1
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Cooper L, Xu H, Polmear J, Kealy L, Szeto C, Pang ES, Gupta M, Kirn A, Taylor JJ, Jackson KJL, Broomfield BJ, Nguyen A, Gago da Graça C, La Gruta N, Utzschneider DT, Groom JR, Martelotto L, Parish IA, O'Keeffe M, Scharer CD, Gras S, Good-Jacobson KL. Type I interferons induce an epigenetically distinct memory B cell subset in chronic viral infection. Immunity 2024; 57:1037-1055.e6. [PMID: 38593796 PMCID: PMC11096045 DOI: 10.1016/j.immuni.2024.03.016] [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: 03/08/2023] [Revised: 11/02/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Memory B cells (MBCs) are key providers of long-lived immunity against infectious disease, yet in chronic viral infection, they do not produce effective protection. How chronic viral infection disrupts MBC development and whether such changes are reversible remain unknown. Through single-cell (sc)ATAC-seq and scRNA-seq during acute versus chronic lymphocytic choriomeningitis viral infection, we identified a memory subset enriched for interferon (IFN)-stimulated genes (ISGs) during chronic infection that was distinct from the T-bet+ subset normally associated with chronic infection. Blockade of IFNAR-1 early in infection transformed the chromatin landscape of chronic MBCs, decreasing accessibility at ISG-inducing transcription factor binding motifs and inducing phenotypic changes in the dominating MBC subset, with a decrease in the ISG subset and an increase in CD11c+CD80+ cells. However, timing was critical, with MBCs resistant to intervention at 4 weeks post-infection. Together, our research identifies a key mechanism to instruct MBC identity during viral infection.
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Affiliation(s)
- Lucy Cooper
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hui Xu
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jack Polmear
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Liam Kealy
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christopher Szeto
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Ee Shan Pang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Mansi Gupta
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Alana Kirn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Benjamin J Broomfield
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Angela Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Catarina Gago da Graça
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Nicole La Gruta
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Daniel T Utzschneider
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Joanna R Groom
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Luciano Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia; University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Ian A Parish
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia; John Curtin School of Medical Research, ANU, Canberra, ACT, Australia
| | - Meredith O'Keeffe
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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Wetzel D, Carter ZA, Monteiro MP, Edwards AN, Scharer CD, McBride SM. The pH-responsive SmrR-SmrT system modulates C. difficile antimicrobial resistance, spore formation, and toxin production. Infect Immun 2024; 92:e0046123. [PMID: 38345371 PMCID: PMC10929453 DOI: 10.1128/iai.00461-23] [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: 11/07/2023] [Accepted: 01/23/2024] [Indexed: 02/27/2024] Open
Abstract
Clostridioides difficile is an anaerobic gastrointestinal pathogen that spreads through the environment as dormant spores. To survive, replicate, and sporulate in the host intestine, C. difficile must adapt to a variety of conditions in its environment, including changes in pH, the availability of metabolites, host immune factors, and a diverse array of other species. Prior studies showed that changes in intestinal conditions, such as pH, can affect C. difficile toxin production, spore formation, and cell survival. However, little is understood about the specific genes and pathways that facilitate environmental adaptation and lead to changes in C. difficile cell outcomes. In this study, we investigated two genes, CD2505 and CD2506, that are differentially regulated by pH to determine if they impact C. difficile growth and sporulation. Using deletion mutants, we examined the effects of both genes (herein smrR and smrT) on sporulation frequency, toxin production, and antimicrobial resistance. We determined that SmrR is a repressor of smrRT that responds to pH and suppresses sporulation and toxin production through regulation of the SmrT transporter. Further, we showed that SmrT confers resistance to erythromycin and lincomycin, establishing a connection between the regulation of sporulation and antimicrobial resistance.IMPORTANCEClostridioides difficile is a mammalian pathogen that colonizes the large intestine and produces toxins that lead to severe diarrheal disease. C. difficile is a major threat to public health due to its intrinsic resistance to antimicrobials and its ability to form dormant spores that are easily spread from host to host. In this study, we examined the contribution of two genes, smrR and smrT, on sporulation, toxin production, and antimicrobial resistance. Our results indicate that SmrR represses smrT expression, while production of SmrT increases spore and toxin production, as well as resistance to antibiotics.
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Affiliation(s)
- Daniela Wetzel
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Zavier A. Carter
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Marcos P. Monteiro
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
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3
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Chen W, Hong SH, Jenks SA, Anam FA, Tipton CM, Woodruff MC, Hom JR, Cashman KS, Faliti CE, Wang X, Kyu S, Wei C, Scharer CD, Mi T, Hicks S, Hartson L, Nguyen DC, Khosroshahi A, Lee S, Wang Y, Bugrovsky R, Ishii Y, Lee FEH, Sanz I. Distinct transcriptomes and autocrine cytokines underpin maturation and survival of antibody-secreting cells in systemic lupus erythematosus. Nat Commun 2024; 15:1899. [PMID: 38429276 PMCID: PMC10907730 DOI: 10.1038/s41467-024-46053-w] [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: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 03/03/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multiple autoantibody types, some of which are produced by long-lived plasma cells (LLPC). Active SLE generates increased circulating antibody-secreting cells (ASC). Here, we examine the phenotypic, molecular, structural, and functional features of ASC in SLE. Relative to post-vaccination ASC in healthy controls, circulating blood ASC from patients with active SLE are enriched with newly generated mature CD19-CD138+ ASC, similar to bone marrow LLPC. ASC from patients with SLE displayed morphological features of premature maturation and a transcriptome epigenetically initiated in SLE B cells. ASC from patients with SLE exhibited elevated protein levels of CXCR4, CXCR3 and CD138, along with molecular programs that promote survival. Furthermore, they demonstrate autocrine production of APRIL and IL-10, which contributed to their prolonged in vitro survival. Our work provides insight into the mechanisms of generation, expansion, maturation and survival of SLE ASC.
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Affiliation(s)
- Weirong Chen
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - So-Hee Hong
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
- Department of Microbiology, Ewha Womans University, Seoul, Republic of Korea
| | - Scott A Jenks
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Fabliha A Anam
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Christopher M Tipton
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jennifer R Hom
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Kevin S Cashman
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Caterina Elisa Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Xiaoqian Wang
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Shuya Kyu
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Chungwen Wei
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Tian Mi
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Sakeenah Hicks
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Louise Hartson
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Doan C Nguyen
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Arezou Khosroshahi
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Saeyun Lee
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Youliang Wang
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Regina Bugrovsky
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yusho Ishii
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - F Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA.
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4
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McManus DT, Valanparambil RM, Medina CB, Hu Y, Scharer CD, Sobierajska E, Chang DY, Wieland A, Lee J, Nasti TH, Hashimoto M, Ross JL, Prokhnevska N, Cardenas MA, Gill AL, Clark EC, Abadie K, Kueh HY, Kaye J, Au-Yeung BB, Kissick HT, Ahmed R. Early generation of a precursor CD8 T cell that can adapt to acute or chronic viral infection. Res Sq 2024:rs.3.rs-3922168. [PMID: 38410458 PMCID: PMC10896375 DOI: 10.21203/rs.3.rs-3922168/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Virus specific PD-1+ TCF-1+ TOX+ stem-like CD8+ T cells are essential for maintaining T cell responses during chronic infection and are also critical for PD-1 directed immunotherapy. In this study we have used the mouse model of chronic LCMV infection to examine when these virus specific stem-like CD8+ T cells are generated during the course of chronic infection and what is the role of antigen in maintaining the stem-like program. We found that these stem-like CD8+ T cells are generated early (day 5) during chronic infection and that antigen is essential for maintaining their stem-like program. This early generation of stem-like CD8+ T cells suggested that the fate commitment to this cell population was agnostic to the eventual outcome of infection and the immune system prepares a priori for a potential chronic infection. Indeed, we found that an identical virus specific stem-cell like CD8+ T cell population was also generated during acute LCMV infection but these cells were lost once the virus was cleared. To determine the fate of these early PD-1+TCF-1+TOX+ stem-like CD8+ T cells that are generated during both acute and chronic LCMV infection we set up two reciprocal adoptive transfer experiments. In the first experiment we transferred day 5 stem-like CD8+ T cells from chronically infected into acutely infected mice and examined their differentiation after viral clearance. We found that these early stem-like CD8+ T cells downregulated canonical markers of the chronic stem-like CD8+ T cells and expressed markers (CD127 and CD62L) associated with central memory CD8+ T cells. In the second experiment, we transferred day 5 stem-like cells from acutely infected mice into chronically infected mice and found that these CD8+ T cells could function like resource cells after transfer into a chronic environment by generating effector CD8+ T cells in both lymphoid and non-lymphoid tissues while also maintaining the number of stem-like CD8+ T cells. These findings provide insight into the generation and maintenance of virus specific stem-like CD8+ T cells that play a critical role in chronic viral infection. In particular, our study highlights the early generation of stem-like CD8+ T cells and their ability to adapt to either an acute or chronic infection. These findings are of broad significance since these novel stem-like CD8+ T cells play an important role in not only viral infections but also in cancer and autoimmunity.
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Affiliation(s)
- Daniel T. McManus
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- These authors contributed equally
| | - Rajesh M. Valanparambil
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- These authors contributed equally
| | - Christopher B. Medina
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Yinghong Hu
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ewelina Sobierajska
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel Y. Chang
- Department of Pathology, Mass General Brigham, Harvard Medical School, Boston, MA, USA
| | - Andreas Wieland
- Department of Otolaryngology, The Ohio State University College of Medicine, Columbus, OH
| | - Judong Lee
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Tahseen H. Nasti
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Masao Hashimoto
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - James L. Ross
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nataliya Prokhnevska
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria A. Cardenas
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Amanda L. Gill
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Elisa C. Clark
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Kathleen Abadie
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jonathan Kaye
- Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Byron B. Au-Yeung
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA
| | - Haydn T. Kissick
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
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5
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Eggert J, Zinzow-Kramer WM, Hu Y, Kolawole EM, Tsai YL, Weiss A, Evavold BD, Salaita K, Scharer CD, Au-Yeung BB. Cbl-b mitigates the responsiveness of naive CD8 + T cells that experience extensive tonic T cell receptor signaling. Sci Signal 2024; 17:eadh0439. [PMID: 38319998 PMCID: PMC10897907 DOI: 10.1126/scisignal.adh0439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/07/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Naive T cells experience tonic T cell receptor (TCR) signaling in response to self-antigens presented by major histocompatibility complex (MHC) in secondary lymphoid organs. We investigated how relatively weak or strong tonic TCR signals influence naive CD8+ T cell responses to stimulation with foreign antigens. The heterogeneous expression of Nur77-GFP, a transgenic reporter of tonic TCR signaling, in naive CD8+ T cells suggests variable intensities or durations of tonic TCR signaling. Although the expression of genes associated with acutely stimulated T cells was increased in Nur77-GFPHI cells, these cells were hyporesponsive to agonist TCR stimulation compared with Nur77-GFPLO cells. This hyporesponsiveness manifested as diminished activation marker expression and decreased secretion of IFN-γ and IL-2. The protein abundance of the ubiquitin ligase Cbl-b, a negative regulator of TCR signaling, was greater in Nur77-GFPHI cells than in Nur77-GFPLO cells, and Cbl-b deficiency partially restored the responsiveness of Nur77-GFPHI cells. Our data suggest that the cumulative effects of previously experienced tonic TCR signaling recalibrate naive CD8+ T cell responsiveness. These changes include gene expression changes and negative regulation partially dependent on Cbl-b. This cell-intrinsic negative feedback loop may enable the immune system to restrain naive CD8+ T cells with higher self-reactivity.
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Affiliation(s)
- Joel Eggert
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, 30322, USA
| | - Wendy M. Zinzow-Kramer
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, 30322, USA
| | - Yuesong Hu
- Department of Chemistry, Emory University; Atlanta, 30322, USA
| | - Elizabeth M. Kolawole
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, 84112, USA
| | - Yuan-Li Tsai
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Departments of Medicine and of Microbiology and Immunology, University of California, San Francisco; San Francisco, 94143, USA
| | - Arthur Weiss
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Departments of Medicine and of Microbiology and Immunology, University of California, San Francisco; San Francisco, 94143, USA
| | - Brian D. Evavold
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, 84112, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University; Atlanta, 30322, USA
| | | | - Byron B. Au-Yeung
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University; Atlanta, 30322, USA
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6
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Uddbäck I, Michalets SE, Saha A, Mattingly C, Kost KN, Williams ME, Lawrence LA, Hicks SL, Lowen AC, Ahmed H, Thomsen AR, Russell CJ, Scharer CD, Boss JM, Koelle K, Antia R, Christensen JP, Kohlmeier JE. Prevention of respiratory virus transmission by resident memory CD8 + T cells. Nature 2024; 626:392-400. [PMID: 38086420 PMCID: PMC11040656 DOI: 10.1038/s41586-023-06937-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
An ideal vaccine both attenuates virus growth and disease in infected individuals and reduces the spread of infections in the population, thereby generating herd immunity. Although this strategy has proved successful by generating humoral immunity to measles, yellow fever and polio, many respiratory viruses evolve to evade pre-existing antibodies1. One approach for improving the breadth of antiviral immunity against escape variants is through the generation of memory T cells in the respiratory tract, which are positioned to respond rapidly to respiratory virus infections2-6. However, it is unknown whether memory T cells alone can effectively surveil the respiratory tract to the extent that they eliminate or greatly reduce viral transmission following exposure of an individual to infection. Here we use a mouse model of natural parainfluenza virus transmission to quantify the extent to which memory CD8+ T cells resident in the respiratory tract can provide herd immunity by reducing both the susceptibility of acquiring infection and the extent of transmission, even in the absence of virus-specific antibodies. We demonstrate that protection by resident memory CD8+ T cells requires the antiviral cytokine interferon-γ (IFNγ) and leads to altered transcriptional programming of epithelial cells within the respiratory tract. These results suggest that tissue-resident CD8+ T cells in the respiratory tract can have important roles in protecting the host against viral disease and limiting viral spread throughout the population.
