1
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Daily KP, Badr A, Eltobgy M, Estfanous S, Whitham O, Tan MH, Carafice C, Krause K, McNamara A, Hamilton K, Houle S, Gupta S, Gupta GA, Madhu S, Fitzgerald J, Saadey AA, Laster B, Yan P, Webb A, Zhang X, Pietrzak M, Kokiko-Cochran ON, Ghoneim HE, Amer AO. DNA hypomethylation promotes the expression of CASPASE-4 which exacerbates inflammation and amyloid-β deposition in Alzheimer's disease. Alzheimers Res Ther 2024; 16:29. [PMID: 38326859 PMCID: PMC10851453 DOI: 10.1186/s13195-024-01390-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Alzheimer's disease (AD) is the sixth leading cause of death in the USA. It is established that neuroinflammation contributes to the synaptic loss, neuronal death, and symptomatic decline of AD patients. Accumulating evidence suggests a critical role for microglia, innate immune phagocytes of the brain. For instance, microglia release pro-inflammatory products such as IL-1β which is highly implicated in AD pathobiology. The mechanisms underlying the transition of microglia to proinflammatory promoters of AD remain largely unknown. To address this gap, we performed reduced representation bisulfite sequencing (RRBS) to profile global DNA methylation changes in human AD brains compared to no disease controls. We identified differential DNA methylation of CASPASE-4 (CASP4), which when expressed promotes the generation of IL-1β and is predominantly expressed in immune cells. DNA upstream of the CASP4 transcription start site was hypomethylated in human AD brains, which was correlated with increased expression of CASP4. Furthermore, microglia from a mouse model of AD (5xFAD) express increased levels of CASP4 compared to wild-type (WT) mice. To study the role of CASP4 in AD, we developed a novel mouse model of AD lacking the mouse ortholog of CASP4 and CASP11, which is encoded by mouse Caspase-4 (5xFAD/Casp4-/-). The expression of CASP11 was associated with increased accumulation of pathologic protein aggregate amyloid-β (Aβ) and increased microglial production of IL-1β in 5xFAD mice. Utilizing RNA-sequencing, we determined that CASP11 promotes unique transcriptomic phenotypes in 5xFAD mouse brains, including alterations of neuroinflammatory and chemokine signaling pathways. Notably, in vitro, CASP11 promoted generation of IL-1β from macrophages in response to cytosolic Aβ through cleavage of downstream effector Gasdermin D (GSDMD). Therefore, here we unravel the role for CASP11 and GSDMD in the generation of IL-1β in response to Aβ and the progression of pathologic inflammation in AD. Overall, our results demonstrate that overexpression of CASP4 due to differential DNA methylation in AD microglia contributes to the progression of AD pathobiology. Thus, we identify CASP4 as a potential target for immunotherapies for the treatment and prevention of AD.
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Affiliation(s)
- Kylene P Daily
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Asmaa Badr
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- Clinical Pathology Department, College of Medicine, Mansoura University, Mansoura, Egypt
| | - Mostafa Eltobgy
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Shady Estfanous
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Owen Whitham
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Michelle H Tan
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Cierra Carafice
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Kathrin Krause
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Andrew McNamara
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Kaitlin Hamilton
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Samuel Houle
- Department of Neuroscience, The Ohio State University, Columbus, OH, 43210, USA
| | - Spandan Gupta
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Gauruv A Gupta
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Shruthi Madhu
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Julie Fitzgerald
- Department of Neuroscience, The Ohio State University, Columbus, OH, 43210, USA
| | - Abbey A Saadey
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Brooke Laster
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Pearlly Yan
- Genomics Shared Resource, Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Xiaoli Zhang
- Center for Biostatistics, Ohio State University, Columbus, OH, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | | | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Amal O Amer
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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2
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Daily KP, Badr A, Eltobgy M, Estfanous S, Whitham O, Tan MH, Carafice C, Krause K, McNamara A, Hamilton K, Houle S, Gupta S, Gupta GA, Madhu S, Fitzgerald J, Saadey AA, Laster B, Yan P, Webb A, Zhang X, Pietrzak M, Kokiko-Cochran ON, Ghoneim HE, Amer AO. DNA hypomethylation promotes the expression of CASPASE-4 which exacerbates neuroinflammation and amyloid-β deposition in Alzheimer's disease The Ohio State University College of Medicine. bioRxiv 2023:2023.08.30.555526. [PMID: 37693600 PMCID: PMC10491177 DOI: 10.1101/2023.08.30.555526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Alzheimer's Disease (AD) is the 6th leading cause of death in the US. It is established that neuroinflammation contributes to the synaptic loss, neuronal death, and symptomatic decline of AD patients. Accumulating evidence suggests a critical role for microglia, innate immune phagocytes of the brain. For instance, microglia release proinflammatory products such as IL-1β which is highly implicated in AD pathobiology. The mechanisms underlying the transition of microglia to proinflammatory promoters of AD remain largely unknown. To address this gap, we performed Reduced Representation Bisulfite Sequencing (RRBS) to profile global DNA methylation changes in human AD brains compared to no disease controls. We identified differential DNA methylation of CASPASE-4 (CASP4), which when expressed, can be involved in generation of IL-1β and is predominantly expressed in immune cells. DNA upstream of the CASP4 transcription start site was hypomethylated in human AD brains, which was correlated with increased expression of CASP4. Furthermore, microglia from a mouse model of AD (5xFAD) express increased levels of CASP4 compared to wild-type (WT) mice. To study the role of CASP4 in AD, we developed a novel mouse model of AD lacking the mouse ortholog of CASP4, CASP11, which is encoded by mouse Caspase-4 (5xFAD/Casp4-/-). The expression of CASP11 was associated with increased accumulation of pathologic protein aggregate amyloid-β (Aβ) and increased microglial production of IL-1β in 5xFAD mice. Utilizing RNA sequencing, we determined that CASP11 promotes unique transcriptomic phenotypes in 5xFAD mouse brains, including alterations of neuroinflammatory and chemokine signaling pathways. Notably, in vitro, CASP11 promoted generation of IL-1β from macrophages in response to cytosolic Aβ through cleavage of downstream effector Gasdermin D (G SDMD). We describe a role for CASP11 and GSDMD in the generation of IL-1β in response to Aβ and the progression of pathologic inflammation in AD. Overall, our results demonstrate that overexpression of CASP4 due to differential methylation in AD microglia contributes to the progression of AD pathobiology, thus identifying CASP4 as a potential target for immunotherapies for the treatment of AD.
