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. 2024 Mar 11;15:2207. doi: 10.1038/s41467-024-46600-5

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a Alluvial plot of differential localization (DL) events (> 0.99 BANDLE DL probability; estimated FDR < 1%) following thapsigargin treatment showing a cohort of proteins moving from the Golgi apparatus (GA) and lysosome towards the plasma membrane (PM) (n = 3). b Spatial map for SLC3A2 (open black circle) in normal (left) and thapsigargin-treated (right) AC16 cells, showing its lysosomal assignment in normal cells and PM assignment in stressed cells. Colors: allocated subcellular compartment. c Ultracentrifugation fraction profile of SLC3A2 and other amino acid transporters SLC7A5, SLC1A4, SLC1A5 and ion channel proteins SLC30A1, ATP1B1, ATP1B3, and ATP2B1 with similar migration patterns. X-axis: fraction 1 to 10 of ultracentrifugation. Y-axis: relative channel abundance. Bold lines: protein of interest; light lines: ultracentrifugation profiles of all proteins classified to the compartment. Colors correspond to subcellular localization in panel b and all AC16 data in the manuscript; numbers within boxes: BANDLE allocation probability to compartment; numbers at arrows: BANDLE DL probability. d Immunofluorescence of SLC3A2 (red) against the lysosome marker LAMP2 (green) and DAPI (blue). Numbers in cell boundary: colocalization score per cell. Scale bar: 90 µm. e Colocalization score (Mander’s correlation coefficient) between SLC3A2 and LAMP2 decreases significantly (two-tailed unpaired t-test P value: 3e–8) in thapsigargin, consistent with movement away from lysosomal fraction (n = 205 normal cells, n = 32 thapsigargin treated cells). Center line: median; box limits: interquartile range; whiskers: 1.5x interquartile range; points: outliers. f Alluvial plot showing the migration of ER, GA, and nucleus proteins toward the peroxisome/endosome containing fraction in thapsigargin treated cells. g Ultracentrifugation fraction profile of stress granule proteins UBAP2, USP10, CNOT1, CNOT2, ZC3H7A, and NUFIP2. RNA Granule Score 7 or above is considered a known stress granule protein. Phi: predicted phase separation participation. Circle denotes a prediction of True within the database. RBP: Annotated RNA binding protein on the RNA Granule Database. One circle denotes known RBP in at least one data set; two circles denote known RBP in multiple datasets.