Human microglial models to study HIV infection and neuropathogenesis: a literature overview and comparative analyses

Abstract

HIV persistence in the CNS despite antiretroviral therapy may cause neurological disorders and poses a critical challenge for HIV cure. Understanding the pathobiology of HIV-infected microglia, the main viral CNS reservoir, is imperative. Here, we provide a comprehensive comparison of human microglial culture models: cultured primary microglia (pMG), microglial cell lines, monocyte-derived microglia (MDMi), stem cell-derived microglia (iPSC-MG), and microglia grown in 3D cerebral organoids (oMG) as potential model systems to advance HIV research on microglia. Functional characterization revealed phagocytic capabilities and responsiveness to LPS across all models. Microglial transcriptome profiles of uncultured pMG showed the highest similarity to cultured pMG and oMG, followed by iPSC-MG and then MDMi. Direct comparison of HIV infection showed a striking difference, with high levels of viral replication in cultured pMG and MDMi and relatively low levels in oMG resembling HIV infection observed in post-mortem biopsies, while the SV40 and HMC3 cell lines did not support HIV infection. Altogether, based on transcriptional similarities to uncultured pMG and susceptibility to HIV infection, MDMi may serve as a first screening tool, whereas oMG, cultured pMG, and iPSC-MG provide more representative microglial culture models for HIV research. The use of current human microglial cell lines (SV40, HMC3) is not recommended.

Keywords: Central nervous system; HIV; HIV-associated neurocognitive disorder; Microglia; Neuropathogenesis; Organoid.

Fig. 1

Morphology of human primary microglia and four different microglial in vitro culture models. a IBA-1 stained microglia in DAB-stained human brain sections of GFM at 40 × magnification. b–e Phase-contrast images of microglial culture models: adult primary microglia at 7 days post isolation b, SV40 microglial cell line c, monocyte-derived microglia d, and organoid-derived microglia e. Magnification = 10 × d and 20 × b, c, e

Fig. 2

Gene expression analysis of microglial culture models on the 500 most variable genes. Legend shows color coding for cell type. a Heatmap depicting the Pearson r correlation effect sizes between cell types based on the 500 most variable genes. Clustering dendrogram is based on Euclidean distances. b PC plot depicting cell-type distances based on expression variance in the 500 most variable genes. Clustering dendrogram is based on Euclidean distances. c Heatmap of log2(CPM) expression values for the 500 most variable genes depicted for each cell type

Fig. 3

Gene expression analysis of microglial culture models on a microglia-specific core signature. a Heatmap depicting Pearson r correlation effect sizes between the cell types based on microglia core gene expression. Clustering dendrogram is based on Euclidean distances. Clustering dendrogram depicts Euclidean distances. b PC plot depicting cell-type similarities based on expression variance within microglia core genes. c Heatmap of log2(CPM) values for microglia core genes extracted from Patir et al. (2019)

Fig. 4

Gene expression analysis of microglia culture models on HIV-relevant genes. a Heatmap of Pearson r for between each cell type (cluster distances are Euclidean). b Boxplot of log2(CPM) for selected HIV genes. c PC plot depicting cell-type distances based on expression variance within selected HIV genes

Fig. 5

HIV infection and virus production in microglial culture models. Adult primary microglia a, MDMi b, oMG c, and microglial cell lines SV40 and HMC3 e were infected with 10 ng (p24 Gag) HIVbal with a luciferase tag and cultured for the indicated days. Supernatant was collected post infection on the indicated days, and virus production was measured with luminescence. d Peak infection day of each culture model

Fig. 6

Gene expression of major HIV receptors in in vitro culture models. Median (IQR) gene expression of CD4, CXCR4, and CCR5 in primary microglia (pMG), monocyte-derived microglia (MDMi), SV40 microglial cell line, CD4 + T-cells and monocytes assessed by RT-PCR and normalized to the reference gene GAPDH. All cells are color-coded according to their Z-value (color bar on the right-hand side)