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Caproni E, Corbellari R, Tomasi M, Isaac SJ, Tamburini S, Zanella I, Grigolato M, Gagliardi A, Benedet M, Baraldi C, Croia L, Di Lascio G, Berti A, Valensin S, Bellini E, Parri M, Grandi A, Grandi G. Anti-Tumor Efficacy of In Situ Vaccination Using Bacterial Outer Membrane Vesicles. Cancers (Basel) 2023; 15:3328. [PMID: 37444437 DOI: 10.3390/cancers15133328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
In situ vaccination (ISV) is a promising cancer immunotherapy strategy that consists of the intratumoral administration of immunostimulatory molecules (adjuvants). The rationale is that tumor antigens are abundant at the tumor site, and therefore, to elicit an effective anti-tumor immune response, all that is needed is an adjuvant, which can turn the immunosuppressive environment into an immunologically active one. Bacterial outer membrane vesicles (OMVs) are potent adjuvants since they contain several microbe-associated molecular patterns (MAMPs) naturally present in the outer membrane and in the periplasmic space of Gram-negative bacteria. Therefore, they appear particularly indicted for ISV. In this work, we first show that the OMVs from E. coli BL21(DE3)Δ60 strain promote a strong anti-tumor activity when intratumorally injected into the tumors of three different mouse models. Tumor inhibition correlates with a rapid infiltration of DCs and NK cells. We also show that the addition of neo-epitopes to OMVs synergizes with the vesicle adjuvanticity, as judged by a two-tumor mouse model. Overall, our data support the use of the OMVs in ISV and indicate that ISV efficacy can benefit from the addition of properly selected tumor-specific neo-antigens.
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Affiliation(s)
- Elena Caproni
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy
| | - Riccardo Corbellari
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Michele Tomasi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Samine J Isaac
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Silvia Tamburini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Ilaria Zanella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Martina Grigolato
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Assunta Gagliardi
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy
| | - Mattia Benedet
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy
| | - Chiara Baraldi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Lorenzo Croia
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | | | - Alvise Berti
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Silvia Valensin
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy
| | - Erika Bellini
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy
| | - Matteo Parri
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Alberto Grandi
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy
- BiOMViS Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Guido Grandi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
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Abstract
Autoimmune type 1 diabetes (T1D) results from the intricate crosstalk of various immune cell types. CD8+ T cells dominate the pro-inflammatory milieu of islet infiltration (insulitis), and are considered as key effectors of beta-cell destruction, through the recognition of MHC Class I-peptide complexes. The pathways generating MHC Class I-restricted antigens in beta cells are poorly documented. Given their specialized insulin secretory function, the associated granule processing and degradation pathways, basal endoplasmic reticulum stress and susceptibility to additional stressors, alternative antigen processing and presentation (APP) pathways are likely to play a significant role in the generation of the beta-cell immunopeptidome. As direct evidence is missing, we here intersect the specificities of beta-cell function and the literature about APP in other cellular models to generate some hypotheses on APPs relevant to beta cells. We further elaborate on the potential role of these pathways in T1D pathogenesis, based on the current knowledge of antigens presented by beta cells. A better understanding of these pathways may pinpoint novel mechanisms amenable to therapeutic targeting to modulate the immunogenicity of beta cells.
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Affiliation(s)
- Alexia Carré
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
| | - Roberto Mallone
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France.,Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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3
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Abstract
PURPOSE OF REVIEW The current review covers recent advances in our knowledge of the newest autoantigen neo-epitopes in type 1 diabetes (T1D): hybrid insulin peptides or HIPs. These ligands for autoreactive T cells are formed by peptide fusion, a novel posttranslational modification process that we first reported in 2016. RECENT FINDINGS Two major HIPs in the nonobese diabetic mouse model, ligands for diabetogenic CD4 T-cell clones, have been incorporated into tetramers and used to track HIP-reactive T cells during progression of disease. HIPs have also been used in strategies for induction of antigen-specific tolerance and show promise for delaying or reversing disease in the nonobese diabetic mouse. Importantly, CD4 T cells reactive to various HIPs have been detected in the islets and peripheral blood mononuclear cell of T1D patients and newly developed human T-cell clones are being employed to gather more data on the phenotype and function of HIP-reactive T cells in patients. SUMMARY These new hybrid insulin peptide epitopes may provide the basis for establishing autoreactive T cells as biomarkers of disease and as potential tolerogens for treatment of T1D.
