markers and the transcription factor Blimp-1 and inducing a transcriptional program overlapping the core TRM transcriptional signature. This reprogramming is driven by Vpr and requires Vpr packaging into virions and manipulation of STAT5. Thus, HIV-1 reprograms resting T cells, with implications for viral replication and persistence.
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Affiliation(s)
- Ann-Kathrin Reuschl
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
| | - Dejan Mesner
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Maitreyi Shivkumar
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Laura J Pallett
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | | | - Rajhmun Madansein
- Department of Cardiothoracic Surgery, University of KwaZulu-Natal, Durban 4091, South Africa; Centre for the AIDS Programme of Research in South Africa, Durban 4091, South Africa
| | - Kaylesh J Dullabh
- Department of Cardiothoracic Surgery, University of KwaZulu-Natal, Durban 4091, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4091, South Africa; Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - John P Thornhill
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3XY, UK; Department of Infectious Disease, Faculty of Medicine, Imperial College, London W2 1NY, UK
| | - Carolina Herrera
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London W2 1NY, UK
| | - Sarah Fidler
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London W2 1NY, UK; Imperial College NIHR Biomedical Research Centre, London W2 1NY, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
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66
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Abstract
T lymphocytes (T cells) are divided into two functionally different subgroups the CD4+ T helper cells (Th) and the CD8+ cytotoxic T lymphocytes (CTL). Adequate CD4 and CD8 T cell activation to proliferation, clonal expansion and effector function is crucial for efficient clearance of infection by pathogens. Failure to do so may lead to T cell exhaustion. Upon activation by antigen presenting cells, T cells undergo metabolic reprograming that support effector functions. In this review we will discuss how metabolic reprograming dictates functionality during viral infections using severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human immunodeficiency virus (HIV) as examples. Moreover, we will briefly discuss T cell metabolic programs during bacterial infections exemplified by Mycobacterium tuberculosis (MT) infection.
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Affiliation(s)
| | - Bjørn Steen Skålhegg
- Division for Molecular Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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67
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Marchingo JM, Cantrell DA. Protein synthesis, degradation, and energy metabolism in T cell immunity. Cell Mol Immunol 2022; 19:303-315. [PMID: 34983947 PMCID: PMC8891282 DOI: 10.1038/s41423-021-00792-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/24/2021] [Indexed: 01/18/2023] Open
Abstract
T cell activation, proliferation, and differentiation into effector and memory states involve massive remodeling of T cell size and molecular content and create a massive increase in demand for energy and amino acids. Protein synthesis is an energy- and resource-demanding process; as such, changes in T cell energy production are intrinsically linked to proteome remodeling. In this review, we discuss how protein synthesis and degradation change over the course of a T cell immune response and the crosstalk between these processes and T cell energy metabolism. We highlight how the use of high-resolution mass spectrometry to analyze T cell proteomes can improve our understanding of how these processes are regulated.
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Affiliation(s)
- Julia M Marchingo
- Cell Signalling and Immunology Division, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Doreen A Cantrell
- Cell Signalling and Immunology Division, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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68
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Abstract
TCF1 and its homologue LEF1 are historically known as effector transcription factors downstream of the WNT signalling pathway and are essential for early T cell development. Recent advances bring TCF1 into the spotlight for its versatile, context-dependent functions in regulating mature T cell responses. In the cytotoxic T cell lineages, TCF1 is required for the self-renewal of stem-like CD8+ T cells generated in response to viral or tumour antigens, and for preserving heightened responses to checkpoint blockade immunotherapy. In the helper T cell lineages, TCF1 is indispensable for the differentiation of T follicular helper and T follicular regulatory cells, and crucially regulates immunosuppressive functions of regulatory T cells. Mechanistic investigations have also identified TCF1 as the first transcription factor that directly modifies histone acetylation, with the capacity to bridge transcriptional and epigenetic regulation. TCF1 also has the potential to become an important clinical biomarker for assessing the prognosis of tumour immunotherapy and the success of viral control in treating HIV and hepatitis C virus infection. Here, we summarize the key findings on TCF1 across the fields of T cell immunity and reflect on the possibility of exploring TCF1 and its downstream transcriptional programmes as therapeutic targets for improving antiviral and antitumour immunity.
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69
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Purohit V, Wagner A, Yosef N, Kuchroo VK. Systems-based approaches to study immunometabolism. Cell Mol Immunol 2022; 19:409-420. [PMID: 35121805 PMCID: PMC8891302 DOI: 10.1038/s41423-021-00783-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Technical advances at the interface of biology and computation, such as single-cell RNA-sequencing (scRNA-seq), reveal new layers of complexity in cellular systems. An emerging area of investigation using the systems biology approach is the study of the metabolism of immune cells. The diverse spectra of immune cell phenotypes, sparsity of immune cell numbers in vivo, limitations in the number of metabolites identified, dynamic nature of cellular metabolism and metabolic fluxes, tissue specificity, and high dependence on the local milieu make investigations in immunometabolism challenging, especially at the single-cell level. In this review, we define the systemic nature of immunometabolism, summarize cell- and system-based approaches, and introduce mathematical modeling approaches for systems interrogation of metabolic changes in immune cells. We close the review by discussing the applications and shortcomings of metabolic modeling techniques. With systems-oriented studies of metabolism expected to become a mainstay of immunological research, an understanding of current approaches toward systems immunometabolism will help investigators make the best use of current resources and push the boundaries of the discipline.
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Affiliation(s)
- Vinee Purohit
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Allon Wagner
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA, 94720, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.
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70
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Smith PR, Pandit SC, Loerch S, Campbell ZT. The space between notes: emerging roles for translationally silent ribosomes. Trends Biochem Sci 2022; 47:477-491. [PMID: 35246374 DOI: 10.1016/j.tibs.2022.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 01/02/2023]
Abstract
In addition to their central functions in translation, ribosomes can adopt inactive structures that are fully assembled yet devoid of mRNA. We describe how the abundance of idle eukaryotic ribosomes is influenced by a broad range of biological conditions spanning viral infection, nutrient deprivation, and developmental cues. Vacant ribosomes may provide a means to exclude ribosomes from translation while also shielding them from degradation, and the variable identity of factors that occlude ribosomes may impart distinct functionality. We propose that regulated changes in the balance of idle and active ribosomes provides a means to fine-tune translation. We provide an overview of idle ribosomes, describe what is known regarding their function, and highlight questions that may clarify their biological roles.
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Affiliation(s)
- Patrick R Smith
- The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX, USA
| | - Sapna C Pandit
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Sarah Loerch
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Zachary T Campbell
- The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX, USA; The Center for Advanced Pain Studies (CAPS), University of Texas at Dallas, Richardson, TX, USA.
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71
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Della Bella E, Koch J, Baerenfaller K. Translation and emerging functions of non-coding RNAs in inflammation and immunity. Allergy 2022; 77:2025-2037. [PMID: 35094406 PMCID: PMC9302665 DOI: 10.1111/all.15234] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Regulatory non‐coding RNAs (ncRNAs) including small non‐coding RNAs (sRNAs), long non‐coding RNAs (lncRNAs), and circular RNAs (circRNAs) have gained considerable attention in the last few years. This is mainly due to their condition‐ and tissue‐specific expression and their various modes of action, which suggests them as promising biomarkers and therapeutic targets. One important mechanism of ncRNAs to regulate gene expression is through translation of short open reading frames (sORFs). These sORFs can be located in lncRNAs, in non‐translated regions of mRNAs where upstream ORFs (uORFs) represent the majority, or in circRNAs. Regulation of their translation can function as a quick way to adapt protein production to changing cellular or environmental cues, and can either depend solely on the initiation and elongation of translation, or on the roles of the produced functional peptides. Due to the experimental challenges to pinpoint translation events and to detect the produced peptides, translational regulation through regulatory RNAs is not well studied yet. In the case of circRNAs, they have only recently started to be recognized as regulatory molecules instead of mere artifacts of RNA biosynthesis. Of the many roles described for regulatory ncRNAs, we will focus here on their regulation during inflammation and in immunity.
