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Abstract
Antibodies are considered the hallmark of the adaptive immune system in that they mediate various key biological functions, such as direct neutralization and recruitment of effector immune cells to eliminate invading pathogens. Antibodies exhibit several unique properties, including high diversity (enabling binding to a wide range of targets), high specificity and structural integrity. These properties and the understanding that antibodies can be utilized in a wide range of applications have motivated the scientific community to develop new approaches for antibody repertoire analysis and rapid monoclonal antibody discovery. Today, antibodies are key modules in the pharmaceutical and diagnostic industries. By virtue of their high affinity and specificity to their targets and the availability of technologies to engineer different antibodies to a wide range of targets, antibodies have become the most promising natural biological molecules in a range of biotechnological applications, such as: highly specific and sensitive nanobiosensors for the diagnostics of different biomarkers; nanoparticle-based targeted drug delivery systems to certain cells or tissues; and nanomachines, which are nanoscale mechanical devices that enable energy conversion into precise mechanical motions in response to specific molecular inputs. In this review, we start by describing the unique properties of antibodies, how antibody diversity is generated, and the available technologies for antibody repertoire analysis and antibody discovery. Thereafter, we provide an overview of some antibody-based nanotechnologies and discuss novel and promising approaches for the application of antibodies in the nanotechnology field. Overall, we aim to bridge the knowledge gap between the nanotechnology and antibody engineering disciplines by demonstrating how technological advances in the antibody field can be leveraged to develop and/or enhance new technological approaches in the nanotechnology field.
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Affiliation(s)
- Yaron Hillman
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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52
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Efficient T cell-B cell collaboration guides autoantibody epitope bias and onset of celiac disease. Proc Natl Acad Sci U S A 2019; 116:15134-15139. [PMID: 31285344 DOI: 10.1073/pnas.1901561116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
B cells play important roles in autoimmune diseases through autoantibody production, cytokine secretion, or antigen presentation to T cells. In most cases, the contribution of B cells as antigen-presenting cells is not well understood. We have studied the autoantibody response against the enzyme transglutaminase 2 (TG2) in celiac disease patients by generating recombinant antibodies from single gut plasma cells reactive with discrete antigen domains and by undertaking proteomic analysis of anti-TG2 serum antibodies. The majority of the cells recognized epitopes in the N-terminal domain of TG2. Antibodies recognizing C-terminal epitopes interfered with TG2 cross-linking activity, and B cells specific for C-terminal epitopes were inefficient at taking up TG2-gluten complexes for presentation to gluten-specific T cells. The bias toward N-terminal epitopes hence reflects efficient T-B collaboration. Production of antibodies against N-terminal epitopes coincided with clinical onset of disease, suggesting that TG2-reactive B cells with certain epitope specificities could be the main antigen-presenting cells for pathogenic, gluten-specific T cells. The link between B cell epitopes, antigen presentation, and disease onset provides insight into the pathogenic mechanisms of a T cell-mediated autoimmune condition.
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53
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MZB1 promotes the secretion of J-chain-containing dimeric IgA and is critical for the suppression of gut inflammation. Proc Natl Acad Sci U S A 2019; 116:13480-13489. [PMID: 31127044 DOI: 10.1073/pnas.1904204116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
IgA is the most abundantly produced antibody in the body and plays a crucial role in gut homeostasis and mucosal immunity. IgA forms a dimer that covalently associates with the joining (J) chain, which is essential for IgA transport into the mucosa. Here, we demonstrate that the marginal zone B and B-1 cell-specific protein (MZB1) interacts with IgA through the α-heavy-chain tailpiece dependent on the penultimate cysteine residue and prevents the intracellular degradation of α-light-chain complexes. Moreover, MZB1 promotes J-chain binding to IgA and the secretion of dimeric IgA. MZB1-deficient mice are impaired in secreting large amounts of IgA into the gut in response to acute inflammation and develop severe colitis. Oral administration of a monoclonal IgA significantly ameliorated the colitis, accompanied by normalization of the gut microbiota composition. The present study identifies a molecular chaperone that promotes J-chain binding to IgA and reveals an important mechanism that controls the quantity, quality, and function of IgA.
