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Yi L, Guo X, Liu Y, Jirimutu, Wang Z. Single-cell 5' RNA sequencing of camelid peripheral B cells provides insights into cellular basis of heavy-chain antibody production. Comput Struct Biotechnol J 2024; 23:1705-1714. [PMID: 38689719 PMCID: PMC11059136 DOI: 10.1016/j.csbj.2024.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Camelids produce both conventional tetrameric antibodies (Abs) and dimeric heavy-chain antibodies (HCAbs). Although B cells that generate these two types of Abs exhibit distinct B cell receptors (BCRs), whether these two B cell populations differ in their phenotypes and developmental processes remains unclear. Here, we performed single-cell 5' RNA profiling of peripheral blood mononuclear cell samples from Bactrian camels before and after immunization. We characterized the functional subtypes and differentiation trajectories of circulating B cells in camels, and reconstructed single-cell BCR sequences. We found that in contrast to humans, the proportion of T-bet+ B cells was high among camelid peripheral B cells. Several marker genes of human B cell subtypes, including CD27 and IGHD, were expressed at low levels in the corresponding camel B cell subtypes. Camelid B cells expressing variable genes of HACbs (VHH) were widely present in various functional subtypes and showed highly overlapping differentiation trajectories with B cells expressing variable genes of conventional Abs (VH). After immunization, the transcriptional changes in VHH+ and VH+ B cells were largely consistent. Through structure modeling, we identified a variety of scaffold types among the reconstructed VHH sequences. Our study provides insights into the cellular context of HCAb production in camels and lays the foundation for developing single-B cell-based camelid single-domain Ab screening.
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Affiliation(s)
- Li Yi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Xin Guo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuexing Liu
- Guangzhou Laboratory, Guangzhou 510005, China
| | - Jirimutu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
- Inner Mongolia China-Kazakhstan Camel Research Institute, Alxa 750306, China
| | - Zhen Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Xu H, Wang Z, Li Y, Xu Z. The distribution and function of teleost IgT. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109281. [PMID: 38092093 DOI: 10.1016/j.fsi.2023.109281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Given the uniquely close relationship between fish and aquatic environments, fish mucosal tissues are constantly exposed to a wide array of pathogenic microorganisms in the surrounding water. To maintain mucosal homeostasis, fish have evolved a distinct mucosal immune system known as mucosal-associated lymphoid tissues (MALTs). These MALTs consist of key effector cells and molecules from the adaptive immune system, such as B cells and immunoglobulins (Igs), which play crucial roles in maintaining mucosal homeostasis and defending against external pathogen infections. Until recently, three primary Ig isotypes, IgM, IgD, and IgT, have been identified in varying proportions within the mucosal secretions of teleost fish. Similar to the role of mucosal IgA in mammals and birds, teleost IgT plays a predominant role in mucosal immunity. Following the identification of the IgT gene in 2005, significant advances have been made in researching the origin, evolution, structure, and function of teleost IgT. Multiple IgT variants have been identified in various species of teleost fish, underscoring the remarkable complexity of IgT in fish. Therefore, this study provides a comprehensive review of the recent advances in various aspects of teleost IgT, including its genomic and structural features, the diverse distribution patterns within various fish mucosal tissues (the skin, gills, gut, nasal, buccal, pharyngeal, and swim bladder mucosa), its interaction with mucosal symbiotic microorganisms, and its immune responses towards diverse pathogens, including bacteria, viruses, and parasites. We also highlight the existing research gaps in the study of teleost IgT, suggesting the need for further investigation into the functional aspects of IgT and IgT+ B cells. This research is aimed at providing valuable insights into the immune functions of IgT and the mechanisms underlying the immune responses of fish against infections.
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Affiliation(s)
- Haoyue Xu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zixuan Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuqing Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Xu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Dübel S. Can antibodies be "vegan"? A guide through the maze of today's antibody generation methods. MAbs 2024; 16:2343499. [PMID: 38634488 PMCID: PMC11028021 DOI: 10.1080/19420862.2024.2343499] [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: 02/28/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
There is no doubt that today's life sciences would look very different without the availability of millions of research antibody products. Nevertheless, the use of antibody reagents that are poorly characterized has led to the publication of false or misleading results. The use of laboratory animals to produce research antibodies has also been criticized. Surprisingly, both problems can be addressed with the same technology. This review charts today's maze of different antibody formats and the various methods for antibody production and their interconnections, ultimately concluding that sequence-defined recombinant antibodies offer a clear path to both improved quality of experimental data and reduced use of animals.
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Affiliation(s)
- Stefan Dübel
- Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
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Xia M, Zhang C, Xiao L, Qiu X. Genetic Characteristics of Non B Cell-Derived Immunoglobulin Genes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1445:37-46. [PMID: 38967748 DOI: 10.1007/978-981-97-0511-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
It is widely acknowledged that immunoglobulins (Igs) are produced solely by B-lineage cells. The Ig gene is created by the rearrangement of a group of gene segments [variable (V), diversity (D), and joining (J) segments rearrangement, or V(D)J recombination], which results in the vast diversity of B cell-derived Ig responsible for recognising various antigens. Ig subsequently undergoes somatic hypermutation (SHM) and class switch recombination (CSR) after exposure to antigens, thus converting the low-affinity IgM to IgG, IgA, or IgE antibodies. IgM and IgD are primarily expressed in naïve B cells that have not been exposed to antigens, they do not undergo somatic hypermutation; hence, their variable region sequences remain the same as those in the germline. In contrast, IgG, IgA, and IgE are expressed in antigen-stimulated memory B cells or plasma cells, and thus, they often possess high-frequency mutations in their variable region sequences. Since the discovery that Ig can be produced by non-B cells, Qiu's group has investigated and compared the genetic characteristics of B cell-derived Ig and non-B cell-derived Ig. These findings demonstrated that non-B cell-derived Ig shares certain similarities with B cell-derived Ig in that the sequence of its constant region is identical to that of B cell-derived Ig, and its variable region is also strictly dependent on the rearrangement of V, D, and J gene segments. Moreover, akin to B cell-derived Ig, the V regions of IgM and IgD are rarely mutated, while IgG, IgA, and IgE produced by cancer cells are frequently mutated. However, the non-B cell-derived Ig V region sequence displays unique characteristics. (1) Unlike the vast diversity of B cell-derived Igs, non-B cell-derived Igs exhibit restricted diversity; cells from the same lineage always select the same V(D)J recombination patterns; (2) Both mRNA and proteins of RAG1/RAG2 recombinase have been detected in Ig positive cancer cell lines and normal tissues. But Ig recombination could also be found in RAG1-/- and RAG2-/- mice, suggesting that they are not necessary for the rearrangement of non-B cell-derived Igs. These features of non-B cell-derived Igs suggest a potentially undiscovered mechanism of V(D)J recombination, ligation, and SHM in non-B cells, which necessitates further investigation with advanced technology in molecular biology.
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Affiliation(s)
- Miaoran Xia
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.
| | - Chi Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Lin Xiao
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
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Wu L, Xia M, Wang C, Yan H, Gong X, Yin CC. Expression, Function, and Significance of Non B Cell-Derived Immunoglobulin in Haematological System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1445:179-188. [PMID: 38967760 DOI: 10.1007/978-981-97-0511-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Acute myeloid leukaemia (AML) is a collection of genetically diverse diseases characterised by abnormal proliferation of immature haematopoietic cells and disruption of normal haematopoiesis. Myeloid cells and lymphocytes originate from different haematopoietic precursors within the bone marrow. It has been traditionally assumed that myeloid cells cannot produce immunoglobulin (Ig), a marker of B cells and plasma cells. However, in recent years, all five Ig classes have been detected in CD34+ haematopoietic stem cells, mature monocytes and neutrophils, differentiated macrophages and tumour-associated macrophages, acute myeloid leukaemia cell lines, as well as myeloblasts of AML. The rearranged V(D)J sequences exhibit unique restricted or biased V gene usage and evidence of somatic mutation. Furthermore, AML-derived Igs could promote cell proliferation, induce apoptosis, and enhance migration. Elevated levels of Ig expression predict inferior clinical outcomes. These findings indicate that AML-derived Ig plays a role in AML pathogenesis and progression, and could serve as a novel biomarker for risk stratification, disease monitoring, and targeted therapy. In this chapter, we provide a comprehensive review of recent literature on the expression, function, and significance of non B cell-derived Ig in the haematological system, with a focus on AML.
