Abstract:
:The B cell antigen receptor repertoire is highly diverse and constantly modified by clonal selection. High-throughput DNA sequencing (HTS) of the lymphocyte repertoire (Rep-Seq) represents a promising technology to explore such diversity ex-vivo and assist in the identification of antigen-specific antibodies based on molecular signatures of clonal selection. Therefore, integrative tools for repertoire reconstruction and analysis from antibody sequences are needed. We developed ImmunediveRity, a stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. Its performance was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Furthermore, ImmunediveRsity was used to mine the B cell repertoire of immunized mice with a model antigen, allowing the identification of previously validated antigen-specific antibodies, and revealing different and unexpected clonal diversity patterns in the post-immunization IgM and IgG compartments. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS. Available at: https://bitbucket.org/ImmunediveRsity/immunediversity/.
journal_name
MAbsjournal_title
mAbsauthors
Cortina-Ceballos B,Godoy-Lozano EE,Sámano-Sánchez H,Aguilar-Salgado A,Velasco-Herrera Mdel C,Vargas-Chávez C,Velázquez-Ramírez D,Romero G,Moreno J,Téllez-Sosa J,Martínez-Barnetche Jdoi
10.1080/19420862.2015.1026502subject
Has Abstractpub_date
2015-01-01 00:00:00pages
516-24issue
3eissn
1942-0862issn
1942-0870journal_volume
7pub_type
杂志文章相关文献
mAbs文献大全abstract::Genomic studies have been revolutionized by the use of next generation sequencing (NGS) that delivers huge amounts of sequence information in a short span of time. The number of applications for NGS is rapidly expanding and significantly transforming many areas of life sciences. The field of antibody research and disc...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.3.1.14169
更新日期:2011-01-01 00:00:00
abstract::Complex cellular targets such as G protein-coupled receptors (GPCRs), ion channels, and other multi-transmembrane proteins represent a significant challenge for therapeutic antibody discovery, primarily because of poor stability of the target protein upon extraction from cell membranes. To assess whether a limited set...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2020.1755069
更新日期:2020-01-01 00:00:00
abstract::A costimulatory signal is required for the full activation of T cells, in addition to the antigen-specific signal via the T cell receptor. The inducible costimulator, ICOS is one of the costimulatory molecules that play an essential role in this process, particularly in the expansion or the development of effector T c...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.1.5.9633
更新日期:2009-09-01 00:00:00
abstract::Biosimilars are designed to be highly similar to approved or licensed (reference) biologics and are evaluated based on the totality of evidence from extensive analytical, nonclinical and clinical studies. As part of the stepwise approach recommended by regulatory agencies, the first step in the clinical evaluation of ...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2016.1171431
更新日期:2016-07-01 00:00:00
abstract::Biological therapies have revolutionized the treatment of several cancers and systemic immune-mediated inflammatory conditions. Expiry of patents protecting a number of biologics has provided the opportunity to commercialize highly similar versions, known as biosimilars. Biosimilars are approved by regulatory agencies...
journal_title:mAbs
pub_type: 杂志文章,评审
doi:10.1080/19420862.2018.1484977
更新日期:2018-08-01 00:00:00
abstract::Bispecific antibodies can uniquely influence cellular responses, but selecting target combinations for optimal functional activity remains challenging. Here we describe a high-throughput, combinatorial, phenotypic screening approach using a new bispecific antibody target discovery format, allowing screening of hundred...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2020.1859049
更新日期:2021-01-01 00:00:00
abstract::Multispecific antibody formats provide a promising platform for the development of novel therapeutic concepts that could facilitate the generation of safer, more effective pharmaceuticals. However, the production and use of such antibody-based multispecifics is often made complicated by: 1) the instability of the anti...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2016.1248012
更新日期:2017-01-01 00:00:00
abstract::Monoclonal antibodies (mAbs) are a burgeoning class of therapeutics, with more than 25 approved in countries worldwide. Novel molecules are entering clinical study at a rate of nearly 40 per year, and the commercial pipeline includes approximately 240 mAb therapeutics in clinical studies that have not yet progressed t...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.2.1.10677
更新日期:2010-01-01 00:00:00
abstract::Tremendous knowledge has been gained in the understanding of various modifications of IgG antibodies, driven mainly by the fact that antibodies are one of the most important groups of therapeutic molecules and because of the development of advanced analytical techniques. Recombinant monoclonal antibody (mAb) therapeut...
