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
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Loss of immune regulation in aged T-cells: A metabolic review to show lack of ability to control responses within the self.
Bharat Singh,Ambak Kumar Rai +1 more
TL;DR: In this paper , the metabolic aspect of T cell function and its possible restoration is reviewed and the IL-7 and mTOR mediated pathways and their association with reactivation of effector T-cell function could help understand the dark side of the compromised adaptive immune system, particularly T cell response, in aging.
Journal ArticleDOI
In chronic infection, HIV gag-specific CD4+ T cell receptor diversity is higher than CD8+ T cell receptor diversity and is associated with less HIV quasispecies diversity.
Mark A. Pilkinton,Wyatt J. McDonnell,Louise Barnett,Abha Chopra,Rama Gangula,Katie D. White,Shay Leary,Jennifer Currenti,Silvana Gaudieri,Silvana Gaudieri,Silvana Gaudieri,Simon Mallal,Simon Mallal,Simon Mallal,Spyros A. Kalams,Spyros A. Kalams +15 more
TL;DR: In this paper, the authors evaluated the TCR diversity of CD4+ and CD8+ T cells responding to HIV-1 Gag to determine if the diversity correlates with clinical or virologic metrics.
Journal ArticleDOI
Human abdominal aortic aneurysm (AAA): Evidence for an autoimmune antigen-driven disease.
Song Lu,John White,Ifeyinwa Nwaneshiudu,Adaobi I. Nwaneshiudu,Dimitri S. Monos,Charalambos C. Solomides,Emilia L. Oleszak,Chris D. Platsoucas +7 more
TL;DR: Abdominal aortic aneurism (AAA) is a complex immunological disease with a strong genetic component, and one of the ten leading causes of death of individuals 55-74 years old worldwide as mentioned in this paper .
Journal ArticleDOI
T Cell Repertoire During Ontogeny and Characteristics in Inflammatory Disorders in Adults and Childhood
TL;DR: In this article, the role of T cell immunity in antigen detection is discussed and the characteristics of a mature TCR repertoire as well as the current state-of-the-art methods of assessment are outlined.
Journal ArticleDOI
Microfluidic T Cell Selection by Cellular Avidity
Julian F. Ashby,Julien Schmidt,Neelima Kc,Armand Kurum,Caroline Koch,Alexandre Harari,Li Tang,Sam H. Au +7 more
TL;DR: A novel microfluidic fluid shear stress‐based approach to identify and recover highly potent T cell clones based on the cellular avidity between living T cells and tumor cells is described.
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