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Affiliation(s)
- Kylene P. Daily
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Asmaa Badr
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Mostafa Eltobgy
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Shady Estfanous
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Owen Whitham
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Michelle H. Tan
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Cierra Carafice
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Kathrin Krause
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Andrew McNamara
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Kaitlin Hamilton
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Samuel Houle
- Department of Neuroscience, The Ohio State University, Columbus, Ohio 43210
| | - Spandan Gupta
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Gauruv A. Gupta
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Shruthi Madhu
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Julie Fitzgerald
- Department of Neuroscience, The Ohio State University, Columbus, Ohio 43210
| | - Abbey A. Saadey
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Brooke Laster
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Pearlly Yan
- Genomics Shared Resource, Comprehensive Cancer Center, USA; Department of Internal Medicine, The Ohio State University, USA; The Ohio State University, Columbus, OH 43210, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Xiaoli Zhang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | | | - Hazem E. Ghoneim
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Amal O. Amer
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
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3
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Read KA, Jones DM, Pokhrel S, Hales EDS, Varkey A, Tuazon JA, Eisele CD, Abdouni O, Saadey A, Leonard MR, Warren RT, Powell MD, Boss JM, Hemann EA, Yount JS, Xin G, Ghoneim HE, Lio CWJ, Freud AG, Collins PL, Oestreich KJ. Aiolos represses CD4 + T cell cytotoxic programming via reciprocal regulation of T FH transcription factors and IL-2 sensitivity. Nat Commun 2023; 14:1652. [PMID: 36964178 PMCID: PMC10039023 DOI: 10.1038/s41467-023-37420-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 03/16/2023] [Indexed: 03/26/2023] Open
Abstract
During intracellular infection, T follicular helper (TFH) and T helper 1 (TH1) cells promote humoral and cell-mediated responses, respectively. Another subset, CD4-cytotoxic T lymphocytes (CD4-CTLs), eliminate infected cells via functions typically associated with CD8+ T cells. The mechanisms underlying differentiation of these populations are incompletely understood. Here, we identify the transcription factor Aiolos as a reciprocal regulator of TFH and CD4-CTL programming. We find that Aiolos deficiency results in downregulation of key TFH transcription factors, and consequently reduced TFH differentiation and antibody production, during influenza virus infection. Conversely, CD4-CTL programming is elevated, including enhanced Eomes and cytolytic molecule expression. We further demonstrate that Aiolos deficiency allows for enhanced IL-2 sensitivity and increased STAT5 association with CD4-CTL gene targets, including Eomes, effector molecules, and IL2Ra. Thus, our collective findings identify Aiolos as a pivotal regulator of CD4-CTL and TFH programming and highlight its potential as a target for manipulating CD4+ T cell responses.
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Affiliation(s)
- Kaitlin A Read
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
| | - Devin M Jones
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
| | - Srijana Pokhrel
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Emily D S Hales
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Aditi Varkey
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Jasmine A Tuazon
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
- Medical Scientist Training Program, Columbus, OH, 43210, USA
| | - Caprice D Eisele
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
- Department of Pathology, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Omar Abdouni
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Abbey Saadey
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
| | - Melissa R Leonard
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Combined Anatomic Pathology Residency/PhD Program, The Ohio State University College of Veterinary Medicine, Columbus, USA
| | - Robert T Warren
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Michael D Powell
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Emily A Hemann
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Infectious Diseases Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Infectious Diseases Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Gang Xin
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Chan-Wang J Lio
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Aharon G Freud
- Department of Pathology, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Patrick L Collins
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Kenneth J Oestreich
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA.
- Infectious Diseases Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA.
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4
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Saadey AA, Yousif A, Osborne N, Shahinfar R, Chen YL, Laster B, Rajeev M, Bauman P, Webb A, Ghoneim HE. Rebalancing TGFβ1/BMP signals in exhausted T cells unlocks responsiveness to immune checkpoint blockade therapy. Nat Immunol 2023; 24:280-294. [PMID: 36543960 DOI: 10.1038/s41590-022-01384-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
T cell dysfunctionality prevents the clearance of chronic infections and cancer. Furthermore, epigenetic programming in dysfunctional CD8+ T cells limits their response to immunotherapies, including immune checkpoint blockade (ICB). However, it is unclear which upstream signals drive acquisition of dysfunctional epigenetic programs, and whether therapeutically targeting these signals can remodel terminally dysfunctional T cells to an ICB-responsive state. Here we innovate an in vitro model system of stable human T cell dysfunction and show that chronic TGFβ1 signaling in posteffector CD8+ T cells accelerates their terminal dysfunction through stable epigenetic changes. Conversely, boosting bone morphogenetic protein (BMP) signaling while blocking TGFβ1 preserved effector and memory programs in chronically stimulated human CD8+ T cells, inducing superior responses to tumors and synergizing the ICB responses during chronic viral infection. Thus, rebalancing TGFβ1/BMP signals provides an exciting new approach to unleash dysfunctional CD8+ T cells and enhance T cell immunotherapies.
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Affiliation(s)
- Abbey A Saadey
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Amir Yousif
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Nicole Osborne
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Roya Shahinfar
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Yu-Lin Chen
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Brooke Laster
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Meera Rajeev
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Parker Bauman
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Amy Webb
- Biomedical Informatics Shared Resources, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA.
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA.
- The Pelotonia Institute for Immuno-Oncology, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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5
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Chen HY, Almonte-Loya A, Lay FY, Hsu M, Johnson E, González-Avalos E, Yin J, Bruno RS, Ma Q, Ghoneim HE, Wozniak DJ, Harrison FE, Lio CWJ. Epigenetic remodeling by vitamin C potentiates plasma cell differentiation. eLife 2022; 11:73754. [PMID: 36069787 PMCID: PMC9451539 DOI: 10.7554/elife.73754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Ascorbate (vitamin C) is an essential micronutrient in humans. The severe chronic deficiency of ascorbate, termed scurvy, has long been associated with increased susceptibility to infections. How ascorbate affects the immune system at the cellular and molecular levels remained unclear. From a micronutrient analysis, we identified ascorbate as a potent enhancer for antibody response by facilitating the IL-21/STAT3-dependent plasma cell differentiation in mouse and human B cells. The effect of ascorbate is unique as other antioxidants failed to promote plasma cell differentiation. Ascorbate is especially critical during early B cell activation by poising the cells to plasma cell lineage without affecting the proximal IL-21/STAT3 signaling and the overall transcriptome. As a cofactor for epigenetic enzymes, ascorbate facilitates TET2/3-mediated DNA modification and demethylation of multiple elements at the Prdm1 locus. DNA demethylation augments STAT3 association at the Prdm1 promoter and a downstream enhancer, thus ensuring efficient gene expression and plasma cell differentiation. The results suggest that an adequate level of ascorbate is required for antibody response and highlight how micronutrients may regulate the activity of epigenetic enzymes to regulate gene expression. Our findings imply that epigenetic enzymes can function as sensors to gauge the availability of metabolites and influence cell fate decisions.
