Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes
René L. Warren,J. Douglas Freeman,Thomas Zeng,Gina Choe,Sarah A. Munro,Richard D. Moore,John R. Webb,Robert A. Holt +7 more
TLDR
It is shown that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy, and a new, directly measured, lower limit on individual T-cell repertoire size is established.Abstract:
Massively parallel sequencing is a useful approach for characterizing T-cell receptor diversity. However, immune receptors are extraordinarily difficult sequencing targets because any given receptor variant may be present in very low abundance and may differ legitimately by only a single nucleotide. We show that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy. At two timepoints, 1 wk apart, we isolated bulk PBMC plus naive (CD45RA+/CD45RO-) and memory (CD45RA-/CD45RO+) T-cell subsets from a healthy donor. From T-cell receptor beta chain (TCRB) mRNA we constructed and sequenced multiple libraries to obtain a total of 1.7 billion paired sequence reads. The sequencing error rate was determined empirically and used to inform a high stringency data filtering procedure. The error filtered data yielded 1,061,522 distinct TCRB nucleotide sequences from this subject which establishes a new, directly measured, lower limit on individual T-cell repertoire size and provides a useful reference set of sequences for repertoire analysis. TCRB nucleotide sequences obtained from two additional donors were compared to those from the first donor and revealed limited sharing (up to 1.1%) of nucleotide sequences among donors, but substantially higher sharing (up to 14.2%) of inferred amino acid sequences. For each donor, shared amino acid sequences were encoded by a much larger diversity of nucleotide sequences than were unshared amino acid sequences. We also observed a highly statistically significant association between numbers of shared sequences and shared HLA class I alleles.read more
Citations
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Converging evolution leads to near maximal junction diversity through parallel mechanisms in B and T cell receptors.
TL;DR: T and B cell receptor (TCR and BCR) complementarity determining region 3 (CDR3) genetic diversity is produced through multiple diversification and selection stages and TCR is as diverse as BCR repertoire, with a biased CDR3 length toward short TCRs and long BCRs.
Journal ArticleDOI
The immune system as a biomonitor: explorations in innate and adaptive immunity
Niclas Thomas,James M. Heather,Gabriel Pollara,Nandi Simpson,Theres Matjeka,John Shawe-Taylor,Mahdad Noursadeghi,Benjamin M. Chain +7 more
TL;DR: Two different and complementary ways of querying the human immune ‘state’ using high-dimensional genomic screening methodologies are considered, and the potentials of these approaches are discussed and some of the technological and computational challenges to be overcome.
Journal ArticleDOI
Avidity of human T cell receptor engineered CD4(+) T cells drives T-helper differentiation fate.
TL;DR: The role of TCR specific antigen avidity in differentiation and maintenance of human Th1, Th2 and Th17 subsets is investigated and it is shown that TCR avidity can control the percentage of IL-4 and IFN-γ co-expression in unskewed TCR engineered cells.
Journal ArticleDOI
A TCR β-Chain Motif Biases toward Recognition of Human CD1 Proteins.
Peter Reinink,Peter Reinink,Adam Shahine,Adam Shahine,Stephanie Gras,Stephanie Gras,Tan Yun Cheng,Rachel Farquhar,Rachel Farquhar,Kattya Lopez,Sara Suliman,Josephine F. Reijneveld,Josephine F. Reijneveld,Josephine F. Reijneveld,Jérôme Le Nours,Jérôme Le Nours,Li Lynn Tan,Li Lynn Tan,Segundo R. Leon,Judith Jimenez,Roger Calderon,Leonid Lecca,Megan Murray,Megan Murray,Jamie Rossjohn,Jamie Rossjohn,Jamie Rossjohn,D. Branch Moody,Ildiko Van Rhijn,Ildiko Van Rhijn +29 more
TL;DR: CD1b tetramer studies and a survey of the 27 published CD1b-restricted TCRs demonstrated a TCR motif in humans defined by the TCR β-chain variable gene 4-1 (TRBV4-1).
Journal ArticleDOI
DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles
TL;DR: The DynaDom method predicts the correct orientation of the TCR Vα/Vβ angles in 96 and 89% of the cases, for the poses with the best RMSD and best interaction energy, respectively, which proves the suitability of the approach for interdomain-angle optimization.
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