1
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Diebold M, Vietzen H, Heinzel A, Haindl S, Herz CT, Mayer K, Doberer K, Kainz A, Faé I, Wenda S, Kühner LM, Berger SM, Puchhammer-Stöckl E, Kozakowski N, Schaub S, Halloran PF, Böhmig GA. Natural killer cell functional genetics and donor-specific antibody-triggered microvascular inflammation. Am J Transplant 2024; 24:743-754. [PMID: 38097018 DOI: 10.1016/j.ajt.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/28/2023] [Accepted: 12/02/2023] [Indexed: 12/31/2023]
Abstract
Antibody-mediated rejection (ABMR) is a leading cause of graft failure. Emerging evidence suggests a significant contribution of natural killer (NK) cells to microvascular inflammation (MVI). We investigated the influence of genetically determined NK cell functionality on ABMR development and activity. The study included 86 kidney transplant recipients subjected to systematic biopsies triggered by donor-specific antibody detection. We performed killer immunoglobulin-like receptor typing to predict missing self and genotyped polymorphisms determining NK cell functionality (FCGR3AV/F158 [rs396991], KLRC2wt/del, KLRK1HNK/LNK [rs1049174], rs9916629-C/T). Fifty patients had ABMR with considerable MVI and elevated NK cell transcripts. Missing self was not related to MVI. Only KLRC2wt/wt showed an association (MVI score: 2 [median; interquartile range: 0-3] vs 0 [0-1] in KLRC2wt/del recipients; P = .001) and remained significant in a proportional odds multivariable model (odds ratio, 7.84; 95% confidence interval, 2.37-30.47; P = .001). A sum score incorporating all polymorphisms and missing self did not outperform a score including only KLRC2 and FCGR3A variants, which were predictive in univariable analysis. NK cell genetics did not affect graft functional decline and survival. In conclusion, a functional KLRC2 polymorphism emerged as an independent determinant of ABMR activity, without a considerable contribution of missing self and other NK cell gene polymorphisms.
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Affiliation(s)
- Matthias Diebold
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria; Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Hannes Vietzen
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Susanne Haindl
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Carsten T Herz
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Katharina Mayer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Konstantin Doberer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Alexander Kainz
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Ingrid Faé
- Department of Blood Group Serology and Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Sabine Wenda
- Department of Blood Group Serology and Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Laura M Kühner
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Sarah M Berger
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | | | | | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, ATAGC, University of Alberta, Edmonton, Alberta, Canada
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria.
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2
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Graninger M, Vietzen H, Puchhammer-Stöckl E. Association between human genetic variants affecting the host NK cell response and the development of herpes simplex virus type 1 encephalitis. J Med Virol 2023; 95:e28759. [PMID: 37212301 DOI: 10.1002/jmv.28759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/22/2023] [Accepted: 04/13/2023] [Indexed: 05/23/2023]
Abstract
Herpes simplex virus encephalitis (HSE) is a rare complication of herpes simplex virus type 1 (HSV-1) infection or reactivation. It is so far unclear why only few patients develop HSE. As natural killer (NK) cells provide an important defense against HSV-1, we investigated whether there is an association between distinct human genetic variants associated with the host NK cell response and HSE. Forty-nine adult patients with confirmed HSE and 247 matched controls were analyzed for the distribution of the following genotypes: CD16A (FcγRIIIA) V/F and IGHG1 G1m3/17, both influencing antibody-dependent cellular cytotoxicity; HLA-E*0101/*0103, associated with NK cell activation; and SLFN13 rs9916629C/T associated with NK cell response. Homozygous HLA-E*0101:0101 and HLA-E*0103:0103 variants as well as the rs9916629CC genotype were overrepresented in HSE patients compared to controls (p ≤ 0.001). Notably, cooccurrence of the homozygous HLA-E*0101 and rs9916629CC genotypes was present in 19% of patients but totally absent in controls (p ≤ 0.0001). Distribution of CD16A and IGHG1 variants did not differ between patients and controls. Our data show that the rare combination of HLA-E*0101:0101 and rs9916629CC is significantly associated with HSE. Possibly, these genetic variations could be useful as clinical markers predicting HSE prognosis and helping to adapt the treatment of HSE in the individual patient.
