The antiviral effector IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry

Abstract

Vesicle-membrane-protein-associated protein A (VAPA) and oxysterol-binding protein (OSBP) regulate intracellular cholesterol homeostasis, which is required for many virus infections. During entry, viruses or virus-containing vesicles can fuse with endosomal membranes to mediate the cytosolic release of virions, and alterations in endosomal cholesterol can inhibit this invasion step. We show that the antiviral effector protein interferon-inducible transmembrane protein 3 (IFITM3) interacts with VAPA and prevents its association with OSBP, thereby disrupting intracellular cholesterol homeostasis and inhibiting viral entry. By altering VAPA-OSBP function, IFITM3 induces a marked accumulation of cholesterol in multivesicular bodies and late endosomes, which inhibits the fusion of intraluminal virion-containing vesicles with endosomal membranes and thereby blocks virus release into the cytosol. Consequently, ectopic expression or depletion of the VAPA gene profoundly affects IFITM3-mediated inhibition of viral entry. Thus, IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry, further underscoring the importance of cholesterol in virus infection.

Figure 1

IFITMs Specifically Interact with VAPA, and IFITM3 Interaction Suppresses the Interaction between VAPA and OSBP (A) Lysates of A549-IFITM1, A549-IFITM2, or A549-IFITM3 cells were used for immunoprecipitation (IP) with anti-VAPA antibody, followed by immunoblotting (IB) with anti-Myc antibody. (B) Lysates of A549-Vector and A549-IFITM3 cells were used for IP and IB with the indicated antibodies. Whole-cell lysates (WCLs) were used for IB with the indicated antibodies. (C) Lysates of A549-Vector-VAPA-FLAG and A549-IFITM3-VAPA-FLAG cells were used for IP and IB with the indicated antibodies. (D) Various fragments of the IFITM3 gene and three fragments of VAPA gene were used for Y2H assay. (E) Various fragments of the VAPA gene and a full-length IFITM3 gene were used for Y2H assay. (F) Bacterially purified GST-VAPA protein was mixed with OSBP-containing cell lysates with increasing amounts of IFITM3-containing cell lysates (left panel), or bacterially purified GST-VAPA protein was mixed with IFITM3-containing cell lysates with increasing amounts of OSBP-containing cell lysates (right panel). Mixtures were incubated for 2 hr at 4°C, followed by GST pull-down (PD) and IB with the indicated antibodies. WCLs were used for IB with the indicated antibodies. See also Figure S1.

Figure 2

VAPA Antagonizes IFITM3-Mediated Inhibition of Viral Entry (A) A549 cells were infected with various multiplicity of infection (m.o.i) of GFP-VSV, and replication levels were monitored by immunofluorescence microscopy (magnification: 4×). (B) A549 cells were infected with VSV (m.o.i = 0.1), and VSV replications were determined by a standard plague assay. Values represent mean ± SD, n = 3 independent experiments. (C) A549 cells were infected with the IAV PR8/H1N1 strain (m.o.i = 0.1), and IAV replications were determined by a standard plague assay. Values represent mean ± SD, n = 3 independent experiments. (D) A549-Vector and A549-IFITM3 cells were infected with lentivirus carrying either VAPA-shRNA (VAPA-sh) or SC-shRNA (SC-sh). After 2 days, A549 cells were infected with the VSV PR8/H1N1 strain (m.o.i = 0.1), and VSV replications were determined by a standard plague assay. Values represent mean ± SD, n = 3 independent experiments. (E) A549-Vector and A549-IFITM3 cells were infected with lentivirus carrying either VAPA-shRNA (VAPA-sh) or SC-shRNA (SC-sh). After 2 days, A549 cells were infected with the IAV PR8/H1N1 strain (m.o.i = 0.1), and IAV replications were determined by a standard plague assay. Values represent mean ± SD, n = 3 independent experiments. (F and G) A549 cells were incubated with MLV-EGFP virus pseudotyped with the indicated envelope protein (VSV, IAV H1N1 [PR8], IAV H3N1 [Udorn], LCMV, MLV, MACH, or LASA). Viral entry is expressed as mean EGFP fluorescence relative to vector control cells, as measured by flow cytometry. Values represent mean ± SD, n ≥ 3 independent experiments. (H) A549-Vector and A549-IFITM3 cell lines were infected with lentivirus carrying either VAPA-shRNA (VAPA-sh) or SC-shRNA (SC-sh). After 2 days, cells were incubated with defective MLV-EGFP pseudotyped with the envelope protein of VSV, IAV H1N1 (PR8), or IAV H3N1 (Udorn). Viral entry is expressed as mean EGFP fluorescence relative to vector control cells, as measured by flow cytometry. Values represent mean ± SD, n ≥ 3 independent experiments. See also Figure S2.

