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Ranek JS, Stallaert W, Milner JJ, Redick M, Wolff SC, Beltran AS, Stanley N, Purvis JE. DELVE: feature selection for preserving biological trajectories in single-cell data. Nat Commun 2024; 15:2765. [PMID: 38553455 PMCID: PMC10980758 DOI: 10.1038/s41467-024-46773-z] [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: 05/18/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Single-cell technologies can measure the expression of thousands of molecular features in individual cells undergoing dynamic biological processes. While examining cells along a computationally-ordered pseudotime trajectory can reveal how changes in gene or protein expression impact cell fate, identifying such dynamic features is challenging due to the inherent noise in single-cell data. Here, we present DELVE, an unsupervised feature selection method for identifying a representative subset of molecular features which robustly recapitulate cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effects of confounding sources of variation, and instead models cell states from dynamic gene or protein modules based on core regulatory complexes. Using simulations, single-cell RNA sequencing, and iterative immunofluorescence imaging data in the context of cell cycle and cellular differentiation, we demonstrate how DELVE selects features that better define cell-types and cell-type transitions. DELVE is available as an open-source python package: https://github.com/jranek/delve .
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Affiliation(s)
- Jolene S Ranek
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Margaret Redick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel C Wolff
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adriana S Beltran
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Natalie Stanley
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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2
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Alvarez-Breckenridge C, Anderson KG, Correia AL, Demehri S, Dinh HQ, Dixon KO, Dunn GP, Evgin L, Goc J, Good Z, Hacohen N, Han P, Hanč P, Hickey J, Kersten K, Liu BC, Buque A, Miao Y‘P, Milner JJ, Pritykin Y, Pucci F, Scharping NE, Sudmeier L, Wang Y, Wieland A, Williams MM. Lessons for the Next Generation of Scientists from the Second Annual Arthur and Sandra Irving Cancer Immunology Symposium. Cancer Immunol Res 2023; 11:1571-1577. [PMID: 37906619 PMCID: PMC10696930 DOI: 10.1158/2326-6066.cir-23-0522] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023]
Abstract
The Arthur and Sandra Irving Cancer Immunology Symposium has been created as a platform for established cancer immunologists to mentor trainees and young investigators as they launch their research career in the field. By sharing their different paths to success, the senior faculty mentors provide an invaluable resource to support the development of the next generation of leaders in the cancer immunology community. This Commentary describes some of the key topics that were discussed during the 2022 symposium: scientific and career trajectory, leadership, mentoring, collaborations, and publishing. For each of these topics, established investigators discussed the elements that facilitate success in these areas as well as mistakes that can hinder progress. Herein, we outline the critical points raised in these discussions for establishing a successful independent research career. These points are highly relevant for the broader scientific community.
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Affiliation(s)
| | - Kristin G. Anderson
- Department of Microbiology, Immunology and Cancer Biology, Carter Center for Immunology Research, University of Virginia, Charlottesville, Virginia
- Department of Obstetrics and Gynecology, University of Virginia, Charlottesville, Virginia
| | | | - Shadmehr Demehri
- Center for Cancer Immunology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Huy Q. Dinh
- McArdle Laboratory for Cancer Research/Department of Oncology, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Karen Olivia Dixon
- Department of Neurology, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Gavin P. Dunn
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Laura Evgin
- Michael Smith Genome Sciences Department, BC Cancer Research Institute, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jeremy Goc
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, New York
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medicine, Cornell University, New York, New York
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, New York
| | - Zinaida Good
- Stanford Cancer Institute and Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
| | - Nir Hacohen
- Center for Cancer Immunology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Patrick Han
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Pavel Hanč
- Department of Immunology, Harvard Medical School, Boston, Massachusetts
| | - John Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Kelly Kersten
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Beiyun C. Liu
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Aitziber Buque
- Department of Radiation Oncology, Weill Cornell Medical College, New York, New York
| | | | - J. Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics and Department of Computer Science, Princeton University, New Jersey
| | - Ferdinando Pucci
- Department of Otolaryngology and Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Nicole E. Scharping
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, California
| | - Lisa Sudmeier
- Department of Radiation Oncology, Winship Cancer Institute and Emory University School of Medicine, Atlanta, Georgia
| | - Yufei Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Andreas Wieland
- Department of Otolaryngology and Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
- James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Michelle M. Williams
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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3
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Ulibarri MR, Lin Y, Ramprashad JR, Han G, Hasan MH, Mithila FJ, Ma C, Gopinath S, Zhang N, Milner JJ, Beura LK. Epithelial organoid supports resident memory CD8 T cell differentiation. bioRxiv 2023:2023.12.01.569395. [PMID: 38076957 PMCID: PMC10705482 DOI: 10.1101/2023.12.01.569395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Resident Memory T cells (TRM) play a vital role in regional immune defense in barrier organs. Although laboratory rodents have been extensively used to study fundamental TRM biology, poor isolation efficiency, sampling bias and low cell survival rates have limited our ability to conduct TRM-focused high-throughput assays. Here, we engineered a murine vaginal epithelial organoid (VEO)-CD8 T cell co-culture system that supports CD8 TRM differentiation in vitro. The three-dimensional VEOs established from murine adult stem cells resembled stratified squamous vaginal epithelium and induced gradual differentiation of activated CD8 T cells into epithelial TRM. These in vitro generated TRM were phenotypically and transcriptionally similar to in vivo TRM, and key tissue residency features were reinforced with a second cognate-antigen exposure during co-culture. TRM differentiation was not affected even when VEOs and CD8 T cells were separated by a semipermeable barrier, indicating soluble factors' involvement. Pharmacological and genetic approaches showed that TGF-β signaling played a crucial role in their differentiation. We found that the VEOs in our model remained susceptible to viral infections and the CD8 T cells were amenable to genetic manipulation; both of which will allow detailed interrogation of antiviral CD8 T cell biology in a reductionist setting. In summary, we established a robust model which captures bonafide TRM differentiation that is scalable, open to iterative sampling, and can be subjected to high throughput assays that will rapidly add to our understanding of TRM.
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Affiliation(s)
- Max R. Ulibarri
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
| | - Ying Lin
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
- Pathobiology Graduate Program, Brown University, Providence, RI, 02912
| | - Julian R. Ramprashad
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
| | - Geongoo Han
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
| | - Mohammad H. Hasan
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
| | - Farha J. Mithila
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
- Molecular Biology, Cell Biology and Biochemistry Graduate Program, Brown University, Providence, RI, 02912
| | - Chaoyu Ma
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX, 78229
| | - Smita Gopinath
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Cambridge, MA, 02115
| | - Nu Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX, 78229
- South Texas Veterans Health Care System, San Antonio, TX, 78229
| | - J. Justin Milner
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599
| | - Lalit K. Beura
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912
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4
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Reina-Campos M, Heeg M, Kennewick K, Mathews IT, Galletti G, Luna V, Nguyen Q, Huang H, Milner JJ, Hu KH, Vichaidit A, Santillano N, Boland BS, Chang JT, Jain M, Sharma S, Krummel MF, Chi H, Bensinger SJ, Goldrath AW. Metabolic programs of T cell tissue residency empower tumour immunity. Nature 2023; 621:179-187. [PMID: 37648857 DOI: 10.1038/s41586-023-06483-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
Tissue resident memory CD8+ T (TRM) cells offer rapid and long-term protection at sites of reinfection1. Tumour-infiltrating lymphocytes with characteristics of TRM cells maintain enhanced effector functions, predict responses to immunotherapy and accompany better prognoses2,3. Thus, an improved understanding of the metabolic strategies that enable tissue residency by T cells could inform new approaches to empower immune responses in tissues and solid tumours. Here, to systematically define the basis for the metabolic reprogramming supporting TRM cell differentiation, survival and function, we leveraged in vivo functional genomics, untargeted metabolomics and transcriptomics of virus-specific memory CD8+ T cell populations. We found that memory CD8+ T cells deployed a range of adaptations to tissue residency, including reliance on non-steroidal products of the mevalonate-cholesterol pathway, such as coenzyme Q, driven by increased activity of the transcription factor SREBP2. This metabolic adaptation was most pronounced in the small intestine, where TRM cells interface with dietary cholesterol and maintain a heightened state of activation4, and was shared by functional tumour-infiltrating lymphocytes in diverse tumour types in mice and humans. Enforcing synthesis of coenzyme Q through deletion of Fdft1 or overexpression of PDSS2 promoted mitochondrial respiration, memory T cell formation following viral infection and enhanced antitumour immunity. In sum, through a systematic exploration of TRM cell metabolism, we reveal how these programs can be leveraged to fuel memory CD8+ T cell formation in the context of acute infections and enhance antitumour immunity.
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Affiliation(s)
- Miguel Reina-Campos
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Maximilian Heeg
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Kelly Kennewick
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ian T Mathews
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Giovanni Galletti
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Vida Luna
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Quynhanh Nguyen
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Hongling Huang
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - J Justin Milner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Kenneth H Hu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Amy Vichaidit
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Natalie Santillano
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mohit Jain
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sonia Sharma
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Matthew F Krummel
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Steven J Bensinger
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ananda W Goldrath
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA.
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5
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Pratt BM, Milner JJ. Cancer immunosurveillance by gut T cells. Science 2023; 380:1011-1012. [PMID: 37289885 DOI: 10.1126/science.adi3357] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
T cells primed in the gut influence immune responses to extraintestinal tumors.