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Affiliation(s)
- Ida Uddbäck
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Sarah E Michalets
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ananya Saha
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Cameron Mattingly
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Kirsten N Kost
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - M Elliott Williams
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Laurel A Lawrence
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Allan R Thomsen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Charles J Russell
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jan P Christensen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob E Kohlmeier
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
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7
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Elliott Williams M, Hardnett FP, Sheth AN, Wein AN, Li ZRT, Radzio-Basu J, Dinh C, Haddad LB, Collins EMB, Ofotokun I, Antia R, Scharer CD, Garcia-Lerma JG, Kohlmeier JE, Swaims-Kohlmeier A. The menstrual cycle regulates migratory CD4 T-cell surveillance in the female reproductive tract via CCR5 signaling. Mucosal Immunol 2024; 17:41-53. [PMID: 37866719 PMCID: PMC10990418 DOI: 10.1016/j.mucimm.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/25/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Despite their importance for immunity against sexually transmitted infections, the composition of female reproductive tract (FRT) memory T-cell populations in response to changes within the local tissue environment under the regulation of the menstrual cycle remains poorly defined. Here, we show that in humans and pig-tailed macaques, the cycle determines distinct clusters of differentiation 4 T-cell surveillance behaviors by subsets corresponding to migratory memory (TMM) and resident memory T cells. TMM displays tissue-itinerant trafficking characteristics, restricted distribution within the FRT microenvironment, and distinct effector responses to infection. Gene pathway analysis by RNA sequencing identified TMM-specific enrichment of genes involved in hormonal regulation and inflammatory responses. FRT T-cell subset fluctuations were discovered that synchronized to cycle-driven CCR5 signaling. Notably, oral administration of a CCR5 antagonist drug blocked TMM trafficking. Taken together, this study provides novel insights into the dynamic nature of FRT memory CD4 T cells and identifies the menstrual cycle as a key regulator of immune surveillance at the site of STI pathogen exposure.
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Affiliation(s)
- M Elliott Williams
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Felica P Hardnett
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anandi N Sheth
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine and Grady Health System, Atlanta, GA, USA
| | - Alexander N Wein
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Zheng-Rong Tiger Li
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jessica Radzio-Basu
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chuong Dinh
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa B Haddad
- Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Elizabeth M B Collins
- Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Igho Ofotokun
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine and Grady Health System, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - J Gerardo Garcia-Lerma
- Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jacob E Kohlmeier
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Alison Swaims-Kohlmeier
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, USA; Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA; Department of Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA, USA.
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8
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Mu DP, Scharer CD, Kaminski NE, Zhang Q. A Multiscale Spatial Modeling Framework for the Germinal Center Response. bioRxiv 2024:2024.01.26.577491. [PMID: 38501122 PMCID: PMC10945589 DOI: 10.1101/2024.01.26.577491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The germinal center response or reaction (GCR) is a hallmark event of adaptive humoral immunity. Unfolding in the B cell follicles of the secondary lymph organs, a GC culminates in the production of high-affinity antibody-secreting plasma cells along with memory B cells. By interacting with follicular dendritic cells (FDC) and T follicular helper (Tfh) cells, GC B cells exhibit complex spatiotemporal dynamics. Driving the B cell dynamics are the intracellular signal transduction and gene regulatory network that responds to cell surface signaling molecules, cytokines, and chemokines. As our knowledge of the GC continues to expand in depth and in scope, mathematical modeling has become an important tool to help disentangle the intricacy of the GCR and inform novel mechanistic and clinical insights. While the GC has been modeled at different granularities, a multiscale spatial simulation framework - integrating molecular, cellular, and tissue-level responses - is still rare. Here, we report our recent progress toward this end with a hybrid stochastic GC framework developed on the Cellular Potts Model-based CompuCell3D platform. Tellurium is used to simulate the B cell intracellular molecular network comprising NF-κB, FOXO1, MYC, AP4, CXCR4, and BLIMP1 that responds to B cell receptor (BCR) and CD40-mediated signaling. The molecular outputs of the network drive the spatiotemporal behaviors of B cells, including cyclic migration between the dark zone (DZ) and light zone (LZ) via chemotaxis; clonal proliferative bursts, somatic hypermutation, and DNA damage-induced apoptosis in the DZ; and positive selection, apoptosis via a death timer, and emergence of plasma cells in the LZ. Our simulations are able to recapitulate key molecular, cellular, and morphological GC events including B cell population growth, affinity maturation, and clonal dominance. This novel modeling framework provides an open-source, customizable, and multiscale virtual GC simulation platform that enables qualitative and quantitative in silico investigations of a range of mechanic and applied research questions in future.
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Sivasami P, Elkins C, Diaz-Saldana PP, Goss K, Peng A, Hamersky M, Bae J, Xu M, Pollack BP, Horwitz EM, Scharer CD, Seldin L, Li C. Obesity-induced dysregulation of skin-resident PPARγ + Treg cells promotes IL-17A-mediated psoriatic inflammation. Immunity 2023; 56:1844-1861.e6. [PMID: 37478855 PMCID: PMC10527179 DOI: 10.1016/j.immuni.2023.06.021] [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: 01/27/2023] [Revised: 05/16/2023] [Accepted: 06/22/2023] [Indexed: 07/23/2023]
Abstract
Obesity is a major risk factor for psoriasis, but how obesity disrupts the regulatory mechanisms that keep skin inflammation in check is unclear. Here, we found that skin was enriched with a unique population of CD4+Foxp3+ regulatory T (Treg) cells expressing the nuclear receptor peroxisome proliferation-activated receptor gamma (PPARγ). PPARγ drove a distinctive transcriptional program and functional suppression of IL-17A+ γδ T cell-mediated psoriatic inflammation. Diet-induced obesity, however, resulted in a reduction of PPARγ+ skin Treg cells and a corresponding loss of control over IL-17A+ γδ T cell-mediated inflammation. Mechanistically, PPARγ+ skin Treg cells preferentially took up elevated levels of long-chain free fatty acids in obese mice, which led to cellular lipotoxicity, oxidative stress, and mitochondrial dysfunction. Harnessing the anti-inflammatory properties of these PPARγ+ skin Treg cells could have therapeutic potential for obesity-associated inflammatory skin diseases.
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Affiliation(s)
- Pulavendran Sivasami
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cody Elkins
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pamela P Diaz-Saldana
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kyndal Goss
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Amy Peng
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael Hamersky
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jennifer Bae
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Miaoer Xu
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Brian P Pollack
- Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA; Department of Dermatology, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Edwin M Horwitz
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lindsey Seldin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA; Department of Dermatology, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chaoran Li
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Dermatology, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA.
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10
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Curtiss ML, Rosenberg AF, Scharer CD, Mousseau B, Benavides NAB, Bradley JE, León B, Steele C, Randall TD, Lund FE. Chitinase-3-like 1 regulates T H2 cells, T FH cells and IgE responses to helminth infection. Front Immunol 2023; 14:1158493. [PMID: 37575256 PMCID: PMC10415220 DOI: 10.3389/fimmu.2023.1158493] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Data from patient cohorts and mouse models of atopic dermatitis, food allergy and asthma strongly support a role for chitinase-3-like-1 protein (CHI3L1) in allergic disease. Methods To address whether Chi3l1 also contributes to TH2 responses following nematode infection, we infected Chi3l1 -/- mice with Heligmosomoides polygyrus (Hp) and analyzed T cell responses. Results As anticipated, we observed impaired TH2 responses in Hp-infected Chi3l1 -/- mice. However, we also found that T cell intrinsic expression of Chi3l1 was required for ICOS upregulation following activation of naïve CD4 T cells and was necessary for the development of the IL-4+ TFH subset, which supports germinal center B cell reactions and IgE responses. We also observed roles for Chi3l1 in TFH, germinal center B cell, and IgE responses to alum-adjuvanted vaccination. While Chi3l1 was critical for IgE humoral responses it was not required for vaccine or infection-induced IgG1 responses. Discussion These results suggest that Chi3l1 modulates IgE responses, which are known to be highly dependent on IL-4-producing TFH cells.
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Affiliation(s)
- Miranda L. Curtiss
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, University of Alabama Birmingham (UAB), Birmingham, AL, United States
- Department of Medicine, Section of Allergy and Immunology, Birmingham VA Medical Center, Birmingham, AL, United States
| | - Alexander F. Rosenberg
- Department of Microbiology, University of Alabama Birmingham (UAB), Birmingham, AL, United States
- Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Betty Mousseau
- Department of Microbiology, University of Alabama Birmingham (UAB), Birmingham, AL, United States
| | - Natalia A. Ballesteros Benavides
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, University of Alabama Birmingham (UAB), Birmingham, AL, United States
- Department of Microbiology, University of Alabama Birmingham (UAB), Birmingham, AL, United States
| | - John E. Bradley
- Department of Medicine, Division of Rheumatology, University of Alabama Birmingham (UAB), Birmingham, AL, United States
| | - Beatriz León
- Department of Microbiology, University of Alabama Birmingham (UAB), Birmingham, AL, United States
| | - Chad Steele
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, United States
| | - Troy D. Randall
- Department of Medicine, Division of Rheumatology, University of Alabama Birmingham (UAB), Birmingham, AL, United States
| | - Frances E. Lund
- Department of Microbiology, University of Alabama Birmingham (UAB), Birmingham, AL, United States
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11
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Chen W, Hong SH, Jenks SA, Anam FA, Tipton CM, Woodruff MC, Hom JR, Cashman KS, Faliti CE, Wang X, Kyu S, Wei C, Scharer CD, Mi T, Hicks S, Hartson L, Nguyen DC, Khosroshahi A, Lee S, Wang Y, Bugrovsky R, Ishii Y, Lee FEH, Sanz I. SLE Antibody-Secreting Cells Are Characterized by Enhanced Peripheral Maturation and Survival Programs. Res Sq 2023:rs.3.rs-3016327. [PMID: 37461641 PMCID: PMC10350208 DOI: 10.21203/rs.3.rs-3016327/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by multiple autoantibodies, some of which are present in high titers in a sustained, B cell-independent fashion consistent with their generation from long-lived plasma cells (LLPC). Active SLE displays high numbers of circulating antibody-secreting cells (ASC). Understanding the mechanisms of generation and survival of SLE ASC would contribute important insight into disease pathogenesis and novel targeted therapies. We studied the properties of SLE ASC through a systematic analysis of their phenotypic, molecular, structural, and functional features. Our results indicate that in active SLE, relative to healthy post-immunization responses, blood ASC contain a much larger fraction of newly generated mature CD19- CD138+ ASC similar to bone marrow (BM) LLPC. SLE ASC were characterized by morphological and structural features of premature maturation. Additionally, SLE ASC express high levels of CXCR4 and CD138, and molecular programs consistent with increased longevity based on pro-survival and attenuated pro-apoptotic pathways. Notably, SLE ASC demonstrate autocrine production of APRIL and IL-10 and experience prolonged in vitro survival. Combined, our findings indicate that SLE ASC are endowed with enhanced peripheral maturation, survival and BM homing potential suggesting that these features likely underlie BM expansion of autoreactive PC.
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Affiliation(s)
- Weirong Chen
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - So-Hee Hong
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Scott A. Jenks
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Fabliha A. Anam
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Christopher M. Tipton
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Matthew C. Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jennifer R. Hom
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Kevin S. Cashman
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Caterina Elisa Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Xiaoqian Wang
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Shuya Kyu
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Chungwen Wei
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Tian Mi
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Sakeenah Hicks
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Louise Hartson
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Doan C. Nguyen
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Arezou Khosroshahi
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Saeyun Lee
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Youliang Wang
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Regina Bugrovsky
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yusho Ishii
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - F. Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
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12
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Zuo Z, Kania AK, Patterson DG, Hicks SL, Maurer J, Gupta M, Boss JM, Scharer CD. CRISPR/Cas9 editing reveals IRF8 regulated gene signatures restraining plasmablast differentiation. Heliyon 2023; 9:e17527. [PMID: 37416674 PMCID: PMC10320122 DOI: 10.1016/j.heliyon.2023.e17527] [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: 11/04/2022] [Revised: 05/24/2023] [Accepted: 06/20/2023] [Indexed: 07/08/2023] Open
Abstract
The transcription factor Interferon regulatory factor 8 (IRF8) is involved in maintaining B cell identity. However, how IRF8 regulates T cell independent B cell responses are not fully characterized. Here, an in vivo CRISPR/Cas9 system was optimized to generate Irf8-deficient murine B cells and used to determine the role of IRF8 in B cells responding to LPS stimulation. Irf8-deficient B cells more readily formed CD138+ plasmablasts in response to LPS with the principal dysregulation occurring at the activated B cell stage. Transcriptional profiling revealed an upregulation of plasma cell associated genes prematurely in activated B cells and a failure to repress the gene expression programs of IRF1 and IRF7 in Irf8-deficient cells. These data expand on the known roles of IRF8 in regulating B cell identity by preventing premature plasma cell formation and highlight how IRF8 helps evolve TLR responses away from the initial activation towards those driving humoral immunity.