journal_title:mAbs
pub_type: 杂志文章,评审
doi:10.4161/mabs.29883
更新日期:2014-01-01 00:00:00
abstract::Antibodies are routinely used to study the activity of transcription factors, using various in vitro and in vivo approaches such as electrophoretic mobility shift assay, enzyme-linked immunosorbent assay, genome-wide method analysis coupled with next generation sequencing, or mass spectrometry. More recently, a new ap...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2018.1451288
更新日期:2018-05-01 00:00:00
abstract::Monoclonal antibodies (mAb) have become a mainstay in tumor therapy. Clinical responses to mAb therapy, however, are far from optimal, with many patients presenting native or acquired resistance or suboptimal responses to a mAb therapy. MAbs exert antitumor activity through different mechanisms of action and we propos...
journal_title:mAbs
pub_type: 杂志文章,评审
doi:10.4161/mabs.22775
更新日期:2013-01-01 00:00:00
abstract::Ectodomains of target antigens for antibody-based therapies can be shed from the target cell surface and found in sera of patients. Shed ectodomains of therapeutic targets not only pose the risk of sequestering therapeutic antibodies but, in a multimeric form, of triggering T cell activation by bispecific antibodies b...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.3.1.14193
更新日期:2011-01-01 00:00:00
abstract::Neutralizing antibody responses to the surface glycoproteins of enveloped viruses play an important role in immunity. Many of these glycoproteins, including the severe acute respiratory syndrome-coronavirus (SARS-CoV) spike (S) protein form trimeric units in the membrane of the native virion. There is substantial expe...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.2.1.10788
更新日期:2010-01-01 00:00:00
abstract::Given the increasing use of combination therapy with multiple monoclonal antibodies (mAbs), there is a clinical need for multiplexing assays. For the frequently co-administered anti-human epidermal growth factor receptor 2 (HER2) mAbs trastuzumab and pertuzumab, we developed a high-throughput and robust hybrid ligand-...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2020.1795492
更新日期:2020-01-01 00:00:00
abstract::Currently, almost all FDA approved therapeutic antibodies (except ReoPro, Lucentis and Cimzia which are Fabs), and the vast majority of those in clinical trials are full-size antibodies mostly in IgG1 format of about 150 kDa size. A fundamental problem for such large molecules is their poor penetration into tissues (e...
journal_title:mAbs
pub_type: 杂志文章,评审
doi:10.4161/mabs.1.1.7480
更新日期:2009-01-01 00:00:00
abstract::Hepatitis B virus (HBV) produces large (L), middle (M), and small (S) envelope proteins, alternatively referred to as hepatitis B surface antigen (HBsAg). Currently, yeast-derived S protein serves as the preventive vaccine, while hepatitis B immune globulin (HBIG) concentrated from pooled plasma of vaccine recipients ...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2015.1134409
更新日期:2016-01-01 00:00:00
abstract::Plasmacytoid dendritic cells (pDCs) play a central role for both innate and adaptive antiviral responses, as they direct immune responses through their unique ability to produce substantial concentrations of type I interferon (IFNs) upon viral encounter while also activating multiple immune cells, including macrophage...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2018.1451283
更新日期:2018-05-01 00:00:00
abstract::Antibody engineering must be accompanied by mapping strategies focused on identifying the epitope recognized by each antibody to define its unique functional identity. High throughput fine specificity determination remains technically challenging. We review recent experiences aimed at revisiting the oldest and most ex...
journal_title:mAbs
pub_type: 杂志文章,评审
doi:10.4161/mabs.36144
更新日期:2014-01-01 00:00:00
abstract::During the past two decades we have seen a phenomenal evolution of bispecific antibodies for therapeutic applications. The 'zoo' of bispecific antibodies is populated by many different species, comprising around 100 different formats, including small molecules composed solely of the antigen-binding sites of two antibo...