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Affiliation(s)
- Heng-Yi Chen
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Ana Almonte-Loya
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Fang-Yun Lay
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Michael Hsu
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Eric Johnson
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Edahí González-Avalos
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Jieyun Yin
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Richard S Bruno
- Human Nutrition Program, The Ohio State University, Columbus, OH, United States
| | - Qin Ma
- Biomedical Informatics, The Ohio State University, Columbus, OH, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Fiona E Harrison
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
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6
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Ghoneim HE, Saadey AA, Yousif A, Osborne N, Chen YL, Laster B, Zayed A, Bauman P. Rebalancing TGFβ1/BMP Signaling Epigenetically Reprograms Fully Exhausted Human CD8 T Cells into a Functional State. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.121.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Epigenetic scarring of exhausted T cells (Tex) remains a major obstacle to achieving durable responses by T cell immunotherapies. While we established that de novo DNA methylation programs are causally linked to T cell’s full exhaustion and poor response to immune checkpoint blockade (ICB), major gaps remain in our current understanding of T cell exhaustion—(1) What are the upstream signals that regulate acquisition of exhaustion-specific epigenetic programs? (2) Can we remodel the epigenetic state of Tex to an ICB-responsive state? To address these questions, we developed a novel in vitro model of human T cell dysfunction. First, we demonstrated that chronic TCR stimulation of CD8 T cells is insufficient to develop T cell exhaustion. Instead, our integrative analyses of epigenetic and transcriptional changes in CD8 T cell subsets during chronic virus infections and cancer revealed TGFβ1 as the most significant upstream regulator linked to full exhaustion in mice and humans. Indeed, we found that post-effector TGFβ1 signaling accelerates full exhaustion in chronically stimulated CD8 T cells through stable epigenetic changes linked to impaired effector function and memory potential. Therapeutic rebalancing of TGFβ1/BMP signals by blocking TGFβ1 while boosting BMP signals not only restored effector function, but also unlocked memory programs in human Tex cells. This new therapeutic approach induced a superior anti-tumor activity of human T cells and synergized the ICB response in a murine model of chronic LCMV infection. Our findings highlight the role of TGFβ1/BMP signals in T cell exhaustion and propose a novel therapeutic strategy to epigenetically reprogram fully exhausted T cells, ultimately enhancing T cell immunotherapies.
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Affiliation(s)
- Hazem E. Ghoneim
- 1Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
- 2The Ohio State University Comprehensive Cancer Center
| | - Abbey A Saadey
- 1Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
| | - Amir Yousif
- 1Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
| | - Nicole Osborne
- 1Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
| | - Yu-Lin Chen
- 1Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
| | - Brooke Laster
- 1Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
| | | | - Parker Bauman
- 1Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
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7
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Read K, Pokhrel S, Jones DM, Saadey A, Eisele C, Warren RT, Collins P, Ghoneim HE, Freud A, Oestreich KJ. Aiolos supports TFH cell differentiation by antagonizing the IL-2/STAT5 signaling pathway. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.112.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
CD4+ T follicular helper (TFH) cells are critical for the generation of robust humoral immune responses, as they provide help to B cells to support the generation of both pathogen-neutralizing antibodies and long-lived plasma cell populations. To date, the mechanisms underlying TFH differentiation are incompletely understood. Here, we identify the transcription factor Aiolos as a key regulator of TFH responses. We find that Aiolos expression is increased in TFH cell populations generated during influenza infection and that Aiolos deficiency results in compromised TFH cell differentiation and B cell helper activity. Mechanistically, loss of Aiolos results in diminished expression of TFH genes, including those encoding the key transcription factors Bcl-6, TCF-1, and Tox. Conversely, expression of genes associated with IL-2/STAT5 signaling, a known antagonist of the TFH gene program, were significantly elevated in Aiolos-deficient settings. Consistent with these data, antigen-specific Aiolos-deficient effector CD4+ T cell populations generated in response to influenza infection exhibited significantly elevated IL-2Rα surface expression. Together, our findings suggest that repression of IL-2/STAT5 signaling represents a novel mechanism by which Aiolos regulates the TFH gene program. These findings are important, as they provide critical insight that may ultimately be leveraged for the development of novel TFH-focused immunotherapies and strategies to improve vaccination approaches.
Supported by a grant from the NIAID (NIH; R01 AI134972), funds through The Ohio State University College of Medicine, and funds through The Ohio State University College of Medicine Advancing Research in Infection and Immunity Fellowship Program
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Affiliation(s)
- Kaitlin Read
- 1Department of Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
- 2Biomedical Sciences Graduate Program, The Ohio State Univ. Col. of Med
| | - Srijana Pokhrel
- 1Department of Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
| | - Devin M Jones
- 1Department of Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
- 2Biomedical Sciences Graduate Program, The Ohio State Univ. Col. of Med
| | - Abbey Saadey
- 1Department of Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
- 2Biomedical Sciences Graduate Program, The Ohio State Univ. Col. of Med
| | - Caprice Eisele
- 2Biomedical Sciences Graduate Program, The Ohio State Univ. Col. of Med
- 3Department of Pathology, The Ohio State Univ. Col. of Med
| | - Robert T Warren
- 1Department of Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
| | - Patrick Collins
- 1Department of Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
- 4Pelotonia Institute for Immuno-oncology, The Ohio State Univ. Col. of Med
| | - Hazem E. Ghoneim
- 1Department of Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
- 4Pelotonia Institute for Immuno-oncology, The Ohio State Univ. Col. of Med
| | - Aharon Freud
- 3Department of Pathology, The Ohio State Univ. Col. of Med
| | - Kenneth J Oestreich
- 1Department of Microbial Infection and Immunity, The Ohio State Univ. Col. of Med
- 4Pelotonia Institute for Immuno-oncology, The Ohio State Univ. Col. of Med
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8
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Abstract
Cell identity and function largely rely on the programming of transcriptomes during development and differentiation. Signature gene expression programs are orchestrated by regulatory circuits consisting of cis-acting promoters and enhancers, which respond to a plethora of cues via the action of transcription factors. In turn, transcription factors direct epigenetic modifications to revise chromatin landscapes, and drive contacts between distal promoter-enhancer combinations. In immune cells, regulatory circuits for effector genes are especially complex and flexible, utilizing distinct sets of transcription factors and enhancers, depending on the cues each cell type receives during an infection, after sensing cellular damage, or upon encountering a tumor. Here, we review major players in the coordination of gene regulatory programs within innate and adaptive immune cells, as well as integrative omics approaches that can be leveraged to decipher their underlying circuitry. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ankita Saini
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Patrick L Collins
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
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9
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Zebley CC, Abdelsamed HA, Ghoneim HE, Alli S, Brown C, Haydar D, Mi T, Harris T, McGargill MA, Krenciute G, Youngblood B. Proinflammatory cytokines promote TET2-mediated DNA demethylation during CD8 T cell effector differentiation. Cell Rep 2021; 37:109796. [PMID: 34644568 PMCID: PMC8593824 DOI: 10.1016/j.celrep.2021.109796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 07/30/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
To gain insight into the signaling determinants of effector-associated DNA methylation programming among CD8 T cells, we explore the role of interleukin (IL)-12 in the imprinting of IFNg expression during CD8 T cell priming. We observe that anti-CD3/CD28-mediated stimulation of human naive CD8 T cells is not sufficient to induce substantial demethylation of the IFNg promoter. However, anti-CD3/CD28 stimulation in the presence of the inflammatory cytokine, IL-12, results in stable demethylation of the IFNg locus that is commensurate with IFNg expression. IL-12-associated demethylation of the IFNg locus is coupled to cell division through TET2-dependent demethylation in an ex vivo human chimeric antigen receptor T cell model system and an in vivo immunologically competent murine system. Collectively, these data illustrate that IL-12 signaling promotes TET2-mediated effector DNA demethylation programming in CD8 T cells and serve as proof of concept that cytokines can guide induction of epigenetically regulated traits for T cell-based immunotherapies.
