Fig. 4: Integration of spatial proteomics with protein levels to characterize organelle metabolic reprogramming.
a, Hierarchical clustering of significantly changed z-score protein profiles in the total proteome over the differentiation time course, for all proteins predicted to be mitochondrial. The values from the four cell models were sorted next to each other at the same time point. GO terms enriched in the clusters compared with the total mitochondrial proteome are highlighted. b, Scheme of BCAA metabolism and its changes during adipogenesis. Upregulated and downregulated proteins are marked in orange and blue, respectively. The colour codes in the boxes display the median protein levels during adipogenesis across all cell models. Thin arrows indicate downregulated reactions and thick pathways indicate upregulated reactions during adipogenesis. The change in the protein localization of BCAT2 during adipogenesis is indicated by a red arrow. Figure were created with BioRender.com. c, Protein profile of BCAT2 and indicated organelle marker profiles. d, Scheme of one-carbon metabolism remodelling during adipogenesis. Upregulated and downregulated proteins are marked in orange and blue, respectively. The colour code in the boxes displays the median protein levels during adipogenesis across all cell models. The direction of the canonical pathway in proliferating preadipocytes is indicated by the grey arrow. Protein translocations of ALDH1L1 and ALDH1L2 are indicated by red arrows. The predicted flux change and reversal based on protein levels and localization are indicated by the arrows. The downregulated mitochondrial part of the cycle is indicated by a thin arrow and the potentially reversed and upregulated cytosolic part of the cycle is indicated by a thick arrow. The figure was created with BioRender.com. e,g, Protein profiles of ALDH1L1 and ALDH1L2 and indicated organelle marker profiles. f,h, Representative immunofluorescence staining for ALDH1L1 and ALDH1L2 in SGBS preadipocytes and adipocytes, respectively. In the overlay, BODIPY is shown in grey, ALDH1L1 and ALDH1A2 are in green and TOM20 is in magenta. Scale bar, 50 µm. Representative images from three experiments are shown.
