In silico modeling indicates the development of HIV-1 resistance to multiple shRNA gene therapy differs to standard antiretroviral therapy.

Tanya Lynn Applegate,Angel Belisario Jaramillo,Geoff Symonds,Glen John Mcintyre,John Michael Murray,Donald John Birkett

doi:10.1186/1742-4690-7-83

Abstract

BackgroundGene therapy has the potential to counter problems that still hamper standard HIV antiretroviral therapy, such as toxicity, patient adherence and the development of resistance. RNA interference can suppress HIV replication as a gene therapeutic via expressed short hairpin RNAs (shRNAs). It is now clear that multiple shRNAs will likely be required to suppress infection and prevent the emergence of resistant virus.ResultsWe have developed the first biologically relevant stochastic model in which multiple shRNAs are introduced into CD34+ hematopoietic stem cells. This model has been used to track the production of gene-containing CD4+ T cells, the degree of HIV infection, and the development of HIV resistance in lymphoid tissue for 13 years. In this model, we found that at least four active shRNAs were required to suppress HIV infection/replication effectively and prevent the development of resistance. The inhibition of incoming virus was shown to be critical for effective treatment. The low potential for resistance development that we found is largely due to a pool of replicating wild-type HIV that is maintained in non-gene containing CD4+ T cells. This wild-type HIV effectively out-competes emerging viral strains, maintaining the viral status quo.ConclusionsThe presence of a group of cells that lack the gene therapeutic and is available for infection by wild-type virus appears to mitigate the development of resistance observed with systemic antiretroviral therapy.

Highlights

Human Immunodeficiency Virus type 1 (HIV-1) is a positive strand RNA retrovirus that can cause Acquired Immunodeficiency Syndrome (AIDS) resulting in destruction of the immune system
Sharing structural similarities to natural microRNA, short hairpin RNAs (shRNAs) consists of a short single stranded RNA transcript that folds into a ‘hairpin’ configuration by virtue of self-complementary regions separated by a short ‘loop’ sequence. shRNA-based gene therapy is an attractive alternative to Highly Active Anti-Retroviral Therapy (HAART) as RNA interference (RNAi) is specific, highly potent, and is likely to be free of the side-effects associated with HAART
There will be two distinct populations of target cells; UNTx cells which have no selective pressure driving the evolution of virus, and Tx cells which have the inhibitory pressure of gene therapy limiting viral replication

Summary

Introduction

Human Immunodeficiency Virus type 1 (HIV-1) is a positive strand RNA retrovirus that can cause Acquired Immunodeficiency Syndrome (AIDS) resulting in destruction of the immune system. HIV infection is currently treated with Highly Active Anti-Retroviral Therapy (HAART), a combination treatment of 3 or more drugs that significantly reduces viral replication and disease progression [1]. These drugs have sideeffects and can lead to low patient adherence resulting in viral breakthrough, one of the greatest challenges of today’s treatment regimes. RNAi can be artificially harnessed to suppress targets of choice by engineering short hairpin RNA (shRNA). RNA interference can suppress HIV replication as a gene therapeutic via expressed short hairpin RNAs (shRNAs). It is clear that multiple shRNAs will likely be required to suppress infection and prevent the emergence of resistant virus

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