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Singh A, Kaileh M, De S, Mazan-Mamczarz K, Bayarsaihan D, Sen R, Roy AL. Transcription factor TFII-I fine tunes innate properties of B lymphocytes. Front Immunol 2023; 14:1067459. [PMID: 36756127 PMCID: PMC9900109 DOI: 10.3389/fimmu.2023.1067459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023] Open
Abstract
The ubiquitously expressed transcription factor TFII-I is a multifunctional protein with pleiotropic roles in gene regulation. TFII-I associated polymorphisms are implicated in Sjögren's syndrome and Lupus in humans and, germline deletion of the Gtf2i gene in mice leads to embryonic lethality. Here we report a unique role for TFII-I in homeostasis of innate properties of B lymphocytes. Loss of Gtf2i in murine B lineage cells leads to an alteration in transcriptome, chromatin landscape and associated transcription factor binding sites, which exhibits myeloid-like features and coincides with enhanced sensitivity to LPS induced gene expression. TFII-I deficient B cells also show increased switching to IgG3, a phenotype associated with inflammation. These results demonstrate a role for TFII-I in maintaining immune homeostasis and provide clues for GTF2I polymorphisms associated with B cell dominated autoimmune diseases in humans.
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Affiliation(s)
- Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Supriyo De
- Laboratory of Genetics & Genomics, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics & Genomics, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Dashzeveg Bayarsaihan
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT, United States
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Ananda L Roy
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
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2
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Docq M, Vétillard M, Gallego C, Jaracz-Ros A, Mercier-Nomé F, Bachelerie F, Schlecht-Louf G. Multi-Tissue Characterization of GILZ Expression in Dendritic Cell Subsets at Steady State and in Inflammatory Contexts. Cells 2021; 10:3153. [PMID: 34831376 PMCID: PMC8623566 DOI: 10.3390/cells10113153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 11/17/2022] Open
Abstract
Dendritic cells (DCs) are key players in the control of tolerance and immunity. Glucocorticoids (GCs) are known to regulate DC function by promoting their tolerogenic differentiation through the induction of inhibitory ligands, cytokines, and enzymes. The GC-induced effects in DCs were shown to critically depend on increased expression of the Glucocorticoid-Induced Leucine Zipper protein (GILZ). GILZ expression levels were further shown to control antigen-presenting cell function, as well as T-cell priming capacity of DCs. However, the pattern of GILZ expression in DC subsets across tissues remains poorly described, as well as the modulation of its expression levels in different pathological settings. To fill in this knowledge gap, we conducted an exhaustive analysis of GILZ relative expression levels in DC subsets from various tissues using multiparametric flow cytometry. This study was performed at steady state, in the context of acute as well as chronic skin inflammation, and in a model of cancer. Our results show the heterogeneity of GILZ expression among DC subsets as well as the complexity of its modulation, that varies in a cell subset- and context-specific manner. Considering the contribution of GILZ in the control of DC functions and its potential as an immune checkpoint in cancer settings, these results are of high relevance for optimal GILZ targeting in therapeutic strategies.
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Affiliation(s)
- Molène Docq
- Inserm U996, Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, 92140 Clamart, France; (M.D.); (M.V.); (C.G.); (A.J.-R.); (F.M.-N.); (F.B.)
| | - Mathias Vétillard
- Inserm U996, Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, 92140 Clamart, France; (M.D.); (M.V.); (C.G.); (A.J.-R.); (F.M.-N.); (F.B.)
| | - Carmen Gallego
- Inserm U996, Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, 92140 Clamart, France; (M.D.); (M.V.); (C.G.); (A.J.-R.); (F.M.-N.); (F.B.)
| | - Agnieszka Jaracz-Ros
- Inserm U996, Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, 92140 Clamart, France; (M.D.); (M.V.); (C.G.); (A.J.-R.); (F.M.-N.); (F.B.)
| | - Françoise Mercier-Nomé
- Inserm U996, Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, 92140 Clamart, France; (M.D.); (M.V.); (C.G.); (A.J.-R.); (F.M.-N.); (F.B.)
- IPSIT SFR-UMS, CNRS, Inserm, Institut Paris Saclay d’Innovation Thérapeutique, Université Paris-Saclay, 92296 Chatenay-Malabry, France
| | - Françoise Bachelerie
- Inserm U996, Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, 92140 Clamart, France; (M.D.); (M.V.); (C.G.); (A.J.-R.); (F.M.-N.); (F.B.)
| | - Géraldine Schlecht-Louf
- Inserm U996, Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, 92140 Clamart, France; (M.D.); (M.V.); (C.G.); (A.J.-R.); (F.M.-N.); (F.B.)