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Affiliation(s)
| | - Hannes Vietzen
- Center for Virology, Medical University of Vienna, Vienna, Austria
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3
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Vietzen H, Furlano PL, Traugott M, Totschnig D, Hoepler W, Strassl R, Zoufaly A, Puchhammer‐Stöckl E. The natural killer cell-associated rs9916629-C allele is a novel genetic risk factor for fatal COVID-19. J Med Virol 2023; 95:e28404. [PMID: 36515427 PMCID: PMC9878105 DOI: 10.1002/jmv.28404] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/09/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
The severity of COVID-19 is associated with individual genetic host factors. Among these, genetic polymorphisms affecting natural killer (NK) cell responses, as variations in the HLA-E- (HLA-E*0101/0103), FcγRIIIa- (FcγRIIIa-158-F/V), and NKG2C- (KLRC2wt/del ) receptor, were associated with severe COVID-19. Recently, the rs9916629-C/T genetic polymorphism was identified that indirectly shape the human NK cell repertoire towards highly pro-inflammatory CD56bright NK cells. We investigated whether the rs9916629-C/T variants alone and in comparison to the other risk factors are associated with a fatal course of COVID-19. We included 1042 hospitalized surviving and 159 nonsurviving COVID-19 patients as well as 1000 healthy controls. rs9916629-C/T variants were genotyped by TaqMan assays and were compared between the groups. The patients' age, comorbidities, HLA-E*0101/0103, FcγRIIIa-158-F/V, and KLRC2wt/del variants were also determined. The presence of the rs9916629-C allele was a risk factor for severe and fatal COVID-19 (p < 0.0001), independent of the patients' age or comorbidities. Fatal COVID-19 was more frequent in younger patients (<69.85 years) carrying the FcγRIIIa-158-V/V (p < 0.006) and in older patients expressing the KLRC2del variant (p < 0.003). Thus, patients with the rs9916629-C allele have a significantly increased risk for fatal COVID-19 and identification of the genetic variants may be used as prognostic marker for hospitalized COVID-19 patients.
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Affiliation(s)
- Hannes Vietzen
- Center for VirologyMedical University of ViennaViennaAustria
| | | | | | | | | | - Robert Strassl
- Division of Clinical VirologyMedical University of ViennaViennaAustria
| | - Alexander Zoufaly
- Department of Medicine IVClinic FavoritenViennaAustria,Faculty of MedicineSigmund Freud UniversityViennaAustria
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4
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Fischietti M, Eckerdt F, Blyth GT, Arslan AD, Mati WM, Oku CV, Perez RE, Lee-Chang C, Kosciuczuk EM, Saleiro D, Beauchamp EM, Lesniak MS, Verzella D, Sun L, Fish EN, Yang GY, Qiang W, Platanias LC. Schlafen 5 as a novel therapeutic target in pancreatic ductal adenocarcinoma. Oncogene 2021; 40:3273-3286. [PMID: 33846574 PMCID: PMC8106654 DOI: 10.1038/s41388-021-01761-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023]
Abstract
We provide evidence that a member of the human Schlafen (SLFN) family of proteins, SLFN5, is overexpressed in human pancreatic ductal adenocarcinoma (PDAC). Targeted deletion of SLFN5 results in decreased PDAC cell proliferation and suppresses PDAC tumorigenesis in in vivo PDAC models. Importantly, high expression levels of SLFN5 correlate with worse outcomes in PDAC patients, implicating SLFN5 in the pathophysiology of PDAC that leads to poor outcomes. Our studies establish novel regulatory effects of SLFN5 on cell cycle progression through binding/blocking of the transcriptional repressor E2F7, promoting transcription of key genes that stimulate S phase progression. Together, our studies suggest an essential role for SLFN5 in PDAC and support the potential for developing new therapeutic approaches for the treatment of pancreatic cancer through SLFN5 targeting.
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Affiliation(s)
- Mariafausta Fischietti
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Frank Eckerdt
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gavin T Blyth
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ahmet D Arslan
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - William M Mati
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Chidera V Oku
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ricardo E Perez
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Catalina Lee-Chang
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ewa M Kosciuczuk
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Diana Saleiro
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elspeth M Beauchamp
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Maciej S Lesniak
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniela Verzella
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Leyu Sun
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eleanor N Fish
- Toronto General Hospital Research Institute, University Health Network and Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Guang-Yu Yang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Wenan Qiang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
- Division of Hematology-Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA.
