1
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Ravichandran S, Erra-Diaz F, Karakaslar OE, Marches R, Kenyon-Pesce L, Rossi R, Chaussabel D, Nehar-Belaid D, LaFon DC, Pascual V, Palucka K, Paust S, Nahm MH, Kuchel GA, Banchereau J, Ucar D. Distinct baseline immune characteristics associated with responses to conjugated and unconjugated pneumococcal polysaccharide vaccines in older adults. Nat Immunol 2024; 25:316-329. [PMID: 38182669 PMCID: PMC10834365 DOI: 10.1038/s41590-023-01717-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/21/2023] [Indexed: 01/07/2024]
Abstract
Pneumococcal infections cause serious illness and death among older adults. The capsular polysaccharide vaccine PPSV23 and conjugated alternative PCV13 can prevent these infections; yet, underlying immunological responses and baseline predictors remain unknown. We vaccinated 39 older adults (>60 years) with PPSV23 or PCV13 and observed comparable antibody responses (day 28) and plasmablast transcriptional responses (day 10); however, the baseline predictors were distinct. Analyses of baseline flow cytometry and bulk and single-cell RNA-sequencing data revealed a baseline phenotype specifically associated with weaker PCV13 responses, which was characterized by increased expression of cytotoxicity-associated genes, increased frequencies of CD16+ natural killer cells and interleukin-17-producing helper T cells and a decreased frequency of type 1 helper T cells. Men displayed this phenotype more robustly and mounted weaker PCV13 responses than women. Baseline expression levels of a distinct gene set predicted PPSV23 responses. This pneumococcal precision vaccinology study in older adults uncovered distinct baseline predictors that might transform vaccination strategies and initiate novel interventions.
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Affiliation(s)
| | - Fernando Erra-Diaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- University of Buenos Aires, School of Medicine, Buenos Aires, Argentina
| | - Onur E Karakaslar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Radu Marches
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Lisa Kenyon-Pesce
- UConn Center on Aging, University of Connecticut, Farmington, CT, USA
| | - Robert Rossi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - David C LaFon
- Division of Pulmonary, Allergy and Critical Care Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Virginia Pascual
- Drukier Institute for Children's Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Silke Paust
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Moon H Nahm
- Division of Pulmonary, Allergy and Critical Care Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - George A Kuchel
- UConn Center on Aging, University of Connecticut, Farmington, CT, USA
| | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Immunoledge LLC, Montclair, NJ, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA.
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2
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Nouri N, Cao RG, Bunsow E, Nehar-Belaid D, Marches R, Xu Z, Smith B, Heinonen S, Mertz S, Leber A, Smits G, van der Klis F, Mejías A, Banchereau J, Pascual V, Ramilo O. Young infants display heterogeneous serological responses and extensive but reversible transcriptional changes following initial immunizations. Nat Commun 2023; 14:7976. [PMID: 38042900 PMCID: PMC10693608 DOI: 10.1038/s41467-023-43758-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Infants necessitate vaccinations to prevent life-threatening infections. Our understanding of the infant immune responses to routine vaccines remains limited. We analyzed two cohorts of 2-month-old infants before vaccination, one week, and one-month post-vaccination. We report remarkable heterogeneity but limited antibody responses to the different antigens. Whole-blood transcriptome analysis in an initial cohort showed marked overexpression of interferon-stimulated genes (ISGs) and to a lesser extent of inflammation-genes at day 7, which normalized one month post-vaccination. Single-cell RNA sequencing in peripheral blood mononuclear cells from a second cohort identified at baseline a predominantly naive immune landscape including ISGhi cells. On day 7, increased expression of interferon-, inflammation-, and cytotoxicity-related genes were observed in most immune cells, that reverted one month post-vaccination, when a CD8+ ISGhi and cytotoxic cluster and B cells expanded. Antibody responses were associated with baseline frequencies of plasma cells, B-cells, and monocytes, and induction of ISGs at day 7.
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Affiliation(s)
- Nima Nouri
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Precision Medicine and Computational Biology, Sanofi, 350 Water Street, Cambridge, MA, 02141, USA
| | - Raquel Giacomelli Cao
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital, and The Ohio State University College of Medicine, Columbus, OH, USA
| | - Eleonora Bunsow
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Radu Marches
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Zhaohui Xu
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bennett Smith
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Santtu Heinonen
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Pediatric Research Center, New Children's Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Sara Mertz
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Leber
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Gaby Smits
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Fiona van der Klis
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Asunción Mejías
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital, and The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Immunai, New York, NY, USA
| | - Virginia Pascual
- Drukier Institute for Children's Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
| | - Octavio Ramilo
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Nationwide Children's Hospital, and The Ohio State University College of Medicine, Columbus, OH, USA.
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA.
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3
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Nehar-Belaid D, Sokolowski M, Ravichandran S, Banchereau J, Chaussabel D, Ucar D. Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS. Semin Immunol 2023; 70:101842. [PMID: 37717525 DOI: 10.1016/j.smim.2023.101842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In fact, while some recipients mount a robust response to vaccination that protects them from the disease, others fail to respond. Multiple clinical and epidemiological factors contribute to this heterogeneity in responsiveness. Systems immunology studies fueled by advances in single-cell biology have been instrumental in uncovering pre-vaccination immune cell types and genomic features (i.e., the baseline immune state, BIS) that have been associated with vaccine responsiveness. Here, we review clinical factors that shape the BIS, and the characteristics of the BIS associated with responsiveness to frequently studied vaccines (i.e., influenza, COVID-19, bacterial pneumonia, malaria). Finally, we discuss potential strategies to enhance vaccine responsiveness in high-risk groups, focusing specifically on older adults.