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Affiliation(s)
- Lina Wu
- Central Laboratory, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China.
| | - Miaoran Xia
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Chong Wang
- Department of Analytical Development, Cell Therapy Technology Product Engine, Oncology Therapeutic Area Unit, Takeda Pharmaceutical Company, Cambridge, MA, USA
| | - Huige Yan
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Gong
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - C Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Xu X, Delves PJ, Huang J, Shao W, Qiu X. Comparison of Non B-Ig and B-Ig. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1445:73-88. [PMID: 38967751 DOI: 10.1007/978-981-97-0511-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Immunoglobulin (Ig) has been widely acknowledged to be produced solely by B-lineage cells. However, growing evidence has demonstrated the expression of Ig in an array of cancer cells, as well as normal cells including epithelial cells, epidermal cells, mesangial cells, monocytes, and neutrophils. Ig has even been found to be expressed in non-B cells at immune-privileged sites such as neurons and spermatogenic cells. Despite these non-B cell-derived Igs (non-B-Igs) sharing the same symmetric structures with conventional Igs (B-Igs), further studies have revealed unique characteristics of non-B-Ig, such as restricted variable region and aberrant glycosylation. Moreover, non-B-Ig exhibits properties of promoting malignant behaviours of cancer cells, therefore it could be utilised in the clinic as a potential therapeutic biomarker or target. The elucidation of the generation and regulation of non-B-Ig will certainly broaden our understanding of immunology.
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Affiliation(s)
- Xiaojun Xu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.
| | - Peter J Delves
- Division of Infection and Immunity, Department of Immunology, UCL (University College London), London, UK
| | - Jing Huang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Wenwei Shao
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China
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Wang R, Li H, Ling C, Zhang X, Lu J, Luan W, Zhang J, Shi L. A novel phenotype of B cells associated with enhanced phagocytic capability and chemotactic function after ischemic stroke. Neural Regen Res 2023; 18:2413-2423. [PMID: 37282471 DOI: 10.4103/1673-5374.371365] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
Accumulating evidence has demonstrated the involvement of B cells in neuroinflammation and neuroregeneration. However, the role of B cells in ischemic stroke remains unclear. In this study, we identified a novel phenotype of macrophage-like B cells in brain-infiltrating immune cells expressing a high level of CD45. Macrophage-like B cells characterized by co-expression of B-cell and macrophage markers, showed stronger phagocytic and chemotactic functions compared with other B cells and showed upregulated expression of phagocytosis-related genes. Gene Ontology analysis found that the expression of genes associated with phagocytosis, including phagosome- and lysosome-related genes, was upregulated in macrophage-like B cells. The phagocytic activity of macrophage-like B cells was verified by immunostaining and three-dimensional reconstruction, in which TREM2-labeled macrophage-like B cells enwrapped and internalized myelin debris after cerebral ischemia. Cell-cell interaction analysis revealed that macrophage-like B cells released multiple chemokines to recruit peripheral immune cells mainly via CCL pathways. Single-cell RNA sequencing showed that the transdifferentiation to macrophage-like B cells may be induced by specific upregulation of the transcription factor CEBP family to the myeloid lineage and/or by downregulation of the transcription factor Pax5 to the lymphoid lineage. Furthermore, this distinct B cell phenotype was detected in brain tissues from mice or patients with traumatic brain injury, Alzheimer's disease, and glioblastoma. Overall, these results provide a new perspective on the phagocytic capability and chemotactic function of B cells in the ischemic brain. These cells may serve as an immunotherapeutic target for regulating the immune response of ischemic stroke.
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Affiliation(s)
- Rui Wang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Huaming Li
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Chenhan Ling
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xiaotao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jianan Lu
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Weimin Luan
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jianmin Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine; Brain Research Institute, Zhejiang University; Stroke Research Center for Diagnostic and Therapeutic Technologies of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Ligen Shi
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine; Clinical Research Center for Neurological Diseases of Zhejiang Province, Hangzhou, Zhejiang Province, China
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Zhu L, Peng Q, Wu Y, Yao X. scBCR-seq revealed a special and novel IG H&L V(D)J allelic inclusion rearrangement and the high proportion dual BCR expressing B cells. Cell Mol Life Sci 2023; 80:319. [PMID: 37804328 PMCID: PMC11073065 DOI: 10.1007/s00018-023-04973-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/09/2023]
Abstract
Since the initial report of V (D) J "allelic exclusion/inclusion" (allelic exclusion rearrangement or allelic inclusion rearrangement) and the concept of the "dual B cell receptor (BCR)" in 1961, despite ongoing discoveries, the precise proportion and source mechanism of dual BCR under physiological conditions have been puzzling immuologists. This study takes advantage of the single cell B cell receptor sequencing (scBCR-seq) technology, which can perfectly match the heavy and light chains of BCR at the level of a single B cell, and obtain the full length mRNA sequence of the complementary determining region 3 (CDR3). Through analyzing the pairing of functional IGH (immunoglobulin heavy chain) and IGL (immunoglobulin light chain) in single B cell from both human and mouse bone marrow and peripheral blood, it was observed that dual BCR B cells exhibit stable and high levels of expression. Among them, the human bone marrow and peripheral blood contain about 10% dual (or multiple) BCR B cells, while in mouse peripheral blood and bone marrow memory B cells, this proportion reaches around 20%. At the same time, we innovatively found that in each research sample of humans and mice, there are three (or more) functional rearrangements (mRNA level) of a single chain in a single B cell. By analyzing the position, direction and other compositional characteristics of the V(D)J gene family, we found that at least two (or more) of them are derived from over two (or more) specific allelic inclusion rearrangements of a single chromosome (mRNA molecular level evidence), our findings also highlighted the necessity of classified single cell sequencing data based on single, dual (or multiple) and cannot be assembled into BCR when analyzing the B cell repertoire. The results of this article provides new methods and modeling references for evaluating the proportion and source mechanisms of dual BCR B cells, as well as potential significance of allelic inclusion (exclusion escape) of V(D)J rearrangement.
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Affiliation(s)
- Lanwei Zhu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation and Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Qi Peng
- Department of Immunology, Center of Immunomolecular Engineering, Innovation and Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Yingjie Wu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation and Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation and Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China.
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Pan YR, Wu CS, Zhong YQ, Zhang YA, Zhang XJ. An Atlas of Grass Carp IgM+ B Cells in Homeostasis and Bacterial Infection Helps to Reveal the Unique Heterogeneity of B Cells in Early Vertebrates. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:964-980. [PMID: 37578390 DOI: 10.4049/jimmunol.2300052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023]
Abstract
Teleost B cells are primitive lymphocytes with both innate and adaptive immune functions. However, the heterogeneity and differentiation trajectory of teleost B cells remain largely unknown. In this study, the landscape of grass carp IgM+ (gcIgM+) B cells was revealed by single-cell RNA sequencing. The results showed that gcIgM+ B cells mainly comprise six populations: (im)mature B cells, innate B cells, proliferating B cells, plasma cells, CD22+ cells, and CD34+ cells, among which innate B cells and proliferating B cells were uncommon B cell subsets with, to our knowledge, new characteristics. Remarkably, three functional IgMs were discovered in grass carp, and a significant percentage of gcIgM+ B cells, especially plasma cells, expressed multiple Igμ genes (Igμ1, Igμ2, and/or Igμ3). More importantly, through single-cell sorting combined with Sanger sequencing, we found that distinct VHDJH recombination patterns of Igμ genes were present in single IgM+ B cells, indicating that individual teleost B cells might produce multiple Abs by coexpressing rearranged IgM subclass genes. Moreover, the percentage of IgM1highIgM2highIgM3high plasma cells increased significantly after bacterial infection, suggesting that individual plasma cells might tend to produce multiple IgMs to resist the infection in teleost fish. In summary, to our knowledge, this study not only helps to uncover the unique heterogeneity of B cells in early vertebrates but also provided significant new evidence supporting the recently proposed "one cell-multiple Abs" paradigm, challenging the classical rule of "one cell-one Ab."
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Affiliation(s)
- Yi-Ru Pan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chang-Song Wu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Ya-Qin Zhong
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yong-An Zhang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xu-Jie Zhang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
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Lutshumba J, Wilcock DM, Monson NL, Stowe AM. Sex-based differences in effector cells of the adaptive immune system during Alzheimer's disease and related dementias. Neurobiol Dis 2023; 184:106202. [PMID: 37330146 PMCID: PMC10481581 DOI: 10.1016/j.nbd.2023.106202] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Neurological conditions such as Alzheimer's disease (AD) and related dementias (ADRD) present with many challenges due to the heterogeneity of the related disease(s), making it difficult to develop effective treatments. Additionally, the progression of ADRD-related pathologies presents differently between men and women. With two-thirds of the population affected with ADRD being women, ADRD has presented itself with a bias toward the female population. However, studies of ADRD generally do not incorporate sex-based differences in investigating the development and progression of the disease, which is detrimental to understanding and treating dementia. Additionally, recent implications for the adaptive immune system in the development of ADRD bring in new factors to be considered as part of the disease, including sex-based differences in immune response(s) during ADRD development. Here, we review the sex-based differences of pathological hallmarks of ADRD presentation and progression, sex-based differences in the adaptive immune system and how it changes with ADRD, and the importance of precision medicine in the development of a more targeted and personalized treatment for this devastating and prevalent neurodegenerative condition.