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Affiliation(s)
- Zhihong Zuo
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Current Address: Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Anna K. Kania
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Dillon G. Patterson
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sakeenah L. Hicks
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jeffrey Maurer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Mansi Gupta
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
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13
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Geitgey DK, Lee M, Cottrill KA, Jaffe M, Pilcher W, Bhasin S, Randall J, Ross AJ, Salemi M, Castillo-Castrejon M, Kilgore MB, Brown AC, Boss JM, Johnston R, Fitzpatrick AM, Kemp ML, English R, Weaver E, Bagchi P, Walsh R, Scharer CD, Bhasin M, Chandler JD, Haynes KA, Wellberg EA, Henry CJ. The 'omics of obesity in B-cell acute lymphoblastic leukemia. J Natl Cancer Inst Monogr 2023; 2023:12-29. [PMID: 37139973 PMCID: PMC10157791 DOI: 10.1093/jncimonographs/lgad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/28/2022] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 05/05/2023] Open
Abstract
The obesity pandemic currently affects more than 70 million Americans and more than 650 million individuals worldwide. In addition to increasing susceptibility to pathogenic infections (eg, SARS-CoV-2), obesity promotes the development of many cancer subtypes and increases mortality rates in most cases. We and others have demonstrated that, in the context of B-cell acute lymphoblastic leukemia (B-ALL), adipocytes promote multidrug chemoresistance. Furthermore, others have demonstrated that B-ALL cells exposed to the adipocyte secretome alter their metabolic states to circumvent chemotherapy-mediated cytotoxicity. To better understand how adipocytes impact the function of human B-ALL cells, we used a multi-omic RNA-sequencing (single-cell and bulk transcriptomic) and mass spectroscopy (metabolomic and proteomic) approaches to define adipocyte-induced changes in normal and malignant B cells. These analyses revealed that the adipocyte secretome directly modulates programs in human B-ALL cells associated with metabolism, protection from oxidative stress, increased survival, B-cell development, and drivers of chemoresistance. Single-cell RNA sequencing analysis of mice on low- and high-fat diets revealed that obesity suppresses an immunologically active B-cell subpopulation and that the loss of this transcriptomic signature in patients with B-ALL is associated with poor survival outcomes. Analyses of sera and plasma samples from healthy donors and those with B-ALL revealed that obesity is associated with higher circulating levels of immunoglobulin-associated proteins, which support observations in obese mice of altered immunological homeostasis. In all, our multi-omics approach increases our understanding of pathways that may promote chemoresistance in human B-ALL and highlight a novel B-cell-specific signature in patients associated with survival outcomes.
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Affiliation(s)
- Delaney K Geitgey
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
| | - Miyoung Lee
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
| | - Kirsten A Cottrill
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Maya Jaffe
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - William Pilcher
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Swati Bhasin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Jessica Randall
- Emory Integrated Computational Core, Emory University, Atlanta, GA, USA
| | - Anthony J Ross
- Riley Children’s Health, Indiana University Health, Indianapolis, IN, USA
| | - Michelle Salemi
- Proteomics Core Facility, University of California Davis Genome Center, Davis, 95616, CA
| | - Marisol Castillo-Castrejon
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew B Kilgore
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ayjha C Brown
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute, Atlanta, GA, USA
| | - Rich Johnston
- Emory Integrated Computational Core, Emory University, Atlanta, GA, USA
| | - Anne M Fitzpatrick
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Melissa L Kemp
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Emory Integrated Proteomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Eric Weaver
- Shimadzu Scientific Instruments, Columbia, MD, USA
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University School of Medicine, Atlanta, GA, USA
| | - Ryan Walsh
- Shimadzu Scientific Instruments, Columbia, MD, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute, Atlanta, GA, USA
| | - Manoj Bhasin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Atlanta, GA, USA
| | - Joshua D Chandler
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Atlanta, GA, USA
| | - Elizabeth A Wellberg
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Curtis J Henry
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
- Winship Cancer Institute, Atlanta, GA, USA
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14
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Nellore A, Zumaquero E, Scharer CD, Fucile CF, Tipton CM, King RG, Mi T, Mousseau B, Bradley JE, Zhou F, Mutneja S, Goepfert PA, Boss JM, Randall TD, Sanz I, Rosenberg AF, Lund FE. A transcriptionally distinct subset of influenza-specific effector memory B cells predicts long-lived antibody responses to vaccination in humans. Immunity 2023; 56:847-863.e8. [PMID: 36958335 PMCID: PMC10113805 DOI: 10.1016/j.immuni.2023.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 02/18/2021] [Revised: 09/20/2022] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Seasonal influenza vaccination elicits hemagglutinin (HA)-specific memory B (Bmem) cells, and although multiple Bmem cell populations have been characterized, considerable heterogeneity exists. We found that HA-specific human Bmem cells differed in the expression of surface marker FcRL5 and transcriptional factor T-bet. FcRL5+T-bet+ Bmem cells were transcriptionally similar to effector-like memory cells, while T-betnegFcRL5neg Bmem cells exhibited stem-like central memory properties. FcRL5+ Bmem cells did not express plasma-cell-commitment factors but did express transcriptional, epigenetic, metabolic, and functional programs that poised these cells for antibody production. Accordingly, HA+ T-bet+ Bmem cells at day 7 post-vaccination expressed intracellular immunoglobulin, and tonsil-derived FcRL5+ Bmem cells differentiated more rapidly into antibody-secreting cells (ASCs) in vitro. The T-bet+ Bmem cell response positively correlated with long-lived humoral immunity, and clonotypes from T-bet+ Bmem cells were represented in the secondary ASC response to repeat vaccination, suggesting that this effector-like population predicts influenza vaccine durability and recall potential.
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Affiliation(s)
- Anoma Nellore
- Department of Medicine, Division of Infectious Disease, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Esther Zumaquero
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christopher F Fucile
- Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christopher M Tipton
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - R Glenn King
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tian Mi
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Betty Mousseau
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - John E Bradley
- Department of Medicine, Division of Clinical Immunology and Rheumatology at The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Fen Zhou
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stuti Mutneja
- Department of Medicine, Division of Infectious Disease, The University of Alabama at Birmingham, Birmingham, AL 35294, USA; ImmuneID, Waltham, MA 02451, USA
| | - Paul A Goepfert
- Department of Medicine, Division of Infectious Disease, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Troy D Randall
- Department of Medicine, Division of Clinical Immunology and Rheumatology at The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alexander F Rosenberg
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA; Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Frances E Lund
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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15
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Rose JR, Akdogan-Ozdilek B, Rahmberg AR, Powell MD, Hicks SL, Scharer CD, Boss JM. Distinct transcriptomic and epigenomic modalities underpin human memory T cell subsets and their activation potential. Commun Biol 2023; 6:363. [PMID: 37012418 PMCID: PMC10070634 DOI: 10.1038/s42003-023-04747-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 03/24/2022] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Human memory T cells (MTC) are poised to rapidly respond to antigen re-exposure. Here, we derived the transcriptional and epigenetic programs of resting and ex vivo activated, circulating CD4+ and CD8+ MTC subsets. A progressive gradient of gene expression from naïve to TCM to TEM is observed, which is accompanied by corresponding changes in chromatin accessibility. Transcriptional changes suggest adaptations of metabolism that are reflected in altered metabolic capacity. Other differences involve regulatory modalities comprised of discrete accessible chromatin patterns, transcription factor binding motif enrichment, and evidence of epigenetic priming. Basic-helix-loop-helix factor motifs for AHR and HIF1A distinguish subsets and predict transcription networks to sense environmental changes. Following stimulation, primed accessible chromatin correlate with an augmentation of MTC gene expression as well as effector transcription factor gene expression. These results identify coordinated epigenetic remodeling, metabolic, and transcriptional changes that enable MTC subsets to ultimately respond to antigen re-encounters more efficiently.
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Affiliation(s)
- James R Rose
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Bagdeser Akdogan-Ozdilek
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Michael D Powell
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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16
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Eggert J, Zinzow-Kramer WM, Hu Y, Tsai YL, Weiss A, Salaita K, Scharer CD, Au-Yeung BB. Accumulation of TCR signaling from self-antigens in naive CD8 T cells mitigates early responsiveness. bioRxiv 2023:2023.01.27.525946. [PMID: 36747815 PMCID: PMC9900884 DOI: 10.1101/2023.01.27.525946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The cumulative effects of T cell receptor (TCR) signal transduction over extended periods of time influences T cell biology, such as the positive selection of immature thymocytes or the proliferative responses of naive T cells. Naive T cells experience recurrent TCR signaling in response to self-antigens in the steady state. However, how these signals influence the responsiveness of naive CD8+ T cells to subsequent agonist TCR stimulation remains incompletely understood. We investigated how naive CD8+ T cells that experienced relatively low or high levels of TCR signaling in response to self-antigens respond to stimulation with foreign antigens. A transcriptional reporter of Nr4a1 (Nur77-GFP) revealed substantial heterogeneity of the amount of TCR signaling naive CD8+ T cells accumulate in the steady state. Nur77-GFPHI cells exhibited diminished T cell activation and secretion of IFNγ and IL-2 relative to Nur77-GFPLO cells in response to agonist TCR stimulation. Differential gene expression analyses revealed upregulation of genes associated with acutely stimulated T cells in Nur77-GFPHI cells but also increased expression of negative regulators such as the phosphatase Sts1. Responsiveness of Nur77-GFPHI cells to TCR stimulation was partially restored at the level of IFNγ secretion by deficiency of Sts1 or the ubiquitin ligase Cbl-b. Our data suggest that extensive accumulation of TCR signaling during steady state conditions induces a recalibration of the responsiveness of naive CD8+ T cells through gene expression changes and negative regulation, at least in part, dependent on Sts1 and Cbl-b. This cell-intrinsic negative feedback loop may allow the immune system to limit the autoreactive potential of highly self-reactive naive CD8+ T cells.
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Affiliation(s)
- Joel Eggert
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University
| | - Wendy M. Zinzow-Kramer
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University
| | - Yuesong Hu
- Department of Chemistry, Emory University
| | - Yuan-Li Tsai
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Departments of Medicine and of Microbiology and Immunology, University of California, San Francisco
| | - Arthur Weiss
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Departments of Medicine and of Microbiology and Immunology, University of California, San Francisco
| | | | | | - Byron B. Au-Yeung
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University
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17
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Powell MD, Lu P, Neeld DK, Kania AK, George-Alexander LEM, Bally AP, Scharer CD, Boss JM. IL-6/STAT3 Signaling Axis Enhances and Prolongs Pdcd1 Expression in Murine CD8 T Cells. Immunohorizons 2022; 6:872-882. [PMID: 36547389 PMCID: PMC10103150 DOI: 10.4049/immunohorizons.2100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/09/2021] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
CD8 cytotoxic T cells are a potent line of defense against invading pathogens. To aid in curtailing aberrant immune responses, the activation status of CD8 T cells is highly regulated. One mechanism in which CD8 T cell responses are dampened is via signaling through the immune-inhibitory receptor Programmed Cell Death Protein-1, encoded by Pdcd1. Pdcd1 expression is regulated through engagement of the TCR, as well as by signaling from extracellular cytokines. Understanding such pathways has influenced the development of numerous clinical treatments. In this study, we showed that signals from the cytokine IL-6 enhanced Pdcd1 expression when paired with TCR stimulation in murine CD8 T cells. Mechanistically, signals from IL-6 were propagated through activation of the transcription factor STAT3, resulting in IL-6-dependent binding of STAT3 to Pdcd1 cis-regulatory elements. Intriguingly, IL-6 stimulation overcame B Lymphocyte Maturation Protein 1-mediated epigenetic repression of Pdcd1, which resulted in a transcriptionally permissive landscape marked by heightened histone acetylation. Furthermore, in vivo-activated CD8 T cells derived from lymphocytic choriomeningitis virus infection required STAT3 for optimal Programmed Cell Death Protein-1 surface expression. Importantly, STAT3 was the only member of the STAT family present at Pdcd1 regulatory elements in lymphocytic choriomeningitis virus Ag-specific CD8 T cells. Collectively, these data define mechanisms by which the IL-6/STAT3 signaling axis can enhance and prolong Pdcd1 expression in murine CD8 T cells.
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Affiliation(s)
- Michael D. Powell
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Peiyuan Lu
- Current Address: Department of Biochemistry and Molecular Biology, School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250021, China
| | - Dennis K. Neeld
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anna K. Kania
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Current Address: Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | | | - Alexander P.R. Bally
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Current Address: Zoetis Inc, 3185 Rampart Rd, Fort Collins, CO 80521, USA
| | - Christopher D. Scharer
- 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
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18
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Lobby JL, Uddbäck I, Scharer CD, Mi T, Boss JM, Thomsen AR, Christensen JP, Kohlmeier JE. Persistent Antigen Harbored by Alveolar Macrophages Enhances the Maintenance of Lung-Resident Memory CD8 + T Cells. J Immunol 2022; 209:1778-1787. [PMID: 36162870 PMCID: PMC9588742 DOI: 10.4049/jimmunol.2200082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/16/2022] [Indexed: 11/07/2022]
Abstract
Lung tissue-resident memory T cells are crucial mediators of cellular immunity against respiratory viruses; however, their gradual decline hinders the development of T cell-based vaccines against respiratory pathogens. Recently, studies using adenovirus (Ad)-based vaccine vectors have shown that the number of protective lung-resident CD8+ TRMs can be maintained long term. In this article, we show that immunization of mice with a replication-deficient Ad serotype 5 expressing influenza (A/Puerto Rico/8/34) nucleoprotein (AdNP) generates a long-lived lung TRM pool that is transcriptionally indistinct from those generated during a primary influenza infection. In addition, we demonstrate that CD4+ T cells contribute to the long-term maintenance of AdNP-induced CD8+ TRMs. Using a lineage tracing approach, we identify alveolar macrophages as a cell source of persistent NP Ag after immunization with AdNP. Importantly, depletion of alveolar macrophages after AdNP immunization resulted in significantly reduced numbers of NP-specific CD8+ TRMs in the lungs and airways. Combined, our results provide further insight to the mechanisms governing the enhanced longevity of Ag-specific CD8+ lung TRMs observed after immunization with recombinant Ad.
