scholarly journals Biochemical patterns of antibody polyreactivity revealed through a bioinformatics-based analysis of CDR loops

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Christopher T Boughter ◽  
Marta T Borowska ◽  
Jenna J Guthmiller ◽  
Albert Bendelac ◽  
Patrick C Wilson ◽  
...  
Keyword(s):  
Biophysical Properties ◽  
Bioinformatic Pipeline ◽  
High Affinity ◽  
Repertoire Analysis ◽  
Single Target ◽  
Binding Surface ◽  
Polyreactive Antibodies ◽  
Automated Pipeline ◽  
Critical Components ◽  
Immune Repertoire Analysis

Antibodies are critical components of adaptive immunity, binding with high affinity to pathogenic epitopes. Antibodies undergo rigorous selection to achieve this high affinity, yet some maintain an additional basal level of low affinity, broad reactivity to diverse epitopes, a phenomenon termed ‘polyreactivity’. While polyreactivity has been observed in antibodies isolated from various immunological niches, the biophysical properties that allow for promiscuity in a protein selected for high-affinity binding to a single target remain unclear. Using a database of over 1000 polyreactive and non-polyreactive antibody sequences, we created a bioinformatic pipeline to isolate key determinants of polyreactivity. These determinants, which include an increase in inter-loop crosstalk and a propensity for a neutral binding surface, are sufficient to generate a classifier able to identify polyreactive antibodies with over 75% accuracy. The framework from which this classifier was built is generalizable, and represents a powerful, automated pipeline for future immune repertoire analysis.

scholarly journals Biochemical Patterns of Antibody Polyreactivity Revealed Through a Bioinformatics-Based Analysis of CDR Loops

2020 ◽  
Author(s):  
Christopher T. Boughter ◽  
Marta T. Borowska ◽  
Jenna J. Guthmiller ◽  
Albert Bendelac ◽  
Patrick C. Wilson ◽  
...  
Keyword(s):  
Biophysical Properties ◽  
Bioinformatic Pipeline ◽  
High Affinity ◽  
Repertoire Analysis ◽  
Single Target ◽  
Binding Surface ◽  
Polyreactive Antibodies ◽  
Automated Pipeline ◽  
Critical Components ◽  
Immune Repertoire Analysis

AbstractAntibodies are critical components of adaptive immunity, binding with high affinity to pathogenic epitopes. Antibodies undergo rigorous selection to achieve this high affinity, yet some maintain an additional basal level of low affinity, broad reactivity to diverse epitopes, a phenomenon termed “polyreactivity”. While polyreactivity has been observed in antibodies isolated from various immunological niches, the biophysical properties that allow for promiscuity in a protein selected for high affinity binding to a single target remain unclear. Using a database of nearly 1,500 polyreactive and non-polyreactive antibody sequences, we created a bioinformatic pipeline to isolate key determinants of polyreactivity. These determinants, which include an increase in inter-loop crosstalk and a propensity for an “inoffensive” binding surface, are sufficient to generate a classifier able to identify polyreactive antibodies with over 75% accuracy. The framework from which this classifier was built is generalizable, and represents a powerful, automated pipeline for future immune repertoire analysis.

scholarly journals ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Anke Fähnrich ◽  
Moritz Krebbel ◽  
Normann Decker ◽  
Martin Leucker ◽  
Felix D. Lange ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Immune Repertoire ◽  
Repertoire Analysis ◽  
Immune Repertoire Analysis

scholarly journals High-throughput immune repertoire analysis with IGoR

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Quentin Marcou ◽  
Thierry Mora ◽  
Aleksandra M. Walczak
Keyword(s):  
High Throughput ◽  
Immune Repertoire ◽  
Repertoire Analysis ◽  
Immune Repertoire Analysis

scholarly journals The pipeline repertoire of Ig-Seq analysis

2018 ◽  
Author(s):  
Laura López-Santibáñez-Jácome ◽  
Selma Eréndira Avendaño-Vázquez ◽  
Carlos Fabián Flores-Jasso
Keyword(s):  
Experimental Design ◽  
High Throughput Sequencing ◽  
Immune Repertoire ◽  
Computational Tools ◽  
Repertoire Analysis ◽  
Strategic Approach ◽  
Antibody Repertoires ◽  
Computational Analyses ◽  
Immune Repertoire Analysis

With the advent of high-throughput sequencing of immunoglobulins (Ig-Seq), the understanding of antibody repertoires and its dynamics among individuals and populations has become and exiting area of research. There are an increasing number of computational tools that aid in every step of the immune repertoire characterization. However, since not all tools function identically, every pipeline has its unique rationale and capabilities, creating a rich blend of useful features that may appear intimidating for newcomer laboratories with the desire to plunge into immune repertoire analysis to expand and improve their research; hence, all pipeline strengths and differences may not seem evident. In this review we provide an organized list of the current set of computational tools, focusing on their most attractive features and differences in order to carry out the characterization of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational analyses of immune repertoires.

scholarly journals A novel, stable, helical scaffold as an alternative binder - construction of phage display libraries.

