HIV and Proteomics: What We Have Learned from High Throughput Studies

Abstract

The accelerated development of technology over the last three decades has driven biological sciences to high-throughput profiling experiments, now broadly referred to as systems biology. The unprecedented improvement of analytical instrumentation has opened new avenues for more complex experimental designs and expands the knowledge in genomics, proteomics, and other omics fields. Despite the collective efforts of hundreds of researchers, gleaning all the expected information from omics experiments is still quite far. This paper summarizes what has been learned from high-throughput proteomics studies thus far, and what is believed should be done to reveal even more valuable information from such studies. It is drawn from the background in using proteomics to study human immunodeficiency virus 1 infection of macrophages and/or T cells, but it is believed that some conclusions will be more broadly applicable.

SWATH‐MS and MRM: Quantification of Ras‐related proteins in HIV‐1 infected and methamphetamine‐exposed human monocyte‐derived macrophages (hMDM)

“…Undoubtfully, cells from different donors react, as expected, differently to the same insult, which is clearly shown in Figure 4 including insult from HIV‐1 infection [7]. This aspect of high‐throughput studies using primary cells has been also discussed as part of our previous study [62] .…”

Multi-omics in HIV: searching insights to understand immunological non-response in PLHIV

“…This analysis identifies and quantifies the proteome in a specific cell type or tissue at a precise developmental or cellular stage ( 79 ). Several translational modifications and diverse patterns of protein expression in different organs and tissues add complexity when interpreting proteomics results ( 80 ) as do internal and external stimuli such as nutritional status, exercise, or diseases that affect proteomic dynamics ( 81 ). High-throughput methods to identify proteins include protein array and mass spectrometry (MS) techniques, but because of the higher accuracy and sensitivity of MS measurements and the advanced software used for data analysis, MS is the preferred technique among proteomics approaches ( 82 ).…”

Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms

“…The effective integration of iTRAQ has also contributed to research in HIV-1 latent infections with cluster of differentiation 4 (CD4)-positive cells. This has allowed the detection of altered protein species and signaling complexity that arises in HIV-1-infected CD4+ cells, including oncogenic disturbances [ 30 ]. The incorporation of iCAT into quantitative proteomics has been demonstrated to be a precise tool to measure the proteoform changes for quantification purposes.…”

“…Other proteomic studies extended their research by identifying novel signaling for personalized medicine in HIV-infected patients with a range of cancer types. Among these molecular signaling targets, researchers have focused on migratory and cytoskeletal components such as cofilin1, cystatins B, and L-plastins [ 30 , 114 , 115 ]. Other proteomic studies focused on identifying the relation between transcriptional behaviors on cellular structures as potential biomarkers in HIV-1 malignancies [ 116 ].…”