IMPre: An Accurate and Efficient Software for Prediction of T- and B-Cell Receptor Germline Genes and Alleles from Rearranged Repertoire Data.

Abstract:

:Large-scale study of the properties of T-cell receptor (TCR) and B-cell receptor (BCR) repertoires through next-generation sequencing is providing excellent insights into the understanding of adaptive immune responses. Variable(Diversity)Joining [V(D)J] germline genes and alleles must be characterized in detail to facilitate repertoire analyses. However, most species do not have well-characterized TCR/BCR germline genes because of their high homology. Also, more germline alleles are required for humans and other species, which limits the capacity for studying immune repertoires. Herein, we developed "Immune Germline Prediction" (IMPre), a tool for predicting germline V/J genes and alleles using deep-sequencing data derived from TCR/BCR repertoires. We developed a new algorithm, "Seed_Clust," for clustering, produced a multiway tree for assembly and optimized the sequence according to the characteristics of rearrangement. We trained IMPre on human samples of T-cell receptor beta (TRB) and immunoglobulin heavy chain and then tested it on additional human samples. Accuracy of 97.7, 100, 92.9, and 100% was obtained for TRBV, TRBJ, IGHV, and IGHJ, respectively. Analyses of subsampling performance for these samples showed IMPre to be robust using different data quantities. Subsequently, IMPre was tested on samples from rhesus monkeys and human long sequences: the highly accurate results demonstrated IMPre to be stable with animal and multiple data types. With rapid accumulation of high-throughput sequence data for TCR and BCR repertoires, IMPre can be applied broadly for obtaining novel genes and a large number of novel alleles. IMPre is available at https://github.com/zhangwei2015/IMPre.

journal_name

Front Immunol

journal_title

Frontiers in immunology

authors

Zhang W,Wang IM,Wang C,Lin L,Chai X,Wu J,Bett AJ,Dhanasekaran G,Casimiro DR,Liu X

doi

10.3389/fimmu.2016.00457

subject

Has Abstract

pub_date

2016-11-04 00:00:00

pages

457

issn

1664-3224

journal_volume

7

pub_type

杂志文章
  • 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

  • Differential chemotactic receptor requirements for NK cell subset trafficking into bone marrow.

    abstract::Responsiveness of maturing natural killer (NK) cells to chemotactic molecules directly affect their retention and relocation in selected bone marrow (BM) microenvironment during development, as well as their localization at sites of immune response during inflammatory diseases. BM is the main site of NK cell generatio...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2013.00012

    authors: Bernardini G,Sciumè G,Santoni A

    更新日期:2013-01-30 00:00:00

  • Endothelial Basement Membrane Laminins as an Environmental Cue in Monocyte Differentiation to Macrophages.

    abstract::Monocyte differentiation to macrophages is triggered by migration across the endothelial barrier, which is constituted by both endothelial cells and their underlying basement membrane. We address here the role of the endothelial basement membrane laminins (laminins 411 and 511) in this monocyte to macrophage switch. C...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.584229

    authors: Li L,Song J,Chuquisana O,Hannocks MJ,Loismann S,Vogl T,Roth J,Hallmann R,Sorokin L

    更新日期:2020-10-30 00:00:00

  • Effective Targeting of TAG72+ Peritoneal Ovarian Tumors via Regional Delivery of CAR-Engineered T Cells.

    abstract::Impressive clinical efficacy of chimeric antigen receptor (CAR)-engineered T cell therapy for hematological malignancies have prompted significant efforts in achieving similar responses in solid tumors. The lack of truly restricted and uniform expression of tumor-associated antigens, as well as limited T cell persiste...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.02268

    authors: Murad JP,Kozlowska AK,Lee HJ,Ramamurthy M,Chang WC,Yazaki P,Colcher D,Shively J,Cristea M,Forman SJ,Priceman SJ