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Affiliation(s)
| | - Mark Sokolowski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | | | - Damien Chaussabel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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4
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Angarola BL, Sharma S, Katiyar N, Gu Kang H, Nehar-Belaid D, Park S, Gott R, Eryilmaz GN, LaBarge MA, Palucka K, Chuang JH, Korstanje R, Ucar D, Anczukow O. Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. bioRxiv 2023:2023.10.20.563147. [PMID: 37961129 PMCID: PMC10634680 DOI: 10.1101/2023.10.20.563147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. We investigate how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory, or cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveal co-localization of aged immune and epithelial cells in situ. Lastly, transcriptional signatures of aging mammary cells are found in human breast tumors, suggesting mechanistic links between aging and cancer. Together, these data uncover that epithelial, immune, and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment, and neoplasia risk.
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Affiliation(s)
| | | | - Neerja Katiyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hyeon Gu Kang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Giray N Eryilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
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5
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Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell 2023; 186:3882-3902.e24. [PMID: 37597510 PMCID: PMC10638861 DOI: 10.1016/j.cell.2023.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [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: 08/17/2022] [Revised: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 08/21/2023]
Abstract
Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.
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Affiliation(s)
- Jin-Gyu Cheong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Siddhartha Sharma
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Simon A Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claire K Wingert
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paoline Laurent
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
| | - Sai Ma
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Lucinda Paddock
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Emin Onur Karakaslar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Vinay K Kartha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Jim K Yee
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Minh Y Mays
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chenyang Jiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew W Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alexia Martinez de Paz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dughan Ahimovic
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Victor Ramos
- The Rockefeller University, New York, NY 10065, USA
| | | | - Erik Nielsen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Ling Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew Earl
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Alisha Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lexi Robbins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Karissa L Weidman
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sabrina Racine-Brzostek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - He S Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David R Price
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Louise Leyre
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - André F Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Junbum Kim
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alain C Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Northwell Health, Greenvale, NY 11548, USA
| | | | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10065, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert J Kaner
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Virginia Pascual
- Department of Pediatrics, Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jason D Buenrostro
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Rachel E Niec
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; The Rockefeller University, New York, NY 10065, USA
| | - Franck J Barrat
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA; HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lindsay Lief
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA.
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6
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Caielli S, Balasubramanian P, Rodriguez-Alcazar J, Balaji U, Wan Z, Baisch J, Smitherman C, Walters L, Sparagana P, Nehar-Belaid D, Marches R, Nassi L, Stewart K, Fuller J, Banchereau JF, Gu J, Wright T, Pascual V. An unconventional mechanism of IL-1β secretion that requires Type I IFN in lupus monocytes. bioRxiv 2023:2023.08.03.551696. [PMID: 37577613 PMCID: PMC10418156 DOI: 10.1101/2023.08.03.551696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Systemic Lupus Erythematosus (SLE) is characterized by autoreactive B cell activation, upregulation of Type I Interferon (IFN) and widespread inflammation. Mitochondrial nucleic acids (NAs) are increasingly recognized as triggers of IFN 1 . Thus, defective removal of mitochondria from mature red blood cells (Mito + RBCs), a feature of SLE, contributes to IFN production by myeloid cells 2 . Here we identify blood monocytes (Mo) that have internalized RBCs and co-express IFN-stimulated genes (ISGs) and interleukin-1β (IL-1β) in SLE patients with active disease. We show that ISG expression requires the interaction between Mito + RBC-derived mitochondrial DNA (mtDNA) and cGAS, while IL-1β production entails Mito + RBC-derived mitochondrial RNA (mtRNA) triggering of RIG-I-like receptors (RLRs). This leads to the cytosolic release of Mo-derived mtDNA that activates the NLRP3 inflammasome. Importantly, IL-1β release depends on the IFN-inducible myxovirus resistant protein 1 (MxA), which enables the translocation of this cytokine into a trans-Golgi network (TGN)-mediated unconventional secretory pathway. Our study highlights a novel and synergistic pathway involving IFN and the NLRP3 inflammasome in SLE.
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7
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Johnson K, Anderson K, Nehar-Belaid D, Varn F, Gujar A, Courtois E, Robson P, Moon HE, Golebiewska A, Paek SH, Niclou S, Verhaak R. EPCO-13. IDENTIFYING REGULATORS OF GLIOMA CELL STATE DIVERSITY AND EVOLUTION VIA JOINT SINGLE NUCLEUS RNA AND CHROMATIN ACCESSIBILITY. Neuro Oncol 2022. [PMCID: PMC9660532 DOI: 10.1093/neuonc/noac209.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Glioma cellular heterogeneity and plasticity represent fundamental obstacles to effective therapies. Understanding the determinants that govern glioma cell diversity and adaptability is critical to overcoming treatment resistance. Recent single cell DNA methylation studies have demonstrated that dynamic epigenetic alterations facilitate glioma cell state shifts and stress response. However, information regarding other modes of epigenetic gene regulation, such as chromatin accessibility, and how therapy shapes cellular heterogeneity remains limited. To determine the critical regulators of glioma cell state plasticity under treatment, we profiled 36 tumors (n = 23 adult patients) with joint single nucleus RNA and ATACseq including 13 longitudinal initial – recurrent pairs that yielded a total of 79,945 cells (37,883 malignant cells). We identified chromatin peaks that were uniquely open in glioma cells (n = 14,462 peaks, FDR < 0.05) compared with tumor microenvironmental cells including neuronal, perivascular, glial, and immune populations. Among malignant cells, differentiated-like cells exhibited more recurrent regions of accessibility than stem-like cells. These populations could be further delineated by differential peak enrichment of transcription factor binding sites in the stem-like (TCF12, ASCL1), differentiated-like (SMARCC1, JUN), and proliferating stem-like (E2F4) malignant cells nominating these transcription factors as master regulators. We confirmed that these cell state-specific open chromatin peaks overlapped enhancer regions via single nucleus multiomics and bulk H3K27ac profiling in 3 patient-derived cell lines. We further demonstrated that there are cell state-specific chromatin changes at recurrence with a trend toward a more open chromatin state that was associated with coordinated transcriptional changes. Finally, we incorporated matched longitudinal whole genome sequencing data to evaluate mutational profiles and differentiate between predominantly epigenetically driven changes and epigenomic co-evolution with the genome. Together, these findings define the key epigenetic switches that shape glioma cell states and facilitate plasticity during tumor progression.