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3
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Lamb D, De Sousa D, Quast K, Fundel-Clemens K, Erjefält JS, Sandén C, Hoffmann HJ, Kästle M, Schmid R, Menden K, Delic D. RORγt inhibitors block both IL-17 and IL-22 conferring a potential advantage over anti-IL-17 alone to treat severe asthma. Respir Res 2021; 22:158. [PMID: 34022896 PMCID: PMC8141258 DOI: 10.1186/s12931-021-01743-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND RORγt is a transcription factor that enables elaboration of Th17-associated cytokines (including IL-17 and IL-22) and is proposed as a pharmacological target for severe asthma. METHODS IL-17 immunohistochemistry was performed in severe asthma bronchial biopsies (specificity confirmed with in situ hybridization). Primary human small airway epithelial cells in air liquid interface and primary bronchial smooth muscle cells were stimulated with recombinant human IL-17 and/or IL-22 and pro-inflammatory cytokines measured. Balb/c mice were challenged intratracheally with IL-17 and/or IL-22 and airway hyperreactivity, pro-inflammatory cytokines and airway neutrophilia measured. Balb/c mice were sensitized intraperitoneally and challenged intratracheally with house dust mite extract and the effect of either a RORγt inhibitor (BIX119) or an anti-IL-11 antibody assessed on airway hyperreactivity, pro-inflammatory cytokines and airway neutrophilia measured. RESULTS We confirmed in severe asthma bronchial biopsies both the presence of IL-17-positive lymphocytes and that an IL-17 transcriptome profile in a severe asthma patient sub-population. Both IL-17 and IL-22 stimulated the release of pro-inflammatory cytokine and chemokine release from primary human lung cells and in mice. Furthermore, IL-22 in combination with IL-17, but neither alone, elicits airway hyperresponsiveness (AHR) in naïve mice. A RORγt inhibitor specifically blocked both IL-17 and IL-22, AHR and neutrophilia in a mouse house dust mite model unlike other registered or advanced pipeline modes of action. Full efficacy versus these parameters was associated with 90% inhibition of IL-17 and 50% inhibition of IL-22. In contrast, anti-IL-17 also blocked IL-17, but not IL-22, AHR or neutrophilia. Moreover, the deregulated genes in the lungs from these mice correlated well with deregulated genes from severe asthma biopsies suggesting that this model recapitulates significant severe asthma-relevant biology. Furthermore, these genes were reversed upon RORγt inhibition in the HDM model. Cell deconvolution suggested that the responsible cells were corticosteroid insensitive γδ-T-cells. CONCLUSION These data strongly suggest that both IL-17 and IL-22 are required for Th2-low endotype associated biology and that a RORγt inhibitor may provide improved clinical benefit in a severe asthma sub-population of patients by blocking both IL-17 and IL-22 biology compared with blocking IL-17 alone.
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MESH Headings
- Adolescent
- Adult
- Aged
- Animals
- Anti-Asthmatic Agents/pharmacology
- Asthma/drug therapy
- Asthma/immunology
- Asthma/metabolism
- Asthma/physiopathology
- Cells, Cultured
- Disease Models, Animal
- Epithelial Cells/drug effects
- Epithelial Cells/immunology
- Epithelial Cells/metabolism
- Female
- Humans
- Interleukin-17/metabolism
- Interleukins/antagonists & inhibitors
- Interleukins/metabolism
- Lung/drug effects
- Lung/immunology
- Lung/metabolism
- Lung/physiopathology
- Male
- Mice, Inbred BALB C
- Middle Aged
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/immunology
- Myocytes, Smooth Muscle/metabolism
- Nuclear Receptor Subfamily 1, Group F, Member 3/antagonists & inhibitors
- Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
- Pyroglyphidae/immunology
- Signal Transduction
- Th17 Cells/drug effects
- Th17 Cells/immunology
- Th17 Cells/metabolism
- Young Adult
- Interleukin-22
- Mice
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Affiliation(s)
- David Lamb
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany.
| | | | - Karsten Quast
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | - Katrin Fundel-Clemens
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | | | | | | | - Marc Kästle
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | - Ramona Schmid
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | - Kevin Menden
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
| | - Denis Delic
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach-an-der-Riss, Germany
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4
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Paiva RA, Sousa AGG, Ramos CV, Ávila M, Lilue J, Paixão T, Martins VC. Self-renewal of double-negative 3 early thymocytes enables thymus autonomy but compromises the β-selection checkpoint. Cell Rep 2021; 35:108967. [PMID: 33852867 DOI: 10.1016/j.celrep.2021.108967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/29/2021] [Accepted: 03/18/2021] [Indexed: 10/21/2022] Open
Abstract
T lymphocyte differentiation in the steady state is characterized by high cellular turnover whereby thymocytes do not self-renew. However, if deprived of competent progenitors, the thymus can temporarily maintain thymopoiesis autonomously. This bears a heavy cost, because prolongation of thymus autonomy causes leukemia. Here, we show that, at an early stage, thymus autonomy relies on double-negative 3 early (DN3e) thymocytes that acquire stem-cell-like properties. Following competent progenitor deprivation, DN3e thymocytes become long lived, are required for thymus autonomy, differentiate in vivo, and include DNA-label-retaining cells. At the single-cell level, the transcriptional programs of thymopoiesis in autonomy and the steady state are similar. However, a new cell population emerges in autonomy that expresses an aberrant Notch target gene signature and bypasses the β-selection checkpoint. In summary, DN3e thymocytes have the potential to self-renew and differentiate in vivo if cell competition is impaired, but this generates atypical cells, probably the precursors of leukemia.
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Affiliation(s)
- Rafael A Paiva
- Lymphocyte Development and Leukemogenesis Laboratory, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - António G G Sousa
- Bioinformatics Unit, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Camila V Ramos
- Lymphocyte Development and Leukemogenesis Laboratory, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Mariana Ávila
- Lymphocyte Development and Leukemogenesis Laboratory, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Jingtao Lilue
- Bioinformatics Unit, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Tiago Paixão
- Quantitative and Digital Science Unit, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Vera C Martins
- Lymphocyte Development and Leukemogenesis Laboratory, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal.
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5
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Wang F, Trier AM, Li F, Kim S, Chen Z, Chai JN, Mack MR, Morrison SA, Hamilton JD, Baek J, Yang TLB, Ver Heul AM, Xu AZ, Xie Z, Dong X, Kubo M, Hu H, Hsieh CS, Dong X, Liu Q, Margolis DJ, Ardeleanu M, Miller MJ, Kim BS. A basophil-neuronal axis promotes itch. Cell 2021; 184:422-440.e17. [PMID: 33450207 PMCID: PMC7878015 DOI: 10.1016/j.cell.2020.12.033] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/09/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023]
Abstract
Itch is an evolutionarily conserved sensation that facilitates expulsion of pathogens and noxious stimuli from the skin. However, in organ failure, cancer, and chronic inflammatory disorders such as atopic dermatitis (AD), itch becomes chronic, intractable, and debilitating. In addition to chronic itch, patients often experience intense acute itch exacerbations. Recent discoveries have unearthed the neuroimmune circuitry of itch, leading to the development of anti-itch treatments. However, mechanisms underlying acute itch exacerbations remain overlooked. Herein, we identify that a large proportion of patients with AD harbor allergen-specific immunoglobulin E (IgE) and exhibit a propensity for acute itch flares. In mice, while allergen-provoked acute itch is mediated by the mast cell-histamine axis in steady state, AD-associated inflammation renders this pathway dispensable. Instead, a previously unrecognized basophil-leukotriene (LT) axis emerges as critical for acute itch flares. By probing fundamental itch mechanisms, our study highlights a basophil-neuronal circuit that may underlie a variety of neuroimmune processes.