journal_title:mAbs
pub_type: 杂志文章,评审
doi:10.1080/19420862.2016.1268307
更新日期:2017-02-01 00:00:00
abstract::Site-specific antibody-drug conjugates (ADCs) are designed to overcome the heterogeneity observed with first-generation ADCs that use random conjugation to surface-exposed lysine residues or conjugation to interchain disulfide bonds. Despite significantly enhanced homogeneity, however, the production of site-specific ...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2019.1624127
更新日期:2019-08-01 00:00:00
abstract::Monoclonal antibodies (mAbs) against human proteins are the primary protein capture reagents for basic research, diagnosis, and molecular therapeutics. The 2 most important attributes of mAbs used in all of these applications are their specificity and avidity. While specificity of a mAb raised against a human protein ...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/19420862.2014.985919
更新日期:2015-01-01 00:00:00
abstract::Process intensification has shown great potential to increase productivity and reduce costs in biomanufacturing. This case study describes the evolution of a manufacturing process from a conventional processing scheme at 1000-L scale (Process A, n = 5) to intensified processing schemes at both 1000-L (Process B, n = 8...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2020.1770669
更新日期:2020-01-01 00:00:00
abstract::A mono-specific antibody may recruit a second antigen binding specificity, thus converting to a dual-specific Two-in-One antibody through mutation at the light chain complementarity-determining regions (CDRs). It is, however, unknown whether mutation at the heavy chain CDRs may evolve such dual specificity. Herein, we...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.28483
更新日期:2014-05-01 00:00:00
abstract::Non-enzymatic glycation is a challenging post-translational modification to characterize due to the structural heterogeneity it generates in proteins. Glycation has become increasingly recognized as an important product quality attribute to monitor, particularly for the biotechnology sector, which produces recombinant...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2015.1046663
更新日期:2015-01-01 00:00:00
abstract::The neonatal Fc receptor (FcRn) is a key membrane protein that plays an integral role in serum immunoglobulin (IgG) recycling, which extends the half-life of antibody. In addition, FcRn is known to traffic antigen-bound immunoglobulins (Ag-IgGs), and to interact with immune complexes to facilitate the antigen cross-pr...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2020.1802135
更新日期:2020-01-01 00:00:00
abstract::Surface and interfacial adsorption of antibody molecules could cause structural unfolding and desorbed molecules could trigger solution aggregation, resulting in the compromise of physical stability. Although antibody adsorption is important and its relevance to many mechanistic processes has been proposed, few techni...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2016.1276141
更新日期:2017-04-01 00:00:00
abstract::During cell line development for an IgG1 antibody candidate (mAb1), a C-terminal extension was identified in 2 product candidate clones expressed in CHO-K1 cell line. The extension was initially observed as the presence of anomalous new peaks in these clones after analysis by cation exchange chromatography (CEX-HPLC) ...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.36222
更新日期:2014-01-01 00:00:00
abstract::A dual-specific, tetravalent immunoglobulin G-like molecule, termed dual variable domain immunoglobulin (DVD-Ig™), is engineered to block two targets. Flexibility modulates Fc receptor and complement binding, but could result in undesirable cross-linking of surface antigens and downstream signaling. Understanding the ...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.24258
更新日期:2013-05-01 00:00:00
abstract::While many antibody therapeutics are formulated at low concentration (~10-20 mg/mL) for intravenous administration, high concentration (> 100 mg/mL) formulations may be required for subcutaneous delivery in certain clinical indications. For such high concentration formulations, product color is more apparent due to th...
journal_title:mAbs
pub_type: 杂志文章
doi:10.4161/mabs.28257
更新日期:2014-05-01 00:00:00
abstract::Glycosylation is a critical attribute for development and manufacturing of therapeutic monoclonal antibodies (mAbs) in the pharmaceutical industry. Conventional antibody glycan analysis is usually achieved by the 2-aminobenzamide (2-AB) hydrophilic interaction liquid chromatography (HILIC) method following the release...
journal_title:mAbs
pub_type: 杂志文章
doi:10.1080/19420862.2016.1156828
更新日期:2016-05-01 00:00:00