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Rodríguez-Rodríguez N, Rosetti F, Crispín JC. CD8 is down(regulated) for tolerance. Trends Immunol 2024; 45:442-453. [PMID: 38782625 DOI: 10.1016/j.it.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024]
Abstract
Activated CD8+ T cells directly kill target cells. Therefore, the regulation of their function is central to avoiding immunopathology. Mechanisms that curb effector functions in CD4+ and CD8+ T cells are mostly shared, yet important differences occur. Here, we focus on the control of CD8+ T cell activity and discuss the importance of a poorly understood aspect of tolerance that directly impairs engagement of target cells: the downregulation of CD8. We contextualize this process and propose that it represents a key element during CD8+ T cell modulation.
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Affiliation(s)
| | - Florencia Rosetti
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José C Crispín
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico; Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Monterrey, Mexico.
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2
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Song J, Liu L, Wang Z, Xie D, Azami NLB, Lu L, Huang Y, Ye W, Zhang Q, Sun M. CCL20 and CD8A as potential diagnostic biomarkers for HBV-induced liver fibrosis in chronic hepatitis B. Heliyon 2024; 10:e28329. [PMID: 38596115 PMCID: PMC11002547 DOI: 10.1016/j.heliyon.2024.e28329] [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: 06/23/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024] Open
Abstract
Background The main cause of the liver fibrosis (LF) remains hepatitis B virus (HBV) infection, especially in China. Histologically, liver fibrosis still occurs progressively in chronic hepatitis B (CHB) patients, even if HBV-DNA is negative or undetectable. The diagnosis of LF is beneficial to control the development of it, also it may promote the reversal of LF. Although liver biopsy is the gold standard of diagnosis in LF at present, it isa traumatic diagnosis. There are no diagnostic biomarkers as yet for the condition. It is badly in need of biomarkers clinically, which is simple to test, minimally invasive, highly specific, and sensitive. Early detection of HBV-LF development is crucial in the prevention, treatment, and prognosis prediction of HBV-LF. Cytokines are closely associated with both immune regulation and inflammation in the progression of hepatitis B virus associated-liver fibrosis (HBV-LF). In this bioinformatic study, we not only analyzed the relationship between HBV-LF and immune infiltration, but also identified key genes to uncover new therapeutic targets. Objectives To find potential biomarkers for liver fibrosis in the development of chronic hepatic B patients. Materials and methods We obtained two sets of data including CHB/healthy control and CHB/HBV-LF from the Integrated Gene Expression (GEO) database to select for differential expression analysis. Protein-protein interaction (PPI) network was also generated, while key genes and important gene modules involved in the occurrence and development of HBV-LF were identified. These key genes were analyzed by functional enrichment analysis, module analysis, and survival analysis. Furthermore, the relationship between these two diseases and immune infiltration was explored. Results Among the identified genes, 150 were individually associated with CHB and healthy control in the differential gene expression (DGE) analysis. While 14 with CHB and HBV-LF. It was also analyzed in the Robust rank aggregation (RRA) analysis, 34 differential genes were further identified by Cytohubba. Among 34 differential genes, two core genes were determined: CCL20 and CD8A. CCL20 was able to predict CHB positivity (area under the receiver operating characteristic curve [AUC-ROC] = 0.883, 95% confidence interval [CI] 0.786-0.963), while HBV-LF positivity ([AUC-ROC] = 0.687, 95% confidence interval [CI] 0.592-0.779). And CD8A was able to predict CHB positivity ([AUC-ROC] = 0.960, 95% confidence interval [CI] 0.915-0.992), while HBV-LF positivity ([AUC-ROC] = 0.773, 95% confidence interval [CI] 0.680-0.856). Relationship between CCL20 gene expression and LF grades was P < 0.05, as well as CD8A. Conclusion CCL20 and CD8A were found to be potential biomarkers and therapeutic targets for HBV-LF. It is instructive for research on the progression of LF in HBV patients, suppression of chronic inflammation, and development of molecularly targeted-therapy for HBV-LF.
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Affiliation(s)
- Jingru Song
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310007, China
| | - Lu Liu
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zheng Wang
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Dong Xie
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Nisma Lena Bahaji Azami
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Lu Lu
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yanping Huang
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Wei Ye
- Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310007, China
| | - Qin Zhang
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Mingyu Sun
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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3
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Minogue E, Cunha PP, Wadsworth BJ, Grice GL, Sah-Teli SK, Hughes R, Bargiela D, Quaranta A, Zurita J, Antrobus R, Velica P, Barbieri L, Wheelock CE, Koivunen P, Nathan JA, Foskolou IP, Johnson RS. Glutarate regulates T cell metabolism and anti-tumour immunity. Nat Metab 2023; 5:1747-1764. [PMID: 37605057 PMCID: PMC10590756 DOI: 10.1038/s42255-023-00855-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/03/2023] [Indexed: 08/23/2023]
Abstract
T cell function and fate can be influenced by several metabolites: in some cases, acting through enzymatic inhibition of α-ketoglutarate-dependent dioxygenases, in others, through post-translational modification of lysines in important targets. We show here that glutarate, a product of amino acid catabolism, has the capacity to do both, and has potent effects on T cell function and differentiation. We found that glutarate exerts those effects both through α-ketoglutarate-dependent dioxygenase inhibition, and through direct regulation of T cell metabolism via glutarylation of the pyruvate dehydrogenase E2 subunit. Administration of diethyl glutarate, a cell-permeable form of glutarate, alters CD8+ T cell differentiation and increases cytotoxicity against target cells. In vivo administration of the compound is correlated with increased levels of both peripheral and intratumoural cytotoxic CD8+ T cells. These results demonstrate that glutarate is an important regulator of T cell metabolism and differentiation with a potential role in the improvement of T cell immunotherapy.
