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

Warren, René L.; Freeman, Jamie; Zeng, Thomas; Choe, Gina; Munro, Sarah A.; Moore, Richard C.; Webb, John R.; Holt, Robert A.

doi:10.1101/gr.115428.110

Cited by 316 publications

(380 citation statements)

References 25 publications

Supporting

Mentioning

363

Contrasting

Unclassified

Order By: Relevance

“…Additionally, within TCRVβ sequences using TRBV7-8, TRBV7-9, and TRBV28, we could identify characteristic amino acid motifs in the center of the CDR3β that were very common within celiac αEβ7 + CD38 + CD8 + T cells compared with healthy reference CDR3β sequences (30) (Fig. 4).…”

Section: Resultsmentioning

confidence: 99%

Dietary gluten triggers concomitant activation of CD4 ⁺ and CD8 ⁺ αβ T cells and γδ T cells in celiac disease

Han

Newell

Glanville

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

175

143

View full text Add to dashboard Cite

Celiac disease is an intestinal autoimmune disease driven by dietary gluten and gluten-specific CD4 + T-cell responses. In celiac patients on a gluten-free diet, exposure to gluten induces the appearance of gluten-specific CD4 + T cells with gut-homing potential in the peripheral blood. Here we show that gluten exposure also induces the appearance of activated, gut-homing CD8 + αβ and γδ T cells in the peripheral blood. Single-cell T-cell receptor sequence analysis indicates that both of these cell populations have highly focused Tcell receptor repertoires, indicating that their induction is antigendriven. These results reveal a previously unappreciated role of antigen in the induction of CD8 + αβ and γδ T cells in celiac disease and demonstrate a coordinated response by all three of the major types of T cells. More broadly, these responses may parallel adaptive immune responses to viral pathogens and other systemic autoimmune diseases.autoimmunity | mucosal immunity

show abstract

Section: Resultsmentioning

confidence: 99%

Dietary gluten triggers concomitant activation of CD4 ⁺ and CD8 ⁺ αβ T cells and γδ T cells in celiac disease

Han

Newell

Glanville

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

175

143

View full text Add to dashboard Cite

show abstract

“…Recent advances in next-generation sequencing (NGS) (2) have enabled any DNA-encodable assay to produce massive amounts of data. Indeed, NGS has enabled unprecedented views into the immune repertoire, as its immune receptor diversity is genetically encoded within a complex collection of lymphocytes (3)(4)(5)(6)(7)(8).…”

mentioning

confidence: 99%

High-resolution antibody dynamics of vaccine-induced immune responses

Laserson

Vigneault

Gadala-Maria

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

175

216

View full text Add to dashboard Cite

The adaptive immune system confers protection by generating a diverse repertoire of antibody receptors that are rapidly expanded and contracted in response to specific targets. Next-generation DNA sequencing now provides the opportunity to survey this complex and vast repertoire. In the present work, we describe a set of tools for the analysis of antibody repertoires and their application to elucidating the dynamics of the response to viral vaccination in human volunteers. By analyzing data from 38 separate blood samples across 2 y, we found that the use of the germ-line library of V and J segments is conserved between individuals over time. Surprisingly, there appeared to be no correlation between the use level of a particular VJ combination and degree of expansion. We found the antibody RNA repertoire in each volunteer to be highly dynamic, with each individual displaying qualitatively different response dynamics. By using combinatorial phage display, we screened selected VH genes paired with their corresponding VL library for affinity against the vaccine antigens. Altogether, this work presents an additional set of tools for profiling the human antibody repertoire and demonstrates characterization of the fast repertoire dynamics through time in multiple individuals responding to an immune challenge.next-generation sequencing | influenza | immunology T he immune system is able to rapidly sense and respond to a vast array of invading organisms. Its arsenal contains systems that are immediately effective against commonly seen patterns (innate immunity) and systems that are capable of responding to novel invaders (adaptive immunity). Given the acute nature and diversity of infections, the immune system must be capable of rapid recognition of a pathogen, amplification of the response, and subsequent contraction of the response after the resolution of the infection. Adaptive immune responses rely on the continuous selection and amplification of specific clones from an enormous library of immune receptors (antibodies and T cell receptors). Specifically, stimulation of B-cell immunity results in the synthesis of antibodies that are secreted into the blood stream or into the mucosa as well as the programming of B memory cells that play a crucial role in the generation of rapid protective responses upon reinfection.Currently, many immunology studies depend on characterizing lymphocyte subsets (e.g., assaying cell-surface receptors) and the ability to correlate them to encoded genetic information (1). Recent advances in next-generation sequencing (NGS) (2) have enabled any DNA-encodable assay to produce massive amounts of data. Indeed, NGS has enabled unprecedented views into the immune repertoire, as its immune receptor diversity is genetically encoded within a complex collection of lymphocytes (3-8).The present study set out to dissect the rapid dynamics of the complete human peripheral antibody response against a controlled immune challenge (vaccination), without the a priori notion of cell state markers or functions...

show abstract

“…Using pyrosequencing, Warren et al recently described limited conservation of CDR3 sequences among human individuals (around 1%) [8]. However, when converted into amino acid sequences, the conservation appeared much higher with up to 14.2% homology between two unrelated donors [8]. Furthermore, a recent study argue that 424.5% of the naïve TCRb amino acid repertoire was shared with at least another donor of the study [9].…”