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Affiliation(s)
- Brandon M Pratt
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - J Justin Milner
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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6
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Nguyen QP, Takehara KK, Deng TZ, O’Shea S, Heeg M, Omilusik KD, Milner JJ, Quon S, Pipkin ME, Choi J, Crotty S, Goldrath AW. Transcriptional programming of CD4 + T RM differentiation in viral infection balances effector- and memory-associated gene expression. Sci Immunol 2023; 8:eabq7486. [PMID: 37172104 PMCID: PMC10350289 DOI: 10.1126/sciimmunol.abq7486] [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: 04/27/2022] [Accepted: 04/19/2023] [Indexed: 05/14/2023]
Abstract
After resolution of infection, T cells differentiate into long-lived memory cells that recirculate through secondary lymphoid organs or establish residence in tissues. In contrast to CD8+ tissue-resident memory T cells (TRM), the developmental origins and transcriptional regulation of CD4+ TRM remain largely undefined. Here, we investigated the phenotypic, functional, and transcriptional profiles of CD4+ TRM in the small intestine (SI) responding to acute viral infection, revealing a shared gene expression program and chromatin accessibility profile with circulating TH1 and the progressive acquisition of a mature TRM program. Single-cell RNA sequencing identified heterogeneity among established CD4+ TRM, which were predominantly located in the lamina propria, and revealed a population of cells that coexpressed both effector- and memory-associated genes, including the transcriptional regulators Blimp1, Id2, and Bcl6. TH1-associated Blimp1 and Id2 and TFH-associated Bcl6 were required for early TRM formation and development of a mature TRM population in the SI. These results demonstrate a developmental relationship between TH1 effector cells and the establishment of early TRM, as well as highlighted differences in CD4+ versus CD8+ TRM populations, providing insights into the mechanisms underlying the origins, differentiation, and persistence of CD4+ TRM in response to viral infection.
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Affiliation(s)
- Quynh P Nguyen
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Kennidy K Takehara
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Tianda Z Deng
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Shannon O’Shea
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Maximilian Heeg
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Kyla D Omilusik
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - J Justin Milner
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Sara Quon
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida
| | - Jinyong Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Ananda W Goldrath
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
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7
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Quon S, Yu B, Russ BE, Tsyganov K, Nguyen H, Toma C, Heeg M, Hocker JD, Milner JJ, Crotty S, Pipkin ME, Turner SJ, Goldrath AW. DNA architectural protein CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8 + T cells. Immunity 2023; 56:959-978.e10. [PMID: 37040762 PMCID: PMC10265493 DOI: 10.1016/j.immuni.2023.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 05/30/2022] [Revised: 11/14/2022] [Accepted: 03/20/2023] [Indexed: 04/13/2023]
Abstract
Although the importance of genome organization for transcriptional regulation of cell-fate decisions and function is clear, the changes in chromatin architecture and how these impact effector and memory CD8+ T cell differentiation remain unknown. Using Hi-C, we studied how genome configuration is integrated with CD8+ T cell differentiation during infection and investigated the role of CTCF, a key chromatin remodeler, in modulating CD8+ T cell fates through CTCF knockdown approaches and perturbation of specific CTCF-binding sites. We observed subset-specific changes in chromatin organization and CTCF binding and revealed that weak-affinity CTCF binding promotes terminal differentiation of CD8+ T cells through the regulation of transcriptional programs. Further, patients with de novo CTCF mutations had reduced expression of the terminal-effector genes in peripheral blood lymphocytes. Therefore, in addition to establishing genome architecture, CTCF regulates effector CD8+ T cell heterogeneity through altering interactions that regulate the transcription factor landscape and transcriptome.
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Affiliation(s)
- Sara Quon
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bingfei Yu
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Kirill Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Hongtuyet Nguyen
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clara Toma
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maximilian Heeg
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - James D Hocker
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - J Justin Milner
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Ananda W Goldrath
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Green WD, Mullins GN, Green JM, Baldwin A, Milner JJ. Molecular regulation of CD8 T cell activity and heterogeneity in pancreatic cancer. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.118.17] [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
T cell dysfunction or ‘exhaustion’ is a hallmark of solid malignancies. Despite the critical importance of CD8 T lymphocytes in controlling tumor growth and immunotherapy efficacy, the mechanisms governing T cell exhaustion remain unclear. Here, we focused on resolving the heterogeneity and molecular programming of exhausted CD8 T cell states in the context of pancreatic cancer. Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with a discouraging 5-year survival rate of approximately 8%. PDAC tumors commonly present as immunologically ‘cold’, devoid of protective T cell populations, and are typically resistant to promising immunotherapies such as immune checkpoint blockade or adoptive cell therapy. Therefore, understanding the unique microenvironmental and CD8 T cell-intrinsic signals governing T cell exhaustion and accumulation in PDAC tumors may reveal crucial insight for engineering CD8 T cells for optimal immunotherapy efficacy. Here, we developed preclinical PDAC models for profiling tumor-specific murine CD8 T cell responses. Through application of spectral flow cytometry and multimodal single-cell sequencing approaches, we have uncovered impressively diverse antigen-specific CD8 T cell states in PDAC tumors. Select CD8 T cell populations identified within the PDAC tumor microenvironment included canonical populations of terminally-exhausted and progenitor-exhausted CD8 T cells as well as unexpected and uncharacterized CD8 T cell populations. Accordingly, we also have identified critical transcription factors controlling key features of CD8 T cell heterogeneity and persistence in PDAC tumors. These findings may ultimately provide insight for tailoring CD8 T cell fate and function in PDAC.
Supported by 2022 AAI Intersect Fellowship for Computational Scientists and Immunologists
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Affiliation(s)
- William D Green
- 1Microbiology & Immunology, University of North Carolina at Chapel Hill
| | | | | | - Albert Baldwin
- 3Cancer Cell Biology, University of North Carolina at Chapel Hill
| | - J Justin Milner
- 2Microbiology & Immunology, Univ. of North Carolina at Chapel Hill
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9
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Mullins GN, Green JM, Green WD, Milner JJ. CD8 T cell exhaustion is dynamically controlled by the chromatin regulator factor BRD4. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.182.05] [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
In the context of chronic viral infections and cancer, the protective potential of CD8 T lymphocytes is often dramatically blunted and characterized by a functionally exhausted cell state. T cell exhaustion contributes to pathogen persistence and can limit responsiveness to promising immunotherapy strategies. Therefore, defining the signals controlling the development and maintenance of an exhausted T cell state has critical implications for global public health. While it has become apparent that T cell exhaustion is a transcriptionally and epigenetically driven process, critical epigenetic mechanisms mediating T cell exhaustion remain unresolved. To this end, we sought to define how the ‘chromatin reader’ BRD4 controls an exhausted state in a CD8 T cell-intrinsic manner during chronic viral infection. Utilizing inducible deletion mouse models and RNAi, we found that BRD4 is a critical regulator of T cell differentiation and function. BRD4 was essential for driving a terminally exhausted CD8 T cell state. Mechanistically, BRD4 was found to bind near and modulate expression of key genes that influence T cell differentiation and exhaustion. These findings provide insights into the epigenetic underpinnings of T cell exhaustion and have important implications for enhancing immunotherapy efficacy.
Supported by grants
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Affiliation(s)
| | | | | | - J Justin Milner
- 1Microbiology and Immunology, Univ. of North Carolina at Chapel Hill
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10
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Green WD, Al-Shaer AE, Shi Q, Gowdy KM, MacIver NJ, Milner JJ, Beck MA, Shaikh SR. Metabolic and functional impairment of CD8 + T cells from the lungs of influenza-infected obese mice. J Leukoc Biol 2022; 111:147-159. [PMID: 33847405 PMCID: PMC8787296 DOI: 10.1002/jlb.4a0120-075rr] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/25/2022] Open
Abstract
Obesity is an independent risk factor for morbidity and mortality in response to influenza infection. However, the underlying mechanisms by which obesity impairs immunity are unclear. Herein, we investigated the effects of diet-induced obesity on pulmonary CD8+ T cell metabolism, cytokine production, and transcriptome as a potential mechanism of impairment during influenza virus infection in mice. Male C57BL/6J lean and obese mice were infected with sub-lethal mouse-adapted A/PR/8/34 influenza virus, generating a pulmonary anti-viral and inflammatory response. Extracellular metabolic flux analyses revealed pulmonary CD8+ T cells from obese mice, compared with lean controls, had suppressed oxidative and glycolytic metabolism at day 10 post-infection. Flow cytometry showed the impairment in pulmonary CD8+ T cell metabolism with obesity was independent of changes in glucose or fatty acid uptake, but concomitant with decreased CD8+ GrB+ IFNγ+ populations. Notably, the percent of pulmonary effector CD8+ GrB+ IFNγ+ T cells at day 10 post-infection correlated positively with total CD8+ basal extracellular acidification rate and basal oxygen consumption rate. Finally, next-generation RNA sequencing revealed complex and unique transcriptional regulation of sorted effector pulmonary CD8+ CD44+ T cells from obese mice compared to lean mice following influenza infection. Collectively, the data suggest diet-induced obesity increases influenza virus pathogenesis, in part, through CD8+ T cell-mediated metabolic reprogramming and impaired effector CD8+ T cell function.
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Affiliation(s)
- William D Green
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Abrar E Al-Shaer
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Qing Shi
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kymberly M Gowdy
- Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Nancie J MacIver
- Department of Immunology, Department of Pediatrics, Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - J Justin Milner
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Melinda A Beck
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Saame Raza Shaikh
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
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11
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Liu C, Qi T, Milner JJ, Lu Y, Cao Y. Speed and Location Both Matter: Antigen Stimulus Dynamics Controls CAR-T Cell Response. Front Immunol 2021; 12:748768. [PMID: 34691062 PMCID: PMC8531752 DOI: 10.3389/fimmu.2021.748768] [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: 07/29/2021] [Accepted: 09/23/2021] [Indexed: 12/18/2022] Open
Abstract
Despite the success in B-cell malignancies, chimeric antigen receptor (CAR)-T cell therapies have not yet demonstrated consistent efficacy across all patients and tumor types, particularly against solid tumors. Higher rates of T cell exhaustion are associated with inferior clinical outcomes following CAR-T cell therapy, which is prevalent in solid tumors. T cell exhaustion may originate from persistent and chronic antigen stimulation by tumor cells that resist and/or evade T cell-mediated killing. We exploited CAR-T exhaustion with a classic negative feedback model (incoherent feedforward loop, IFFL) to investigate the balance between CAR-T cell activation and exhaustion under different antigen presentation dynamics. Built upon the experimental and clinical data, we hypothesize that the speed and anatomical location of antigenic stimulation are both crucial to CAR-T cell response. Chronic antigenic stimulation as well as the harsh tumor microenvironment present multiple barriers to CAR-T cell efficacy in solid tumors. Many therapeutic strategies are individually insufficient to improve of CAR-T responses against solid tumors, as they clear but one of the many barriers CAR-T cells face in solid tumors. A combination strategy targeting multiple barriers holds promise to improve CAR-T therapy in solid tumors.