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54
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IgA Responses to Microbiota. Immunity 2019; 49:211-224. [PMID: 30134201 DOI: 10.1016/j.immuni.2018.08.011] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/03/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
Various immune mechanisms are deployed in the mucosa to confront the immense diversity of resident bacteria. A substantial fraction of the commensal microbiota is coated with immunoglobulin A (IgA) antibodies, and recent findings have established the identities of these bacteria under homeostatic and disease conditions. Here we review the current understanding of IgA biology, and present a framework wherein two distinct types of humoral immunity coexist in the gastrointestinal mucosa. Homeostatic IgA responses employ a polyreactive repertoire to bind a broad but taxonomically distinct subset of microbiota. In contrast, mucosal pathogens and vaccines elicit high-affinity, T cell-dependent antibody responses. This model raises fundamental questions including how polyreactive IgA specificities are generated, how these antibodies exert effector functions, and how they exist together with other immune responses during homeostasis and disease.
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55
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Breedveld A, van Egmond M. IgA and FcαRI: Pathological Roles and Therapeutic Opportunities. Front Immunol 2019; 10:553. [PMID: 30984170 PMCID: PMC6448004 DOI: 10.3389/fimmu.2019.00553] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/01/2019] [Indexed: 12/12/2022] Open
Abstract
Immunoglobulin A (IgA) is the most abundant antibody class present at mucosal surfaces. The production of IgA exceeds the production of all other antibodies combined, supporting its prominent role in host-pathogen defense. IgA closely interacts with the intestinal microbiota to enhance its diversity, and IgA has a passive protective role via immune exclusion. Additionally, inhibitory ITAMi signaling via the IgA Fc receptor (FcαRI; CD89) by monomeric IgA may play a role in maintaining homeostatic conditions. By contrast, IgA immune complexes (e.g., opsonized pathogens) potently activate immune cells via cross-linking FcαRI, thereby inducing pro-inflammatory responses resulting in elimination of pathogens. The importance of IgA in removal of pathogens is emphasized by the fact that several pathogens developed mechanisms to break down IgA or evade FcαRI-mediated activation of immune cells. Augmented or aberrant presence of IgA immune complexes can result in excessive neutrophil activation, potentially leading to severe tissue damage in multiple inflammatory, or autoimmune diseases. Influencing IgA or FcαRI-mediated functions therefore provides several therapeutic possibilities. On the one hand (passive) IgA vaccination strategies can be developed for protection against infections. Furthermore, IgA monoclonal antibodies that are directed against tumor antigens may be effective as cancer treatment. On the other hand, induction of ITAMi signaling via FcαRI may reduce allergy or inflammation, whereas blocking FcαRI with monoclonal antibodies, or peptides may resolve IgA-induced tissue damage. In this review both (patho)physiological roles as well as therapeutic possibilities of the IgA-FcαRI axis are addressed.
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Affiliation(s)
- Annelot Breedveld
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam, Netherlands
| | - Marjolein van Egmond
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam, Netherlands
- Department of Surgery, Amsterdam UMC, Amsterdam, Netherlands
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56
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Abstract
Coeliac disease is an immune-mediated enteropathy against dietary gluten present in wheat, rye and barley and is one of the most common lifelong food-related disorders worldwide. Coeliac disease is also considered to be a systemic disorder characterized by a variable combination of gluten-related signs and symptoms and disease-specific antibodies in addition to enteropathy. The ingestion of gluten leads to the generation of harmful gluten peptides, which, in predisposed individuals, can induce adaptive and innate immune responses. The clinical presentation is extremely variable; patients may have severe gastrointestinal symptoms and malabsorption, extraintestinal symptoms or have no symptoms at all. Owing to the multifaceted clinical presentation, diagnosis remains a challenge and coeliac disease is heavily underdiagnosed. The diagnosis of coeliac disease is achieved by combining coeliac disease serology and small intestinal mucosal histology during a gluten-containing diet. Currently, the only effective treatment for coeliac disease is a lifelong strict gluten-free diet; however, the diet is restrictive and gluten is difficult to avoid. Optimizing diagnosis and care in coeliac disease requires continuous research and education of both patients and health-care professionals.