Figure 3

IFITM3 Induces Cholesterol-Laden Endosomal Compartments (A and B) A549-Vector or A549-IFITM3 cells were stained with filipin (A) or Nile Red (B), together with anti-Myc (IFITM3) or anti-CD63 antibody. Scale bars, 10 and 20 μm. The inserts at the right panels show the magnified images. The metric values (mean ± SD) in the inserts represent colocalization quantification of either filipin with IFITM3 (0.52 ± 0.11) or Nile Red with IFITM3 (0.42 ± 0.09) calculated by Pearson’s correlation coefficient based on ≥20 cells. (C) A549-IFITM3 cells were stained with filipin, together with anti-Myc (IFITM3) and anti-LBPA antibody. Scale bar, 5 μm. Colocalization between LBPA and IFITM3 was quantified as 0.38 ± 0.10 (Pearson’s coefficient, mean ± SD, n ≥ 20). (D) A549-Vector, A549-IFITM3, A549-VAPA, and A549-IFITM3-VAPA cells were stained with Nile Red dye to measure their intracellular cholesterol levels by flow cytometry. The mean fluorescence intensities (MFI) were compared and presented as relative folds compared with those of A549-Vector cells. As a positive control, A549-Vector cells were treated with 2 μg/ml U18666A (U18), a cholesterol transport inhibitor, to induce cholesterol accumulation in endosomal compartments. Values represent mean ± SD, n > 3 independent experiments. Significant differences (p value < 0.05), compared to IFITM3, are marked by an asterisk. (E) A549-IFITM3 cells were washed 3–5 times with PBS and then treated with different concentrations (mM) of MβCD in free-serum media at 37°C for 45 min. Cells were then washed three times and incubated with defective MLV-EGFP pseudotyped with VSVgp. Viral entry is expressed as mean EGFP fluorescence relative to A549-Vector cells, as measured by flow cytometry. Values represent mean ± SD, n ≥ 3 independent experiments. (F) A549-Vector and A549-IFITM3 were infected with lentivirus carrying VAPA-shRNA or SC-shRNA. After two days, cells then fixed, stained with Nile Red, and subjected to flow cytometry analysis to measure intracellular cholesterol levels. See also Figure S3.

