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Orecchioni M, Wolf D, Suryawanshi V, Winkels H, Kobiyama K, Makings J, Kiosses WB, Ley K. Deleting interleukin-10 from myeloid cells exacerbates atherosclerosis in Apoe -/- mice. Cell Mol Life Sci 2022; 80:10. [PMID: 36496494 PMCID: PMC10141524 DOI: 10.1007/s00018-022-04649-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/05/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022]
Abstract
Atherosclerosis is initiated by subendothelial retention of lipoproteins and cholesterol, which triggers a non-resolving inflammatory process that over time leads to plaque progression in the artery wall. Myeloid cells and in particular macrophages are the primary drivers of the inflammatory response and plaque formation. Several immune cells including macrophages, T cells and B cells secrete the anti-inflammatory cytokine IL-10, known to be essential for the atherosclerosis protection. The cellular source of IL-10 in natural atherosclerosis progression is unknown. This study aimed to determine the main IL10-producing cell type in atherosclerosis. To do so, we crossed VertX mice, in which IRES-green fluorescent protein (eGFP) was placed downstream of exon 5 of the Il10 gene, with atherosclerosis-prone Apoe-/- mice. We found that myeloid cells express high levels of IL-10 in VertX Apoe-/- mice in both chow and western-diet fed mice. By single cell RNA sequencing and flow cytometry analysis, we identified resident and inflammatory macrophages in atherosclerotic plaques as the main IL-10 producers. To address whether IL-10 secreted by myeloid cells is essential for the protection, we utilized LyzMCre+Il10fl/fl mice crossed into the Apoe-/- background and confirmed that macrophages were unable to secrete IL-10. Chow and western diet-fed LyzMCre+Il10fl/fl Apoe-/- mice developed significantly larger atherosclerotic plaques as measured by en face morphometry than LyzMCre-Il10 fl/flApoe-/-. Flow cytometry and cytokine measurements suggest that the depletion of IL-10 in myeloid cells increases Th17 cells with elevated CCL2, and TNFα in blood plasma. We conclude that macrophage-derived IL-10 is critical for limiting atherosclerosis in mice.
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Affiliation(s)
- Marco Orecchioni
- La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA.
| | - Dennis Wolf
- Cardiology and Angiology I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vasantika Suryawanshi
- La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Holger Winkels
- Department of Cardiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kouji Kobiyama
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jeffrey Makings
- La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - William B Kiosses
- Histology and Microscopy Core Facility, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Klaus Ley
- La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Immunology Center of Georgia (IMMCG), Augusta University, Augusta, GA, 30912, USA.
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Nettersheim FS, Armstrong SS, Durant C, Blanco-Dominguez R, Roy P, Orecchioni M, Suryawanshi V, Ley K. Titration of 124 antibodies using CITE-Seq on human PBMCs. Sci Rep 2022; 12:20817. [PMID: 36460735 PMCID: PMC9718773 DOI: 10.1038/s41598-022-24371-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 09/14/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-Seq) is widely used to characterize immune cell populations. However, mRNA levels correlate poorly with expression of surface proteins, which are well established to define immune cell types. CITE-Seq (cellular indexing of transcriptomes and epitopes by sequencing) utilizes oligonucleotide-tagged antibodies to simultaneously analyze surface phenotypes and transcriptomes. Considering the high costs of adding surface phenotyping to scRNA-Seq, we aimed to determine which of 188 tested CITE-Seq antibodies can detect their antigens on human peripheral blood mononuclear cells (PBMCs), a commonly interrogated cell population in immunology, and find the optimal concentration for staining. The recommended concentration was optimal for 76 antibodies, whereas staining quality of 7 antibodies improved when the concentration was doubled. 33 and 8 antibodies still worked well when the concentration was reduced to 1/5 or 1/25, respectively. 64 antigens were not detected at any antibody concentration. Optimizing the antibody panel by removing antibodies not able to detect their target antigens and adjusting concentrations of the remaining antibodies will improve the analysis and may reduce costs. In conclusion, our data are a resource for building an informative and cost-effective panel of CITE-Seq antibodies and use them at their optimal concentrations in future CITE-seq experiments on human PBMCs.