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5
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Mechanisms of Resistance to NK Cell Immunotherapy. Cancers (Basel) 2020; 12:cancers12040893. [PMID: 32272610 PMCID: PMC7226138 DOI: 10.3390/cancers12040893] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/19/2022] Open
Abstract
Immunotherapy has recently been a major breakthrough in cancer treatment. Natural killer (NK) cells are suitable targets for immunotherapy owing to their potent cytotoxic activity that may target cancer cells in a major histocompatibility complex (MHC) and antigen-unrestricted manner. Current therapies targeting NK cells include monoclonal antibodies that promote NK cell antibody-dependent cell-mediated cytotoxicity (ADCC), hematopoietic stem cell transplantation (HSCT), the adoptive transfer of NK cells, the redirection of NK cells using chimeric antigen receptor (CAR)-NK cells and the use of cytokines and immunostimulatory drugs to boost the anti-tumor activity of NK cells. Despite some encouraging clinical results, patients receiving these therapies frequently develop resistance, and a myriad of mechanisms of resistance affecting both the immune system and cancer cells have been reported. A first contributing factor that modulates the efficacy of the NK cell therapy is the genetic profile of the individual, which regulates all aspects of NK cell biology. Additionally, the resistance of cancer cells to apoptosis and the immunoediting of cancer cells, a process that decreases their immunogenicity and promotes immunosuppression, are major determinants of the resistance to NK cell therapy. Consequently, the efficacy of NK cell anti-tumor therapy is specific to each patient and disease. The elucidation of such immunosubversive mechanisms is crucial to developing new procedures and therapeutic strategies to fully harness the anti-tumor potential of NK cells.
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6
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Ranu N, Villani AC, Hacohen N, Blainey PC. Targeting individual cells by barcode in pooled sequence libraries. Nucleic Acids Res 2019; 47:e4. [PMID: 30256981 PMCID: PMC6326790 DOI: 10.1093/nar/gky856] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/12/2018] [Indexed: 01/02/2023] Open
Abstract
Transcriptional profiling of thousands of single cells in parallel by RNA-seq is now routine. However, due to reliance on pooled library preparation, targeting analysis to particular cells of interest is difficult. Here, we present a multiplexed PCR method for targeted sequencing of select cells from pooled single-cell sequence libraries. We demonstrated this molecular enrichment method on multiple cell types within pooled single-cell RNA-seq libraries produced from primary human blood cells. We show how molecular enrichment can be combined with FACS to efficiently target ultra-rare cell types, such as the recently identified AXL+SIGLEC6+ dendritic cell (AS DC) subset, in order to reduce the required sequencing effort to profile single cells by 100-fold. Our results demonstrate that DNA barcodes identifying cells within pooled sequencing libraries can be used as targets to enrich for specific molecules of interest, for example reads from a set of target cells.
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Affiliation(s)
- Navpreet Ranu
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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7
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Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Landscape of X chromosome inactivation across human tissues. Nature 2017; 550:244-248. [PMID: 29022598 PMCID: PMC5685192 DOI: 10.1038/nature24265] [Citation(s) in RCA: 630] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/28/2017] [Indexed: 12/16/2022]
Abstract
X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of 'escape' from inactivation varying between genes and individuals. The extent to which XCI is shared between cells and tissues remains poorly characterized, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression and phenotypic traits. Here we describe a systematic survey of XCI, integrating over 5,500 transcriptomes from 449 individuals spanning 29 tissues from GTEx (v6p release) and 940 single-cell transcriptomes, combined with genomic sequence data. We show that XCI at 683 X-chromosomal genes is generally uniform across human tissues, but identify examples of heterogeneity between tissues, individuals and cells. We show that incomplete XCI affects at least 23% of X-chromosomal genes, identify seven genes that escape XCI with support from multiple lines of evidence and demonstrate that escape from XCI results in sex biases in gene expression, establishing incomplete XCI as a mechanism that is likely to introduce phenotypic diversity. Overall, this updated catalogue of XCI across human tissues helps to increase our understanding of the extent and impact of the incompleteness in the maintenance of XCI.