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Affiliation(s)
- Caitlin C Zebley
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shanta Alli
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charmaine Brown
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dalia Haydar
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tian Mi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tarsha Harris
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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10
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LeMessurier KS, Rooney R, Ghoneim HE, Liu B, Li K, Smallwood HS, Samarasinghe AE. Influenza A virus directly modulates mouse eosinophil responses. J Leukoc Biol 2020; 108:151-168. [PMID: 32386457 DOI: 10.1002/jlb.4ma0320-343r] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 12/14/2022] Open
Abstract
Allergic asthma and influenza are common respiratory diseases with a high probability of co-occurrence. During the 2009 influenza pandemic, hospitalized patients with influenza experienced lower morbidity if asthma was an underlying condition. We have previously demonstrated that acute allergic asthma protects mice from severe influenza and have implicated eosinophils in the airways of mice with allergic asthma as participants in the antiviral response. However, very little is known about how eosinophils respond to direct exposure to influenza A virus (IAV) or the microenvironment in which the viral burden is high. We hypothesized that eosinophils would dynamically respond to the presence of IAV through phenotypic, transcriptomic, and physiologic changes. Using our mouse model of acute fungal asthma and influenza, we showed that eosinophils in lymphoid tissues were responsive to IAV infection in the lungs and altered surface expression of various markers necessary for cell activation in a niche-specific manner. Siglec-F expression was altered in a subset of eosinophils after virus exposure, and those expressing high Siglec-F were more active (IL-5Rαhi CD62Llo ). While eosinophils exposed to IAV decreased their overall transcriptional activity and mitochondrial oxygen consumption, transcription of genes encoding viral recognition proteins, Ddx58 (RIG-I), Tlr3, and Ifih1 (MDA5), were up-regulated. CD8+ T cells from IAV-infected mice expanded in response to IAV PB1 peptide-pulsed eosinophils, and CpG methylation in the Tbx21 promoter was reduced in these T cells. These data offer insight into how eosinophils respond to IAV and help elucidate alternative mechanisms by which they regulate antiviral immune responses during IAV infection.
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Affiliation(s)
- Kim S LeMessurier
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Children's Foundation Research Institute, Memphis, Tennessee, USA
| | - Robert Rooney
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Department of Genetics, Genomics & Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Children's Foundation Research Institute, Memphis, Tennessee, USA
| | - Hazem E Ghoneim
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Microbial Infection and Immunity, College of Medicine, Ohio State University, Columbus, Ohio, USA
| | - Baoming Liu
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kui Li
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Heather S Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Children's Foundation Research Institute, Memphis, Tennessee, USA
| | - Amali E Samarasinghe
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Children's Foundation Research Institute, Memphis, Tennessee, USA
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11
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Quarnstrom CF, Fonseca R, Beura LK, Ghoneim HE, Fan Y, Zebley CC, Scott MC, Fares-Frederickson NJ, Wijeyesinghe SP, Thompson EA, da Silva HB, Vezys V, Youngblood BA, Masopust D. Developmental plasticity allows outside-in immune responses by resident memory T cells. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.81.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Central memory T (TCM) cells patrol lymph nodes and perform conventional memory responses upon re-stimulation: proliferation, migration, and differentiation into diverse T cell subsets while also self-renewing. Resident memory T (TRM) cells are parked within single organs, share properties with terminal effectors, and contribute to rapid host protection. We observed that reactivated TRM cells rejoined the circulating pool. Epigenetic analyses revealed that TRM cells align closely with conventional memory T cell populations, bearing little resemblance to recently activated effectors. Fully differentiated TRM cells isolated from small intestine epithelium exhibited the potential to differentiate into TCM, TEM, and TRM cells upon recall. Ex-TRM cells, former intestinal TRM that rejoined the circulating pool, heritably maintained a predilection for homing back to their tissue of origin upon subsequent reactivation and a heightened capacity to re-differentiate into TRM cells. Thus, TRM cells can rejoin the circulation but are advantaged to re-form local TRM when called upon.