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Affiliation(s)
- Felix Sebastian Nettersheim
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Department of Cardiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | | | | | - Rafael Blanco-Dominguez
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Centro Nacional de Investigaciones Cardiovasculares, 28029, Madrid, Spain
| | - Payel Roy
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | | | | | - Klaus Ley
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.
- Department of Bioengineering, University of California, San Diego, San Diego, CA, 92093, USA.
- Immunology Center of Georgia (IMMCG), Augusta University, Augusta, GA, 30912, USA.
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Vallejo J, Saigusa R, Gulati R, Suthahar SSA, Suryawanshi V, Alimadadi A, Durant CP, Ghosheh Y, Roy P, Ehinger E, Pattarabanjird T, Hanna DB, Landay AL, Tracy RP, Lazar JM, Mack WJ, Weber KM, Adimora AA, Hodis HN, Tien PC, Ofotokun I, Heath SL, Shemesh A, McNamara CA, Lanier LL, Hedrick CC, Kaplan RC, Ley K. Author Correction: Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells. BMC Biol 2022; 20:237. [PMID: 36266696 PMCID: PMC9585771 DOI: 10.1186/s12915-022-01440-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jenifer Vallejo
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Ryosuke Saigusa
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Rishab Gulati
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | | | | | - Ahmad Alimadadi
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | | | - Yanal Ghosheh
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Payel Roy
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Erik Ehinger
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Tanyaporn Pattarabanjird
- Carter Immunology Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - David B Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Jason M Lazar
- Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Wendy J Mack
- Department of Medicine and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Atherosclerosis Research Unit, University of Southern California, Los Angeles, CA, USA
| | - Kathleen M Weber
- Cook County Health/Hektoen Institute of Medicine, Chicago, IL, USA
| | - Adaora A Adimora
- Department of Medicine, University of North Carolina School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Howard N Hodis
- Department of Medicine and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Atherosclerosis Research Unit, University of Southern California, Los Angeles, CA, USA
| | - Phyllis C Tien
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Igho Ofotokun
- Department of Medicine, Infectious Disease Division and Grady Health Care System, Emory University School of Medicine, Atlanta, GA, USA
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Avishai Shemesh
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Coleen A McNamara
- Carter Immunology Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Lewis L Lanier
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Catherine C Hedrick
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
| | - Klaus Ley
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA.
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Vallejo J, Saigusa R, Gulati R, Armstrong Suthahar SS, Suryawanshi V, Alimadadi A, Durant CP, Ghosheh Y, Roy P, Ehinger E, Pattarabanjird T, Hanna DB, Landay AL, Tracy RP, Lazar JM, Mack WJ, Weber KM, Adimora AA, Hodis HN, Tien PC, Ofotokun I, Heath SL, Shemesh A, McNamara CA, Lanier LL, Hedrick CC, Kaplan RC, Ley K. Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells. BMC Biol 2022; 20:193. [PMID: 36045343 PMCID: PMC9434837 DOI: 10.1186/s12915-022-01382-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Cryopreserved peripheral blood mononuclear cells (PBMCs) are frequently collected and provide disease- and treatment-relevant data in clinical studies. Here, we developed combined protein (40 antibodies) and transcript single-cell (sc)RNA sequencing (scRNA-seq) in PBMCs. RESULTS Among 31 participants in the Women's Interagency HIV Study (WIHS), we sequenced 41,611 cells. Using Boolean gating followed by Seurat UMAPs (tool for visualizing high-dimensional data) and Louvain clustering, we identified 50 subsets among CD4+ T, CD8+ T, B, NK cells, and monocytes. This resolution was superior to flow cytometry, mass cytometry, or scRNA-seq without antibodies. Combined protein and transcript scRNA-seq allowed for the assessment of disease-related changes in transcriptomes and cell type proportions. As a proof-of-concept, we showed such differences between healthy and matched individuals living with HIV with and without cardiovascular disease. CONCLUSIONS In conclusion, combined protein and transcript scRNA sequencing is a suitable and powerful method for clinical investigations using PBMCs.