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Affiliation(s)
| | - Jana Koch
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Swiss Institute of Bioinformatics (SIB) Davos Switzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Swiss Institute of Bioinformatics (SIB) Davos Switzerland
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72
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De Silva D, Ferguson L, Chin GH, Smith BE, Apathy RA, Roth TL, Blaeschke F, Kudla M, Marson A, Ingolia NT, Cate JHD. Robust T cell activation requires an eIF3-driven burst in T cell receptor translation. eLife 2021; 10:e74272. [PMID: 34970966 PMCID: PMC8758144 DOI: 10.7554/elife.74272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Activation of T cells requires a rapid surge in cellular protein synthesis. However, the role of translation initiation in the early induction of specific genes remains unclear. Here, we show human translation initiation factor eIF3 interacts with select immune system related mRNAs including those encoding the T cell receptor (TCR) subunits TCRA and TCRB. Binding of eIF3 to the TCRA and TCRB mRNA 3'-untranslated regions (3'-UTRs) depends on CD28 coreceptor signaling and regulates a burst in TCR translation required for robust T cell activation. Use of the TCRA or TCRB 3'-UTRs to control expression of an anti-CD19 chimeric antigen receptor (CAR) improves the ability of CAR-T cells to kill tumor cells in vitro. These results identify a new mechanism of eIF3-mediated translation control that can aid T cell engineering for immunotherapy applications.
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Affiliation(s)
- Dasmanthie De Silva
- Department of Molecular and Cell Biology, University of California-BerkeleyBerkeleyUnited States
- The J. David Gladstone InstitutesSan FranciscoUnited States
| | - Lucas Ferguson
- Department of Molecular and Cell Biology, University of California-BerkeleyBerkeleyUnited States
| | - Grant H Chin
- Department of Molecular and Cell Biology, University of California-BerkeleyBerkeleyUnited States
| | - Benjamin E Smith
- School of Optometry, University of California, BerkeleyBerkeleyUnited States
| | - Ryan A Apathy
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
| | - Theodore L Roth
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
| | | | - Marek Kudla
- Department of Molecular and Cell Biology, University of California-BerkeleyBerkeleyUnited States
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Department of Medicine, University of California, San FranciscoSan FranciscoUnited States
- Parker Institute for Cancer ImmunotherapySan FranciscoUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California-BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
| | - Jamie HD Cate
- Department of Molecular and Cell Biology, University of California-BerkeleyBerkeleyUnited States
- The J. David Gladstone InstitutesSan FranciscoUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California-BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
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73
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Yan M, Hu J, Yuan H, Xu L, Liao G, Jiang Z, Zhu J, Pang B, Ping Y, Zhang Y, Xiao Y, Li X. Dynamic regulatory networks of T cell trajectory dissect transcriptional control of T cell state transition. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1115-1129. [PMID: 34786214 PMCID: PMC8577129 DOI: 10.1016/j.omtn.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/13/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022]
Abstract
T cells exhibit heterogeneous functional states, which correlate with responsiveness to immune checkpoint blockade and prognosis of tumor patients. However, the molecular regulatory mechanisms underlying the dynamic process of T cell state transition remain largely unknown. Based on single-cell transcriptome data of T cells in non-small cell lung cancer, we combined cell states and pseudo-times to propose a pipeline to construct dynamic regulatory networks for dissecting the process of T cell dysfunction. Candidate regulators at different stages were revealed in the process of tumor-infiltrating T cell dysfunction. Through comparing dynamic networks across the T cell state transition, we revealed frequent regulatory interaction rewiring and further refined critical regulators mediating each state transition. Several known regulators were identified, including TCF7, EOMES, ID2, and TOX. Notably, one of the critical regulators, TSC22D3, was frequently identified in the state transitions from the intermediate state to the pre-dysfunction and dysfunction state, exerting diverse roles in each state transition by regulatory interaction rewiring. Moreover, higher expression of TSC22D3 was associated with the clinical outcome of tumor patients. Our study embedded transcription factors (TFs) within the temporal dynamic networks, providing a comprehensive view of dynamic regulatory mechanisms controlling the process of T cell state transition.
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Affiliation(s)
- Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Huating Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin, Heilongjiang 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin, Heilongjiang 150081, China
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74
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Rogers D, Sood A, Wang H, van Beek JJP, Rademaker TJ, Artusa P, Schneider C, Shen C, Wong DC, Bhagrath A, Lebel MÈ, Condotta SA, Richer MJ, Martins AJ, Tsang JS, Barreiro LB, François P, Langlais D, Melichar HJ, Textor J, Mandl JN. Pre-existing chromatin accessibility and gene expression differences among naive CD4 + T cells influence effector potential. Cell Rep 2021; 37:110064. [PMID: 34852223 DOI: 10.1016/j.celrep.2021.110064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/26/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
CD4+ T cells have a remarkable potential to differentiate into diverse effector lineages following activation. Here, we probe the heterogeneity present among naive CD4+ T cells before encountering their cognate antigen to ask whether their effector potential is modulated by pre-existing transcriptional and chromatin landscape differences. Single-cell RNA sequencing shows that key drivers of variability are genes involved in T cell receptor (TCR) signaling. Using CD5 expression as a readout of the strength of tonic TCR interactions with self-peptide MHC, and sorting on the ends of this self-reactivity spectrum, we find that pre-existing transcriptional differences among naive CD4+ T cells impact follicular helper T (TFH) cell versus non-TFH effector lineage choice. Moreover, our data implicate TCR signal strength during thymic development in establishing differences in naive CD4+ T cell chromatin landscapes that ultimately shape their effector potential.