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Affiliation(s)
- Jenna L Lobby
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
| | - Ida Uddbäck
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
| | - Tian Mi
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
| | - Allan R Thomsen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jan P Christensen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob E Kohlmeier
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
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19
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Hashimoto M, Araki K, Cardenas MA, Li P, Jadhav RR, Kissick HT, Hudson WH, McGuire DJ, Obeng RC, Wieland A, Lee J, McManus DT, Ross JL, Im SJ, Lee J, Lin JX, Hu B, West EE, Scharer CD, Freeman GJ, Sharpe AH, Ramalingam SS, Pellerin A, Teichgräber V, Greenleaf WJ, Klein C, Goronzy JJ, Umaña P, Leonard WJ, Smith KA, Ahmed R. PD-1 combination therapy with IL-2 modifies CD8 + T cell exhaustion program. Nature 2022; 610:173-181. [PMID: 36171288 PMCID: PMC9793890 DOI: 10.1038/s41586-022-05257-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/15/2021] [Accepted: 08/22/2022] [Indexed: 12/30/2022]
Abstract
Combination therapy with PD-1 blockade and IL-2 is highly effective during chronic lymphocytic choriomeningitis virus infection1. Here we examine the underlying basis for this synergy. We show that PD-1 + IL-2 combination therapy, in contrast to PD-1 monotherapy, substantially changes the differentiation program of the PD-1+TCF1+ stem-like CD8+ T cells and results in the generation of transcriptionally and epigenetically distinct effector CD8+ T cells that resemble highly functional effector CD8+ T cells seen after an acute viral infection. The generation of these qualitatively superior CD8+ T cells that mediate viral control underlies the synergy between PD-1 and IL-2. Our results show that the PD-1+TCF1+ stem-like CD8+ T cells, also referred to as precursors of exhausted CD8+ T cells, are not fate-locked into the exhaustion program and their differentiation trajectory can be changed by IL-2 signals. These virus-specific effector CD8+ T cells emerging from the stem-like CD8+ T cells after combination therapy expressed increased levels of the high-affinity IL-2 trimeric (CD25-CD122-CD132) receptor. This was not seen after PD-1 blockade alone. Finally, we show that CD25 engagement with IL-2 has an important role in the observed synergy between IL-2 cytokine and PD-1 blockade. Either blocking CD25 with an antibody or using a mutated version of IL-2 that does not bind to CD25 but still binds to CD122 and CD132 almost completely abrogated the synergistic effects observed after PD-1 + IL-2 combination therapy. There is considerable interest in PD-1 + IL-2 combination therapy for patients with cancer2,3, and our fundamental studies defining the underlying mechanisms of how IL-2 synergizes with PD-1 blockade should inform these human translational studies.
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Affiliation(s)
- Masao Hashimoto
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Koichi Araki
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Maria A Cardenas
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rohit R Jadhav
- Department of Immunology, Mayo Clinic School of Medicine and Sciences, Rochester, MN, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haydn T Kissick
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - William H Hudson
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Donald J McGuire
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Rebecca C Obeng
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pathology and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Andreas Wieland
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Otolaryngology, The Ohio State University College of Medicine, Columbus, OH, USA
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Judong Lee
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel T McManus
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - James L Ross
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Se Jin Im
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Immunology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Junghwa Lee
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Jian-Xin Lin
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Bin Hu
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erin E West
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
- Complement and Inflammation Research Section (CIRS), National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Suresh S Ramalingam
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jorg J Goronzy
- Department of Immunology, Mayo Clinic School of Medicine and Sciences, Rochester, MN, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pablo Umaña
- Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kendall A Smith
- Department of Medicine, Division of Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.
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20
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Zinzow-Kramer WM, Kolawole EM, Eggert J, Evavold BD, Scharer CD, Au-Yeung BB. Strong Basal/Tonic TCR Signals Are Associated with Negative Regulation of Naive CD4 + T Cells. Immunohorizons 2022; 6:671-683. [PMID: 36100367 DOI: 10.4049/immunohorizons.2200051] [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] [Received: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/19/2022] Open
Abstract
T cells experience varying intensities of tonic or basal TCR signaling in response to self-peptides presented by MHC (self-pMHC) in vivo. We analyzed four subpopulations of mouse naive CD4+ cells that express different levels of Nur77-GFP and Ly6C, surrogate markers that positively and inversely correlate with the strength of tonic TCR signaling, respectively. Adoptive transfer studies suggest that relatively weak or strong Nur77-GFP intensity in thymocytes tends to be maintained in mature T cells. Two-dimensional affinity measurements were lowest for Nur77-GFPloLy6C+ cells and highest for Nur77-GFPhiLy6C- cells, highlighting a positive correlation between apparent TCR affinity and tonic TCR signal strength. Despite experiencing the strongest tonic TCR signaling, Nur77-GFPhiLy6C- cells were least responsive to multiple concentrations of a cognate or suboptimal pMHC. Gene expression analyses suggest that Nur77-GFPhiLy6C- cells induce a gene expression program that has similarities with that of acutely stimulated T cells. However, strong tonic TCR signaling also correlates with increased expression of genes with inhibitory functions, including coinhibitory receptors. Similarly, assay for transposase-accessible chromatin with sequencing analyses suggested that increased tonic TCR signal strength correlated with increased chromatin accessibility associated with genes that have positive and inhibitory roles in T cell activation. Strikingly, Nur77-GFPhiLy6C- cells exhibited differential accessibility within regions of Cd200r1 and Tox that were similar in location to differentially accessible regions previously identified in exhausted CD8+ T cells. We propose that constitutive strong tonic TCR signaling triggers adaptations detectable at both the transcriptional and epigenetic levels, ultimately contributing to the tuning of T cell responsiveness.
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Affiliation(s)
- Wendy M Zinzow-Kramer
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Elizabeth M Kolawole
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT; and
| | - Joel Eggert
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Brian D Evavold
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT; and
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Byron B Au-Yeung
- Division of Immunology, Lowance Center for Human Immunology, Department of Medicine, Emory University School of Medicine, Atlanta, GA;
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21
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Lee M, Geitgey DK, Hamilton JAG, Boss JM, Scharer CD, Spangle JM, Haynes KA, Henry CJ. Adipocyte-mediated epigenomic instability in human T-ALL cells is cytotoxic and phenocopied by epigenetic-modifying drugs. Front Cell Dev Biol 2022; 10:909557. [PMID: 36060800 PMCID: PMC9438935 DOI: 10.3389/fcell.2022.909557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
The world’s population with obesity is reaching pandemic levels. If current trends continue, it is predicted that there will be 1.5 billion people with obesity by 2030. This projection is alarming due to the association of obesity with numerous diseases including cancer, with recent studies demonstrating a positive association with acute myeloid leukemia (AML) and B cell acute lymphoblastic leukemia (B-ALL). Interestingly, several epidemiological studies suggest the converse relationship may exist in patients with T cell acute lymphoblastic leukemia (T-ALL). To determine the relationship between obesity and T-ALL development, we employed the diet-induced obesity (DIO) murine model and cultured human T-ALL cells in adipocyte-conditioned media (ACM), bone marrow stromal cell-conditioned media, stromal conditioned media (SCM), and unconditioned media to determine the functional impact of increased adiposity on leukemia progression. Whereas only 20% of lean mice transplanted with T-ALL cells survived longer than 3 months post-inoculation, 50%–80% of obese mice with leukemia survived over this same period. Furthermore, culturing human T-ALL cells in ACM resulted in increased histone H3 acetylation (K9/K14/K18/K23/K27) and methylation (K4me3 and K27me3) posttranslational modifications (PTMs), which preceded accelerated cell cycle progression, DNA damage, and cell death. Adipocyte-mediated epigenetic changes in human T-ALL cells were recapitulated with the H3K27 demethylase inhibitor GSK-J4 and the pan-HDAC inhibitor vorinostat. These drugs were also highly cytotoxic to human T-ALL cells at low micromolar concentrations. In summary, our data support epidemiological studies demonstrating that adiposity suppresses T-ALL pathogenesis. We present data demonstrating that T-ALL cell death in adipose-rich microenvironments is induced by epigenetic modifications, which are not tolerated by leukemia cells. Similarly, GSK-J4 and vorinostat treatment induced epigenomic instability and cytotoxicity profiles that phenocopied the responses of human T-ALL cells to ACM, which provides additional support for the use of epigenetic modifying drugs as a treatment option for T-ALL.
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Affiliation(s)
- Miyoung Lee
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Delaney K. Geitgey
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Jamie A. G. Hamilton
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Jennifer M. Spangle
- Winship Cancer Institute, Atlanta, GA, United States
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, United States
| | - Karmella A. Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Curtis J. Henry
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA, United States
- Winship Cancer Institute, Atlanta, GA, United States
- *Correspondence: Curtis J. Henry,
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22
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Zhou C, Uluisik R, Rowley JW, David C, Jones CL, Scharer CD, Noetzli L, Fisher MH, Kirkpatrick GD, Bark K, Boss JM, Henry CJ, Pietras EM, Di Paola J, Porter CC. Germline ETV6 mutation promotes inflammation and disrupts lymphoid development of early hematopoietic progenitors. Exp Hematol 2022; 112-113:24-34. [PMID: 35803545 PMCID: PMC9885892 DOI: 10.1016/j.exphem.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/29/2022] [Revised: 06/10/2022] [Accepted: 06/26/2022] [Indexed: 02/01/2023]
Abstract
Germline mutations in ETV6 are associated with a syndrome of thrombocytopenia and leukemia predisposition, and ETV6 is among the most commonly mutated genes in leukemias, especially childhood B-cell acute lymphoblastic leukemia. However, the mechanisms underlying disease caused by ETV6 dysfunction are poorly understood. To address these gaps in knowledge, using CRISPR/Cas9, we developed a mouse model of the most common recurrent, disease-causing germline mutation in ETV6. We found defects in hematopoiesis related primarily to abnormalities of the multipotent progenitor population 4 (MPP4) subset of hematopoietic progenitor cells and evidence of sterile inflammation. Expression of ETV6 in Ba/F3 cells altered the expression of several cytokines, some of which were also detected at higher levels in the bone marrow of the mice with Etv6 mutation. Among these, interleukin-18 and interleukin-13 abrogated B-cell development of sorted MPP4 cells, but not common lymphoid progenitors, suggesting that inflammation contributes to abnormal hematopoiesis by impairing lymphoid development. These data, along with those from humans, support a model in which ETV6 dysfunction promotes inflammation, which adversely affects thrombopoiesis and promotes leukemogenesis.
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Affiliation(s)
- Chengjing Zhou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Rizvan Uluisik
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Jesse W Rowley
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT
| | - Camille David
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | | | - Christopher D Scharer
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA
| | | | - Marlie H Fisher
- Medical Scientist Training Program, University of Colorado School of Medicine, Aurora, CO
| | | | - Katrina Bark
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Jeremy M Boss
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA
| | - Curtis J Henry
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Eric M Pietras
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Jorge Di Paola
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Christopher C Porter
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA; Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA.
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23
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Rose JR, Rahmberg AR, Powell MD, Scharer CD, Boss JM. Epigenome accessibility changes before and after activation reveal distinct and progressive differentiation for human memory T cell subsets. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.57.02] [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
Memory T cells (MTC), an indispensable part of adaptive immune memory, have historically been categorized by the cell surface proteins CCR7 and CD45RA into specialized subtypes (TCM, TEM, and TEMRA), each with unique functions. However, the epigenetic characteristics that distinguish the MTC subsets as well as the gene regulatory networks governing each MTC subsets’ response to activation remain poorly understood. Here we define and categorize the transcriptional and epigenetic differences of MTC and their respective primary subsets found in human blood, both in a resting state and after ex-vivo stimulation. Resting TCM were found to be relatively more similar to naïve cells in both CD4 and CD8 lineages, while TEM exhibited greater numbers of differentially expressed genes (DEG) and alterations to chromatin accessibility. Differentially accessible regions (DAR) discerning memory subsets contained binding motifs for factors thought to regulate memory formation from the bZIP, T-box and HMG families, as well as sites for novel bHLH factors MSC and AHR that may function in MTC development. Examining the effect of stimulation on MTC gene expression and chromatin identified unique DAR and DEG modules, some of which may have initially been primed by previous activation events in naive progenitors. Primed DAR were correlated with augmented expression of important genes in MTC after stimulation, suggesting an epigenetic mechanism of regulation. Ultimately these results describe the accumulation of epigenetic alterations during primary activation and during memory development that distinguish MTC from naïve T cells, enable differentiation into distinct subsets, and influence how MTC respond to secondary activation.
Supported by grants from NIH (RO1 AI113021,T32 GM0008490)
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Affiliation(s)
- James R Rose
- 1Department of Microbiology & Immunology, Emory Univ. Sch. of Med
| | | | - Michael D Powell
- 1Department of Microbiology & Immunology, Emory Univ. Sch. of Med
| | | | - Jeremy M Boss
- 1Department of Microbiology & Immunology, Emory Univ. Sch. of Med
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24
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Dale GA, Wilkins DJ, Rowley J, Scharer CD, Tipton CM, Hom J, Boss JM, Corces V, Sanz I, Jacob J. Somatic Diversification of Rearranged Antibody Gene Segments by Intra- and Interchromosomal Templated Mutagenesis. J Immunol 2022; 208:2141-2153. [PMID: 35418472 PMCID: PMC9047068 DOI: 10.4049/jimmunol.2100434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The ability of the humoral immune system to generate Abs capable of specifically binding a myriad of Ags is critically dependent on the somatic hypermutation program. This program induces both templated mutations (i.e., gene conversion) and untemplated mutations. In humans, somatic hypermutation is widely believed to result in untemplated point mutations. In this study, we demonstrate detection of large-scale templated events that occur in human memory B cells and circulating plasmablasts. We find that such mutations are templated intrachromosomally from IGHV genes and interchromosomally from IGHV pseudogenes as well as other homologous regions unrelated to IGHV genes. These same donor regions are used in multiple individuals, and they predominantly originate from chromosomes 14, 15, and 16. In addition, we find that exogenous sequences placed at the IgH locus, such as LAIR1, undergo templated mutagenesis and that homology appears to be the major determinant for donor choice. Furthermore, we find that donor tracts originate from areas in proximity with open chromatin, which are transcriptionally active, and are found in spatial proximity with the IgH locus during the germinal center reaction. These donor sequences are inserted into the Ig gene segment in association with overlapping activation-induced cytidine deaminase hotspots. Taken together, these studies suggest that diversity generated during the germinal center response is driven by untemplated point mutations as well as templated mutagenesis using local and distant regions of the genome.