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Affiliation(s)
- Taru Tukiainen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Angela Yen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Manuel A. Rivas
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Jamie L. Marshall
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- New York Genome Center, New York, NY 10013, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Matt Aguirre
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Laura Gauthier
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark Fleharty
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew Kirby
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beryl B. Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stephane E. Castel
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Konrad J. Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrea Byrnes
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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8
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Villani AC, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane AA, Haniffa M, Regev A, Hacohen N. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 2017; 356:eaah4573. [PMID: 28428369 PMCID: PMC5775029 DOI: 10.1126/science.aah4573] [Citation(s) in RCA: 1512] [Impact Index Per Article: 216.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/07/2017] [Indexed: 12/16/2022]
Abstract
Dendritic cells (DCs) and monocytes play a central role in pathogen sensing, phagocytosis, and antigen presentation and consist of multiple specialized subtypes. However, their identities and interrelationships are not fully understood. Using unbiased single-cell RNA sequencing (RNA-seq) of ~2400 cells, we identified six human DCs and four monocyte subtypes in human blood. Our study reveals a new DC subset that shares properties with plasmacytoid DCs (pDCs) but potently activates T cells, thus redefining pDCs; a new subdivision within the CD1C+ subset of DCs; the relationship between blastic plasmacytoid DC neoplasia cells and healthy DCs; and circulating progenitor of conventional DCs (cDCs). Our revised taxonomy will enable more accurate functional and developmental analyses as well as immune monitoring in health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Department of Medicine, Boston, MA, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- New York Genome Center, New York University Center for Genomics and Systems Biology, New York, NY, USA
- New York University Center for Genomics and Systems Biology, New York, NY, USA
| | - Gary Reynolds
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - James Fletcher
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Morgane Griesbeck
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
| | - Andrew Butler
- New York Genome Center, New York University Center for Genomics and Systems Biology, New York, NY, USA
- New York University Center for Genomics and Systems Biology, New York, NY, USA
| | - Shiwei Zheng
- New York Genome Center, New York University Center for Genomics and Systems Biology, New York, NY, USA
- New York University Center for Genomics and Systems Biology, New York, NY, USA
| | - Suzan Lazo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Laura Jardine
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - David Dixon
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - David McDonald
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Weibo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Department of Medicine, Boston, MA, USA
| | - Philip L De Jager
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School
| | | | - Andrew A Lane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, UK
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology and Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Department of Medicine, Boston, MA, USA
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9
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Sips M, Liu Q, Draghi M, Ghebremichael M, Berger CT, Suscovich TJ, Sun Y, Walker BD, Carrington M, Altfeld M, Brouckaert P, De Jager PL, Alter G. HLA-C levels impact natural killer cell subset distribution and function. Hum Immunol 2016; 77:1147-1153. [PMID: 27521484 PMCID: PMC6684021 DOI: 10.1016/j.humimm.2016.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 07/09/2016] [Accepted: 08/10/2016] [Indexed: 01/11/2023]
Abstract
Differences in HLA-C expression are inversely correlated with HIV viral load set-point and slower progression to AIDS, linked to enhanced cytotoxic T cell immunity. Yet, beyond T cells, HLA-C serves as a dominant ligand for natural killer (NK) cell killer immunoglobulin-like receptors (KIR). Thus, we speculated that HLA-C expression levels may also impact NK activity, thereby modulating HIV antiviral control. Phenotypic and functional profiling was performed on freshly isolated PBMCs. HLA-C expression was linked to changes in NK subset distribution and licensing, particularly in HLA-C1/C1, KIR2DL3+2DL2-individuals. Moreover, high levels of HLA-C, were associated with reduced frequencies of anergic CD56neg NKs and lower frequencies of KIR2DL1/2/3+ NK cells, pointing to an HLA-C induced influence on the NK cell development in the absence of disease. In HIV infection, several spontaneous controllers, that expressed higher levels of HLA-C demonstrated robust NK-IFN-γ secretion in response to target cells, highlighting a second disease induced licensing phenotype. Thus this population study points to a potential role for HLA-C levels both in NK cell education and development.