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Affiliation(s)
- Dakota Rogers
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Aditi Sood
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada; Department of Microbiology, Immunology, and Infectious Disease, Université de Montréal, Montreal, QC, Canada
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Jasper J P van Beek
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | | | - Patricio Artusa
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Caitlin Schneider
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Connie Shen
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Dylan C Wong
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Aanya Bhagrath
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Marie-Ève Lebel
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
| | - Stephanie A Condotta
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Martin J Richer
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis B Barreiro
- Department of Medicine, Genetic Section, University of Chicago, Chicago, IL, USA
| | - Paul François
- Department of Physics, McGill University, Montreal, QC, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill University Genome Centre, Montreal, QC, Canada
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Judith N Mandl
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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75
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Zandhuis ND, Nicolet BP, Wolkers MC. RNA-Binding Protein Expression Alters Upon Differentiation of Human B Cells and T Cells. Front Immunol 2021; 12:717324. [PMID: 34867946 PMCID: PMC8635512 DOI: 10.3389/fimmu.2021.717324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/27/2021] [Indexed: 12/25/2022] Open
Abstract
B cells and T cells are key players in the defence against infections and malignancies. To exert their function, B cells and T cells differentiate into effector and memory cells. Tight regulation of these differentiation processes is key to prevent their malfunction, which can result in life-threatening disease. Lymphocyte differentiation relies on the appropriate timing and dosage of regulatory molecules, and post-transcriptional gene regulation (PTR) is a key player herein. PTR includes the regulation through RNA-binding proteins (RBPs), which control the fate of RNA and its translation into proteins. To date, a comprehensive overview of the RBP expression throughout lymphocyte differentiation is lacking. Using transcriptome and proteome analyses, we here catalogued the RBP expression for human B cells and T cells. We observed that even though the overall RBP expression is conserved, the relative RBP expression is distinct between B cells and T cells. Differentiation into effector and memory cells alters the RBP expression, resulting into preferential expression of different classes of RBPs. For instance, whereas naive T cells express high levels of translation-regulating RBPs, effector T cells preferentially express RBPs that modulate mRNA stability. Lastly, we found that cytotoxic CD8+ and CD4+ T cells express a common RBP repertoire. Combined, our study reveals a cell type-specific and differentiation-dependent RBP expression landscape in human lymphocytes, which will help unravel the role of RBPs in lymphocyte function.
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Affiliation(s)
- Nordin D. Zandhuis
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Benoit P. Nicolet
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Monika C. Wolkers
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
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76
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De Ponte Conti B, Miluzio A, Grassi F, Abrignani S, Biffo S, Ricciardi S. mTOR-dependent translation drives tumor infiltrating CD8 + effector and CD4 + Treg cells expansion. eLife 2021; 10:69015. [PMID: 34787568 PMCID: PMC8598161 DOI: 10.7554/elife.69015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/06/2021] [Indexed: 12/03/2022] Open
Abstract
We performed a systematic analysis of the translation rate of tumor-infiltrating lymphocytes (TILs) and the microenvironment inputs affecting it, both in humans and in mice. Measurement of puromycin incorporation, a proxy of protein synthesis, revealed an increase of translating CD4+ and CD8+ cells in tumors, compared to normal tissues. High translation levels are associated with phospho-S6 labeling downstream of mTORC1 activation, whereas low levels correlate with hypoxic areas, in agreement with data showing that T cell receptor stimulation and hypoxia act as translation stimulators and inhibitors, respectively. Additional analyses revealed the specific phenotype of translating TILs. CD8+ translating cells have enriched expression of IFN-γ and CD-39, and reduced SLAMF6, pointing to a cytotoxic phenotype. CD4+ translating cells are mostly regulatory T cells (Tregs) with enriched levels of CTLA-4 and Ki67, suggesting an expanding immunosuppressive phenotype. In conclusion, the majority of translationally active TILs is represented by cytotoxic CD8+ and suppressive CD4+ Tregs, implying that other subsets may be largely composed by inactive bystanders.
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Affiliation(s)
- Benedetta De Ponte Conti
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Annarita Miluzio
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Fabio Grassi
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Bellinzona, Switzerland.,Department of Medical Biotechnology and Translational Medicine, Universita` degli Studi di Milano, Milan, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Stefano Biffo
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Bioscience Department, Università degli Studi di Milano, Milan, Italy
| | - Sara Ricciardi
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Bioscience Department, Università degli Studi di Milano, Milan, Italy
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77
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Nicolet BP, Zandhuis ND, Lattanzio VM, Wolkers MC. Sequence determinants as key regulators in gene expression of T cells. Immunol Rev 2021; 304:10-29. [PMID: 34486113 PMCID: PMC9292449 DOI: 10.1111/imr.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
T cell homeostasis, T cell differentiation, and T cell effector function rely on the constant fine-tuning of gene expression. To alter the T cell state, substantial remodeling of the proteome is required. This remodeling depends on the intricate interplay of regulatory mechanisms, including post-transcriptional gene regulation. In this review, we discuss how the sequence of a transcript influences these post-transcriptional events. In particular, we review how sequence determinants such as sequence conservation, GC content, and chemical modifications define the levels of the mRNA and the protein in a T cell. We describe the effect of different forms of alternative splicing on mRNA expression and protein production, and their effect on subcellular localization. In addition, we discuss the role of sequences and structures as binding hubs for miRNAs and RNA-binding proteins in T cells. The review thus highlights how the intimate interplay of post-transcriptional mechanisms dictate cellular fate decisions in T cells.
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Affiliation(s)
- Benoit P. Nicolet
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Nordin D. Zandhuis
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - V. Maria Lattanzio
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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78
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Titelbaum M, Brant B, Baumel D, Burstein-Willensky A, Perez S, Barsheshet Y, Avni O. Ezh2 harnesses the intranuclear actin cytoskeleton to remodel chromatin in differentiating Th cells. iScience 2021; 24:103093. [PMID: 34622148 PMCID: PMC8479699 DOI: 10.1016/j.isci.2021.103093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/20/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022] Open
Abstract
Following their first interaction with the antigen, quiescent naive T-helper (Th; CD4+) cells enlarge, differentiate, and proliferate; these processes are accompanied by substantial epigenetic alterations. We showed previously that the epigenetic regulators the polycomb-group (PcG) proteins have a dual function as both positive and negative transcriptional regulators; however, the underlying mechanisms remain poorly understood. Here, we demonstrate that during Th cell differentiation the methyltransferase activity of the PcG protein Ezh2 regulates post-transcriptionally inducible assembly of intranuclear actin filaments. These filaments are colocalized with the actin regulators Vav1 and WASp, vertically oriented to the T cell receptor, and intermingle with the chromatin fibers. Ezh2 and Vav1 are observed together at chromatin-actin intersections. Furthermore, the inducible assembly of nuclear actin filaments is required for chromatin spreading and nuclear growth. Altogether these findings delineate a model in which the epigenetic machinery orchestrates the dynamic mechanical force of the intranuclear cytoskeleton to reorganize chromatin during differentiation. Ezh2 regulates post-transcriptionally the inducible assembly of intranuclear F-actin F-actin is oriented toward the TCR and intermingled with the chromatin fibers F-actin is required for chromatin spreading and nuclear growth The epigenetic machinery harnesses intranuclear cytoskeleton to reorganize chromatin
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Affiliation(s)
- Moran Titelbaum
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Boris Brant
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Daniel Baumel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | - Shira Perez
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | - Orly Avni
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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79
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Dynamic changes in tRNA modifications and abundance during T cell activation. Proc Natl Acad Sci U S A 2021; 118:2106556118. [PMID: 34642250 DOI: 10.1073/pnas.2106556118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA (transfer RNA) supply and mRNA (messenger RNA) demand during cancerous proliferation. Yet dynamic changes may also occur during physiologically normal proliferation, and these are less well characterized. We examined the tRNA and mRNA pools of T cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observed a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool relaxed back to the basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T cell activation. These modifications occur in the anticodon loops of two tRNAs that decode "slippery codons," which are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with an HIV gag-pol frameshifting site reporter. These results may explain HIV's specific tropism toward proliferating T cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a layer of translation regulation during T cell proliferation and expose a potential tradeoff between cellular growth and translation fidelity.