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Affiliation(s)
- Fang Wang
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Dermatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Anna M Trier
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fengxian Li
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong 510282, China; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Seonyoung Kim
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhen Chen
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Jiani N Chai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Madison R Mack
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie A Morrison
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Jinok Baek
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Dermatology, College of Medicine, Gachon University, Incheon 21565, Korea
| | - Ting-Lin B Yang
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aaron M Ver Heul
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amy Z Xu
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zili Xie
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xintong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Masato Kubo
- Laboratory for Cytokine Regulation, Center for Integrative Medical Science, RIKEN Yokohama Institute, Yokohama 230-0045, Kanagawa Prefecture, Japan; Division of Molecular Pathology, Research Institute for Biomedical Science, Tokyo University of Science, Noda 278-0022, Chiba Prefecture, Japan
| | - Hongzhen Hu
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chyi-Song Hsieh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qin Liu
- Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David J Margolis
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Mark J Miller
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian S Kim
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch and Sensory Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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7
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Kim EY, Ner-Gaon H, Varon J, Cullen AM, Guo J, Choi J, Barragan-Bradford D, Higuera A, Pinilla-Vera M, Short SA, Arciniegas-Rubio A, Tamura T, Leaf DE, Baron RM, Shay T, Brenner MB. Post-sepsis immunosuppression depends on NKT cell regulation of mTOR/IFN-γ in NK cells. J Clin Invest 2020; 130:3238-3252. [PMID: 32154791 PMCID: PMC7260006 DOI: 10.1172/jci128075] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
As treatment of the early, inflammatory phase of sepsis improves, post-sepsis immunosuppression and secondary infection have increased in importance. How early inflammation drives immunosuppression remains unclear. Although IFN-γ typically helps microbial clearance, we found that increased plasma IFN-γ in early clinical sepsis was associated with the later development of secondary Candida infection. Consistent with this observation, we found that exogenous IFN-γ suppressed macrophage phagocytosis of zymosan in vivo, and antibody blockade of IFN-γ after endotoxemia improved survival of secondary candidemia. Transcriptomic analysis of innate lymphocytes during endotoxemia suggested that NKT cells drove IFN-γ production by NK cells via mTORC1. Activation of invariant NKT (iNKT) cells with glycolipid antigen drove immunosuppression. Deletion of iNKT cells in Cd1d-/- mice or inhibition of mTOR by rapamycin reduced immunosuppression and susceptibility to secondary Candida infection. Thus, although rapamycin is typically an immunosuppressive medication, in the context of sepsis, rapamycin has the opposite effect. These results implicated an NKT cell/mTOR/IFN-γ axis in immunosuppression following endotoxemia or sepsis. In summary, in vivo iNKT cells activated mTORC1 in NK cells to produce IFN-γ, which worsened macrophage phagocytosis, clearance of secondary Candida infection, and mortality.
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Affiliation(s)
- Edy Y. Kim
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Masachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Hadas Ner-Gaon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Jack Varon
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Masachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | | | - Jingyu Guo
- Division of Rheumatology, Inflammation and Immunity and
| | - Jiyoung Choi
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Masachusetts, USA
| | - Diana Barragan-Bradford
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Masachusetts, USA
| | - Angelica Higuera
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Masachusetts, USA
| | - Mayra Pinilla-Vera
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Masachusetts, USA
| | - Samuel A.P. Short
- Division of Renal (Kidney) Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Tomoyoshi Tamura
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Masachusetts, USA
| | - David E. Leaf
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Renal (Kidney) Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Rebecca M. Baron
- Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Masachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tal Shay
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael B. Brenner
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Inflammation and Immunity and
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8
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The pseudo-allergic/neurogenic route of mast cell activation via MRGPRX2: discovery, functional programs, regulation, relevance to disease, and relation with allergic stimulation. ACTA ACUST UNITED AC 2020. [DOI: 10.1097/itx.0000000000000032] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Chao T, Liu Z, Zhang Y, Zhang L, Huang R, He L, Gu Y, Chen Z, Zheng Q, Shi L, Zheng W, Qi X, Kong E, Zhang Z, Lawrence T, Liang Y, Lu L. Precise and Rapid Validation of Candidate Gene by Allele Specific Knockout With CRISPR/Cas9 in Wild Mice. Front Genet 2019; 10:124. [PMID: 30838037 PMCID: PMC6390232 DOI: 10.3389/fgene.2019.00124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/04/2019] [Indexed: 11/13/2022] Open
Abstract
It is a tempting goal to identify causative genes underlying phenotypic differences among inbred strains of mice, which is a huge reservoir of genetic resources to understand mammalian pathophysiology. In particular, the wild-derived mouse strains harbor enormous genetic variations that have been acquired during evolutionary divergence over 100s of 1000s of years. However, validating the genetic variation in non-classical strains was extremely difficult, until the advent of CRISPR/Cas9 genome editing tools. In this study, we first describe a T cell phenotype in both wild-derived PWD/PhJ parental mice and F1 hybrids, from a cross to C57BL/6 (B6) mice, and we isolate a genetic locus on Chr2, using linkage mapping and chromosome substitution mice. Importantly, we validate the identification of the functional gene controlling this T cell phenotype, Cd44, by allele specific knockout of the PWD copy, leaving the B6 copy completely intact. Our experiments using F1 mice with a dominant phenotype, allowed rapid validation of candidate genes by designing sgRNA PAM sequences that only target the DNA of the PWD genome. We obtained 10 animals derived from B6 eggs fertilized with PWD sperm cells which were subjected to microinjection of CRISPR/Cas9 gene targeting machinery. In the newborns of F1 hybrids, 80% (n = 10) had allele specific knockout of the candidate gene Cd44 of PWD origin, and no mice showed mistargeting of the B6 copy. In the resultant allele-specific knockout F1 mice, we observe full recovery of T cell phenotype. Therefore, our study provided a precise and rapid approach to functionally validate genes that could facilitate gene discovery in classic mouse genetics. More importantly, as we succeeded in genetic manipulation of mice, allele specific knockout could provide the possibility to inactivate disease alleles while keeping the normal allele of the gene intact in human cells.