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Affiliation(s)
- Jenny Lutshumba
- Department of Neurology, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Donna M Wilcock
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States of America; Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Nancy L Monson
- Department of Neurology and Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Ann M Stowe
- Department of Neurology, College of Medicine, University of Kentucky, Lexington, KY, United States of America; Center for Advanced Translational Stroke Science, University of Kentucky, Lexington, KY, United States of America.
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Zhu L, Peng Q, Li J, Wu Y, Wang J, Zhou D, Ma L, Yao X. scRNA-seq revealed the special TCR β & α V(D)J allelic inclusion rearrangement and the high proportion dual (or more) TCR-expressing cells. Cell Death Dis 2023; 14:487. [PMID: 37524693 PMCID: PMC10390570 DOI: 10.1038/s41419-023-06004-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Allelic exclusion, one lymphocyte expresses one antigen receptor, is a fundamental mechanism of immunological self-tolerance and highly specific immune responses to pathogens. However, the phenomenon of V(D)J allelic inclusion (incomplete allelic exclusion or allelic escape) rearrangement and dual TCR T cells have been discovered by multiple laboratories. Despite continuous new discoveries, the proportion and underlying mechanism of dual TCR has been puzzling immunologists. In this study, we observed the presence of single T cells expressing multiple TCR chains in all samples, with the proportion of 15%, 10%, and 20% in the human thymus, human peripheral blood, and mouse lymphoid organs, respectively. The proportion of T cells possessing multiple T-cell receptors (TCR) varied significantly in different physiological states and developmental stages. By analyzing RSS category, RSS direction, and V(D)J gene position at TR locus of T cells which contain multiple TCR chains, we creatively found that one of TCR β (or TCR α) should originate from the transcription of V(D)J combination in T-cell receptor excision circle (TREC) formed after the twice successful rearrangement in the same chromosome. Moreover, human V30 (or mouse V31) gene may participate in reverse recombination and transcription to prevent allelic exclusion. In general, high proportion of T cells with multiple TCR at the transcriptome level was first made public, and we proposed a novel mechanism of secondary (or more) TCR rearrangement on a single chromosome. Our findings also indicated that the single-cell sequencing data should be classified according to the single, multiple, and abnormal TCR when analyzing the T-cell repertoire.
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Affiliation(s)
- Lanwei Zhu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Qi Peng
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Jun Li
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Yingjie Wu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Jiayi Wang
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Dewei Zhou
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China.
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12
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Zou J, Li J, Zhong X, Tang D, Fan X, Chen R. Liver in infections: a single-cell and spatial transcriptomics perspective. J Biomed Sci 2023; 30:53. [PMID: 37430371 PMCID: PMC10332047 DOI: 10.1186/s12929-023-00945-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
The liver is an immune organ that plays a vital role in the detection, capture, and clearance of pathogens and foreign antigens that invade the human body. During acute and chronic infections, the liver transforms from a tolerant to an active immune state. The defence mechanism of the liver mainly depends on a complicated network of intrahepatic and translocated immune cells and non-immune cells. Therefore, a comprehensive liver cell atlas in both healthy and diseased states is needed for new therapeutic target development and disease intervention improvement. With the development of high-throughput single-cell technology, we can now decipher heterogeneity, differentiation, and intercellular communication at the single-cell level in sophisticated organs and complicated diseases. In this concise review, we aimed to summarise the advancement of emerging high-throughput single-cell technologies and re-define our understanding of liver function towards infections, including hepatitis B virus, hepatitis C virus, Plasmodium, schistosomiasis, endotoxemia, and corona virus disease 2019 (COVID-19). We also unravel previously unknown pathogenic pathways and disease mechanisms for the development of new therapeutic targets. As high-throughput single-cell technologies mature, their integration into spatial transcriptomics, multiomics, and clinical data analysis will aid in patient stratification and in developing effective treatment plans for patients with or without liver injury due to infectious diseases.
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Affiliation(s)
- Ju Zou
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jie Li
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiao Zhong
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xuegong Fan
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ruochan Chen
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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13
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Ramirez Valdez K, Nzau B, Dorey-Robinson D, Jarman M, Nyagwange J, Schwartz JC, Freimanis G, Steyn AW, Warimwe GM, Morrison LJ, Mwangi W, Charleston B, Bonnet-Di Placido M, Hammond JA. A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies. Vaccines (Basel) 2023; 11:1099. [PMID: 37376488 PMCID: PMC10302312 DOI: 10.3390/vaccines11061099] [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: 05/12/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Studying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resolution in any species. Here, we detail a flexible and customizable suite of methods from flow cytometry, single cell sorting, heavy and light chain amplification to antibody sequencing in cattle. These methods were used successfully, including adaptation to the 10x Genomics platform, to isolate native heavy-light chain pairs. When combined with the Ig-Sequence Multi-Species Annotation Tool, this suite represents a powerful toolkit for studying the cattle antibody response with high resolution and precision. Using three workflows, we processed 84, 96, and 8313 cattle B cells from which we sequenced 24, 31, and 4756 antibody heavy-light chain pairs, respectively. Each method has strengths and limitations in terms of the throughput, timeline, specialist equipment, and cost that are each discussed. Moreover, the principles outlined here can be applied to study antibody responses in other mammalian species.
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Affiliation(s)
| | - Benjamin Nzau
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | | | | | - James Nyagwange
- The Pirbright Institute, Pirbright GU24 0NF, UK
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | | | | | | | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | - Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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14
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Beisel C, Jordan-Paiz A, Köllmann S, Ahrenstorf AE, Padoan B, Barkhausen T, Addo MM, Altfeld M. Sex differences in the percentage of IRF5 positive B cells are associated with higher production of TNF-α in women in response to TLR9 in humans. Biol Sex Differ 2023; 14:11. [PMID: 36814288 PMCID: PMC9945365 DOI: 10.1186/s13293-023-00495-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND The clinical course and outcome of many diseases differ between women and men, with women experiencing a higher prevalence and more severe pathogenesis of autoimmune diseases. The precise mechanisms underlying these sex differences still remain to be fully understood. IRF5 is a master transcription factor that regulates TLR/MyD88-mediated responses to pathogen-associated molecular patterns (PAMPS) in DCs and B cells. B cells are central effector cells involved in autoimmune diseases via the production of antibodies and pro-inflammatory cytokines as well as mediating T cell help. Dysregulation of IRF5 expression has been reported in autoimmune diseases, including systemic lupus erythematosus, primary Sjögren syndrome, and rheumatoid arthritis. METHODS In the current study, we analyzed whether the percentage of IRF5 positive B cells differs between women and men and assessed the resulting consequences for the production of inflammatory cytokines after TLR7- or TLR9 stimulation. RESULTS The percentage of IRF5 positive B cells was significantly higher in B cells of women compared to men in both unstimulated and TLR7- or TLR9-stimulated B cells. B cells of women produced higher levels of TNF-α in response to TLR9 stimulation. CONCLUSIONS Taken together, our data contribute to the understanding of sex differences in immune responses and may identify IRF5 as a potential therapeutic target to reduce harmful B cell-mediated immune responses in women.
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Affiliation(s)
- Claudia Beisel
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany. .,German Center for Infection Research (DZIF), University Medical Center Hamburg-Eppendorf, Lübeck-Borstel-Riems, Hamburg, Germany. .,Research Department Virus Immunology, Leibniz Institute of Virology, 20251, Hamburg, Germany. .,Department of Internal Medicine IV, Gastroenterology and Infectious Diseases, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.
| | - Ana Jordan-Paiz
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Sandra Köllmann
- grid.13648.380000 0001 2180 3484I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany ,grid.13648.380000 0001 2180 3484German Center for Infection Research (DZIF), University Medical Center Hamburg-Eppendorf, Lübeck-Borstel-Riems, Hamburg, Germany
| | | | - Benedetta Padoan
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Tanja Barkhausen
- grid.13648.380000 0001 2180 3484German Center for Infection Research (DZIF), University Medical Center Hamburg-Eppendorf, Lübeck-Borstel-Riems, Hamburg, Germany ,Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Marylyn M. Addo
- grid.13648.380000 0001 2180 3484I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany ,grid.13648.380000 0001 2180 3484German Center for Infection Research (DZIF), University Medical Center Hamburg-Eppendorf, Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marcus Altfeld
- grid.13648.380000 0001 2180 3484German Center for Infection Research (DZIF), University Medical Center Hamburg-Eppendorf, Lübeck-Borstel-Riems, Hamburg, Germany ,Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
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15
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Inoue K, Qin Y, Xia Y, Han J, Yuan R, Sun J, Xu R, Jiang JX, Greenblatt MB, Zhao B. Bone marrow Adipoq-lineage progenitors are a major cellular source of M-CSF that dominates bone marrow macrophage development, osteoclastogenesis, and bone mass. eLife 2023; 12:e82118. [PMID: 36779851 PMCID: PMC10005769 DOI: 10.7554/elife.82118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 02/12/2023] [Indexed: 02/14/2023] Open
Abstract
M-CSF is a critical growth factor for myeloid lineage cells, including monocytes, macrophages, and osteoclasts. Tissue-resident macrophages in most organs rely on local M-CSF. However, it is unclear what specific cells in the bone marrow produce M-CSF to maintain myeloid homeostasis. Here, we found that Adipoq-lineage progenitors but not mature adipocytes in bone marrow or in peripheral adipose tissue, are a major cellular source of M-CSF, with these Adipoq-lineage progenitors producing M-CSF at levels much higher than those produced by osteoblast lineage cells. The Adipoq-lineage progenitors with high CSF1 expression also exist in human bone marrow. Deficiency of M-CSF in bone marrow Adipoq-lineage progenitors drastically reduces the generation of bone marrow macrophages and osteoclasts, leading to severe osteopetrosis in mice. Furthermore, the osteoporosis in ovariectomized mice can be significantly alleviated by the absence of M-CSF in bone marrow Adipoq-lineage progenitors. Our findings identify bone marrow Adipoq-lineage progenitors as a major cellular source of M-CSF in bone marrow and reveal their crucial contribution to bone marrow macrophage development, osteoclastogenesis, bone homeostasis, and pathological bone loss.