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Affiliation(s)
- Jenifer Vallejo
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Ryosuke Saigusa
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Rishab Gulati
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | | | | | - Ahmad Alimadadi
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | | | - Yanal Ghosheh
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Payel Roy
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Erik Ehinger
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Tanyaporn Pattarabanjird
- Carter Immunology Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - David B Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Jason M Lazar
- Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Wendy J Mack
- Department of Medicine and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Atherosclerosis Research Unit, University of Southern California, Los Angeles, CA, USA
| | - Kathleen M Weber
- Cook County Health/Hektoen Institute of Medicine, Chicago, IL, USA
| | - Adaora A Adimora
- Department of Medicine, University of North Carolina School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Howard N Hodis
- Department of Medicine and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Atherosclerosis Research Unit, University of Southern California, Los Angeles, CA, USA
| | - Phyllis C Tien
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Igho Ofotokun
- Department of Medicine, Infectious Disease Division and Grady Health Care System, Emory University School of Medicine, Atlanta, GA, USA
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Avishai Shemesh
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Coleen A McNamara
- Carter Immunology Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Lewis L Lanier
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Catherine C Hedrick
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
| | - Klaus Ley
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA.
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Roy P, Sidney J, Lindestam Arlehamn CS, Phillips E, Mallal S, Suthahar SSA, Billitti M, Rubiro P, Marrama D, Drago F, Vallejo J, Suryawanshi V, Orecchioni M, Makings J, Kim PJ, McNamara CA, Peters B, Sette A, Ley K. Immunodominant MHC-II (Major Histocompatibility Complex II) Restricted Epitopes in Human Apolipoprotein B. Circ Res 2022; 131:258-276. [PMID: 35766025 PMCID: PMC9536649 DOI: 10.1161/circresaha.122.321116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND CD (cluster of differentiation) 4+ T-cell responses to APOB (apolipoprotein B) are well characterized in atherosclerotic mice and detectable in humans. CD4+ T cells recognize antigenic peptides displayed on highly polymorphic HLA (human leukocyte antigen)-II. Immunogenicity of individual APOB peptides is largely unknown in humans. Only 1 HLA-II-restricted epitope was validated using the DRB1*07:01-APOB3036-3050 tetramer. We hypothesized that human APOB may contain discrete immunodominant CD4+ T-cell epitopes that trigger atherosclerosis-related autoimmune responses in donors with diverse HLA alleles. METHODS We selected 20 APOB-derived peptides (APOB20) from an in silico screen and experimentally validated binding to the most commonly occurring human HLA-II alleles. We optimized a restimulation-based workflow to evaluate antigenicity of multiple candidate peptides in HLA-typed donors. This included activation-induced marker assay, intracellular cytokine staining, IFNγ (interferon gamma) enzyme-linked immunospot and cytometric bead array. High-throughput sequencing revealed TCR (T-cell receptor) clonalities of APOB-reactive CD4+ T cells. RESULTS Using stringent positive, negative, and crossover stimulation controls, we confirmed specificity of expansion-based protocols to detect CD4+ T cytokine responses to the APOB20 pool. Ex vivo assessment of AIM+CD4+ T cells revealed a statistically significant autoimmune response to APOB20 but not to a ubiquitously expressed negative control protein, actin. Resolution of CD4+ T responses to the level of individual peptides using IFNγ enzyme-linked immunospot led to the discovery of 6 immunodominant epitopes (APOB6) that triggered robust CD4+ T activation in most donors. APOB6-specific responding CD4+ T cells were enriched in unique expanded TCR clonotypes and preferentially expressed memory markers. Cytometric bead array analysis detected APOB6-induced secretion of both proinflammatory and regulatory cytokines. In clinical samples from patients with angiographically verified coronary artery disease, APOB6 stimulation induced higher activation and memory phenotypes and augmented secretion of proinflammatory cytokines TNF (tumor necrosis factor) and IFNγ, compared with patients with low coronary artery disease. CONCLUSIONS Using 3 cohorts, each with ≈20 donors, we discovered and validated 6 immunodominant, HLA-II-restricted APOB epitopes. The immune response to these APOB epitopes correlated with coronary artery disease severity.