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Affiliation(s)
- Tianzhu Chao
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Zhuangzhuang Liu
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Yu Zhang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Lichen Zhang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Rong Huang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Le He
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Yanrong Gu
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Zhijun Chen
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Qianqian Zheng
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Lijin Shi
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Laboratory of Genetic Regulators in the Immune System, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Wenping Zheng
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Xinhui Qi
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Eryan Kong
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Zhongjian Zhang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Toby Lawrence
- Centre for Inflammation Biology and Cancer Immunology, King's College London, London, United Kingdom
| | - Yinming Liang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China.,Laboratory of Genetic Regulators in the Immune System, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Liaoxun Lu
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China.,Laboratory of Genetic Regulators in the Immune System, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
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10
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Targeted PET imaging strategy to differentiate malignant from inflamed lymph nodes in diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A 2017; 114:E7441-E7449. [PMID: 28827325 DOI: 10.1073/pnas.1705013114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma in adults. DLBCL exhibits highly aggressive and systemic progression into multiple tissues in patients, particularly in lymph nodes. Whole-body 18F-fluodeoxyglucose positron emission tomography ([18F]FDG-PET) imaging has an essential role in diagnosing DLBCL in the clinic; however, [18F]FDG-PET often faces difficulty in differentiating malignant tissues from certain nonmalignant tissues with high glucose uptake. We have developed a PET imaging strategy for DLBCL that targets poly[ADP ribose] polymerase 1 (PARP1), the expression of which has been found to be much higher in DLBCL than in healthy tissues. In a syngeneic DLBCL mouse model, this PARP1-targeted PET imaging approach allowed us to discriminate between malignant and inflamed lymph nodes, whereas [18F]FDG-PET failed to do so. Our PARP1-targeted PET imaging approach may be an attractive addition to the current PET imaging strategy to differentiate inflammation from malignancy in DLBCL.
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11
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Te Velde AA, Bezema T, van Kampen AHC, Kraneveld AD, 't Hart BA, van Middendorp H, Hack EC, van Montfrans JM, Belzer C, Jans-Beken L, Pieters RH, Knipping K, Huber M, Boots AMH, Garssen J, Radstake TR, Evers AWM, Prakken BJ, Joosten I. Embracing Complexity beyond Systems Medicine: A New Approach to Chronic Immune Disorders. Front Immunol 2016; 7:587. [PMID: 28018353 PMCID: PMC5149516 DOI: 10.3389/fimmu.2016.00587] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/28/2016] [Indexed: 12/21/2022] Open
Abstract
In order to combat chronic immune disorders (CIDs), it is an absolute necessity to understand the bigger picture, one that goes beyond insights at a one-disease, molecular, cellular, and static level. To unravel this bigger picture we advocate an integral, cross-disciplinary approach capable of embracing the complexity of the field. This paper discusses the current knowledge on common pathways in CIDs including general psychosocial and lifestyle factors associated with immune functioning. We demonstrate the lack of more in-depth psychosocial and lifestyle factors in current research cohorts and most importantly the need for an all-encompassing analysis of these factors. The second part of the paper discusses the challenges of understanding immune system dynamics and effectively integrating all key perspectives on immune functioning, including the patient’s perspective itself. This paper suggests the use of techniques from complex systems science in describing and simulating healthy or deviating behavior of the immune system in its biopsychosocial surroundings. The patient’s perspective data are suggested to be generated by using specific narrative techniques. We conclude that to gain more insight into the behavior of the whole system and to acquire new ways of combatting CIDs, we need to construct and apply new techniques in the field of computational and complexity science, to an even wider variety of dynamic data than used in today’s systems medicine.
