Fig 2: (a) Volcano plot with − log10 p-value vs. log2 FC (mouse anti-ITM2B/unspecific antibody). Each point represents an identified protein. Proteins with significantly different abundances (in red 0.01 < p-value < 0.05, in green p-value < 0.01) are above the horizontal red line. On the right side are the proteins enriched with the mouse anti-ITM2B antibody with a FC > 2 while on the left side are the proteins enriched with the unspecific antibody with FC > 2. (b) Co-immunoprecipitation of APP and APLP2 from the human retina. The IP for negative controls (NC) was performed using Dynabeads and mouse IgG (isotypic control). Raw data of Western blots are presented in Supplementary Fig. S9.

Fig 3: Experimental design. ITM2B is composed of several domains: CD: cytosolic domain, TMD: transmembrane domain, BRICHOS, Bri23 and two linker domains (in light grey). Two distinct anti-ITM2B antibodies were used for immunoprecipitation. The first antibody is a rabbit polyclonal antibody raised against the 15–264 aminoacidic region of ITM2B and the second antibody is a mouse monoclonal antibody raised against the N-terminal 1–54 aminoacidic region of the protein. A third unspecific IgG mouse antibody was used as negative control. After ITM2B immunoprecipitation, protein complexes were digested with trypsin and peptide mixtures were analyzed by LC–MS/MS. A label-free quantitative proteomic analysis was then performed to identify and quantify ITM2B partners.

Fig 4: ITM2B interactome in the retina with the 360 proteins purified with the rabbit antibody (FC > 2 and p-value < 0.01). (A) GO-term network analysis. (B) Functional clusters and pathways identified with enriched proteins. %Genes/Term corresponds to the proportion of genes enriched in the functional clusters. Bars with the same color belong to the same functional cluster.

Fig 5: ITM2B interactome in the retina with the 254 proteins purified with the mouse antibody (FC > 2 and p-value < 0.01). (a) GO-term network analysis. (b) Functional clusters and pathways enriched within the ITM2B interactors. %Genes/Term corresponds to the proportion of genes enriched in the functional clusters. Bars with the same color belong to the same functional cluster.