Figure 4

IFITM3-VAPA Interaction Is Required to Restrict Viral Entry (A) Schematic illustration of IFITM3 chimera carrying the CD4 transmembrane (IFITM-CD4) or transferrin receptor transmembrane (IFITM3-TR). WCLs were used for IB with the indicated antibodies. (B) A549-Vector, A549-IFITM3, A549-IFITM3-CD4, and A549-IFITM3-TR cells were fixed and stained with anti-Myc (IFITM3), anti-CD63, or Nile Red dye for confocal microscopy. DAPI was used to stain the nucleus. Scale bar, 5 μm. The metric values (mean ± SD) represent the quantitative assessment of the colocalization of CD63 (top panel) and Nile Red (bottom panel) with IFITM3 WT and chimeras (Pearson’s coefficient, mean ± SD, n ≥ 20). (C) Lysates of A549-Vector, A549-IFITM3, A549-IFITM3-CD4, and A549-IFITM3-TR cells were used for IP and IB. WCLs were used for IB analysis to show expressions of VAPA, IFITMs, and tubulin. (D) A549-Vector, A549-IFITM3, A549-IFITM3-CD4, and A549-IFITM3-TR cells were infected with GFP-VSV (top panel) or GFP-IAV PR8 (bottom panel). At 48 hr postinfection, cells were photographed under immunofluorescence microscopy (magnification: 4×). (E) A549-Vector, A549-IFITM3, A549-IFITM3-CD4, and A549-IFITM3-TR cells were infected with defective MLV-EGFP pseudotyped with the envelope proteins of VSV, IAV H1N1 (PR8), or IAV H3N1 (Udorn). Viral entry is expressed as mean EGFP fluorescence relative to vector control cells, as measured by flow cytometry. Values represent mean ± SD, n ≥ 3 independent experiments. See also Figure S4.

Figure 5

Effects of IFITM3 and VAPA Expression on MVB Structures (A) A549-IFITM3 and A549-IFITM3-VAPA cells were stained with filipin, anti-Myc (IFITM3), and anti-CD63 for confocal microscopy. The inserts at the right panels show the magnified images of the “filled form” (top panel) or the “ring form” (bottom panel) of endosomal compartments. Scale bar, 10 μm. The numbers indicate the Pearson’s correlation coefficient for colocalization of filipin and IFITM3 within endosomal compartments (mean ± SD, n ≥ 100 endosomal compartments). (B and C) A549-IFITM3 and A549-IFITM3-VAPA cells were subjected to TEM and immunogold EM (anti-Myc and 15 nm gold particle-conjugated secondary antibody) as described in the Experimental Procedures. Magnified images of the inserts are shown in the bottom of the panel. Scale bar, 0.2 μm. (D) Bar graphs represent the percentages of the “filled form” or the “ring form” structure of endosomal compartments within A549-IFITM3 and A549-IFITM3-VAPA cells from TEM images (n ≥ 100 endosomal compartments). See also Figure S5.

Figure 6

TEM and Immunogold EM of VSV-Infected A549-IFITM3 and A549-IFITM3-VAPA Cells (A and B) A549-IFITM3 and A549-IFITM3-VAPA were mock infected (left panel) or with high titers of VSV for 1 hr (rest of panels). Then cells were washed to remove unbound viruses and subjected to TEM (scale bar, 0.1 μm) and immunogold EM (scale bar, 0.2 μm) as described in the Experimental Procedures. Dual immunogold labeling was performed with anti-Myc antibody and 15 nm gold particle-conjugated secondary antibody (IFITM3, filled triangle) and anti-VSVgp antibody and 30 nm gold particle-conjugated secondary antibody (VSVgp, open arrow). The areas of particular MVBs are marked by dashed lines. See also Figure S6.

Figure 7

Schematic Model of IFITM3-Mediated Inhibition of Viral Entry Schematic model represents viral infection in the absence (left panel) or presence (right panel) of IFITM induction. Virions (depicted as stars) enter the cell by endocytosis, are subsequently transferred to early endosome (EE), and are finally transferred to late endosome/multivesicular body (LE/MVB). In the absence of IFITM induction under normal cholesterol (depicted as its chemical shape) homeostasis conditions, the intraluminal virion-cargo-containing vesicles or virion particles finally fuse with the limiting membrane to release viral genome or nucleocapsid to the cytosol. In the presence of IFITM induction, IFITM-VAPA interaction disturbs intracellular cholesterol homeostasis, leading to the accumulation of cholesterol in LE/MVB. This consequently blocks the fusion of the intraluminal virion-cargo-containing vesicles or virion particles with the limiting membrane of LE/MVB compartments.