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Affiliation(s)
- Eleanor Minogue
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Pedro P Cunha
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Brennan J Wadsworth
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Guinevere L Grice
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Shiv K Sah-Teli
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Centre for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - Rob Hughes
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - David Bargiela
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Alessandro Quaranta
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Javier Zurita
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Pedro Velica
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Barbieri
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Centre for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Iosifina P Foskolou
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Randall S Johnson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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4
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Guo S, Jiang H, Deng Y, Dong Y, Yin A, Wang Q, Lan Q, Zhang Y, Xu C. Reduced 2,4-dienoyl-CoA reductase 1 is served as an unfavorable biomarker and is related to immune infiltration in cervical cancer. J Obstet Gynaecol Res 2023; 49:2475-2486. [PMID: 37497824 DOI: 10.1111/jog.15751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Worldwide, cervical cancer (CC) remains the most prevalent malignancy of the female reproductive system, posing a threat to women's life and health, and increasing the medical and economic burden on society. Therefore, the search for tumor biomarkers for CC remains an important research direction. Immunotherapy has significantly improved patient outcomes, and genes related to tumor immune infiltration have been clinically relevant and highly reproducible biomarkers that affect the prognosis and response to treatment of CC. 2,4-dienoyl-CoA reductase 1 (DECR1) was considered to be an oncogene in a previous study, but relationship between DECR1 and immune infiltration was not mentioned. Our study aimed to reveal the clinical value of DECR1 in CC and to investigate its relationship with immune infiltration. METHODS Human Protein Atlas was used to identify the localization of DECR1. The Ualcan database, TCGA, and IHC were used to assess the prognostic value of DECR1. GSEA was used to assess the possible signaling pathways of DECR1 in CC. The TIMER database was applied to reveal the relevance between DECR1 and immune infiltration. GEPIA was conducted to detect the co-relationship among DECR1, immune markers, and typical molecules of apoptosis. RESULTS DECR1 was mainly distributed in the cytoplasm and overlapped with the endoplasmic reticulum. DECR1 was downregulated in CC compared to adjacent tissue. Survival analysis showed that patients with lower expression of DECR1 have a worse prognosis in CC. GSEA suggested that DECR1 was closely related to apoptosis signaling. TIMER showed that DECR1 was positively correlated with CD8+ T cell and CD4+ T cell but not with B cell in CC. CONCLUSION DECR1 may be a potential cancer suppressor in CC and may be involved in apoptotic pathways and associated with immune infiltration.
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Affiliation(s)
- Suiqun Guo
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Huiping Jiang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yuanrun Deng
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yanqi Dong
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Aiqi Yin
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Qinghai Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Qiudai Lan
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yilin Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Caiqiu Xu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China
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5
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Chen J, Yu S, Lang Z, Jin Y, Zhou G, Tao Q, Wang X, Zheng J. Development and validation of a potential biomarker to improve the assessment of liver fibrosis progression in patients with chronic hepatitis B. J Med Virol 2023; 95:e28239. [PMID: 36258661 DOI: 10.1002/jmv.28239] [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: 06/08/2022] [Revised: 09/16/2022] [Accepted: 10/16/2022] [Indexed: 01/12/2023]
Abstract
We aimed to develop and validate a novel combined score to improve the assessment of liver fibrosis progression in patients with chronic hepatitis B (CHB). In this study, a total of 331 CHB patients from three cohorts who underwent liver biopsy were enrolled, and the Scheuer system was used for liver fibrosis classification. The combined score was derived by principal component analysis of key differentially expressed genes. For significant liver fibrosis (≥S2), the areas under the receiver operating characteristics curves (AUROCs) of the combined score were 0.838, 0.842, and 0.881 in the three cohorts, respectively. And for advanced liver fibrosis (≥S3), the AUROCs were 0.794, 0.801, and 0.901, respectively. Compared with the results of AUROCs for aspartate aminotransferase≥to≥platelet ratio (APRI) and fibrosis index based on four factors (FIB-4) in the validation cohorts, better clinical diagnostic value for assessing the progression of liver fibrosis was found in the combined score. Additionally, univariate ordered logistic regression analysis indicated that the combined score could serve as a more superior and stable risk factor than APRI and FIB-4 in the assessment of liver fibrosis. For CHB patients with normal alanine aminotransferase (ALT), our results further emphasized the diagnostic value of the combined score for significant fibrosis (≥S2) and advanced fibrosis (≥S3). Moreover, it was found that patients with the high combined score, who were associated with the advanced fibrosis stage, had higher levels of drug sensitivity and immune checkpoint expression. In conclusion, the novel combined score could serve as a potential biomarker and contribute to improving the assessment of fibrosis stage in CHB patients.