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Affiliation(s)
- Clare F Quarnstrom
- 1Dept. of Microbiology and Immunology, Center for Immunology, University of Minnesota
| | - Raissa Fonseca
- 2The Peter Doherty Institute for Infection and Immunity, Univ. Melbourne
| | - Lalit K Beura
- 3Dept. of Molecular Microbiology and Immunology, Brown University
| | | | | | | | - Milcah C Scott
- 1Dept. of Microbiology and Immunology, Center for Immunology, University of Minnesota
| | | | - Sathi P Wijeyesinghe
- 1Dept. of Microbiology and Immunology, Center for Immunology, University of Minnesota
| | - Emily A Thompson
- 1Dept. of Microbiology and Immunology, Center for Immunology, University of Minnesota
| | | | - Vaiva Vezys
- 1Dept. of Microbiology and Immunology, Center for Immunology, University of Minnesota
| | | | - David Masopust
- 1Dept. of Microbiology and Immunology, Center for Immunology, University of Minnesota
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12
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Read K, Sreekumar B, Powell MD, Jones DM, Zafar S, Ghoneim HE, Collins PL, Oestreich KJ. Eos supports TH1 differentiation through feed-forward propagation of the IL-2/STAT5 signaling pathway. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.76.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The Ikaros zinc finger (IkZF) transcription factor Eos is a known regulator of CD4+ regulatory T cell (TREG) populations. However, its role in the differentiation of other CD4+ T cell subsets is unknown. Here, we find that Eos deficiency results in both compromised TH1 cell differentiation and reduced production of the TH1 effector cytokine IFN-γ. Historically, IkZF factors have been associated with changes in gene expression via the alteration of chromatin structure. However, ATAC-seq analysis indicated that there were minimal changes in chromatin accessibility between wild type and Eos-deficient cells cultured under TH1-polarizing conditions. Rather, we find that IL-2 signaling promotes the STAT5-dependent induction of Eos expression, and that Eos both interacts with STAT5 and supports tyrosine phosphorylation-mediated STAT5 activation. Consequently, STAT5 enrichment is reduced at TH1 target genes in the absence of Eos. Thus, modulation of STAT5 signaling represents a novel mechanism by which Eos positively regulates the TH1 gene program. Given the important role for IL-2/STAT5 signaling in the differentiation of TH2, TH9, and TREG cell subsets, it will be of interest to determine whether this mechanism is conserved across additional CD4+ T cell populations.
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13
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Abdelsamed HA, Zebley CC, Nguyen H, Rutishauser RL, Fan Y, Ghoneim HE, Crawford JC, Alfei F, Alli S, Ribeiro SP, Castellaw AH, McGargill MA, Jin H, Boi SK, Speake C, Serti E, Turka LA, Busch ME, Stone M, Deeks SG, Sekaly RP, Zehn D, James EA, Nepom GT, Youngblood B. Beta cell-specific CD8 + T cells maintain stem cell memory-associated epigenetic programs during type 1 diabetes. Nat Immunol 2020; 21:578-587. [PMID: 32231298 PMCID: PMC7183435 DOI: 10.1038/s41590-020-0633-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 02/08/2020] [Indexed: 12/22/2022]
Abstract
The pool of beta cell-specific CD8+ T-cells in type 1 diabetes (T1D) sustains an autoreactive potential despite having access to a constant source of antigen. To investigate the long-lived nature of these cells, we established a DNA methylation-based T cell “multipotency index” and found that beta cell-specific CD8+ T-cells retained a stem-like epigenetic multipotency score. Single cell ATAC-seq analysis confirmed the co-existence of naive and effector-associated epigenetic programs in individual beta cell-specific CD8+ T-cells. Assessment of beta cell-specific CD8+ T-cell anatomical distribution and the establishment of stem-associated epigenetic programs revealed that self-reactive CD8+ T-cells isolated from murine lymphoid tissue retained developmentally plastic phenotypic and epigenetic profiles relative to the same cells isolated from the pancreas. Collectively, these data provide new insight into the longevity of beta cell-specific CD8+ T cell responses, and document the utility of this novel methylation-based multipotency index for investigating human and mouse CD8+ T-cell differentiation.
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Affiliation(s)
- Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Caitlin C Zebley
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hai Nguyen
- Translational Research Program, Benaroya Research Institute, Seattle, WA, USA
| | - Rachel L Rutishauser
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Francesca Alfei
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Shanta Alli
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ashley H Castellaw
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shannon K Boi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cate Speake
- Diabetes Research Program, Benaroya Research Institute, Seattle, WA, USA
| | | | - Laurence A Turka
- Immune Tolerance Network, Bethesda, MD, USA.,Center for Translational Sciences, Department of Surgery, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | | | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Eddie A James
- Translational Research Program, Benaroya Research Institute, Seattle, WA, USA
| | - Gerald T Nepom
- Translational Research Program, Benaroya Research Institute, Seattle, WA, USA.,Immune Tolerance Network, Bethesda, MD, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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14
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Fonseca R, Beura LK, Quarnstrom CF, Ghoneim HE, Fan Y, Zebley CC, Scott MC, Fares-Frederickson NJ, Wijeyesinghe S, Thompson EA, Borges da Silva H, Vezys V, Youngblood B, Masopust D. Developmental plasticity allows outside-in immune responses by resident memory T cells. Nat Immunol 2020; 21:412-421. [PMID: 32066954 PMCID: PMC7096285 DOI: 10.1038/s41590-020-0607-7] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/17/2020] [Indexed: 01/02/2023]
Abstract
Central memory T (TCM) cells patrol lymph nodes and perform conventional memory responses on restimulation: proliferation, migration and differentiation into diverse T cell subsets while also self-renewing. Resident memory T (TRM) cells are parked within single organs, share properties with terminal effectors and contribute to rapid host protection. We observed that reactivated TRM cells rejoined the circulating pool. Epigenetic analyses revealed that TRM cells align closely with conventional memory T cell populations, bearing little resemblance to recently activated effectors. Fully differentiated TRM cells isolated from small intestine epithelium exhibited the potential to differentiate into TCM cells, effector memory T cells and TRM cells on recall. Ex-TRM cells, former intestinal TRM cells that rejoined the circulating pool, heritably maintained a predilection for homing back to their tissue of origin on subsequent reactivation and a heightened capacity to redifferentiate into TRM cells. Thus, TRM cells can rejoin the circulation but are advantaged to re-form local TRM when called on.
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Affiliation(s)
- Raissa Fonseca
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA.,Department of Microbiology and Immunology, University of Melbourne and the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lalit K Beura
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA.,Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Clare F Quarnstrom
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Hazem E Ghoneim
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.,Department of Microbial Infection and Immunity, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Yiping Fan
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Caitlin C Zebley
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Milcah C Scott
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Nancy J Fares-Frederickson
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Sathi Wijeyesinghe
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Emily A Thompson
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Henrique Borges da Silva
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Vaiva Vezys
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Benjamin Youngblood
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David Masopust
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA.
