(A) Mass spectrometry of proteins isolated from EMC3 coimmunoprecipitates in MLE-15 cells identified 26 proteins as potential EMC3 binding partners. For each experimental pair, MLE-15 cells were transfected with empty vector or vector encoding Myc-tagged EMC3 (Myc-EMC3). Myc antibody coimmunoprecipitates were isolated from cell lysates using μMACS c-myc Isolation Kit (Miltenyi Biotec) and analyzed by mass spectrometry. Five independent pairs of co-IP assays were performed and analyzed. The R package apmsWAPP, sub package TSPM, was used to determine significant EMC3 interacting partners, P < 0.05. Significant EMC3 PPI partners were visualized in a z score–transformed heatmap of the normalized spectral counts. (B) Functional enrichment analyses of potential EMC3 interaction partners were performed using Toppfun. A subset of significant relationships was represented by graphing the corresponding –log₁₀ (P value). (C) Normalized VCP protein levels were measured from the proteomic analysis in Figure 4A. Mean ± SEM; **P < 0.01 using 2-way ANOVA multiple comparisons test, n = 4/group. (D) VCP inhibitor, CB5083, was given every other day (q.o.d.) by oral gavage at 50 mg/kg/dose to 6–8 week-old I73T/I73T mice for 14 days. Representative H&E-stained lung sections are shown. Scale bar: 200 μm. (E) ImageJ was used to quantify the H&E staining results in D. Mean ± SEM; **P < 0.01, ***P < 0.001, ****P < 0.0001 using 1-way ANOVA multiple comparisons test, n = 6. (F) Lung sections from adult mice treated in D were stained for proSP-C and cell-surface marker WGA. Scale bars: 20 μm. (G) Quantification of the ratio of cell-surface proSP-C stained in F by ImageJ. For each group, 20 AT2 cells from 4 mice were quantified. (H) Western blot of lysates from AT2 cells isolated from CB5083 or vehicle treated adult mice as in D. Emc3 deletion did not change levels of proSP-C(I73T).