Combining high throughput sequencing with novel mathematical modelling and bioinformatics to estimate T and B cell repertoires in patients with HIV

Supervisors: Professor Nigel Klein, Dr Mike Hubank and Professor Robin Callard

Current guidelines for HIV infected children recommend initiation of antiretroviral therapy (ART) at age-related CD4 T-cell thresholds that are based on the risk of short-term disease progression [1,2]. However, with survival for ART treated children into adulthood now increasingly likely, it has become important to understand how ART initiation influences long-term immune reconstitution and immunological health. Although good long term CD4 T-cell reconstitution can now be obtained and has been found to correlate with initial CD4 T-cell count and with age when treatment was first initiated [3], one of the major unanswered questions is whether the recovered T cell population includes sufficient diversity of antigen recognition to provide long term immunity to a range of pathogens. We have recently developed and characterised a novel technique for high throughput sequencing of T-cell and B-cell receptors that can be used with appropriate mathematical and statistical models to compare T-cell receptor diversity required for recognition of pathogens. In this project, T-cell receptor sequences will be analysed in a large cohort of HIV-infected children successfully treated with ART and related to important parameters such as age treatment commenced and starting CD4 numbers. There is considerable discussion as to when to start ART and how long to continue therapy. This project will help inform these important questions and enable treatment decisions to be made early on for these children that will optimise immune reconstitution in later life. This approach to assessing TCR and BCR diversity will also have implications for other disease such as children undergoing stem cell transplant therapy.

The objectives of the proposed investigation:
i) Utilise the sure select capture method recently devised by us to obtain TCR and BCR sequences from HIV infected children on ART. The cohorts to be used will include children from the GOSH HIV clinic, a large study of children in the ARROW trial performed in Africa and from children who have undergone periods of treatment interruption at GOSH. The focus will be on the impact of early and sustained treatment with ART as compared to those who did not initiate treatment because they were considered to be long-term non-progressors and those who have undergone a period of structured treatment interruption.
ii) Develop a mathematical model for estimating TCR and BCR diversity from the sequencing data.
iii) Incorporate the TCR and BCR diversity estimates with nonlinear mixed effects models developed by us to correlate diversity with T cell reconstitution, age of treatment initiation, initial CD4 T cell count and thymus output.

These results will then be used to inform future treatment guidelines through our connections with the MRC clinical trials unit, the Paediatric European Network for Treatment of AIDS (PENTA) and WHO.

1) World Health Organization. Antiretroviral therapy for HIV infection in adults and adolescents: recommendations for a public health approach 2010 revision. Geneva, Switzerland: World Health Organization, 2010.
2) Paediatric European Network for Treatment of AIDS (PENTA) Steering Committee. PENTA 2009 guidelines for the use of antiretroviral therapy in paediatric HIV-1 infection. HIV Med 2010; 10:591–613.
3) Lewis J, Walker AS, Klein N, Callard R. CD31+ cell percenage correlation with speed of CD4+ T cell recovery in HIV-infected adults is reversed in children: higher thymic output may be responsible. Clin Infect Dis. 2012;55(2):304-307.