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Affiliation(s)
- Magdalena Sips
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Qingquan Liu
- Department of Endocrinology, Tangdu Hospital, Fourth Military Medical University, Xi'an, ShaanXi, China
| | - Monia Draghi
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Christoph T Berger
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; University Hospital Basel, Basel, Switzerland
| | | | - Yongtao Sun
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, ShaanXi, China
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marcus Altfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Peter Brouckaert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Womens Hospital, Boston, MA, USA; Harvard Medical School, Cambridge, MA, USA; Program in Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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10
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Chang HH, Liu GY, Dwivedi N, Sun B, Okamoto Y, Kinslow JD, Deane KD, Demoruelle MK, Norris JM, Thompson PR, Sparks JA, Rao DA, Karlson EW, Hung HC, Holers VM, Ho IC. A molecular signature of preclinical rheumatoid arthritis triggered by dysregulated PTPN22. JCI Insight 2016; 1:e90045. [PMID: 27777982 DOI: 10.1172/jci.insight.90045] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A unique feature of rheumatoid arthritis (RA) is the presence of anti-citrullinated protein antibodies (ACPA). Several risk factors for RA are known to increase the expression or activity of peptidyl arginine deiminases (PADs), which catalyze citrullination and, when dysregulated, can result in hypercitrullination. However, the consequence of hypercitrullination is unknown and the function of each PAD has yet to be defined. Th cells of RA patients are hypoglycolytic and hyperproliferative due to impaired expression of PFKFB3 and ATM, respectively. Here, we report that these features are also observed in peripheral blood mononuclear cells (PBMCs) from healthy at-risk individuals (ARIs). PBMCs of ARIs are also hypercitrullinated and produce more IL-2 and Th17 cytokines but fewer Th2 cytokines. These abnormal features are due to impaired induction of PTPN22, a phosphatase that also suppresses citrullination independently of its phosphatase activity. Attenuated phosphatase activity of PTPN22 results in aberrant expression of IL-2, ATM, and PFKFB3, whereas diminished nonphosphatase activity of PTPN22 leads to hypercitrullination mediated by PADs. PAD2- or PAD4-mediated hypercitrullination reduces the expression of Th2 cytokines. By contrast, only PAD2-mediated hypercitrullination can increase the expression of Th17 cytokines. Taken together, our data depict a molecular signature of preclinical RA that is triggered by impaired induction of PTPN22.
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Affiliation(s)
- Hui-Hsin Chang
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Guang-Yaw Liu
- Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan.,Division of Allergy, Immunology and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Nishant Dwivedi
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Bo Sun
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Yuko Okamoto
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jennifer D Kinslow
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kevin D Deane
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - M Kristen Demoruelle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Deepak A Rao
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth W Karlson
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Hui-Chih Hung
- Department of Life Sciences and.,Agricultural Biotechnology Center and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - V Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - I-Cheng Ho
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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11
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Chang HH, Dwivedi N, Nicholas AP, Ho IC. The W620 Polymorphism in PTPN22 Disrupts Its Interaction With Peptidylarginine Deiminase Type 4 and Enhances Citrullination and NETosis. Arthritis Rheumatol 2015; 67:2323-34. [DOI: 10.1002/art.39215] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/19/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Hui-Hsin Chang
- Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Nishant Dwivedi
- Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Anthony P. Nicholas
- University of Alabama at Birmingham and Birmingham VA Medical Center; Birmingham Alabama
| | - I-Cheng Ho
- Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
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12
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Detection of IL-17A-producing peripheral blood monocytes in Langerhans cell histiocytosis patients. Clin Immunol 2014; 153:112-22. [DOI: 10.1016/j.clim.2014.04.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 03/03/2014] [Accepted: 04/07/2014] [Indexed: 01/13/2023]
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13
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Cichocki F, Sitnicka E, Bryceson YT. NK cell development and function – Plasticity and redundancy unleashed. Semin Immunol 2014; 26:114-26. [DOI: 10.1016/j.smim.2014.02.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/02/2014] [Accepted: 02/04/2014] [Indexed: 01/16/2023]
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14
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Abstract
The initiation and perpetuation of autoimmunity recognize numerous checkpoints, from the genomic susceptibility to the breakdown of tolerance. This latter phenomenon includes the loss of B cell anergy and T regulatory cell failure, as well as the production of autoantibodies and autoreactive T cells. These mechanisms ultimately lead to tissue injury via different mechanisms that span from the production of proinflammatory cytokines to the chemotaxis of immune cells to the target sites. The pathways to autoimmunity have been widely investigated over the past year and resulted in a number of articles in peer-reviewed journals that has increased by nearly 10 % compared to 2011. We herein follow on the attempt to provide a brief discussion of the majority of articles on autoimmune diseases that were published in the major immunology journals in the previous solar year. The selection is necessarily arbitrary and may thus not be seen as comprehensive but reflects current research trends. Indeed, 2012 articles were mostly dedicated to define new and old mechanisms with potential therapeutic implications in autoimmunity in general, though based on specific clinical conditions or animal models. As paradigmatic examples, the environmental influence on autoimmunity, Th17 changes modulating the autoimmune response, serum autoantibodies and B cell changes as biomarkers and therapeutic targets were major issues addressed by experimental articles in 2012. Further, a growing number of studies investigated the sex bias of autoimmunity and supported different working hypotheses to explain the female predominance, including sex chromosome changes and reproductive life factors. In conclusion, the resulting scenario illustrates that common factors may underlie different autoimmune diseases and this is well represented by the observed alterations in interferon-α and TGFβ or by the shared signaling pathways.