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Affiliation(s)
- Gordon A Dale
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA
| | - Daniel J Wilkins
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA
| | - Jordan Rowley
- Department of Biology, Emory University, Atlanta, GA
| | | | - Christopher M Tipton
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA
| | - Jennifer Hom
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA
| | - Jeremy M Boss
- Emory University School of Medicine, Emory University, Atlanta, GA; and
| | - Victor Corces
- Department of Biology, Emory University, Atlanta, GA
| | - Ignacio Sanz
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA
| | - Joshy Jacob
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA;
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25
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Powell MD, Rose JR, Neeld D, Rahmberg AR, Scharer CD, Boss JM. Defining the cis- and trans-regulatory architecture for human PD-1 in T Follicular Helper Cells. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.112.21] [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: 01/03/2023]
Abstract
Abstract
The surface immune checkpoint inhibitor Programed Death-1 (PD-1), encoded by PDCD1, is expressed throughout the immune system. Notably, PD-1 expression is amongst its highest in a specialized subset of CD4+ T follicular helper (TFH) cells. TFH cells primarily function by engaging with cognate B cells, facilitating the generation of high affinity vaccine- and pathogen-specific antibodies. Despite the proven clinical benefit of therapies targeting the PD-1 pathway, very little is known regarding the mechanisms by which human PDCD1 is transcriptionally regulated in humans. Here, we seek to elucidate both the cis- and trans-regulatory mechanisms that govern PDCD1 expression in TFH cells. Human TFH cells were sourced from discarded tonsil tissue, circulating blood, or through an ex vivo differentiation model to generate ‘TFH-like’ cells. RNA-seq analysis revealed that ex vivo-derived ‘TFH-like’ cells resembled bona-fide in vivo TFH cells, including induction of PDCD1. Furthermore, ATAC-sequencing experiments identified 8 conserved regions in the PDCD1 locus that exhibited altered accessibility in TFH cells. These cis-regulatory elements were determined to have distinct functions in controlling PDCD1 expression. Additionally, bioinformatic analysis revealed a core TFH gene program, implicating the transcription factors BCL-6, ASCL2, TOX, TOX2, and AIOLOS as regulators of PDCD1 and TFH fate. Taken together, these findings uncover the molecular mechanisms that control PDCD1 expression, informing the design of future therapies aimed at manipulating PD-1.
Supported by National Institute of Health grants: RO1 AI113021 to J.M.B, F32 AI161857 to M.D.P
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Affiliation(s)
| | - James R Rose
- 2Department of Microbiology & Immunology, Emory University School of Medicine
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26
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Kania AK, Price MJ, George-Alexander LE, Patterson DG, Hicks SL, Scharer CD, Boss JM. H3K27me3 Demethylase UTX Restrains Plasma Cell Formation. J I 2022; 208:1873-1885. [PMID: 35346967 PMCID: PMC9012698 DOI: 10.4049/jimmunol.2100948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/02/2022] [Indexed: 11/19/2022]
Abstract
B cell differentiation is associated with substantial transcriptional, metabolic, and epigenetic remodeling, including redistribution of histone 3 lysine 27 trimethylation (H3K27me3), which is associated with a repressive chromatin state and gene silencing. Although the role of the methyltransferase EZH2 (Enhancer of zeste homolog 2) in B cell fate decisions has been well established, it is not known whether H3K27me3 demethylation is equally important. In this study, we showed that simultaneous genetic deletion of the two H3K27 demethylases UTX and JMJD3 (double-knockout [Utx fl/fl Jmjd3 fl/fl Cd19 cre/+] [dKO]) led to a significant increase in plasma cell (PC) formation after stimulation with the T cell-independent Ags LPS and NP-Ficoll. This phenotype occurred in a UTX-dependent manner as UTX single-knockout mice, but not JMJD3 single-knockout mice, mimicked the dKO. Although UTX- and JMJD3-deficient marginal zone B cells showed increased proliferation, dKO follicular B cells also showed increased PC formation. PCs from dKO mice upregulated genes associated with oxidative phosphorylation and exhibited increased spare respiratory capacity. Mechanistically, deletion of Utx and Jmjd3 resulted in higher levels of H3K27me3 at proapoptotic genes and resulted in reduced apoptosis of dKO PCs in vivo. Furthermore, UTX regulated chromatin accessibility at regions containing ETS and IFN regulatory factor (IRF) transcription factor family motifs, including motifs of known repressors of PC fate. Taken together, these data demonstrate that the H3K27me3 demethylases restrain B cell differentiation.
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Affiliation(s)
- Anna K Kania
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Madeline J Price
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | | | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
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27
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Liu M, Starenki D, Scharer CD, Silva-Sanchez A, Molina PA, Pollock JS, Cooper SJ, Arend RC, Rosenberg AF, Randall TD, Meza-Perez S. Circulating Tregs accumulate in omental tumors and acquire adipose-resident features. Cancer Immunol Res 2022; 10:641-655. [PMID: 35263766 DOI: 10.1158/2326-6066.cir-21-0880] [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] [Received: 10/14/2021] [Revised: 01/20/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022]
Abstract
Tumors that metastasize in the peritoneal cavity typically end up in the omental adipose tissue, a particularly immune-suppressive environment that includes specialized adipose-resident regulatory T cells (Tregs). Tregs rapidly accumulate in the omentum after tumor implantation and potently suppress anti-tumor immunity. However, it is unclear whether these Tregs are recruited from the circulation or derived from pre-existing adipose-resident Tregs by clonal expansion. Here we show that Tregs in tumor-bearing omenta predominantly have thymus-derived characteristics. Moreover, naïve tumor antigen-specific CD4+ T cells fail to differentiate into Tregs in tumor-bearing omenta. In fact, Tregs derived from the pre-tumor repertoire are sufficient to suppress anti-tumor immunity and promote tumor growth. However, tumor implantation in the omentum does not promote Treg clonal expansion, but instead leads to increased clonal diversity. Parabiosis experiments show that despite tissue-resident (non-circulating) characteristics of omental Tregs in naïve mice, tumor implantation promotes a rapid influx of circulating Tregs, many of which come from the spleen. Finally, we show that newly recruited Tregs rapidly acquire characteristics of adipose-resident Tregs in tumor-bearing omenta. These data demonstrate that most Tregs in omental tumors are recruited from the circulation and adapt to their environment by altering their homing, transcriptional and metabolic properties.
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Affiliation(s)
- Mingyong Liu
- University of Alabama at Birmingham, Birmingham, AL, United States
| | | | | | | | - Patrick A Molina
- University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Rebecca C Arend
- University of Alabama at Birmingham, Birmingham, Alabama, United States
| | | | - Troy D Randall
- University of Alabama at Birmingham, Birmingham, AL, United States
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28
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Lee M, Hamilton JAG, Talekar GR, Ross AJ, Michael L, Rupji M, Dwivedi B, Raikar SS, Boss J, Scharer CD, Graham DK, DeRyckere D, Porter CC, Henry CJ. Obesity-induced galectin-9 is a therapeutic target in B-cell acute lymphoblastic leukemia. Nat Commun 2022; 13:1157. [PMID: 35241678 PMCID: PMC8894417 DOI: 10.1038/s41467-022-28839-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 09/17/2019] [Accepted: 02/11/2022] [Indexed: 12/25/2022] Open
Abstract
The incidence of obesity is rising with greater than 40% of the world’s population expected to be overweight or suffering from obesity by 2030. This is alarming because obesity increases mortality rates in patients with various cancer subtypes including leukemia. The survival differences between lean patients and patients with obesity are largely attributed to altered drug pharmacokinetics in patients receiving chemotherapy; whereas, the direct impact of an adipocyte-enriched microenvironment on cancer cells is rarely considered. Here we show that the adipocyte secretome upregulates the surface expression of Galectin-9 (GAL-9) on human B-acute lymphoblastic leukemia cells (B-ALL) which promotes chemoresistance. Antibody-mediated targeting of GAL-9 on B-ALL cells induces DNA damage, alters cell cycle progression, and promotes apoptosis in vitro and significantly extends the survival of obese but not lean mice with aggressive B-ALL. Our studies reveal that adipocyte-mediated upregulation of GAL-9 on B-ALL cells can be targeted with antibody-based therapies to overcome obesity-induced chemoresistance. Obesity has been reported to promote tumourigenesis and chemoresistance but the underlying mechanisms are not completely understood. Here, the authors show that adipocytes induce Galectin-9 (GAL-9) expression in B-acute lymphoblastic leukaemia (B-ALL) cells which leads to chemoresistance and antibody-mediated blockade of GAL-9 increases survival in preclinical B-ALL murine models.
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Affiliation(s)
- Miyoung Lee
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jamie A G Hamilton
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Ganesh R Talekar
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Anthony J Ross
- Riley Pediatric Cancer and Blood Diseases, Riley Children's Health, Indiana University School of Medicine, Indianapolis, Indiana, IN, USA
| | | | - Manali Rupji
- Bioinformatics and Biostatistics Shared Resource, Winship Cancer Institute, Atlanta, GA, USA
| | - Bhakti Dwivedi
- Bioinformatics and Biostatistics Shared Resource, Winship Cancer Institute, Atlanta, GA, USA
| | - Sunil S Raikar
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jeremy Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Douglas K Graham
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Deborah DeRyckere
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Christopher C Porter
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Curtis J Henry
- Department of Pediatrics, Emory University School of Medicine and Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA.
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29
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Budd RC, Scharer CD, Barrantes-Reynolds R, Legunn S, Fortner KA. T Cell Homeostatic Proliferation Promotes a Redox State That Drives Metabolic and Epigenetic Upregulation of Inflammatory Pathways in Lupus. Antioxid Redox Signal 2022; 36:410-422. [PMID: 34328790 PMCID: PMC8982120 DOI: 10.1089/ars.2021.0078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Significance: Numerous abnormalities in T cells have been described in patients with systemic lupus erythematosus (SLE), including lymphopenia, DNA demethylation, expression of endogenous retroviruses (ERVs), increased cell death, enlarged mitochondria, production of reactive oxygen species (ROS), and the appearance of unusual CD4-CD8- T cells. Our studies propose a model in which accelerated homeostatic proliferation of T cells promotes an epigenetic and metabolic program, leading to this cluster of abnormalities. Recent Advances: Growing knowledge of the innate immune disorders in SLE has included increased mitochondrial size and ROS production that induces oligomerization of the mitochondrial antiviral signaling (MAVS) protein and type I interferon production, as well as DNA demethylation, upregulation of inflammatory genes, and expression of certain ERVs in SLE peripheral blood mononuclear cells. All these events are part of the cellular program that occurs during homeostatic proliferation of T cells. Evidence from a murine model of SLE as well as in human SLE reveals that increased T cell homeostatic proliferation may be a driving factor in these processes. Critical Issues: Despite extensive knowledge of the myriad autoantibodies in SLE and other immune abnormalities, a cogent model has been lacking to link the numerous and seemingly disparate immune aberrations. This may partly explain the general lack of new drugs specifically for SLE in over 50 years. A more coherent model of SLE would not only unify the variety of immune abnormalities is SLE but would also suggest new therapies. Future Directions: The model of augmented homeostatic proliferation leading to increased mitochondrial mass, ROS, DNA demethylation, and upregulation of inflammatory genes suggests strategic new targets for SLE, including antioxidants and certain inhibitors of metabolism. Antioxid. Redox Signal. 36, 410-422.
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Affiliation(s)
- Ralph C Budd
- Department of Medicine, Vermont Center for Immunology and Infectious Diseases, Larner College of Medicine, The University of Vermont, Burlington, Vermont, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Ramiro Barrantes-Reynolds
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, The University of Vermont, Burlington, Vermont, USA
| | - Scott Legunn
- Department of Medicine, Vermont Center for Immunology and Infectious Diseases, Larner College of Medicine, The University of Vermont, Burlington, Vermont, USA
| | - Karen A Fortner
- Department of Medicine, Vermont Center for Immunology and Infectious Diseases, Larner College of Medicine, The University of Vermont, Burlington, Vermont, USA
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30
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Joyner CJ, Ley AM, Nguyen DC, Ali M, Corrado A, Tipton C, Scharer CD, Mi T, Woodruff MC, Hom J, Boss JM, Duan M, Gibson G, Roberts D, Andrews J, Lonial S, Sanz I, Lee FEH. Generation of human long-lived plasma cells by developmentally regulated epigenetic imprinting. Life Sci Alliance 2022; 5:e202101285. [PMID: 34952892 PMCID: PMC8739272 DOI: 10.26508/lsa.202101285] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
Antibody secreting cells (ASCs) circulate after vaccination and infection and migrate to the BM where a subset known as long-lived plasma cells (LLPCs) persists and secrete antibodies for a lifetime. The mechanisms by which circulating ASCs become LLPCs are not well elucidated. Here, we show that human blood ASCs have distinct morphology, transcriptomes, and epigenetics compared with BM LLPCs. Compared with blood ASCs, BM LLPCs have decreased nucleus/cytoplasm ratio but increased endoplasmic reticulum and numbers of mitochondria. LLPCs up-regulate pro-survival genes MCL1, BCL2, and BCL-XL while simultaneously down-regulating pro-apoptotic genes HRK1, CASP3, and CASP8 Consistent with reduced gene expression, the pro-apoptotic gene loci are less accessible in LLPCs. Of the pro-survival genes, only BCL2 is concordant in gene up-regulation and loci accessibility. Using a novel in vitro human BM mimetic, we show that blood ASCs undergo similar morphological and molecular changes that resemble ex vivo BM LLPCs. Overall, our study demonstrates that early-minted blood ASCs in the BM microniche must undergo morphological, transcriptional, and epigenetic changes to mature into apoptotic-resistant LLPCs.