2012 ◽  
Vol 59 (3) ◽  
Author(s):  
Anna Cyranka-Czaja ◽  
Jacek Otlewski
Keyword(s):  
Phage Display ◽  
Measles Virus ◽  
In Vitro Selection ◽  
Biophysical Properties ◽  
Phage Display Technology ◽  
High Affinity ◽  
Promising Tool ◽  
Phage Display Libraries ◽  
Display Technology

Specific, high affinity binding macromolecules are of great importance for biomedical and biotechnological applications. The most popular classical antibody-based molecules have recently been challenged by alternative scaffolds with desirable biophysical properties. Phage display technology applied to such scaffolds allows generation of potent affinity reagents by in vitro selection. Here, we report identification and characterization of a novel helical polypeptide with advantageous biophysical properties as a template for construction of phage display libraries. A three-helix bundle structure, based on Measles virus phosphoprotein P shows a very favourable stability and solubility profile. We designed, constructed and characterized six different types of phage display libraries based on the proposed template. Their functional size of over 10(9) independent clones, balanced codon bias and decent display level are key parameters attesting to the quality and utility of the libraries. The new libraries are a promising tool for isolation of high affinity binders based on a small helical scaffold which could become a convenient alternative to antibodies.

scholarly journals α-Helical peptidic scaffolds to target α-synuclein toxic species with nanomolar affinity

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jaime Santos ◽  
Pablo Gracia ◽  
Susanna Navarro ◽  
Samuel Peña-Díaz ◽  
Jordi Pujols ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Cell Damage ◽  
Biophysical Properties ◽  
Functional Protein ◽  
Guided Search ◽  
Toxic Species ◽  
High Affinity ◽  
Key Driver ◽  
The Brain ◽  
Therapeutic Avenue

Abstractα-Synuclein aggregation is a key driver of neurodegeneration in Parkinson’s disease and related syndromes. Accordingly, obtaining a molecule that targets α-synuclein toxic assemblies with high affinity is a long-pursued objective. Here, we exploit the biophysical properties of toxic oligomers and amyloid fibrils to identify a family of α-helical peptides that bind to these α-synuclein species with low nanomolar affinity, without interfering with the monomeric functional protein. This activity is translated into a high anti-aggregation potency and the ability to abrogate oligomer-induced cell damage. Using a structure-guided search we identify a human peptide expressed in the brain and the gastrointestinal tract with analogous binding, anti-aggregation, and detoxifying properties. The chemical entities we describe here may represent a therapeutic avenue for the synucleinopathies and are promising tools to assist diagnosis by discriminating between native and toxic α-synuclein species.

scholarly journals The pipeline repertoire of Ig-Seq analysis

2018 ◽  
Author(s):  
Laura López-Santibáñez-Jácome ◽  
Selma Eréndira Avendaño-Vázquez ◽  
Carlos Fabián Flores-Jasso
Keyword(s):  
Experimental Design ◽  
High Throughput Sequencing ◽  
Immune Repertoire ◽  
Computational Tools ◽  
Repertoire Analysis ◽  
Strategic Approach ◽  
Antibody Repertoires ◽  
Computational Analyses ◽  
Immune Repertoire Analysis

With the advent of high-throughput sequencing of immunoglobulins (Ig-Seq), the understanding of antibody repertoires and its dynamics among individuals and populations has become and exiting area of research. There are an increasing number of computational tools that aid in every step of the immune repertoire characterization. However, since not all tools function identically, every pipeline has its unique rationale and capabilities, creating a rich blend of useful features that may appear intimidating for newcomer laboratories with the desire to plunge into immune repertoire analysis to expand and improve their research; hence, all pipeline strengths and differences may not seem evident. In this review we provide an organized list of the current set of computational tools, focusing on their most attractive features and differences in order to carry out the characterization of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational analyses of immune repertoires.

scholarly journals Scalable Design of paired CRISPR Guide RNAs for Genomic Deletion

2016 ◽  
Author(s):  
Carlos Pulido-Quetglas ◽  
Estel Aparicio-Prat ◽  
Carme Arnan ◽  
Taisia Polidori ◽  
Toni Hermoso ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Model Organisms ◽  
High Coverage ◽  
Bioinformatic Pipeline ◽  
Genomic Deletion ◽  
C Elegans ◽  
Guide Rnas ◽  
Single Target ◽  
Sgrna Design ◽  
Scalable Design

AbstractUsing CRISPR/Cas9, diverse genomic elements may be studied in their endogenous context. Pairs of single guide RNAs (sgRNAs) are used to delete regulatory elements and small RNA genes, while longer RNAs can be silenced through promoter deletion. We here present CRISPETa, a bioinformatic pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target. Any number of targets can be analyzed in parallel, making CRISPETa equally appropriate for studies of individual elements, or complex library screens. Fast run-times are achieved using a precomputed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present a series of pre-designed, high-coverage library designs for entire classes of non-coding elements in human, mouse, zebrafish, Drosophila and C. elegans. Using an improved version of the DECKO deletion vector, together with a quantitative deletion assay, we test CRISPETa designs by deleting an enhancer and exonic fragment of the MALAT1 oncogene. These achieve efficiencies of ≥50%, resulting in production of mutant RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales.

scholarly journals IGoR: a tool for high-throughput immune repertoire analysis

2017 ◽  
Author(s):  
Quentin Marcou ◽  
Thierry Mora ◽  
Aleksandra M. Walczak
Keyword(s):  
T Cell ◽  
B Cells ◽  
High Throughput ◽  
T Cell Receptors ◽  
Diagnostic Tools ◽  
Biological Complexity ◽  
Immune Repertoire ◽  
Repertoire Analysis ◽  
Repertoire Sequencing ◽  
Immune Repertoire Analysis

High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of these datasets. We present IGoR - a new comprehensive tool that takes B or T-cell receptors sequence reads and quantitatively characterizes the statistics of receptor generation from both cDNA and gDNA. It probabilistically annotates sequences and its modular structure can investigate models of increasing biological complexity for different organisms. For B-cells IGoR returns the hypermutation statistics, which we use to reveal co-localization of hypermutations along the sequence. We demonstrate that IGoR outperforms existing tools in accuracy and estimate the sample sizes needed for reliable repertoire characterization.

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