Quantitative longitudinal analysis of T cell receptor repertoire expression in HIV-infected patients on antiretroviral and interleukin-2 therapy

Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family

The BRASSINAZOLE-RESISTANT (BZR) family of transcription factors (TFs) are positive regulators in the biosynthesis of brassinosteroids. The latter is a class of steroid hormones that affect a variety of developmental and physiological processes in plants. BZR TFs play essential roles in the regulation of plant growth and development, including multiple stress-resistance functions. However, the evolutionary history and individual expression patterns of the legume BZR genes has not been determined. In this study, we performed a genome-wide investigation of the BZR gene family in seven legume species. In total, 52 BZR genes were identified and characterized. By analyzing their phylogeny, we divided these BZR genes into five groups by comparison with orthologs/paralogs in Arabidopsis thaliana. The intron/exon structural patterns and conserved protein motifs of each gene were analyzed and showed high group-specificities. Legume BZR genes were unevenly distributed among their corresponding genomes. Genome and gene sequence comparisons revealed that gene expansion of the BZR TF family in legumes mainly resulted from segmental duplications and that this family has undergone purifying selection. Synteny analysis showed that BZR genes tended to localize within syntenic blocks conserved across legume genomes. The expression patterns of BZR genes among various legume vegetative tissues and in response to different abiotic stresses were analyzed using a combination of public transcriptome data and quantitative PCR. The patterns indicated that many BZR genes regulate legume organ development and differentiation, and significantly respond to drought and salt stresses. This study may provide valuable information for understanding the evolution of BZR gene structure and expression, and lays a foundation for future functional analysis of the legume BZR genes by species and by gene.

CD8 TCR β chain repertoire expansions and deletions are related with immunologic markers in HIV-1-infected patients during treatment interruption

BACKGROUND

HIV-1-infected individuals progressively loss CD4(+) T cells leading to immunosuppression and raising the risk of opportunistic infections. CD8(+) T-cells play an important role in the immune response against virus infections through their TCR.

OBJECTIVE

To evaluate the CD8-TCR repertoire and immunologic markers in HIV-1-infected patients.

STUDY DESIGN

Ten chronic HIV-1-infected individuals on prolonged effective antiretroviral treatment (ART) were analyzed at baseline (before treatment interruption), after at least one year of treatment interruption (TI) and after at least one year from ART resume (TR). Twenty-four TCR-Vβ gene families were analyzed by a modified CDR3 spectratyping method in isolated CD8(+) T-cells. Immune activation, exhaustion and subpopulation markers were analyzed by flow cytometry.

RESULTS

Expansion of Vβ10, Vβ14 and Vβ15 families, associated with low cell activation and stable exhaustion markers, were found at TI. Moreover, an increment of effector memory cells was found. Besides, depletion of Vβ20, Vβ28, and Vβ29 families, associated with an increase in cell activation and exhaustion markers, at TI were also found. These alterations seemed to be more pronounced in patients who had longer time from diagnosis. ART seemed to restore altered CD8(+) T-cell repertoire and most of the immunologic markers.

CONCLUSIONS

During TI (that was more pronounced in patients with longer HIV-1 infection) it was observed the expansion of Vβ families correlated with decreased cell activation, while Vβ families correlated with cell activation and exhaustion were depleted. These specific repertoire alterations reverted after ART resume.

Measurement of absolute T cell receptor rearrangement diversity

T cell receptor (TCR) diversity is critical for adaptive immunity. Existing methods for measuring such diversity are qualitative, expensive, and/or of uncertain accuracy. Here, we describe a method and associated reagents for estimating the absolute number of unique TCR Vβ rearrangements present in a given number of cells or volume of blood. Compared to next generation sequencing, this method is rapid, reproducible, and affordable. Diversity of a sample is calculated based on three independent measurements of one Vβ-Jβ family of TCR rearrangements at a time. The percentage of receptors using the given Vβ gene is determined by flow cytometric analysis of T cells stained with anti-Vβ family antibodies. The percentage of receptors using the Vβ gene in combination with the chosen Jβ gene is determined by quantitative PCR. Finally, the absolute clonal diversity of the Vβ-Jβ family is determined with the AmpliCot method of DNA hybridization kinetics, by interpolation relative to PCR standards of known sequence diversity. These three component measurements are reproducible and linear. Using titrations of known numbers of input cells, we show that the TCR diversity estimates obtained by this approach approximate expected values within a two-fold error, have a coefficient of variation of 20%, and yield similar results when different Vβ-Jβ pairs are chosen. The ability to obtain accurate measurements of the total number of different TCR gene rearrangements in a cell sample should be useful for basic studies of the adaptive immune system as well as in clinical studies of conditions such as HIV disease, transplantation, aging, and congenital immunodeficiencies.

A brief review of potential mechanisms of immune reconstitution inflammatory syndrome in HIV following antiretroviral therapy

A subset of HIV-infected individuals who receive antiretroviral therapy (ART) develop a paradoxical pathological response that significantly increases morbidity and sometimes mortality. Following the induction of highly active ART, a rapid decline in the viral load results within weeks and coincides with a steep rise in the CD4(+) T-cell counts and immune hyperactivation. Although no mechanistic pathway has been elucidated for the development of immune reconstitution inflammatory syndrome (IRIS), it is thought that change in the nature of the immune response is a predominant factor in the development of reconstitution disease. In this article, we review the current state of knowledge in this field and provide a model for the development of IRIS.

The application of real-time PCR to the analysis of T cell repertoires

The diversity of T-cell populations is determined by the spectrum of antigen-specific T-cell receptors (TCRs) that are heterodimers of alpha and beta subunits encoded by rearranged combinations of variable (AV and BV), joining (AJ and BJ), and constant region genes (AC and BC). We have developed a novel approach for analysis of beta transcript diversity in mice with a real-time PCR-based method that uses a matrix of BV- and BJ-specific primers to amplify 240 distinct BV-BJ combinations. Defined endpoints (Ct values) and dissociation curves are generated for each BV-BJ combination and the Ct values are consolidated in a matrix that characterizes the beta transcript diversity of each RNA sample. Relative diversities of BV-BJ combinations in individual RNA samples are further described by estimates of scaled entropy. A skin allograft system was used to demonstrate that dissection of repertoires into 240 BV-BJ combinations increases efficiency of identifying and sequencing beta transcripts that are overrepresented at inflammatory sites. These BV-BJ matrices should generate greater investigation in laboratory and clinical settings due to increased throughput, resolution and identification of overrepresented TCR transcripts.