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Affiliation(s)
- Kazuki Inoue
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special SurgeryNew YorkUnited States
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Yongli Qin
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special SurgeryNew YorkUnited States
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Yuhan Xia
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special SurgeryNew YorkUnited States
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Jie Han
- The first Affiliated Hospital of Xiamen University-ICMRS Collaborating Center for Skeletal Stem Cells, State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen UniversityXiamenChina
| | - Ruoxi Yuan
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special SurgeryNew YorkUnited States
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Jun Sun
- Pathology and Laboratory Medicine, Weill Cornell Medical CollegeNew YorkUnited States
| | - Ren Xu
- The first Affiliated Hospital of Xiamen University-ICMRS Collaborating Center for Skeletal Stem Cells, State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen UniversityXiamenChina
| | - Jean X Jiang
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San AntonioSan AntonioUnited States
| | - Matthew B Greenblatt
- Pathology and Laboratory Medicine, Weill Cornell Medical CollegeNew YorkUnited States
- Research Institute, Hospital for Special SurgeryNew YorkUnited States
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special SurgeryNew YorkUnited States
- Department of Medicine, Weill Cornell Medical CollegeNew YorkUnited States
- Graduate Program in Cell and Development Biology, Weill Cornell Graduate School of Medical SciencesNew YorkUnited States
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16
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Krechetov SP, Vtorushina VV, Inviyaeva EV, Gorodnova EA, Kolesnik SV, Kudlay DA, Borovikov PI, Krechetova LV, Dolgushina NV, Sukhikh GT. T-Cell Immunity in COVID-19-Recovered Individuals and Individuals Vaccinated with the Combined Vector Vaccine Gam-COVID-Vac. Int J Mol Sci 2023; 24:ijms24031930. [PMID: 36768254 PMCID: PMC9916700 DOI: 10.3390/ijms24031930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/21/2023] Open
Abstract
The COVID-19 pandemic has required extensive research on the new coronavirus SARS-CoV-2 and the creation of new highly effective vaccines. The presence of T-cells in the body that respond to virus antigens suggests adequate antiviral immunity. We investigated T-cell immunity in individuals who recovered from mild and moderate COVID-19 and in individuals vaccinated with the Gam-COVID-Vac combined vector vaccine. The ELISPOT method was used to determine the number of T-cells responding with IFN-γ synthesis to stimulation by peptides containing epitopes of the S-protein or N-, M-, ORF3, and ORF7 proteins, using peripheral blood mononuclear cells (PBMCs). At the same time, the multiplex method was used to determine the accumulation of IFN-γ and other cytokines in the culture medium. According to the data obtained, the proportion of positive conclusions about the T-cell immune response to SARS-CoV-2 antigens in control, recovered, and vaccinated individuals was 12%, 70%, and 52%, respectively. At the same time, more than half of the vaccinated individuals with a T-cell response were sensitized to the antigens of N-, M-, ORF3, and ORF7 proteins not produced by Gam-COVID-Vac, indicating a high likelihood of asymptomatic SARS-CoV-2 infection. Increased IFN-γ release by single sensitized T-cells in response to specific stimulation in recovered and vaccinated individuals did not result in the accumulation of this and other cytokines in the culture medium. These findings suggest a balance between cytokine production and utilization by immunocompetent cells as a prerequisite for providing a controlled cytokine signal and avoiding a "cytokine storm".
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Affiliation(s)
- Sergey Petrovich Krechetov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Valentina Valentinovna Vtorushina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Evgenia Vladimirovna Inviyaeva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Elena Aleksandrovna Gorodnova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-(916)564-77-69
| | - Svetlana Vladimirovna Kolesnik
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Dmitry Anatolievich Kudlay
- NRC Institute of Immunology FMBA of Russia, 115522 Moscow, Russia
- Department of Pharmacology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Pavel Igorevich Borovikov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Liubov Valentinovna Krechetova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Nataliya Vitalievna Dolgushina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
- Department of Obstetrics, Gynecology, Perinatology and Reproductology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Gennady Tikhonovich Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
- Department of Obstetrics, Gynecology, Perinatology and Reproductology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
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17
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Wang Z, Wang G, Lu H, Li H, Tang M, Tong A. Development of therapeutic antibodies for the treatment of diseases. MOLECULAR BIOMEDICINE 2022; 3:35. [PMID: 36418786 PMCID: PMC9684400 DOI: 10.1186/s43556-022-00100-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/24/2022] [Indexed: 11/25/2022] Open
Abstract
Since the first monoclonal antibody drug, muromonab-CD3, was approved for marketing in 1986, 165 antibody drugs have been approved or are under regulatory review worldwide. With the approval of new drugs for treating a wide range of diseases, including cancer and autoimmune and metabolic disorders, the therapeutic antibody drug market has experienced explosive growth. Monoclonal antibodies have been sought after by many biopharmaceutical companies and scientific research institutes due to their high specificity, strong targeting abilities, low toxicity, side effects, and high development success rate. The related industries and markets are growing rapidly, and therapeutic antibodies are one of the most important research and development areas in the field of biology and medicine. In recent years, great progress has been made in the key technologies and theoretical innovations provided by therapeutic antibodies, including antibody-drug conjugates, antibody-conjugated nuclides, bispecific antibodies, nanobodies, and other antibody analogs. Additionally, therapeutic antibodies can be combined with technologies used in other fields to create new cross-fields, such as chimeric antigen receptor T cells (CAR-T), CAR-natural killer cells (CAR-NK), and other cell therapy. This review summarizes the latest approved or in regulatory review therapeutic antibodies that have been approved or that are under regulatory review worldwide, as well as clinical research on these approaches and their development, and outlines antibody discovery strategies that have emerged during the development of therapeutic antibodies, such as hybridoma technology, phage display, preparation of fully human antibody from transgenic mice, single B-cell antibody technology, and artificial intelligence-assisted antibody discovery.
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Affiliation(s)
- Zeng Wang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guoqing Wang
- grid.13291.380000 0001 0807 1581Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, China
| | - Huaqing Lu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongjian Li
- grid.12527.330000 0001 0662 3178Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Mei Tang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Aiping Tong
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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18
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Yang R, Avery DT, Jackson KJL, Ogishi M, Benhsaien I, Du L, Ye X, Han J, Rosain J, Peel JN, Alyanakian MA, Neven B, Winter S, Puel A, Boisson B, Payne KJ, Wong M, Russell AJ, Mizoguchi Y, Okada S, Uzel G, Goodnow CC, Latour S, Bakkouri JE, Bousfiha A, Preece K, Gray PE, Keller B, Warnatz K, Boisson-Dupuis S, Abel L, Pan-Hammarström Q, Bustamante J, Ma CS, Casanova JL, Tangye SG. Human T-bet governs the generation of a distinct subset of CD11c highCD21 low B cells. Sci Immunol 2022; 7:eabq3277. [PMID: 35867801 PMCID: PMC9413977 DOI: 10.1126/sciimmunol.abq3277] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
High-level expression of the transcription factor T-bet characterizes a phenotypically distinct murine B cell population known as "age-associated B cells" (ABCs). T-bet-deficient mice have reduced ABCs and impaired humoral immunity. We describe a patient with inherited T-bet deficiency and largely normal humoral immunity including intact somatic hypermutation, affinity maturation and memory B cell formation in vivo, and B cell differentiation into Ig-producing plasmablasts in vitro. Nevertheless, the patient exhibited skewed class switching to IgG1, IgG4, and IgE, along with reduced IgG2, both in vivo and in vitro. Moreover, T-bet was required for the in vivo and in vitro development of a distinct subset of human B cells characterized by reduced expression of CD21 and the concomitantly high expression of CD19, CD20, CD11c, FCRL5, and T-bet, a phenotype that shares many features with murine ABCs. Mechanistically, human T-bet governed CD21loCD11chi B cell differentiation by controlling the chromatin accessibility of lineage-defining genes in these cells: FAS, IL21R, SEC61B, DUSP4, DAPP1, SOX5, CD79B, and CXCR4. Thus, human T-bet is largely redundant for long-lived protective humoral immunity but is essential for the development of a distinct subset of human CD11chiCD21lo B cells.