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Affiliation(s)
- Carlo Selmi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy,
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15
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Recher M, Karjalainen-Lindsberg ML, Lindlöf M, Söderlund-Venermo M, Lanzi G, Väisänen E, Kumar A, Sadeghi M, Berger CT, Alitalo T, Anttila P, Kolehmainen M, Franssila R, Chen T, Siitonen S, Delmonte OM, Walter JE, Pessach I, Hess C, Simpson MA, Navarini AA, Giliani S, Hedman K, Seppänen M, Notarangelo LD. Genetic variation in schlafen genes in a patient with a recapitulation of the murine Elektra phenotype. J Allergy Clin Immunol 2013; 133:1462-5, 1465.e1-5. [PMID: 24373355 DOI: 10.1016/j.jaci.2013.10.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 10/21/2013] [Accepted: 10/23/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Mike Recher
- Division of Immunology and the Manton Center for Orphan Disease Research, Children's Hospital, Boston, Mass; Clinic for Primary Immunodeficiency, Medical Outpatient Clinic and Immunobiology Lab, University Hospital, Basel, Switzerland.
| | | | - Mikael Lindlöf
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | - Maria Söderlund-Venermo
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | - Gaetana Lanzi
- Department of Pediatrics, "Angelo Nocivelli" Institute for Molecular Medicine, and the Department of Pathology, Laboratory of Genetic Disorders of Childhood, Children's Hospital, Brescia, Italy
| | - Elina Väisänen
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | - Arun Kumar
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | - Mohammadreza Sadeghi
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | - Christoph T Berger
- Clinic for Primary Immunodeficiency, Medical Outpatient Clinic and Immunobiology Lab, University Hospital, Basel, Switzerland
| | - Tiina Alitalo
- Genetics Laboratory, HUSLAB, Helsinki University Central Hospital, Helsinki, Finland
| | - Pekka Anttila
- Helsinki University Central Hospital, Helsinki, Finland
| | | | - Rauli Franssila
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | - Tingting Chen
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | - Sanna Siitonen
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | - Ottavia M Delmonte
- Division of Immunology and the Manton Center for Orphan Disease Research, Children's Hospital, Boston, Mass
| | - Jolan E Walter
- Division of Immunology and the Manton Center for Orphan Disease Research, Children's Hospital, Boston, Mass
| | - Itai Pessach
- Division of Immunology and the Manton Center for Orphan Disease Research, Children's Hospital, Boston, Mass; Department of Pediatric Critical Care, Sheba Medical Center, Tel-Hashomer, and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Christoph Hess
- Clinic for Primary Immunodeficiency, Medical Outpatient Clinic and Immunobiology Lab, University Hospital, Basel, Switzerland
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, School of Medicine, King's College London, Guy's Hospital, London, United Kingdom
| | - Alexander A Navarini
- Division of Genetics and Molecular Medicine, School of Medicine, King's College London, Guy's Hospital, London, United Kingdom
| | - Silvia Giliani
- Department of Pediatrics, "Angelo Nocivelli" Institute for Molecular Medicine, and the Department of Pathology, Laboratory of Genetic Disorders of Childhood, Children's Hospital, Brescia, Italy
| | - Klaus Hedman
- Haartman Institute, University of Helsinki, and Helsinki University Central Hospital Laboratory Division, Helsinki, Finland
| | | | - Luigi D Notarangelo
- Division of Immunology and the Manton Center for Orphan Disease Research, Children's Hospital, Boston, Mass
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16
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Ottoboni L, Frohlich IY, Lee M, Healy BC, Keenan BT, Xia Z, Chitnis T, Guttmann CR, Khoury SJ, Weiner HL, Hafler DA, De Jager PL. Clinical relevance and functional consequences of the TNFRSF1A multiple sclerosis locus. Neurology 2013; 81:1891-9. [PMID: 24174586 DOI: 10.1212/01.wnl.0000436612.66328.8a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE We set out to characterize the clinical impact and functional consequences of rs1800693(G), the multiple sclerosis (MS) susceptibility allele found in the TNFRSF1A locus. METHODS We analyzed prospectively collected data on patients with MS to assess the role of the TNFRSF1A locus on disease course and treatment response. Using archival serum samples and freshly isolated monocytes from patients with MS and healthy subjects, we evaluated the effects of rs1800693(G) and a second risk allele, R92Q, on immune function. RESULTS In 772 patients with MS, we see no evidence that rs1800693(G) strongly influences clinical or radiographic indices of disease course and treatment response; thus, rs1800693(G) appears to be primarily involved in the onset of MS. At the molecular level, this validated susceptibility allele generates an RNA isoform, TNFRSF1A Δ6, that lacks the transmembrane and cytoplasmic domains. While there was no measurable effect on serum levels of soluble TNFRSF1A, rs1800693(G) appears to alter the state of monocytes, which demonstrate a more robust transcriptional response of CXCL10 and other genes in response to tumor necrosis factor (TNF)-α. We also report that activation of the TNF-α pathway results in altered expression of 6 other MS susceptibility genes, including T-cell activation rho GTPase activating protein (TAGAP) and regulator of G-protein signaling 1 (RGS1), which are not previously known to be responsive to TNF-α. CONCLUSIONS The MS rs1800693(G) susceptibility allele affects the magnitude of monocyte responses to TNF-α stimulation, and the TNF pathway may be one network in which the effect of multiple MS genes becomes integrated.
