1
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Xian W, Asad M, Wu S, Bai Z, Li F, Lu J, Zu G, Brintnell E, Chen H, Mao Y, Zhou G, Liao B, Wu J, Wang E, You L. Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq analysis. Front Med 2024; 18:147-168. [PMID: 37955814 DOI: 10.1007/s11684-023-1017-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/24/2023] [Indexed: 11/14/2023]
Abstract
The association of neurogenesis and gliogenesis with glioma remains unclear. By conducting single-cell RNA-seq analyses on 26 gliomas, we reported their classification into primitive oligodendrocyte precursor cell (pri-OPC)-like and radial glia (RG)-like tumors and validated it in a public cohort and TCGA glioma. The RG-like tumors exhibited wild-type isocitrate dehydrogenase and tended to carry EGFR mutations, and the pri-OPC-like ones were prone to carrying TP53 mutations. Tumor subclones only in pri-OPC-like tumors showed substantially down-regulated MHC-I genes, suggesting their distinct immune evasion programs. Furthermore, the two subgroups appeared to extensively modulate glioma-infiltrating lymphocytes in distinct manners. Some specific genes not expressed in normal immune cells were found in glioma-infiltrating lymphocytes. For example, glial/glioma stem cell markers OLIG1/PTPRZ1 and B cell-specific receptors IGLC2/IGKC were expressed in pri-OPC-like and RG-like glioma-infiltrating lymphocytes, respectively. Their expression was positively correlated with those of immune checkpoint genes (e.g., LGALS33) and poor survivals as validated by the increased expression of LGALS3 upon IGKC overexpression in Jurkat cells. This finding indicated a potential inhibitory role in tumor-infiltrating lymphocytes and could provide a new way of cancer immune evasion.
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Affiliation(s)
- Weiwei Xian
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Mohammad Asad
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Shuai Wu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zhixin Bai
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Fengjiao Li
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Junfeng Lu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Gaoyu Zu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Erin Brintnell
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Guomin Zhou
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai, 200040, China
| | - Bo Liao
- School of Mathematics and Statistics, Hainan Normal University, Haikou, 570100, China
| | - Jinsong Wu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai, 200040, China.
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2
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Wang Q, Feng D, Jia S, Lu Q, Zhao M. B-Cell Receptor Repertoire: Recent Advances in Autoimmune Diseases. Clin Rev Allergy Immunol 2024; 66:76-98. [PMID: 38459209 DOI: 10.1007/s12016-024-08984-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
In the field of contemporary medicine, autoimmune diseases (AIDs) are a prevalent and debilitating group of illnesses. However, they present extensive and profound challenges in terms of etiology, pathogenesis, and treatment. A major reason for this is the elusive pathophysiological mechanisms driving disease onset. Increasing evidence suggests the indispensable role of B cells in the pathogenesis of autoimmune diseases. Interestingly, B-cell receptor (BCR) repertoires in autoimmune diseases display a distinct skewing that can provide insights into disease pathogenesis. Over the past few years, advances in high-throughput sequencing have provided powerful tools for analyzing B-cell repertoire to understand the mechanisms during the period of B-cell immune response. In this paper, we have provided an overview of the mechanisms and analytical methods for generating BCR repertoire diversity and summarize the latest research progress on BCR repertoire in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), primary Sjögren's syndrome (pSS), multiple sclerosis (MS), and type 1 diabetes (T1D). Overall, B-cell repertoire analysis is a potent tool to understand the involvement of B cells in autoimmune diseases, facilitating the creation of innovative therapeutic strategies targeting specific B-cell clones or subsets.