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57
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Corthésy B, Monnerat J, Lötscher M, Vonarburg C, Schaub A, Bioley G. Oral Passive Immunization With Plasma-Derived Polyreactive Secretory-Like IgA/M Partially Protects Mice Against Experimental Salmonellosis. Front Immunol 2018; 9:2970. [PMID: 30619327 PMCID: PMC6305475 DOI: 10.3389/fimmu.2018.02970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/03/2018] [Indexed: 01/29/2023] Open
Abstract
Secretory immunoglobulins have a critical role in defense of the gastrointestinal tract and are known to act by preventing bacterial acquisition. A stringent murine model of bacterial infection with Salmonella enterica Typhimurium was used to examine protection mediated by oral passive immunization with human plasma-derived polyreactive IgA and IgM antibodies (Abs) reconstituted as secretory-like immunoglobulins (SCIgA/M). This reagent has been shown to trigger Salmonella agglutination and to limit the entry of bacterium into intestinal Peyer's patches via immune exclusion. We now demonstrate that upon administration into ligated intestinal loops, SCIgA/M properly anchors in the mucus and is protected from degradation to a better extent that IgA/M or IgG. Moreover, prophylactic oral administration of SCIgA/M before intragastric infection of mice with a virulent strain of S. enterica Typhimurium allows to protect infected animals, as reflected by reduced colonization of both mucosal and systemic compartments, and conserved integrity of intestinal tissues. In comparison with IgA/M or IgG administration, SCIgA/M provided the highest degree of protection. Moreover, such protective efficacy is also observed after therapeutic oral delivery of SCIgA/M. Either prophylactic or therapeutic treatment with passively delivered SCIgA/M ensured survival of up to 50% of infected mice, while untreated animals all died. Our findings unravel the potential of oral passive immunization with plasma-derived polyreactive SCIgA/M Abs to fight gastrointestinal infections.
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Affiliation(s)
- Blaise Corthésy
- R&D Laboratory, Division of Immunology and Allergy, Lausanne University Hospital (CHUV), Épalinges, Switzerland
| | - Justine Monnerat
- R&D Laboratory, Division of Immunology and Allergy, Lausanne University Hospital (CHUV), Épalinges, Switzerland
| | | | | | | | - Gilles Bioley
- R&D Laboratory, Division of Immunology and Allergy, Lausanne University Hospital (CHUV), Épalinges, Switzerland
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58
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Fadlallah J, Sterlin D, Fieschi C, Parizot C, Dorgham K, El Kafsi H, Autaa G, Ghillani-Dalbin P, Juste C, Lepage P, Malphettes M, Galicier L, Boutboul D, Clément K, André S, Marquet F, Tresallet C, Mathian A, Miyara M, Oksenhendler E, Amoura Z, Yssel H, Larsen M, Gorochov G. Synergistic convergence of microbiota-specific systemic IgG and secretory IgA. J Allergy Clin Immunol 2018; 143:1575-1585.e4. [PMID: 30554723 DOI: 10.1016/j.jaci.2018.09.036] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 08/24/2018] [Accepted: 09/04/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Commensals induce local IgA responses essential to the induction of tolerance to gut microbiota, but it remains unclear whether antimicrobiota responses remain confined to the gut. OBJECTIVE The aim of this study was to investigate systemic and intestinal responses against the whole microbiota under homeostatic conditions and in the absence of IgA. METHODS We analyzed blood and feces from healthy donors, patients with selective IgA deficiency (SIgAd), and patients with common variable immunodeficiency (CVID). Immunoglobulin-coated bacterial repertoires were analyzed by using combined bacterial fluorescence-activated cell sorting and 16S rRNA sequencing. Bacterial lysates were probed by using Western blot analysis with healthy donor sera. RESULTS Although absent from the healthy gut, serum antimicrobiota IgG are present in healthy subjects and increased in patients with SIgAd. IgG converges with nonoverlapping secretory IgA specificities to target the same bacteria. Each individual subject targets a diverse microbiota repertoire with a proportion that correlates inversely with systemic inflammation. Finally, intravenous immunoglobulin preparations target CVID gut microbiota much less efficiently than healthy microbiota. CONCLUSION Secretory IgA and systemic IgG converge to target gut microbiota at the cellular level. SIgAd-associated inflammation is inversely correlated with systemic anticommensal IgG responses, which might serve as a second line of defense. We speculate that patients with SIgAd could benefit from oral IgA supplementation. Our data also suggest that intravenous immunoglobulin preparations can be supplemented with IgG from IgA-deficient patient pools to offer better protection against gut bacterial translocations in patients with CVID.