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Affiliation(s)
- Payel Roy
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Cecilia S. Lindestam Arlehamn
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Simon Mallal
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Sujit Silas Armstrong Suthahar
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Monica Billitti
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Daniel Marrama
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
| | - Fabrizio Drago
- Cardiovascular Research Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville
| | - Jenifer Vallejo
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Vasantika Suryawanshi
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Marco Orecchioni
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Jeffrey Makings
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
| | - Paul J. Kim
- Division of Cardiovascular Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Coleen A. McNamara
- Cardiovascular Research Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Klaus Ley
- Center for Autoimmune Disease, Laboratory of Inflammation Biology, La Jolla Institute for Immunology, 9420 Athena Circle Drive, La Jolla, CA, 92037, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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Orecchioni M, Wolf D, Suryawanshi V, Winkels H, Kobiyama K, Makings J, Kiosses WB, Ley K. Myeloid cell interleukin-10 is essential for atherosclerosis protection in Apoe−/− mice. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.54.22] [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
Atherosclerosis, the disease underlying stroke, myocardial infarction and ischemic heart failure, is initiated by the subendothelial retention of lipoproteins and cholesterol, which then triggers a non-resolving inflammatory process driving plaque progression in the artery wall. Myeloid cells and in particular macrophages are the primary driver of this process. IL10 is a prototypic anti-inflammatory cytokine made by several immune cells such as macrophages. IL10 is also essential for the protection against atherosclerosis. However, it is not known which cells are responsible for the IL10 production mediating protection from atherosclerosis. Here, we crossed the VertX mouse model, in which an IRES-enhanced green fluorescent protein (eGFP) fusion protein was placed downstream of exon 5 of the IL-10 gene, to the atherosclerosis-prone Apoe−/− background. We found that myeloid cells express high levels of IL10 GFP in VertX-Apoe−/− mice. By scRNAseq we found that macrophages especially inflammatory macrophages in plaques are the main producers of IL10 in atherosclerosis. To address whether IL10 secreted by myeloid cells is essential for the protection, we developed a LyzMCreIL-10flox/flox mouse crossed in the Apoe−/− background and confirmed that macrophages were unable to secrete IL-10. We discovered that the LyzMCreIL-10flox/floxApoe−/− mice developed significantly more atherosclerosis than LyzMCreIL-10+/+Apoe−/−, both on chow and lipid-rich diet. Flow cytometry data and cytokine measurements suggest that the depletion of IL-10 in myeloid cells increases Th17 cells with elevated IL-17a, IL-17f and CCL20 in blood plasma. These data underscore the critical roles of macrophage-derived IL-10 in limiting atherosclerosis.
Supported by grants NIH HL 115232, 145241, and HL088093.
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Affiliation(s)
| | | | | | - Holger Winkels
- 4Department of Internal Medicine III, Division of Cardiology, Heart Center, University Hospital of Cologne, Germany
| | | | | | | | - Klaus Ley
- 3La Jolla Institute for Immunology
- 6University of California San Diego
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Abstract
The transcriptomic information obtained by single cell RNA sequencing (scRNA-seq) can be supplemented by information on the cell surface phenotype by using oligonucleotide-tagged monoclonal antibodies (scAb-Seq). This is of particular importance in immune cells, where the correlation between mRNA and cell surface expression is very weak. scAb-Seq is facilitated by the availability of commercial antibodies and antibody mixes. Now panels of up to 200 antibodies are available for human and mouse cells. Proteins are detected by antibodies conjugated to a tripartite DNA sequence that contains a primer for amplification and sequencing, a unique oligonucleotide that acts as an antibody barcode and a poly(dA) sequence, simultaneously detecting extension of antibody-specific DNA sequences and cDNAs in the same poly(dT)-primed reaction. For each cell, surface protein expression is captured and sequenced along with the cell's transcriptome. Here, we list the steps needed to produce antibody sequencing data from tissue or blood cells.