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Affiliation(s)
- Can Liu
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Timothy Qi
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - J. Justin Milner
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yong Lu
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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12
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Milner JJ, Toma C, Quon S, Omilusik K, Scharping NE, Dey A, Reina-Campos M, Nguyen H, Getzler AJ, Diao H, Yu B, Delpoux A, Yoshida TM, Li D, Qi J, Vincek A, Hedrick SM, Egawa T, Zhou MM, Crotty S, Ozato K, Pipkin ME, Goldrath AW. Bromodomain protein BRD4 directs and sustains CD8 T cell differentiation during infection. J Exp Med 2021; 218:e20202512. [PMID: 34037670 PMCID: PMC8160575 DOI: 10.1084/jem.20202512] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/24/2020] [Revised: 03/10/2021] [Accepted: 05/03/2021] [Indexed: 12/26/2022] Open
Abstract
In response to infection, pathogen-specific CD8 T cells differentiate into functionally diverse effector and memory T cell populations critical for resolving disease and providing durable immunity. Through small-molecule inhibition, RNAi studies, and induced genetic deletion, we reveal an essential role for the chromatin modifier and BET family member BRD4 in supporting the differentiation and maintenance of terminally fated effector CD8 T cells during infection. BRD4 bound diverse regulatory regions critical to effector T cell differentiation and controlled transcriptional activity of terminal effector-specific super-enhancers in vivo. Consequentially, induced deletion of Brd4 or small molecule-mediated BET inhibition impaired maintenance of a terminal effector T cell phenotype. BRD4 was also required for terminal differentiation of CD8 T cells in the tumor microenvironment in murine models, which we show has implications for immunotherapies. Taken together, these data reveal an unappreciated requirement for BRD4 in coordinating activity of cis regulatory elements to control CD8 T cell fate and lineage stability.
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Affiliation(s)
- J. Justin Milner
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Clara Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Sara Quon
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Kyla Omilusik
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Nicole E. Scharping
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Anup Dey
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Miguel Reina-Campos
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Hongtuyet Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Adam J. Getzler
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL
| | - Huitian Diao
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL
| | - Bingfei Yu
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Arnaud Delpoux
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Tomomi M. Yoshida
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
| | - Deyao Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Adam Vincek
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Stephen M. Hedrick
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Matthew E. Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL
| | - Ananda W. Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, CA
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13
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Clark M, Kroger CJ, Ke Q, Zhang R, Statum K, Milner JJ, Martin AJ, Wang B, Tisch R. Coreceptor therapy has distinct short- and long-term tolerogenic effects intrinsic to autoreactive effector T cells. JCI Insight 2021; 6:e149130. [PMID: 34314385 PMCID: PMC8492310 DOI: 10.1172/jci.insight.149130] [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: 02/26/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Immunotherapies are needed in the clinic that effectively suppress beta cell autoimmunity and reestablish long-term self-tolerance in type 1 diabetes. We previously demonstrated that nondepleting αCD4 and αCD8α antibodies establish rapid and indefinite remission in recent-onset diabetic NOD mice. Diabetes reversal by coreceptor therapy (CoRT) is induced by suppression of pathogenic effector T cells (Teff) and the selective egress of T cells from the pancreatic lymph nodes and islets that remain free of infiltration long-term. Here, we defined CoRT-induced events regulating early Teff function and pancreatic residency, and long-term tolerance. TCR-driven gene expression controlling autoreactive Teff expansion and proinflammatory activity was suppressed by CoRT, and islet T cell egress was sphingosine-1 phosphate-dependent. In both murine and human T cells, CoRT upregulated the Foxo1 transcriptional axis, which in turn was required for suppression and efficient pancreatic egress of Teff. Interestingly, long-term tolerance induced in late-preclinical NOD mice was marked by reseeding of the pancreas by a reduced CD8+ Teff pool exhibiting an exhausted phenotype. Notably, PD-1 blockade, which rescues exhausted Teff, resulted in diabetes onset in protected animals. These findings demonstrate that CoRT has distinct intrinsic effects on Teff that impact events early in induction and later in maintenance of self-tolerance.
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Affiliation(s)
- Matthew Clark
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Charles J Kroger
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Qi Ke
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Rui Zhang
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Karen Statum
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - J Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Aaron J Martin
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Bo Wang
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Roland Tisch
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
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14
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Kurd NS, He Z, Louis TL, Milner JJ, Omilusik KD, Jin W, Tsai MS, Widjaja CE, Kanbar JN, Olvera JG, Tysl T, Quezada LK, Boland BS, Huang WJ, Murre C, Goldrath AW, Yeo GW, Chang JT. Early precursors and molecular determinants of tissue-resident memory CD8 + T lymphocytes revealed by single-cell RNA sequencing. Sci Immunol 2020; 5:5/47/eaaz6894. [PMID: 32414833 DOI: 10.1126/sciimmunol.aaz6894] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/16/2020] [Indexed: 01/06/2023]
Abstract
During an immune response to microbial infection, CD8+ T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (TRM) cells that mediate potent protection within nonlymphoid tissues. Here, we used single-cell RNA sequencing to examine the gene expression patterns of individual CD8+ T cells in the spleen and small intestine intraepithelial lymphocyte (siIEL) compartment throughout the course of their differentiation in response to viral infection. These analyses revealed previously unknown transcriptional heterogeneity within the siIEL CD8+ T cell population at several stages of differentiation, representing functionally distinct TRM cell subsets and a subset of TRM cell precursors within the tissue early in infection. Together, these findings may inform strategies to optimize CD8+ T cell responses to protect against microbial infection and cancer.
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Affiliation(s)
- Nadia S Kurd
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.,Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tiani L Louis
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J Justin Milner
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kyla D Omilusik
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Matthew S Tsai
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Jad N Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jocelyn G Olvera
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren K Quezada
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wendy J Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cornelis Murre
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ananda W Goldrath
- Division of Biologic Sciences, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. .,Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA. .,Division of Gastroenterology, VA San Diego Healthcare System, San Diego, CA, USA
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15
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Boland BS, He Z, Tsai MS, Olvera JG, Omilusik KD, Duong HG, Kim ES, Limary AE, Jin W, Milner JJ, Yu B, Patel SA, Louis TL, Tysl T, Kurd NS, Bortnick A, Quezada LK, Kanbar JN, Miralles A, Huylebroeck D, Valasek MA, Dulai PS, Singh S, Lu LF, Bui JD, Murre C, Sandborn WJ, Goldrath AW, Yeo GW, Chang JT. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses. Sci Immunol 2020; 5:5/50/eabb4432. [PMID: 32826341 PMCID: PMC7733868 DOI: 10.1126/sciimmunol.abb4432] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel disease (IBD) encompasses a spectrum of gastrointestinal disorders driven by dysregulated immune responses against gut microbiota. We integrated single-cell RNA and antigen receptor sequencing to elucidate key components, cellular states, and clonal relationships of the peripheral and gastrointestinal mucosal immune systems in health and ulcerative colitis (UC). UC was associated with an increase in IgG1+ plasma cells in colonic tissue, increased colonic regulatory T cells characterized by elevated expression of the transcription factor ZEB2, and an enrichment of a γδ T cell subset in the peripheral blood. Moreover, we observed heterogeneity in CD8+ tissue-resident memory T (TRM) cells in colonic tissue, with four transcriptionally distinct states of differentiation observed across health and disease. In the setting of UC, there was a marked shift of clonally related CD8+ TRM cells toward an inflammatory state, mediated, in part, by increased expression of the T-box transcription factor Eomesodermin. Together, these results provide a detailed atlas of transcriptional changes occurring in adaptive immune cells in the context of UC and suggest a role for CD8+ TRM cells in IBD.
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Affiliation(s)
- Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Matthew S Tsai
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jocelyn G Olvera
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kyla D Omilusik
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Han G Duong
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Eleanor S Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abigail E Limary
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - J Justin Milner
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Bingfei Yu
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shefali A Patel
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiani L Louis
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiffani Tysl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nadia S Kurd
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alexandra Bortnick
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lauren K Quezada
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jad N Kanbar
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ara Miralles
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Danny Huylebroeck
- Department of Development and Regeneration, University of Leuven, Leuven, Belgium.,Department of Cell Biology, Erasmus University Medical Center Rotterdam, 3015 CN Rotterdam, Netherlands
| | - Mark A Valasek
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Siddharth Singh
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Li-Fan Lu
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jack D Bui
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Cornelis Murre
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - William J Sandborn
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ananda W Goldrath
- Division of Biologic Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Division of Gastroenterology, VA San Diego Healthcare System, San Diego, CA, USA
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16
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Milner JJ, Toma C, He Z, Kurd NS, Nguyen QP, McDonald B, Quezada L, Widjaja CE, Witherden DA, Crowl JT, Shaw LA, Yeo GW, Chang JT, Omilusik KD, Goldrath AW. Heterogenous Populations of Tissue-Resident CD8 + T Cells Are Generated in Response to Infection and Malignancy. Immunity 2020; 52:808-824.e7. [PMID: 32433949 PMCID: PMC7784612 DOI: 10.1016/j.immuni.2020.04.007] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [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: 08/04/2019] [Revised: 01/21/2020] [Accepted: 04/17/2020] [Indexed: 11/23/2022]
Abstract
Tissue-resident memory CD8+ T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8+ T cells, including a Blimp1hiId3lo tissue-resident effector cell population most prominent in the early phase of acute viral and bacterial infections and a molecularly distinct Blimp1loId3hi tissue-resident memory population that subsequently accumulated at later infection time points. These Trm populations exhibited distinct cytokine production, secondary memory potential, and transcriptional programs including differential roles for transcriptional regulators Blimp1, T-bet, Id2, and Id3 in supporting and maintaining intestinal Trm. Extending our analysis to malignant tissue, we also identified discrete populations of effector-like and memory-like CD8+ T cell populations with tissue-resident gene-expression signatures that shared features of terminally exhausted and progenitor-exhausted T cells, respectively. Our findings provide insight into the development and functional heterogeneity of Trm cells, which has implications for enhancing vaccination and immunotherapy approaches.