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Affiliation(s)
- Chester J Joyner
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Center for Vaccines and Immunology, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - Ariel M Ley
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - Doan C Nguyen
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - Mohammad Ali
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Alessia Corrado
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Christopher Tipton
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Tian Mi
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Matthew C Woodruff
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Jennifer Hom
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Meixue Duan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Greg Gibson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Danielle Roberts
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Joel Andrews
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Inaki Sanz
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, USA
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
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31
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Di Pietro A, Polmear J, Cooper L, Damelang T, Hussain T, Hailes L, O'Donnell K, Udupa V, Mi T, Preston S, Shtewe A, Hershberg U, Turner SJ, La Gruta NL, Chung AW, Tarlinton DM, Scharer CD, Good-Jacobson KL. Targeting BMI-1 in B cells restores effective humoral immune responses and controls chronic viral infection. Nat Immunol 2022; 23:86-98. [PMID: 34845392 DOI: 10.1038/s41590-021-01077-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 10/20/2021] [Indexed: 01/12/2023]
Abstract
Ineffective antibody-mediated responses are a key characteristic of chronic viral infection. However, our understanding of the intrinsic mechanisms that drive this dysregulation are unclear. Here, we identify that targeting the epigenetic modifier BMI-1 in mice improves humoral responses to chronic lymphocytic choriomeningitis virus. BMI-1 was upregulated by germinal center B cells in chronic viral infection, correlating with changes to the accessible chromatin landscape, compared to acute infection. B cell-intrinsic deletion of Bmi1 accelerated viral clearance, reduced splenomegaly and restored splenic architecture. Deletion of Bmi1 restored c-Myc expression in B cells, concomitant with improved quality of antibody and coupled with reduced antibody-secreting cell numbers. Specifically, BMI-1-deficiency induced antibody with increased neutralizing capacity and enhanced antibody-dependent effector function. Using a small molecule inhibitor to murine BMI-1, we could deplete antibody-secreting cells and prohibit detrimental immune complex formation in vivo. This study defines BMI-1 as a crucial immune modifier that controls antibody-mediated responses in chronic infection.
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Affiliation(s)
- Andrea Di Pietro
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jack Polmear
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Lucy Cooper
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Timon Damelang
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Tabinda Hussain
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Lauren Hailes
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kristy O'Donnell
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, Victoria, Australia
| | - Vibha Udupa
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.,Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Tian Mi
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Simon Preston
- Divisions of Immunology and Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Areen Shtewe
- Department of Human Biology, Faculty of Science, University of Haifa, Haifa, Israel
| | - Uri Hershberg
- Department of Human Biology, Faculty of Science, University of Haifa, Haifa, Israel
| | - Stephen J Turner
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Amy W Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - David M Tarlinton
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, Victoria, Australia
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia. .,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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32
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Kania AK, Guo M, Scharer CD, Boss JM. Inhibition of H3K27me3 Demethylases Promotes Plasmablast Formation. Immunohorizons 2021; 5:918-930. [PMID: 34880105 DOI: 10.4049/immunohorizons.2000087] [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] [Received: 10/02/2020] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
B cell differentiation into Ab-secreting plasma cells requires transcriptional, metabolic, and epigenetic remodeling. Histone H3 lysine 27 trimethylation (H3K27me3), a histone modification associated with gene silencing, is dynamically regulated during B cell differentiation. Although several studies have focused on mechanisms involving the gain of this modification in plasmablasts (PB), the role of active demethylation of H3K27me3 by ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX) and Jumonji domain-containing protein 3 (JMDJ3) during B cell differentiation has not been examined. In this study, this process was assessed using a pharmacological inhibitor of UTX and JMJD3, GSK-J4. Treatment of ex vivo stimulated mouse B cells with GSK-J4 led to an increase in PB frequency without affecting the ability of the newly formed PB to secrete Abs. Consistent with the role of UTX and JMJD3 in promoting gene expression, the majority of differentially expressed were downregulated upon GSK-J4 treatment. GSK-J4-treated cells downregulated genes associated with signaling and P53 pathways. Inhibitor treated cells upregulated genes associated with cell cycle and proliferation, which correlated with an increase in actively proliferating cells. Unexpectedly, a majority of the downregulated transcripts corresponded to genes that in the wild-type setting were genes that gain H3K27me3 and downregulated in PB. Together, our results show that UTX and JMDJ3 are required to restrain B cell differentiation and suggest that they function as a rheostat for H3K27me3 to control this process.
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Affiliation(s)
- Anna K Kania
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Muyao Guo
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
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33
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Patterson DG, Kania AK, Price MJ, Rose JR, Scharer CD, Boss JM. An IRF4-MYC-mTORC1 Integrated Pathway Controls Cell Growth and the Proliferative Capacity of Activated B Cells during B Cell Differentiation In Vivo. J Immunol 2021; 207:1798-1811. [PMID: 34470852 DOI: 10.4049/jimmunol.2100440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022]
Abstract
Cell division is an essential component of B cell differentiation to Ab-secreting plasma cells, with critical reprogramming occurring during the initial stages of B cell activation. However, a complete understanding of the factors that coordinate early reprogramming events in vivo remain to be determined. In this study, we examined the initial reprogramming by IRF4 in activated B cells using an adoptive transfer system and mice with a B cell-specific deletion of IRF4. IRF4-deficient B cells responding to influenza, 4-hydroxy-3-nitrophenylacetyl-Ficoll, and LPS divided but stalled during the proliferative response. Gene expression profiling of IRF4-deficient B cells at discrete divisions revealed IRF4 was critical for inducing MYC target genes, oxidative phosphorylation, and glycolysis. Moreover, IRF4-deficient B cells maintained an inflammatory gene expression signature. Complementary chromatin accessibility analyses established a hierarchy of IRF4 activity and identified networks of dysregulated transcription factor families in IRF4-deficient B cells, including E-box binding bHLH family members. Indeed, B cells lacking IRF4 failed to fully induce Myc after stimulation and displayed aberrant cell cycle distribution. Furthermore, IRF4-deficient B cells showed reduced mTORC1 activity and failed to initiate the B cell activation unfolded protein response and grow in cell size. Myc overexpression in IRF4-deficient cells was sufficient to overcome the cell growth defect. Together, these data reveal an IRF4-MYC-mTORC1 relationship critical for controlling cell growth and the proliferative response during B cell differentiation.
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Affiliation(s)
- Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and.,The Emory Vaccine Center, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Anna K Kania
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and.,The Emory Vaccine Center, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Madeline J Price
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and.,The Emory Vaccine Center, Emory University School of Medicine, Emory University, Atlanta, GA
| | - James R Rose
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and.,The Emory Vaccine Center, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and.,The Emory Vaccine Center, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and .,The Emory Vaccine Center, Emory University School of Medicine, Emory University, Atlanta, GA
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34
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Rivas MA, Durmaz C, Kloetgen A, Chin CR, Chen Z, Bhinder B, Koren A, Viny AD, Scharer CD, Boss JM, Elemento O, Mason CE, Melnick AM. Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. Front Immunol 2021; 12:688493. [PMID: 34621263 PMCID: PMC8490713 DOI: 10.3389/fimmu.2021.688493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/30/2021] [Accepted: 08/24/2021] [Indexed: 01/10/2023] Open
Abstract
The cohesin complex plays critical roles in genomic stability and gene expression through effects on 3D architecture. Cohesin core subunit genes are mutated across a wide cross-section of cancers, but not in germinal center (GC) derived lymphomas. In spite of this, haploinsufficiency of cohesin ATPase subunit Smc3 was shown to contribute to malignant transformation of GC B-cells in mice. Herein we explored potential mechanisms and clinical relevance of Smc3 deficiency in GC lymphomagenesis. Transcriptional profiling of Smc3 haploinsufficient murine lymphomas revealed downregulation of genes repressed by loss of epigenetic tumor suppressors Tet2 and Kmt2d. Profiling 3D chromosomal interactions in lymphomas revealed impaired enhancer-promoter interactions affecting genes like Tet2, which was aberrantly downregulated in Smc3 deficient lymphomas. Tet2 plays important roles in B-cell exit from the GC reaction, and single cell RNA-seq profiles and phenotypic trajectory analysis in Smc3 mutant mice revealed a specific defect in commitment to the final steps of plasma cell differentiation. Although Smc3 deficiency resulted in structural abnormalities in GC B-cells, there was no increase of somatic mutations or structural variants in Smc3 haploinsufficient lymphomas, suggesting that cohesin deficiency largely induces lymphomas through disruption of enhancer-promoter interactions of terminal differentiation and tumor suppressor genes. Strikingly, the presence of the Smc3 haploinsufficient GC B-cell transcriptional signature in human patients with GC-derived diffuse large B-cell lymphoma (DLBCL) was linked to inferior clinical outcome and low expression of cohesin core subunits. Reciprocally, reduced expression of cohesin subunits was an independent risk factor for worse survival int DLBCL patient cohorts. Collectively, the data suggest that Smc3 functions as a bona fide tumor suppressor for lymphomas through non-genetic mechanisms, and drives disease by disrupting the commitment of GC B-cells to the plasma cell fate.
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MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/immunology
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cells, Cultured
- Chondroitin Sulfate Proteoglycans/genetics
- Chondroitin Sulfate Proteoglycans/immunology
- Chondroitin Sulfate Proteoglycans/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/immunology
- Chromosomal Proteins, Non-Histone/metabolism
- Coculture Techniques
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Databases, Genetic
- Dioxygenases/genetics
- Dioxygenases/metabolism
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Germinal Center/immunology
- Germinal Center/metabolism
- Haploinsufficiency
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Phenotype
- Plasma Cells/immunology
- Plasma Cells/metabolism
- Transcription, Genetic
- Mice
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Affiliation(s)
- Martin A. Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Ceyda Durmaz
- Graduate Program on Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, New York, NY, United States
| | - Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cristopher R. Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medical College, New York, NY, United States
| | - Bhavneet Bhinder
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Aaron D. Viny
- Division of Hematology/Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, United States
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY, United States
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
| | - Ari M. Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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35
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Corrado A, Ramonell RP, Woodruff MC, Tipton C, Wise S, Levy J, DelGaudio J, Kuruvilla ME, Magliocca KR, Tomar D, Garimalla S, Scharer CD, Boss JM, Wu H, Gumber S, Fucile C, Gibson G, Rosenberg A, Sanz I, Lee FEH. Extrafollicular IgD+ B cells generate IgE antibody secreting cells in the nasal mucosa. Mucosal Immunol 2021; 14:1144-1159. [PMID: 34050324 PMCID: PMC8160425 DOI: 10.1038/s41385-021-00410-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 04/05/2021] [Accepted: 04/24/2021] [Indexed: 02/04/2023]
Abstract
Increased IgE is a typical feature of allergic rhinitis. Local class-switch recombination has been intimated but B cell precursors and mechanisms remain elusive. Here we describe the dynamics underlying the generation of IgE-antibody secreting cells (ASC) in human nasal polyps (NP), mucosal tissues rich in ASC without germinal centers (GC). Using VH next generation sequencing, we identified an extrafollicular (EF) mucosal IgD+ naïve-like intermediate B cell population with high connectivity to the mucosal IgE ASC. Mucosal IgD+ B cells, express germline epsilon transcripts and predominantly co-express IgM. However, a small but significant fraction co-express IgG or IgA instead which also show connectivity to ASC IgE. Phenotypically, NP IgD+ B cells display an activated profile and molecular evidence of BCR engagement. Transcriptionally, mucosal IgD+ B cells reveal an intermediate profile between naïve B cells and ASC. Single cell IgE ASC analysis demonstrates lower mutational frequencies relative to IgG, IgA, and IgD ASC consistent with IgE ASC derivation from mucosal IgD+ B cell with low mutational load. In conclusion, we describe a novel mechanism of GC-independent, extrafollicular IgE ASC formation at the nasal mucosa whereby activated IgD+ naïve B cells locally undergo direct and indirect (through IgG and IgA), IgE class switch.
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Affiliation(s)
- Alessia Corrado
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Richard P Ramonell
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Matthew C Woodruff
- Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology Emory University, Atlanta, GA, USA
| | - Christopher Tipton
- Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology Emory University, Atlanta, GA, USA
| | - Sarah Wise
- Department of Otolaryngology, Emory University, Atlanta, GA, USA
| | - Joshua Levy
- Department of Otolaryngology, Emory University, Atlanta, GA, USA
| | - John DelGaudio
- Department of Otolaryngology, Emory University, Atlanta, GA, USA
| | - Merin E Kuruvilla
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Kelly R Magliocca
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Deepak Tomar
- Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology Emory University, Atlanta, GA, USA
| | - Swetha Garimalla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Sanjeev Gumber
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Chris Fucile
- Department of Microbiology and Immunology, Informatics Institute, University of Alabama, Birmingham, AL, USA
| | - Greg Gibson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alexander Rosenberg
- Department of Microbiology and Immunology, Informatics Institute, University of Alabama, Birmingham, AL, USA
| | - Iñaki Sanz
- Division of Rheumatology, Department of Medicine, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology Emory University, Atlanta, GA, USA
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA.
- Lowance Center for Human Immunology Emory University, Atlanta, GA, USA.