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Affiliation(s)
- Anje A Te Velde
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center , Amsterdam , Netherlands
| | | | - Antoine H C van Kampen
- Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB), Academic Medical Center, Amsterdam, Netherlands; Biosystems Data Analysis, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands; Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bert A 't Hart
- Department of Immunobiology, Biomedical Primate Research Centre, Rijswijk, Netherlands; Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Neuroscience, University Medical Center, University of Groningen, Groningen, Netherlands
| | - Henriët van Middendorp
- Institute of Psychology, Health, Medical, and Neuropsychology Unit, Faculty of Social and Behavioural Sciences, Leiden University , Leiden , Netherlands
| | - Erik C Hack
- Laboratory of Translational Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Joris M van Montfrans
- Division of Pediatrics, Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht , Utrecht , Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University , Wageningen , Netherlands
| | - Lilian Jans-Beken
- Department of Psychology and Educational Sciences, Open University , Heerlen , Netherlands
| | - Raymond H Pieters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands; Institute for Life Sciences and Chemistry, HU University of Applied Sciences Utrecht, Utrecht, Netherlands
| | - Karen Knipping
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands; Immunology Platform, Nutricia Research, Utrecht, Netherlands
| | - Machteld Huber
- Institute for Positive Health , Amersfoort , Netherlands
| | - Annemieke M H Boots
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands; Immunology Platform, Nutricia Research, Utrecht, Netherlands
| | - Tim R Radstake
- Laboratory of Translational Immunology, Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Andrea W M Evers
- Institute of Psychology, Health, Medical, and Neuropsychology Unit, Faculty of Social and Behavioural Sciences, Leiden University , Leiden , Netherlands
| | - Berent J Prakken
- Laboratory of Translational Immunology, Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht , Utrecht , Netherlands
| | - Irma Joosten
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Centre , Nijmegen , Netherlands
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12
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Yang IV, Pedersen BS, Liu AH, O'Connor GT, Pillai D, Kattan M, Misiak RT, Gruchalla R, Szefler SJ, Khurana Hershey GK, Kercsmar C, Richards A, Stevens AD, Kolakowski CA, Makhija M, Sorkness CA, Krouse RZ, Visness C, Davidson EJ, Hennessy CE, Martin RJ, Togias A, Busse WW, Schwartz DA. The nasal methylome and childhood atopic asthma. J Allergy Clin Immunol 2016; 139:1478-1488. [PMID: 27745942 DOI: 10.1016/j.jaci.2016.07.036] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 06/24/2016] [Accepted: 07/14/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Given the strong environmental influence on both epigenetic marks and allergic asthma in children, the epigenetic alterations in respiratory epithelia might provide insight into allergic asthma. OBJECTIVE We sought to identify DNA methylation and gene expression changes associated with childhood allergic persistent asthma. METHODS We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma (n = 36) versus healthy control subjects (n = 36). Results were validated in an independent population of asthmatic children (n = 30) by using a shared healthy control population (n = 36) and in an independent population of white adult atopic asthmatic patients (n = 12) and control subjects (n = 12). RESULTS We identified 186 genes with significant methylation changes, differentially methylated regions or differentially methylated probes, after adjustment for age, sex, race/ethnicity, batch effects, inflation, and multiple comparisons. Genes differentially methylated included those with established roles in asthma and atopy and genes related to extracellular matrix, immunity, cell adhesion, epigenetic regulation, and airflow obstruction. The methylation changes were substantial (median, 9.5%; range, 2.6% to 29.5%). Hypomethylated and hypermethylated genes were associated with increased and decreased gene expression, respectively (P < 2.8 × 10-6 for differentially methylated regions and P < 7.8 × 10-10 for differentially methylated probes). Quantitative analysis in 53 differentially expressed genes demonstrated that 32 (60%) have significant methylation-expression relationships within 5 kb of the gene. Ten loci selected based on the relevance to asthma, magnitude of methylation change, and methylation-expression relationships were validated in an independent cohort of children with atopic asthma. Sixty-seven of 186 genes also have significant asthma-associated methylation changes in nasal epithelia of adult white asthmatic patients. CONCLUSIONS Epigenetic marks in respiratory epithelia are associated with allergic asthma and gene expression changes in inner-city children.
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Affiliation(s)
- Ivana V Yang
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo; National Jewish Health, Denver, Colo; Department of Epidemiology, Colorado School of Public Health, Aurora, Colo.
| | - Brent S Pedersen
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | | | - Meyer Kattan
- Columbia University Medical Center, New York, NY
| | | | | | - Stanley J Szefler
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado, School of Medicine, Aurora, Colo
| | | | | | - Adam Richards
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | | | | | - Christine A Sorkness
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | | | | | - Elizabeth J Davidson
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | - Corinne E Hennessy
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md; and University of Colorado, Aurora, CO
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - David A Schwartz
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo; National Jewish Health, Denver, Colo; Department of Immunology, University of Colorado, Aurora, Colo.
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13
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Coppola CJ, C Ramaker R, Mendenhall EM. Identification and function of enhancers in the human genome. Hum Mol Genet 2016; 25:R190-R197. [PMID: 27402881 DOI: 10.1093/hmg/ddw216] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/31/2022] Open
Abstract
The study of gene regulation has rapidly advanced by leveraging next-generation sequencing to identify and characterize the cis and trans elements that are critical for defining cell identity. These advances have paralleled a movement towards whole genome sequencing in clinics. These two tracks have increasingly synergized to underscore the importance of cis-regulatory elements in development as well produce countless studies implicating these elements in human disease. Other studies have emphasized the clinical phenotypes associated with variation or mutations in trans factors, including non-coding RNAs and chromatin regulators. These studies highlight the importance of obtaining a comprehensive understanding of mammalian gene regulation for predicting the impact of genetic variation on patient phenotypes. Currently lagging behind the generation of vast datasets and annotations is our ability to examine these putative elements in the dynamic context of a developing organism.