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Affiliation(s)
- Rui Yang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA,Department of Pediatrics, Weill Cornell Medicine, New York, NY, 10065, USA,Corresponding authors: Rui Yang (); Jean-Laurent Casanova (); Stuart Tangye ()
| | - Danielle T. Avery
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW Australia
| | | | - Masato Ogishi
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Ibtihal Benhsaien
- Laboratory of Clinical Immunology, Inflammation, and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco,Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Likun Du
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Stockholm, Sweden, EU
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Stockholm, Sweden, EU
| | - Jing Han
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Jessica N. Peel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Marie-Alexandra Alyanakian
- Immunology Laboratory, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), 75015 Paris, France, EU
| | - Bénédicte Neven
- Department of Pediatric Immunology, Hematology and Rheumatology, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Sarah Winter
- Paris Cité University, Imagine Institute, 75015 Paris, France,Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Bertrand Boisson
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Kathryn J. Payne
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW Australia
| | - Melanie Wong
- Children’s Hospital at Westmead, NSW, Australia,Faculty of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Amanda J. Russell
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW Australia
| | - Yoko Mizoguchi
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Christopher C. Goodnow
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW Australia,St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, Australia
| | - Sylvain Latour
- Paris Cité University, Imagine Institute, 75015 Paris, France,Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, 75015 Paris, France
| | - Jalila El Bakkouri
- Laboratory of Clinical Immunology, Inflammation, and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco,Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation, and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco,Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Kahn Preece
- John Hunter Children's Hospital, Newcastle, New South Wales, Australia
| | - Paul E. Gray
- School of Women's and Children's Health, UNSW Sydney, Sydney, New South Wales, Australia.,Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Baerbel Keller
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stéphanie Boisson-Dupuis
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Stockholm, Sweden, EU
| | - Jacinta Bustamante
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | - Cindy S. Ma
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW Australia,St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, Australia
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,Howard Hughes Medical Institute, New York, NY, USA,Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France,Corresponding authors: Rui Yang (); Jean-Laurent Casanova (); Stuart Tangye ()
| | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW Australia,St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, Australia,Corresponding authors: Rui Yang (); Jean-Laurent Casanova (); Stuart Tangye ()
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19
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Khaliq AM, Erdogan C, Kurt Z, Turgut SS, Grunvald MW, Rand T, Khare S, Borgia JA, Hayden DM, Pappas SG, Govekar HR, Kam AE, Reiser J, Turaga K, Radovich M, Zang Y, Qiu Y, Liu Y, Fishel ML, Turk A, Gupta V, Al-Sabti R, Subramanian J, Kuzel TM, Sadanandam A, Waldron L, Hussain A, Saleem M, El-Rayes B, Salahudeen AA, Masood A. Refining colorectal cancer classification and clinical stratification through a single-cell atlas. Genome Biol 2022; 23:113. [PMID: 35538548 PMCID: PMC9092724 DOI: 10.1186/s13059-022-02677-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/21/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironments is required to elucidate mechanisms of tumor and stroma cell contributions to pathogenesis which may advance subtype-specific therapeutic development. We interrogate racially diverse human CRC samples and analyze multiple independent external cohorts for a total of 487,829 single cells enabling high-resolution depiction of the cellular diversity and heterogeneity within the tumor and microenvironmental cells. RESULTS Tumor cells recapitulate individual CMS subgroups yet exhibit significant intratumoral CMS heterogeneity. Both CMS1 microsatellite instability (MSI-H) CRCs and microsatellite stable (MSS) CRC demonstrate similar pathway activations at the tumor epithelial level. However, CD8+ cytotoxic T cell phenotype infiltration in MSI-H CRCs may explain why these tumors respond to immune checkpoint inhibitors. Cellular transcriptomic profiles in CRC exist in a tumor immune stromal continuum in contrast to discrete subtypes proposed by studies utilizing bulk transcriptomics. We note a dichotomy in tumor microenvironments across CMS subgroups exists by which patients with high cancer-associated fibroblasts (CAFs) and C1Q+TAM content exhibit poor outcomes, providing a higher level of personalization and precision than would distinct subtypes. Additionally, we discover CAF subtypes known to be associated with immunotherapy resistance. CONCLUSIONS Distinct CAFs and C1Q+ TAMs are sufficient to explain CMS predictive ability and a simpler signature based on these cellular phenotypes could stratify CRC patient prognosis with greater precision. Therapeutically targeting specific CAF subtypes and C1Q + TAMs may promote immunotherapy responses in CRC patients.
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Affiliation(s)
- Ateeq M Khaliq
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cihat Erdogan
- Isparta University of Applied Sciences, Isparta, Turkey
| | - Zeyneb Kurt
- Northumbria University, Newcastle Upon Tyne, UK
| | | | | | - Tim Rand
- Tempus Labs, Inc., Chicago, IL, USA
| | | | | | | | - Sam G Pappas
- Rush University Medical Center, Chicago, IL, USA
| | | | - Audrey E Kam
- Rush University Medical Center, Chicago, IL, USA
| | | | | | - Milan Radovich
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yong Zang
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yingjie Qiu
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Anita Turk
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vineet Gupta
- Rush University Medical Center, Chicago, IL, USA
| | - Ram Al-Sabti
- Rush University Medical Center, Chicago, IL, USA
| | | | | | | | - Levi Waldron
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
| | - Arif Hussain
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Bassel El-Rayes
- University of Alabama, O'Neil Comprehensive Cancer Institute, Birmingham, AL, USA
| | | | - Ashiq Masood
- Indiana University School of Medicine, Indianapolis, IN, USA.
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20
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Rodgers CB, Mustard CJ, McLean RT, Hutchison S, Pritchard AL. A B-cell or a key player? The different roles of B-cells and antibodies in melanoma. Pigment Cell Melanoma Res 2022; 35:303-319. [PMID: 35218154 PMCID: PMC9314792 DOI: 10.1111/pcmr.13031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 02/01/2022] [Accepted: 02/21/2022] [Indexed: 12/17/2022]
Abstract
The B‐cell system plays an important role in the melanoma immune response; however, consensus has yet to be reached in many facets. Here, we comprehensively review human studies only, due to fundamental differences in the humoral response with animal models. Tumour‐infiltrating B‐cells are associated with contradictory prognostic values, reflecting a lack of agreement between studies on cell subset classification and differences in the markers used, particularly the common use of a single marker not differentiating multiple subsets. Tertiary lymphoid structures (TLS) organise T‐cells and B‐cells within tumours to generate a local anti‐tumour response and TLS presence associates with improved survival in response to immune checkpoint blockade, in late‐stage disease. Autoantibody production is increased in melanoma patients and has been proposed as biomarkers for diagnosis, prognosis and treatment/toxicity response; however, no consistent targets are yet identified. The function of antibodies in an anti‐tumour response is determined by its isotype and subclass; IgG4 is immune‐suppressive and robustly correlate with poor patient survival in melanoma. We conclude that the current B‐cell literature needs careful interpretation based on the methods used and that we need a consensus of markers to define B‐cells and associated lymphoid organs. Furthermore, future studies need to not only examine antibody targets, but also isotypes when considering functional roles.
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Affiliation(s)
- Chloe B Rodgers
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
| | - Colette J Mustard
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
| | - Ryan T McLean
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
| | - Sharon Hutchison
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
| | - Antonia L Pritchard
- Genetics and Immunology Department, Division of Biomedical Research, Institute of Health Research and Innovation, University of the Highlands and Islands, Inverness, UK
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21
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Sinkora M, Stepanova K, Butler JE, Sinkora M, Sinkora S, Sinkorova J. Comparative Aspects of Immunoglobulin Gene Rearrangement Arrays in Different Species. Front Immunol 2022; 13:823145. [PMID: 35222402 PMCID: PMC8873125 DOI: 10.3389/fimmu.2022.823145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022] Open
Abstract
Studies in humans and mice indicate the critical role of the surrogate light chain in the selection of the productive immunoglobulin repertoire during B cell development. However, subsequent studies using mutant mice have also demonstrated that alternative pathways are allowed. Our recent investigation has shown that some species, such as pig, physiologically use preferential rearrangement of authentic light chains, and become independent of surrogate light chains. Here we summarize the findings from swine and compare them with results in other species. In both groups, allelic and isotypic exclusions remain intact, so the different processes do not alter the paradigm of B-cell monospecificity. Both groups also retained some other essential processes, such as segregated and sequential rearrangement of heavy and light chain loci, preferential rearrangement of light chain kappa before lambda, and functional κ-deleting element recombination. On the other hand, the respective order of heavy and light chains rearrangement may vary, and rearrangement of the light chain kappa and lambda on different chromosomes may occur independently. Studies have also confirmed that the surrogate light chain is not required for the selection of the productive repertoire of heavy chains and can be substituted by authentic light chains. These findings are important for understanding evolutional approaches, redundancy and efficiency of B-cell generation, dependencies on other regulatory factors, and strategies for constructing therapeutic antibodies in unrelated species. The results may also be important for explaining interspecies differences in the proportional use of light chains and for the understanding of divergences in rearrangement processes. Therefore, the division into two groups may not be definitive and there may be more groups of intermediate species.