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80
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Brenes AJ, Vandereyken M, James OJ, Watt H, Hukelmann J, Spinelli L, Dikovskaya D, Lamond AI, Swamy M. Tissue environment, not ontogeny, defines murine intestinal intraepithelial T lymphocytes. eLife 2021; 10:e70055. [PMID: 34473623 PMCID: PMC8463072 DOI: 10.7554/elife.70055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Tissue-resident intestinal intraepithelial T lymphocytes (T-IEL) patrol the gut and have important roles in regulating intestinal homeostasis. T-IEL include both induced T-IEL, derived from systemic antigen-experienced lymphocytes, and natural T-IEL, which are developmentally targeted to the intestine. While the processes driving T-IEL development have been elucidated, the precise roles of the different subsets and the processes driving activation and regulation of these cells remain unclear. To gain functional insights into these enigmatic cells, we used high-resolution, quantitative mass spectrometry to compare the proteomes of induced T-IEL and natural T-IEL subsets, with naive CD8+ T cells from lymph nodes. This data exposes the dominant effect of the gut environment over ontogeny on T-IEL phenotypes. Analyses of protein copy numbers of >7000 proteins in T-IEL reveal skewing of the cell surface repertoire towards epithelial interactions and checkpoint receptors; strong suppression of the metabolic machinery indicating a high energy barrier to functional activation; upregulated cholesterol and lipid metabolic pathways, leading to high cholesterol levels in T-IEL; suppression of T cell antigen receptor signalling and expression of the transcription factor TOX, reminiscent of chronically activated T cells. These novel findings illustrate how T-IEL integrate multiple tissue-specific signals to maintain their homeostasis and potentially function.
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Affiliation(s)
- Alejandro J Brenes
- Centre for Gene Regulation and Expression, University of DundeeDundeeUnited Kingdom
- Division of Cell Signalling and Immunology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Maud Vandereyken
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Olivia J James
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Harriet Watt
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Jens Hukelmann
- Centre for Gene Regulation and Expression, University of DundeeDundeeUnited Kingdom
| | - Laura Spinelli
- Division of Cell Signalling and Immunology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Dina Dikovskaya
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, University of DundeeDundeeUnited Kingdom
| | - Mahima Swamy
- Division of Cell Signalling and Immunology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
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81
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Hoefig KP, Reim A, Gallus C, Wong EH, Behrens G, Conrad C, Xu M, Kifinger L, Ito-Kureha T, Defourny KAY, Geerlof A, Mautner J, Hauck SM, Baumjohann D, Feederle R, Mann M, Wierer M, Glasmacher E, Heissmeyer V. Defining the RBPome of primary T helper cells to elucidate higher-order Roquin-mediated mRNA regulation. Nat Commun 2021; 12:5208. [PMID: 34471108 PMCID: PMC8410761 DOI: 10.1038/s41467-021-25345-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 07/28/2021] [Indexed: 01/01/2023] Open
Abstract
Post-transcriptional gene regulation in T cells is dynamic and complex as targeted transcripts respond to various factors. This is evident for the Icos mRNA encoding an essential costimulatory receptor that is regulated by several RNA-binding proteins (RBP), including Roquin-1 and Roquin-2. Here, we identify a core RBPome of 798 mouse and 801 human T cell proteins by utilizing global RNA interactome capture (RNA-IC) and orthogonal organic phase separation (OOPS). The RBPome includes Stat1, Stat4 and Vav1 proteins suggesting unexpected functions for these transcription factors and signal transducers. Based on proximity to Roquin-1, we select ~50 RBPs for testing coregulation of Roquin-1/2 targets by induced expression in wild-type or Roquin-1/2-deficient T cells. Besides Roquin-independent contributions from Rbms1 and Cpeb4 we also show Roquin-1/2-dependent and target-specific coregulation of Icos by Celf1 and Igf2bp3. Connecting the cellular RBPome in a post-transcriptional context, we find contributions from multiple RBPs to the prototypic regulation of mRNA targets by individual trans-acting factors. An extensive RNA binding protein atlas (RBPome) for primary T cells would be a useful resource. Here the authors use two different methods to characterise the mouse and human T cell RBPome and show regulation of Roquin-1/2 dependent and independent pathways.
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Affiliation(s)
- Kai P Hoefig
- Research Unit Molecular Immune Regulation, Helmholtz Center Munich, Munich, Germany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Christian Gallus
- Institute of Diabetes and Obesity, Helmholtz Center Munich, Munich, Germany
| | - Elaine H Wong
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Gesine Behrens
- Research Unit Molecular Immune Regulation, Helmholtz Center Munich, Munich, Germany
| | - Christine Conrad
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Meng Xu
- Research Unit Molecular Immune Regulation, Helmholtz Center Munich, Munich, Germany
| | - Lisa Kifinger
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Taku Ito-Kureha
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Kyra A Y Defourny
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.,Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Josef Mautner
- Research Unit Gene Vectors, Helmholtz Center Munich & Children's Hospital, TU Munich, Munich, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, Munich, Germany
| | - Dirk Baumjohann
- Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.,Medical Clinic III for Oncology, Immuno-Oncology and Rheumatology University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility and Research Group, Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany. .,Proteomics Research Infrastructure, University of Copenhagen, Copenhagen, Denmark.
| | - Elke Glasmacher
- Institute of Diabetes and Obesity, Helmholtz Center Munich, Munich, Germany. .,Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
| | - Vigo Heissmeyer
- Research Unit Molecular Immune Regulation, Helmholtz Center Munich, Munich, Germany. .,Institute for Immunology, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.
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82
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Jurgens AP, Popović B, Wolkers MC. T cells at work: How post-transcriptional mechanisms control T cell homeostasis and activation. Eur J Immunol 2021; 51:2178-2187. [PMID: 34180545 PMCID: PMC8457102 DOI: 10.1002/eji.202049055] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/07/2021] [Indexed: 12/19/2022]
Abstract
T cells are central players of the adaptive immune system by protecting us from recurring infections and by killing malignant cells. Protective T cell responses rely on the concerted production of effector molecules such as cytolytic mediators, granzymes, and perforins, as well as pro-inflammatory cytokines and chemokines. Once activated, T cells drastically change their gene expression and rapidly respond to insults by producing ample amounts of effector molecules. In the absence of antigen, T cells remain in a quiescent state and survey our body for possible pathogenic insults. Resting T cells are, however, not inert, but continuously regulate their protein production to survive and to be prepared for possible re-infections. Here, we review our current knowledge on the regulation of gene expression in activated and quiescent T cells. We specifically focus on post-transcriptional mechanisms that define the protein output and that allow dormant cells to undergo active signaling and selective translation, keeping them poised for activation. Finally, we discuss which signals drive T cell survival and their preparedness to respond to insults and which mechanisms are involved in these processes.