    更新日期:2018-11-19 00:00:00

  • Gene Expression Profiling of PDGFRA Mutant GIST Reveals Immune Signatures as a Specific Fingerprint of D842V Exon 18 Mutation.

    abstract::Platelet Derived Growth Factor Receptor Alpha (PDGFRA) mutations occur in only about 5-7% of gastrointestinal stromal tumors (GIST), notably with alterations on exons 12/14/18. The most frequent PDGFRA mutation is the exon 18 D842V, which is correlated to specific clinico-pathological features, such as primary imatini...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.00851

    authors: Indio V,Ravegnini G,Astolfi A,Urbini M,Saponara M,De Leo A,Gruppioni E,Tarantino G,Angelini S,Pession A,Pantaleo MA,Nannini M

    更新日期:2020-06-02 00:00:00

  • The Antidiabetic and Antinephritic Activities of Auricularia cornea (An Albino Mutant Strain) via Modulation of Oxidative Stress in the db/db Mice.

    abstract::This study first systematically analyzed the constituents of an albino mutant strain of Auricularia cornea (AU). After 8 weeks of continuous treatment with metformin (Met) (0.1 g/kg) and AU (0.1 and 0.4 g/kg), db/db mice showed hypoglycemic functioning, indicated by reduced bodyweight, food intake, plasma glucose, ser...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2019.01039

    authors: Wang D,Jiang X,Teng S,Zhang Y,Liu Y,Li X,Li Y

    更新日期:2019-05-08 00:00:00

  • The Enigma of Heat Shock Proteins in Immune Tolerance.

    abstract::The fundamental problem of autoimmune diseases is the failure of the immune system to downregulate its own potentially dangerous cells, which leads to destruction of tissue expressing the relevant autoantigens. Current immunosuppressive therapies offer relief but fail to restore the basic condition of self-tolerance. ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2017.01599

    authors: van Eden W,Jansen MAA,Ludwig I,van Kooten P,van der Zee R,Broere F

    更新日期:2017-11-21 00:00:00

  • Excess of Mortality in Adults and Elderly and Circulation of Subtypes of Influenza Virus in Southern Brazil.

    abstract:Purpose:In the elderly population, the influenza infection and its clinical complications are important causes of hospitalization and death, particularly, in longer-lived age. The objective of this study is to analyze the impact of influenza virus circulation on mortality in the elderly and adults, in years with differ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.01903

    authors: Freitas ARR,Donalisio MR

    更新日期:2018-01-08 00:00:00

  • Role of Tumor-Mediated Dendritic Cell Tolerization in Immune Evasion.

    abstract::The vast majority of cancer-related deaths are due to metastasis, a process that requires evasion of the host immune system. In addition, a significant percentage of cancer patients do not benefit from our current immunotherapy arsenal due to either primary or secondary immunotherapy resistance. Importantly, select su...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2019.02876

    authors: DeVito NC,Plebanek MP,Theivanthiran B,Hanks BA

    更新日期:2019-12-10 00:00:00

  • CD36 Shunts Eicosanoid Metabolism to Repress CD14 Licensed Interleukin-1β Release and Inflammation.

    abstract::Interleukin (IL)-1β is a potential target for treatment of several inflammatory diseases, including envenomation by the scorpion Tityus serrulatus. In this context, bioactive lipids such as prostaglandin (PG)E2 and leukotriene (LT)B4 modulate the production of IL-1β by innate immune cells. Pattern recognition receptor...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.00890

    authors: Zoccal KF,Gardinassi LG,Sorgi CA,Meirelles AFG,Bordon KCF,Glezer I,Cupo P,Matsuno AK,Bollela VR,Arantes EC,Guimarães FS,Faccioli LH

    更新日期:2018-04-27 00:00:00

  • Mode of Proximal Tubule Damage: Differential Cause for the Release of TFF3?