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Affiliation(s)
| | | | | | | | - Amit Gujar
- The Jackson Laboratory , Farmington , USA
| | | | | | - Hyo-Eun Moon
- Seoul National University College of Medicine and Seoul National University Hospital , Seoul , Republic of Korea
| | | | - Sun Ha Paek
- Seoul National University College of Medicine and Seoul National University Hospital , Seoul , Republic of Korea
| | - Simone Niclou
- Luxembourg Institute of Health , Luxembourg , Luxembourg
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8
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George PJ, Marches R, Nehar-Belaid D, Banchereau J, Lustigman S. The Th1/Tfh-like biased responses elicited by the rASP-1 innate adjuvant are dependent on TRIF and Type I IFN receptor pathways. Front Immunol 2022; 13:961094. [PMID: 36119026 PMCID: PMC9478378 DOI: 10.3389/fimmu.2022.961094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
Abstract
Ov-ASP-1 (rASP-1), a parasite-derived protein secreted by the helminth Onchocerca volvulus, is an adjuvant which enhances the potency of the influenza trivalent vaccine (IIV3), even when used with 40-fold less IIV3. This study is aimed to provide a deeper insight into the molecular networks that underline the adjuvanticity of rASP-1. Here we show that rASP-1 stimulates mouse CD11c+ bone marrow-derived dendritic (BMDCs) to secrete elevated levels of IL-12p40, TNF-α, IP-10 and IFN-β in a TRIF-dependent but MyD88-independent manner. rASP-1-activated BMDCs promoted the differentiation of naïve CD4+ T cells into Th1 cells (IFN-γ+) that was TRIF- and type I interferon receptor (IFNAR)-dependent, and into Tfh-like cells (IL21+) and Tfh1 (IFN-γ+ IL21+) that were TRIF-, MyD88- and IFNAR-dependent. rASP-1-activated BMDCs promoted the differentiation of naïve CD4+ T cells into Th17 (IL-17+) cells only when the MyD88 pathway was inhibited. Importantly, rASP-1-activated human blood cDCs expressed upregulated genes that are associated with DC maturation, type I IFN and type II IFN signaling, as well as TLR4-TRIF dependent signaling. These activated cDCs promoted the differentiation of naïve human CD4+ T cells into Th1, Tfh-like and Th17 cells. Our data thus confirms that the rASP-1 is a potent innate adjuvant that polarizes the adaptive T cell responses to Th1/Tfh1 in both mouse and human DCs. Notably, the rASP-1-adjuvanted IIV3 vaccine elicited protection of mice from a lethal H1N1 infection that is also dependent on the TLR4-TRIF axis and IFNAR signaling pathway, as well as on its ability to induce anti-IIV3 antibody production.
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Affiliation(s)
- Parakkal Jovvian George
- Laboratory Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Radu Marches
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | | | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Sara Lustigman
- Laboratory Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
- *Correspondence: Sara Lustigman,
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9
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Varn FS, Johnson KC, Martinek J, Huse JT, Nasrallah MP, Wesseling P, Cooper LAD, Malta TM, Wade TE, Sabedot TS, Brat D, Gould PV, Wöehrer A, Aldape K, Ismail A, Sivajothi SK, Barthel FP, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon HE, Pollock S, Goldfarb C, Lee GH, Garofano L, Anderson KJ, Nehar-Belaid D, Barnholtz-Sloan JS, Bakas S, Byrne AT, D'Angelo F, Gan HK, Khasraw M, Migliozzi S, Ormond DR, Paek SH, Van Meir EG, Walenkamp AME, Watts C, Weiss T, Weller M, Palucka K, Stead LF, Poisson LM, Noushmehr H, Iavarone A, Verhaak RGW. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell 2022; 185:2184-2199.e16. [PMID: 35649412 PMCID: PMC9189056 DOI: 10.1016/j.cell.2022.04.038] [Citation(s) in RCA: 138] [Impact Index Per Article: 69.0] [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: 04/18/2021] [Revised: 01/22/2022] [Accepted: 04/28/2022] [Indexed: 12/21/2022]
Abstract
The factors driving therapy resistance in diffuse glioma remain poorly understood. To identify treatment-associated cellular and genetic changes, we analyzed RNA and/or DNA sequencing data from the temporally separated tumor pairs of 304 adult patients with isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant glioma. Tumors recurred in distinct manners that were dependent on IDH mutation status and attributable to changes in histological feature composition, somatic alterations, and microenvironment interactions. Hypermutation and acquired CDKN2A deletions were associated with an increase in proliferating neoplastic cells at recurrence in both glioma subtypes, reflecting active tumor growth. IDH-wild-type tumors were more invasive at recurrence, and their neoplastic cells exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. Mesenchymal transition was associated with the presence of a myeloid cell state defined by specific ligand-receptor interactions with neoplastic cells. Collectively, these recurrence-associated phenotypes represent potential targets to alter disease progression.