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Affiliation(s)
- Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Sujie Jia
- Department of Pharmacy, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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3
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Zhang Y, Guo C, Zhou Y, Zhang W, Zhu Z, Wang W, Wan Y. A biphenotypic lymphocyte subset displays both T- and B-cell functionalities. Commun Biol 2024; 7:28. [PMID: 38182721 PMCID: PMC10770049 DOI: 10.1038/s42003-023-05719-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
T cell/B cell mixed phenotypic lymphocytes have been observed in different disease contexts, yet their presence and function in physiological conditions remain elusive. Here, we provide evidence for the existence of a lymphocyte subset endogenously expressing both T- and B-cell lineage markers in mice. The majority of these T/B phenotypic lymphocytes (CD3+CD19+) show an origin of pro/pre B cells and distribute widely in mouse bone marrow, lymph nodes, spleen, and peripheral blood. Functional assays show that these biphenotypic lymphocytes can be activated through stimulating TCR or BCR signaling pathways. Moreover, we show that these cells actively participate both the humoral and cellular immune responses elicited by vaccination. Compared to conventional T cells, these biphenotypic lymphocytes can secrete a higher level of IL-2 but a lower level of TNF-α upon antigen specific stimulation. An equivalent lymphocyte subset is found in freshly isolated human PBMCs and exhibits similar functionality, albeit at a lower frequency than in mice.
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Affiliation(s)
- Yifan Zhang
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
| | - Cuiyuan Guo
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yigong Zhou
- Life Science Department, Faculty of Agricultural and Environmental Sciences, Macdonald Campus of McGill University, Quebec, Canada
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China.
| | - Wanhai Wang
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, China.
| | - Yanmin Wan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China.
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4
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Levi R, Dvorkin S, Louzoun Y. Shared bias in H chain V-J pairing in naive and memory B cells. Front Immunol 2023; 14:1166116. [PMID: 37790930 PMCID: PMC10543446 DOI: 10.3389/fimmu.2023.1166116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction H chain rearrangement in B cells is a two-step process where first DH binds JH, and only then VH is joined to the complex. As such, there is no direct rearrangement between VH and JH. Results Nevertheless, we here show that the VHJH combinations frequency in humans deviates from the one expected based on each gene usage frequency. This bias is observed mainly in functional rearrangements, and much less in out-of-frame rearrangements. The bias cannot be explained by preferred binding for DH genes or a preferred reading frame. Preferred VH JH combinations are shared between donors. Discussion These results suggest a common structural mechanism for these biases. Through development, thepreferred VH JH combinations evolve during peripheral selection to become stronger, but less shared. We propose that peripheral Heavy chain VH JH usage is initially shaped by a structural selection before the naive B cellstate, followed by pathogen-induced selection for host specific VH-JH pairs.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
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5
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Shapiro MR, Dong X, Perry DJ, McNichols JM, Thirawatananond P, Posgai AL, Peters LD, Motwani K, Musca RS, Muir A, Concannon P, Jacobsen LM, Mathews CE, Wasserfall CH, Haller MJ, Schatz DA, Atkinson MA, Brusko MA, Bacher R, Brusko TM. Human immune phenotyping reveals accelerated aging in type 1 diabetes. JCI Insight 2023; 8:e170767. [PMID: 37498686 PMCID: PMC10544250 DOI: 10.1172/jci.insight.170767] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023] Open
Abstract
The proportions and phenotypes of immune cell subsets in peripheral blood undergo continual and dramatic remodeling throughout the human life span, which complicates efforts to identify disease-associated immune signatures in type 1 diabetes (T1D). We conducted cross-sectional flow cytometric immune profiling on peripheral blood from 826 individuals (stage 3 T1D, their first-degree relatives, those with ≥2 islet autoantibodies, and autoantibody-negative unaffected controls). We constructed an immune age predictive model in unaffected participants and observed accelerated immune aging in T1D. We used generalized additive models for location, shape, and scale to obtain age-corrected data for flow cytometry and complete blood count readouts, which can be visualized in our interactive portal (ImmScape); 46 parameters were significantly associated with age only, 25 with T1D only, and 23 with both age and T1D. Phenotypes associated with accelerated immunological aging in T1D included increased CXCR3+ and programmed cell death 1-positive (PD-1+) frequencies in naive and memory T cell subsets, despite reduced PD-1 expression levels on memory T cells. Phenotypes associated with T1D after age correction were predictive of T1D status. Our findings demonstrate advanced immune aging in T1D and highlight disease-associated phenotypes for biomarker monitoring and therapeutic interventions.
