Structurally Mapping Antibody Repertoires.

Abstract:

:Every human possesses millions of distinct antibodies. It is now possible to analyze this diversity via next-generation sequencing of immunoglobulin genes (Ig-seq). This technique produces large volume sequence snapshots of B-cell receptors that are indicative of the antibody repertoire. In this paper, we enrich these large-scale sequence datasets with structural information. Enriching a sequence with its structural data allows better approximation of many vital features, such as its binding site and specificity. Here, we describe the structural annotation of antibodies pipeline that maps the outputs of large Ig-seq experiments to known antibody structures. We demonstrate the viability of our protocol on five separate Ig-seq datasets covering ca. 35 m unique amino acid sequences from ca. 600 individuals. Despite the great theoretical diversity of antibodies, we find that the majority of sequences coming from such studies can be reliably mapped to an existing structure.

journal_name

Front Immunol

journal_title

Frontiers in immunology

authors

Krawczyk K,Kelm S,Kovaltsuk A,Galson JD,Kelly D,Trück J,Regep C,Leem J,Wong WK,Nowak J,Snowden J,Wright M,Starkie L,Scott-Tucker A,Shi J,Deane CM

doi

10.3389/fimmu.2018.01698

subject

Has Abstract

pub_date

2018-07-23 00:00:00

pages

1698

issn

1664-3224

journal_volume

9

pub_type

杂志文章
  • Phylogenetic conservation of the 3' cryptic recombination signal sequence (3'cRSS) in the VH genes of jawed vertebrates.

    abstract::The VH replacement process is a RAG-mediated secondary recombination in which the variable region of a rearranged VHDJH is replaced by a different germline VH gene. In almost all human and mouse VH genes, two sequence features appear to be crucial for VH replacement. First, an embedded heptamer, which is located near ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2012.00392

    authors: Sun Y,Liu Z,Li Z,Lian Z,Zhao Y

    更新日期:2012-12-20 00:00:00

  • Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses.

    abstract::About 8% of our genome is composed of sequences with viral origin, namely human Endogenous Retroviruses (HERVs). HERVs are relics of ancient infections that affected the primates' germ line along the last 100 million of years, and became stable elements at the interface between self and foreign DNA. Intriguingly, HERV...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.02039

    authors: Grandi N,Tramontano E

    更新日期:2018-09-10 00:00:00

  • Effects of Omalizumab on FcεRI and IgE Expression in Lesional Skin of Bullous Pemphigoid.

    abstract::Recent studies suggest an important role of immunoglobulin E (IgE) as an alternative pathogenic pathway in the development of bullous pemphigoid (BP), as the most frequent subepidermal blistering disease of the skin Use of IgE targeted therapies, such as omalizumab, has been shown promising in recent studies. The aim ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2019.01919

    authors: Seyed Jafari SM,Gadaldi K,Feldmeyer L,Yawalkar N,Borradori L,Schlapbach C

    更新日期:2019-08-14 00:00:00

  • Dynamic Interplay of Innate and Adaptive Immunity During Sterile Retinal Inflammation: Insights From the Transcriptome.

    abstract::The pathogenesis of many retinal degenerations, such as age-related macular degeneration (AMD), is punctuated by an ill-defined network of sterile inflammatory responses. The delineation of innate and adaptive immune milieu among the broad leukocyte infiltrate, and the gene networks, which construct these responses, a...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.01666

    authors: Natoli R,Mason E,Jiao H,Chuah A,Patel H,Fernando N,Valter K,Wells CA,Provis J,Rutar M

    更新日期:2018-07-18 00:00:00

  • Inhibition of Host Arginase Activity Against Staphylococcal Bloodstream Infection by Different Metabolites.

    abstract::Staphylococcus aureus is a notorious bacterial pathogen that often causes soft tissue and bloodstream infections and invariably garners resistance mechanisms against new antibiotics. Modulation of the host immune response by metabolites is a powerful tool against bacterial infections, but has not yet been used against...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.01639

    authors: Pang R,Zhou H,Huang Y,Su Y,Chen X

    更新日期:2020-07-28 00:00:00

  • PRINS Non-Coding RNA Regulates Nucleic Acid-Induced Innate Immune Responses of Human Keratinocytes.

    abstract::Cytosolic DNA fragments are recognized as pathogen- and danger-associated molecular patterns that induce a cascade of innate immune responses. Moreover, excessive cytosolic DNA can enhance chronic inflammation, predominantly by activating inflammasomes, and thereby contributing to the pathogenesis of chronic diseases,...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.01053

    authors: Danis J,Göblös A,Bata-Csörgő Z,Kemény L,Széll M

    更新日期:2017-08-29 00:00:00

  • Immune Tolerance Maintained by Cooperative Interactions between T Cells and Antigen Presenting Cells Shapes a Diverse TCR Repertoire.