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Affiliation(s)
- Ji Chen
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Suhui Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhichao Lang
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yan Jin
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guangyao Zhou
- Department of Infectious Diseases, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiqi Tao
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaodong Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianjian Zheng
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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6
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Turner SJ, Bennett TJ, Gruta NLL. CD8 + T-Cell Memory: The Why, the When, and the How. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a038661. [PMID: 33648987 PMCID: PMC8091951 DOI: 10.1101/cshperspect.a038661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The generation of effective adaptive T-cell memory is a cardinal feature of the adaptive immune system. The establishment of protective T-cell immunity requires the differentiation of CD8+ T cells from a naive state to one where pathogen-specific memory CD8+ T cells are capable of responding to a secondary infection more rapidly and robustly without the need for further differentiation. The study of factors that determine the fate of activated CD8+ T cells into either effector or memory subsets has a long history. The advent of new technologies is now providing new insights into how epigenetic regulation not only impacts acquisition and maintenance of effector function, but also the maintenance of the quiescent yet primed memory state. There is growing appreciation that rather than distinct subsets, memory T-cell populations may reflect different points on a spectrum between the starting naive T-cell population and a terminally differentiated effector CD8+ T-cell population. Interestingly, there is growing evidence that the molecular mechanisms that underpin the rapid effector function of memory T cells are also observed in innate immune cells such as macrophages and natural killer (NK) cells. This raises an interesting hypothesis that the memory/effector T-cell state represents a default innate-like response to antigen recognition, and that it is the naive state that is the defining feature of adaptive immunity. These issues are discussed.
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Affiliation(s)
- Stephen J Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Taylah J Bennett
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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7
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Abstract
PURPOSE OF REVIEW TCRαβ+CD4-CD8- double-negative T (DNT) cells, a principal subset of mature T lymphocytes, have been closely linked with autoimmune/inflammatory conditions. However, controversy persists regarding their ontogeny and function. Here, we present an overview on DNT cells in different autoimmune diseases to advance a deeper understanding of the contribution of this population to disease pathogenesis. RECENT FINDINGS DNT cells have been characterized in various chronic inflammatory diseases and they have been proposed to display pathogenic or regulatory function. The tissue location of DNT cells and the effector cytokines they produce bespeak to their active involvement in chronic inflammatory diseases. SUMMARY By producing various cytokines, expanded DNT cells in inflamed tissues contribute to the pathogenesis of a variety of autoimmune inflammatory diseases. However, it is unclear whether this population represents a stable lineage consisting of different subsets similar to CD4+ T helper cell subset. Better understanding of the possible heterogeneity and plasticity of DNT cells is needed to reveal interventional therapeutic opportunities.
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Affiliation(s)
- Hao Li
- Division of Rheumatology and Clinical Immunology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
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8
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Rezinciuc S, Tian Z, Wu S, Hengel S, Pasa-Tolic L, Smallwood HS. Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells. Viruses 2020; 12:v12121409. [PMID: 33302437 PMCID: PMC7762524 DOI: 10.3390/v12121409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 12/25/2022] Open
Abstract
T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.
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Affiliation(s)
- Svetlana Rezinciuc
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Zhixin Tian
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Shawna Hengel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Heather S. Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
- Children’s Foundation Research Institute, Memphis, TN 38105, USA
- Correspondence: ; Tel.: +1-(901)-448–3068
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9
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Siefker DT, Vu L, You D, McBride A, Taylor R, Jones TL, DeVincenzo J, Cormier SA. Respiratory Syncytial Virus Disease Severity Is Associated with Distinct CD8 + T-Cell Profiles. Am J Respir Crit Care Med 2020; 201:325-334. [PMID: 31644878 DOI: 10.1164/rccm.201903-0588oc] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Rationale: Respiratory syncytial virus (RSV) causes significant morbidity and mortality in infants worldwide. Although T-helper type 2 (Th2) cell pathology is implicated in severe disease, the mechanisms underlying the development of immunopathology are incompletely understood.Objectives: We aimed to identify local immune responses associated with severe RSV in infants. Our hypothesis was that disease severity would correlate with enhanced Th2 cellular responses.Methods: Nasal aspirates were collected from infants hospitalized with severe (admitted to the pediatric ICU) or moderate (maintained in the general ward) RSV disease at 5 to 9 days after enrollment. The immune response was investigated by evaluating T-lymphocyte cellularity, cytokine concentration, and viral load.Measurements and Main Results: Patients with severe disease had increased proportions of CD8 (cluster of differentiation 8)-positive T cells expressing IL-4 (Tc2) and reduced proportions of CD8+ T cells expressing IFNγ (Tc1). Nasal aspirates from patients with severe disease had reduced concentrations of IL-17. Patients with greater frequencies of Tc1, CD8+ T cells expressing IL-17 (Tc17), and CD4+ T cells expressing IL-17 (Th17) had shorter durations of hospitalization.Conclusions: Severe RSV disease was associated with distinct T-cell profiles. Tc1, Tc17, and Th17 were associated with shorter hospital stay and may play a protective role, whereas Tc2 cells may play a previously underappreciated role in pathology.
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Affiliation(s)
- David T Siefker
- Department of Biological Sciences, College of Science, and Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
| | - Luan Vu
- Department of Biological Sciences, College of Science, and Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
| | - Dahui You
- Department of Pediatrics, and.,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | | | | | - Tamekia L Jones
- Department of Pediatrics, and.,Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee; and.,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - John DeVincenzo
- Department of Pediatrics, and.,Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Stephania A Cormier
- Department of Biological Sciences, College of Science, and Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
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10
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Pace L, Amigorena S. Epigenetics of T cell fate decision. Curr Opin Immunol 2020; 63:43-50. [PMID: 32066083 DOI: 10.1016/j.coi.2020.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
The changes of transcription factor activity and chromatin dynamics guide functional differentiation of T cell subsets, including commitment to short-lived effectors and long-term survival of memory T cells. Understanding the lineage relationships among the different stages of effector and memory differentiation has profound therapeutic implications for the development of new vaccine and immunotherapy protocols. Here we review the contribution of chromatin architecture to T cell specification, focusing on the interplay between epigenetic changes and transcriptional programs linked to T cell plasticity, commitment and memory. We will also discuss the translational implications of epigenetic control in the context of infections and cancer.
