Fig. 7: Interactome analysis reveals that LRMDA similarly binds to Retriever.

Volcano plot (a) and heat map (b) of VPS35L-interacting proteins quantified by mass spectrometry after coimmunoprecipitation of HA-tagged VPS35L, using indicated HeLa stable cell lines shown in Fig. 4d. Two-sided Student’s t test and Benjamini–Hochberg false discovery rate (FDR) correction were applied in data analyses. Colored dots (blue or green) denote proteins with FDR-corrected p value < 0.05; green dots depict hits that also had >10-fold change between WT and EV control samples. Dot size is proportional to the position on the y axis (depicting statistical significance). Protein spectral counts, fold change between indicated cells, and corresponding p-values are depicted. c Cartoon presentation of LRMDA domain organization and constructs used in e. d Immunoprecipitation of VPS35L (HA) followed by immunoblotting for LRMDA and CCDC93 in indicated stable HeLa cell lines. e Immunoprecipitation of LRMDA full-length (FL), NT, and CT in Lenti-X 293 T cells, followed by immunoblotting for indicated Retriever and CCC subunits. The experiment in a and b was performed once, with three biological replicates included in each group. Detailed proteomic data are provided in Supplementary Data 2 and deposited in MassIVE repository as detailed in the data availability section. Western blot experiments in d and e were performed three times. Representative results are shown.