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Affiliation(s)
- Anouk P. Jurgens
- Department of HematopoiesisSanquin ResearchLandsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamOncode InstituteUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Branka Popović
- Department of HematopoiesisSanquin ResearchLandsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamOncode InstituteUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin ResearchLandsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamOncode InstituteUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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83
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Omilusik KD, Nadjsombati MS, Yoshida TM, Shaw LA, Goulding J, Goldrath AW. Ubiquitin Specific Protease 1 Expression and Function in T Cell Immunity. THE JOURNAL OF IMMUNOLOGY 2021; 207:1377-1387. [PMID: 34380645 PMCID: PMC8387442 DOI: 10.4049/jimmunol.2100303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/30/2021] [Indexed: 12/24/2022]
Abstract
T cells are essential mediators of immune responses against infectious diseases and provide long-lived protection from reinfection. The differentiation of naive to effector T cells and the subsequent differentiation and persistence of memory T cell populations in response to infection is a highly regulated process. E protein transcription factors and their inhibitors, Id proteins, are important regulators of both CD4+ and CD8+ T cell responses; however, their regulation at the protein level has not been explored. Recently, the deubiquitinase USP1 was shown to stabilize Id2 and modulate cellular differentiation in osteosarcomas. In this study, we investigated a role for Usp1 in posttranslational control of Id2 and Id3 in murine T cells. We show that Usp1 was upregulated in T cells following activation in vitro or following infection in vivo, and the extent of Usp1 expression correlated with the degree of T cell expansion. Usp1 directly interacted with Id2 and Id3 following T cell activation. However, Usp1 deficiency did not impact Id protein abundance in effector T cells or alter effector T cell expansion or differentiation following a primary infection. Usp1 deficiency resulted in a gradual loss of memory CD8+ T cells over time and reduced Id2 protein levels and proliferation of effector CD8+ T cell following reinfection. Together, these results identify Usp1 as a player in modulating recall responses at the protein level and highlight differences in regulation of T cell responses between primary and subsequent infection encounters. Finally, our observations reveal differential regulation of Id2/3 proteins between immune versus nonimmune cell types.
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Affiliation(s)
- Kyla D Omilusik
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA
| | - Marija S Nadjsombati
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA
| | - Tomomi M Yoshida
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA
| | - Laura A Shaw
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA
| | - John Goulding
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA
| | - Ananda W Goldrath
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA
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84
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Galloway A, Kaskar A, Ditsova D, Atrih A, Yoshikawa H, Gomez-Moreira C, Suska O, Warminski M, Grzela R, Lamond AI, Darzynkiewicz E, Jemielity J, Cowling V. Upregulation of RNA cap methyltransferase RNMT drives ribosome biogenesis during T cell activation. Nucleic Acids Res 2021; 49:6722-6738. [PMID: 34125914 PMCID: PMC8266598 DOI: 10.1093/nar/gkab465] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/17/2021] [Indexed: 01/07/2023] Open
Abstract
The m7G cap is ubiquitous on RNAPII-transcribed RNA and has fundamental roles in eukaryotic gene expression, however its in vivo role in mammals has remained unknown. Here, we identified the m7G cap methyltransferase, RNMT, as a key mediator of T cell activation, which specifically regulates ribosome production. During T cell activation, induction of mRNA expression and ribosome biogenesis drives metabolic reprogramming, rapid proliferation and differentiation generating effector populations. We report that RNMT is induced by T cell receptor (TCR) stimulation and co-ordinates the mRNA, snoRNA and rRNA production required for ribosome biogenesis. Using transcriptomic and proteomic analyses, we demonstrate that RNMT selectively regulates the expression of terminal polypyrimidine tract (TOP) mRNAs, targets of the m7G-cap binding protein LARP1. The expression of LARP1 targets and snoRNAs involved in ribosome biogenesis is selectively compromised in Rnmt cKO CD4 T cells resulting in decreased ribosome synthesis, reduced translation rates and proliferation failure. By enhancing ribosome abundance, upregulation of RNMT co-ordinates mRNA capping and processing with increased translational capacity during T cell activation.
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Affiliation(s)
- Alison Galloway
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Aneesa Kaskar
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dimitrinka Ditsova
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Abdelmadjid Atrih
- FingerPrints Proteomics Facility, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Harunori Yoshikawa
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Carolina Gomez-Moreira
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Olga Suska
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Marcin Warminski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Edward Darzynkiewicz
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, and Division of Physics, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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85
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Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation. Sci Rep 2021; 11:14101. [PMID: 34238961 PMCID: PMC8266878 DOI: 10.1038/s41598-021-93509-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 06/22/2021] [Indexed: 12/23/2022] Open
Abstract
T-cell activation induces context-specific gene expression programs that promote energy generation and biosynthesis, progression through the cell cycle and ultimately cell differentiation. The aim of this study was to apply the omni ATAC-seq method to characterize the landscape of chromatin changes induced by T-cell activation in mature naïve CD4+ T-cells. Using a well-established ex vivo protocol of canonical T-cell receptor signaling, we generated genome-wide chromatin maps of naïve T-cells from pediatric donors in quiescent or recently activated states. We identified thousands of individual chromatin accessibility peaks that are associated with T-cell activation, the majority of which were annotated intronic and intergenic enhancer regions. A core set of 3268 gene promoters underwent chromatin remodeling and concomitant changes in gene expression in response to activation, and were enriched in multiple pathways controlling cell cycle regulation, metabolism, inflammatory response genes and cell survival. Leukemia inhibitory factor (LIF) was among those factors that gained the highest accessibility and expression, in addition to IL2-STAT5 dependent chromatin remodeling in the T-cell activation response. Using publicly available data we found the chromatin response was far more dynamic at 24-h compared with 72-h post-activation. In total 546 associations were reproduced at both time-points with similar strength of evidence and directionality of effect. At the pathways level, the IL2-STAT5, KRAS signalling and UV response pathways were replicable at both time-points, although differentially modulated from 24 to 72 h post-activation.
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86
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Martin-Cofreces NB, Valpuesta JM, Sánchez-Madrid F. T cell asymmetry and metabolic crosstalk can fine-tune immunological synapses. Trends Immunol 2021; 42:649-653. [PMID: 34226146 DOI: 10.1016/j.it.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
T cell asymmetry upon specific cell-cell interactions during mammalian immunological synapse (IS) contacts requires mammalian target of rapamycin complex (mTORC) activation and chaperones, such as the eukaryotic chaperonin containing TCP1 (CCT) for protein synthesis and folding. This mechanism can control cytoskeleton dynamics, and regulate mitochondrial fate, respiration, and metabolic rates, ultimately underlying cell reprogramming events that are relevant for CD4+ T cell functional outcomes.
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Affiliation(s)
- Noa Beatriz Martin-Cofreces
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006, Spain; Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029, Spain; Centro de Investigación Básica en Red Cardiovascular, CIBERCV, Madrid, 28029, Spain.
| | - Jose Maria Valpuesta
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain.
| | - Francisco Sánchez-Madrid
- Immunology Service, Hospital Universitario de la Princesa, UAM, IIS-IP. Madrid, 28006, Spain; Area of Vascular Pathophysiology, Laboratory of Intercellular Communication, Fundación Centro Nacional de Investigaciones Cardiovasculares-Carlos III, Madrid, 28029, Spain; Centro de Investigación Básica en Red Cardiovascular, CIBERCV, Madrid, 28029, Spain.
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87
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Su Z, Dutta A. De-stressing the T cells in need. Science 2021; 372:683-684. [PMID: 33986167 DOI: 10.1126/science.abi7265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Zhangli Su
- Department of Genetics, University of Alabama, Birmingham, AL 35233, USA
| | - Anindya Dutta
- Department of Genetics, University of Alabama, Birmingham, AL 35233, USA.