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Boichard A, Pham TV, Yeerna H, Goodman A, Tamayo P, Lippman S, Frampton GM, Tsigelny IF, Kurzrock R. APOBEC-related mutagenesis and neo-peptide hydrophobicity: implications for response to immunotherapy. Oncoimmunology 2018; 8:1550341. [PMID: 30723579 PMCID: PMC6350681 DOI: 10.1080/2162402x.2018.1550341] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/11/2018] [Accepted: 11/10/2018] [Indexed: 01/07/2023] Open
Abstract
Tumor-associated neo-antigens are mutated peptides that allow the immune system to recognize the affected cell as foreign. Cells carrying excessive mutation load often develop mechanisms of tolerance. PD-L1/PD-1 checkpoint immunotherapy is a highly promising approach to overcome these protective signals and induce tumor shrinkage. Yet, the nature of the neo-antigens driving those beneficial responses remains unclear. Here, we show that APOBEC-related mutagenesis - a mechanism at the crossroads between anti-viral immunity and endogenous nucleic acid editing - increases neo-peptide hydrophobicity (a feature of immunogenicity), as demonstrated by in silico computation and in the TCGA pan-cancer cohort, where APOBEC-related mutagenesis was also strongly associated with immune marker expression. Moreover, APOBEC-related mutagenesis correlated with immunotherapy response in a cohort of 99 patients with diverse cancers, and this correlation was independent of the tumor mutation burden (TMB). Combining APOBEC-related mutagenesis estimate and TMB resulted in greater predictive ability than either parameter alone. Based on these results, further investigation of APOBEC-related mutagenesis as a marker of response to anti-cancer checkpoint blockade is warranted.
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Affiliation(s)
- Amélie Boichard
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA
| | | | - Huwate Yeerna
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA
| | - Aaron Goodman
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA.,Division of Blood and Marrow Transplantation, University of California, Moores Cancer Center, La Jolla, CA, USA
| | - Pablo Tamayo
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA.,Division of Medical Genetics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Scott Lippman
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA
| | | | - Igor F Tsigelny
- CureMatch Inc., San Diego, CA, USA.,San Diego Supercomputer Center and Neuroscience Department, University of California San Diego, La Jolla, CA, USA
| | - Razelle Kurzrock
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA
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Li X, Cai Y. Methylation-Based Classification of Cervical Squamous Cell Carcinoma into Two New Subclasses Differing in Immune-Related Gene Expression. Int J Mol Sci 2018; 19:ijms19113607. [PMID: 30445744 PMCID: PMC6275080 DOI: 10.3390/ijms19113607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/13/2022] Open
Abstract
Cervical cancer is traditionally classified into two major histological subtypes, cervical squamous cell carcinoma (CSCC) and cervical adenocarcinoma (CA). However, heterogeneity exists among patients, comprising possible subpopulations with distinct molecular profiles. We applied consensus clustering to 307 methylation samples with cervical cancer from The Cancer Genome Atlas (TCGA). Fisher’s exact test was used to perform transcription factors (TFs) and genomic region enrichment. Gene expression profiles were downloaded from TCGA to assess expression differences. Immune cell fraction was calculated to quantify the immune cells infiltration. Putative neo-epitopes were predicted from somatic mutations. Three subclasses were identified: Class 1 correlating with the CA subtype and Classes 2 and 3 dividing the CSCC subtype into two subclasses. We found the hypomethylated probes in Class 3 exhibited strong enrichment in promoter region as compared with Class 2. Five TFs significantly enriched in the hypomethylated promoters and their highly expressed target genes in Class 3 functionally involved in the immune pathway. Gene function analysis revealed that immune-related genes were significantly increased in Class 3, and a higher level of immune cell infiltration was estimated. High expression of 24 immune genes exhibited a better overall survival and correlated with neo-epitope burden. Additionally, we found only two immune-related driver genes, CARD11 and JAK3, to be significantly increased in Class 3. Our analyses provide a classification of the largest CSCC subtype into two new subclasses, revealing they harbored differences in immune-related gene expression.
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Affiliation(s)
- Xia Li
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China.
| | - Yunpeng Cai
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China.