Section: Discussionmentioning

confidence: 99%

“…In this line, an interesting study recently proposed a numerical model of mouse TCR Va/Ja gene accessibility that pointed out unbalanced V-J associations resulting from preferential access to gene rearrangements [6]. Despite studies using high-throughput sequencing of TCR b chains [2,[7][8][9], a global view on the distribution of V-J rearrangement combinations of the TCR b chain in humans was lacking. Here, we have reanalyzed T-cell repertoire data that we generated in humanized NOD.SCID.gc À/À (NSG) mice [5] with the aim to determine the extent of the overlap between the T-cell repertoire of humans and humanized mice at the level of V-J rearrangements.…”

Section: Introductionmentioning

confidence: 99%

“…This idea is further supported by the fact that IL-7 adjunction greatly improved both T-cell reconstitution and repertoire diversity [4]. Using pyrosequencing, Warren et al recently described limited conservation of CDR3 sequences among human individuals (around 1%) [8]. However, when converted into amino acid sequences, the conservation appeared much higher with up to 14.2% homology between two unrelated donors [8].…”

mentioning

confidence: 99%

See 1 more Smart Citation

Half of the T‐cell repertoire combinatorial diversity is genetically determined in humans and humanized mice

Pham

Manuel²,

Petit

et al. 2011

Eur J Immunol

View full text Add to dashboard Cite

In humanized mice, the T-cell repertoire is derived from genetically identical human progenitors in distinct animals. Thus, careful comparison of the T-cell repertoires of humanized mice with those of humans may reveal the contribution of genetic determinism on T-cell repertoire formation. Here, we performed a comprehensive assessment of the distribution of V-J combinations of the human b chain of the T-cell receptor (hTRBV) in NOD.SCID.cc À/À (NSG) humanized mice. We observed that numerous V-J combinations were equally distributed in the thymus and in the periphery of humanized mice compared with human references. A global analysis of the data, comparing repertoire perturbation indices in humanized NSG mice and unrelated human PBMCs, reveals that 50% of the hTRBV families significantly overlapped. Using multivariate ranking and bootstrap analyses, we found that 18% of all possible V-J combinations contributed close to 50% of the expressed diversity, with significant over-representation of BV5-J1.111.2 and BV6-J1.111.2 rearrangements. Finally, comparison of CD3 À and CD3 1 thymocyte repertoires indicated that the observed V-J combination overlap was already present before TCR-MHC selection in the thymus. Altogether, our results show that half of the T-cell repertoire combinatorial diversity in humans is genetically determined.Key words: Humanized mice . ISEApeaks . Multivariate score . T-cell repertoire . V-J rearrangements Supporting Information available online Introduction T-cell repertoire diversity is based upon tightly ordered genetic rearrangements of the T-cell receptor V, D and J genes. The available numbers of these genes in the genome constitutes a first level of diversity: to date, 33 and 65 genes encoding variable elements of the human T-cell receptor b chain (hTRBV) from 30 hTRBV families have been characterized in mice and humans respectively (according to the ImMunoGeneTics (IMGT) database (http://www.imgt.org)). An additional level of diversity comes from the association of single V, (D) and J elements together. The major determinant of repertoire diversity is then random addition of nucleotides at the junction of these V(D)J gene segments, constituting the CDR3 of the TCR. Finally, a fourth level of complexity originates from the association of the rearranged a and b chains of the TCR. In theory, these sequential processes occurring during T-cell differentiation in the thymus could Eur. J. Immunol. 2012. 42: 760-770 760 generate up to 10 15 different TCRs, a number far in excess of the number of T-cells in the body. The 'real' size of the repertoire is probably much lower though, with recent estimations of unique TCR b chains ranging from 10 6 to 4.10 6 in humans [1,2]. Mice reconstituted with a human immune system generated from hematopoietic precursors represent a new animal model for human immunology studies. The extent of the human T-cell repertoire diversity generated in mice may represent an important functional indicator [3], useful for immunological studies in the models. However, a...

show abstract

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

Cited by 316 publications

References 25 publications

Dietary gluten triggers concomitant activation of CD4 ⁺ and CD8 ⁺ αβ T cells and γδ T cells in celiac disease

Dietary gluten triggers concomitant activation of CD4 ⁺ and CD8 ⁺ αβ T cells and γδ T cells in celiac disease

High-resolution antibody dynamics of vaccine-induced immune responses

Half of the T‐cell repertoire combinatorial diversity is genetically determined in humans and humanized mice

Contact Info

Product

Resources

About

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

Cited by 316 publications

References 25 publications

Dietary gluten triggers concomitant activation of CD4 + and CD8 + αβ T cells and γδ T cells in celiac disease

Dietary gluten triggers concomitant activation of CD4 + and CD8 + αβ T cells and γδ T cells in celiac disease

High-resolution antibody dynamics of vaccine-induced immune responses

Half of the T‐cell repertoire combinatorial diversity is genetically determined in humans and humanized mice

Contact Info

Product

Resources

About

Dietary gluten triggers concomitant activation of CD4 ⁺ and CD8 ⁺ αβ T cells and γδ T cells in celiac disease

Dietary gluten triggers concomitant activation of CD4 ⁺ and CD8 ⁺ αβ T cells and γδ T cells in celiac disease