Ultra-sensitive detection of rare T cell clones

Robins, Harlan; Desmarais, Cindy; Matthis, Jessica; Livingston, Robert; Andriesen, Jessica; Reijonen, Helena; Carlson, Christopher; Nepom, Gerald T.; Yee, Cassian; Cerosaletti, Karen

doi:10.1016/j.jim.2011.09.001

Cited by 170 publications

(152 citation statements)

References 20 publications

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“…Data were analysed using the ImmunoSEQ analyser toolset. This approach is capable of detecting one cell in 40,000 T cells using the Survey level, or one cell in 200,000 using the Deep level 53 .…”

Section: Methodsmentioning

confidence: 99%

Parallel T-cell cloning and deep sequencing of human MAIT cells reveal stable oligoclonal TCRβ repertoire

et al. 2014

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Mucosal-associated invariant T (MAIT) cells are abundant in humans and recognize conserved bacterial antigens derived from riboflavin precursors, presented by the nonpolymorphic MHC class I-like molecule MR1. Here we show that human MAIT cells are remarkably oligoclonal in both the blood and liver, display high inter-individual homology and exhibit a restricted length CDR3b domain of the TCRVb chain. We extend this analysis to a second sub-population of MAIT cells expressing a semi-invariant TCR conserved between individuals. Similar to 'conventional' MAIT cells, these lymphocytes react to riboflavin-synthesizing microbes in an MR1-restricted manner and infiltrate solid tissues. Both MAIT cell types release Th0, Th1 and Th2 cytokines, and sCD40L in response to bacterial infection, show cytotoxic capacity against infected cells and promote killing of intracellular bacteria, thus suggesting important protective and immunoregulatory functions of these lymphocytes.

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Section: Methodsmentioning

confidence: 99%

Parallel T-cell cloning and deep sequencing of human MAIT cells reveal stable oligoclonal TCRβ repertoire

et al. 2014

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“…We adapted technology that we previously developed for TCRb deep sequencing (21,23,24) to collect rearranged human germline IgH sequences from the genomic DNA of naive B cells that had been purified from normal human peripheral blood samples. Naive B cells were purified from PBMCs with Ab-coated magnetic beads.…”

Section: Sampling Of Human Germline Igh Repertoires With Deep Sequencingmentioning

confidence: 99%

Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing

Larimore

McCormick

Robins

et al. 2012

The Journal of Immunology

153

171

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To understand better how selection processes balance the benefits of Ig repertoire diversity with the risks of autoreactivity and nonfunctionality of highly variable IgH CDR3s, we collected millions of rearranged germline IgH CDR3 sequences by deep sequencing of DNA from mature human naive B cells purified from four individuals and analyzed the data with computational methods. Long HCDR3 regions, often components of HIV-neutralizing Abs, appear to derive not only from incorporation of long D genes and insertion of large N regions but also by usage of multiple D gene segments in tandem. However, comparison of productive and out-of-frame IgH rearrangements revealed a selection bias against long HCDR3 loops, suggesting these may be disproportionately either poorly functional or autoreactive. Our data suggest that developmental selection removes HCDR3 loops containing patches of hydrophobicity, which are commonly found in some auto-antibodies, and at least 69% of the initial productive IgH rearrangements are removed from the repertoire during B cell development. Additionally, we have demonstrated the potential utility of this new technology for vaccine development with the identification in all four individuals of related candidate germline IgH precursors of the HIV-neutralizing Ab 4E10.

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“…High-throughput T-cell receptor sequencing TCRB complementarity determining regions (CDR3β) were amplified and sequenced by Adaptive Biotechnologies Corp. (Seattle, WA, USA) using ImmunoSEQ assay Survey level analysis, which is capable of detecting one cell in 40,000 T cells. 20 The TCRB sequencing method is described in the Online Supplementary Appendix.…”

Section: Deep Targeted Sequencing and Capillary Sequencing Of Stat3 Ementioning

confidence: 99%

The analysis of clonal diversity and therapy responses using STAT3 mutations as a molecular marker in large granular lymphocytic leukemia

et al. 2014

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Ultra-sensitive detection of rare T cell clones

Cited by 170 publications

References 20 publications

Parallel T-cell cloning and deep sequencing of human MAIT cells reveal stable oligoclonal TCRβ repertoire

Parallel T-cell cloning and deep sequencing of human MAIT cells reveal stable oligoclonal TCRβ repertoire

Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing

The analysis of clonal diversity and therapy responses using STAT3 mutations as a molecular marker in large granular lymphocytic leukemia

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