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Affiliation(s)
- Marek Sinkora
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czechia
- *Correspondence: Marek Sinkora,
| | - Katerina Stepanova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czechia
| | - John E. Butler
- Department of Microbiology, University of Iowa, Iowa City, IA, United States
| | - Marek Sinkora
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czechia
| | - Simon Sinkora
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czechia
| | - Jana Sinkorova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czechia
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22
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Nicaise AJ, McDonald A, Sears ER, Sturgis T, Kaplan BLF. TCDD Inhibition of IgG1 Production in Experimental Autoimmune Encephalomyelitis (EAE) and In Vitro. Antibodies (Basel) 2022; 11:4. [PMID: 35076460 PMCID: PMC8788515 DOI: 10.3390/antib11010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/02/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The environmental contaminant 2,3,7,8-tetrachlorodibenzo-para-dioxin (TCDD) is a ligand for the aryl hydrocarbon receptor (AhR). TCDD is well-characterized to produce immunotoxicity, including suppression of antibody production. Previously we showed that TCDD inhibited myelin oligodendrocyte glycoprotein (MOG) peptide-specific IgG and attenuated disease in experimental autoimmune encephalomyelitis (EAE) model in mice. Thus, the purpose of this study was to characterize the effects of TCDD on IgG subclasses in EAE and in vitro and assess effects in B cells derived from various tissues. TCDD modestly suppressed intracellular IgG expression in splenocytes (SPLC), but not bone marrow (BM) or lymph node (LN) cells. To further understand TCDD's effects on IgG, we utilized LPS and LPS + IL-4 in vitro to stimulate IgG3 and IgG1 production, respectively. TCDD preferentially suppressed IgG1+ cell surface expression, especially in SPLC. However, TCDD was able to suppress IgG1 and IgG3 secretion from SPLC and B cells, but not BM cells. Lastly, we revisited the EAE model and determined that TCDD suppressed MOG-specific IgG1 production. Together these data show that the IgG1 subclass of IgG is a sensitive target of suppression by TCDD. Part of the pathophysiology of EAE involves production of pathogenic antibodies that can recruit cytolytic cells to destroy MOG-expressing cells that comprise myelin, so inhibition of IgG1 likely contributes to TCDD's EAE disease attenuation.
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Affiliation(s)
| | | | | | | | - Barbara L. F. Kaplan
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (A.J.N.); (A.M.); (E.R.S.); (T.S.)
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23
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OGIHARA K, NAYA Y, KAMIE J, HISAMATSU S, KODAMA M, ISHIKAWA Y, KADOTA K. A porcine lymphoma-derived cell line co-expressing IgM, IgG and IgA. J Vet Med Sci 2022; 84:760-765. [PMID: 35400671 PMCID: PMC9246694 DOI: 10.1292/jvms.21-0508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A cell line (PL38PB) was established from blood samples of a 6-month-old pig that was
diagnosed with lymphoma with CD5 expression. Histopathological examination revealed
neoplastic lesions in the spleen, liver and lymph nodes. Tumor cells were
immunohistochemically positive for CD20 and immunoglobulin heavy chains (μ, γ and α).
Membranous CD5 and cytoplasmic Immunoglobulin M (IgM), Immunoglobulin G (IgG) and
Immunoglobulin A (IgA) were detected in PL38PB cells by flow cytometry. In addition, the
cytoplasm of PL38PB cells were positive for IgM, IgG and IgA by immunofluorescent.
However, no Ig secretion was detected in culture supernatant by Ouchterlony gel diffusion
method. Results suggest that PL38PB cells express three Ig isotypes that are produced but
not secreted.
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Affiliation(s)
- Kikumi OGIHARA
- Laboratory of Pathology, School of Life and Environmental Science, Azabu University
| | - Yuko NAYA
- Laboratory of Pathology, School of Life and Environmental Science, Azabu University
| | - Junichi KAMIE
- Laboratory of Veteinary Pathology, School of Veterinary Medicine, Azabu University
| | - Shin HISAMATSU
- Laboratory of Environmental Analysis, School of Life and Environmental Science, Azabu University
| | - Michi KODAMA
- Hokkaido Research Station, National Institute of Animal Health
| | | | - Koichi KADOTA
- Hokkaido Research Station, National Institute of Animal Health
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24
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Khatri I, Diks AM, van den Akker EB, Oosten LEM, Zwaginga JJ, Reinders MJT, van Dongen JJM, Berkowska MA. Longitudinal Dynamics of Human B-Cell Response at the Single-Cell Level in Response to Tdap Vaccination. Vaccines (Basel) 2021; 9:1352. [PMID: 34835283 PMCID: PMC8617659 DOI: 10.3390/vaccines9111352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/08/2021] [Accepted: 11/13/2021] [Indexed: 01/28/2023] Open
Abstract
To mount an adequate immune response against pathogens, stepwise mutation and selection processes are crucial functions of the adaptive immune system. To better characterize a successful vaccination response, we performed longitudinal (days 0, 5, 7, 10, and 14 after Boostrix vaccination) analysis of the single-cell transcriptome as well as the B-cell receptor (BCR) repertoire (scBCR-rep) in plasma cells of an immunized donor and compared it with baseline B-cell characteristics as well as flow cytometry findings. Based on the flow cytometry knowledge and literature findings, we discriminated individual B-cell subsets in the transcriptomics data and traced over-time maturation of plasmablasts/plasma cells (PB/PCs) and identified the pathways associated with the plasma cell maturation. We observed that the repertoire in PB/PCs differed from the baseline B-cell repertoire e.g., regarding expansion of unique clones in post-vaccination visits, high usage of IGHG1 in expanded clones, increased class-switching events post-vaccination represented by clonotypes spanning multiple IGHC classes and positive selection of CDR3 sequences over time. Importantly, the Variable gene family-based clustering of BCRs represented a similar measure as the gene-based clustering, but certainly improved the clustering of BCRs, as BCRs from duplicated Variable gene families could be clustered together. Finally, we developed a query tool to dissect the immune response to the components of the Boostrix vaccine. Using this tool, we could identify the BCRs related to anti-tetanus and anti-pertussis toxoid BCRs. Collectively, we developed a bioinformatic workflow which allows description of the key features of an ongoing (longitudinal) immune response, such as activation of PB/PCs, Ig class switching, somatic hypermutation, and clonal expansion, all of which are hallmarks of antigen exposure, followed by mutation & selection processes.
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Affiliation(s)
- Indu Khatri
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (I.K.); (A.M.D.); (M.A.B.)
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (E.B.v.d.A.); (M.J.T.R.)
| | - Annieck M. Diks
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (I.K.); (A.M.D.); (M.A.B.)
| | - Erik B. van den Akker
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (E.B.v.d.A.); (M.J.T.R.)
- Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Liesbeth E. M. Oosten
- Department of Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (L.E.M.O.); (J.J.Z.)
| | - Jaap Jan Zwaginga
- Department of Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (L.E.M.O.); (J.J.Z.)
| | - Marcel J. T. Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (E.B.v.d.A.); (M.J.T.R.)
- Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Jacques J. M. van Dongen
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (I.K.); (A.M.D.); (M.A.B.)
| | - Magdalena A. Berkowska
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (I.K.); (A.M.D.); (M.A.B.)
