Molecular analysis of the complementarity determining region 3 of the human T cell receptor beta chain. Establishment of a reference panel of CDR3 lengths from phytohaemagglutinin activated lymphocytes

The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis

T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a "next-generation" of repertoire analysis.

Retrovirus mediated gene transduction of human T-cell subsets

PURPOSE

Allogeneic bone marrow transplantation (AlloBMT) can be curative for patients with leukaemia. Graft versus host disease (GVHD) is a potentially life threatening complication of AlloBMT mediated by the T cells contained within the graft. In order to be able to control GVHD, the allogeneic T cells may be transduced with a suicide gene such as herpes simplex virus thymidine kinase (HSV-tk). For this strategy to be successful, all subsets of T cells should be transduced to a similar extent. Also, the transduction protocol should not induce expression of unwanted homing receptors, nor should it lead to unwanted skewing of the T-cell receptor repertoire. We have studied the transduction efficiency of naïve and memory subsets of CD4+ and CD8+ T cells, and examined the transduced T-cell subsets for possible changes in T-cell receptor (TCR) repertoire and homing receptor expression.

METHODS

The cells were transduced using a Moloney murine retroviral vector carrying a conjugate of the genes encoding the truncated form of the cell surface marker, low affinity nerve growth factor receptor (DeltaLNGFR) and HSV-tk. Transduction efficiency and homing receptor expression were quantified by flow cytometry. TCR repertoire was determined by spectratyping.

RESULTS

We obtained a transduction efficiency of 30-50% of the cells, with no difference between the T-cell subsets. Cell surface receptors responsible for homing to skin, gastrointestinal tract or lymph nodes were practically absent at the end of 2 weeks in culture. The activation procedure seemed to favour the expansion of certain T-cell clones over polyclonal populations. However, there was no difference in the TCR repertoire between transduced and non-transduced cells.

CONCLUSION

Changes in the composition of the T-cell subsets at the end of the cell culture were the results of the activation, and not the suicide gene transduction. The transduced T cells did not express unwanted homing receptors.

Characterization of the Interstitial Lung and Peripheral Blood T Cell Receptor Repertoire in Cigarette Smokers

T lymphocytes modulate the pulmonary inflammatory response. The aim of this study was to evaluate the clonality within the interstitial lung and peripheral blood T cell receptor (TCR) repertoire in smokers. Interstitial T lymphocytes were isolated from surplus tissue of 16 patients (63 +/- 9 [+/- SD] yr old, 11 male) undergoing surgery due to lung cancer (n = 15) or emphysema. TCR clonality was assessed by PCR amplification followed by spectratyping. Nearly all TCR of interstitial lung lymphocytes showed oligoclonal bands (CD4(+) subset 13/16 patients, 81%; CD8(+) 100%) indicating a specific differentiation. Peripheral blood T lymphocytes (PBL) TCR (especially CD4(+)) had less oligoclonal bands (CD4(+) 31%, CD8(+) 88%). Likewise, more oligoclonal bands were seen in lung TCR (total of 168 bands; 37 CD4(+); 131 CD8(+)), compared with 59 bands in PBL TCR (13 CD4(+); 46 CD8(+)). Intraindividual comparison revealed a more prominent difference in TCR oligoclonality between lung and blood in CD8(+) T cells (median of difference lung minus blood 5; interquartile range 1-10; P = 0.002) compared with CD4(+) T cells (median 2, 0-3, P = 0.039). Thus, TCR oligoclonality is preferentially found in the CD8(+) T cell subset, most distinctive in the lung. These findings indicate a specific interstitial T cell differentiation in response to local stimuli.

Estimate of the total number of CD8+ clonal expansions in healthy adults using a new DNA heteroduplex-tracking assay for CDR3 repertoire analysis

A T-cell receptor heteroduplex-tracking assay (TCR-HTA) was developed to analyze the sequence diversity of the TCR beta-chain mRNA of each of the 24 T-cell receptor beta-chain variable region (TRBV). TCR-HTA allowed an estimation of the number of expanded CD8 T-cell clones whose distinct CDR3 domain mRNA made up 2% or more of the transcript of each TRBV subfamily. An average of 40 CD8+ clonal expansions (range 34-49) was detected in three healthy adults. Correct sampling of the complex mRNA transcript populations was documented by the reproducible generation of TCR-HTA patterns using independently generated PCR amplicons. The CDR3 sequence of expanded T-cell clones could be rapidly determined by direct sequencing of DNA heteroduplex bands. CD4+ and CD8+ clonal expansions were found predominantly although not exclusively in CD45RO+ CD62L- effector/memory cells and the majority of expanded T-cell clones were stable over a period of at least 6 months. Fewer CD4+ than CD8+ clonal expansions were detected in peripheral blood cells. By providing a high-resolution method for the detection of clonally expanded T-cell clones and by simplifying the pattern generated using traditional DNA heteroduplex analysis, TCR-HTA is shown to be a sensitive method for assessing levels of oligoclonality and changes in TRBV repertoires.