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15
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Alfei F, Kanev K, Hofmann M, Wu M, Ghoneim HE, Roelli P, Utzschneider DT, von Hoesslin M, Cullen JG, Fan Y, Eisenberg V, Wohlleber D, Steiger K, Merkler D, Delorenzi M, Knolle PA, Cohen CJ, Thimme R, Youngblood B, Zehn D. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 2019; 571:265-269. [DOI: 10.1038/s41586-019-1326-9] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 05/30/2019] [Indexed: 02/07/2023]
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16
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Youngblood BA, Ghoneim HE, Abdelsamed HA, Moustaki A, Fan Y, Crawford J, Thomas PG, Stewart E, Federico S. De novo DNA methylation programs regulate T cell exhaustion and limit T cell-based immunotherapies. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.134.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
T cell-based immunotherapies have emerged as one of the most promising frontiers in the fight against cancer and chronic infections. However, it has become clear that prolonged exposure of T cells to their cognate antigen drives them toward a terminally differentiated state, limiting their capacity to mount an effector response. The commitment of T cells to this “exhausted” fate is currently a major barrier in the advancement of T cell immunotherapy efforts. To better understand mechanisms that reinforce the T cell exhaustion gene expression program, we investigated the role of de novo epigenetic programming in establishing exhausted T cells that are non-responsive during immune checkpoint blockade (ICB) therapy. Using mouse models of tumor and chronic viral infection, we observed that genetic deletion of the de novo DNA methyltransferase, Dnmt3a, in antigen-specific T cells that are chronically stimulated allowed them to remain highly functional despite expressing high levels of the checkpoint inhibitory receptor PD-1. Furthermore, PD-1 blockade treatment resulted in massive expansion of PD-1+ Dnmt3a-deficient antigen-specific T cells. Building upon the findings from our murine studies, we have generated whole-genome DNA methylation profiles of human CD8 T cells from a wide array of differentiation states, and established an epigenetic-based human T cell multipotency index. Using this index, we report that tumor-associated PD-1hi CD8 T cells from pediatric solid tumors acquire an epigenetically reinforced terminal differentiation program. Collectively, these data establish Dnmt3a-mediated de novo DNA methylation programming as a key factor in limiting CD8 T cell-based immunotherapuetic approaches.
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17
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Ghoneim HE, Fan Y, Moustaki A, Abdelsamed H, Dash P, Dogra P, Carter R, Awad W, Neale G, Thomas PG, Youngblood B. Abstract A26: De novo epigenetic programming restrains PD-1 blockade-mediated T cell rejuvenation. Cancer Immunol Res 2018. [DOI: 10.1158/2326-6074.tumimm17-a26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immune checkpoint blockade (ICB)-mediated rejuvenation of exhausted T cells has emerged as a promising approach for treating various cancers and chronic infections. However, T cells that become fully exhausted during prolonged antigen exposure remain refractory to ICB-mediated rejuvenation. Given that many of the impaired effector properties of terminally exhausted CD8 T cells appear to be heritably maintained even in the absence of antigen, we investigated the role of de novo DNA methylation programming as a cell-intrinsic mechanism for establishing the ICB-nonresponsive state of T-cell exhaustion. We report that blocking de novo DNA methylation in activated CD8 T cells allows them to retain their effector functions despite chronic stimulation during a persistent viral infection. Whole-genome bisulfite sequencing of antigen-specific murine CD8 T cells at the effector and exhaustion stages of an immune response identified progressively acquired heritable de novo methylation programs that restrict T cell expansion and clonal diversity during PD-1 blockade treatment. Moreover, these exhaustion-associated DNA methylation programs were acquired in tumor-infiltrating PD-1hi CD8 T cells. Therapeutic approaches to reverse these programs can enhance ICB-mediated T cell rejuvenation and ultimately facilitate the control of chronic viral infections and tumor growth. These data establish de novo DNA methylation programming as a regulator of T cell exhaustion and barrier of ICB therapy.
Citation Format: Hazem E. Ghoneim, Yiping Fan, Ardiana Moustaki, Hossam Abdelsamed, Pradyot Dash, Pranay Dogra, Robert Carter, Walid Awad, Geoff Neale, Paul G. Thomas, Ben Youngblood. De novo epigenetic programming restrains PD-1 blockade-mediated T cell rejuvenation [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr A26.
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Affiliation(s)
| | - Yiping Fan
- St. Jude Children’s Research Hospital, Memphis, TN
| | | | | | - Pradyot Dash
- St. Jude Children’s Research Hospital, Memphis, TN
| | - Pranay Dogra
- St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Walid Awad
- St. Jude Children’s Research Hospital, Memphis, TN
| | - Geoff Neale
- St. Jude Children’s Research Hospital, Memphis, TN
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Youngblood B, Hale JS, Kissick HT, Ahn E, Xu X, Wieland A, Araki K, West EE, Ghoneim HE, Fan Y, Dogra P, Davis CW, Konieczny BT, Antia R, Cheng X, Ahmed R. Effector CD8 T cells dedifferentiate into long-lived memory cells. Nature 2017; 552:404-409. [PMID: 29236683 PMCID: PMC5965677 DOI: 10.1038/nature25144] [Citation(s) in RCA: 315] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/17/2017] [Indexed: 01/20/2023]
Abstract
Memory CD8 T cells that circulate in the blood and are present in lymphoid organs are an essential component of long-lived T cell immunity. These memory CD8 T cells remain poised to rapidly elaborate effector functions upon re-exposure to pathogens, but also have many properties in common with naive cells, including pluripotency and the ability to migrate to the lymph nodes and spleen. Thus, memory cells embody features of both naive and effector cells, fuelling a long-standing debate centred on whether memory T cells develop from effector cells or directly from naive cells. Here we show that long-lived memory CD8 T cells are derived from a subset of effector T cells through a process of dedifferentiation. To assess the developmental origin of memory CD8 T cells, we investigated changes in DNA methylation programming at naive and effector cell-associated genes in virus-specific CD8 T cells during acute lymphocytic choriomeningitis virus infection in mice. Methylation profiling of terminal effector versus memory-precursor CD8 T cell subsets showed that, rather than retaining a naive epigenetic state, the subset of cells that gives rise to memory cells acquired de novo DNA methylation programs at naive-associated genes and became demethylated at the loci of classically defined effector molecules. Conditional deletion of the de novo methyltransferase Dnmt3a at an early stage of effector differentiation resulted in reduced methylation and faster re-expression of naive-associated genes, thereby accelerating the development of memory cells. Longitudinal phenotypic and epigenetic characterization of the memory-precursor effector subset of virus-specific CD8 T cells transferred into antigen-free mice revealed that differentiation to memory cells was coupled to erasure of de novo methylation programs and re-expression of naive-associated genes. Thus, epigenetic repression of naive-associated genes in effector CD8 T cells can be reversed in cells that develop into long-lived memory CD8 T cells while key effector genes remain demethylated, demonstrating that memory T cells arise from a subset of fate-permissive effector T cells.