    abstract::The T cell population in an individual needs to avoid harmful activation by self peptides while maintaining the ability to respond to an unknown set of foreign peptides. This property is acquired by a combination of thymic and extra-thymic mechanisms. We extend current models for the development of self/non-self discr...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2015.00360

    authors: Best K,Chain B,Watkins C

    更新日期:2015-08-07 00:00:00

  • Alum Activates the Bovine NLRP3 Inflammasome.

    abstract::There has been a move away from vaccines composed of whole or inactivated antigens toward subunit-based vaccines, which although safe, provide less immunological protection. As a result, the use of adjuvants to enhance and direct adaptive immune responses has become the focus of much targeted bovine vaccine research. ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.01494

    authors: Harte C,Gorman AL,McCluskey S,Carty M,Bowie AG,Scott CJ,Meade KG,Lavelle EC

    更新日期:2017-11-09 00:00:00

  • Persistence of Activated and Adaptive-Like NK Cells in HIV+ Individuals despite 2 Years of Suppressive Combination Antiretroviral Therapy.

    abstract::Innate immune dysfunction persists in HIV+ individuals despite effective combination antiretroviral therapy (cART). We recently demonstrated that an adaptive-like CD56dim NK cell population lacking the signal transducing protein FcRγ is expanded in HIV+ individuals. Here, we analyzed a cohort of HIV+ men who have sex ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.00731

    authors: Hearps AC,Agius PA,Zhou J,Brunt S,Chachage M,Angelovich TA,Cameron PU,Giles M,Price P,Elliott J,Jaworowski A

    更新日期:2017-06-30 00:00:00

  • Class-Switch Recombination (CSR)/Hyper-IgM (HIGM) Syndromes and Phosphoinositide 3-Kinase (PI3K) Defects.

    abstract::Antibody production and function represent an essential part of the immune response, particularly in fighting bacterial and viral infections. Multiple immunological phenotypes can result in dysregulation of the immune system humoral compartment, including class-switch recombination (CSR) defects associated with hyper-...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.02172

    authors: Jhamnani RD,Nunes-Santos CJ,Bergerson J,Rosenzweig SD

    更新日期:2018-09-26 00:00:00

  • Interaction Between Macrophage Migration Inhibitory Factor and CD74 in Human Immunodeficiency Virus Type I Infected Primary Monocyte-Derived Macrophages Triggers the Production of Proinflammatory Mediators and Enhances Infection of Unactivated CD4+ T Cell

    abstract::Understanding the mechanisms of human immunodeficiency virus type I (HIV-1) pathogenesis would facilitate the identification of new therapeutic targets to control the infection in face of current antiretroviral therapy limitations. CD74 membrane expression is upregulated in HIV-1-infected cells and the magnitude of it...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.01494

    authors: Trifone C,Salido J,Ruiz MJ,Leng L,Quiroga MF,Salomón H,Bucala R,Ghiglione Y,Turk G

    更新日期:2018-06-27 00:00:00

  • Humoral Responses Elicited by Adenovirus Displaying Epitopes Are Induced Independently of the Infection Process and Shaped by the Toll-Like Receptor/MyD88 Pathway.

    abstract::The use of serotype 5 adenovirus (Ad)-derived vectors in vaccination is confronted to preexisting anti-Ad immunity. Epitope display on Ad capsid is currently being investigated as an alternative approach of vaccination. The present study seeks to better understand virus- and host-related factors controlling the effica...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.00124

    authors: Anchim A,Raddi N,Zig L,Perrieau P,Le Goffic R,Ryffel B,Benihoud K

    更新日期:2018-02-05 00:00:00

  • Immunometabolic Regulations Mediated by Coinhibitory Receptors and Their Impact on T Cell Immune Responses.

    abstract::Host immunity provides wide spectrum protection that serves to eradicate pathogens and cancer cells, while maintaining self-tolerance and immunological homeostasis. Ligation of the T cell receptor (TCR) by antigen activates signaling pathways that coordinately induce aerobic glycolysis, mitochondrial activity, anaboli...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2017.00330

    authors: Patsoukis N,Weaver JD,Strauss L,Herbel C,Seth P,Boussiotis VA

    更新日期:2017-04-11 00:00:00

  • The Role of the Immune Response in Chlamydia trachomatis Infection of the Male Genital Tract: A Double-Edged Sword.

    abstract::Chlamydia trachomatis (CT) is the most prevalent bacterial sexually transmitted infection in the world, with more than 100 million cases reported annually. While there have been extensive studies into the adverse effects that CT infection has on the female genital tract, and on the subsequent ability of these women to...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2014.00534

    authors: Redgrove KA,McLaughlin EA

    更新日期:2014-10-27 00:00:00

  • CAR T Cell Therapy of Non-hematopoietic Malignancies: Detours on the Road to Clinical Success.