Role of interferon-alpha and clonally expanded T cells in the immunotherapy of chronic myelogenous leukemia

Twenty five percent of patients in the chronic phase of chronic myelogenous leukemia (CML) are treated with interferon-alpha (IFN-alpha) to induce a cytogenic remission. In addition to its direct effects on leukemic cells, IFN-alpha has been shown to induce immunologic alterations, including upregulation of the expression of major histocompatibility (MHC) antigens in antigen-presenting cells (APCs), as well as augmentation of the activity of the lymphocytes against tumor cells. However, there has been little direct evidence supporting a causal interaction between cellular immunoreactivity and clinical responsiveness to IFN-alpha. We have shown that one approach to elucidate the immunological mechanisms by which IFN-alpha exerts its anti-CML activity is by analyzing therapy-induced modulation in T-cell receptor (TCR) Vbeta chain usage, using the reverse transcription-polymerase chain reaction (RT-PCR) followed by single-strand conformation (SSCP) analysis. This method is particularly attractive, since it provides an index of antigen-specific T cell expansion, but does not require the extraction and purification of the antigens involved in the T-cell response. T cell clones that express the Vbeta 10, 12, and 14 families predominate in the peripheral blood (PB) of CML patients. The enhanced expression of the Vbeta 9 and 20 families has been detected in IFN-alpha responsive patients but not patients who are poorly responsive to this agent. This suggests that expansion of T cells expressing these TCR Vbeta gene families may serve as a prognostic factors of the clinical responsiveness of CML patients to IFN-alpha. In addition, since T cell clones that express certain Vbeta families may react with a discrete set of antigenic peptides presented on the surface of malignant cells, a better understanding of the immunobiology of T cells in CML may allow for the design of increasing efficacious immune therapy for this disease.

Normal CD4 T-cell receptor repertoire in tonsillar tissue despite perturbed repertoire in peripheral blood in HIV-1 infected individuals

OBJECTIVE

To compare the T-cell receptor (TCR) repertoire of T-cell subsets in peripheral blood and lymphoid tissue from HIV-1 infected individuals.

DESIGN

Biopsies of tonsillar tissue and samples of peripheral blood were obtained from 10, mostly treatment-naive, HIV-1-infected individuals. CD4 and CD8 T-cell subsets were quantified, the TCR repertoire was analysed within 'naive' and 'memory' subsets, and results compared between identical subsets in tonsillar tissue and blood.

METHODS

Cell subsets were quantified by flow cytometry. CD4 T cells and CD8 T cells were isolated by immunomagnetic beads. Populations were in most cases further subdivided by immunomagnetic selection on the basis of CD45RO expression. TCR repertoire was studied by spectratyping of the TCR beta variable (BV) complementarity determining region 3 (CDR3) transcripts.

RESULTS

Amongst CD4 T cells, an abnormal TCR repertoire was found in median 25% (range, 0-88%) of BV families in peripheral blood, but in 0% (0-7%) in tonsillar tissue (P<0.05). Large peaks suggestive of expanded clones were common within CD8 T-cells, both in peripheral blood and tonsillar tissue. However, the expanded clones were rarely identical in the two compartments. Expanded CDR3 peaks, suggesting the presence of clonally expanded cells, were observed within both CD45RO+ and CD45RO- cells from all T-cell subsets, but, again they were mainly of different lengths.

CONCLUSION

CD4 T cells were preserved in number and TCR repertoire in tonsillar tissue compared with blood in HIV-1 infected individuals. T-cells collected from the peripheral blood may not be representative of those residing in lymphoid tissue.

The T cell receptor repertoire of CD8+CD28- T lymphocytes is dominated by expanded clones that persist over time

The costimulatory molecule CD28 is expressed on almost all CD4+ T cells, but on only a portion of CD8+ T cells in healthy human adults. alpha beta T cells may thus be divided into three phenotypically and functionally different subsets: CD4+, CD8+CD28+ and CD8+CD28-. Using peripheral blood lymphocytes from six healthy adults, we have studied the T cell receptor (TCR) repertoire within these subsets by analysis of the distribution of lengths of the complementarity determining region 3 (CDR3) of the beta variable (BV) transcripts and flow cytometric analysis of TCR V beta usage. Expanded CDR3 lengths were identified in 86% of BV families within CD8+CD28- T cells, but in only 4% within CD4+ T cells, and 35% within CD8+CD28+ T cells (P < 0.01). When sequenced, the majority of expanded peaks were found to be dominated by single clones. Identical expanded clones were found within both CD8+CD28+ and CD8+CD28- subsets, consistent with the belief that CD8+CD28- T cells descend directly from CD8+CD28+ T cells. Greatly expanded CD28- clones were found within both CD8+ and CD4+ subsets and persisted at the same magnitude for up to 4.5 years of observation. The finding of a small proportion of cells expressing Ki-67 showed that some of these clonally expanded cells were in the active stages of the cell cycle, but few of the cells expressed activation markers CD69, CD25, CD71 or CD122. One likely explanation for the persistence of expanded peripheral lymphocyte populations in healthy individuals is the presence of persistent antigen.