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Affiliation(s)
| | | | | | - Klaus Ley
- La Jolla Institute for Immunology, La Jolla, CA, USA.
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8
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Winkels H, Ghosheh Y, Kobiyama K, Kiosses WB, Orecchioni M, Ehinger E, Suryawanshi V, Herrera-De La Mata S, Marchovecchio P, Riffelmacher T, Thiault N, Kronenberg M, Wolf D, Seumois G, Vijayanand P, Ley K. Thymus-Derived CD4 +CD8 + Cells Reside in Mediastinal Adipose Tissue and the Aortic Arch. J Immunol 2021; 207:2720-2732. [PMID: 34740961 DOI: 10.4049/jimmunol.2100208] [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] [Received: 03/02/2021] [Accepted: 09/04/2021] [Indexed: 11/19/2022]
Abstract
Double-positive CD4+CD8αβ+ (DP) cells are thought to reside as T cell progenitors exclusively within the thymus. We recently discovered an unexpected CD4+ and CD8αβ+ immune cell population in healthy and atherosclerotic mice by single-cell RNA sequencing. Transcriptomically, these cells resembled thymic DPs. Flow cytometry and three-dimensional whole-mount imaging confirmed DPs in thymus, mediastinal adipose tissue, and aortic adventitia, but nowhere else. Deep transcriptional profiling revealed differences between DP cells isolated from the three locations. All DPs were dependent on RAG2 expression and the presence of the thymus. Mediastinal adipose tissue DPs resided in close vicinity to invariant NKT cells, which they could activate in vitro. Thymus transplantation failed to reconstitute extrathymic DPs, and frequencies of extrathymic DPs were unaltered by pharmacologic inhibition of S1P1, suggesting that their migration may be locally confined. Our results define two new, transcriptionally distinct subsets of extrathymic DPs that may play a role in aortic vascular homeostasis.
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Affiliation(s)
- Holger Winkels
- La Jolla Institute for Immunology, La Jolla, CA; .,Department of Cardiology, Clinic III for Internal Medicine, University of Cologne, Cologne, Germany
| | | | | | | | | | | | | | | | | | | | | | | | - Dennis Wolf
- University Hospital Freiburg, Freiburg, Germany; and
| | | | | | - Klaus Ley
- La Jolla Institute for Immunology, La Jolla, CA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA
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Suryawanshi GW, Arokium H, Kim S, Khamaikawin W, Lin S, Shimizu S, Chupradit K, Lee Y, Xie Y, Guan X, Suryawanshi V, Presson AP, An DS, Chen ISY. Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias. Stem Cell Res Ther 2021; 12:528. [PMID: 34620229 PMCID: PMC8499514 DOI: 10.1186/s13287-021-02601-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/27/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Current understanding of hematopoiesis is largely derived from mouse models that are physiologically distant from humans. Humanized mice provide the most physiologically relevant small animal model to study human diseases, most notably preclinical gene therapy studies. However, the clonal repopulation dynamics of human hematopoietic stem and progenitor cells (HSPC) in these animal models is only partially understood. Using a new clonal tracking methodology designed for small sample volumes, we aim to reveal the underlying clonal dynamics of human cell repopulation in a mouse environment. METHODS Humanized bone marrow-liver-thymus (hu-BLT) mice were generated by transplanting lentiviral vector-transduced human fetal liver HSPC (FL-HSPC) in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice implanted with a piece of human fetal thymus. We developed a methodology to track vector integration sites (VIS) in a mere 25 µl of mouse blood for longitudinal and quantitative clonal analysis of human HSPC repopulation in mouse environment. We explored transcriptional and epigenetic features of human HSPC for possible VIS bias. RESULTS A total of 897 HSPC clones were longitudinally tracked in hu-BLT mice-providing a first-ever demonstration of clonal dynamics and coordinated expansion of therapeutic and control vector-modified human cell populations simultaneously repopulating in the same humanized mice. The polyclonal repopulation stabilized at 19 weeks post-transplant and the contribution of the largest clone doubled within 4 weeks. Moreover, 550 (~ 60%) clones persisted over 6 weeks and were highly shared between different organs. The normal clonal profiles confirmed the safety of our gene therapy vectors. Multi-omics analysis of human FL-HSPC revealed that 54% of vector integrations in repopulating clones occurred within ± 1 kb of H3K36me3-enriched regions. CONCLUSIONS Human repopulation in mice is polyclonal and stabilizes more rapidly than that previously observed in humans. VIS preference for H3K36me3 has no apparent negative effects on HSPC repopulation. Our study provides a methodology to longitudinally track clonal repopulation in small animal models extensively used for stem cell and gene therapy research and with lentiviral vectors designed for clinical applications. Results of this study provide a framework for understanding the clonal behavior of human HPSC repopulating in a mouse environment, critical for translating results from humanized mice models to the human settings.