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Affiliation(s)
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eric M Mendenhall
- University of Alabama in Huntsville, Huntsville, AL, USA HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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14
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Clancy T, Hovig E. Profiling networks of distinct immune-cells in tumors. BMC Bioinformatics 2016; 17:263. [PMID: 27377892 PMCID: PMC4932723 DOI: 10.1186/s12859-016-1141-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Abstract
Background It is now clearly evident that cancer outcome and response to therapy is guided by diverse immune-cell activity in tumors. Presently, a key challenge is to comprehensively identify networks of distinct immune-cell signatures present in complex tissue, at higher-resolution and at various stages of differentiation, activation or function. This is particularly so for closely related immune-cells with diminutive, yet critical, differences. Results To predict networks of infiltrated distinct immune-cell phenotypes at higher resolution, we explored an integrated knowledge-based approach to select immune-cell signature genes integrating not only expression enrichment across immune-cells, but also an automatic capture of relevant immune-cell signature genes from the literature. This knowledge-based approach was integrated with resources of immune-cell specific protein networks, to define signature genes of distinct immune-cell phenotypes. We demonstrate the utility of this approach by profiling signatures of distinct immune-cells, and networks of immune-cells, from metastatic melanoma patients who had undergone chemotherapy. The resultant bioinformatics strategy complements immunohistochemistry from these tumors, and predicts both tumor-killing and immunosuppressive networks of distinct immune-cells in responders and non-responders, respectively. The approach is also shown to capture differences in the immune-cell networks of BRAF versus NRAS mutated metastatic melanomas, and the dynamic changes in resistance to targeted kinase inhibitors in MAPK signalling. Conclusions This integrative bioinformatics approach demonstrates that capturing the protein network signatures and ratios of distinct immune-cell in the tumor microenvironment maybe an important factor in predicting response to therapy. This may serve as a computational strategy to define network signatures of distinct immune-cells to guide immuno-pathological discovery. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1141-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Trevor Clancy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. .,Department of Cancer Immunology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Biomedical Research Group, Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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15
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Abstract
Imaging reveals complex structures and dynamic interactive processes, located deep inside the body, that are otherwise difficult to decipher. Numerous imaging modalities harness every last inch of the energy spectrum. Clinical modalities include magnetic resonance imaging (MRI), X-ray computed tomography (CT), ultrasound, and light-based methods [endoscopy and optical coherence tomography (OCT)]. Research modalities include various light microscopy techniques (confocal, multiphoton, total internal reflection, superresolution fluorescence microscopy), electron microscopy, mass spectrometry imaging, fluorescence tomography, bioluminescence, variations of OCT, and optoacoustic imaging, among a few others. Although clinical imaging and research microscopy are often isolated from one another, we argue that their combination and integration is not only informative but also essential to discovering new biology and interpreting clinical datasets in which signals invariably originate from hundreds to thousands of cells per voxel.
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16
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Kidd BA, Wroblewska A, Boland MR, Agudo J, Merad M, Tatonetti NP, Brown BD, Dudley JT. Mapping the effects of drugs on the immune system. Nat Biotechnol 2015; 34:47-54. [PMID: 26619012 PMCID: PMC4706827 DOI: 10.1038/nbt.3367] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 08/11/2015] [Indexed: 11/18/2022]
Abstract
Understanding how drugs affect the immune system has consequences for treating disease and minimizing unwanted side effects. Here we present an integrative computational approach for predicting interactions between drugs and immune cells in a system-wide manner. The approach matches gene sets between transcriptional signatures to determine their similarity. We apply the method to model the interactions between 1,309 drugs and 221 immune cell types and predict 69,995 known and novel interactions. The resulting immune-cell pharmacology map is used to predict how 5 drugs influence 4 immune cell types in humans and mice. To validate the predictions, we analyzed patient records and examined cell population changes from in vivo experiments. Our method offers a tool for screening thousands of interactions to identify relationships between drugs and the immune system.
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Affiliation(s)
- Brian A Kidd
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Aleksandra Wroblewska
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mary R Boland
- Department of Biomedical Informatics, Systems Biology and Medicine, Columbia University Medical Center, New York, New York, USA
| | - Judith Agudo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Systems Biology and Medicine, Columbia University Medical Center, New York, New York, USA
| | - Brian D Brown
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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17
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Tsang JS. Utilizing population variation, vaccination, and systems biology to study human immunology. Trends Immunol 2015; 36:479-93. [PMID: 26187853 PMCID: PMC4979540 DOI: 10.1016/j.it.2015.06.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 12/27/2022]
Abstract
The move toward precision medicine has highlighted the importance of understanding biological variability within and across individuals in the human population. In particular, given the prevalent involvement of the immune system in diverse pathologies, an important question is how much and what information about the state of the immune system is required to enable accurate prediction of future health and response to medical interventions. Towards addressing this question, recent studies using vaccination as a model perturbation and systems-biology approaches are beginning to provide a glimpse of how natural population variation together with multiplexed, high-throughput measurement and computational analysis can be used to uncover predictors of immune response quality in humans. Here I discuss recent developments in this emerging field, with emphasis on baseline correlates of vaccination responses, sources of immune-state variability, as well as relevant features of study design, data generation, and computational analysis.
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Affiliation(s)
- John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD 20892, USA; Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD 20892, USA.
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18
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Touzot M, Dahirel A, Cappuccio A, Segura E, Hupé P, Soumelis V. Using Transcriptional Signatures to Assess Immune Cell Function: From Basic Mechanisms to Immune-Related Disease. J Mol Biol 2015; 427:3356-67. [PMID: 25986308 DOI: 10.1016/j.jmb.2015.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 12/24/2022]
Abstract
Assessing human immune response remains a challenge as it involves multiple cell types in specific tissues. The use of microarray-based expression profiling as a tool for assessing the immune response has grown increasingly over the past decade. Transcriptome analyses provide investigators with a global perspective of the complex molecular and cellular events that unfold during the development of an immune response. In this review, we will detail the broad use of gene expression profiling to decipher the complexity of immune responses from disease biomarkers identification to cell activation, polarisation or functional specialisation. We will also describe how such data-driven strategies revealed the flexibility of immune function with common and specific transcriptional programme under multiple stimuli.
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Affiliation(s)
- Maxime Touzot
- INSERM U932, 26 rue d'Ulm, 75005 Paris, France; Institut Curie, Section Recherche, 26 rue d'Ulm, 75005 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, 26 rue d'Ulm, 75005 Paris, France
| | - Alix Dahirel
- INSERM U932, 26 rue d'Ulm, 75005 Paris, France; Institut Curie, Section Recherche, 26 rue d'Ulm, 75005 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, 26 rue d'Ulm, 75005 Paris, France
| | - Antonio Cappuccio
- INSERM U932, 26 rue d'Ulm, 75005 Paris, France; Institut Curie, Section Recherche, 26 rue d'Ulm, 75005 Paris, France; Service de Bioinformatique, INSERM U900, Institut Curie, 26 rue d'Ulm, 75248 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, 26 rue d'Ulm, 75005 Paris, France
| | - Elodie Segura
- INSERM U932, 26 rue d'Ulm, 75005 Paris, France; Institut Curie, Section Recherche, 26 rue d'Ulm, 75005 Paris, France
| | - Philippe Hupé
- Institut Curie, Section Recherche, 26 rue d'Ulm, 75005 Paris, France; Service de Bioinformatique, INSERM U900, Institut Curie, 26 rue d'Ulm, 75248 Paris, France; CNRS UMR 144
| | - Vassili Soumelis
- INSERM U932, 26 rue d'Ulm, 75005 Paris, France; Institut Curie, Section Recherche, 26 rue d'Ulm, 75005 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, 26 rue d'Ulm, 75005 Paris, France.