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Affiliation(s)
- Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jan Martinek
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jason T Huse
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - MacLean P Nasrallah
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pieter Wesseling
- Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Lee A D Cooper
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tathiane M Malta
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Brazil, Ribeirao Preto, São Paulo, Brazil
| | - Taylor E Wade
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Thais S Sabedot
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Daniel Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Peter V Gould
- service d'anatomopathologie, Hôpital de l'Enfant-Jésus du Centre hospitalier universitaire de Québec, Université Laval, Quebec City, QC, Canada
| | - Adelheid Wöehrer
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | | | - Azzam Ismail
- Department of Cellular and Molecular Pathology, Leeds Teaching Hospital NHS Trust, St James's University Hospital, Leeds, UK
| | | | - Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Cancer and Cell Biology Division, the Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Biopharmaceutical Convergence, Department of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeong gi-do, South Korea
| | - Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital Essen, Essen, Germany
| | | | - Kieron White
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Indrani Datta
- Department of Public Health Sciences, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Hyo-Eun Moon
- Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | | | | | - Ga-Hyun Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Luciano Garofano
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Kevin J Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Jill S Barnholtz-Sloan
- Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH, USA; Center for Biomedical Informatics and Information Technology & Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Spyridon Bakas
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Annette T Byrne
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Fulvio D'Angelo
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Hui K Gan
- Olivia Newton-John Cancer Research Institute, Austin Health, Melbourne, Australia
| | - Mustafa Khasraw
- Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Simona Migliozzi
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - D Ryan Ormond
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sun Ha Paek
- Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - Erwin G Van Meir
- Department of Neurosurgery, School of Medicine and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Annemiek M E Walenkamp
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | - Colin Watts
- Academic Department of Neurosurgery, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zürich, Switzerland
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zürich, Switzerland
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Laila M Poisson
- Department of Public Health Sciences, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA; Department of Neurology, Columbia University Medical Center, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Neurosurgery, Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands.
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10
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Dérian N, Pham HP, Nehar-Belaid D, Tchitchek N, Klatzmann D, Eric V, Six A. The Tsallis generalized entropy enhances the interpretation of transcriptomics datasets. PLoS One 2022; 17:e0266618. [PMID: 35446844 PMCID: PMC9022844 DOI: 10.1371/journal.pone.0266618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 03/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background
Identifying differentially expressed genes between experimental conditions is still the gold-standard approach to interpret transcriptomic profiles. Alternative approaches based on diversity measures have been proposed to complement the interpretation of such datasets but are only used marginally.
Methods
Here, we reinvestigated diversity measures, which are commonly used in ecology, to characterize mice pregnancy microenvironments based on a public transcriptome dataset. Mainly, we evaluated the Tsallis entropy function to explore the potential of a collection of diversity measures for capturing relevant molecular event information.
Results
We demonstrate that the Tsallis entropy function provides additional information compared to the traditional diversity indices, such as the Shannon and Simpson indices. Depending on the relative importance given to the most abundant transcripts based on the Tsallis entropy function parameter, our approach allows appreciating the impact of biological stimulus on the inter-individual variability of groups of samples. Moreover, we propose a strategy for reducing the complexity of transcriptome datasets using a maximation of the beta diversity.
Conclusions
We highlight that a diversity-based analysis is suitable for capturing complex molecular events occurring during physiological events. Therefore, we recommend their use through the Tsallis entropy function to analyze transcriptomics data in addition to differential expression analyses.
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Affiliation(s)
- Nicolas Dérian
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | | | - Djamel Nehar-Belaid
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America
| | - Nicolas Tchitchek
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Vicaut Eric
- APHP, Hôpitaux Saint-Louis Lariboisière, Univ Paris 07, Unité de recherche clinique, UMR 942, Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
- * E-mail:
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11
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Thibodeau A, Eroglu A, McGinnis CS, Lawlor N, Nehar-Belaid D, Kursawe R, Marches R, Conrad DN, Kuchel GA, Gartner ZJ, Banchereau J, Stitzel ML, Cicek AE, Ucar D. AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Genome Biol 2021; 22:252. [PMID: 34465366 PMCID: PMC8408950 DOI: 10.1186/s13059-021-02469-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples. AMULET has high precision, estimated via donor-based multiplexing, and high recall, estimated via simulated multiplets, compared to alternatives and identifies multiplets most effectively when a certain read depth of 25K median valid reads per nucleus is achieved.