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36
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Patterson DG, Kania AK, Zuo Z, Scharer CD, Boss JM. Epigenetic gene regulation in plasma cells. Immunol Rev 2021; 303:8-22. [PMID: 34010461 DOI: 10.1111/imr.12975] [Citation(s) in RCA: 9] [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] [Received: 04/05/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
Humoral immunity provides protection from pathogenic infection and is mediated by antibodies following the differentiation of naive B cells (nBs) to antibody-secreting cells (ASCs). This process requires substantial epigenetic and transcriptional rewiring to ultimately repress the nB program and replace it with one conducive to ASC physiology and function. Notably, these reprogramming events occur within the framework of cell division. Efforts to understand the relationship of cell division with reprogramming and ASC differentiation in vivo have uncovered the timing and scope of reprogramming, as well as key factors that influence these events. Herein, we discuss the unique physiology of ASC and how nBs undergo epigenetic and genome architectural reorganization to acquire the necessary functions to support antibody production. We also discuss the stage-wise manner in which reprogramming occurs across cell divisions and how key molecular determinants can influence B cell fate outcomes.
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Affiliation(s)
- Dillon G Patterson
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Anna K Kania
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Zhihong Zuo
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Xiangya School of Medicine, Central South University, Changsha, China
| | | | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
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37
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Risley CA, Scharer CD, Boss JM, Lund FE. T-bet expression marks a transcriptionally and functionally distinct population of memory B cells. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.114.18] [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: 02/10/2023]
Abstract
Abstract
Memory B cells (Bmem) rapidly differentiate and mount antibody (Ab) responses to previously encountered antigen (Ag). Mouse Bmem can be subdivided using BCR isotype or expression of CD73, CD80, and PD-L2. Many of these Bmem populations were discovered following vaccination with alum-adjuvanted Ag, which drives a distinct immune response from those generated after infection with IFN-inducing viruses. We previously demonstrated that the IFNγ-inducible transcription factor T-bet is required for Bmem recall responses to influenza but not nematode infections, suggesting that T-bet might regulate anti-viral Bmem. Therefore, we hypothesized that the anti-viral Bmem compartment likely contained cells that were distinct from the established subpopulations. Here, we show that T-bet expression within the flu-specific Bmem is heterogeneous and not restricted to any of the previously described Bmem subsets. Furthermore, B cell-intrinsic T-bet ablation caused the loss of one of these Bmem subpopulations, and inducible deletion of T-bet in Bmem caused the loss of the same subpopulation. To determine how T-bet regulates the Bmem compartment, we performed single-cell RNAseq and CITEseq on flu infection-induced Bmem. We identified numerous transcriptionally distinct clusters of Bmem, several of which express T-bet as well as genes associated with plasma cell function. Consistent with this, in vitro assays show that T-bet+ Bmem differentiate more robustly than T-betneg Bmem. These data show that the anti-viral Bmem compartment is heterogeneous and includes a T-bet expressing subpopulation that appears poised for rapid Ab responses. Thus, T-bet appears to be important for the maintenance and function of some, but not all, Bmem.
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Affiliation(s)
| | | | - Jeremy M. Boss
- 2Department of Microbiology and Immunology, Emory University
| | - Frances E Lund
- 1Department of Microbiology, University of Alabama at Birmingham
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38
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Zuo Z, Kania AK, Patterson DG, Scharer CD, Boss JM. Genomic Screening of B cell differentiation by using CRIPSR/Cas9. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.98.35] [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: 02/10/2023]
Abstract
Abstract
The differentiation of naïve B cells to antibody secreting plasma cells plays a crucial role in humoral immunity. This process is regulated by multiple factors including, transcription factors and epigenetic modifiers. Type II, clustered, regularly interspaced, short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems can be used to identify genes that influence a phenotype of interest. Herein, we established this system to identify novel regulators of plasma cell differentiation. To accomplish this, we transduced hematopoietic stem cells derived from mice expressing Cas9 specifically in B cells (Rosa26-Cas9, Cd19-Cre) with lentiviral based gRNAs targeting Ptprc (CD45), Irf8 and Bach2 and transplanted the stem cells into congenically disparate hosts. Hematopoietic stem cells are enriched with lineage depletion kit and then sorted by C-kit and Sca-1, followed by culture for 24 hours and spin-infection with corresponding lentivirus. After another 24-hour recovery, these cells are transferred to radioactively immune system destroyed hosts. Following immune constitution, B cells were isolated and the deletion of CD45, IRF8 and BACH2 was confirmed. Consistent with previous findings, deletion of IRF8 and BACH2 augmented plasma cell formation in ex vivo differentiation assays. Additionally, we used a genome-wide CRISPR gRNA lentiviral library targeting 18,424 genes to screen for factors that influenced B cell differentiation to LPS, IL-2 and IL-5. In conclusion, the CRISPR/Cas9 system allows us to rapidly generate genetic deletions to explore B cell differentiation in vivo and to discover novel factors that regulate plasma cell formation.
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Affiliation(s)
- Zhihong Zuo
- 1Department of Microbiology and Immunology, Emory University
- 2Xiangya School of Medicine, Central South University, China
| | - Anna K. Kania
- 1Department of Microbiology and Immunology, Emory University
| | | | | | - Jeremy M. Boss
- 1Department of Microbiology and Immunology, Emory University
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George-Alexander LE, Kania A, Mi T, Scharer CD, Boss JM. H3K9 dimethyltransferase G9a deficiency modulates B-cell response to LPS. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.63.08] [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: 02/09/2023]
Abstract
Abstract
B cell differentiation is a tightly regulated process coordinated by the timed expression of various transcription factors and chromatin accessibility changes mediated by histone modifying enzymes. The histone methyltransferase (HMT) G9a, dimethylates histone H3 lysine 9 (H3K9) at promoters and inhibits gene expression through recruitment of proteins that impair chromatin accessibility. HMTs are expressed ubiquitously but display distinct enzymatic activities and patterns of chromosomal localization. G9a is most known for co-localizing with Blimp-1 to silence genes associated with the B cell phenotype in plasma cells. However, our findings show a constitutive expression of G9a during B-cell division. In addition, B cell processes that are modulated by G9a mediated dimethylation remain to be elucidated. To study G9a’s involvement at various stages of B-cell differentiation, we crossed G9afl/fl mice onto the CD19Cre/+ background (G9aKO mice). Phenotypic characterization of these mice identified a skewing within the mature B cell population towards marginal zone (MZ) B cells in G9aKO mice. Upon challenge with LPS significantly elevated activated B-cell and plasmablast frequencies were observed in G9aKO mice. Regions with chromatin accessibility and expression changes identified by ATAC-Seq and RNA-Seq elucidated the B cell processes that are modulated in G9a deficient mice. B cell processes that are subject to direct modulation by G9a will be elucidated using CUT&Tag. Together, our data shows the importance of G9a in epigenetic modulation required for B cell function.
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Affiliation(s)
| | - Anna Kania
- 1Department of Microbiology and Immunology, Emory School of Medicine
| | - Tian Mi
- 1Department of Microbiology and Immunology, Emory School of Medicine
| | | | - Jeremy M Boss
- 1Department of Microbiology and Immunology, Emory School of Medicine
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Uddback IEM, Mattingly C, Thomas J, Kost KN, Li ZRT, Thomsen AR, Scharer CD, Christensen JP, Kohlmeier JE. Resident Memory CD8+ T cells in the respiratory tract prevent transmission of respiratory viruses. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.103.01] [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: 02/10/2023]
Abstract
Abstract
Tissue-resident memory CD8+ T cells (TRM) in the respiratory tract reduce viral replication and limit pathology following respiratory virus infections. In infection with heterosubtypic influenza viruses, where pre-existing antibodies does not proved sterilizing immunity, TRM are critical for protection. However, in addition to protecting the host against disease vaccine programs are also designed to limit viral spread in a population. Due to the lack of an animal model to study the effect of TRM on transmission through longitudinal tracking, and with immunological parameters easily identified and manipulated available, this hasn’t been studied before. To solve these issues, we used a luciferase expressing Sendai virus, a natural mouse parainfluenza virus that readily transmits via the aerosol and contact routes, as well as a recombinant influenza virus expressing the immunodominant Sendai NP324-332/Kb epitope to generate SenNP+ memory CD8+ T cells. By utilizing IVIS imaging to non-invasively measure Sendai virus infection over time, we found that mice with pre-existing SenNP+ TRM in the respiratory system don’t transmit Sendai virus to naïve mice when co-housed. In contrast, mice with pre-existing circulating SenNP+ effector memory CD8+ T cells, but no TRM, failed to prevent transmission of Sendai virus to naïve mice when co-housed. In addition, we found that the prevention of transmission was dependent on the production of IFNγ. These findings demonstrates notably that antigen specific lung TRM contributes to herd immunity by preventing respiratory virus transmission. This underscores the importance, and potential, of TRMs generated by vaccines for protection against respiratory viruses.
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Lobby JL, Uddback IEM, Scharer CD, Mi T, Boss JM, Thomsen AR, Christensen JP, Kohlmeier JE. Identifying mechanisms that enhance the longevity of tissue-resident memory CD8+ T cells in the lung. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.103.24] [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: 02/10/2023]
Abstract
Abstract
Lung tissue-resident memory CD8+ T cells (TRM) are crucial mediators of cellular immunity against influenza viruses, but the number of these cells in the lung tissue gradually declines in the months following influenza infection. Recently, we showed that intranasal immunization with a replication-deficient adenovirus that expresses the nucleoprotein from influenza A virus (AdNP) results in long-term maintenance of lung CD8+ TRM for up to 1-year post-immunization. However, the mechanism(s) that promote this enhanced longevity of FluNP-specific CD8+ lung TRM remain unknown. Using a combination of mouse infection models, flow cytometry, and RNA-sequencing, we compared CD8+ T cells from the airways, lungs, and spleen of AdNP-immunized or influenza x31-infected mice. We found that CD8+ TRM in the lungs of AdNP-immunized mice show increased homeostatic turnover and hallmarks of persistent antigen stimulation in the lung. However, RNA-sequencing analysis comparing lung CD8+ TRM from AdNP-immunized and x31-infected mice at 1-month and 1-year post-immunization showed only minor variations that did not fully explain the differences in lung TRM persistence. Lineage tracing experiments using a Cre recombinase-expressing Adenovirus (AdCre) identified alveolar macrophages as the primary cell type harboring persistent antigen in the lung. Together, these results define one mechanism for enhancing the durability of lung TRM, which is an important consideration for the design of future cell-mediated influenza vaccines
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Affiliation(s)
- Jenna L Lobby
- 1Department of Microbiology and Immunology, Emory University School of Medicine
| | | | | | - Tian Mi
- 1Department of Microbiology and Immunology, Emory University School of Medicine
| | - Jeremy M. Boss
- 1Department of Microbiology and Immunology, Emory University School of Medicine
| | - Allan R Thomsen
- 2Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | | | - Jacob E Kohlmeier
- 1Department of Microbiology and Immunology, Emory University School of Medicine
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Majumder P, Lee JT, Barwick BG, Patterson DG, Bally APR, Scharer CD, Boss JM. The Murine MHC Class II Super Enhancer IA/IE-SE Contains a Functionally Redundant CTCF-Binding Component and a Novel Element Critical for Maximal Expression. J Immunol 2021; 206:2221-2232. [PMID: 33863790 DOI: 10.4049/jimmunol.2001089] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/01/2021] [Indexed: 11/19/2022]
Abstract
In both humans and mice, CTCF-binding elements form a series of interacting loops across the MHC class II (MHC-II) locus, and CTCF is required for maximal MHC-II gene expression. In humans, a CTCF-bound chromatin insulator termed XL9 and a super enhancer (SE) DR/DQ-SE situated in the intergenic region between HLA-DRB1 and HLA-DQA1 play critical roles in regulating MHC-II expression. In this study, we identify a similar SE, termed IA/IE-SE, located between H2-Eb1 and H2-Aa of the mouse that contains a CTCF site (C15) and a novel region of high histone H3K27 acetylation. A genetic knockout of C15 was created and its role on MHC-II expression tested on immune cells. We found that C15 deletion did not alter MHC-II expression in B cells, macrophages, and macrophages treated with IFN-γ because of functional redundancy of the remaining MHC-II CTCF sites. Surprisingly, embryonic fibroblasts derived from C15-deleted mice failed to induce MHC-II gene expression in response to IFN-γ, suggesting that at least in this developmental lineage, C15 was required. Examination of the three-dimensional interactions with C15 and the H2-Eb1 and H2-Aa promoters identified interactions within the novel region of high histone acetylation within the IA/IE-SE (termed N1) that contains a PU.1 binding site. CRISPR/Cas9 deletion of N1 altered chromatin interactions across the locus and resulted in reduced MHC-II expression. Together, these data demonstrate the functional redundancy of the MHC-II CTCF elements and identify a functionally conserved SE that is critical for maximal expression of MHC-II genes.
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Affiliation(s)
- Parimal Majumder
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Joshua T Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Benjamin G Barwick
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Alexander P R Bally
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
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Price MJ, Scharer CD, Kania AK, Randall TD, Boss JM. Conserved Epigenetic Programming and Enhanced Heme Metabolism Drive Memory B Cell Reactivation. J Immunol 2021; 206:1493-1504. [PMID: 33627377 DOI: 10.4049/jimmunol.2000551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/25/2021] [Indexed: 02/01/2023]
Abstract
Memory B cells (MBCs) have enhanced capabilities to differentiate to plasma cells and generate a rapid burst of Abs upon secondary stimulation. To determine if MBCs harbor an epigenetic landscape that contributes to increased differentiation potential, we derived the chromatin accessibility and transcriptomes of influenza-specific IgM and IgG MBCs compared with naive cells. MBCs possessed an accessible chromatin architecture surrounding plasma cell-specific genes, as well as altered expression of transcription factors and genes encoding cell cycle, chemotaxis, and signal transduction processes. Intriguingly, this MBC signature was conserved between humans and mice. MBCs of both species possessed a heightened heme signature compared with naive cells. Differentiation in the presence of hemin enhanced oxidative phosphorylation metabolism and MBC differentiation into Ab-secreting plasma cells. Thus, these data define conserved MBC transcriptional and epigenetic signatures that include a central role for heme and multiple other pathways in augmenting MBC reactivation potential.
