Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation

Table 3 Limitations of the present studies that identify differentially expressed genes between latently infected and uninfected cells and possible solutions that may enable identification of solid candidate biomarkers of latency

Limitations	Solutions
Small percentage of latently infected cells	Isolate latently infected cells using reporter system OR perform gene expression profiling on a single-cell level
Effect from the exposure to the virus without infection	Use aldrithiol-2 inactivated virus[123] instead of mock-infection to compare to latently infected cell model
Identified differentially expressed genes are ubiquitously expressed on all CD4+ T cells	Identify a panel of biomarkers that best differentiates between latently infected and uninfected cells
Different models represent different aspects of latency establishment	Include additional models into analysis; use same statistical approaches to ensure differences in biomarkers are biological, not technical differences
Gene expression profiling can only identify candidate biomarkers	Perform experimental validation that latently infected cells can be detected using these biomarkers