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Affiliation(s)
- Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Alper Eroglu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Nathan Lawlor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | | | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Radu Marches
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Daniel N Conrad
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - George A Kuchel
- University of Connecticut Center on Aging, UConn Health Center, Farmington, CT, 06030, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, 94158, USA
- NSF Center for Cellular Construction, San Francisco, CA, 94158, USA
| | | | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - A Ercument Cicek
- Computer Engineering Department, Bilkent University, 06800, Ankara, Turkey
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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12
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Lawlor N, Nehar-Belaid D, Grassmann JDS, Stoeckius M, Smibert P, Stitzel ML, Pascual V, Banchereau J, Williams A, Ucar D. Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28. Front Immunol 2021; 12:636720. [PMID: 33815388 PMCID: PMC8010670 DOI: 10.3389/fimmu.2021.636720] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Immune cell activation assays have been widely used for immune monitoring and for understanding disease mechanisms. However, these assays are typically limited in scope. A holistic study of circulating immune cell responses to different activators is lacking. Here we developed a cost-effective high-throughput multiplexed single-cell RNA-seq combined with epitope tagging (CITE-seq) to determine how classic activators of T cells (anti-CD3 coupled with anti-CD28) or monocytes (LPS) alter the cell composition and transcriptional profiles of peripheral blood mononuclear cells (PBMCs) from healthy human donors. Anti-CD3/CD28 treatment activated all classes of lymphocytes either directly (T cells) or indirectly (B and NK cells) but reduced monocyte numbers. Activated T and NK cells expressed senescence and effector molecules, whereas activated B cells transcriptionally resembled autoimmune disease- or age-associated B cells (e.g., CD11c, T-bet). In contrast, LPS specifically targeted monocytes and induced two main states: early activation characterized by the expression of chemoattractants and a later pro-inflammatory state characterized by expression of effector molecules. These data provide a foundation for future immune activation studies with single cell technologies (https://czi-pbmc-cite-seq.jax.org/).
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Affiliation(s)
- Nathan Lawlor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | | | | | | | | | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States.,Institute of Systems Genomics, University of Connecticut, Farmington, CT, United States.,Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, United States
| | - Virginia Pascual
- Ronay Menschel Professor of Pediatrics, Drukier Institute, Weill Cornell Medicine, New York, NY, United States
| | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States.,Institute of Systems Genomics, University of Connecticut, Farmington, CT, United States.,Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, United States
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States.,Institute of Systems Genomics, University of Connecticut, Farmington, CT, United States.,Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, United States
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13
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Nehar-Belaid D, Hong S, Marches R, Chen G, Bolisetty M, Baisch J, Walters L, Punaro M, Rossi RJ, Chung CH, Huynh RP, Singh P, Flynn WF, Tabanor-Gayle JA, Kuchipudi N, Mejias A, Collet MA, Lucido AL, Palucka K, Robson P, Lakshminarayanan S, Ramilo O, Wright T, Pascual V, Banchereau JF. Mapping systemic lupus erythematosus heterogeneity at the single-cell level. Nat Immunol 2020; 21:1094-1106. [PMID: 32747814 PMCID: PMC7442743 DOI: 10.1038/s41590-020-0743-0] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/20/2020] [Indexed: 12/12/2022]
Abstract
Patients with systemic lupus erythematosus (SLE) display a complex blood transcriptome whose cellular origin is poorly resolved. Using single-cell RNA sequencing, we profiled ~276,000 peripheral blood mononuclear cells from 33 children with SLE with different degrees of disease activity and 11 matched controls. Increased expression of interferon-stimulated genes (ISGs) distinguished cells from children with SLE from healthy control cells. The high ISG expression signature (ISGhi) derived from a small number of transcriptionally defined subpopulations within major cell types, including monocytes, CD4+ and CD8+ T cells, natural killer cells, conventional and plasmacytoid dendritic cells, B cells and especially plasma cells. Expansion of unique subpopulations enriched in ISGs and/or in monogenic lupus-associated genes classified patients with the highest disease activity. Profiling of ~82,000 single peripheral blood mononuclear cells from adults with SLE confirmed the expansion of similar subpopulations in patients with the highest disease activity. This study lays the groundwork for resolving the origin of the SLE transcriptional signatures and the disease heterogeneity towards precision medicine applications.
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Affiliation(s)
| | - Seunghee Hong
- Drukier Institute for Children's Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Radu Marches
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Guo Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mohan Bolisetty
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeanine Baisch
- Drukier Institute for Children's Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | | | - Marilynn Punaro
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA
- UT Southwestern Medical Center, Dallas, TX, USA
| | - Robert J Rossi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Cheng-Han Chung
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Richie P Huynh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Prashant Singh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - William F Flynn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Joy-Ann Tabanor-Gayle
- Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Navya Kuchipudi
- Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Asuncion Mejias
- Division of Pediatric Infectious Diseases, Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH, USA
| | - Magalie A Collet
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Anna Lisa Lucido
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Institute for Systems Genomics and Department of Genetics & Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | | | - Octavio Ramilo
- Division of Pediatric Infectious Diseases, Nationwide Children's Hospital and the Ohio State University School of Medicine, Columbus, OH, USA
| | - Tracey Wright
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA
- UT Southwestern Medical Center, Dallas, TX, USA
| | - Virginia Pascual
- Drukier Institute for Children's Health and Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
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14
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Pereira BI, De Maeyer RPH, Covre LP, Nehar-Belaid D, Lanna A, Ward S, Marches R, Chambers ES, Gomes DCO, Riddell NE, Maini MK, Teixeira VH, Janes SM, Gilroy DW, Larbi A, Mabbott NA, Ucar D, Kuchel GA, Henson SM, Strid J, Lee JH, Banchereau J, Akbar AN. Sestrins induce natural killer function in senescent-like CD8 + T cells. Nat Immunol 2020; 21:684-694. [PMID: 32231301 PMCID: PMC10249464 DOI: 10.1038/s41590-020-0643-3] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/26/2020] [Indexed: 12/29/2022]
Abstract
Aging is associated with remodeling of the immune system to enable the maintenance of life-long immunity. In the CD8+ T cell compartment, aging results in the expansion of highly differentiated cells that exhibit characteristics of cellular senescence. Here we found that CD27-CD28-CD8+ T cells lost the signaling activity of the T cell antigen receptor (TCR) and expressed a protein complex containing the agonistic natural killer (NK) receptor NKG2D and the NK adaptor molecule DAP12, which promoted cytotoxicity against cells that expressed NKG2D ligands. Immunoprecipitation and imaging cytometry indicated that the NKG2D-DAP12 complex was associated with sestrin 2. The genetic inhibition of sestrin 2 resulted in decreased expression of NKG2D and DAP12 and restored TCR signaling in senescent-like CD27-CD28-CD8+ T cells. Therefore, during aging, sestrins induce the reprogramming of non-proliferative senescent-like CD27-CD28-CD8+ T cells to acquire a broad-spectrum, innate-like killing activity.