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88
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Freen-van Heeren JJ. Post-transcriptional control of T-cell cytokine production: Implications for cancer therapy. Immunology 2021; 164:57-72. [PMID: 33884612 DOI: 10.1111/imm.13339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/05/2023] Open
Abstract
As part of the adaptive immune system, T cells are vital for the eradication of infected and malignantly transformed cells. To perform their protective function, T cells produce effector molecules that are either directly cytotoxic, such as granzymes, perforin, interferon-γ and tumour necrosis factor α, or attract and stimulate (immune) cells, such as interleukin-2. As these molecules can also induce immunopathology, tight control of their production is required. Indeed, inflammatory cytokine production is regulated on multiple levels. Firstly, locus accessibility and transcription factor availability and activity determine the amount of mRNA produced. Secondly, post-transcriptional mechanisms, influencing mRNA splicing/codon usage, stability, decay, localization and translation rate subsequently determine the amount of protein that is produced. In the immune suppressive environments of tumours, T cells gradually lose the capacity to produce effector molecules, resulting in tumour immune escape. Recently, the role of post-transcriptional regulation in fine-tuning T-cell effector function has become more appreciated. Furthermore, several groups have shown that exhausted or dysfunctional T cells from cancer patients or murine models possess mRNA for inflammatory mediators, but fail to produce effector molecules, hinting that post-transcriptional events also play a role in hampering tumour-infiltrating lymphocyte effector function. Here, the post-transcriptional regulatory events governing T-cell cytokine production are reviewed, with a specific focus on the importance of post-transcriptional regulation in anti-tumour responses. Furthermore, potential approaches to circumvent tumour-mediated dampening of T-cell effector function through the (dis)engagement of post-transcriptional events are explored, such as CRISPR/Cas9-mediated genome editing or chimeric antigen receptors.
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89
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ElTanbouly MA, Noelle RJ. Rethinking peripheral T cell tolerance: checkpoints across a T cell's journey. Nat Rev Immunol 2021; 21:257-267. [PMID: 33077935 DOI: 10.1038/s41577-020-00454-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 01/10/2023]
Abstract
Following their exit from the thymus, T cells are endowed with potent effector functions but must spare host tissue from harm. The fate of these cells is dictated by a series of checkpoints that regulate the quality and magnitude of T cell-mediated immunity, known as tolerance checkpoints. In this Perspective, we discuss the mediators and networks that control the six main peripheral tolerance checkpoints throughout the life of a T cell: quiescence, ignorance, anergy, exhaustion, senescence and death. At the naive T cell stage, two intrinsic checkpoints that actively maintain tolerance are quiescence and ignorance. In the presence of co-stimulation-deficient T cell activation, anergy is a dominant hallmark that mandates T cell unresponsiveness. When T cells are successfully stimulated and reach the effector stage, exhaustion and senescence can limit excessive inflammation and prevent immunopathology. At every stage of the T cell's journey, cell death exists as a checkpoint to limit clonal expansion and to terminate unrestrained responses. Here, we compare and contrast the T cell tolerance checkpoints and discuss their specific roles, with the aim of providing an integrated view of T cell peripheral tolerance and fate regulation.
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Affiliation(s)
- Mohamed A ElTanbouly
- Department of Microbiology and Immunology, Geisel School of Medicine, Norris Cotton Cancer Center, Dartmouth College, Hanover, NH, USA
| | - Randolph J Noelle
- Department of Microbiology and Immunology, Geisel School of Medicine, Norris Cotton Cancer Center, Dartmouth College, Hanover, NH, USA.
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90
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Tang R, Liu X, Liang C, Hua J, Xu J, Wang W, Meng Q, Liu J, Zhang B, Yu X, Shi S. Deciphering the Prognostic Implications of the Components and Signatures in the Immune Microenvironment of Pancreatic Ductal Adenocarcinoma. Front Immunol 2021; 12:648917. [PMID: 33777046 PMCID: PMC7987951 DOI: 10.3389/fimmu.2021.648917] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/12/2021] [Indexed: 12/21/2022] Open
Abstract
Background: The treatment modalities for pancreatic ductal adenocarcinoma (PDAC) are limited and unsatisfactory. Although many novel drugs targeting the tumor microenvironment, such as immune checkpoint inhibitors, have shown promising efficacy for some tumors, few of them significantly prolong the survival of patients with PDAC due to insufficient knowledge on the tumor microenvironment. Methods: A single-cell RNA sequencing (scRNA-seq) dataset and seven PDAC cohorts with complete clinical and bulk sequencing data were collected for bioinformatics analysis. The relative proportions of each cell type were estimated using the gene set variation analysis (GSVA) algorithm based on the signatures identified by scRNA-seq or previous literature. Results: A meta-analysis of 883 PDAC patients showed that neutrophils are associated with worse overall survival (OS) for PDAC, while CD8+ T cells, CD4+ T cells, and B cells are related to prolonged OS for PDAC, with marginal statistical significance. Seventeen cell categories were identified by clustering analysis based on single-cell sequencing. Among them, CD8+ T cells and NKT cells were universally exhausted by expressing exhaustion-associated molecular markers. Interestingly, signatures of CD8+ T cells and NKT cells predicted prolonged OS for PDAC only in the presence of “targets” for pyroptosis and ferroptosis induction. Moreover, a specific state of T cells with overexpression of ribosome-related proteins was associated with a good prognosis. In addition, the hematopoietic stem cell (HSC)-like signature predicted prolonged OS in PDAC. Weighted gene co-expression network analysis identified 5 hub genes whose downregulation may mediate the observed survival benefits of the HSC-like signature. Moreover, trajectory analysis revealed that myeloid cells evolutionarily consisted of 7 states, and antigen-presenting molecules and complement-associated genes were lost along the pseudotime flow. Consensus clustering based on the differentially expressed genes between two states harboring the longest pseudotime span identified two PDAC groups with prognostic differences, and more infiltrated immune cells and activated immune signatures may account for the survival benefits. Conclusion: This study systematically investigated the prognostic implications of the components of the PDAC tumor microenvironment by integrating single-cell sequencing and bulk sequencing, and future studies are expected to develop novel targeted agents for PDAC treatment.
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Affiliation(s)
- Rong Tang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xiaomeng Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Chen Liang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jie Hua
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Qingcai Meng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jiang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
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91
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Roy DG, Kaymak I, Williams KS, Ma EH, Jones RG. Immunometabolism in the Tumor Microenvironment. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2021. [DOI: 10.1146/annurev-cancerbio-030518-055817] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Advances in immunotherapy have underscored the importance of antitumor immune responses in controlling cancer. However, the tumor microenvironment (TME) imposes several obstacles to the proper function of immune cells, including a metabolically challenging and immunosuppressive microenvironment. The increased metabolic activity of tumor cells can lead to the depletion of key nutrients required by immune cells and the accumulation of byproducts that hamper antitumor immunity. Furthermore, the presence of suppressive immune cells, such as regulatory T cells and myeloid-derived suppressor cells, and the expression of immune inhibitory receptors can negatively impact immune cell metabolism and function. This review summarizes the metabolic reprogramming that is characteristic of various immune cell subsets, discusses how the metabolism and function of immune cells are shaped by the TME, and highlights how therapeutic interventions aimed at improving the metabolic fitness of immune cells and alleviating the metabolic constraints in the TME can boost antitumor immunity.