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Affiliation(s)
- J Justin Milner
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Clara Toma
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Zhaoren He
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nadia S Kurd
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Quynh P Nguyen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Bryan McDonald
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lauren Quezada
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Deborah A Witherden
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - John T Crowl
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Laura A Shaw
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kyla D Omilusik
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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17
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Omilusik K, Milner JJ, Kurd N, Toma C, Chang JT, Goldrath AW. Identification of TRM subsets with distinct cellular states and memory potential. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.60.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The memory CD8+ T cell population consists of distinct subsets that collaborate to provide robust immunological protection. Within the circulation, two broad classes exist – the shorter-lived effector and effector memory (TEM) cells with heightened effector function for immediate protection and the longer-lived central memory (TCM) cells with stem-like qualities and increased proliferation potential. Tissue-resident memory (TRM) cells are the prominent cell type permanently residing in non-lymphoid tissues acting as sentinels against reinfection. Despite the critical importance of the TRM subset, the extent of their phenotypic and functional heterogeneity remains unknown. Using single-cell gene expression analyses, we assessed small intestine intraepithelial TRM cells over the course of acute infection. Distinct subsets were identified and distinguished by reciprocal expression of effector- and memory-associated transcriptional regulators, Blimp1 and Id3, respectively. While the Blimp1hi subset was prominent at early time points, the Id3hi population persisted and was more abundant over time. Importantly, examination of the subset-specific transcriptional profiles revealed considerable enrichment for the effector/effector-memory gene signature within the Blimp1hiTRM subset and the central-memory gene signature within the Id3hi TRM population. Furthermore, Id3hi TRM cells exhibited more stem-like characteristics including increased capacity to proliferate following rechallenge. Taken together, this study reveals that similar to circulating memory, the TRM population is heterogeneous, comprising cells with contrasting differentiation states and memory potential.
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Affiliation(s)
- Kyla Omilusik
- 1Division of Biological Sciences, University of California San Diego (UCSD)
| | - J Justin Milner
- 1Division of Biological Sciences, University of California San Diego (UCSD)
| | - Nadia Kurd
- 2Department of Medicine, University of California San Diego (UCSD)
| | - Clara Toma
- 1Division of Biological Sciences, University of California San Diego (UCSD)
| | - John T. Chang
- 2Department of Medicine, University of California San Diego (UCSD)
| | - Ananda W Goldrath
- 1Division of Biological Sciences, University of California San Diego (UCSD)
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18
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Milner JJ, Toma C, Omilusik K, Nguyen H, Yu B, Delpoux A, Yoshida T, Quon S, Dey A, Hedrick SM, Ozato K, Crotty S, Pipkin ME, Goldrath AW. Epigenetic targeting of Brd4 constrains CD8+ T cell differentiation during infection and cancer. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.138.6] [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
Memory CD8+ T cells afford long-lived, durable protection against infection and malignancy. Despite the critical relevance of memory T cells to vaccination and immunotherapies, the transcriptional and epigenetic signals instructing memory T cell fate remain unclear. Here, we utilized a pooled RNA interference screen to evaluate the activity of transcription factors and chromatin modifiers governing memory T cell differentiation in vivo. The epigenetic ‘reader,’ Brd4 of the BET protein family, emerged as a top regulator of memory T cell differentiation. Through RNA interference, small molecule inhibition and inducible genetic deletion, we established a central role for Brd4 in mediating CD8+ T cell proliferation, differentiation and function during acute viral infection. Brd4 was required for optimal expression of fate-specifying transcription factors, and a deficiency of Brd4 activity resulted in diminished formation of effector memory and CD103+ tissue-resident memory CD8+ T cells. Given that BET inhibition has emerged as a powerful approach for suppressing tumor growth, we also evaluated how BET inhibition and Brd4-deficiency influence T cell activity during cancer. Brd4 was required for intratumoral accumulation and function of T cells in a mouse model of melanoma, and BET inhibition suppressed T cell-mediated control of tumor growth. However, epigenetic targeting of Brd4 constrained terminal differentiation of T cells within tumors, biasing tumor-resident T cells towards a reprogrammable TCF1-expressing phenotype. These studies establish a novel role for Brd4 in CD8+ T cell biology and provide insight for immunotherapy approaches designed to leverage the dynamic activity of CD8+ T cells in tumors.
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Affiliation(s)
| | - Clara Toma
- 2Division of Biological Sciences, University of California San Diego (UCSD)
| | - Kyla Omilusik
- 2Division of Biological Sciences, University of California San Diego (UCSD)
| | | | | | | | | | - Sara Quon
- 1University of California, San Diego
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19
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Nguyen H, Toma C, Omilusik K, Goldrath AW, Milner JJ. Long-lived effector CD8+ T cells are transcriptionally and functionally distinct from effector memory cells. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.189.12] [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
In response to an infection or vaccination, antigen-specific CD8+ T cells have the capacity to differentiate into long-lived memory T cells that ultimately confer critical protection against re-infection. The memory CD8+ T cell population is heterogeneous and comprised of circulating effector memory (Tem) and central memory (Tcm) cells as well as non-circulating memory cells or tissue-resident memory cells (Trm). Each memory T cell subset is characterized by distinct phenotypic and functional attributes as well as localization patterns. It has previously been demonstrated that circulating memory subsets can be further subdivided based on effector function or migration patterns. Here, we contribute to the clarification of this heterogeneity by characterizing the gene expression, functional activity and differentiation requirements of long-lived CD127loCD62Llo effector cells (LLE) that can persist at least one year after infection in mice. LLE were found to be phenotypically and functionally distinct from CD127hiCD62Llo Tem and CD127hiCD62LhiTcm subsets. LLE exhibited a unique transcriptional profile, with genes expressed in common with both CD127loKLRG1hi short-lived effector cells and Tem. Further, we refine roles for key fate-specifying transcription factors in controlling the differentiation of LLE versus Tem subsets. These studies further highlight the extent of memory T cell heterogeneity and may inform novel vaccination strategies.
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Affiliation(s)
- Hong Nguyen
- 1Division of Biological Sciences, University of California San Diego (UCSD)
| | - Clara Toma
- 1Division of Biological Sciences, University of California San Diego (UCSD)
| | - Kyla Omilusik
- 1Division of Biological Sciences, University of California San Diego (UCSD)
| | - Ananda W. Goldrath
- 1Division of Biological Sciences, University of California San Diego (UCSD)
| | - J. Justin Milner
- 1Division of Biological Sciences, University of California San Diego (UCSD)
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20
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Freemerman AJ, Zhao L, Pingili AK, Teng B, Cozzo AJ, Fuller AM, Johnson AR, Milner JJ, Lim MF, Galanko JA, Beck MA, Bear JE, Rotty JD, Bezavada L, Smallwood HS, Puchowicz MA, Liu J, Locasale JW, Lee DP, Bennett BJ, Abel ED, Rathmell JC, Makowski L. Myeloid Slc2a1-Deficient Murine Model Revealed Macrophage Activation and Metabolic Phenotype Are Fueled by GLUT1. J Immunol 2019; 202:1265-1286. [PMID: 30659108 PMCID: PMC6360258 DOI: 10.4049/jimmunol.1800002] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 12/03/2018] [Indexed: 12/15/2022]
Abstract
Macrophages (MΦs) are heterogeneous and metabolically flexible, with metabolism strongly affecting immune activation. A classic response to proinflammatory activation is increased flux through glycolysis with a downregulation of oxidative metabolism, whereas alternative activation is primarily oxidative, which begs the question of whether targeting glucose metabolism is a viable approach to control MΦ activation. We created a murine model of myeloid-specific glucose transporter GLUT1 (Slc2a1) deletion. Bone marrow-derived MΦs (BMDM) from Slc2a1M-/- mice failed to uptake glucose and demonstrated reduced glycolysis and pentose phosphate pathway activity. Activated BMDMs displayed elevated metabolism of oleate and glutamine, yet maximal respiratory capacity was blunted in MΦ lacking GLUT1, demonstrating an incomplete metabolic reprogramming. Slc2a1M-/- BMDMs displayed a mixed inflammatory phenotype with reductions of the classically activated pro- and anti-inflammatory markers, yet less oxidative stress. Slc2a1M-/- BMDMs had reduced proinflammatory metabolites, whereas metabolites indicative of alternative activation-such as ornithine and polyamines-were greatly elevated in the absence of GLUT1. Adipose tissue MΦs of lean Slc2a1M-/- mice had increased alternative M2-like activation marker mannose receptor CD206, yet lack of GLUT1 was not a critical mediator in the development of obesity-associated metabolic dysregulation. However, Ldlr-/- mice lacking myeloid GLUT1 developed unstable atherosclerotic lesions. Defective phagocytic capacity in Slc2a1M-/- BMDMs may have contributed to unstable atheroma formation. Together, our findings suggest that although lack of GLUT1 blunted glycolysis and the pentose phosphate pathway, MΦ were metabolically flexible enough that inflammatory cytokine release was not dramatically regulated, yet phagocytic defects hindered MΦ function in chronic diseases.