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Affiliation(s)
- Branca I Pereira
- Division of Infection and Immunity, University College London, London, UK
| | - Roel P H De Maeyer
- Division of Infection and Immunity, University College London, London, UK
| | - Luciana P Covre
- Division of Infection and Immunity, University College London, London, UK
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | | | - Alessio Lanna
- Division of Infection and Immunity, University College London, London, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie Ward
- Department of Medicine, Imperial College London, London, UK
| | - Radu Marches
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Emma S Chambers
- Division of Infection and Immunity, University College London, London, UK
| | - Daniel C O Gomes
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Natalie E Riddell
- Division of Infection and Immunity, University College London, London, UK
- Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Mala K Maini
- Division of Infection and Immunity, University College London, London, UK
| | - Vitor H Teixeira
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Samuel M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Derek W Gilroy
- Division of Medicine, University College London, London, UK
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Neil A Mabbott
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - George A Kuchel
- University of Connecticut Center on Aging, University of Connecticut, Farmington, CT, USA
| | - Sian M Henson
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jessica Strid
- Department of Medicine, Imperial College London, London, UK
| | - Jun H Lee
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Arne N Akbar
- Division of Infection and Immunity, University College London, London, UK.
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15
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Hong S, Banchereau R, Maslow BSL, Guerra MM, Cardenas J, Baisch J, Branch DW, Porter TF, Sawitzke A, Laskin CA, Buyon JP, Merrill J, Sammaritano LR, Petri M, Gatewood E, Cepika AM, Ohouo M, Obermoser G, Anguiano E, Kim TW, Nulsen J, Nehar-Belaid D, Blankenship D, Turner J, Banchereau J, Salmon JE, Pascual V. Longitudinal profiling of human blood transcriptome in healthy and lupus pregnancy. J Exp Med 2019; 216:1154-1169. [PMID: 30962246 PMCID: PMC6504211 DOI: 10.1084/jem.20190185] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022] Open
Abstract
Healthy and uncomplicated lupus pregnancies exhibit early and sustained transcriptional modulation of lupus-related pathways. This might contribute to fetal tolerance while predisposing pregnant women to certain infections. Failure to modulate these pathways is associated with lupus pregnancy complications. Systemic lupus erythematosus carries an increased risk of pregnancy complications, including preeclampsia and fetal adverse outcomes. To identify the underlying molecular mechanisms, we longitudinally profiled the blood transcriptome of 92 lupus patients and 43 healthy women during pregnancy and postpartum and performed multicolor flow cytometry in a subset of them. We also profiled 25 healthy women undergoing assisted reproductive technology to monitor transcriptional changes around embryo implantation. Sustained down-regulation of multiple immune signatures, including interferon and plasma cells, was observed during healthy pregnancy. These changes appeared early after embryo implantation and were mirrored in uncomplicated lupus pregnancies. Patients with preeclampsia displayed early up-regulation of neutrophil signatures that correlated with expansion of immature neutrophils. Lupus pregnancies with fetal complications carried the highest interferon and plasma cell signatures as well as activated CD4+ T cell counts. Thus, blood immunomonitoring reveals that both healthy and uncomplicated lupus pregnancies exhibit early and sustained transcriptional modulation of lupus-related signatures, and a lack thereof associates with adverse outcomes.