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Affiliation(s)
- Dominic G. Roy
- Goodman Cancer Research Centre, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Irem Kaymak
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Kelsey S. Williams
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Eric H. Ma
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Russell G. Jones
- Metabolic and Nutritional Programming, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
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92
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Leoni C, Bianchi N, Vincenzetti L, Monticelli S. An optimized workflow for CRISPR-Cas9 deletion of surface and intracellular factors in primary human T lymphocytes. PLoS One 2021; 16:e0247232. [PMID: 33600503 PMCID: PMC7891767 DOI: 10.1371/journal.pone.0247232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
The appropriate regulation of T lymphocyte functions is key to achieve protective immune responses, while at the same time limiting the risks of tissue damage and chronic inflammation. Deciphering the mechanisms underpinning T cell responses in humans may therefore be beneficial for a range of infectious and chronic diseases. Recently, the development of methods based on CRISPR-Cas9 gene-editing has greatly expanded the available tool-box for the mechanistic studies of primary human T cell responses. While the deletion of a surface protein has become a relatively straightforward task, as long as an antibody for detection is available, the identification and selection of cells lacking an intracellular protein, a non-coding RNA or a protein for which no antibody is available, remain more problematic. Here, we discuss the options currently available to scientists interested in performing gene-editing in primary human T lymphocytes and we describe the optimization of a workflow for the screening and analysis of lymphocytes following gene-editing with CRISPR-Cas9 based on T cell cloning and T7 endonuclease I cleavage assay.
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MESH Headings
- CRISPR-Cas Systems/genetics
- Cell Cycle Proteins/deficiency
- Cell Cycle Proteins/genetics
- Cells, Cultured
- Endoribonucleases/deficiency
- Endoribonucleases/genetics
- Gene Editing/methods
- Humans
- Membrane Proteins/deficiency
- Membrane Proteins/genetics
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/deficiency
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- T-Box Domain Proteins/deficiency
- T-Box Domain Proteins/genetics
- T-Lymphocytes/cytology
- T-Lymphocytes/metabolism
- Transcription Factors/deficiency
- Transcription Factors/genetics
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Affiliation(s)
- Cristina Leoni
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Niccolò Bianchi
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Lucia Vincenzetti
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
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93
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Xia L, Oyang L, Lin J, Tan S, Han Y, Wu N, Yi P, Tang L, Pan Q, Rao S, Liang J, Tang Y, Su M, Luo X, Yang Y, Shi Y, Wang H, Zhou Y, Liao Q. The cancer metabolic reprogramming and immune response. Mol Cancer 2021; 20:28. [PMID: 33546704 PMCID: PMC7863491 DOI: 10.1186/s12943-021-01316-8] [Citation(s) in RCA: 398] [Impact Index Per Article: 132.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
The overlapping metabolic reprogramming of cancer and immune cells is a putative determinant of the antitumor immune response in cancer. Increased evidence suggests that cancer metabolism not only plays a crucial role in cancer signaling for sustaining tumorigenesis and survival, but also has wider implications in the regulation of antitumor immune response through both the release of metabolites and affecting the expression of immune molecules, such as lactate, PGE2, arginine, etc. Actually, this energetic interplay between tumor and immune cells leads to metabolic competition in the tumor ecosystem, limiting nutrient availability and leading to microenvironmental acidosis, which hinders immune cell function. More interestingly, metabolic reprogramming is also indispensable in the process of maintaining self and body homeostasis by various types of immune cells. At present, more and more studies pointed out that immune cell would undergo metabolic reprogramming during the process of proliferation, differentiation, and execution of effector functions, which is essential to the immune response. Herein, we discuss how metabolic reprogramming of cancer cells and immune cells regulate antitumor immune response and the possible approaches to targeting metabolic pathways in the context of anticancer immunotherapy. We also describe hypothetical combination treatments between immunotherapy and metabolic intervening that could be used to better unleash the potential of anticancer therapies.
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Affiliation(s)
- Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Jinguan Lin
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Yaqian Han
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Pin Yi
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China.,University of South China, 421001, Hengyang, Hunan, China
| | - Lu Tang
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China.,University of South China, 421001, Hengyang, Hunan, China
| | - Qing Pan
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China.,University of South China, 421001, Hengyang, Hunan, China
| | - Shan Rao
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Jiaxin Liang
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Yiqing Yang
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Yingrui Shi
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Hui Wang
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, 410013, Changsha, Hunan, China.
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94
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Curdy N, Lanvin O, Cadot S, Laurent C, Fournié JJ, Franchini DM. Stress Granules in the Post-transcriptional Regulation of Immune Cells. Front Cell Dev Biol 2021; 8:611185. [PMID: 33520991 PMCID: PMC7841200 DOI: 10.3389/fcell.2020.611185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022] Open
Abstract
Immune cell activation triggers transcriptional and translational programs eliciting cellular processes, such as differentiation or proliferation, essential for an efficient immune response. These dynamic processes require an intricate orchestration of regulatory mechanisms to control the precise spatiotemporal expression of proteins. Post-transcriptional regulation ensures the control of messenger RNA metabolism and appropriate translation. Among these post-transcriptional regulatory mechanisms, stress granules participate in the control of protein synthesis. Stress granules are ribonucleoprotein complexes that form upon stress, typically under control of the integrated stress response. Such structures assemble upon stimulation of immune cells where they control selective translational programs ensuring the establishment of accurate effector functions. In this review, we summarize the current knowledge about post-transcriptional regulation in immune cells and highlight the role of stress sensors and stress granules in such regulation.
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Affiliation(s)
- Nicolas Curdy
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Olivia Lanvin
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Sarah Cadot
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Camille Laurent
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France.,Département de Pathologie, Centre Hospitalier Universitaire (CHU) de Toulouse, Toulouse, France
| | - Jean-Jacques Fournié
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Don-Marc Franchini
- Cancer Research Center of Toulouse (CRCT), INSERM UMR 1037, CNRS ERL 5294, Toulouse, France.,Université Toulouse III Paul Sabatier, Toulouse, France.,Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
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95
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The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function. Int J Mol Sci 2020; 22:ijms22010275. [PMID: 33383959 PMCID: PMC7795831 DOI: 10.3390/ijms22010275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022] Open
Abstract
CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. The activation and functional status of CD4+ T cells is important for adequate responses to pathogen infections but has also been associated with auto-immune disorders and survival in several cancers. In the current study, we carried out a label-free high-resolution FTMS-based proteomic profiling of resting and T cell receptor-activated (72 h) primary human CD4+ T cells from peripheral blood of healthy donors as well as SUP-T1 cells. We identified 5237 proteins, of which significant alterations in the levels of 1119 proteins were observed between resting and activated CD4+ T cells. In addition to identifying several known T-cell activation-related processes altered expression of several stimulatory/inhibitory immune checkpoint markers between resting and activated CD4+ T cells were observed. Network analysis further revealed several known and novel regulatory hubs of CD4+ T cell activation, including IFNG, IRF1, FOXP3, AURKA, and RIOK2. Comparison of primary CD4+ T cell proteomic profiles with human lymphoblastic cell lines revealed a substantial overlap, while comparison with mouse CD+ T cell data suggested interspecies proteomic differences. The current dataset will serve as a valuable resource to the scientific community to compare and analyze the CD4+ proteome.
