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
Fluctuating fitness shapes the clone-size distribution of immune repertoires
TL;DR: Effective models of somatic evolution where cell fate depends on an effective fitness are proposed and fluctuations in the fitness acting specifically on clones are identified as the essential ingredient leading to the observed distributions.
Journal ArticleDOI
Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire
Jennifer S. Sims,Boris Grinshpun,Yaping Feng,Timothy H. Ung,Justin A. Neira,Jorge Samanamud,Peter Canoll,Yufeng Shen,Peter A. Sims,Jeffrey N. Bruce +9 more
TL;DR: A TCR signature strongly inversely correlated with the VJ-independent divergence between the peripheral and tissue-infiltrating repertoires of patients is discovered, and this signature is detectable in peripheral blood and could serve as a means of noninvasively monitoring immune response in patients.
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Studying the antibody repertoire after vaccination: practical applications.
TL;DR: Recent findings based on antibody repertoire sequencing are reviewed, and potential applications of these new technologies and of the analyses of the increasing volume of antibody sequence data in the context of vaccine development are discussed.
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New tools for classification and monitoring of autoimmune diseases
Holden T. Maecker,Tamsin M. Lindstrom,William H. Robinson,Paul J. Utz,Matthew Hale,Scott D. Boyd,Shai S. Shen-Orr,C. Garrison Fathman +7 more
TL;DR: This Review provides an introduction to these powerful technologies that could promote the identification of actionable biomarkers, including mass cytometry, protein arrays, and immunoglobulin and T-cell receptor high-throughput sequencing.
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Clinically Relevant Cytotoxic Immune Cell Signatures and Clonal Expansion of T-Cell Receptors in High-Risk MYCN-Not-Amplified Human Neuroblastoma.
Jun S. Wei,Igor B. Kuznetsov,Shile Zhang,Young K. Song,Shahab Asgharzadeh,Sivasish Sindiri,Xinyu Wen,Rajesh Patidar,Sushma Najaraj,Ashley Walton,Jaime M. Guidry Auvil,Daniela S. Gerhard,Aysen Yuksel,Daniel Catchpoole,Stephen M. Hewitt,Paul M. Sondel,Robert C. Seeger,John M. Maris,Javed Khan +18 more
TL;DR: Evidence is provided that RNA signatures of cytotoxic TIL are associated with the presence of activated NK/T cells and improved outcomes in high-risk neuroblastoma patients harboring MYCN-NA tumors, indicating an immune-suppressive microenvironment in these neuroblastomas.
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