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25
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Wu ZX, Wang F, Li L, Yao Y, Long J, Luo QQ, Zhao ZB, Li WL, Cao J, Lian ZX. The Clinical Significance of Mesenteric Lymphocytes in Human Colorectal Cancer. Front Oncol 2021; 11:685577. [PMID: 34604029 PMCID: PMC8481834 DOI: 10.3389/fonc.2021.685577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/27/2021] [Indexed: 01/08/2023] Open
Abstract
Objective The mesentery is a potential site of residual tumor in patients with colorectal cancer (CRC). However, the mesenteric immune microenvironment remains unclear. In this study, we investigated the immune landscape of the mesentery, particularly the role of lymphocytes and its association with the clinicopathological characteristics of CRC. Methods Flow cytometry was used to detect lymphocytes in the paired mesenteric tissue specimens adjacent to the colorectal tumors and normal mesenteric tissue specimens 10 cm away from the colorectal tumor edge and preoperative peripheral blood samples obtained from patients with CRC who underwent surgery. T-distributed stochastic neighbor embedding was utilized to analyze multiparameter flow cytometry data. Multiplex immunohistochemistry was performed to evaluate T cells subsets in the paired mesentery adjacent to the colorectal tumors and normal mesentery. The Fisher’s exact test and non-parametric Wilcoxon’s matched-pairs tests were used for statistical analysis. The non-parametric Mann-Whitney U test was used to determine associations between percentage data and clinical parameters of patients with CRC. Results We found that immune cells in the normal mesentery were mainly of lymphoid lineage. Compared with peripheral blood, the normal mesentery showed decreased NK cells and the CD4/CD8 ratio and increased CD3+ CD56+, memory CD4+ T, memory CD8+ T, CD4+ tissue-resident memory T (TRM), and CD8+ TRM cells. Compared with the normal mesentery, the mesentery adjacent to the colorectal tumor showed increased B and regulatory T cells and decreased NK, CD3+ CD56+, CD4+ TRM, and CD8+ TRM cells. Moreover, memory CD8+ T cells and plasmablasts are negatively correlated with the depth of invasion of CRC. Increased memory CD4+ T cells are associated with distant metastasis of CRC and high preoperative serum carcinoembryonic antigen levels. Conclusion The mesentery shows a specific immune microenvironment, which differs from that observed in peripheral blood. CRC can alter the mesenteric immune response to promote tumor progression.
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Affiliation(s)
- Zi-Xin Wu
- Department of Colorectal Surgery, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Fei Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Liang Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yuan Yao
- Department of Colorectal Surgery, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China
| | - Jie Long
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qing-Qing Luo
- Department of Colorectal Surgery, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Zhi-Bin Zhao
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Wang-Lin Li
- Department of Colorectal Surgery, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Jie Cao
- Department of Colorectal Surgery, The Second Affiliated Hospital of South China University of Technology, Guangzhou, China
| | - Zhe-Xiong Lian
- School of Medicine, South China University of Technology, Guangzhou, China
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26
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Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol 2021; 40:463-481. [PMID: 34535228 DOI: 10.1016/j.tibtech.2021.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022]
Abstract
Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.
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27
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Perdiguero P, Morel E, Díaz-Rosales P, Tafalla C. Individual B cells transcribe multiple rearranged immunoglobulin light chains in teleost fish. iScience 2021; 24:102615. [PMID: 34142062 PMCID: PMC8188548 DOI: 10.1016/j.isci.2021.102615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/14/2021] [Accepted: 05/19/2021] [Indexed: 11/01/2022] Open
Abstract
B cells express a unique antibody protein which comprises two pairs of immunoglobulin (Ig) heavy (H) and light (L) chains. In addition to an invariable constant (C) region, IgH and IgL chains encompass a variable (V) region mediating antigen binding. This unique region stems from Ig V(D)J gene recombination, which generates diversity by assembling these gene segments into VHDJH and VLJL genes. To ensure that one B cell only expresses one antibody, VHDJH rearrangement occurs only in one IgH locus (allelic exclusion), whereas VLJL rearrangement only in either the κ or λ locus (isotype exclusion). However, teleosts express multiple IgLs encoded by distinct CL genes. Using single-cell transcriptomics, we have demonstrated the transcription of distinct rearranged VLJLCL genes in single rainbow trout B cells. Our results highlight the laxity of isotype exclusion in teleosts and strongly suggest that fish B cells can produce antibodies of different specificities.
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Affiliation(s)
- Pedro Perdiguero
- Animal Health Research Center (CISA-INIA), Valdeolmos, Madrid 28130, Spain
| | - Esther Morel
- Animal Health Research Center (CISA-INIA), Valdeolmos, Madrid 28130, Spain
| | | | - Carolina Tafalla
- Animal Health Research Center (CISA-INIA), Valdeolmos, Madrid 28130, Spain
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28
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Jin X, Zhou W, Luo M, Wang P, Xu Z, Ma K, Cao H, Xu C, Huang Y, Cheng R, Xiao L, Lin X, Pang F, Li Y, Nie H, Jiang Q. Global characterization of B cell receptor repertoire in COVID-19 patients by single-cell V(D)J sequencing. Brief Bioinform 2021; 22:6278607. [PMID: 34015809 PMCID: PMC8194558 DOI: 10.1093/bib/bbab192] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 04/14/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
The world is facing a pandemic of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Adaptive immune responses are essential for SARS-CoV-2 virus clearance. Although a large body of studies have been conducted to investigate the immune mechanism in COVID-19 patients, we still lack a comprehensive understanding of the BCR repertoire in patients. In this study, we used the single-cell V(D)J sequencing to characterize the BCR repertoire across convalescent COVID-19 patients. We observed that the BCR diversity was significantly reduced in disease compared with healthy controls. And BCRs tend to skew toward different V gene segments in COVID-19 and healthy controls. The CDR3 sequences of heavy chain in clonal BCRs in patients were more convergent than that in healthy controls. In addition, we discovered increased IgG and IgA isotypes in the disease, including IgG1, IgG3 and IgA1. In all clonal BCRs, IgG isotypes had the most frequent class switch recombination events and the highest somatic hypermutation rate, especially IgG3. Moreover, we found that an IgG3 cluster from different clonal groups had the same IGHV, IGHJ and CDR3 sequences (IGHV4-4-CARLANTNQFYDSSSYLNAMDVW-IGHJ6). Overall, our study provides a comprehensive characterization of the BCR repertoire in COVID-19 patients, which contributes to the understanding of the mechanism for the immune response to SARS-CoV-2 infection.
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Affiliation(s)
- Xiyun Jin
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Wenyang Zhou
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Meng Luo
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Pingping Wang
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Zhaochun Xu
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Kexin Ma
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Huimin Cao
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Chang Xu
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Yan Huang
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Rui Cheng
- Harbin Institute of Technology, China
| | - Lixing Xiao
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | | | | | - Yiqun Li
- Harbin Institute of Technology, China
| | - Huan Nie
- School of Life Science and Technology at the Harbin Institute of Technology, China
| | - Qinghua Jiang
- School of Life Science and Technology at the Harbin Institute of Technology, China
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Single-Cell Sequencing Confirms Transcripts and V HDJ H Rearrangements of Immunoglobulin Genes in Human Podocytes. Genes (Basel) 2021; 12:genes12040472. [PMID: 33806147 PMCID: PMC8064494 DOI: 10.3390/genes12040472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 11/17/2022] Open
Abstract
Most glomerular diseases are associated with inflammation caused by deposited pathogenic immunoglobulins (Igs), which are believed to be produced by B cells. However, our previous study indicated that the human podocyte cell line can produce IgG. In this study, we aimed to confirm the transcripts and characterize the repertoires of Igs in primary podocytes at single cell level. First, single-cell RNA sequencing of cell suspensions from “normal” kidney cortexes by a 10xGenomics Chromium system detected Ig transcripts in 7/360 podocytes and Ig gene segments in 106/360 podocytes. Then, we combined nested PCR with Sanger sequencing to detect the transcripts and characterize the repertoires of Igs in 48 single podocytes and found that five classes of Ig heavy chains were amplified in podocytes. Four-hundred and twenty-nine VHDJH rearrangement sequences were analyzed; podocyte-derived Igs exhibited classic VHDJH rearrangements with nucleotide additions and somatic hypermutations, biased VH1 usage and restricted diversity. Moreover, compared with the podocytes from healthy control that usually expressed one class of Ig and one VHDJH pattern, podocytes from patients expressed more classes of Ig, VHDJH patterns and somatic hypermutations. These findings suggested that podocytes can express Igs in normal condition and increase diversity in pathological situations.
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30
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Raybould MIJ, Marks C, Kovaltsuk A, Lewis AP, Shi J, Deane CM. Public Baseline and shared response structures support the theory of antibody repertoire functional commonality. PLoS Comput Biol 2021; 17:e1008781. [PMID: 33647011 PMCID: PMC7951972 DOI: 10.1371/journal.pcbi.1008781] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 03/11/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022] Open
Abstract
The naïve antibody/B-cell receptor (BCR) repertoires of different individuals ought to exhibit significant functional commonality, given that most pathogens trigger an effective antibody response to immunodominant epitopes. Sequence-based repertoire analysis has so far offered little evidence for this phenomenon. For example, a recent study estimated the number of shared ('public') antibody clonotypes in circulating baseline repertoires to be around 0.02% across ten unrelated individuals. However, to engage the same epitope, antibodies only require a similar binding site structure and the presence of key paratope interactions, which can occur even when their sequences are dissimilar. Here, we search for evidence of geometric similarity/convergence across human antibody repertoires. We first structurally profile naïve ('baseline') antibody diversity using snapshots from 41 unrelated individuals, predicting all modellable distinct structures within each repertoire. This analysis uncovers a high (much greater than random) degree of structural commonality. For instance, around 3% of distinct structures are common to the ten most diverse individual samples ('Public Baseline' structures). Our approach is the first computational method to find levels of BCR commonality commensurate with epitope immunodominance and could therefore be harnessed to find more genetically distant antibodies with same-epitope complementarity. We then apply the same structural profiling approach to repertoire snapshots from three individuals before and after flu vaccination, detecting a convergent structural drift indicative of recognising similar epitopes ('Public Response' structures). We show that Antibody Model Libraries derived from Public Baseline and Public Response structures represent a powerful geometric basis set of low-immunogenicity candidates exploitable for general or target-focused therapeutic antibody screening.