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Yukl SA, Khan S, Chen TH, Trapecar M, Wu F, Xie G, Telwatte S, Fulop D, Pico AR, Laird GM, Ritter KD, Jones NG, Lu CM, Siliciano RF, Roan NR, Milush JM, Somsouk M, Deeks SG, Hunt PW, Sanjabi S. Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103 + and Gut CD4 + T Cells. J Virol 2020; 95:e01331-20. [PMID: 33115867 PMCID: PMC7944458 DOI: 10.1128/jvi.01331-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Latent HIV infection is the main barrier to cure, and most HIV-infected cells reside in the gut, where distinct but unknown mechanisms may promote viral latency. Transforming growth factor β (TGF-β), which induces the expression of CD103 on tissue-resident memory T cells, has been implicated in HIV latency. Using CD103 as a surrogate marker to identify cells that have undergone TGF-β signaling, we compared the HIV RNA/DNA contents and cellular transcriptomes of CD103+ and CD103- CD4 T cells from the blood and rectum of HIV-negative (HIV-) and antiretroviral therapy (ART)-suppressed HIV-positive (HIV+) individuals. Like gut CD4+ T cells, circulating CD103+ cells harbored more HIV DNA than did CD103- cells but transcribed less HIV RNA per provirus. Circulating CD103+ cells also shared a gene expression profile that is closer to that of gut CD4 T cells than to that of circulating CD103- cells, with significantly lower expression levels of ribosomal proteins and transcriptional and translational pathways associated with HIV expression but higher expression levels of a subset of genes implicated in suppressing HIV transcription. These findings suggest that blood CD103+ CD4 T cells can serve as a model to study the molecular mechanisms of HIV latency in the gut and reveal new cellular factors that may contribute to HIV latency.IMPORTANCE The ability of HIV to establish a reversibly silent, "latent" infection is widely regarded as the main barrier to curing HIV. Most HIV-infected cells reside in tissues such as the gut, but it is unclear what mechanisms maintain HIV latency in the blood or gut. We found that circulating CD103+ CD4+ T cells are enriched for HIV-infected cells in a latent-like state. Using RNA sequencing (RNA-seq), we found that CD103+ T cells share a cellular transcriptome that more closely resembles that of CD4+ T cells from the gut, suggesting that they are homing to or from the gut. We also identified the cellular genes whose expression distinguishes gut CD4+ or circulating CD103+ T cells from circulating CD103- T cells, including some genes that have been implicated in HIV expression. These genes may contribute to latent HIV infection in the gut and may serve as new targets for therapies aimed at curing HIV.
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Affiliation(s)
- Steven A Yukl
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Shahzada Khan
- Gladstone Institutes, San Francisco, California, USA
| | - Tsui-Hua Chen
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- University of California, San Francisco, San Francisco, California, USA
| | | | - Frank Wu
- Gladstone Institutes, San Francisco, California, USA
| | - Guorui Xie
- Gladstone Institutes, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
| | - Sushama Telwatte
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Daniel Fulop
- Gladstone Institutes, San Francisco, California, USA
| | | | | | | | - Norman G Jones
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Chuanyi M Lu
- San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- University of California, San Francisco, San Francisco, California, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Nadia R Roan
- Gladstone Institutes, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
| | - Jeffrey M Milush
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Ma Somsouk
- Division of Gastroenterology, University of California, San Francisco, San Francisco, California, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Peter W Hunt
- Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, California, USA
| | - Shomyseh Sanjabi
- Gladstone Institutes, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
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97
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Running to Stand Still: Naive CD8 + T Cells Actively Maintain a Program of Quiescence. Int J Mol Sci 2020; 21:ijms21249773. [PMID: 33371448 PMCID: PMC7767439 DOI: 10.3390/ijms21249773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
CD8+ T cells play a pivotal role in clearing intracellular pathogens and combatting tumours. Upon infection, naïve CD8+ T cells differentiate into effector and memory cells, and this program is underscored by large-scale and coordinated changes in the chromatin architecture and gene expression. Importantly, recent evidence demonstrates that the epigenetic mechanisms that regulate the capacity for rapid effector function of memory T cells are shared by innate immune cells such as natural killer (NK) cells. Thus, it appears that the crucial difference between innate and adaptive immunity is the presence of the naïve state. This important distinction raises an intriguing new hypothesis, that the naïve state was evolutionary installed to restrain a default program of effector and memory differentiation in response to antigen recognition. We argue that the hallmark of adaptive T immunity is therefore the naïve program, which actively maintains CD8+ T cell quiescence until receipt of appropriate activation signals. In this review, we examine the mechanistic control of naïve CD8+ T cell quiescence and summarise the multiple levels of restraint imposed in naïve cells in to limit spontaneous and inappropriate activation. This includes epigenetic mechanisms and transcription factor (TF) regulation of gene expression, in addition to novel inhibitory receptors, abundance of RNA, and protein degradation.
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98
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020; 20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023] Open
Abstract
In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
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Affiliation(s)
- Alison Barbara Ross
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Julian David Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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99
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Ross SH, Cantrell DA. Of Mosaicism and Mechanisms: How JAK1 Goes Awry. Immunity 2020; 53:481-484. [PMID: 32937149 DOI: 10.1016/j.immuni.2020.08.010] [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] [Indexed: 11/19/2022]
Abstract
Personalized medicines require understanding the molecular causes of disease. In this issue of Immunity, Gruber et al. reveal that a gain-of-function JAK1 genetic variant results in a mutant protein with mosaic expression that drives multi-organ immune dysregulation via kinase dependent and independent mechanisms. The work highlights how biochemistry can inform therapies to resolve complex immune disorders.
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Affiliation(s)
- Sarah H Ross
- Lymphocyte Signaling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Doreen A Cantrell
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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100
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Milam AAV, Bartleson JM, Buck MD, Chang CH, Sergushichev A, Donermeyer DL, Lam WY, Pearce EL, Artyomov MN, Allen PM. Tonic TCR Signaling Inversely Regulates the Basal Metabolism of CD4 + T Cells. Immunohorizons 2020; 4:485-497. [PMID: 32769180 DOI: 10.4049/immunohorizons.2000055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/28/2022] Open
Abstract
The contribution of self-peptide-MHC signaling in CD4+ T cells to metabolic programming has not been definitively established. In this study, we employed LLO118 and LLO56, two TCRtg CD4+ T cells that recognize the same Listeria epitope. We previously have shown that LLO56 T cells are highly self-reactive and respond poorly in a primary infection, whereas LLO118 cells, which are less self-reactive, respond well during primary infection. We performed metabolic profiling and found that naive LLO118 had a dramatically higher basal respiration rate, a higher maximal respiration rate, and a higher glycolytic rate relative to LLO56. The LLO118 cells also exhibited a greater uptake of 2-NBD-glucose, in vitro and in vivo. We extended the correlation of low self-reactivity (CD5lo) with high basal metabolism using two other CD4+ TCRtg cells with known differences in self-reactivity, AND and Marilyn. We hypothesized that the decreased metabolism resulting from a strong interaction with self was mediated through TCR signaling. We then used an inducible knock-in mouse expressing the Scn5a voltage-gated sodium channel. This channel, when expressed in peripheral T cells, enhanced basal TCR-mediated signaling, resulting in decreased respiration and glycolysis, supporting our hypothesis. Genes and metabolites analysis of LLO118 and LLO56 T cells revealed significant differences in their metabolic pathways, including the glycerol phosphate shuttle. Inhibition of this pathway reverts the metabolic state of the LLO118 cells to be more LLO56 like. Overall, these studies highlight the critical relationship between peripheral TCR-self-pMHC interaction, metabolism, and the immune response to infection.
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Affiliation(s)
- Ashley A Viehmann Milam
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Juliet M Bartleson
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Michael D Buck
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany.,The Francis Crick Institute, London NW1 1AT, United Kingdom
| | | | | | - David L Donermeyer
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Wing Y Lam
- Amgen Research, Amgen, Inc., South San Francisco, CA 94080
| | - Erika L Pearce
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Maxim N Artyomov
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Paul M Allen
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110;
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