    abstract::Proximal tubular epithelial cells are particularly sensitive to damage. In search of a biomarker, this study evaluated the potential of different cell activation models (hypoxia/replenishment and protein overload) to lead to a release of trefoil factor 3 (TFF3). Surprisingly, we found disparity in the ability of the d...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2016.00122

    authors: Zwaini Z,Alammari D,Byrne S,Stover C

    更新日期:2016-03-30 00:00:00

  • Differences in the composition of the human antibody repertoire by B cell subsets in the blood.

    abstract::The vast initial diversity of the antibody repertoire is generated centrally by means of a complex series of V(D)J gene rearrangement events, variation in the site of gene segment joining, and TdT catalyzed N-region addition. Although the diversity is great, close inspection has revealed distinct and unique characteri...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2014.00096

    authors: Mroczek ES,Ippolito GC,Rogosch T,Hoi KH,Hwangpo TA,Brand MG,Zhuang Y,Liu CR,Schneider DA,Zemlin M,Brown EE,Georgiou G,Schroeder HW Jr

    更新日期:2014-03-19 00:00:00

  • MTBVAC: Attenuating the Human Pathogen of Tuberculosis (TB) Toward a Promising Vaccine against the TB Epidemic.

    abstract::Bacille Calmette-Guérin (BCG) is a live-attenuated strain of Mycobacterium bovis developed a century ago by repeated subculture. It remains the only vaccine against tuberculosis (TB) in use today, and it offers variable protection against the respiratory forms of TB responsible for transmission. The principal genetic ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2017.01803

    authors: Gonzalo-Asensio J,Marinova D,Martin C,Aguilo N

    更新日期:2017-12-15 00:00:00

  • Association of Clinical Phenotypes in Haploinsufficiency A20 (HA20) With Disrupted Domains of A20.

    abstract::Background: Haploinsufficiency A20 (HA20) is a newly described monogenic disease characterized by a wide spectrum of manifestations and caused by heterozygous mutations in TNFAIP3 which encodes A20 protein. TNFAIP3 mutation leads to disruption of the A20 ovarian tumor (OTU) domain and/or the zinc finger (ZnF) domain. ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.574992

    authors: Chen Y,Ye Z,Chen L,Qin T,Seidler U,Tian D,Xiao F

    更新日期:2020-09-23 00:00:00

  • Thioredoxin Modulates Protein Arginine Deiminase 4 (PAD4)-Catalyzed Citrullination.

    abstract::Protein citrullination is a post-translational modification catalyzed by the protein arginine deiminases (PADs). This modification plays a crucial role in the pathophysiology of numerous autoimmune disorders including RA. Recently, there has been a growing interest in investigating physiological regulators of PAD acti...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2019.00244

    authors: Nagar M,Tilvawala R,Thompson PR

    更新日期:2019-02-19 00:00:00

  • Uncovering the Role of RNA-Binding Proteins in Gene Expression in the Immune System.

    abstract::Fighting external pathogens requires an ever-changing immune system that relies on tight regulation of gene expression. Transcriptional control is the first step to build efficient responses while preventing immunodeficiencies and autoimmunity. Post-transcriptional regulation of RNA editing, location, stability, and t...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.01094

    authors: Díaz-Muñoz MD,Turner M

    更新日期:2018-05-23 00:00:00

  • Transcription Factor KLF10 Constrains IL-17-Committed Vγ4+ γδ T Cells.

    abstract::γδ T cells, known to be an important source of innate IL-17 in mice, provide critical contributions to host immune responses. Development and function of γδ T cells are directed by networks of diverse transcription factors (TFs). Here, we examine the role of the zinc finger TFs, Kruppel-like factor 10 (KLF10), in the ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.00196

    authors: Kim G,Gu MJ,Kim SJ,Ko KH,Kye YC,Kim CG,Cho JH,Lee WK,Song KD,Chu H,Park YM,Han SH,Yun CH

    更新日期:2018-02-28 00:00:00

  • Cell Versus Cytokine - Directed Therapies for Hemophagocytic Lymphohistiocytosis (HLH) in Inborn Errors of Immunity.