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Affiliation(s)
- Luigia Pace
- Armenise-Harvard Immune Regulation Unit, IIGM, FPO-IRCCS Candiolo, Turin, Italy.
| | - Sebastian Amigorena
- Institut Curie, PSL Research University, Paris, France; INSERM U932, France.
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11
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Chen J, Lin M, Zhang S. Identification of key miRNA‑mRNA pairs in septic mice by bioinformatics analysis. Mol Med Rep 2019; 20:3858-3866. [PMID: 31432183 PMCID: PMC6755251 DOI: 10.3892/mmr.2019.10594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/26/2019] [Indexed: 11/06/2022] Open
Abstract
Sepsis is one of the most common causes of death among critically ill patients in intensive care units worldwide; however, the microRNAs (miRNAs/miRs) involved in the sepsis process (and their target genes) are largely unknown. The present study integrated miRNA and mRNA datasets to elucidate key sepsis-related miRNA-mRNA pairs. The datasets, GSE74952 and GSE55238 were downloaded from the Gene Expression Omnibus. By performing bioinformatics analysis such as GEO2R, miRNA target gene prediction, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis and miRNA-mRNA network analysis, a total of four sepsis-related miRNA-mRNA pairs were successfully obtained. Mmu-miR-370-3p, cluster of differentiation (CD)8a, CD247, Zap70 and inhibitor of nuclear factor κ B kinase subunit β (Ikbkb) were identified as the components involved in these pairs, and these genes were enriched in the T-cell receptor signaling pathway. Finally, reverse transcription-quantitative PCR results validated that the expression levels of the four genes (CD8a, CD247, Zap70 and Ikbkb) in the sepsis model mice were consistent with the microarray analysis. In conclusion, the present study identified four sepsis-related miRNA-mRNA pairs using bioinformatics analysis. These results indicated that the candidate miRNA-mRNA pairs may be involved in the regulation of immunity in sepsis, which may in turn act as indicators or therapeutic targets for sepsis.
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Affiliation(s)
- Jianxin Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Min Lin
- School of Information Engineering, Putian University, Putian, Fujian 351100, P.R. China
| | - Sen Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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12
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Abstract
A fundamental question in developmental immunology is how bipotential thymocyte precursors generate both CD4+ helper and CD8+ cytotoxic T cell lineages. The MHC specificity of αβ T cell receptors (TCRs) on precursors is closely correlated with cell fate-determining processes, prompting studies to characterize how variations in TCR signaling are linked with genetic programs establishing lineage-specific gene expression signatures, such as exclusive CD4 or CD8 expression. The key transcription factors ThPOK and Runx3 have been identified as mediating development of helper and cytotoxic T cell lineages, respectively. Together with increasing knowledge of epigenetic regulators, these findings have advanced our understanding of the transcription factor network regulating the CD4/CD8 dichotomy. It has also become apparent that CD4+ T cells retain developmental plasticity, allowing them to acquire cytotoxic activity in the periphery. Despite such advances, further studies are necessary to identify the molecular links between TCR signaling and the nuclear machinery regulating expression of ThPOK and Runx3.
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Affiliation(s)
- Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan;
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13
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Prier JE, Li J, Gearing LJ, Olshansky M, Sng XYX, Hertzog PJ, Turner SJ. Early T-BET Expression Ensures an Appropriate CD8 + Lineage-Specific Transcriptional Landscape after Influenza A Virus Infection. THE JOURNAL OF IMMUNOLOGY 2019; 203:1044-1054. [PMID: 31227580 DOI: 10.4049/jimmunol.1801431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/31/2019] [Indexed: 01/12/2023]
Abstract
Virus infection triggers large-scale changes in the phenotype and function of naive CD8+ T cells, resulting in the generation of effector and memory T cells that are then critical for immune clearance. The T-BOX family of transcription factors (TFs) are known to play a key role in T cell differentiation, with mice deficient for the TF T-BET (encoded by Tbx21) unable to generate optimal virus-specific effector responses. Although the importance of T-BET in directing optimal virus-specific T cell responses is accepted, the precise timing and molecular mechanism of action remains unclear. Using a mouse model of influenza A virus infection, we demonstrate that although T-BET is not required for early CD8+ T cell activation and cellular division, it is essential for early acquisition of virus-specific CD8+ T cell function and sustained differentiation and expansion. Whole transcriptome analysis at this early time point showed that Tbx21 deficiency resulted in global dysregulation in early programming events with inappropriate lineage-specific signatures apparent with alterations in the potential TF binding landscape. Assessment of histone posttranslational modifications within the Ifng locus demonstrated that Tbx21 -/- CD8+ T cells were unable to activate "poised" enhancer elements compared with wild-type CD8+ T cells, correlating with diminished Ifng transcription. In all, these data support a model whereby T-BET serves to promote appropriate chromatin remodeling at specific gene loci that underpins appropriate CD8+ T cell lineage-specific commitment and differentiation.
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Affiliation(s)
- Julia E Prier
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jasmine Li
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Linden J Gearing
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia; and
| | - Moshe Olshansky
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Paul J Hertzog
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia; and
| | - Stephen J Turner
- Department of Microbiology and Immunology, the Doherty Institute at the University of Melbourne, Parkville, Victoria 3010, Australia; .,Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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14
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Arenas-Ramirez N, Sahin D, Boyman O. Epigenetic mechanisms of tumor resistance to immunotherapy. Cell Mol Life Sci 2018; 75:4163-4176. [PMID: 30140960 PMCID: PMC11105392 DOI: 10.1007/s00018-018-2908-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/10/2018] [Accepted: 08/16/2018] [Indexed: 12/14/2022]
Abstract
The recent impact of cancer immunotherapies has firmly established the ability and importance of the immune system to fight malignancies. However, the intimate interaction between the highly dynamic tumor and immune cells leads to a selection process driven by genetic and epigenetic processes. As the molecular pathways of cancer resistance mechanisms to immunotherapy become increasingly known, novel therapeutic targets are being tested in combination with immune-stimulating approaches. We here review recent insights into the molecular mechanisms of tumor resistance with particular emphasis on epigenetic processes and place these in the context of previous models.