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Brentville VA, Atabani S, Cook K, Durrant LG. Novel tumour antigens and the development of optimal vaccine design. Ther Adv Vaccines Immunother 2018; 6:31-47. [PMID: 29998219 DOI: 10.1177/2515135518768769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/23/2018] [Indexed: 12/13/2022] Open
Abstract
The interplay between tumours and the immune system has long been known to involve complex interactions between tumour cells, immune cells and the tumour microenvironment. The progress of checkpoint inhibitors in the clinic in the last decade has highlighted again the role of the immune system in the fight against cancer. Numerous efforts have been undertaken to develop ways of stimulating the cellular immune response to eradicate tumours. These interventions include the identification of appropriate tumour antigens as targets for therapy. In this review, we summarize progress in selection of target tumour antigen. Targeting self antigens has the problem of thymic deletion of high-affinity T-cell responses leaving a diminished repertoire of low-affinity T cells that fail to kill tumour cells. Thymic regulation appears to be less stringent for differentiation of cancer-testis antigens, as many tumour rejection antigens fall into this category. More recently, targeting neo-epitopes or post-translational modifications such as a phosphorylation or stress-induced citrullination has shown great promise in preclinical studies. Of particular interest is that the responses can be mediated by both CD4 and CD8 T cells. Previous vaccines have targeted CD8 T-cell responses but more recently, the central role of CD4 T cells in orchestrating inflammation within tumours and also differentiating into potent killer cells has been recognized. The design of vaccines to induce such immune responses is discussed herein. Liposomally encoded ribonucleic acid (RNA), targeted deoxyribonucleic acid (DNA) or long peptides linked to toll-like receptor (TLR) adjuvants are the most promising new vaccine approaches. These exciting new approaches suggest that the 'Holy Grail' of a simple nontoxic cancer vaccine may be on the horizon. A major hurdle in tumour therapy is also to overcome the suppressive tumour environment. We address current progress in combination therapies and suggest that these are likely to show the most promise for the future.
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Affiliation(s)
| | - Suha Atabani
- Academic Department of Clinical Oncology, University of Nottingham, Nottingham, UK
| | - Katherine Cook
- Academic Department of Clinical Oncology, University of Nottingham, Nottingham, UK
| | - Lindy G Durrant
- Scancell Limited, Academic Department of Clinical Oncology, University of Nottingham, City Hospital, Hucknall Road, Nottingham, NG5 1PB, UK
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Maccalli C, Parmiani G, Ferrone S. Immunomodulating and Immunoresistance Properties of Cancer-Initiating Cells: Implications for the Clinical Success of Immunotherapy. Immunol Invest 2017; 46:221-238. [PMID: 28287848 DOI: 10.1080/08820139.2017.1280051] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cancer-initiating cells (CICs) represent a relatively rare subpopulation of cells endowed with self-renewal, stemness properties, tumorigenicity in immunodeficient mice, and resistance to standard therapies as well as to immunotherapy. Here, we review the biological and immunological characteristics of CICs with special focus on the immunomodulating mechanisms they utilize to escape from immunosurveillance. The recently developed immunotherapeutic strategies have yielded remarkable clinical results in many types of tumors, indicating that indeed a patient's immune system can mount an immune response, which is effective in controlling tumor growth. However, a high proportion of patients is resistant or acquires resistance to these therapeutic strategies. The latter findings may reflect, at least in some cases, the inability of the immunotherapeutic strategies used to eradicate CICs. The CICs that escape immune recognition and destruction may give rise to new tumors in the same organ site or through the metastatic colonization in other anatomic sites. Identification of novel therapeutic approaches that can eradicate CICs is a major challenge in the cancer therapy area. An improved understanding of the interactions of CICs with immune system and with tumor microenvironment may contribute to optimize the available therapies and to design novel combination treatments for cancer therapy. ABBREVIATIONS ALDH, aldehyde dehydrogenase; APC, antigen-presenting cells; APM, antigen-processing machinery; CAR: chimeric antigen receptor; CHK1, checkpoint serine/threonine protein kinase; CIC, cancer-initiating cell; CRC, colorectal cancer; CTLA-4, cytotoxic T lymphocyte antigen-4; GBM, glioblastoma multiforme; GDF-15, growth differentiation factor-15; CSPG4: chondroitin sulfate proteoglycan-4; IFN, interferon; IL-4, interleukin-4; IL-10, interleukin-10; IL-13, interleukin-13; IL-13α2, α2 chain of IL-13 receptor; mAb, monoclonal antibody; MDSC, myeloid-derived suppressor cell; MHC, major histocompatibility complex; PD-1, programmed death-1; PD-L1 programmed death ligand-1; PDK, 3-phosphoinositide-dependent protein kinase-1; PGE2, prostaglandin E2; STAT3, signal transducer and activator of transcription 3; TGFB-1, transforming growth factor beta-1; Treg, T regulatory cell.
