scholarly journals Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information

2021 ◽  
Author(s):  
James M Heather ◽  
Matthew J Spindler ◽  
Marta Herrero Alonso ◽  
Yifang Ivana Shui ◽  
David G Millar ◽  
...  
Keyword(s):  
T Cell Receptors ◽  
Modular Design ◽  
Software Tool ◽  
Nucleotide Sequences ◽  
Jurkat Cells ◽  
Antigen Specificity ◽  
Data Repositories ◽  
Coding Sequences ◽  
Repeatability And Reproducibility ◽  
Gene Symbols

The study and manipulation of T cell receptors (TCRs) is central to multiple fields across basic and translational immunology research. Produced by V(D)J recombination, TCRs are often only recorded in the literature and data repositories as a combination of their V and J gene symbols, plus their hypervariable CDR3 amino acid sequence. However, numerous applications require full-length coding nucleotide sequences. Here we present Stitchr, a software tool developed to specifically address this limitation. Given minimal V/J/CDR3 information, Stitchr produces complete coding sequences representing a fully spliced TCR cDNA. Due to its modular design, Stitchr can be used for TCR engineering using either published germline or novel/modified variable and constant region sequences. Sequences produced by Stitchr were validated by synthesizing and transducing TCR sequences into Jurkat cells, recapitulating the expected antigen specificity of the parental TCR. Using a companion script, Thimble, we demonstrate that Stitchr can process a million TCRs in under ten minutes using a standard desktop personal computer. By systemizing the production and modification of TCR sequences, we propose that Stitchr will increase the speed, repeatability, and reproducibility of TCR research. Stitchr is available on GitHub.

scholarly journals Functionally specialized human CD4+ T-cell subsets express physicochemically distinct TCRs

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Sofya A Kasatskaya ◽  
Kristin Ladell ◽  
Evgeniy S Egorov ◽  
Kelly L Miners ◽  
Alexey N Davydov ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Cell Receptors ◽  
Adaptive Immune System ◽  
T Cell Subsets ◽  
Effector Memory ◽  
Intrinsic Properties ◽  
Antigen Specificity ◽  
Adaptive Immune ◽  
Transition Pathways

The organizational integrity of the adaptive immune system is determined by functionally discrete subsets of CD4+ T cells, but it has remained unclear to what extent lineage choice is influenced by clonotypically expressed T-cell receptors (TCRs). To address this issue, we used a high-throughput approach to profile the αβ TCR repertoires of human naive and effector/memory CD4+ T-cell subsets, irrespective of antigen specificity. Highly conserved physicochemical and recombinatorial features were encoded on a subset-specific basis in the effector/memory compartment. Clonal tracking further identified forbidden and permitted transition pathways, mapping effector/memory subsets related by interconversion or ontogeny. Public sequences were largely confined to particular effector/memory subsets, including regulatory T cells (Tregs), which also displayed hardwired repertoire features in the naive compartment. Accordingly, these cumulative repertoire portraits establish a link between clonotype fate decisions in the complex world of CD4+ T cells and the intrinsic properties of somatically rearranged TCRs.

Recovery of Paired T Cell Receptors from Single-cell Seq-Well Libraries

2019 ◽  
Author(s):  
Ang A. Tu ◽  
Todd M. Gierahn ◽  
Brinda Monian ◽  
Duncan M. Morgan ◽  
Naveen K. Mehta ◽  
...  
Keyword(s):  
T Cells ◽  
Food Allergy ◽  
T Cell ◽  
Single Cell ◽  
T Cell Receptors ◽  
Immune Cell ◽  
Cost Effective ◽  
Antigen Specificity ◽  
Activated T Cells ◽  
Cell Receptors