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Affiliation(s)
- Alex J. Freemerman
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 25799
| | - Liyang Zhao
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 25799
| | - Ajeeth K. Pingili
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Bin Teng
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Alyssa J. Cozzo
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 25799
| | - Ashley M. Fuller
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Amy R. Johnson
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 25799
| | - J. Justin Milner
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 25799
| | - Maili F. Lim
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 25799
| | - Joseph A. Galanko
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Melinda A. Beck
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 25799
| | - James E. Bear
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jeremy D. Rotty
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Lavanya Bezavada
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Heather S. Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Michelle A. Puchowicz
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Duke University, Durham, NC 27710
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Duke University, Durham, NC 27710
| | | | - Brian J. Bennett
- U.S. Department of Agriculture Western Human Nutrition Research Center, Davis, CA 95616
| | - E. Dale Abel
- Division of Endocrinology and Metabolism, University of Iowa Carver College of Medicine, Iowa City, IA 52242;,Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242; and
| | - Jeff C. Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN 37232
| | - Liza Makowski
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 25799; .,Department of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163
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21
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Milner JJ, Goldrath AW. Transcriptional programming of tissue-resident memory CD8 + T cells. Curr Opin Immunol 2018; 51:162-169. [PMID: 29621697 PMCID: PMC5943164 DOI: 10.1016/j.coi.2018.03.017] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/18/2018] [Indexed: 01/28/2023]
Abstract
Tissue-resident memory CD8+ T cells (TRM) are localized in non-lymphoid tissues throughout the body where they mediate long-lived protective immunity at common sites of pathogen exposure. As the signals controlling TRM differentiation are uncovered, it is becoming apparent that the dynamic activities of numerous transcription factors are intricately involved in TRM formation. Here, we highlight known transcriptional regulators of TRM differentiation and discuss how understanding the transcriptional programming of CD8+ T cell residency in non-lymphoid tissues can be leveraged to prevent or treat disease.
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Affiliation(s)
- J Justin Milner
- Division of Biological Sciences, University of California, San Diego , La Jolla, CA, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California, San Diego , La Jolla, CA, USA.
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22
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Omilusik KD, Nadjsombati MS, Shaw LA, Yu B, Milner JJ, Goldrath AW. Sustained Id2 regulation of E proteins is required for terminal differentiation of effector CD8 + T cells. J Exp Med 2018; 215:773-783. [PMID: 29440362 PMCID: PMC5839762 DOI: 10.1084/jem.20171584] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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: 08/28/2017] [Revised: 12/07/2017] [Accepted: 01/18/2018] [Indexed: 02/01/2023] Open
Abstract
CD8+ T cells responding to infection differentiate into short-lived effector cells destined to die or memory cells that provide long-lived protection. Omilusik et al. demonstrate that commitment to an effector cell fate is not necessarily terminal and that sustained transcriptional regulation is required to maintain subset-specific properties. CD8+ T cells responding to infection differentiate into a heterogeneous population composed of progeny that are short-lived and participate in the immediate, acute response and those that provide long-lasting host protection. Although it is appreciated that distinct functional and phenotypic CD8+ T cell subsets persist, it is unclear whether there is plasticity among subsets and what mechanisms maintain subset-specific differences. Here, we show that continued Id2 regulation of E-protein activity is required to maintain the KLRG1hi CD8+ T cell population after lymphocytic choriomeningitis virus infection. Induced deletion of Id2 phenotypically and transcriptionally transformed the KLRG1hi “terminal” effector/effector-memory CD8+ T cell population into a KLRG1lo memory-like population, promoting a gene-expression program that resembled that of central memory T cells. Our results question the idea that KLRG1hi CD8+ T cells are necessarily terminally programmed and suggest that sustained regulation is required to maintain distinct CD8+ T cell states.
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Affiliation(s)
- Kyla D Omilusik
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA
| | - Marija S Nadjsombati
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA
| | - Laura A Shaw
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA
| | - J Justin Milner
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA
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23
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Kosaraju R, Guesdon W, Crouch MJ, Teague HL, Sullivan EM, Karlsson EA, Schultz-Cherry S, Gowdy K, Bridges LC, Reese LR, Neufer PD, Armstrong M, Reisdorph N, Milner JJ, Beck M, Shaikh SR. B Cell Activity Is Impaired in Human and Mouse Obesity and Is Responsive to an Essential Fatty Acid upon Murine Influenza Infection. J Immunol 2017; 198:4738-4752. [PMID: 28500069 DOI: 10.4049/jimmunol.1601031] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 04/10/2017] [Indexed: 02/06/2023]
Abstract
Obesity is associated with increased risk for infections and poor responses to vaccinations, which may be due to compromised B cell function. However, there is limited information about the influence of obesity on B cell function and underlying factors that modulate B cell responses. Therefore, we studied B cell cytokine secretion and/or Ab production across obesity models. In obese humans, B cell IL-6 secretion was lowered and IgM levels were elevated upon ex vivo anti-BCR/TLR9 stimulation. In murine obesity induced by a high fat diet, ex vivo IgM and IgG were elevated with unstimulated B cells. Furthermore, the high fat diet lowered bone marrow B cell frequency accompanied by diminished transcripts of early lymphoid commitment markers. Murine B cell responses were subsequently investigated upon influenza A/Puerto Rico/8/34 infection using a Western diet model in the absence or presence of docosahexaenoic acid (DHA). DHA, an essential fatty acid with immunomodulatory properties, was tested because its plasma levels are lowered in obesity. Relative to controls, mice consuming the Western diet had diminished Ab titers whereas the Western diet plus DHA improved titers. Mechanistically, DHA did not directly target B cells to elevate Ab levels. Instead, DHA increased the concentration of the downstream specialized proresolving lipid mediators (SPMs) 14-hydroxydocosahexaenoic acid, 17-hydroxydocosahexaenoic acid, and protectin DX. All three SPMs were found to be effective in elevating murine Ab levels upon influenza infection. Collectively, the results demonstrate that B cell responses are impaired across human and mouse obesity models and show that essential fatty acid status is a factor influencing humoral immunity, potentially through an SPM-mediated mechanism.
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Affiliation(s)
- Rasagna Kosaraju
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834.,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834
| | - William Guesdon
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834.,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834
| | - Miranda J Crouch
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834.,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834
| | - Heather L Teague
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834.,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834
| | - E Madison Sullivan
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834.,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834
| | - Erik A Karlsson
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Kymberly Gowdy
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University, Greenville, NC 27834
| | - Lance C Bridges
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834.,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834
| | - Lauren R Reese
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834.,Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC 27834
| | - P Darrell Neufer
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834.,Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC 27834
| | - Michael Armstrong
- Department of Pharmaceutical Sciences, University of Colorado, Denver, CO 80045; and
| | - Nichole Reisdorph
- Department of Pharmaceutical Sciences, University of Colorado, Denver, CO 80045; and
| | - J Justin Milner
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Melinda Beck
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Saame Raza Shaikh
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC 27834; .,East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834
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24
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Yu B, Zhang K, Milner JJ, Toma C, Chen R, Scott-Browne JP, Pereira RM, Crotty S, Chang JT, Pipkin ME, Wang W, Goldrath AW. Epigenetic landscapes reveal transcription factors that regulate CD8 + T cell differentiation. Nat Immunol 2017; 18:573-582. [PMID: 28288100 PMCID: PMC5395420 DOI: 10.1038/ni.3706] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/07/2017] [Indexed: 12/14/2022]
Abstract
Dynamic changes in the expression of transcription factors (TFs) can influence specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TF among differentially-fated precursor cells suggests additional underlying mechanisms. Here, we profiled genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8+ T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that TF expression and binding contributed to establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal novel TFs influencing the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8+ T cell differentiation, regulated the formation of terminal-effector and memory-precursor cell-fates, respectively. Our data define the epigenetic landscape of differentiation intermediates, facilitating identification of TFs with previously unappreciated roles in CD8+ T cell differentiation.
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Affiliation(s)
- Bingfei Yu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Kai Zhang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - J Justin Milner
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Clara Toma
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Runqiang Chen
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, USA
| | - James P Scott-Browne
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Renata M Pereira
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.,Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Matthew E Pipkin
- Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, USA
| | - Wei Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Ananda W Goldrath
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
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25
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Antoniak S, Tatsumi K, Hisada Y, Milner JJ, Neidich SD, Shaver CM, Pawlinski R, Beck MA, Bastarache JA, Mackman N. Tissue factor deficiency increases alveolar hemorrhage and death in influenza A virus-infected mice. J Thromb Haemost 2016; 14:1238-48. [PMID: 26947929 PMCID: PMC5892427 DOI: 10.1111/jth.13307] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 10/19/2015] [Accepted: 02/15/2016] [Indexed: 12/23/2022]
Abstract
UNLABELLED Essentials H1N1 Influenza A virus (IAV) infection is a hemostatic challenge for the lung. Tissue factor (TF) on lung epithelial cells maintains lung hemostasis after IAV infection. Reduced TF-dependent activation of coagulation leads to alveolar hemorrhage. Anticoagulation might increase the risk for hemorrhages into the lung during severe IAV infection. SUMMARY Background Influenza A virus (IAV) infection is a common respiratory tract infection that causes considerable morbidity and mortality worldwide. Objective To investigate the effect of genetic deficiency of tissue factor (TF) in a mouse model of IAV infection. Methods Wild-type mice, low-TF (LTF) mice and mice with the TF gene deleted in different cell types were infected with a mouse-adapted A/Puerto Rico/8/34 H1N1 strain of IAV. TF expression was measured in the lungs, and bronchoalveolar lavage fluid (BALF) was collected to measure extracellular vesicle TF, activation of coagulation, alveolar hemorrhage, and inflammation. Results IAV infection of wild-type mice increased lung TF expression, activation of coagulation and inflammation in BALF, but also led to alveolar hemorrhage. LTF mice and mice with selective deficiency of TF in lung epithelial cells had low basal levels of TF and failed to increase TF expression after infection; these two strains of mice had more alveolar hemorrhage and death than controls. In contrast, deletion of TF in either myeloid cells or endothelial cells and hematopoietic cells did not increase alveolar hemorrhage or death after IAV infection. These results indicate that TF expression in the lung, particularly in epithelial cells, is required to maintain alveolar hemostasis after IAV infection. Conclusion Our study indicates that TF-dependent activation of coagulation is required to limit alveolar hemorrhage and death after IAV infection.