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Affiliation(s)
- Cristina Maccalli
- a Department of Translational Medicine , Sidra Medical and Research Center , Doha , Qatar
| | - Giorgio Parmiani
- b Italian Network for Biotherapy, University Hospital of Siena , Siena , Italy
| | - Soldano Ferrone
- c Department of Surgery , Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
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Koşaloğlu Z, Zörnig I, Halama N, Kaiser I, Buchhalter I, Grabe N, Eils R, Schlesner M, Califano A, Jäger D. Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases. Oncoimmunology 2016; 5:e1213931. [PMID: 27999735 DOI: 10.1080/2162402x.2016.1213931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/30/2016] [Accepted: 07/12/2016] [Indexed: 12/22/2022] Open
Abstract
Neuroendocrine tumors (NETs) of the gastrointestinal tract are a rare and heterogeneous group of neoplasms with unique tumor biology and clinical management issues. While surgery is the only curative treatment option in patients with early stage NETs, the optimal management strategy for patients with advanced metastatic NETs is unknown. Based on the tremendous success of immunotherapeutic approaches, we sought to investigate such approaches in a case of metastatic rectal NET. Here, we apply an integrative approach using various computational and experimental methods to explore several aspects of the tumor-host immune interactions for immunotherapeutic options. Sequencing of six different liver metastases revealed a quite homogenous set of mutations, and further analysis of these mutations for immunogenicity revealed few neo-epitopes with pre-existing T cell reactivity, which can be used in therapeutic vaccines. Staining for immunomodulatory proteins and cytokine profiling showed that the immune setting is surprisingly different, when compared to liver metastases of colorectal cancer for instance. Taken together, our results highlight the broad range and complexity of tumor-host immune interaction and underline the value of an integrative approach.
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Affiliation(s)
- Zeynep Koşaloğlu
- Clinical Cooperation Unit "Applied Tumor Immunity", National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Heidelberg, Germany
| | - Inka Zörnig
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg , Heidelberg, Germany
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg , Heidelberg, Germany
| | - Iris Kaiser
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg , Heidelberg, Germany
| | - Ivo Buchhalter
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ) , Heidelberg, Germany
| | - Niels Grabe
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg , Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ) , Heidelberg, Germany
| | - Andrea Califano
- Department of Biomedical Informatics, Department of Systems Biology, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University , New York, NY, USA
| | - Dirk Jäger
- Clinical Cooperation Unit "Applied Tumor Immunity", National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Heidelberg, Germany
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9
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Abstract
INTRODUCTION The complement system is an essential part of the immune system of vertebrates. The central event of the complement activation cascade is the sequential proteolytic activation of C3, which is associated with profound alterations in the molecule's structure and conformation and is responsible for triggering most of the biological effects of complement. MATERIAL AND METHODS Here, we have studied the conformation of C3 fragments deposited onto an IgG-coated surface from human serum during complement activation, using a set of unique monoclonal antibodies (mAbs) that are all specific for the C3dg portion of bound iC3b. RESULTS; We were able to identify two conformational forms of target-bound iC3b: the first recognized by mAb 7D18.1, and the second by mAb 7D323.1. The first species of iC3b bound recombinant complement receptor 1 (CR1), while the second bound CR2. Since CR1 and CR2 are expressed by different subsets of leukocytes, this difference in receptor-binding capacity implies that there is a biological difference between the two forms of surface-bound iC3b. CONCLUSION We propose that mAbs 7D18.1 and 7D323.1 can act as surrogate markers for CR1 and CR2, respectively, and that they may be useful tools for studying the immune complexes that are generated in various autoimmune diseases.
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Affiliation(s)
- Ulf R. Nilsson
- Division of Clinical Immunology, Rudbeck Laboratory C5, Uppsala UniversitySweden
| | - Lillemor Funke
- Division of Clinical Immunology, Rudbeck Laboratory C5, Uppsala UniversitySweden
| | - Bo Nilsson
- Division of Clinical Immunology, Rudbeck Laboratory C5, Uppsala UniversitySweden
| | - Kristina N. Ekdahl
- Division of Clinical Immunology, Rudbeck Laboratory C5, Uppsala UniversitySweden
- Department of Natural Sciences, Linneaus University, KalmarSweden
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