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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Journal ArticleDOI
Genetic and environmental determinants of human TCR repertoire diversity.
TL;DR: It is shown that TCR repertoire diversity is positively associated with polymorphism at the human leukocyte antigen class I (HLA-I) loci, and diminishes with age and cytomegalovirus (CMV) infection and a mechanism underlying the evolutionary fitness advantage of HLA-I heterozygosity is suggested.
Journal ArticleDOI
Next generation sequencing: new tools in immunology and hematology
TL;DR: Recently, a novel technology known as next generation sequencing has been developed; this allows the recognition of unique sequences and provides depth of coverage, heterogeneity, and accuracy of sequencing, and provides a powerful tool that, along with microarray analysis for gene expression, may become integral in resolving the remaining key problems in hematology.
Journal ArticleDOI
Enteric immunity, the gut microbiome, and sepsis: Rethinking the germ theory of disease
TL;DR: It is hypothesized that sepsis induces imbalances in microbial populations residing in the gut, along with compromises in epithelial integrity, and normal antigen sampling becomes impaired, and proliferative cues are intermixed with inhibitory signals, which situates the microbiome, the Gut, and its complex immune network of cells and bacteria, at the center of aberrant immune responses during and after septis.
Journal ArticleDOI
Mother and Child T Cell Receptor Repertoires: Deep Profiling Study
Ekaterina V. Putintseva,Olga V. Britanova,Dmitriy B. Staroverov,Ekaterina M. Merzlyak,Maria A. Turchaninova,Mikhail Shugay,Dmitriy A. Bolotin,Mikhail V. Pogorelyy,Ilgar Z. Mamedov,Vlasta Bobrynina,M.A. Maschan,Yuri B. Lebedev,Dmitriy M. Chudakov,Dmitriy M. Chudakov +13 more
TL;DR: It is shown that thymic selection essentially and similarly shapes the initial output of the TCR recombination machinery in both related and unrelated pairs, with minor effect from inherited differences.
Journal ArticleDOI
Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy.
TL;DR: The T cells are key players of the response to checkpoint blockade immunotherapy and monitoring the strength and specificity of antitumor T-cell reactivity remains a crucial but elusive component of precision immunotherapy.
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