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Affiliation(s)
- Ben Youngblood
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - J Scott Hale
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Haydn T Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Eunseon Ahn
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Xiaojin Xu
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Andreas Wieland
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Koichi Araki
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Erin E West
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Pranay Dogra
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Carl W Davis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Bogumila T Konieczny
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Dogra P, Ghoneim HE, Abdelsamed HA, Youngblood B. Generating long-lived CD8(+) T-cell memory: Insights from epigenetic programs. Eur J Immunol 2017; 46:1548-62. [PMID: 27230488 DOI: 10.1002/eji.201545550] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/28/2016] [Accepted: 05/24/2016] [Indexed: 12/13/2022]
Abstract
T-cell-based immunological memory has the potential to provide the host with life-long protection against pathogen reexposure and thus offers tremendous promise for the design of vaccines targeting chronic infections or cancer. In order to exploit this potential in the design of new vaccines, it is necessary to understand how and when memory T cells acquire their poised effector potential, and moreover, how they maintain these properties during homeostatic proliferation. To gain insight into the persistent nature of memory T-cell functions, investigators have turned their attention to epigenetic mechanisms. Recent efforts have revealed that many of the properties acquired among memory T cells are coupled to stable changes in DNA methylation and histone modifications. Furthermore, it has recently been reported that the delineating features among memory T cells subsets are also linked to distinct epigenetic events, such as permissive and repressive histone modifications and DNA methylation programs, providing exciting new hypotheses regarding their cellular ancestry. Here, we review recent studies focused on epigenetic programs acquired during effector and memory T-cell differentiation and discuss how these data may shed new light on the developmental path for generating long-lived CD8(+) T-cell memory.
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Affiliation(s)
- Pranay Dogra
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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Ghoneim HE, Fan Y, Moustaki A, Abdelsamed HA, Dash P, Dogra P, Carter R, Awad W, Neale G, Thomas PG, Youngblood B. De Novo Epigenetic Programs Inhibit PD-1 Blockade-Mediated T Cell Rejuvenation. Cell 2017. [PMID: 28648661 DOI: 10.1016/j.cell.2017.06.007] [Citation(s) in RCA: 482] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immune-checkpoint-blockade (ICB)-mediated rejuvenation of exhausted T cells has emerged as a promising approach for treating various cancers and chronic infections. However, T cells that become fully exhausted during prolonged antigen exposure remain refractory to ICB-mediated rejuvenation. We report that blocking de novo DNA methylation in activated CD8 T cells allows them to retain their effector functions despite chronic stimulation during a persistent viral infection. Whole-genome bisulfite sequencing of antigen-specific murine CD8 T cells at the effector and exhaustion stages of an immune response identified progressively acquired heritable de novo methylation programs that restrict T cell expansion and clonal diversity during PD-1 blockade treatment. Moreover, these exhaustion-associated DNA-methylation programs were acquired in tumor-infiltrating PD-1hi CD8 T cells, and approaches to reverse these programs improved T cell responses and tumor control during ICB. These data establish de novo DNA-methylation programming as a regulator of T cell exhaustion and barrier of ICB-mediated T cell rejuvenation.
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Affiliation(s)
- Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ardiana Moustaki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pranay Dogra
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert Carter
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Geoff Neale
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Abdelsamed HA, Moustaki A, Fan Y, Dogra P, Ghoneim HE, Zebley CC, Triplett BM, Sekaly RP, Youngblood B. Human memory CD8 T cell effector potential is epigenetically preserved during in vivo homeostasis. J Exp Med 2017; 214:1593-1606. [PMID: 28490440 PMCID: PMC5461005 DOI: 10.1084/jem.20161760] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 02/16/2017] [Accepted: 04/04/2017] [Indexed: 12/15/2022] Open
Abstract
Abdelsamed et al. demonstrate that the poised effector potential of human memory CD8 T cells is coupled to maintenance of effector-associated DNA methylation programs during in vitro and in vivo homeostatic proliferation. Antigen-independent homeostasis of memory CD8 T cells is vital for sustaining long-lived T cell–mediated immunity. In this study, we report that maintenance of human memory CD8 T cell effector potential during in vitro and in vivo homeostatic proliferation is coupled to preservation of acquired DNA methylation programs. Whole-genome bisulfite sequencing of primary human naive, short-lived effector memory (TEM), and longer-lived central memory (TCM) and stem cell memory (TSCM) CD8 T cells identified effector molecules with demethylated promoters and poised for expression. Effector-loci demethylation was heritably preserved during IL-7– and IL-15–mediated in vitro cell proliferation. Conversely, cytokine-driven proliferation of TCM and TSCM memory cells resulted in phenotypic conversion into TEM cells and was coupled to increased methylation of the CCR7 and Tcf7 loci. Furthermore, haploidentical donor memory CD8 T cells undergoing in vivo proliferation in lymphodepleted recipients also maintained their effector-associated demethylated status but acquired TEM-associated programs. These data demonstrate that effector-associated epigenetic programs are preserved during cytokine-driven subset interconversion of human memory CD8 T cells.
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Affiliation(s)
- Hossam A Abdelsamed
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Ardiana Moustaki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Pranay Dogra
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Caitlin C Zebley
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Brandon M Triplett
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105
| | | | - Ben Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
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Ghoneim HE, Zamora AE, Thomas PG, Youngblood BA. Cell-Intrinsic Barriers of T Cell-Based Immunotherapy. Trends Mol Med 2016; 22:1000-1011. [PMID: 27825667 DOI: 10.1016/j.molmed.2016.10.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
Prolonged exposure of CD8+ T cells to their cognate antigen can result in exhaustion of effector functions enabling the persistence of infected or transformed cells. Recent advances in strategies to rejuvenate host effector function using Immune Checkpoint Blockade have resulted in tremendous success towards the treatment of several cancers. However, it is unclear if T cell rejuvenation results in long-lived antitumor functions. Emerging evidence suggests that T cell exhaustion may also represent a significant impediment in sustaining long-lived antitumor activity by chimeric antigen receptor T cells. Here, we discuss current findings regarding transcriptional regulation during T cell exhaustion and address the hypothesis that epigenetics may be a potential barrier to achieving the maximum benefit of T cell-based immunotherapies.