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Affiliation(s)
- Seunghee Hong
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
| | - Romain Banchereau
- Baylor Institute for Immunology Research, Dallas, TX.,Oncology Biomarker Development, Genentech, South San Francisco, CA
| | | | - Marta M Guerra
- Department of Medicine and Program in Inflammation and Autoimmunity, Hospital for Special Surgery, New York, NY
| | | | - Jeanine Baisch
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
| | - D Ware Branch
- University of Utah Health Sciences Center, Salt Lake City, UT.,Intermountain Healthcare, Salt Lake City, UT
| | - T Flint Porter
- University of Utah Health Sciences Center, Salt Lake City, UT.,Intermountain Healthcare, Salt Lake City, UT
| | - Allen Sawitzke
- University of Utah Health Sciences Center, Salt Lake City, UT
| | - Carl A Laskin
- Mount Sinai Hospital and the University of Toronto, Toronto, Ontario, Canada
| | - Jill P Buyon
- New York University School of Medicine, New York, NY
| | - Joan Merrill
- Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Lisa R Sammaritano
- Department of Medicine and Program in Inflammation and Autoimmunity, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Michelle Petri
- Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | - Marina Ohouo
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
| | | | | | - Tae Whan Kim
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
| | - John Nulsen
- University of Connecticut School of Medicine, Farmington, CT
| | | | | | - Jacob Turner
- Baylor Institute for Immunology Research, Dallas, TX
| | | | - Jane E Salmon
- Department of Medicine and Program in Inflammation and Autoimmunity, Hospital for Special Surgery, New York, NY.,Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Virginia Pascual
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY.,Department of Pediatrics, Weill Cornell Medicine, New York, NY.,Baylor Institute for Immunology Research, Dallas, TX
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16
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Nordor AV, Nehar-Belaid D, Richon S, Klatzmann D, Bellet D, Dangles-Marie V, Fournier T, Aryee MJ. The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors. Epigenetics 2017; 12:793-803. [PMID: 28678605 PMCID: PMC5739102 DOI: 10.1080/15592294.2017.1342912] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 12/31/2022] Open
Abstract
The placenta relies on phenotypes that are characteristic of cancer to successfully implant the embryo in the uterus during early pregnancy. Notably, it has to invade its host tissues, promote angiogenesis—while surviving hypoxia—, and escape the immune system. Similarities in DNA methylation patterns between the placenta and cancers suggest that common epigenetic mechanisms may be involved in regulating these behaviors. We show here that megabase-scale patterns of hypomethylation distinguish first from third trimester chorionic villi in the placenta, and that these patterns mirror those that distinguish many tumors from corresponding normal tissues. We confirmed these findings in villous cytotrophoblasts isolated from the placenta and identified a time window at the end of the first trimester, when these cells come into contact with maternal blood, as the likely time period for the methylome alterations. Furthermore, the large genomic regions affected by these patterns of hypomethylation encompass genes involved in pathways related to epithelial-mesenchymal transition, immune response, and inflammation. Analyses of expression profiles corresponding to genes in these hypomethylated regions in colon adenocarcinoma tumors point to networks of differentially expressed genes previously implicated in carcinogenesis and placentogenesis, where nuclear factor kappa B is a key hub. Taken together, our results suggest the existence of epigenetic switches involving large-scale changes of methylation in the placenta during pregnancy and in tumors during neoplastic transformation. The characterization of such epigenetic switches might lead to the identification of biomarkers and drug targets in oncology as well as in obstetrics and gynecology.
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Affiliation(s)
- Akpéli V Nordor
- a Institut Curie, PSL Research University , Département de Recherche Translationnelle , Paris , France.,b Chimie ParisTech, PSL Research University, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS) , Paris , France.,c CNRS, UTCBS UMR 8258 , Paris , France.,d Université Paris Descartes, Sorbonne-Paris-Cité, UTCBS , Paris , France.,e INSERM, UTCBS U 1022 , Paris , France.,f Massachusetts General Hospital and Harvard Medical School , Department of Pathology and Center for Cancer Research , Charlestown , Massachusetts , USA
| | - Djamel Nehar-Belaid
- g Sorbonne Universités, UPMC University of Paris , Paris , France.,h INSERM UMR_S 959 , Paris , France
| | - Sophie Richon
- i Institut Curie, PSL Research University, CNRS , UMR 144, France
| | - David Klatzmann
- g Sorbonne Universités, UPMC University of Paris , Paris , France.,h INSERM UMR_S 959 , Paris , France.,j AP-HP, Groupe Hospitalier Pitié-Salpêtrière , Department of Biotherapies, Clinical Investigation Center in Biotherapy and Inflammation-Immunopathology-Biotherapy Department (DHU I2B) , Paris , France
| | - Dominique Bellet
- b Chimie ParisTech, PSL Research University, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS) , Paris , France.,c CNRS, UTCBS UMR 8258 , Paris , France.,d Université Paris Descartes, Sorbonne-Paris-Cité, UTCBS , Paris , France.,e INSERM, UTCBS U 1022 , Paris , France.,k Institut Curie, PSL Research University, Hôpital René Huguenin , Laboratoire d'Oncobiologie, Pôle Pathologie-Génétique-Immunologie-Hémobiologie , Saint-Cloud , France
| | - Virginie Dangles-Marie
- a Institut Curie, PSL Research University , Département de Recherche Translationnelle , Paris , France.,l Laboratoire d'immunologie, Faculté de Pharmacie de Paris , Université Paris Descartes, Sorbonne-Paris-Cité , Paris , France
| | - Thierry Fournier
- m INSERM, U1139 , Faculté de Pharmacie de Paris , Paris , France.,n Université Paris Descartes, Sorbonne-Paris-Cité , UMR-S1139, Paris , France.,o PremUp Foundation , Paris , France
| | - Martin J Aryee
- f Massachusetts General Hospital and Harvard Medical School , Department of Pathology and Center for Cancer Research , Charlestown , Massachusetts , USA.,p Department of Biostatistics , Harvard T.H. Chan School of Public Health , Boston , Massachusetts , USA
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17
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Courau T, Nehar-Belaid D, Florez L, Levacher B, Vazquez T, Brimaud F, Bellier B, Klatzmann D. TGF- β and VEGF cooperatively control the immunotolerant tumor environment and the efficacy of cancer immunotherapies. JCI Insight 2016; 1:e85974. [PMID: 27699271 DOI: 10.1172/jci.insight.85974] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Tregs imprint an early immunotolerant tumor environment that prevents effective antitumor immune responses. Using transcriptomics of tumor tissues, we identified early upregulation of VEGF and TGF-β pathways compatible with tolerance imprinting. Silencing of VEGF or TGF-β in tumor cells induced early and pleiotropic modulation of immune-related transcriptome signatures in tumor tissues. These were surprisingly similar for both silenced tumors and related to common downstream effects on Tregs. Silencing of VEGF or TGF-β resulted in dramatically delayed tumor growth, associated with decreased Tregs and myeloid-derived suppressor cells and increased effector T cell activation in tumor infiltrates. Strikingly, co-silencing of TGF-β and VEGF led to a substantial spontaneous tumor eradication rate and the combination of their respective inhibitory drugs was synergistic. VEGF and/or TGF-β silencing also restored tumor sensitivity to tumor-specific cell therapies and markedly improved the efficacy of anti-PD-1/anti-CTLA-4 treatment. Thus, TGF-β and VEGF cooperatively control the tolerant environment of tumors and are targets for improved cancer immunotherapies.