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Affiliation(s)
- Melanie R. Shapiro
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Xiaoru Dong
- Diabetes Institute and
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Daniel J. Perry
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - James M. McNichols
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Puchong Thirawatananond
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Amanda L. Posgai
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Leeana D. Peters
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Keshav Motwani
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Richard S. Musca
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Andrew Muir
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Patrick Concannon
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
- Genetics Institute and
| | - Laura M. Jacobsen
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Clive H. Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Michael J. Haller
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Desmond A. Schatz
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mark A. Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Maigan A. Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Rhonda Bacher
- Diabetes Institute and
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Todd M. Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
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6
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Cantley J, Eizirik DL, Latres E, Dayan CM. Islet cells in human type 1 diabetes: from recent advances to novel therapies - a symposium-based roadmap for future research. J Endocrinol 2023; 259:e230082. [PMID: 37493471 PMCID: PMC10502961 DOI: 10.1530/joe-23-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/25/2023] [Indexed: 07/27/2023]
Abstract
There is a growing understanding that the early phases of type 1 diabetes (T1D) are characterised by a deleterious dialogue between the pancreatic beta cells and the immune system. This, combined with the urgent need to better translate this growing knowledge into novel therapies, provided the background for the JDRF-DiabetesUK-INNODIA-nPOD symposium entitled 'Islet cells in human T1D: from recent advances to novel therapies', which took place in Stockholm, Sweden, in September 2022. We provide in this article an overview of the main themes addressed in the symposium, pointing to both promising conclusions and key unmet needs that remain to be addressed in order to achieve better approaches to prevent or reverse T1D.
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Affiliation(s)
- J Cantley
- School of Medicine, University of Dundee, Dundee, United Kingdom of Great Britain and Northern Ireland
| | - D L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles Faculté de Médecine, Bruxelles, Belgium
| | - E Latres
- JDRF International, New York, NY, USA
| | - C M Dayan
- Cardiff University School of Medicine, Cardiff, United Kingdom of Great Britain and Northern Ireland
| | - the JDRF-DiabetesUK-INNODIA-nPOD Stockholm Symposium 2022
- School of Medicine, University of Dundee, Dundee, United Kingdom of Great Britain and Northern Ireland
- ULB Center for Diabetes Research, Université Libre de Bruxelles Faculté de Médecine, Bruxelles, Belgium
- JDRF International, New York, NY, USA
- Cardiff University School of Medicine, Cardiff, United Kingdom of Great Britain and Northern Ireland
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7
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Salnikov MY, Fonseca GJ, Mymryk JS. Differences in the Tumor Microenvironment of EBV-Associated Gastric Cancers Revealed Using Single-Cell Transcriptome Analysis. Cancers (Basel) 2023; 15:3178. [PMID: 37370788 DOI: 10.3390/cancers15123178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Epstein-Barr virus (EBV) is a gamma-herpesvirus associated with nearly 10% of gastric cancers (GCs). These EBV-associated GCs (EBVaGCs) are molecularly, histopathologically, and clinically distinct from EBV-negative GCs (EBVnGCs). While viral genes in EBVaGCs contribute to the carcinogenesis process, viral proteins also represent foreign antigens that could trigger enhanced immune responses compared to EBVnGCs. Despite prior investigations of the EBVaGC tumor microenvironment (TME), the cellular composition has not been thoroughly explored. In this study, cellular subpopulations overrepresented in EBVaGCs were identified and molecularly characterized. Genes consistently expressed across both bulk tumor and single-cell RNA sequencing data were highlighted, with the expression across the identified cellular subpopulations analyzed. As expected, based on existing histopathological analysis, EBVaGC is characterized by abundant lymphocytic infiltration of the stroma. Our molecular analysis identified three unique immune cell subpopulations in EBVaGC: T and B cells expressing high levels of proliferation markers and B cells expressing T cell features. The proliferating T cell cluster also expressed markers of follicular T helper cells. Overall, EBVaGC also exhibited unique features indicative of a higher inflammatory response. These substantial differences within the TME suggest that further detailed exploration of the cellular composition of EBVaGCs is needed, which may identify cellular subpopulations and phenotypes associated with patient outcomes.