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Affiliation(s)
| | - Dilara Sahin
- Department of Immunology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, 8091, Zurich, Switzerland.
- Faculty of Medicine, University of Zurich, 8006, Zurich, Switzerland.
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15
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Harland KL, Fox A, Nüssing S, Hensen L, Kedzierska K, Turner SJ, Kelso A. Limited Phenotypic and Functional Plasticity of Influenza Virus–Specific Memory CD8+T Cells during Activation in an Alternative Cytokine Environment. THE JOURNAL OF IMMUNOLOGY 2018; 201:3282-3293. [DOI: 10.4049/jimmunol.1701672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 09/17/2018] [Indexed: 12/21/2022]
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16
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Liu F, Zhao Y, Gong C, Xu T, Zhang Y, Mei J, Lu J, Feng X, Rong Y, Wu Y. Identification of Methylated Gene Markers in Childhood Atopic Asthma by Integrating Gene Expression and Methylation Profiles Based on Bioinformatic Analysis. PEDIATRIC ALLERGY, IMMUNOLOGY, AND PULMONOLOGY 2018. [DOI: 10.1089/ped.2017.0793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Fang Liu
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
| | - YuHua Zhao
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
| | - ChunHua Gong
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
| | - Tong Xu
- Department of Pediatrics, Changzheng Hospital Affiliated to the Second Military Medical University, Shanghai, China
| | - YanBin Zhang
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
| | - Jun Mei
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
| | - JieMin Lu
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
| | - XiaoYan Feng
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
| | - YanMing Rong
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
| | - YaHui Wu
- Department of Pediatrics, Shanghai East Hospital affiliated to Tongji University, Shanghai, China
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17
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Fox A, Harland KL, Kedzierska K, Kelso A. Exposure of Human CD8 + T Cells to Type-2 Cytokines Impairs Division and Differentiation and Induces Limited Polarization. Front Immunol 2018; 9:1141. [PMID: 29892290 PMCID: PMC5985406 DOI: 10.3389/fimmu.2018.01141] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/07/2018] [Indexed: 12/18/2022] Open
Abstract
Effector CD8+ T cells generally produce type-1 cytokines and mediators of the perforin/granzyme cytolytic pathway, yet type-2-polarized CD8+ cells (Tc2) are detected in type-2 (T2) cytokine-driven diseases such as asthma. It is unclear whether T2 cytokine exposure during activation is sufficient to polarize human CD8+ T cells. To address this question, a protocol was developed for high-efficiency activation of human CD8+ T cells in which purified single cells or populations were stimulated with plate-bound anti-CD3 and anti-CD11a mAb for up to 8 days in T2 polarizing or neutral conditions, before functional analysis. Activation of CD8+ naïve T cells (TN) in T2 compared with neutral conditions decreased the size of single-cell clones, although early division kinetics were equivalent, indicating an effect on overall division number. Activation of TN in T2 conditions followed by brief anti-CD3 mAb restimulation favored expression of T2 cytokines, GATA3 and Eomes, and lowered expression of type-1 cytokines, Prf1, Gzmb, T-BET, and Prdm1. However, IL-4 was only weakly expressed, and PMA and ionomycin restimulation favored IFN-γ over IL-4 expression. Activation of TN in T2 compared with neutral conditions prevented downregulation of costimulatory (CD27, CD28) and lymph-node homing receptors (CCR7) and CD95 acquisition, which typically occur during differentiation into effector phenotypes. CD3 was rapidly and substantially induced after activation in neutral, but not T2 conditions, potentially contributing to greater division and differentiation in neutral conditions. CD8+ central memory T cells (TCM) were less able to enter division upon reactivation in T2 compared with neutral conditions, and were more refractory to modulating IFN-γ and IL-4 production than CD8+ TN. In summary, while activation of TN in T2 conditions can generate T2 cytokine-biased cells, IL-4 expression is weak, T2 bias is lost upon strong restimulation, differentiation, and division are arrested, and reactivation of TCM is reduced in T2 conditions. Taken together, this suggests that exposure to T2 cytokines during activation may not be sufficient to generate and retain human Tc2 cells.
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Affiliation(s)
- Annette Fox
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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18
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Abstract
During differentiation of CD4+CD8+ double-positive (DP) thymocytes into the CD4-CD8+ single-positive (CD8SP) thymocytes committed to the cytotoxic T cell lineage, Cd8a transcription is temporally terminated after positive selection and is subsequently reinitiated, a process known as coreceptor reversal. Despite the identification of a transcriptional enhancer in the Cd8a gene that directs reporter transgene expression specifically in CD8SP thymocytes, the molecular mechanisms controlling reactivation of the Cd8a gene are not fully understood. Here, we show that, after positive selection, hCD2 reporter expression from the Cd8a locus, which was generated by insertion of hCD2 cDNA into the first exon of the Cd8a gene, requires the incorporation of intron sequences into the hCD2 transcript. The presence of polyadenylation signals after hCD2 cDNA inhibited hCD2 expression in mature CD8+ T cells, whereas hCD2 expression in DP thymocytes recapitulated the Cd8a expression. Incorporation of the endogenous short intron structure and heterologous intron structure of the Cd4 locus restored hCD2 expression in mature CD8+ T cells in a variegated manner. Interestingly, stage-specific DNA demethylation was impaired in Cd8a reporter alleles that failed to express hCD2 in CD8+ T cells, and intron sequences lacking RNA splicing signals still restored hCD2 expression. These observations indicate that "intron-mediated enhancement" is involved in a stage-specific reactivation of the Cd8a locus harboring hCD2 cDNA. However, the Cd8a gene was transcribed in mature CD8+ T cells, albeit at a lower level, from a mutant Cd8a locus lacking intron structures, suggesting that protein-coding sequences in transcripts affect sensitivity to intron-mediated enhancement.