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Affiliation(s)
- Linda Ottoboni
- From the Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry (L.O., I.Y.F., M.L., B.T.K., Z.X., P.L.D.), Department of Neurology, Partners MS Center, Center for Neurologic Diseases (B.C.H., T.C., S.J.K., H.L.W., P.L.D.), and Center for Neurological Imaging, Department of Radiology (C.R.G.), Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Program in Medical & Population Genetics (L.O., I.Y.F., M.L., B.T.K., Z.X., P.L.D.), Broad Institute of Harvard University and the Massachusetts Institute of Technology, Cambridge; and the Department of Neurology and Immunobiology (D.A.H.), Yale School of Medicine, New Haven, CT
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17
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De Jager PL, Bennett DA. An inflection point in gene discovery efforts for neurodegenerative diseases: from syndromic diagnoses toward endophenotypes and the epigenome. JAMA Neurol 2013; 70:719-26. [PMID: 23571780 DOI: 10.1001/jamaneurol.2013.275] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We are at an inflection point in our study of the human genome as it relates to neurodegenerative disease. The sequencing of the human genome, and its associated cataloging of human genetic variation and technological as well as methodological development, introduced a period of rapid gene discovery over the past decade. These efforts have yielded many new insights and will continue to uncover the genetic architecture of syndromically defined neurodegenerative diseases in the coming decades. More recently, these successful study designs have been applied to the investigation of intermediate traits that relate to and inform our understanding of clinical syndromes and to exploration of the epigenome, the higher-order structure of DNA that dictates the expression of a given genetic risk factor. While still nascent, given the challenges of accumulating large numbers of subjects with detailed phenotypes and technological hurdles in characterizing the state of chromatin, these efforts represent key investments that will enable the study of the functional consequences of a genetic risk factor and, eventually, its contribution to the clinical manifestations of a given disease. As a community of investigators, we are therefore at an exciting inflection point at which gene discovery efforts are transitioning toward the functional characterization of implicated genetic variation; this transition is crucial for understanding the molecular, cellular, and systemic events that lead to a syndromic diagnosis for a neurodegenerative disease.
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Affiliation(s)
- Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women’s Hospital, Boston, Massachusetts, USA.
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18
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Chang HH, Miaw SC, Tseng W, Sun YW, Liu CC, Tsao HW, Ho IC. PTPN22 modulates macrophage polarization and susceptibility to dextran sulfate sodium-induced colitis. THE JOURNAL OF IMMUNOLOGY 2013; 191:2134-43. [PMID: 23913970 DOI: 10.4049/jimmunol.1203363] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PTPN22, a protein tyrosine phosphatase expressed mainly in hematopoietic cells, has been linked to many autoimmune diseases. A C-to-T single nucleotide polymorphism (SNP) at position 1858 of human PTPN22 cDNA decreases the risk of Crohn's disease. However, the function of PTPN22 and the mechanism by which this SNP reduces the risk of Crohn's disease are poorly understood. We find that PTPN22 is expressed in macrophages. It suppresses M1 macrophage polarization and reciprocally promotes the expression of M2-associated genes. PTPN22-deficient mice develop severe colitis induced by dextran sulfate sodium, and their intestinal macrophages express higher levels of M1 genes but lower levels of M2-associated genes. Furthermore, the protective T allele of the C1858T SNP is associated with attenuated expression of inflammatory cytokines and a higher level of PTPN22 in human M1 macrophages. This T allele-associated aberrant expression of PTPN22 is partly attributed to an autoinhibition mechanism, in which PTPN22 suppresses its own expression in M1 but not M2 macrophages. Our data not only demonstrate a critical role of PTPN22 in regulating macrophage polarization but also provide a molecular explanation for the protective effect of the C1858T SNP in Crohn's disease.