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19
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Kottyan LC, Weirauch MT, Rothenberg ME. Making it big in allergy. J Allergy Clin Immunol 2015; 135:43-5. [PMID: 25567041 DOI: 10.1016/j.jaci.2014.10.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 10/30/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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20
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Wang F, Tian Z, Wei H. Genomic expression profiling of NK cells in health and disease. Eur J Immunol 2014; 45:661-78. [PMID: 25476835 DOI: 10.1002/eji.201444998] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/01/2014] [Accepted: 12/01/2014] [Indexed: 12/15/2022]
Abstract
NK cells are important components of innate and adaptive immunity. Functionally, they play key roles in host defense against tumors and infectious pathogens. Within the past few years, genomic-scale experiments have provided us with a plethora of gene expression data that reveal an extensive molecular and biological map underlying gene expression programs. In order to better explore and take advantage of existing datasets, we review here the genomic expression profiles of NK cells and their subpopulations in resting or stimulated states, in diseases, and in different organs; moreover, we contrast these expression data to those of other lymphocytes. We have also compiled a comprehensive list of genomic profiling studies of both human and murine NK cells in this review.
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Affiliation(s)
- Fuyan Wang
- Institute of Immunology, School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China; Diabetes Center, School of Medicine, Ningbo University, Ningbo, China
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21
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Paczesny S, Duncan C, Jacobsohn D, Krance R, Leung K, Carpenter P, Bollard C, Renbarger J, Cooke K. Opportunities and challenges of proteomics in pediatric patients: circulating biomarkers after hematopoietic stem cell transplantation as a successful example. Proteomics Clin Appl 2014; 8:837-50. [PMID: 25196024 DOI: 10.1002/prca.201400033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/30/2014] [Accepted: 09/03/2014] [Indexed: 11/06/2022]
Abstract
Biomarkers have the potential to improve diagnosis and prognosis, facilitate-targeted treatment, and reduce health care costs. Thus, there is great hope that biomarkers will be integrated in all clinical decisions in the near future. A decade ago, the biomarker field was launched with great enthusiasm because MS revealed that blood contains a rich library of candidate biomarkers. However, biomarker research has not yet delivered on its promise due to several limitations: (i) improper sample handling and tracking as well as limited sample availability in the pediatric population, (ii) omission of appropriate controls in original study designs, (iii) lability and low abundance of interesting biomarkers in blood, and (iv) the inability to mechanistically tie biomarker presence to disease biology. These limitations as well as successful strategies to overcome them are discussed in this review. Several advances in biomarker discovery and validation have been made in hematopoietic stem cell transplantation, the current most effective tumor immunotherapy, and these could serve as examples for other conditions. This review provides fresh optimism that biomarkers clinically relevant in pediatrics are closer to being realized based on: (i) a uniform protocol for low-volume blood collection and preservation, (ii) inclusion of well-controlled independent cohorts, (iii) novel technologies and instrumentation with low analytical sensitivity, and (iv) integrated animal models for exploring potential biomarkers and targeted therapies.
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Affiliation(s)
- Sophie Paczesny
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
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22
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Kim HJ, Cantor H. The path to reactivation of antitumor immunity and checkpoint immunotherapy. Cancer Immunol Res 2014; 2:926-36. [PMID: 25281320 DOI: 10.1158/2326-6066.cir-14-0153] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cancer immunology has recently made major therapeutic inroads that represent clinical application of basic insights into mechanisms that govern immunity against tumors. Research into fundamental elements of T-cell and natural killer-cell biology, including the basis of antigen recognition, activation, proliferation, and survival, has informed the design of new therapeutic approaches to augment the body's natural anticancer immune response. Here, we describe some of the key steps that have provided the foundation for current strategies of immunotherapy.
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Affiliation(s)
- Hye-Jung Kim
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts. Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Harvey Cantor
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts. Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts.
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23
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Differential protein network analysis of the immune cell lineage. BIOMED RESEARCH INTERNATIONAL 2014; 2014:363408. [PMID: 25309909 PMCID: PMC4189771 DOI: 10.1155/2014/363408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/28/2014] [Accepted: 07/12/2014] [Indexed: 01/16/2023]
Abstract
Recently, the Immunological Genome Project (ImmGen) completed the first phase of the goal to understand the molecular circuitry underlying the immune cell lineage in mice. That milestone resulted in the creation of the most comprehensive collection of gene expression profiles in the immune cell lineage in any model organism of human disease. There is now a requisite to examine this resource using bioinformatics integration with other molecular information, with the aim of gaining deeper insights into the underlying processes that characterize this immune cell lineage. We present here a bioinformatics approach to study differential protein interaction mechanisms across the entire immune cell lineage, achieved using affinity propagation applied to a protein interaction network similarity matrix. We demonstrate that the integration of protein interaction networks with the most comprehensive database of gene expression profiles of the immune cells can be used to generate hypotheses into the underlying mechanisms governing the differentiation and the differential functional activity across the immune cell lineage. This approach may not only serve as a hypothesis engine to derive understanding of differentiation and mechanisms across the immune cell lineage, but also help identify possible immune lineage specific and common lineage mechanism in the cells protein networks.