    abstract::Chimeric antigen receptor (CAR)-engineered T cells represent a breakthrough in personalized medicine. In this strategy, a patient's own T lymphocytes are genetically reprogrammed to encode a synthetic receptor that binds a tumor antigen, allowing T cells to recognize and kill antigen-expressing cancer cells. As a resu...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.02740

    authors: Long KB,Young RM,Boesteanu AC,Davis MM,Melenhorst JJ,Lacey SF,DeGaramo DA,Levine BL,Fraietta JA

    更新日期:2018-12-03 00:00:00

  • Refractory Chronic Spontaneous Urticaria Treated With Omalizumab in an Adolescent With Common Variable Immunodeficiency.

    abstract::Chronic spontaneous urtcaria (CSU) can represent the leading sign of a wide spectrum of systemic diseases, including primary immunodeficiencies. We describe the case of a young adult female with coexisting CSU and common variable immunodeficiency (CVID) successfully treated with omalizumab. The patient, with a history...

    journal_title:Frontiers in immunology

    pub_type:

    doi:10.3389/fimmu.2019.01700

    authors: Comberiati P,Costagliola G,Carli N,Legitimo A,D'Elios S,Consolini R,Peroni DG

    更新日期:2019-07-17 00:00:00

  • Human Serum Albumin Binds Streptolysin O (SLO) Toxin Produced by Group A Streptococcus and Inhibits Its Cytotoxic and Hemolytic Effects.

    abstract::The pathogenicity of group A Streptococcus (GAS) is mediated by direct bacterial invasivity and toxin-associated damage. Among the extracellular products, the exotoxin streptolysin O (SLO) is produced by almost all GAS strains. SLO is a pore forming toxin (PFT) hemolitically active and extremely toxic in vivo. Recent ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.507092

    authors: Vita GM,De Simone G,Leboffe L,Montagnani F,Mariotti D,Di Bella S,Luzzati R,Gori A,Ascenzi P,di Masi A

    更新日期:2020-12-08 00:00:00

  • The critical role of the tumor microenvironment in shaping natural killer cell-mediated anti-tumor immunity.

    abstract::Considerable evidence has been gathered over the last 10 years showing that the tumor microenvironment (TME) is not simply a passive recipient of immune cells, but an active participant in the establishment of immunosuppressive conditions. It is now well documented that hypoxia, within the TME, affects the functions o...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2013.00490

    authors: Baginska J,Viry E,Paggetti J,Medves S,Berchem G,Moussay E,Janji B

    更新日期:2013-12-25 00:00:00

  • Further Advances in Cancer Immunotherapy: Going Beyond Checkpoint Blockade.

    abstract::Significant advances have been made to identify effective therapies that either restore or generate de novo a patient's immune response to cancer, so-called immunotherapy or immuno-oncology (IO) therapies. Some tumors overcome immune surveillance by promoting mechanisms to evade or suppress the immune system. This con...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.01082

    authors: Wilkinson RW,Leishman AJ

    更新日期:2018-06-01 00:00:00

  • Serum microRNA Profiles Serve as Novel Biomarkers for Autoimmune Diseases.

    abstract::Autoimmune diseases involve a complex dysregulation of immunity. Autoimmune diseases include many members [e.g., rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE)], and most of them are classified according to what organs and tissues are targeted by the damaging immune response. Many studies have focuse...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.02381

    authors: Jin F,Hu H,Xu M,Zhan S,Wang Y,Zhang H,Chen X

    更新日期:2018-10-16 00:00:00

  • MIF and CXCL12 in Cardiovascular Diseases: Functional Differences and Similarities.

    abstract::Coronary artery disease (CAD) as part of the cardiovascular diseases is a pathology caused by atherosclerosis, a chronic inflammatory disease of the vessel wall characterized by a massive invasion of lipids and inflammatory cells into the inner vessel layer (intima) leading to the formation of atherosclerotic lesions;...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2015.00373

    authors: van der Vorst EP,Döring Y,Weber C

    更新日期:2015-07-21 00:00:00

  • Notch Signaling Pathway Expression in the Skin of Leprosy Patients: Association With Skin and Neural Damage.

    abstract::Introduction: Leprosy is an infectious disease caused by Mycobacterium leprae, a debilitating disease that affects the skin and peripheral nerves. It is possible that tissue changes during infection with leprosy are related to alterations in the activity of the Notch signaling pathway, an innate signaling pathway in t...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.00368

    authors: Serrano-Coll H,Ospina JP,Salazar-Peláez L,Cardona-Castro N

    更新日期:2020-03-19 00:00:00

  • Neonatal Diet Impacts Circulatory miRNA Profile in a Porcine Model.