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19
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Acetylation of the Cd8 Locus by KAT6A Determines Memory T Cell Diversity. Cell Rep 2018; 16:3311-3321. [PMID: 27653692 DOI: 10.1016/j.celrep.2016.08.056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/21/2016] [Accepted: 08/17/2016] [Indexed: 11/20/2022] Open
Abstract
How functionally diverse populations of pathogen-specific killer T cells are generated during an immune response remains unclear. Here, we propose that fine-tuning of CD8αβ co-receptor levels via histone acetylation plays a role in lineage fate. We show that lysine acetyltransferase 6A (KAT6A) is responsible for maintaining permissive Cd8 gene transcription and enabling robust effector responses during infection. KAT6A-deficient CD8(+) T cells downregulated surface CD8 co-receptor expression during clonal expansion, a finding linked to reduced Cd8α transcripts and histone-H3 lysine 9 acetylation of the Cd8 locus. Loss of CD8 expression in KAT6A-deficient T cells correlated with reduced TCR signaling intensity and accelerated contraction of the effector-like memory compartment, whereas the long-lived memory compartment appeared unaffected, a result phenocopied by the removal of the Cd8 E8I enhancer element. These findings suggest a direct role of CD8αβ co-receptor expression and histone acetylation in shaping functional diversity within the cytotoxic T cell pool.
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20
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Brandt D, Hedrich CM. TCRαβ +CD3 +CD4 -CD8 - (double negative) T cells in autoimmunity. Autoimmun Rev 2018; 17:422-430. [PMID: 29428806 DOI: 10.1016/j.autrev.2018.02.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022]
Abstract
TCRαβ+CD3+CD4-CD8- "double negative" (DN) T cells comprise a small subset of mature peripheral T cells. The origin and function of DN T cells are somewhat unclear and discussed controversially. While DN T cells resemble a rare and heterogeneous T cell subpopulation in healthy individuals, numbers of TCRαβ+ DN T cells are expanded in several inflammatory conditions, where they also exhibit distinct effector phenotypes and infiltrate inflamed tissues. Thus, DN T cells may be involved in systemic inflammation and tissue damage in autoimmune/inflammatory conditions, including SLE, Sjögren's syndrome, and psoriasis. Here, the current understanding of the origin and phenotype of DN T cells, and their role in the instruction of immune responses, autoimmunity and inflammation will be discussed in health and disease.
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Affiliation(s)
- D Brandt
- Division of Pediatric Rheumatology and Immunology, Children's Hospital Dresden, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - C M Hedrich
- Division of Pediatric Rheumatology and Immunology, Children's Hospital Dresden, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany; Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, UK; Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK.
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21
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Falanga YT, Frascoli M, Kaymaz Y, Forconi C, Ong'echa JM, Bailey JA, Berg LJ, Moormann AM. High pathogen burden in childhood promotes the development of unconventional innate-like CD8+ T cells. JCI Insight 2017; 2:93814. [PMID: 28768916 DOI: 10.1172/jci.insight.93814] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/20/2017] [Indexed: 11/17/2022] Open
Abstract
Cellular and humoral constituents of the immune system differ significantly between children and adults, yet very little is known about the impact of early-life pathogen exposure on this immunologic transition. We examined CD4+ and CD8+ T cell subsets defined by CCR7 and CD45RA expression in two longitudinal pediatric cohorts experiencing divergent levels of pathogen burden. Using multiparameter flow cytometry, along with serological, cytokine, and transcriptomic data, we show that cumulative pathogen burden promotes the development of atypical CD8dim T cells with an innate-like profile (Granzyme Bhi, IFNγlow, TNFαlow, PLFZhi, ID2hi, IKZF2hi) in contrast to age-matched children residing in a low pathogen-exposure area who display a more conventional CD8bright profile (IFNγ+, TNFα+, CCL4+). Furthermore, these unconventional T cells had stunted proliferation, distinct transcriptional programs, and impaired T cell receptor signaling and were enriched in hallmark TNFα, NF-κB, and IL-6 gene signaling pathways, reminiscent of NK cells and type-1 innate lymphoid cells. Our findings suggest that these unconventional CD8dim T cells arise in a very particular immunological context and may provide a deeper understanding of the heterogeneity in human immune responses.