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Affiliation(s)
- Jehane Fadlallah
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France; Université Paris Diderot Paris 7, Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Delphine Sterlin
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Claire Fieschi
- Université Paris Diderot Paris 7, Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Christophe Parizot
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Karim Dorgham
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Hela El Kafsi
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Gaëlle Autaa
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Pascale Ghillani-Dalbin
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Catherine Juste
- Micalis Institute, INRA, AgroParisTech, Universite Paris-Saclay, 78350 Jouy-en-Josas, Paris, France
| | - Patricia Lepage
- Micalis Institute, INRA, AgroParisTech, Universite Paris-Saclay, 78350 Jouy-en-Josas, Paris, France
| | - Marion Malphettes
- Université Paris Diderot Paris 7, Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Lionel Galicier
- Université Paris Diderot Paris 7, Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - David Boutboul
- Université Paris Diderot Paris 7, Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Karine Clément
- Sorbonne Universite, INSERM, UMRS1166, NutriOmics team, ICAN, Paris, France; Assistance Publique Hôpitaux de Paris, Nutrition department, Pitié-Salpêtrière Hospital, Paris, France
| | - Sébastien André
- Sorbonne Universite, INSERM, UMRS1166, NutriOmics team, ICAN, Paris, France
| | - Florian Marquet
- Sorbonne Universite, INSERM, UMRS1166, NutriOmics team, ICAN, Paris, France
| | - Christophe Tresallet
- Department of Surgery, Assistance Publique Hôpitaux de Paris, Pitiè-Salpêtrière Hospital, Paris, France
| | - Alexis Mathian
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Makoto Miyara
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Eric Oksenhendler
- Université Paris Diderot Paris 7, Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Zahir Amoura
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Hans Yssel
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Martin Larsen
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France.
| | - Guy Gorochov
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Assistance Publique-Hôpitaux de Paris (AP-HP), Groupement Hospitalier Pitié-Salpêtrière, Département d'Immunologie, Paris, France.
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59
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Hietikko M, Koskinen O, Kurppa K, Laurila K, Saavalainen P, Salmi T, Ilus T, Huhtala H, Kaukinen K, Lindfors K. Small-intestinal TG2-specific plasma cells at different stages of coeliac disease. BMC Immunol 2018; 19:36. [PMID: 30522434 PMCID: PMC6282384 DOI: 10.1186/s12865-018-0275-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/27/2018] [Indexed: 11/30/2022] Open
Abstract
Background In coeliac disease, ingestion of gluten induces the production of transglutaminase 2 (TG2)-targeted autoantibodies by TG2-specific plasma cells present at high frequency in the small intestinal mucosa in untreated disease. During treatment with a gluten-free diet (GFD), the number of these cells decreases considerably. It has not been previously investigated whether the cells are also present prior to development of villous atrophy, or in non-responsive patients and those with dietary lapses. We aimed to define the frequency of small bowel mucosal TG2-specific plasma cells in coeliac disease patients with varying disease activity, and to investigate whether the frequency correlates with serum and small intestinal TG2-targeting antibodies as well as mucosal morphology and the number of intraepithelial lymphocytes. Results Mucosal TG2-specific plasma cells were found in 79% of patients prior to development of mucosal damage, in all patients with villous atrophy, and in 63% of the patients after 1 year on GFD. In these disease stages, TG2-specific plasma cells accounted for median of 2.3, 4.3, and 0.7% of all mucosal plasma cells, respectively. After long-term treatment, the cells were present in 20% of the patients in clinical remission (median 0%) and in 60% of the patients with poor dietary adherence (median 5.8%). In patients with non-responsive coeliac disease despite strict GFD, the cells were found in only one (9%) subject; the