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Affiliation(s)
- Silvio Antoniak
- Department of Medicine, Division of Hematology and Oncology, UNC McAllister Heart Institute, University of North Carolina at Chapel Hill, 111 Mason Farm Road Campus Box 7126, Chapel Hill, North Carolina, USA
| | - Kohei Tatsumi
- Department of Medicine, Division of Hematology and Oncology, UNC McAllister Heart Institute, University of North Carolina at Chapel Hill, 111 Mason Farm Road Campus Box 7126, Chapel Hill, North Carolina, USA
| | - Yohei Hisada
- Department of Medicine, Division of Hematology and Oncology, UNC McAllister Heart Institute, University of North Carolina at Chapel Hill, 111 Mason Farm Road Campus Box 7126, Chapel Hill, North Carolina, USA
| | - J. Justin Milner
- Department of Nutrition, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive Campus Box 7461, Chapel Hill, North Carolina, USA
| | - Scott D. Neidich
- Department of Nutrition, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive Campus Box 7461, Chapel Hill, North Carolina, USA
| | - Ciara M. Shaver
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, T-1218 MCN, Nashville, TN, USA
| | - Rafal Pawlinski
- Department of Medicine, Division of Hematology and Oncology, UNC McAllister Heart Institute, University of North Carolina at Chapel Hill, 111 Mason Farm Road Campus Box 7126, Chapel Hill, North Carolina, USA
| | - Melinda A. Beck
- Department of Nutrition, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive Campus Box 7461, Chapel Hill, North Carolina, USA
| | - Julie A. Bastarache
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, T-1218 MCN, Nashville, TN, USA
| | - Nigel Mackman
- Department of Medicine, Division of Hematology and Oncology, UNC McAllister Heart Institute, University of North Carolina at Chapel Hill, 111 Mason Farm Road Campus Box 7126, Chapel Hill, North Carolina, USA
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26
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Milner JJ, Rebeles J, Dhungana S, Stewart DA, Sumner SCJ, Meyers MH, Mancuso P, Beck MA. Obesity Increases Mortality and Modulates the Lung Metabolome during Pandemic H1N1 Influenza Virus Infection in Mice. J Immunol 2015; 194:4846-59. [PMID: 25862817 DOI: 10.4049/jimmunol.1402295] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 03/11/2015] [Indexed: 01/20/2023]
Abstract
Obese individuals are at greater risk for hospitalization and death from infection with the 2009 pandemic H1N1 influenza virus (pH1N1). In this study, diet-induced and genetic-induced obese mouse models were used to uncover potential mechanisms by which obesity increases pH1N1 severity. High-fat diet-induced and genetic-induced obese mice exhibited greater pH1N1 mortality, lung inflammatory responses, and excess lung damage despite similar levels of viral burden compared with lean control mice. Furthermore, obese mice had fewer bronchoalveolar macrophages and regulatory T cells during infection. Obesity is inherently a metabolic disease, and metabolic profiling has found widespread usage in metabolic and infectious disease models for identifying biomarkers and enhancing understanding of complex mechanisms of disease. To further characterize the consequences of obesity on pH1N1 infection responses, we performed global liquid chromatography-mass spectrometry metabolic profiling of lung tissue and urine. A number of metabolites were perturbed by obesity both prior to and during infection. Uncovered metabolic signatures were used to identify changes in metabolic pathways that were differentially altered in the lungs of obese mice such as fatty acid, phospholipid, and nucleotide metabolism. Taken together, obesity induces distinct alterations in the lung metabolome, perhaps contributing to aberrant pH1N1 immune responses.
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Affiliation(s)
- J Justin Milner
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jenny Rebeles
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Suraj Dhungana
- Systems and Translational Science Center, RTI International, Research Triangle Park, NC 27709; and
| | - Delisha A Stewart
- Systems and Translational Science Center, RTI International, Research Triangle Park, NC 27709; and
| | - Susan C J Sumner
- Systems and Translational Science Center, RTI International, Research Triangle Park, NC 27709; and
| | - Matthew H Meyers
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Peter Mancuso
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109
| | - Melinda A Beck
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
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Milner JJ, Wang J, Sheridan PA, Ebbels T, Beck MA, Saric J. 1H NMR-based profiling reveals differential immune-metabolic networks during influenza virus infection in obese mice. PLoS One 2014; 9:e97238. [PMID: 24844920 PMCID: PMC4028207 DOI: 10.1371/journal.pone.0097238] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [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: 02/12/2014] [Accepted: 04/16/2014] [Indexed: 11/18/2022] Open
Abstract
Obese individuals are at greater risk for death from influenza virus infection. Paralleling human evidence, obese mice are also more susceptible to influenza infection mortality. However, the underlying mechanisms driving greater influenza severity in the obese remain unclear. Metabolic profiling has been utilized in infectious disease models to enhance prognostic or diagnostic methods, and to gain insight into disease pathogenesis by providing a more global picture of dynamic infection responses. Herein, metabolic profiling was used to develop a deeper understanding of the complex processes contributing to impaired influenza protection in obese mice and to facilitate generation of new explanatory hypotheses. Diet-induced obese and lean mice were infected with influenza A/Puerto Rico/8/34. 1H nuclear magnetic resonance-based metabolic profiling of urine, feces, lung, liver, mesenteric white adipose tissue, bronchoalveolar lavage fluid and serum revealed distinct metabolic signatures in infected obese mice, including perturbations in nucleotide, vitamin, ketone body, amino acid, carbohydrate, choline and lipid metabolic pathways. Further, metabolic data was integrated with immune analyses to obtain a more comprehensive understanding of potential immune-metabolic interactions. Of interest, uncovered metabolic signatures in urine and feces allowed for discrimination of infection status in both lean and obese mice at an early influenza time point, which holds prognostic and diagnostic implications for this methodology. These results confirm that obesity causes distinct metabolic perturbations during influenza infection and provide a basis for generation of new hypotheses and use of this methodology in detection of putative biomarkers and metabolic patterns to predict influenza infection outcome.
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Affiliation(s)
- J. Justin Milner
- Gillings School of Global Public Health, Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jue Wang
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Patricia A. Sheridan
- Gillings School of Global Public Health, Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tim Ebbels
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Melinda A. Beck
- Gillings School of Global Public Health, Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (MAB); (JS)
| | - Jasmina Saric
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, United Kingdom
- * E-mail: (MAB); (JS)
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Affiliation(s)
- J Justin Milner
- Gillings School of Global Public Health, Department of Nutrition, UNC Chapel Hill, Chapel Hill, 27514, NC, USA
| | - Melinda A Beck
- Gillings School of Global Public Health, Department of Nutrition, UNC Chapel Hill, Chapel Hill, 27514, NC, USA
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Freemerman AJ, Johnson AR, Sacks GN, Milner JJ, Kirk EL, Troester MA, Macintyre AN, Goraksha-Hicks P, Rathmell JC, Makowski L. Metabolic reprogramming of macrophages: glucose transporter 1 (GLUT1)-mediated glucose metabolism drives a proinflammatory phenotype. J Biol Chem 2014; 289:7884-96. [PMID: 24492615 DOI: 10.1074/jbc.m113.522037] [Citation(s) in RCA: 593] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glucose is a critical component in the proinflammatory response of macrophages (MΦs). However, the contribution of glucose transporters (GLUTs) and the mechanisms regulating subsequent glucose metabolism in the inflammatory response are not well understood. Because MΦs contribute to obesity-induced inflammation, it is important to understand how substrate metabolism may alter inflammatory function. We report that GLUT1 (SLC2A1) is the primary rate-limiting glucose transporter on proinflammatory-polarized MΦs. Furthermore, in high fat diet-fed rodents, MΦs in crown-like structures and inflammatory loci in adipose and liver, respectively, stain positively for GLUT1. We hypothesized that metabolic reprogramming via increased glucose availability could modulate the MΦ inflammatory response. To increase glucose uptake, we stably overexpressed the GLUT1 transporter in RAW264.7 MΦs (GLUT1-OE MΦs). Cellular bioenergetics analysis, metabolomics, and radiotracer studies demonstrated that GLUT1 overexpression resulted in elevated glucose uptake and metabolism, increased pentose phosphate pathway intermediates, with a complimentary reduction in cellular oxygen consumption rates. Gene expression and proteome profiling analysis revealed that GLUT1-OE MΦs demonstrated a hyperinflammatory state characterized by elevated secretion of inflammatory mediators and that this effect could be blunted by pharmacologic inhibition of glycolysis. Finally, reactive oxygen species production and evidence of oxidative stress were significantly enhanced in GLUT1-OE MΦs; antioxidant treatment blunted the expression of inflammatory mediators such as PAI-1 (plasminogen activator inhibitor 1), suggesting that glucose-mediated oxidative stress was driving the proinflammatory response. Our results indicate that increased utilization of glucose induced a ROS-driven proinflammatory phenotype in MΦs, which may play an integral role in the promotion of obesity-associated insulin resistance.
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Affiliation(s)
- Alex J Freemerman
- From the Department of Nutrition, Gillings School of Global Public Health
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Sundaram S, Freemerman AJ, Johnson AR, Milner JJ, McNaughton KK, Galanko JA, Bendt KM, Darr DB, Perou CM, Troester MA, Makowski L. Role of HGF in obesity-associated tumorigenesis: C3(1)-TAg mice as a model for human basal-like breast cancer. Breast Cancer Res Treat 2013; 142:489-503. [PMID: 24218051 DOI: 10.1007/s10549-013-2741-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/16/2013] [Indexed: 11/29/2022]
Abstract
Obesity is associated with basal-like breast cancer (BBC), an aggressive breast cancer subtype. The objective of this study was to determine whether obesity promotes BBC onset in adulthood and to evaluate the role of stromal-epithelial interactions in obesity-associated tumorigenesis. We hypothesized that hepatocyte growth factor (HGF) plays a promoting role in BBC, which express the HGF receptor, c-Met. In C3(1)-T(Ag) mice, a murine model of BBC, we demonstrated that obesity leads to a significant increase in HGF secretion and an associated decrease in tumor latency. By immunohistochemical analysis, normal mammary gland exhibited obesity-induced HGF, c-Met and phospho-c-Met, indicating that the activation of the cascade was obesity-driven. HGF secretion was also increased from primary mammary fibroblasts isolated from normal mammary glands and tumors of obese mice compared to lean. These results demonstrate that obesity-induced elevation of HGF expression is a stable phenotype, maintained after several passages, and after removal of dietary stimulation. Conditioned media from primary tumor fibroblasts from obese mice drove tumor cell proliferation. In co-culture, neutralization of secreted HGF blunted tumor cell migration, further linking obesity-mediated HGF-dependent effects to in vitro measures of tumor aggressiveness. In sum, these results demonstrate that HGF/c-Met plays an important role in obesity-associated carcinogenesis. Understanding the effects of obesity on risk and progression is important given that epidemiologic studies imply a portion of BBC could be eliminated by reducing obesity.