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Affiliation(s)
- Hazem E Ghoneim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA; Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Anthony E Zamora
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ben A Youngblood
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Youngblood BA, Ghoneim HE, Abdelsamed HA, Carter R, Hale JS, Ahn E, Im S, Ahmed R. T cell exhaustion is Reinforced by Progressive De novo DNA Methylation Programming. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.214.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Antigen-specific CD8 T cells play a critical role in controlling chronic infections and cancer, but progressively lose their effector functions during prolonged antigen exposure. Repression of CD8 T cell effector functions, commonly referred to as T cell exhaustion, limits the ability of the immune system to purge the chronic pathogen from the host. It has recently become recognized that CD8 T cell exhaustion programs can be reinforced and heritably maintained. Therefore in order to develop and/or improve current therapeutic approaches that utilize host antigen-specific T cells to treat chronic infections or cancer a major challenge for the field is to identify mechanisms that stabilize T cell exhaustion. We have recently found that epigenetic modifications acquired in pathogen-specific CD8 T cells during prolonged antigen exposure reinforce T cell exhaustion. Using the LCMV model system of chronic viral infection we investigated the role of Dnmt3a mediated de novo DNA methylation in regulating CD8 T cell exhaustion. Strikingly, conditional deletion of Dnmt3a in activated CD8 T cells blocked the cells from becoming exhausted. Longitudinal analysis of whole-genome methylation programming of WT and Dnmt3a cKO CD8 T cells from chronically infected animals reveals progressive acquisition of Dnmt3a-dependent DNA methylation programs in genes, including interferon gamma, that are coupled to the progressive decline of effector functions. These results have significant implications for therapeutic strategies that utilize reactivation of host pathogen-specific CD8 T cells to control chronic viral infections or cancer and provide a nucleotide-resolution map of epigenetic programs progressively acquired during T cell exhaustion.
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Ghoneim HE, McCullers JA. Adjunctive corticosteroid therapy improves lung immunopathology and survival during severe secondary pneumococcal pneumonia in mice. J Infect Dis 2013; 209:1459-68. [PMID: 24273183 DOI: 10.1093/infdis/jit653] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Secondary bacterial pneumonia is a significant cause of morbidity and mortality during influenza, despite routine use of standard antibiotics. Antibiotic-induced immunopathology associated with bacterial cell wall lysis has been suggested to contribute to these poor outcomes. Using Streptococcus pneumoniae in a well-established murine model of secondary bacterial pneumonia (SBP) following influenza, we stratified disease severity based on pneumococcal load in the lungs via in vivo bioluminescence imaging. Ampicillin treatment cured mice with mild pneumonia but was ineffective against severely pneumonic mice, despite effective bacterial killing. Adjunctive dexamethasone therapy improved ampicillin-induced immunopathology and improved outcomes in mice with severe SBP. However, early dexamethasone therapy during primary influenza infection impaired lung adaptive immunity as manifest by increased viral titers, with an associated loss of its protective functions in SBP. These data support adjunctive clinical use of corticosteroids in severe cases of community-acquired pneumonia.
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Affiliation(s)
- Hazem E Ghoneim
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
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Ghoneim HE, Thomas PG, McCullers JA. Depletion of alveolar macrophages during influenza infection facilitates bacterial superinfections. J Immunol 2013; 191:1250-9. [PMID: 23804714 DOI: 10.4049/jimmunol.1300014] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Viruses such as influenza suppress host immune function by a variety of methods. This may result in significant morbidity through several pathways, including facilitation of secondary bacterial pneumonia from pathogens such as Streptococcus pneumoniae. PKH26-phagocytic cell labeling dye was administered intranasally to label resident alveolar macrophages (AMs) in a well-established murine model before influenza infection to determine turnover kinetics during the course of infection. More than 90% of resident AMs were lost in the first week after influenza, whereas the remaining cells had a necrotic phenotype. To establish the impact of this innate immune defect, influenza-infected mice were challenged with S. pneumoniae. Early AM-mediated bacterial clearance was significantly impaired in influenza-infected mice: ~50% of the initial bacterial inoculum could be harvested from the alveolar airspace 3 h later. In mock-infected mice, by contrast, >95% of inocula up to 50-fold higher was efficiently cleared. Coinfection during the AM depletion phase caused significant body weight loss and mortality. Two weeks after influenza, the AM population was fully replenished with successful re-establishment of early innate host protection. Local GM-CSF treatment partially restored the impaired early bacterial clearance with efficient protection against secondary pneumococcal pneumonia. We conclude that resident AM depletion occurs during influenza infection. Among other potential effects, this establishes a niche for secondary pneumococcal infection by altering early cellular innate immunity in the lungs, resulting in pneumococcal outgrowth and lethal pneumonia. This novel mechanism will inform development of novel therapeutic approaches to restore lung innate immunity against bacterial superinfections.
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Affiliation(s)
- Hazem E Ghoneim
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Marcelin G, Aldridge JR, Duan S, Ghoneim HE, Rehg J, Marjuki H, Boon ACM, McCullers JA, Webby RJ. Fatal outcome of pandemic H1N1 2009 influenza virus infection is associated with immunopathology and impaired lung repair, not enhanced viral burden, in pregnant mice. J Virol 2011; 85:11208-19. [PMID: 21865394 PMCID: PMC3194964 DOI: 10.1128/jvi.00654-11] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 08/10/2011] [Indexed: 01/22/2023] Open
Abstract
Pandemic A (H1N1) 2009 influenza virus (pH1N1) infection in pregnant women can be severe. The mechanisms that affect infection outcome in this population are not well understood. To address this, pregnant and nonpregnant BALB/c mice were inoculated with the wild-type pH1N1 strain A/California/04/09. To determine whether innate immune responses are associated with severe infection, we measured the innate cells trafficking into the lungs of pregnant versus nonpregnant animals. Increased infiltration of pulmonary neutrophils and macrophages strongly correlated with an elevated mortality in pregnant mice. In agreement with this, the product of nitric oxide (nitrite) and several cytokines associated with recruitment and/or function of these cells were increased in the lungs of pregnant animals. Surprisingly, increased mortality in pregnant mice was not associated with higher virus load because equivalent virus titers and immunohistochemical staining were observed in the nasal cavities or lungs of all mice. To determine whether exacerbated inflammatory responses and elevated cellularity resulted in lung injury, epithelial regeneration was measured. The lungs of pregnant mice exhibited reduced epithelial regeneration, suggesting impaired lung repair. Despite these immunologic alterations, pregnant animals demonstrated equivalent percentages of pulmonary influenza virus-specific CD8(+) T lymphocytes, although they displayed elevated levels of T-regulator lymphocytes (Tregs) in the lung. Also, pregnant mice mounted equal antibody titers in response to virus or immunization with a monovalent inactivated pH1N1 A/California/07/09 vaccine. Therefore, immunopathology likely caused by elevated cellular recruitment is an implicated mechanism of severe pH1N1 infection in pregnant mice.
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Affiliation(s)
| | | | - Susu Duan
- Department of Infectious Diseases, Division of Virology
| | | | - Jerold Rehg
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105
| | - Henju Marjuki
- Department of Infectious Diseases, Division of Virology
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