cells accounted for 2.4% of all plasma cells. A positive correlation between the percentage of TG2-specific plasma cells and serum TG2 antibody levels (rS = 0.69, P < 0.001) and the intensity of mucosal TG2-targeting IgA deposits (rS = 0.43, P < 0.001) was observed. Conclusions Our results show that TG2-specific plasma cells are already detectable prior to villous atrophy, and that generally their frequency increases during overt disease. By contrast, on GFD, the percentage of these cells decreases. Overall, the presence of TG2-specific plasma cells in the small bowel mucosa mirrors the presence of gluten in the diet, but the frequency is not always parallel to the level of serum or intestinal TG2 antibodies. These findings increase the knowledge about the development of the TG2 plasma cell responses especially in the early phases of coeliac disease. Electronic supplementary material The online version of this article (10.1186/s12865-018-0275-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Minna Hietikko
- Celiac Disease Research Center, Faculty of Medicine and Life Sciences, University of Tampere, P.O. Box 100, 33014, Tampere, Finland
| | - Outi Koskinen
- Celiac Disease Research Center, Faculty of Medicine and Life Sciences, University of Tampere, P.O. Box 100, 33014, Tampere, Finland
| | - Kalle Kurppa
- Tampere Center for Child Health Research, University of Tampere, Tampere, Finland.,Department of Paediatrics, Tampere University Hospital, Tampere, Finland
| | - Kaija Laurila
- Celiac Disease Research Center, Faculty of Medicine and Life Sciences, University of Tampere, P.O. Box 100, 33014, Tampere, Finland
| | - Päivi Saavalainen
- Department of Medical and Clinical Genetics and the Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Teea Salmi
- Celiac Disease Research Center, Faculty of Medicine and Life Sciences, University of Tampere, P.O. Box 100, 33014, Tampere, Finland.,Department of Dermatology, Tampere University Hospital, Tampere, Finland
| | - Tuire Ilus
- Celiac Disease Research Center, Faculty of Medicine and Life Sciences, University of Tampere, P.O. Box 100, 33014, Tampere, Finland.,Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Heini Huhtala
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
| | - Katri Kaukinen
- Celiac Disease Research Center, Faculty of Medicine and Life Sciences, University of Tampere, P.O. Box 100, 33014, Tampere, Finland.,Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
| | - Katri Lindfors
- Celiac Disease Research Center, Faculty of Medicine and Life Sciences, University of Tampere, P.O. Box 100, 33014, Tampere, Finland.
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60
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Neu KE, Guthmiller JJ, Huang M, La J, Vieira MC, Kim K, Zheng NY, Cortese M, Tepora ME, Hamel NJ, Rojas KT, Henry C, Shaw D, Dulberger CL, Pulendran B, Cobey S, Khan AA, Wilson PC. Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination. J Clin Invest 2018; 129:93-105. [PMID: 30457979 DOI: 10.1172/jci121341] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
Vaccines are among the most effective public health tools for combating certain infectious diseases such as influenza. The role of the humoral immune system in vaccine-induced protection is widely appreciated; however, our understanding of how antibody specificities relate to B cell function remains limited due to the complexity of polyclonal antibody responses. To address this, we developed the Spec-seq framework, which allows for simultaneous monoclonal antibody (mAb) characterization and transcriptional profiling from the same single cell. Here, we present the first application of the Spec-seq framework, which we applied to human plasmablasts after influenza vaccination in order to characterize transcriptional differences governed by B cell receptor (BCR) isotype and vaccine reactivity. Our analysis did not find evidence of long-term transcriptional specialization between plasmablasts of different isotypes. However, we did find enhanced transcriptional similarity between clonally related B cells, as well as distinct transcriptional signatures ascribed by BCR vaccine recognition. These data suggest IgG and IgA vaccine-positive plasmablasts are largely similar, whereas IgA vaccine-negative cells appear to be transcriptionally distinct from conventional, terminally differentiated, antigen-induced peripheral blood plasmablasts.
