Jinmin Ma:
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Human immunodeficiency virus-1 (HIV-1) is a retrovirus that primarily infects components of
the human immune system such as CD4+ T cells, macrophages and dendritic cells. HIV directly
and indirectly destroys CD4+ T cells, which leads to severe immunodeficiency and enhanced
susceptibility to opportunistic infections in most infected patients.
Highly active antiretroviral treatment (HAART) is able to suppress viral replication, lower the
amount of virus (viral load) in a patients body, and partially restore circulating CD4+ T cells so
that the immune system is better able to deal with HIV-1 infections. However, the accumulative
side effects or problems have emerged with ART in patients. The increasing number of patients
with issues of drug toxicity, emergence of drug resistant viruses, immune reconstitution
inflammatory syndrome (IRIS) following the initiation of HAART and unable to normalize
immune activation in HIV-infected individuals posed new challenges to the fight against AIDS.
Furthermore, Tuberculosis (TB) is still one of the worlds greatest public health threats.
Combined with HIV, the two diseases can be much more devastating. TB infection is the most
common opportunistic infection in the HIV/AIDS positive patients, and the proportion reaches
30%~60%, even more, nearly 50%-80% HIV/AIDS patients die because of TB infecting. Highly
Active Antiretroviral Therapy (HAART) is a useful method for therapy these patients, but
Tuberculosis-associated Immune Reconstitution Inflammatory Syndrome (TB-IRIS) is a
common complication of HAART in HIV-TB co-infected patients. However, the disease
mechanism is poorly understood, prognosis of TB-IRIS is currently impossible, and diagnosis is
highly challenging.
Genome-wide gene expression profiling is an informative method used to reveal global changes
of the immune system in health and disease, and has been particularly useful in identifying
biomarkers, examining the disease states, and investigating immune responses. Although a
number of transcriptome studies in HIV infection have been conducted, most of them based on
conventional microarray technologies that focused on a limited number of genes. Recently,
Next-generation sequencing (NGS) technology has provided a new method for both mapping
and quantifying transcriptomes. This method, termed RNA-Seq (RNA sequencing), provides
highly accurate measurements of genome-wide gene expression through high-throughput DNA
sequencing and generates high quality transcriptome data, including transcript abundance, gene
structure, alternative splicing, profiles of non-coding RNA species and genetic polymorphisms.
Such data may provide a more complete and comprehensive understanding of HIV pathogenesis.