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Affiliation(s)
- Yves T Falanga
- Department of Pathology.,Program in Molecular Medicine, and
| | | | - Yasin Kaymaz
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | | | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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22
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Issuree PDA, Ng CP, Littman DR. Heritable Gene Regulation in the CD4:CD8 T Cell Lineage Choice. Front Immunol 2017; 8:291. [PMID: 28382035 PMCID: PMC5360760 DOI: 10.3389/fimmu.2017.00291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 12/04/2022] Open
Abstract
The adaptive immune system is dependent on functionally distinct lineages of T cell antigen receptor αβ-expressing T cells that differentiate from a common progenitor in the thymus. CD4+CD8+ progenitor thymocytes undergo selection following interaction with MHC class I and class II molecules bearing peptide self-antigens, giving rise to CD8+ cytotoxic and CD4+ helper or regulatory T cell lineages, respectively. The strict correspondence of CD4 and CD8 expression with distinct cellular phenotypes has made their genes useful surrogates for investigating molecular mechanisms of lineage commitment. Studies of Cd4 and Cd8 transcriptional regulation have uncovered cis-regulatory elements that are critical for mediating epigenetic modifications at distinct stages of development to establish heritable transcriptional programs. In this review, we examine the epigenetic mechanisms involved in Cd4 and Cd8 gene regulation during T cell lineage specification and highlight the features that make this an attractive system for uncovering molecular mechanisms of heritability.
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Affiliation(s)
- Priya D A Issuree
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine , New York, NY , USA
| | - Charles P Ng
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine , New York, NY , USA
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
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23
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Tyrakis PA, Palazon A, Macias D, Lee KL, Phan AT, Veliça P, You J, Chia GS, Sim J, Doedens A, Abelanet A, Evans CE, Griffiths JR, Poellinger L, Goldrath AW, Johnson RS. S-2-hydroxyglutarate regulates CD8 + T-lymphocyte fate. Nature 2016; 540:236-241. [PMID: 27798602 PMCID: PMC5149074 DOI: 10.1038/nature20165] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/18/2016] [Indexed: 12/28/2022]
Abstract
R-2-hydroxyglutarate accumulates to millimolar levels in cancer cells with gain-of-function isocitrate dehydrogenase 1/2 mutations. These levels of R-2-hydroxyglutarate affect 2-oxoglutarate-dependent dioxygenases. Both metabolite enantiomers, R- and S-2-hydroxyglutarate, are detectible in healthy individuals, yet their physiological function remains elusive. Here we show that 2-hydroxyglutarate accumulates in mouse CD8+ T cells in response to T-cell receptor triggering, and accumulates to millimolar levels in physiological oxygen conditions through a hypoxia-inducible factor 1-alpha (HIF-1α)-dependent mechanism. S-2-hydroxyglutarate predominates over R-2-hydroxyglutarate in activated T cells, and we demonstrate alterations in markers of CD8+ T-cell differentiation in response to this metabolite. Modulation of histone and DNA demethylation, as well as HIF-1α stability, mediate these effects. S-2-hydroxyglutarate treatment greatly enhances the in vivo proliferation, persistence and anti-tumour capacity of adoptively transferred CD8+ T cells. Thus, S-2-hydroxyglutarate acts as an immunometabolite that links environmental context, through a metabolic-epigenetic axis, to immune fate and function.
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Affiliation(s)
- Petros A. Tyrakis
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Asis Palazon
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - David Macias
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - Kian. L. Lee
- Cancer Science Institute of Singapore, National University of Singapore, Republic of Singapore
| | | | - Pedro Veliça
- Department of Cell and Molecular Biology, Karolinska Institute, Sweden
| | - Jia You
- Cancer Science Institute of Singapore, National University of Singapore, Republic of Singapore
| | - Grace S. Chia
- Cancer Science Institute of Singapore, National University of Singapore, Republic of Singapore
| | - Jingwei Sim
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - Andrew Doedens
- Molecular Biology Section, UC San Diego, La Jolla, CA, USA
| | - Alice Abelanet
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - Colin E. Evans
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
| | - John R. Griffiths
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Lorenz Poellinger
- Cancer Science Institute of Singapore, National University of Singapore, Republic of Singapore
- Department of Cell and Molecular Biology, Karolinska Institute, Sweden
| | | | - Randall S. Johnson
- Department of Physiology, Development and Neuroscience, University of Cambridge, UK
- Department of Cell and Molecular Biology, Karolinska Institute, Sweden
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24
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Liu M, Zhou J, Chen Z, Cheng ASL. Understanding the epigenetic regulation of tumours and their microenvironments: opportunities and problems for epigenetic therapy. J Pathol 2016; 241:10-24. [PMID: 27770445 DOI: 10.1002/path.4832] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/06/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022]
Abstract
The tumour microenvironment plays an instrumental role in cancer development, progression and treatment response/resistance. Accumulating evidence is underscoring the fundamental importance of epigenetic regulation in tumour immune evasion. Following many pioneering discoveries demonstrating malignant transformation through epigenetic anomalies ('epimutations'), there is also a growing emphasis on elucidating aberrant epigenetic mechanisms that reprogramme the milieu of tumour-associated immune and stromal cells towards an immunosuppressive state. Pharmacological inhibition of DNA methylation and histone modifications can augment the efficiency of immune checkpoint blockage, and unleash anti-tumour T-cell responses. However, these non-specific agents also represent a 'double-edged sword', as they can also reactivate gene transcription of checkpoint molecules, interrupting immune surveillance programmes. By understanding the impact of epigenetic control on the tumour microenvironment, rational combinatorial epigenetic and checkpoint blockage therapies have the potential to harness the immune system for the treatment of cancer. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Man Liu
- School of Biomedical Sciences and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Jingying Zhou
- School of Biomedical Sciences and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
| | - Zhiwei Chen
- AIDS Institute and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, PR China
| | - Alfred Sze-Lok Cheng
- School of Biomedical Sciences and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China
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25
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Wiencke JK, Butler R, Hsuang G, Eliot M, Kim S, Sepulveda MA, Siegel D, Houseman EA, Kelsey KT. The DNA methylation profile of activated human natural killer cells. Epigenetics 2016; 11:363-80. [PMID: 26967308 DOI: 10.1080/15592294.2016.1163454] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Natural killer (NK) cells are now recognized to exhibit characteristics akin to cells of the adaptive immune system. The generation of adaptive memory is linked to epigenetic reprogramming including alterations in DNA methylation. The study herein found reproducible genome wide DNA methylation changes associated with human NK cell activation. Activation led predominately to CpG hypomethylation (81% of significant loci). Bioinformatics analysis confirmed that non-coding and gene-associated differentially methylated sites (DMS) are enriched for immune related functions (i.e., immune cell activation). Known DNA methylation-regulated immune loci were also identified in activated NK cells (e.g., TNFA, LTA, IL13, CSF2). Twenty-one loci were designated high priority and further investigated as potential markers of NK activation. BHLHE40 was identified as a viable candidate for which a droplet digital PCR assay for demethylation was developed. The assay revealed high demethylation in activated NK cells and low demethylation in naïve NK, T- and B-cells. We conclude the NK cell methylome is plastic with potential for remodeling. The differentially methylated region signature of activated NKs revealed similarities with T cell activation, but also provided unique biomarker candidates of NK activation, which could be useful in epigenome-wide association studies to interrogate the role of NK subtypes in global methylation changes associated with exposures and/or disease states.