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Affiliation(s)
- Karlynn E Neu
- The Committee on Immunology.,The Department of Medicine, Section of Rheumatology
| | | | - Min Huang
- The Department of Medicine, Section of Rheumatology
| | - Jennifer La
- The Department of Pathology, Molecular Pathogenesis and Molecular Medicine, and
| | - Marcos C Vieira
- The Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Kangchon Kim
- The Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | | | - Mario Cortese
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | | | | | | | - Carole Henry
- The Department of Medicine, Section of Rheumatology
| | - Dustin Shaw
- The Committee on Immunology.,The Department of Medicine, Section of Rheumatology
| | - Charles L Dulberger
- The Department of Biochemistry and Molecular Biophysics, The University of Chicago, Chicago, Illinois, USA
| | - Bali Pulendran
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Sarah Cobey
- The Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Aly A Khan
- Toyota Technological Institute at Chicago, Chicago, Illinois, USA
| | - Patrick C Wilson
- The Committee on Immunology.,The Department of Medicine, Section of Rheumatology
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61
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Tellier J, Nutt SL. Plasma cells: The programming of an antibody‐secreting machine. Eur J Immunol 2018; 49:30-37. [DOI: 10.1002/eji.201847517] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/28/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Julie Tellier
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology University of Melbourne Parkville Victoria Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology University of Melbourne Parkville Victoria Australia
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62
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Wang JJ, Colella AD, Beroukas D, Chataway TK, Gordon TP. Precipitating anti-dsDNA peptide repertoires in lupus. Clin Exp Immunol 2018; 194:273-282. [PMID: 30086185 DOI: 10.1111/cei.13197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/15/2022] Open
Abstract
Anti-double-stranded (ds)DNA autoantibodies are prototypical serological markers of systemic lupus erythematosus (SLE), but little is known about their immunoglobulin variable (IgV) region composition at the level of the secreted (serum) proteome. Here, we use a novel proteomic workflow based on de novo mass spectrometric sequencing of anti-dsDNA precipitins to analyse IgV subfamily expression and mutational signatures of high-affinity, precipitating anti-dsDNA responses. Serum anti-dsDNA proteomes were oligoclonal with shared (public) expression of immunoglobulin (Ig)G heavy chain variable region (IGHV) and kappa chain variable region (IGKV) subfamilies. IgV peptide maps from eight subjects showed extensive public and random (private) amino acid replacement mutations with prominent arginine substitutions across heavy (H)- and light (L)-chains. Shared sets of L-chain complementarity determining region 3 (CDR3) peptides specified by arginine substitutions were sequenced from the dominantly expressed IGKV3-20 subfamily, with changes in expression levels of a clonal L-chain CDR3 peptide by quantitative multiple reaction monitoring (MRM) paralleling the rise and fall of anti-dsDNA levels by Farr radioimmunoassays (RIA). The heavily mutated IgV peptide signatures of precipitating anti-dsDNA autoantibody proteomes reflect the strong selective forces that shape humoral anti-dsDNA responses in germinal centres. Direct sequencing of agarose gel precipitins using microlitre volumes of stored sera streamlines the antibody sequencing workflow and is generalizable to other precipitating serum antibodies.
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Affiliation(s)
- J J Wang
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, SA, Australia
| | - A D Colella
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, SA, Australia
| | - D Beroukas
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, SA, Australia
| | - T K Chataway
- Flinders Proteomics Facility, Flinders University, Bedford Park, SA, Australia
| | - T P Gordon
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, SA, Australia
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63
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Avram O, Vaisman-Mentesh A, Yehezkel D, Ashkenazy H, Pupko T, Wine Y. ASAP - A Webserver for Immunoglobulin-Sequencing Analysis Pipeline. Front Immunol 2018; 9:1686. [PMID: 30105017 PMCID: PMC6077260 DOI: 10.3389/fimmu.2018.01686] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022] Open
Abstract
Reproducible and robust data on antibody repertoires are invaluable for basic and applied immunology. Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology, providing quantitative molecular information on antibody polyclonal composition. However, major computational challenges exist when analyzing antibody sequences, from error handling to hypermutation profiles and clonal expansion analyses. In this work, we developed the ASAP (A webserver for Immunoglobulin-Seq Analysis Pipeline) webserver (https://asap.tau.ac.il). The input to ASAP is a paired-end sequence dataset from one or more replicates, with or without unique molecular identifiers. These datasets can be derived from NGS of human or murine antibody variable regions. ASAP first filters and annotates the sequence reads using public or user-provided germline sequence information. The ASAP webserver next performs various calculations, including somatic hypermutation level, CDR3 lengths, V(D)J family assignments, and V(D)J combination distribution. These analyses are repeated for each replicate. ASAP provides additional information by analyzing the commonalities and differences between the repeats (“joint” analysis). For example, ASAP examines the shared variable regions and their frequency in each replicate to determine which sequences are less likely to be a result of a sample preparation derived and/or sequencing errors. Moreover, ASAP clusters the data to clones and reports the identity and prevalence of top ranking clones (clonal expansion analysis). ASAP further provides the distribution of synonymous and non-synonymous mutations within the V genes somatic hypermutations. Finally, ASAP provides means to process the data for proteomic analysis of serum/secreted antibodies by generating a variable region database for liquid chromatography high resolution tandem mass spectrometry (LC-MS/MS) interpretation. ASAP is user-friendly, free, and open to all users, with no login requirement. ASAP is applicable for researchers interested in basic questions related to B cell development and differentiation, as well as applied researchers who are interested in vaccine development and monoclonal antibody engineering. By virtue of its user-friendliness, ASAP opens the antibody analysis field to non-expert users who seek to boost their research with immune repertoire analysis.