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Affiliation(s)
- Mikhail Y Salnikov
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
| | - Gregory J Fonseca
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC H3G 2M1, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, QC H3A 0G4, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
- Department of Otolaryngology, Western University, London, ON N6A 5W9, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
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8
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Walsh ES, Tollison TS, Brochu HN, Shaw BI, Diveley KR, Chou H, Law L, Kirk AD, Gale M, Peng X. Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques. J Immunol 2022; 208:762-771. [PMID: 34987112 PMCID: PMC8820446 DOI: 10.4049/jimmunol.2100824] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/17/2021] [Indexed: 02/03/2023]
Abstract
Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired H and L chains of Igs and VDJ and VJ chains of TCRs from thousands of single cells simultaneously in humans and mice. Despite rhesus macaques being one of the most well-studied model organisms for the human adaptive immune response, high-throughput single-cell immune repertoire sequencing assays are not yet available due to the complexity of these polyclonal receptors. We used custom primers that capture all known rhesus macaque Ig and TCR isotypes and chains that are fully compatible with a commercial solution for single-cell immune repertoire profiling. Using these rhesus-specific assays, we sequenced Ig and TCR repertoires in >60,000 cells from cryopreserved rhesus PBMCs, splenocytes, and FACS-sorted B and T cells. We were able to recover every Ig isotype and TCR chain, measure clonal expansion in proliferating T cells, and pair Ig and TCR repertoires with gene expression profiles of the same single cells. Our results establish the ability to perform high-throughput immune repertoire analysis in rhesus macaques at the single-cell level.
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Affiliation(s)
- Evan S. Walsh
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607,Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Tammy S. Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
| | - Hayden N. Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607,Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Brian I. Shaw
- Department of Surgery, Duke University, Durham, NC 27710
| | - Kayleigh R. Diveley
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607,Genetics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Hsuan Chou
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Allan D. Kirk
- Department of Surgery, Duke University, Durham, NC 27710
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA 98109,Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109,Washington National Primate Research Center, University of Washington, Seattle, WA 98121
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607,Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695,Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695
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9
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany. .,Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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10
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Eugster A, Bostick ML, Gupta N, Mariotti-Ferrandiz E, Kraus G, Meng W, Soto C, Trück J, Stervbo U, Luning Prak ET; AIRR Community. AIRR Community Guide to Planning and Performing AIRR-Seq Experiments. Methods Mol Biol 2022; 2453:261-78. [PMID: 35622331 DOI: 10.1007/978-1-0716-2115-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.
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11
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Hanna SJ, Tatovic D, Thayer TC, Dayan CM. Insights From Single Cell RNA Sequencing Into the Immunology of Type 1 Diabetes- Cell Phenotypes and Antigen Specificity. Front Immunol 2021; 12:751701. [PMID: 34659258 PMCID: PMC8519581 DOI: 10.3389/fimmu.2021.751701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/14/2021] [Indexed: 01/10/2023] Open
Abstract
In the past few years, huge advances have been made in techniques to analyse cells at an individual level using RNA sequencing, and many of these have precipitated exciting discoveries in the immunology of type 1 diabetes (T1D). This review will cover the first papers to use scRNAseq to characterise human lymphocyte phenotypes in T1D in the peripheral blood, pancreatic lymph nodes and islets. These have revealed specific genes such as IL-32 that are differentially expressed in islet -specific T cells in T1D. scRNAseq has also revealed wider gene expression patterns that are involved in T1D and can predict its development even predating autoantibody production. Single cell sequencing of TCRs has revealed V genes and CDR3 motifs that are commonly used to target islet autoantigens, although truly public TCRs remain elusive. Little is known about BCR repertoires in T1D, but scRNAseq approaches have revealed that insulin binding BCRs commonly use specific J genes, share motifs between donors and frequently demonstrate poly-reactivity. This review will also summarise new developments in scRNAseq technology, the insights they have given into other diseases and how they could be leveraged to advance research in the type 1 diabetes field to identify novel biomarkers and targets for immunotherapy.