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Affiliation(s)
- John K Wiencke
- a Department of Neurological Surgery , University of California San Francisco , San Francisco , CA
| | - Rondi Butler
- b Brown University , Department of Epidemiology , Providence , RI
| | - George Hsuang
- a Department of Neurological Surgery , University of California San Francisco , San Francisco , CA
| | - Melissa Eliot
- b Brown University , Department of Epidemiology , Providence , RI
| | - Stephanie Kim
- b Brown University , Department of Epidemiology , Providence , RI
| | - Manuel A Sepulveda
- d Janssen Oncology Therapeutic Area, Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson , 1400 Welsh and McKean Roads, Spring House , PA
| | - Derick Siegel
- d Janssen Oncology Therapeutic Area, Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson , 1400 Welsh and McKean Roads, Spring House , PA
| | - E Andres Houseman
- e University of Oregon, College of Public Health and Human Science , Corvallis , OR
| | - Karl T Kelsey
- b Brown University , Department of Epidemiology , Providence , RI.,c Department of Laboratory Medicine and Pathology , Providence , RI
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26
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Baz A, Groves P, Buttigieg K, Apte SH, Kienzle N, Kelso A. Quantitative assessment of the functional plasticity of memory CD8(+) T cells. Eur J Immunol 2016; 46:863-73. [PMID: 26799367 DOI: 10.1002/eji.201545726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 11/29/2015] [Accepted: 01/15/2016] [Indexed: 01/28/2023]
Abstract
While the functional plasticity of memory CD4(+) T cells has been studied extensively, less is known about this property in memory CD8(+) T cells. Here, we report the direct measurement of plasticity by paired daughter analysis of effector and memory OT-I CD8(+) T cells primed in vivo with ovalbumin. Naïve, effector, and memory OT-I cells were isolated and activated in single-cell culture; then, after the first division, their daughter cells were transferred to new cultures with and without IL-4; expression of IFN-γ and IL-4 mRNAs was measured 5 days later in the resultant subclones. Approximately 40% of clonogenic memory CD8(+) T cells were bipotential in this assay, giving rise to an IL-4(-) subclone in the absence of IL-4 and an IL-4(+) subclone in the presence of IL-4. The frequency of bipotential cells was lower among memory cells than naïve cells but markedly higher than among 8-day effectors. Separation based on high or low expression of CD62L, CD122, CD127, or Ly6C did not identify a phenotypic marker of the bipotential cells. Functional plasticity in memory CD8(+) T-cell populations can therefore reflect modulation at the level of a single memory cell and its progeny.
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Affiliation(s)
- Adriana Baz
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Penny Groves
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Kathy Buttigieg
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Simon H Apte
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Norbert Kienzle
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
| | - Anne Kelso
- Cooperative Research Centre for Vaccine Technology, QIMR Berghofer Medical Research Institute, QLD, Australia
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Nguyen MLT, Jones SA, Prier JE, Russ BE. Transcriptional Enhancers in the Regulation of T Cell Differentiation. Front Immunol 2015; 6:462. [PMID: 26441967 PMCID: PMC4563239 DOI: 10.3389/fimmu.2015.00462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/24/2015] [Indexed: 12/24/2022] Open
Abstract
The changes in phenotype and function that characterize the differentiation of naïve T cells to effector and memory states are underscored by large-scale, coordinated, and stable changes in gene expression. In turn, these changes are choreographed by the interplay between transcription factors and epigenetic regulators that act to restructure the genome, ultimately ensuring lineage-appropriate gene expression. Here, we focus on the mechanisms that control T cell differentiation, with a particular focus on the role of regulatory elements encoded within the genome, known as transcriptional enhancers (TEs). We discuss the central role of TEs in regulating T cell differentiation, both in health and disease.
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Affiliation(s)
- Michelle L T Nguyen
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, VIC , Australia
| | - Sarah A Jones
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health , Melbourne, VIC , Australia
| | - Julia E Prier
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, VIC , Australia
| | - Brendan E Russ
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, VIC , Australia
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Ranasinghe C, Trivedi S, Wijesundara DK, Jackson RJ. IL-4 and IL-13 receptors: Roles in immunity and powerful vaccine adjuvants. Cytokine Growth Factor Rev 2014; 25:437-42. [DOI: 10.1016/j.cytogfr.2014.07.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 07/15/2014] [Indexed: 01/01/2023]
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