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24
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Erratum: Consortium biology in immunology: the perspective from the Immunological Genome Project. Nat Rev Immunol 2014. [DOI: 10.1038/nri3714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Altboum Z, Steuerman Y, David E, Barnett-Itzhaki Z, Valadarsky L, Keren-Shaul H, Meningher T, Mendelson E, Mandelboim M, Gat-Viks I, Amit I. Digital cell quantification identifies global immune cell dynamics during influenza infection. Mol Syst Biol 2014; 10:720. [PMID: 24586061 PMCID: PMC4023392 DOI: 10.1002/msb.134947] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hundreds of immune cell types work in coordination to maintain tissue homeostasis. Upon infection, dramatic changes occur with the localization, migration, and proliferation of the immune cells to first alert the body of the danger, confine it to limit spreading, and finally extinguish the threat and bring the tissue back to homeostasis. Since current technologies can follow the dynamics of only a limited number of cell types, we have yet to grasp the full complexity of global in vivo cell dynamics in normal developmental processes and disease. Here, we devise a computational method, digital cell quantification (DCQ), which combines genome‐wide gene expression data with an immune cell compendium to infer in vivo changes in the quantities of 213 immune cell subpopulations. DCQ was applied to study global immune cell dynamics in mice lungs at ten time points during 7 days of flu infection. We find dramatic changes in quantities of 70 immune cell types, including various innate, adaptive, and progenitor immune cells. We focus on the previously unreported dynamics of four immune dendritic cell subtypes and suggest a specific role for CD103+CD11b−DCs in early stages of disease and CD8+pDC in late stages of flu infection.
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Affiliation(s)
- Zeev Altboum
- Department of Immunology, Weizmann Institute, Rehovot, Israel
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26
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Kim CC, Lanier LL. Beyond the transcriptome: completion of act one of the Immunological Genome Project. Curr Opin Immunol 2013; 25:593-7. [PMID: 24168965 DOI: 10.1016/j.coi.2013.09.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 12/24/2022]
Abstract
The Immunological Genome Consortium has generated a public resource (www.immgen.org) that provides a compendium of gene expression profiles of ∼270 leukocyte subsets in the mouse. This effort established carefully standardized operating procedures that resulted in a transcriptional dataset of unprecedented comprehensiveness and quality. The findings have been detailed recently in a series of publications providing molecular insights into the development, heterogeneity, and/or function of these cellular lineages and distinct subpopulations. Here, we review the key findings of these studies, highlighting what has been gained and how the knowledge can be used to accelerate progress toward a comprehensive understanding of the immune system.
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Affiliation(s)
- Charles C Kim
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA 94110, United States
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27
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Bronevetsky Y, Ansel KM. Regulation of miRNA biogenesis and turnover in the immune system. Immunol Rev 2013; 253:304-16. [PMID: 23550654 DOI: 10.1111/imr.12059] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) have emerged as important regulators of gene expression in diverse biological processes ranging from cell proliferation and survival to organ development and immunity. Here, we review mechanisms that regulate the expression of miRNAs themselves in the immune system. Like protein-coding genes, miRNAs can be regulated at the transcriptional level, downstream of signaling pathways and circuits that activate or inhibit transcription factors and chromatin remodeling. The resulting primary miRNAs are processed into active mature miRNAs through a series of biochemical steps, and miRNA abundance can be regulated at each step of this biogenesis pathway. Recent work has uncovered regulation of mature miRNA turnover in the immune system as well. A better understanding of these processes and their regulation by immunogenic stimuli is critical for integrating miRNAs into current models of gene expression networks that determine cell identity and immune function.
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Affiliation(s)
- Yelena Bronevetsky
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
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28
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Shay T, Kang J. Immunological Genome Project and systems immunology. Trends Immunol 2013; 34:602-9. [PMID: 23631936 DOI: 10.1016/j.it.2013.03.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/20/2013] [Accepted: 03/24/2013] [Indexed: 12/23/2022]
Abstract
Immunological studies of single proteins in a single cell type have been complemented in recent years by larger studies, enabled by emerging high-throughput technologies. This trend has recently been exemplified by the discovery of gene networks controlling regulatory and effector αβ T cell subset development and human hematopoiesis. The Immunological Genome Project (ImmGen) aims to decipher the gene networks underpinning mouse hematopoiesis. The first phase, completed in 2012, profiled the transcriptome of 249 immune cell types. We discuss the utilities of the datasets in high-resolution mapping of the hematopoietic system. The immune transcriptome compendium has revealed unsuspected cell lineage relations and the network reconstruction has identified novel regulatory factors of hematopoiesis.
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Affiliation(s)
- Tal Shay
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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29
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Tamari M, Tanaka S, Hirota T. Genome-wide association studies of allergic diseases. Allergol Int 2013; 62:21-28. [PMID: 23439055 DOI: 10.2332/allergolint.13-rai-0539] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Indexed: 12/12/2022] Open
Abstract
Allergic diseases are complex diseases caused by a combination of genetic and environmental factors. To determine the genetic components of these diseases and to discover the genes and cellular pathways underlying them, a large number of genetic studies have been conducted. Progress in genetics enables us to conduct genome-wide association studies (GWASs), which is a comprehensive and unbiased approach to identify susceptibility loci for multifactorial diseases. Recent GWASs have convincingly detected a large number of loci associated with allergic diseases. Candidate genes in the susceptibility loci suggest roles for epithelial barrier functions, innate-adaptive immunity, IL-1 family signaling, regulatory T cells and the vitamin D pathway in the pathogenesis of allergic diseases. Interestingly, the IL1RL1, HLA, IL13 and C11orf30 regions are overlapping susceptibility loci among atopic dermatitis and asthma or allergic rhinitis. Although a more complete collection of associated genes and pathways is needed, biologic insights revealed by GWASs improve our understanding of the pathophysiology of human allergic diseases and contribute to the development of better treatment and preventive strategies.
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Affiliation(s)
- Mayumi Tamari
- Laboratory for Respiratory Diseases, Center for Genomic Medicine, Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan.
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