    abstract::microRNAs (miRNAs) are conserved non-coding small nucleotide molecules found in nearly all species and breastmilk. miRNAs present in breastmilk are very stable to freeze-thaw, RNase treatment, and low pH as they are protected inside exosomes. They are involved in regulating several physiologic and pathologic processes...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.01240

    authors: Carr LE,Bowlin AK,Elolimy AA,Byrum SD,Washam CL,Randolph CE,MacLeod SL,Yeruva L

    更新日期:2020-06-23 00:00:00

  • Therapeutic implications of immunogenic cell death in human cancer.

    abstract::Dendritic cells (DCs) are central to the adoptive immune response, and their function is regulated by diverse signals in a context-specific manner. Different DCs have been described in physiologic conditions, inflammation, and cancer, prompting a series of questions on how adoptive immune responses, or tolerance, deve...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2013.00503

    authors: Palombo F,Focaccetti C,Barnaba V

    更新日期:2014-01-06 00:00:00

  • Remote Activation of a Latent Epitope in an Autoantigen Decoded With Simulated B-Factors.

    abstract::Mutants of a catalytically inactive variant of Proteinase 3 (PR3)-iPR3-Val103 possessing a Ser195Ala mutation relative to wild-type PR3-Val103-offer insights into how autoantigen PR3 interacts with antineutrophil cytoplasmic antibodies (ANCAs) in granulomatosis with polyangiitis (GPA) and whether such interactions can...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2019.02467

    authors: Pang YP,Casal Moura M,Thompson GE,Nelson DR,Hummel AM,Jenne DE,Emerling D,Volkmuth W,Robinson WH,Specks U

    更新日期:2019-10-25 00:00:00

  • The new deal: a potential role for secreted vesicles in innate immunity and tumor progression.

    abstract::Tumors must evade the immune system to survive and metastasize, although the mechanisms that lead to tumor immunoediting and their evasion of immune surveillance are far from clear. The first line of defense against metastatic invasion is the innate immune system that provides immediate defense through humoral immunit...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2015.00066

    authors: Benito-Martin A,Di Giannatale A,Ceder S,Peinado H

    更新日期:2015-02-24 00:00:00

  • Antimicrobial activities of chemokines: not just a side-effect?

    abstract::The large family of chemoattractant cytokines (chemokines) embraces multiple, in part unrelated functions that go well beyond chemotaxis. Undoubtedly, the control of immune cell migration (chemotaxis) is the single, unifying response mediated by all chemokines, which involves the sequential engagement of chemokine rec...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2012.00213

    authors: Wolf M,Moser B

    更新日期:2012-07-23 00:00:00

  • Prenatal Administration of Betamethasone Causes Changes in the T Cell Receptor Repertoire Influencing Development of Autoimmunity.

    abstract::Prenatal glucocorticoids are routinely administered to pregnant women at risk of preterm delivery in order to improve survival of the newborn. However, in half of the cases, birth occurs outside the beneficial period for lung development. Glucocorticoids are potent immune modulators and cause apoptotic death of immatu...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.01505

    authors: Gieras A,Gehbauer C,Perna-Barrull D,Engler JB,Diepenbruck I,Glau L,Joosse SA,Kersten N,Klinge S,Mittrücker HW,Friese MA,Vives-Pi M,Tolosa E

    更新日期:2017-11-13 00:00:00

  • Complement Activation in Autoimmune Bullous Dermatoses: A Comprehensive Review.

    abstract::Autoimmune bullous dermatoses (AIBD) are characterized by circulating autoantibodies that are either directed against epidermal antigens or deposited as immune complexes in the basement membrane zone (BMZ). The complement system (CS) can be activated by autoantibodies, thereby triggering activation of specific complem...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2019.01477

    authors: Edwards G,Diercks GFH,Seelen MAJ,Horvath B,van Doorn MBA,Damman J

    更新日期:2019-06-26 00:00:00

  • B Cell Functions Can Be Modulated by Antimicrobial Peptides in Rainbow Trout Oncorhynchus mykiss: Novel Insights into the Innate Nature of B Cells in Fish.

    abstract::B cells in fish were recently proven to have potent innate immune activities like macrophages. This inspired us to further explore the innate nature of B cells in fish. Moreover, antimicrobial peptides (AMPs) are representative molecules of innate immunity, and they can modulate the functions of macrophages. These mak...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.00388

    authors: Zhang XJ,Wang P,Zhang N,Chen DD,Nie P,Li JL,Zhang YA

    更新日期:2017-04-04 00:00:00