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Affiliation(s)
- Madeline J Price
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Anna K Kania
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - Troy D Randall
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322; .,Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322
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44
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Squires KE, Gerber KJ, Tillman MC, Lustberg DJ, Montañez-Miranda C, Zhao M, Ramineni S, Scharer CD, Saha RN, Shu FJ, Schroeder JP, Ortlund EA, Weinshenker D, Dudek SM, Hepler JR. Human genetic variants disrupt RGS14 nuclear shuttling and regulation of LTP in hippocampal neurons. J Biol Chem 2021; 296:100024. [PMID: 33410399 PMCID: PMC7949046 DOI: 10.1074/jbc.ra120.016009] [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: 09/11/2020] [Revised: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
The human genome contains vast genetic diversity as naturally occurring coding variants, yet the impact of these variants on protein function and physiology is poorly understood. RGS14 is a multifunctional signaling protein that suppresses synaptic plasticity in dendritic spines of hippocampal neurons. RGS14 also is a nucleocytoplasmic shuttling protein, suggesting that balanced nuclear import/export and dendritic spine localization are essential for RGS14 functions. We identified genetic variants L505R (LR) and R507Q (RQ) located within the nuclear export sequence (NES) of human RGS14. Here we report that RGS14 encoding LR or RQ profoundly impacts protein functions in hippocampal neurons. RGS14 membrane localization is regulated by binding Gαi-GDP, whereas RGS14 nuclear export is regulated by Exportin 1 (XPO1). Remarkably, LR and RQ variants disrupt RGS14 binding to Gαi1-GDP and XPO1, nucleocytoplasmic equilibrium, and capacity to inhibit long-term potentiation (LTP). Variant LR accumulates irreversibly in the nucleus, preventing RGS14 binding to Gαi1, localization to dendritic spines, and inhibitory actions on LTP induction, while variant RQ exhibits a mixed phenotype. When introduced into mice by CRISPR/Cas9, RGS14-LR protein expression was detected predominantly in the nuclei of neurons within hippocampus, central amygdala, piriform cortex, and striatum, brain regions associated with learning and synaptic plasticity. Whereas mice completely lacking RGS14 exhibit enhanced spatial learning, mice carrying variant LR exhibit normal spatial learning, suggesting that RGS14 may have distinct functions in the nucleus independent from those in dendrites and spines. These findings show that naturally occurring genetic variants can profoundly alter normal protein function, impacting physiology in unexpected ways.
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Affiliation(s)
- Katherine E Squires
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta Georgia, USA
| | - Kyle J Gerber
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta Georgia, USA
| | | | - Daniel J Lustberg
- Department of Human Genetics, Emory University, Atlanta Georgia, USA
| | | | - Meilan Zhao
- National Institute of Environmental Health Sciences, Research Triangle Park, Raleigh North Carolina, USA
| | - Suneela Ramineni
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta Georgia, USA
| | | | - Ramendra N Saha
- Department of Molecular & Cell Biology, University of California-Merced, Merced California, USA
| | - Feng-Jue Shu
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta Georgia, USA
| | - Jason P Schroeder
- Department of Human Genetics, Emory University, Atlanta Georgia, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University, Atlanta Georgia, USA
| | - David Weinshenker
- Department of Human Genetics, Emory University, Atlanta Georgia, USA
| | - Serena M Dudek
- National Institute of Environmental Health Sciences, Research Triangle Park, Raleigh North Carolina, USA
| | - John R Hepler
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta Georgia, USA.
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45
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Wiggins KJ, Scharer CD. Roadmap to a plasma cell: Epigenetic and transcriptional cues that guide B cell differentiation. Immunol Rev 2020; 300:54-64. [PMID: 33278036 DOI: 10.1111/imr.12934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 10/03/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022]
Abstract
Antibody-secreting cells (ASCs) or plasma cells secrete antibodies and form a cornerstone of humoral immunity. B cells that receive activation signals in the presence or absence of T cells initiate a differentiation program that requires epigenetic and transcriptional reprogramming in order to ultimately form ASC. Reprogramming is accomplished through the interplay of transcription factors that initiate gene expression programs and epigenetic mechanisms that maintain these programs and cell fates. An important consideration is that all of these factors are operating in the context of cell division. Recent technical advances now allow mechanistic studies to move beyond genetic studies to identify the promoters and enhancer repertoires that are regulated by epigenetic mechanisms and transcription factors in rare cell types and differentiation stages in vivo. This review will detail efforts to integrate transcriptional and epigenetic changes during B cell differentiation with cell division in vivo. What has emerged is a multiphased differentiation model that requires distinct transcription factors and epigenetic programs at each step. The identification of markers that define each phase will help facilitate the manipulation of B cell differentiation for vaccine development or to treat diseases where antibodies are a component.
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Affiliation(s)
- Keenan J Wiggins
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
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Scharer CD, Fortner KA, Dragon JA, Tighe S, Boss JM, Budd RC. Selective DNA Demethylation Accompanies T Cell Homeostatic Proliferation and Gene Regulation in Lupus-Prone lpr Mice. Immunohorizons 2020; 4:679-687. [PMID: 33097564 PMCID: PMC8141279 DOI: 10.4049/immunohorizons.2000078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/06/2020] [Indexed: 11/19/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is characterized by increased DNA demethylation in T cells, although it is unclear whether this occurs primarily in a subset of SLE T cells. The process driving the DNA demethylation and the consequences on overall gene expression are also poorly understood and whether this represents a secondary consequence of SLE or a primary contributing factor. Lupus-prone lpr mice accumulate large numbers of T cells with age because of a mutation in Fas (CD95). The accumulating T cells include an unusual population of CD4-CD8-TCR-αβ+ (DN) T cells that arise from CD8+ precursors and are also found in human SLE. We have previously observed that T cell accumulation in lpr mice is due to dysregulation of T cell homeostatic proliferation, which parallels an increased expression of numerous genes in the DN subset, including several proinflammatory molecules and checkpoint blockers. We thus determined the DNA methylome in lpr DN T cells compared with their CD8+ precursors. Our findings show that DN T cells manifest discrete sites of extensive demethylation throughout the genome, and these sites correspond to the location of a large proportion of the upregulated genes. Thus, dysregulated homeostatic proliferation in lpr mice and consequent epigenetic alterations may be a contributing factor to lupus pathogenesis.
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Affiliation(s)
- Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322;
| | - Karen A Fortner
- Vermont Center for Immunology and Infectious Diseases, Department of Medicine, University of Vermont Larner College of Medicine, Burlington, VT 05405; and
| | - Julie A Dragon
- Vermont Integrative Genomics Resource, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Scott Tighe
- Vermont Integrative Genomics Resource, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Jeremy M Boss
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322
| | - Ralph C Budd
- Vermont Center for Immunology and Infectious Diseases, Department of Medicine, University of Vermont Larner College of Medicine, Burlington, VT 05405; and
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47
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Inglis GAS, Zhou Y, Patterson DG, Scharer CD, Han Y, Boss JM, Wen Z, Escayg A. Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons. Hum Mol Genet 2020; 29:2579-2595. [PMID: 32794569 PMCID: PMC7471504 DOI: 10.1093/hmg/ddaa150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/09/2020] [Accepted: 07/11/2020] [Indexed: 12/13/2022] Open
Abstract
GABAergic interneurons (GINs) are a heterogeneous population of inhibitory neurons that collectively contribute to the maintenance of normal neuronal excitability and network activity. Identification of the genetic regulatory elements and transcription factors that contribute toward GIN function may provide new insight into the pathways underlying proper GIN activity while also indicating potential therapeutic targets for GIN-associated disorders, such as schizophrenia and epilepsy. In this study, we examined the temporal changes in gene expression and chromatin accessibility during GIN development by performing transcriptomic and epigenomic analyses on human induced pluripotent stem cell-derived neurons at 22, 50 and 78 days (D) post-differentiation. We observed 13 221 differentially accessible regions (DARs) of chromatin that associate with temporal changes in gene expression at D78 and D50, relative to D22. We also classified families of transcription factors that are increasingly enriched at DARs during differentiation, indicating regulatory networks that likely drive GIN development. Collectively, these data provide a resource for examining the molecular networks regulating GIN functionality.
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Affiliation(s)
- George Andrew S Inglis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ying Zhou
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yanfei Han
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, 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
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew Escayg
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Scharer CD, Patterson DG, Mi T, Price MJ, Hicks SL, Boss JM. Antibody-secreting cell destiny emerges during the initial stages of B-cell activation. Nat Commun 2020; 11:3989. [PMID: 32778653 PMCID: PMC7417592 DOI: 10.1038/s41467-020-17798-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 05/04/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023] Open
Abstract
Upon stimulation, B cells assume heterogeneous cell fates, with only a fraction differentiating into antibody-secreting cells (ASC). Here we investigate B cell fate programming and heterogeneity during ASC differentiation using T cell-independent models. We find that maximal ASC induction requires at least eight cell divisions in vivo, with BLIMP-1 being required for differentiation at division eight. Single cell RNA-sequencing of activated B cells and construction of differentiation trajectories reveal an early cell fate bifurcation. The ASC-destined branch requires induction of IRF4, MYC-target genes, and oxidative phosphorylation, with the loss of CD62L expression serving as a potential early marker of ASC fate commitment. Meanwhile, the non-ASC branch expresses an inflammatory signature, and maintains B cell fate programming. Finally, ASC can be further subseted based on their differential responses to ER-stress, indicating multiple development branch points. Our data thus define the cell division kinetics of B cell differentiation in vivo, and identify the molecular trajectories of B cell fate and ASC formation.
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Affiliation(s)
- Christopher D Scharer
- Department of Microbiology and Immunology and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Dillon G Patterson
- Department of Microbiology and Immunology and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tian Mi
- Department of Microbiology and Immunology and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Madeline J Price
- Department of Microbiology and Immunology and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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Saini A, Duan M, Mi T, Hicks S, Lee EH, Scharer CD, Boss JM, Gibson G, Sanz I. Defining altered regulome structured in response to antigen co-receptors, toll-like receptors, and cytokine receptors stimuli to predispose early developing B cells for pathogenic fate in Systemic lupus erythematosus. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.218.6] [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: 01/03/2023]
Abstract
Abstract
A TLR7-IFNg driven IL-21 mediated unique extra-follicular pathway of ASC differentiation of activated naïve B cells through an intermediary DN2 B cell subset has been characterized in pathogenesis of SLE. It has been correlated to distinct priming of naïve B cells characterized by the presence of SLE disease signatures which indicates towards the convergence of TLR, and cytokine signaling along with BCR signaling in the expansion and differentiation of peripheral B cells in SLE. Thus, we hypothesize that distinct combinations of innate, cytokines and antigen driven stimuli cause pathogenesis of SLE by maneuvering disease-related epigenetic programs and molecular networks during B cell development resulting in perturbed activation and differentiation. Indeed, initial data from bulk RNA-seq show enrichment of Type I interferon production and signature genes in HSCs to transitional B cells in SLE BM. Confounded by scRNA-seq, these populations also show profound type II interferon signature genes in SLE BM. Interestingly, BCR devoid Pro-B cells show reduced expression of BCR signaling intermediates with enhanced proliferation. However, expression of Pre-BCR or BCR on the surface of Pre-B cells or Immature B cells respectively are accompanied by increased expression of BCR co-receptors in SLE BM. On the other hand, metabolically SLE early BM B cells are less dependent on oxidative phosphorylation with reduced protein synthesis and processing. Together, these initial findings provide evidence that the proinflammatory microenvironment in SLE BM exerts its effect by differentially regulating BCR signaling factors and co-receptors in early B cell populations and thereby could define the pathogenic fate of B cell in periphery in SLE.
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Patterson D, Scharer CD, Mi T, Hicks SL, Zhang Q, Boss JM. IRF4 regulates the proliferative capacity of activated B cells during B cell differentiation. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.151.26] [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
Cell division is essential for B cell differentiation to a plasma cell (PC). While the cell division coupled changes in the expression of transcription factors that coordinate the PC program have been described, little is known regarding how these factors coordinate the proliferative program. To address this, we exploited an adoptive transfer system and monitored the cell division/differentiation kinetics in response to lipopolysaccharide (LPS). In this system, wildtype (WT) B cells undergo at least 8 cell divisions before differentiating into PC, and the same requirement is also observed following NP-ficoll or influenza immune challenge. Modeling division rates over time identified a proliferative burst between 48 and 60 hours following LPS injection. In contrast, Interferon Regulatory Factor 4-deficient (IRF4−/−) B cells divided but failed to undergo the proliferative burst, stalling at divisions 2–6. To assess the scope of IRF4-dependent reprogramming, WT and IRF4−/− B cells at divisions 0, 1, and 3–6 were sorted for ATAC- and RNA-seq. RNA-seq data revealed hundreds of differentially expressed genes (DEGs) when IRF4 was deleted, a subset of which included MYC target genes. Indeed, IRF4−/− cells failed to upregulate MYC compared to WT cells and consequently, we observed little increase in cell size following immune challenge. Furthermore, IRF4−/− B cells exhibited aberrant cell cycle distribution when compared to WT cells at the same timepoint and division. ATAC-seq data also exposed hundreds of differentially accessible regions, the majority of which contained a known IRF4 binding motif and mapped to a corresponding DEG. Together, these data reveal a critical role for IRF4 in maintaining the proliferative response.
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