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Affiliation(s)
- Hui-Hsin Chang
- Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
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19
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Altered natural killer cell subset homeostasis and defective chemotactic responses in paroxysmal nocturnal hemoglobinuria. Blood 2013; 122:1887-90. [PMID: 23881915 DOI: 10.1182/blood-2013-06-507574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In paroxysmal nocturnal hemoglobinuria (PNH), hematopoietic cells lacking glycosylphosphatidylinositol (GPI)-linked proteins on their surface (GPI(neg)) exist alongside normal (GPI+) cells. Analysis of natural killer (NK) cell subsets in 47 PNH patients revealed that the ratio of CD56(bright):CD56(dim) NK cells differed in the GPI+ and GPI(neg) populations, with GPI(neg)CD56(bright) NK cells significantly more abundant in peripheral blood than their normal GPI+ counterparts. Indeed, GPI+CD56(bright) NK cells were not detected in the peripheral blood of some patients, suggesting their trafficking to a niche unavailable to the GPI(neg)CD56(bright) NK cell population. Defective cellular trafficking in this disease was supported by findings showing differential chemokine receptor expression between GPI+ and GPI(neg) NK cells and impaired stromal cell-derived factor 1 (SDF-1)-induced chemotaxis of GPI(neg) NK cells. Our results indicate a role for GPI-linked proteins in NK cell subset homeostasis and suggest that differential chemokine responses might contribute to the balance of GPI+ and GPI(neg) populations in this disease.
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20
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Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci. Nat Genet 2013; 45:730-8. [PMID: 23749187 DOI: 10.1038/ng.2667] [Citation(s) in RCA: 619] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 05/15/2013] [Indexed: 02/07/2023]
Abstract
Ankylosing spondylitis is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. In addition to HLA-B*27 alleles, 12 loci have previously been identified that are associated with ankylosing spondylitis in populations of European ancestry, and 2 associated loci have been identified in Asians. In this study, we used the Illumina Immunochip microarray to perform a case-control association study involving 10,619 individuals with ankylosing spondylitis (cases) and 15,145 controls. We identified 13 new risk loci and 12 additional ankylosing spondylitis-associated haplotypes at 11 loci. Two ankylosing spondylitis-associated regions have now been identified encoding four aminopeptidases that are involved in peptide processing before major histocompatibility complex (MHC) class I presentation. Protective variants at two of these loci are associated both with reduced aminopeptidase function and with MHC class I cell surface expression.
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21
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Stranger BE, De Jager PL. Coordinating GWAS results with gene expression in a systems immunologic paradigm in autoimmunity. Curr Opin Immunol 2012; 24:544-51. [PMID: 23040211 DOI: 10.1016/j.coi.2012.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 08/31/2012] [Accepted: 09/05/2012] [Indexed: 11/28/2022]
Abstract
There has been considerable progress in our understanding of the genetic architecture of susceptibility to inflammatory diseases in recent years: several hundred susceptibility loci have been discovered in genome-wide association studies (GWAS) of human populations. This success has created an important challenge in identifying the functional consequences of these risk-associated variants and in elucidating how the repercussions of individual susceptibility loci integrate to yield dysregulation of immune pathways and, ultimately, syndromic clinical phenotypes. The integration of GWAS association signals with high-resolution transcriptome and other genomic data that capture the dynamics of cellular state and function in the context of individual's collection of susceptibility alleles has proven to be a successful avenue of investigation. The rapid pace of methodological development in this area has been coupled with an accumulation of experimental data that makes the elucidation of complex biological networks underlying susceptibility to these common inflammatory diseases a reasonable goal in the near future.
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Affiliation(s)
- Barbara E Stranger
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
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