Combined gene expression analysis in HIV Associated Dementia, Alzheimer’s disease and Parkinson’s disease- An in-silico approach

Abstract

Human immunodeficiency virus (HIV) Type 1 infection predominantly affects the immune system. Nevertheless, scientific studies have proven its association with the Central Nervous system (CNS) causing several neurological complications leading to HIV Associated Dementia (HAD). HAD is characterized by a progressive, disabling decline in essential CNS functions such as cognition, motor control and behavior. These are the general characteristics of the most common Neuro degenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). The genetics of AD and PD is widely studied and clinical studies have shown cohesion in the pathology of HAD, AD and PD. Analysing the concurrent expression patterns of large number of genes amongst these related diseases will aid in establishing correlations between the genes and their functions. We have analysed the gene expression datasets of HAD, AD and PD from GEO database to determine the overlapping genes and transcription factors involved. The datasets were normalized using R-Bioconductor, and statistical analysis was performed to identify the significant genes using limma and related packages in R. Although substantial amount of common proteins among HAD and other Neuro degenerative diseases have been previously reported, our findings can help in expanding the pool of target genes and further enhancing the knowledge about the convergent pathways among HAD, AD and PD. These common markers identified will provide insights into parallel pathways of disease mechanisms and further assist in the understanding of progression of HAD pathogenesis.