    abstract::Hemophagocytic lymphohistiocytosis (HLH) is a heterogeneous hyperinflammatory syndrome with different pathways of pathogenesis resulting in similar clinical presentations. It is best defined and understood if presenting in the context of genetic immunodeficiencies associated with defects of lymphocyte cytotoxicity. In...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2020.00808

    authors: Wegehaupt O,Wustrau K,Lehmberg K,Ehl S

    更新日期:2020-05-08 00:00:00

  • Targeting Interleukin-2-Inducible T-Cell Kinase (ITK) Differentiates GVL and GVHD in Allo-HSCT.

    abstract::Allogeneic hematopoietic stem cell transplantation is a potentially curative procedure for many malignant diseases. Donor T cells prevent disease recurrence via graft-versus-leukemia (GVL) effect. Donor T cells also contribute to graft-versus-host disease (GVHD), a debilitating and potentially fatal complication. Nove...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2020.593863

    authors: Mammadli M,Huang W,Harris R,Sultana A,Cheng Y,Tong W,Pu J,Gentile T,Dsouza S,Yang Q,Bah A,August A,Karimi M

    更新日期:2020-11-26 00:00:00

  • Dynamic Perturbations of the T-Cell Receptor Repertoire in Chronic HIV Infection and following Antiretroviral Therapy.

    abstract::HIV infection profoundly affects many parameters of the immune system and ultimately leads to AIDS, yet which factors are most important for determining resistance, pathology, and response to antiretroviral treatment - and how best to monitor them - remain unclear. We develop a quantitative high-throughput sequencing ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2015.00644

    authors: Heather JM,Best K,Oakes T,Gray ER,Roe JK,Thomas N,Friedman N,Noursadeghi M,Chain B

    更新日期:2016-01-11 00:00:00

  • Neonatal Immunization: Rationale, Current State, and Future Prospects.

    abstract::Infections take their greatest toll in early life necessitating robust approaches to protect the very young. Here, we review the rationale, current state, and future research directions for one such approach: neonatal immunization. Challenges to neonatal immunization include natural concern about safety as well as a d...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2018.00532

    authors: Whittaker E,Goldblatt D,McIntyre P,Levy O

    更新日期:2018-04-04 00:00:00

  • High-Speed Single-Molecule Tracking of CXCL13 in the B-Follicle.

    abstract::Soluble factors are an essential means of communication between cells and their environment. However, many molecules readily interact with extracellular matrix components, giving rise to multiple modes of diffusion. The molecular quantification of diffusion in situ is thus a challenging imaging frontier, requiring ver...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.01073

    authors: Miller H,Cosgrove J,Wollman AJM,Taylor E,Zhou Z,O'Toole PJ,Coles MC,Leake MC

    更新日期:2018-05-22 00:00:00

  • The Inflammatory Role of Platelets via Their TLRs and Siglec Receptors.

    abstract::Platelets are non-nucleated cells that play central roles in the processes of hemostasis, innate immunity, and inflammation; however, several reports show that these distinct functions are more closely linked than initially thought. Platelets express numerous receptors and contain hundreds of secretory products. These...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2015.00083

    authors: Cognasse F,Nguyen KA,Damien P,McNicol A,Pozzetto B,Hamzeh-Cognasse H,Garraud O

    更新日期:2015-03-02 00:00:00

  • The Essential Role Played by B Cells in Supporting Protective Immunity Against Trichuris muris Infection Is by Controlling the Th1/Th2 Balance in the Mesenteric Lymph Nodes and Depends on Host Genetic Background.

    abstract::How B cells contribute to protective immunity against parasitic nematodes remains unclear, with their importance as accessory cells underexplored. In this study, anti-CD20 monoclonal antibody (α-CD20 mAb)-mediated depletion of B cells from C57BL/6 mice revealed an important role for B cells in supporting Th2 immune re...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2019.02842

    authors: Sahputra R,Ruckerl D,Couper KN,Muller W,Else KJ

    更新日期:2019-12-10 00:00:00

  • A New Tool for Complement Research: In vitro Reconstituted Human Classical Complement Pathway.