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Affiliation(s)
- Gajendra W Suryawanshi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Hubert Arokium
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Sanggu Kim
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Wannisa Khamaikawin
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Samantha Lin
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | - Saki Shimizu
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | | | - YooJin Lee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Yiming Xie
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Xin Guan
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Vasantika Suryawanshi
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Angela P Presson
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, 84108, USA
- Department of Biostatistics, University of California, Los Angeles, 90095, USA
| | - Dong-Sung An
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | - Irvin S Y Chen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA.
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA.
- Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
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Ithnin M, Vu WT, Shin MG, Suryawanshi V, Sherbina K, Zolkafli SH, Serdari NM, Amiruddin MD, Abdullah N, Mustaffa S, Marjuni M, Nookiah R, Kushairi A, Marjoram P, Nuzhdin SV, Chang PL, Singh R. Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm. Plant Sci 2021; 304:110731. [PMID: 33568284 DOI: 10.1016/j.plantsci.2020.110731] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 05/15/2023]
Abstract
Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.
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Affiliation(s)
- Maizura Ithnin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Wendy T Vu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Siti Hazirah Zolkafli
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norziha Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ahmad Kushairi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Paul Marjoram
- Department of Preventative Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia.
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Suryawanshi V, Talke IN, Weber M, Eils R, Brors B, Clemens S, Krämer U. Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. BMC Genomics 2016; 17:1034. [PMID: 28155655 PMCID: PMC5259951 DOI: 10.1186/s12864-016-3319-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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] [Indexed: 11/17/2022] Open
Abstract
Background Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation. In plants, copy number expansions of single genes were implicated in cultivar- or species-specific tolerance of high levels of soil boron, aluminium or calamine-type heavy metals, respectively. Arabidopsis halleri is a zinc- and cadmium-hyperaccumulating extremophile species capable of growing on heavy-metal contaminated, toxic soils. In contrast, its non-accumulating sister species A. lyrata and the closely related reference model species A. thaliana exhibit merely basal metal tolerance. Results For a genome-wide assessment of the role of copy number divergence (CND) in lineage-specific environmental adaptation, we conducted cross-species array comparative genome hybridizations of three plant species and developed a global signal scaling procedure to adjust for sequence divergence. In A. halleri, transition metal homeostasis functions are enriched twofold among the genes detected as copy number expanded. Moreover, biotic stress functions including mostly disease Resistance (R) gene-related genes are enriched twofold among genes detected as copy number reduced, when compared to the abundance of these functions among all genes. Conclusions Our results provide genome-wide support for a link between evolutionary adaptation and CND in A. halleri as shown previously for Heavy metal ATPase4. Moreover our results support the hypothesis that elemental defences, which result from the hyperaccumulation of toxic metals, allow the reduction of classical defences against biotic stress as a trade-off. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3319-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vasantika Suryawanshi
- Department of Plant Physiology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, 44801, Germany.,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany
| | - Ina N Talke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany
| | - Michael Weber
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 280, Heidelberg, 69121, Germany.,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 280, Heidelberg, 69121, Germany
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany
| | - Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, 44801, Germany. .,BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.
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