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Affiliation(s)
- Sneha Sundaram
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, University of North Carolina at Chapel Hill, CB 7461, 2203 McGavran Greenberg Hall, Chapel Hill, NC, 27599-7461, USA,
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Milner JJ, Sheridan PA, Karlsson EA, Schultz-Cherry S, Shi Q, Beck MA. Diet-induced obese mice exhibit altered heterologous immunity during a secondary 2009 pandemic H1N1 infection. J Immunol 2013; 191:2474-85. [PMID: 23904168 PMCID: PMC3756476 DOI: 10.4049/jimmunol.1202429] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
During the 2009 pandemic H1N1 influenza A virus (pH1N1) outbreak, obese individuals were at greater risk for morbidity and mortality from pandemic infection. However, the mechanisms contributing to greater infection severity in obese individuals remain unclear. Although most individuals lacked pre-existing, neutralizing Ab protection to the novel pH1N1 virus, heterologous defenses conferred from exposure to circulating strains or vaccination have been shown to impart protection against pH1N1 infection in humans and mice. Because obese humans and mice have impaired memory T cell and Ab responses following influenza vaccination or infection, we investigated the impact of obesity on heterologous protection from pH1N1 infection using a mouse model of diet-induced obesity. Lean and obese mice were infected with influenza A/Puerto Rico/8/34 (PR8) and 5 wk later challenged with a lethal dose of heterologous pH1N1. Cross-neutralizing Ab protection was absent in this model, but obese mice exhibited a significantly lower level of nonneutralizing, cross-reactive pH1N1 nucleoprotein Abs following the primary PR8 infection. Further, obese mice had elevated viral titers, greater lung inflammation and lung damage, and more cytotoxic memory CD8(+) T cells in the lung airways. Although obese mice had more regulatory T cells (Tregs) in the lung airways than did lean controls during the pH1N1 challenge, Tregs isolated from obese mice were 40% less suppressive than Tregs isolated from lean mice. In sum, excessive inflammatory responses to pH1N1 infection, potentially owing to greater viral burden and impaired Treg function, may be a novel mechanism by which obesity contributes to greater pH1N1 severity.
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Affiliation(s)
- J. Justin Milner
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patricia A. Sheridan
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erik A. Karlsson
- Department of Infectious Diseases, St. Jude Children’s Research Hospital Memphis, Memphis, TN, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital Memphis, Memphis, TN, USA
| | - Qing Shi
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melinda A. Beck
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Milner JJ, Sheridan PA, Karlsson EA, Schultz‐Cherry S, Shi Q, Beck MA. Diet‐induced obese mice exhibit heightened lung inflammatory and cross‐reactive CD8 T cell responses during a secondary 2009 pandemic H1N1 influenza infection. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.357.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
As humans evolved, perhaps the two strongest selection determinants of survival were a robust immune response able to clear bacterial, viral, and parasitic infection and an ability to efficiently store nutrients to survive times when food sources were scarce. These traits are not mutually exclusive. It is now apparent that critical proteins necessary for regulating energy metabolism, such as peroxisome proliferator-activated receptors, Toll-like receptors, and fatty acid-binding proteins, also act as links between nutrient metabolism and inflammatory pathway activation in immune cells. Obesity in humans is a symptom of energy imbalance: the scale has been tipped such that energy intake exceeds energy output and may be a result, in part, of evolutionary selection toward a phenotype characterized by efficient energy storage. As discussed in this review, obesity is a state of low-grade, chronic inflammation that promotes the development of insulin resistance and diabetes. Ironically, the formation of systemic and/or local, tissue-specific insulin resistance upon inflammatory cell activation may actually be a protective mechanism that co-evolved to repartition energy sources within the body during times of stress during infection. However, the point has been reached where a once beneficial adaptive trait has become detrimental to the health of the individual and an immense public health and economic burden. This article reviews the complex relationship between obesity, insulin resistance/diabetes, and inflammation, and although the liver, brain, pancreas, muscle, and other tissues are relevant, we focus specifically on how the obese adipose microenvironment can promote immune cell influx and sustain damaging inflammation that can lead to the onset of insulin resistance and diabetes. Finally, we address how substrate metabolism may regulate the immune response and discuss how fuel uptake and metabolism may be a targetable approach to limit or abrogate obesity-induced inflammation.
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Affiliation(s)
- Amy R Johnson
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Milner JJ, Paich HA, Sheridan PA, Beck MA. Regulatory T cells: a mechanism for impaired immunity to influenza infection in obese mice? FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.127.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Milner JJ, Karlsson EA, Beck M. Leptin treatment alters the response of respiratory epithelial cells to influenza infection. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.723.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- J Justin Milner
- NutritionUniversity of North Carolina Chapel HillChapel HillNC
| | - Erik A Karlsson
- NutritionUniversity of North Carolina Chapel HillChapel HillNC
| | - Melinda Beck
- NutritionUniversity of North Carolina Chapel HillChapel HillNC
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Abstract
Schraudolph proposed an excellent exponential approximation providing increased performance particularly suited to the logistic squashing function used within many neural networking applications. This note applies Intel's streaming SIMD Extensions 2 (SSE2), where SIMD is single instruction multiple data, of the Pentium IV class processor to Schraudolph's technique, further increasing the performance of the logistic squashing function. It was found that the calculation of the new 32-bit SSE2 logistic squashing function described here was up to 38 times faster than the conventional exponential function and up to 16 times faster than a Schraudolph-style 32-bit method on an Intel Pentium D 3.6 GHz CPU.
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Affiliation(s)
- J J Milner
- School of Computing and Mathematical Sciences, University of Greenwich, Greenwich, London, U.K.
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Abstract
The dielectric properties of the Tobacco Mosaic Virus (TMV) have been measured using time domain dielectric spectroscopy (TDDS) in the temperature range from 1 to 40 degrees C. A single dielectric dispersion is observed in the MHz range. The activation energy of the process is found to be in the range 1-2 kcal/mol. The experimental data could not be completely accounted for by current theoretical models, but evidence indicates that the dielectric loss arises from polarisation of charge on and around the virus.
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Affiliation(s)
- I Ermolina
- Bioelectronics Research Centre, Department of Electronics and Electrical Engineering, University of Glasgow, Rankine Building, Glasgow G12 8LT, Scotland, UK
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Covey SN, McCallum DG, Turner DS, Al-Kaff NS, Dale P, Cecchini E, Milner JJ. Pararetrovirus-crucifer interactions: attack and defence or modus vivendi? Mol Plant Pathol 2000; 1:77-86. [PMID: 20572954 DOI: 10.1046/j.1364-3703.2000.00011.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Abstract The compatible infection of plants by viruses usually leads to the development of systemic symptoms. Symptom expression of this kind is generally understood to be a host response that indicates an inability of the host to defend itself from attack. We have been studying compatible interactions between the plant pararetrovirus cauliflower mosaic virus (CaMV) and its crucifer hosts in order to understand the relationship between viral activity, symptom expression and plant defence. A CaMV protein (P6) appears to play a major role in eliciting symptom expression. This host response leads to a regulation of the viral multiplication cycle that is associated with leaf mosaics. The host regulation of CaMV appears to operate at the transcriptional level through an effect on the 35S promoter, or at the post-transcriptional level by a process that is akin to gene silencing, and can lead to host recovery depending upon the genetic background of the host. The plant apex is a focus for antiviral defence mechanisms, presumably because viral infection of the apical meristem would rapidly compromise the ability of the plant to generate new leaves and flowers for reproduction. The balance of interactions between CaMV and crucifers can provide a sustainable source of host plants to ensure viral propagation and viral exposure allows the host to adapt and develop its repertoire of defence mechanisms.
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Affiliation(s)
- S N Covey
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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Geri C, Cecchini E, Giannakou ME, Covey SN, Milner JJ. Altered patterns of gene expression in Arabidopsis elicited by cauliflower mosaic virus (CaMV) infection and by a CaMV gene VI transgene. Mol Plant Microbe Interact 1999; 12:377-384. [PMID: 10226370 DOI: 10.1094/mpmi.1999.12.5.377] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Cauliflower mosaic virus (CaMV) gene VI protein (P6) is an important determinant of symptom expression. Differential display polymerase chain reaction (PCR) was used to identify changes in gene expression in Arabidopsis elicited by a P6 transgene that causes a symptomatic phenotype. We used slot blot hybridization to measure the abundance of mRNAs complementary to 66 candidate PCR products in transgenic, CaMV-infected, and uninfected Arabidopsis plants. CaMV-infected and P6 transgenic plants showed broadly similar changes in abundance of mRNA species. In P6 transgenic plants we detected 18 PCR products that showed unambiguous changes in abundance plus another 15 that showed more limited changes (approximately twofold). CaMV-infected plants showed 17 unambiguous and 13 limited changes. Down-regulated species include those encoding a novel, phenol-like sulfotransferase, and a glycine-rich, RNA-binding protein. Up-regulated species included ones encoding an myb protein, glycine-rich and stress-inducible proteins, and a member of a previously unreported gene family. CaMV infection causes alterations in expression of many Arabidopsis genes. Transgene-mediated expression of P6 mimics virus infection in its effect on host gene expression, providing a potential mechanism for this process.
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Affiliation(s)
- C Geri
- Plant Molecular Science Group, Glasgow University, Scotland, U.K
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40
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Affiliation(s)
- J J Milner
- Divn of Biochemistry and Molecular Biology, University of Glasgow, UK.
