Idiosyncratic T-cell receptor repertoire perturbation and loss of diversity in HIV-positive individuals revealed by deep-sequencing

⚫ We have developed and applied a protocol for the unbiased amplification, high-throughput DNA sequencing and error-corrected computational analysis of αβ T-cell receptor (TCR) repertoires.
⚫ This technology currently represents the highest resolution tool for investigating TCR repertoires, and thus presents an exciting opportunity for investigating many questions relating to immunity and infection.
⚫ Using this protocol, we have investigated the effect of HIV infection and subsequent anti-retroviral therapy (ART) on the TCR repertoire.
⚫ Two bleeds were taken: one before treatment (v1) and one after three months of ART (v2). Each TCR DNA sequence was translated and its complementarity determining region 3 (CDR3) extracted.

⚫ CD8 T-cell expansion, as well as CD4 death, drives formation of heavily perturbed idiosyncratic repertoires during HIV infection.
⚫ ART fails to rectify the majority of disrupted repertoire features.
⚫ High-throughput DNA sequencing permits population and clonotype level analyses of TCR repertoires.