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Affiliation(s)
- Oren Avram
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Anna Vaisman-Mentesh
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Dror Yehezkel
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Haim Ashkenazy
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Tal Pupko
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Yariv Wine
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
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64
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Tutturen AEV, Dørum S, Clancy T, Reims HM, Christophersen A, Lundin KEA, Sollid LM, de Souza GA, Stamnaes J. Characterization of the Small Intestinal Lesion in Celiac Disease by Label-Free Quantitative Mass Spectrometry. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:1563-1579. [PMID: 29684362 DOI: 10.1016/j.ajpath.2018.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 12/16/2022]
Abstract
Global characterization of tissue proteomes from small amounts of biopsy material has become feasible because of advances in mass spectrometry and bioinformatics tools. In celiac disease (CD), dietary gluten induces an immune response that is accompanied by pronounced remodeling of the small intestine. Removal of gluten from the diet abrogates the immune response, and the tissue architecture normalizes. In this study, differences in global protein expression of small intestinal biopsy specimens from CD patients were quantified by analyzing formalin-fixed, paraffin-embedded material using liquid chromatography-mass spectrometry and label-free protein quantitation. Protein expression was compared in biopsy specimens collected from the same patients before and after 1-year treatment with gluten-free diet (n = 10) or before and after 3-day gluten provocation (n = 4). Differential expression of proteins in particular from mature enterocytes, neutrophils, and plasma cells could distinguish untreated from treated CD mucosa, and Ig variable region IGHV5-51 expression was found to serve as a CD-specific marker of ongoing immune activation. In patients who had undergone gluten challenge, coordinated up-regulation of wound response proteins, including the CD autoantigen transglutaminase 2, was observed. Our study provides a global and unbiased assessment of antigen-driven changes in protein expression in the celiac intestinal mucosa.
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Affiliation(s)
- Astrid E V Tutturen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway; Proteomics Core Facility, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Siri Dørum
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Trevor Clancy
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Henrik M Reims
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - Knut E A Lundin
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway; Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway; KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Gustavo A de Souza
- Proteomics Core Facility, Oslo University Hospital-Rikshospitalet, Oslo, Norway; The Brain Institute, Universidade Federal do Rio Grande do Norte, Natal-RN, Brazil
| | - Jorunn Stamnaes
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.
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65
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Miho E, Yermanos A, Weber CR, Berger CT, Reddy ST, Greiff V. Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires. Front Immunol 2018; 9:224. [PMID: 29515569 PMCID: PMC5826328 DOI: 10.3389/fimmu.2018.00224] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/26/2018] [Indexed: 12/21/2022] Open
Abstract
The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity and to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic, and (iv) machine learning methods applied to dissect, quantify, and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology toward coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.
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Affiliation(s)
- Enkelejda Miho
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- aiNET GmbH, ETH Zürich, Basel, Switzerland
| | - Alexander Yermanos
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Cédric R. Weber
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christoph T. Berger
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
- Department of Internal Medicine, Clinical Immunology, University Hospital Basel, Basel, Switzerland
| | - Sai T. Reddy
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Department of Immunology, University of Oslo, Oslo, Norway
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