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41
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Abstract
Seeds of transgenic Arabidopsis, containing a negatively selectable suicide marker, a 35Stms2 construct introduced as a transgene, were gamma-irradiated at a range of doses from 20-120 krad. Batches of M2 seeds, from M1 plants irradiated at doses of 40, 45 and 60 krad, were screened by germinating them on medium containing NAM under conditions that selectively inhibited growth of plants expressing the tms2 gene product. Nine candidate loss-of-transgene mutants were isolated. The frequency of such mutations (0.0125 to 0.025%) did not vary significantly with irradiation dose or M1 pool size. DNA from the mutants and the parent was hybridized in Southern blots, using probes complementary to various regions of the transgene. All nine mutants were null for both the tms2 coding sequence and the 35S promoter. Six of the nine mutants were null for the entire transgene construct of 9 kbp. DNA from one mutant contained one of the T-DNA borders and gave a hybridization pattern consistent with a deletion at least 5 kbp. The two remaining mutant lines gave identical patterns of hybridization, consistent with a 5.6-kbp internal deletion within the transgene. From the Southern blots, and on the basis of lineage, the nine lines represent the progeny of either seven or eight independent mutations. We have established conditions capable of producing deletion mutations of at least 5 kbp, but without apparently introducing small deletions or rearrangements. Such deletion mutations are ideally suited for cloning by subtractive hybridization, and should also be readily detectable by RFLP analysis, facilitating map-based cloning procedures.
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Affiliation(s)
- E Cecchini
- Plant Molecular Science Group, Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, Glasgow University, Glasgow G12 8QQ, Scotland, UK
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Cecchini E, Gong Z, Geri C, Covey SN, Milner JJ. Transgenic Arabidopsis lines expressing gene VI from cauliflower mosaic virus variants exhibit a range of symptom-like phenotypes and accumulate inclusion bodies. Mol Plant Microbe Interact 1997; 10:1094-101. [PMID: 9390424 DOI: 10.1094/mpmi.1997.10.9.1094] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Gene VI of cauliflower mosaic virus (CaMV) is an important determinant of symptom expression during infection. We have constructed a series of transgenic Arabidopsis lines that express gene VI protein (P6) from two CaMV isolates (Bari-1 and Cabb B-JI) that cause mild and severe symptoms, respectively, in Arabidopsis, and from a recombinant virus (Baji-31) with a hybrid gene VI that causes very severe symptoms. From 41 transgenic lines analyzed, 17 showed symptom-like phenotypes that ranged from mild vein chlorosis to severe chlorosis and stunting. P6 levels in transgenic lines varied from undetectable in the lowest expressors to levels greater than those in CaMV-infected plants. There was a strong correlation between phenotype severity and the level of P6, and with the gene VI origin in the order, Baji-31 > B-JI > Bari-1. This was similar to symptom severity in Arabidopsis infected with the respective CaMV variant. We also found that transgenic P6 accumulated in inclusion bodies that were similar to those found in infected plants but lacking virions. We conclude that expression of P6, in the absence of virus replication, elicits a subset of the host symptom responses normally observed during infection and that the level, sequence, and possibly the form of P6 are important in potentiating the process.
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Affiliation(s)
- E Cecchini
- Division of Biochemistry & Molecular Biology, Glasgow University, Scotland, U.K
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Abstract
A non-uniform alternating electric field induces motion in polarisable particles called dielectrophoresis. The effect is governed by the relative magnitudes of the dielectric properties of the medium and the particles. The technology has been used to manipulate particles for biotechnological applications, including purification, fractionation and concentration of cells and microorganisms. However, the lower size limit for the dielectrophoretic manipulation of particles was believed to be about 1 micron, but recent work has proved otherwise. The dielectrophoretic movement and properties of latex beads and a simple rod-shaped virus, tobacco mosaic virus (TMV), have been measured using microfabricated electrode structures. Measurements have been made over a range of suspending medium conductivities, applied frequencies and electric field strengths. It is shown that under appropriate conditions both latex beads and tobacco mosaic virus particles can be selectively attracted to regions of high electric field strength located at the tips of microfabricated electrode structures. The ability to selectively trap and separate bio-particles has many potential applications in the area of biotechnology.
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Affiliation(s)
- N G Green
- Department of Electronics and Electrical Engineering, University of Glasgow, Scotland, UK
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Abstract
Nucleic acid sequences that differ in abundance between two populations (target sequences) can be cloned by multiple rounds of subtractive hybridization and amplification by PCR. These sequences can be cDNAs representing up-regulated mRNAs, or genomic DNAs from deletion mutants. We have derived an equation that describes the recovery of such sequences, and have used this to simulate the outcome of up to 10 rounds of subtractive hybridization and PCR amplification. When the model was tested by comparing its predictions with the published results from genomic and cDNA subtractions, the predictions of the model were generally in good agreement with the published data. We have modelled the outcomes of genomic subtractions, for a variety of genomes, and have used it to compare various strategies for enriching targets. The model predicts that for genomes of less than 5 x 10(8) bp, deletions of as small as 1 kbp should represent > 99% of the DNA after three to six rounds of hybridization (depending on the enrichment procedure). As genomes increase in size, the kinetics of hybridization become an important limiting factor. However, even for genomes as large as 3 x 10(9) bp, it should be possible to isolate deletions of 5 kbp using the appropriate conditions. These simulations suggest that such methods offer a realistic alternative to chromosome walking for identifying genomic deletions for which there are known phenotypes, thereby considerably reducing time and effort. For cDNA subtractive hybridization, the model predicts that after six rounds of hybridization, sequences that do not differ in abundance between the tester and driver populations (the background) will represent < 1% of the subtracted population, and even quite modestly upregulated cDNAs should be successfully enriched. Where several up-regulated cDNAs are present, the predicted final representation is dependent on both the initial abundance and the degree of up-regulation.
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Affiliation(s)
- J J Milner
- Plant Molecular Science Group, Institute of Biomedical and Life Sciences, Glasgow University
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Cecchini E, Dominy PJ, Geri C, Kaiser K, Sentry J, Milner JJ. Identification of genes up-regulated in dedifferentiating Nicotania glauca pith tissue, using an improved method for constructing a subtractive cDNA library. Nucleic Acids Res 1993; 21:5742-7. [PMID: 8284223 PMCID: PMC310543 DOI: 10.1093/nar/21.24.5742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Pith explants of Nicotiana glauca grown in vitro in synthetic medium supplemented with 2,4 dichlorophenoxyacetic acid (2, 4 D), are induced to dedifferentiate. Treatment with actinomycin D within the first 4-8 h of culture (but not later) is lethal and the explants die, implying a requirement for de novo transcription. The genes expressed during the initial period of culture are presumably critical for subsequent cell survival and proliferation, but so far their identity is unknown. We have constructed a subtractive cDNA library, enriched in sequences more abundant in dedifferentiating tissue than in pith. The subtractive library contains approximately seven major species, two of which, NGSUB7 and NGSUB8, are highly abundant. In Northern blots, these two hybridized to mRNA species whose abundance increased significantly but transiently during the first 4 to 8 h of culture. The sequence of NGSUB7 showed no significant homology at a nucleotide or derived amino acid level with any previously reported sequence. NGSUB8 however, showed significant homology over part of the derived amino acid sequence to several yeast and bacterial proteins with DNA binding function. We propose that the two recombinants represent transcripts from two novel genes edeA and edeB, which are expressed early in dedifferentiation.
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Affiliation(s)
- E Cecchini
- Department of Botany, Glasgow University, UK
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Abstract
Polyadenylated RNA, isolated from total cellular RNA of photoautotrophically grown Euglena gracilis, comprised 2.1% of the total cellular RNA and contained 6.2% polyadenylic acid. Polyadenylated RNA, labeled in vitro with (125)I, hybridized at saturating levels to an average 7.7% of the chloroplast DNA. In the presence of excess chloroplast rRNA, hybridization of polyadenylated RNA was reduced, but was still observed at a level corresponding to 2.8% of the chloroplast DNA. Polyadenylic acid was not detected in mRNA prepared from chloroplast polyribosomes, indicating a level of less than 0.1% polyadenylic acid in mature chloroplast mRNA. Of the total RNA isolated from cytoplasmic polyribosomes, 2.0% contained polyadenylic acid. This latter polyadenylated RNA did not hybridize to chloroplast DNA.
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Affiliation(s)
- J J Milner
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801
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Mielenz JR, Milner JJ, Hershberger CL. Analysis of Euglena gracilis chloroplast deoxyribonucleic acid with a restriction endonuclease, EcoRI. J Bacteriol 1977; 130:860-8. [PMID: 233724 PMCID: PMC235292 DOI: 10.1128/jb.130.2.860-868.1977] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cleavage of chloroplast deoxyribonucleic acid (DNA) of Euglena gracilis Z with restriction endonuclease RI from Escherichia coli (EcoRI) yielded 23 bands upon electrophoresis in gels of agarose. Four of the bands contained twice the stoichiometric amount of DNA. One of these bands contained two similarly sized fragments. The sum of the molecular weight of the 24 different fragments equaled the molecular weight of the circular molecule. The restriction fragments had different buoyant densities, with four having distinctly heavy densities in CsCl. Restriction fragments with a high buoyant density were preferentially lost when broken chloroplast DNA was purified by equilibrium density gradient centrifugation. Hybridization of chloroplast ribosomal ribonucleic acid to intact chloroplast DNA determined that there are two cistrons for 16S and 23S ribosomal ribonucleic acid. These two cistrons are located on six restriction fragments, all of which have buoyant densities greater than the intact molecule of chloroplast DNA.
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Abstract
The digestion of E. coli 16S RNA with a single-strand-specific nuclease produced two fractions separable by gel filtration. One fraction was small oligonucleotides, the other, comprising 67.5% of the total RNA, was highly structured double helical fragments of mol. wt. 7,600. There are thus about 44 helical loops of average size corresponding to 12 base pairs in each 16S RNA. 10% of the RNA could be digested from native 30S subunits. Nuclease attack was primarily in the intraloop single-stranded region but two major sites of attack were located in the interloop single-stranded regions. Nuclease digestion of unfolded subunits produced three classes of fragments, two of which, comprising 80% of the total RNA, were identical to fragments from 16S RNA. The third, consisting of 20% RNA, together with an equal weight of peotein, was a resistant core (sedimentation coefficient 7S).
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