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Affiliation(s)
- Stephanie J. Hanna
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Danijela Tatovic
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Terri C. Thayer
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Department of Biological and Chemical Sciences, School of Natural and Social Sciences, Roberts Wesleyan College, Rochester, NY, United States
| | - Colin M. Dayan
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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Ahmed R, Omidian Z, Giwa A, Donner T, Jie C, Hamad ARA. A reply to "TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes". Cell 2021; 184:840-3. [PMID: 33545037 DOI: 10.1016/j.cell.2020.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/05/2020] [Accepted: 11/19/2020] [Indexed: 11/22/2022]
Abstract
We have recently identified a novel lymphocyte that is a dual expresser (DE) of TCRαβ and BCR. DEs in T1D patients are predominated by a public BCR clonotype (clone-x) that encodes a potent autoantigen that cross-activates insulin-reactive T cells. Betts and colleagues were able to detect DEs but alleged to not detect high DE frequency, clone-x, or similar clones in T1D patients. Unfortunately, the authors did not follow our methods and when they did, their flow cytometric data at two sites were conflicting. Moreover, contrary to their claim, we identified clones similar to clone-x in their data along with clones bearing the core motif (DTAMVYYFDYW). Additionally, their report of no increased usage of clone-x VH/DH genes by bulk B cells confirms rather than challenges our results. Finally, the authors failed to provide data verifying purity of their sorted DEs, making it difficult to draw reliable conclusion of their repertoire analysis. This Matters Arising Response paper addresses the Japp et al. (2021) Matters Arising paper, published concurrently in Cell.
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Wadenpohl J, Seyfarth J, Hehenkamp P, Hoffmann M, Kummer S, Reinauer C, Döing C, Förtsch K, Mayatepek E, Meissner T, Jacobsen M. CD5-expressing CD8 + T-cell subsets differ between children with type 1 diabetes and controls. Immunol Cell Biol 2021; 99:1077-1084. [PMID: 34133790 DOI: 10.1111/imcb.12488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 01/14/2023]
Abstract
Different lymphocyte subsets are involved in autoimmune pathogenesis of type 1 diabetes (T1D). Previous studies suggested a role of CD5-expressing T and B cells including rare unconventional lymphocytes with combined T- and B-cell features [dual expressing (DE) cells]. We performed algorithm-supported multiparameter flow cytometry and quantitative PCR to investigate immune cell subsets and DE cells in children with T1D (n = 20) and matched controls (n = 20). Comparisons of conventional immune cells detected increased proportions of CD3+ T cells in T1D patients, whereas CD19+ B-cell proportions were comparable to controls. Self-organizing maps for flow cytometry analyses (FlowSOM) showed highly similar CD5-expressing B-cell subsets and no differences for DE cells were detected between the study groups by flow cytometry or specific quantitative PCR. Notably, differences in CD8+ T cells were indicated by FlowSOM and similarity-based t-distributed stochastic neighbor embedding (tSNE) analyses. Study group comparisons confirmed significantly reduced CD8+ T-cell proportions with moderate or low CD5 expression in T1D patients. Finally, in vitro experiments showed stable CD5 expression differences of CD8+ T cells after T-cell activation, cytokine stimulation and culture. We observed differences of T-cell coreceptor CD5 expression in T1D patients with potential relevance for immune regulation of CD8+ T-cell activation.
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Affiliation(s)
- Josefine Wadenpohl
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Julia Seyfarth
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Paul Hehenkamp
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Maximilian Hoffmann
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Sebastian Kummer
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Christina Reinauer
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Carsten Döing
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Katharina Förtsch
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Thomas Meissner
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | - Marc Jacobsen
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
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