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Affiliation(s)
- Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Claire Marks
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Aleksandr Kovaltsuk
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Alan P. Lewis
- Data and Computational Sciences, GlaxoSmithKline Research and Development, Stevenage, United Kingdom
| | - Jiye Shi
- Chemistry Department, UCB Pharma, Slough, United Kingdom
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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31
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Reily C, Xu N, Crossman DK. Assigning immunoglobulin class from single-cell transcriptomes in IgA1-secreting versus membrane subpopulations. Biotechniques 2021; 70:89-99. [PMID: 33307788 PMCID: PMC7983040 DOI: 10.2144/btn-2020-0044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/29/2020] [Indexed: 01/30/2023] Open
Abstract
IgA nephropathy (IgAN) is an autoimmune disease characterized by renal glomerular immunodeposits enriched for galactose-deficient IgA1 (Gd-IgA1; autoantigen) with the corresponding IgG autoantibodies. Despite the known contribution of Gd-IgA1 to IgAN, little is known concerning IgA1-secreting subpopulations responsible for autoantigen production. The goal of this study is to identify IgA1-secreting and membrane subpopulations from single-cell transcriptomic analysis. We developed a novel single-cell analytics workflow to discern cells expressing IgA1 secreted isoform or membrane-bound isoform. Multiple approaches were compared to assess immunoglobulin-isotype identity in single cells, and multiple immunoglobulin heavy-chain genes expressed in the same cells were found. To better identify specific immunoglobulin heavy-chain transcripts, we merged a software platform called Alteryx with the existing single-cell R toolkit program Seurat. This process allowed for improved calls on IgA1-secreting subpopulations based on secreting versus membrane splice-variant expression levels.
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Affiliation(s)
- Colin Reily
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Nuo Xu
- Department of Management, Information Systems & Quantitative Methods, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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32
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Moraes JZ, Hamaguchi B, Braggion C, Speciale ER, Cesar FBV, Soares GDFDS, Osaki JH, Pereira TM, Aguiar RB. Hybridoma technology: is it still useful? CURRENT RESEARCH IN IMMUNOLOGY 2021; 2:32-40. [PMID: 35492397 PMCID: PMC9040095 DOI: 10.1016/j.crimmu.2021.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
The isolation of single monoclonal antibodies (mAbs) against a given antigen was only possible with the introduction of the hybridoma technology, which is based on the fusion of specific B lymphocytes with myeloma cells. Since then, several mAbs were described for therapeutic, diagnostic, and research purposes. Despite being an old technique with low complexity, hybridoma-based strategies have limitations that include the low efficiency on B lymphocyte-myeloma cell fusion step, and the need to use experimental animals. In face of that, several methods have been developed to improve mAb generation, ranging from changes in hybridoma technique to the advent of completely new technologies, such as the antibody phage display and the single B cell antibody ones. In this review, we discuss the hybridoma technology along with emerging mAb isolation approaches, taking into account their advantages and limitations. Finally, we explore the usefulness of the hybridoma technology nowadays. Hybridoma technology is the most popular technique to obtain monoclonal antibodies. Hybridoma technology variants include B cell and stereospecific targeting protocols. Phage display and single B cell methods are hybridoma technology alternatives.
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33
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Deng Z, Wang X, Liu Y, Tian X, Deng S, Sun Y, Wang S, Zheng D, Cui Z, Pan Y, A L, Yan H, Qiu X, Wang Y. Single-cell RNA sequencing confirms IgG transcription and limited diversity of V HDJ H rearrangements in proximal tubular epithelial cells. Sci Rep 2020; 10:19657. [PMID: 33184300 PMCID: PMC7661700 DOI: 10.1038/s41598-020-75013-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/29/2020] [Indexed: 01/19/2023] Open
Abstract
Increasing evidence has confirmed that immunoglobulins (Igs) can be expressed in non-B cells. Our previous work demonstrated that mesangial cells and podocytes express IgA and IgG, respectively. The aim of this work was to reveal whether proximal tubular epithelial cells (PTECs) express Igs. High-throughput single-cell RNA sequencing (scRNA-seq) detected Igs in a small number of PTECs, and then we combined nested PCR with Sanger sequencing to detect the transcripts and characterize the repertoires of Igs in PTECs. We sorted PTECs from the normal renal cortex of two patients with renal cancer by FACS and further confirmed their identify by LRP2 gene expression. Only the transcripts of the IgG heavy chain were successfully amplified in 91/111 single PTECs. We cloned and sequenced 469 VHDJH transcripts from 91 single PTECs and found that PTEC-derived IgG exhibited classic VHDJH rearrangements with nucleotide additions at the junctions and somatic hypermutations. Compared with B cell-derived IgG, PTEC-derived IgG displayed less diversity of VHDJH rearrangements, predominant VH1-24/DH2-15/JH4 sequences, biased VH1 usage, centralized VH gene segment location at the 3′ end of the genome and non-Gaussian distribution of the CDR3 length. These results demonstrate that PTECs can express a distinct IgG repertoire that may have implications for their role in the renal tubular epithelial-mesenchymal transition.
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Affiliation(s)
- Zhenling Deng
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Xinyao Wang
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Yue Liu
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Xinyu Tian
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Shaohui Deng
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Yingchun Sun
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Song Wang
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Danxia Zheng
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Zhuan Cui
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Yuejuan Pan
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Lata A
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China
| | - Huige Yan
- Department of Immunology, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, People's Republic of China
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, People's Republic of China.
| | - Yue Wang
- Department of Nephrology, Peking University Third Hospital, 49 Huayuanbei Road, Beijing, 100191, People's Republic of China.
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Sinkora M, Stepanova K, Sinkorova J. Immunoglobulin light chain κ precedes λ rearrangement in swine but a majority of λ + B cells are generated earlier. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 111:103751. [PMID: 32454063 DOI: 10.1016/j.dci.2020.103751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Developmental pathways for B cell lymphogenesis are sufficiently known only in mice and humans. However, both of these species rearrange immunoglobulin heavy chains (IgH) before light chains (IgL) while IgL precedes IgH rearrangement in swine. We demonstrate here that this reversed order of rearrangements have some concealed consequences: (1) we confirmed that although IgLκ rearrangement is initial, most IgLλ+ B cells are generated earlier and before IgH rearrangements, while most IgLκ+ B cells later and after IgH rearrangements, (2) the second IgLκ rearrangement can occur after IgLλ rearrangement, (3) early formed B cells bear only single in-frame IgH rearrangements, (4) many IgLκ+ B cells carry IgLλ rearrangements that can be productive and occurring on both alleles in one cell, and (5) although VpreB and λ5 genes are present in swine, they are preferentially expressed in non-B cells. In summary, our findings reveal that swine use an alternative B cell developmental pathway as compared to mice and humans.
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Affiliation(s)
- Marek Sinkora
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic.
| | - Katerina Stepanova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic
| | - Jana Sinkorova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic
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35
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Ma A, McDermaid A, Xu J, Chang Y, Ma Q. Integrative Methods and Practical Challenges for Single-Cell Multi-omics. Trends Biotechnol 2020; 38:1007-1022. [PMID: 32818441 PMCID: PMC7442857 DOI: 10.1016/j.tibtech.2020.02.013] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 12/19/2022]
Abstract
Fast-developing single-cell multimodal omics (scMulti-omics) technologies enable the measurement of multiple modalities, such as DNA methylation, chromatin accessibility, RNA expression, protein abundance, gene perturbation, and spatial information, from the same cell. scMulti-omics can comprehensively explore and identify cell characteristics, while also presenting challenges to the development of computational methods and tools for integrative analyses. Here, we review these integrative methods and summarize the existing tools for studying a variety of scMulti-omics data. The various functionalities and practical challenges in using the available tools in the public domain are explored through several case studies. Finally, we identify remaining challenges and future trends in scMulti-omics modeling and analyses.
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Affiliation(s)
- Anjun Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43235, USA
| | - Adam McDermaid
- Imagenetics, Sanford Health, Sioux Falls, SD 57104, USA; Department of Internal Medicine, University of South Dakota, Virmillion, SD 57069, USA
| | - Jennifer Xu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43235, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yuzhou Chang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43235, USA
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43235, USA.
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