Abstract High-throughput 3’ single-cell RNA-Sequencing (scRNA-Seq) allows for cost-effective, detailed characterization of thousands of individual immune cells from healthy and diseased tissues. Current techniques, however, are limited in their ability to elucidate essential immune cell features, including the variable sequences of T cell receptors (TCRs) that confer antigen specificity in T cells. Here, we present an enrichment strategy that enables simultaneous analysis of TCR variable sequences and corresponding full transcriptomes from 3’ barcoded scRNA-Seq samples. This approach is compatible with common 3’ scRNA-Seq methods, and adaptable to processed samples post hoc. We applied the technique to resolve clonotype-to-phenotype relationships among antigen-activated T cells from immunized mice and from patients with food allergy. We observed diverse but preferential cellular phenotypes manifest among subsets of expanded clonotypes, including functional Th2 states associated with food allergy. These results demonstrate the utility of our method when studying complex diseases in which clonotype-driven immune responses are critical to understanding the underlying biology.

scholarly journals Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors

2020 ◽  
Vol 11 ◽  
Author(s):  
Chloe H. Lee ◽  
Mariolina Salio ◽  
Giorgio Napolitani ◽  
Graham Ogg ◽  
Alison Simmons ◽  
...  
Keyword(s):  
T Cell ◽  
T Cell Receptors ◽  
Cross Reactivity ◽  
Antigen Specificity ◽  
Cell Receptors

scholarly journals Distraction index measurement on the dog's hip joint using a dedicated software

2020 ◽  
Vol 72 (4) ◽  
pp. 1241-1247 ◽  
Author(s):  
S. Alves-Pimenta ◽  
A. Santana ◽  
J. Martins ◽  
B. Colaço ◽  
L. Gonçalves ◽  
...  
Keyword(s):  
Computer Software ◽  
Software Tool ◽  
Measurement Tool ◽  
Specific Training ◽  
Hip Joints ◽  
Index Measurement ◽  
Analysis Center ◽  
Good Repeatability ◽  
Repeatability And Reproducibility ◽  
Measurement Repeatability

ABSTRACT The aim of this study was to test the accuracy of a new automated computer software tool for the assessment of passive hip laxity. The hip laxity was estimated using the dedicated computer software by two blinded evaluators, one previously trained and one without specific training for distraction index measurement, in two independent sessions using 230 hip joints from 115 dogs that underwent screening for passive hip laxity using the distraction view. Previously, all of these radiographs were sent to PennHIP Analysis Center for an official distraction index record. The measurement repeatability of the two sessions was adequate for both evaluators. The reproducibility of the official distraction index measurement, mean distraction index±standard deviation 0.44±0.15, was adequate (P>0.05) for the trained evaluator, 0.44±0.15, and non-adequate (P<0.05), for the non-trained evaluator 0.47±0.17. The distraction index measurement tool proposed can be used with confidence for hip laxity evaluation by trained evaluators, as it provided good repeatability and reproducibility of official reports. The simplicity of the process described leads to a less time-consuming and more affordable procedure.

scholarly journals TCR3d: The T cell receptor structural repertoire database

2019 ◽  
Vol 35 (24) ◽  
pp. 5323-5325 ◽  
Author(s):  
Ragul Gowthaman ◽  
Brian G Pierce
Keyword(s):  
T Cell ◽  
T Cell Receptors ◽  
Adaptive Immune System ◽  
Cell Receptor ◽  
Binding Mode ◽  
Computational Techniques ◽  
Antigen Specificity ◽  
Cell Receptors ◽  
Gene Usage ◽  
Mechanistic Basis

Abstract Summary T cell receptors (TCRs) are critical molecules of the adaptive immune system, capable of recognizing diverse antigens, including peptides, lipids and small molecules, and represent a rapidly growing class of therapeutics. Determining the structural and mechanistic basis of TCR targeting of antigens is a major challenge, as each individual has a vast and diverse repertoire of TCRs. Despite shared general recognition modes, diversity in TCR sequence and recognition represents a challenge to predictive modeling and computational techniques being developed to predict antigen specificity and mechanistic basis of TCR targeting. To this end, we have developed the TCR3d database, a resource containing all known TCR structures, with a particular focus on antigen recognition. TCR3d provides key information on antigen binding mode, interface features, loop sequences and germline gene usage. Users can interactively view TCR complex structures, search sequences of interest against known structures and sequences, and download curated datasets of structurally characterized TCR complexes. This database is updated on a weekly basis, and can serve the community as a centralized resource for those studying T cell receptors and their recognition. Availability and implementation The TCR3d database is available at https://tcr3d.ibbr.umd.edu/.

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