    abstract::The complement, as part of the innate immune system, represents the first line of defense against Gram-negative bacteria invading the bloodstream. The complement system is a zymogen cascade that ultimately assemble into the so-called membrane attack complex (MAC), which lyses Gram-negative bacteria upon insertion into...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.02770

    authors: Mutti M,Ramoni K,Nagy G,Nagy E,Szijártó V

    更新日期:2018-12-04 00:00:00

  • Allies or Enemies-The Multifaceted Role of Myeloid Cells in the Tumor Microenvironment.

    abstract::For decades, cancer was considered a disease driven by genetic mutations in tumor cells, therefore afflicting a single cell type. This simplified view was slowly replaced by the understanding that interactions between malignant cells and neighboring stromal and immune cells-the tumor microenvironment (TME)-profoundly ...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2019.02746

    authors: Haas L,Obenauf AC

    更新日期:2019-11-28 00:00:00

  • Systems Approach Reveals Nuclear Factor Erythroid 2-Related Factor 2/Protein Kinase R Crosstalk in Human Cutaneous Leishmaniasis.

    abstract::Leishmania parasites infect macrophages, causing a wide spectrum of human diseases, from cutaneous to visceral forms. In search of novel therapeutic targets, we performed comprehensive in vitro and ex vivo mapping of the signaling pathways upstream and downstream of antioxidant transcription factor [nuclear factor ery...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2017.01127

    authors: Vivarini ÁC,Calegari-Silva TC,Saliba AM,Boaventura VS,França-Costa J,Khouri R,Dierckx T,Dias-Teixeira KL,Fasel N,Barral AMP,Borges VM,Van Weyenbergh J,Lopes UG

    更新日期:2017-09-15 00:00:00

  • Bovine Neonatal Pancytopenia-Associated Alloantibodies Recognize Individual Bovine Leukocyte Antigen 1 Alleles.

    abstract::Bovine neonatal pancytopenia (BNP) was a vaccine-induced alloimmune disease observed in young calves and characterized by hemorrhages, pancytopenia, and severe destruction of the hematopoietic tissues. BNP was induced by alloreactive maternal antibodies present in the colostrum of certain cows vaccinated with a highly...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2018.01902

    authors: Kasonta R,Mauritz J,Spohr C,Sauter-Louis C,Duchow K,Cussler K,Holsteg M,Bastian M

    更新日期:2018-08-14 00:00:00

  • Activated IL-1RI Signaling Pathway Induces Th17 Cell Differentiation via Interferon Regulatory Factor 4 Signaling in Patients with Relapsing-Remitting Multiple Sclerosis.

    abstract::IL-1β plays a crucial role in the differentiation of human Th17 cells. We report here that IL-1RI expression is significantly increased in both naive and memory CD4+ T cells derived from relapsing-remitting multiple sclerosis (RR MS) patients in comparison to healthy controls. Interleukin 1 receptor (IL-1R)I expressio...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章

    doi:10.3389/fimmu.2016.00543

    authors: Sha Y,Markovic-Plese S

    更新日期:2016-11-29 00:00:00

  • Natural Killer Cells for Immunotherapy - Advantages of the NK-92 Cell Line over Blood NK Cells.

    abstract::Natural killer (NK) cells are potent cytotoxic effector cells for cancer therapy and potentially for severe viral infections. However, there are technical challenges to obtain sufficient numbers of functionally active NK cells from a patient's blood since they represent only 10% of the lymphocytes and are often dysfun...

    journal_title:Frontiers in immunology

    pub_type: 杂志文章,评审

    doi:10.3389/fimmu.2016.00091

    authors: Klingemann H,Boissel L,Toneguzzo F

    更新日期:2016-03-14 00:00:00