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Affiliation(s)
- Tristan Courau
- Sorbonne Universités, UPMC University of Paris, Paris, France.,INSERM UMR_S 959, Paris, France
| | - Djamel Nehar-Belaid
- Sorbonne Universités, UPMC University of Paris, Paris, France.,INSERM UMR_S 959, Paris, France
| | - Laura Florez
- Sorbonne Universités, UPMC University of Paris, Paris, France.,INSERM UMR_S 959, Paris, France
| | - Béatrice Levacher
- Sorbonne Universités, UPMC University of Paris, Paris, France.,INSERM UMR_S 959, Paris, France
| | - Thomas Vazquez
- Sorbonne Universités, UPMC University of Paris, Paris, France.,INSERM UMR_S 959, Paris, France
| | - Faustine Brimaud
- Sorbonne Universités, UPMC University of Paris, Paris, France.,INSERM UMR_S 959, Paris, France.,AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Biotherapies, Clinical Investigation Center in Biotherapy and Inflamation-Immunopathology-Biotherapy Department (DHU I2B), F-75013, Paris, France
| | - Bertrand Bellier
- Sorbonne Universités, UPMC University of Paris, Paris, France.,INSERM UMR_S 959, Paris, France
| | - David Klatzmann
- Sorbonne Universités, UPMC University of Paris, Paris, France.,INSERM UMR_S 959, Paris, France.,AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Biotherapies, Clinical Investigation Center in Biotherapy and Inflamation-Immunopathology-Biotherapy Department (DHU I2B), F-75013, Paris, France
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18
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Nehar-Belaid D, Chen T, Darrasse-Jèze G, Courau T, Dérian N, Florez L, Ruocco M, Klatzmann D. Is the immune system mistaking tumors for fetuses? J Reprod Immunol 2016. [DOI: 10.1016/j.jri.2016.04.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Nehar-Belaid D, Courau T, Dérian N, Florez L, Ruocco MG, Klatzmann D. Regulatory T Cells Orchestrate Similar Immune Evasion of Fetuses and Tumors in Mice. J Immunol 2015; 196:678-90. [PMID: 26643476 DOI: 10.4049/jimmunol.1501834] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/05/2015] [Indexed: 01/16/2023]
Abstract
Embryos and tumors are both masses of dividing cells expressing foreign Ags, but they are not rejected by the immune system. We hypothesized that similar tolerogenic mechanisms prevent their rejection. Global comparison of fetal and tumor microenvironments through transcriptomics in mice revealed strikingly similar and dramatic decreases in expression of numerous immune-related pathways, including Ag presentation and T cell signaling. Unsupervised analyses highlighted the parallel kinetics and similarities of immune signature downregulation, from the very first days after tumor or embryo implantation. Besides upregulated signatures related to cell proliferation, the only significant signatures shared by the two conditions across all biological processes and all time points studied were downmodulated immune response signatures. Regulatory T cell depletion completely reverses this immune downmodulation to an immune upregulation that leads to fetal or tumor immune rejection. We propose that evolutionarily selected mechanisms that protect mammalian fetuses from immune attack are hijacked to license tumor development.
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Affiliation(s)
- Djamel Nehar-Belaid
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Laboratoire I3 (Immunologie-Immunopathologie-Immunothérapie), F-75013 Paris, France; INSERM, UMR_S 959, F-75013 Paris, France; CNRS, FRE3632, F-75013 Paris, France; and
| | - Tristan Courau
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Laboratoire I3 (Immunologie-Immunopathologie-Immunothérapie), F-75013 Paris, France; INSERM, UMR_S 959, F-75013 Paris, France; CNRS, FRE3632, F-75013 Paris, France; and
| | - Nicolas Dérian
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Laboratoire I3 (Immunologie-Immunopathologie-Immunothérapie), F-75013 Paris, France; INSERM, UMR_S 959, F-75013 Paris, France; CNRS, FRE3632, F-75013 Paris, France; and
| | - Laura Florez
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Laboratoire I3 (Immunologie-Immunopathologie-Immunothérapie), F-75013 Paris, France; INSERM, UMR_S 959, F-75013 Paris, France; CNRS, FRE3632, F-75013 Paris, France; and
| | - Maria Grazia Ruocco
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Laboratoire I3 (Immunologie-Immunopathologie-Immunothérapie), F-75013 Paris, France; INSERM, UMR_S 959, F-75013 Paris, France; CNRS, FRE3632, F-75013 Paris, France; and
| | - David Klatzmann
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Laboratoire I3 (Immunologie-Immunopathologie-Immunothérapie), F-75013 Paris, France; INSERM, UMR_S 959, F-75013 Paris, France; CNRS, FRE3632, F-75013 Paris, France; and Assistance-Publique Hopitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Biothérapies et Centre d'Investigation Clinique en Biothérapie, F-75013 Paris, France
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20
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Nehar-Belaid D, Courau T, Dérian N, Florez L, Ruocco MG, Klatzmann D. Tregs orchestrate similar immune evasion of fetuses and tumors. J Reprod Immunol 2015. [DOI: 10.1016/j.jri.2015.06.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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