Supplemental Information RAB7 Controls Melanoma ... - Cell Press

Cancer Cell, Volume 26

Supplemental Information

RAB7 Controls Melanoma Progression by Exploiting a Lineage-Specific Wiring of the Endolysosomal Pathway Direna Alonso-Curbelo, Erica Riveiro-Falkenbach, Eva Pérez-Guijarro, Metehan Cifdaloz, Panagiotis Karras, Lisa Osterloh, Diego Megías, Estela Cañón, Tonantzin G. Calvo, David Olmeda, Gonzalo Gómez-López, Osvaldo Graña, Víctor Javier Sánchez-Arévalo Lobo, David G. Pisano, Hao-Wei Wang, Pablo Ortiz-Romero, Damià Tormo, Keith Hoek, José L. Rodríguez-Peralto, Johanna A. Joyce, and María S. Soengas

SUPPLEMENTAL DATA Table S1, related to Figure 1. GO-“CELLULAR COMPONENT” and “BIOLOGICAL PROCESSES“ selectively enriched in melanoma.

GO -Term and Description GO:0005773 Vacuole GO:0000323 Lytic vacuole GO:0005764 Lysosome GO:0048066 developmental pigmentation GO:0005739 mitochondrion GO:0042438 melanin biosynthetic process GO:0006582 melanin metabolic process GO:0044429 mitochondrial part GO:0031090 organelle membrane GO:0042470 melanosome GO:0030318 melanocyte differentiation GO:0046148 pigment biosynthetic process GO:0031966 mitochondrial membrane GO:0005740 mitochondrial envelope GO:0031988 membrane-bounded vesicle GO:0016023 cytoplasmic membrane-bounded vesicle GO:0043218 compact myelin GO:0031410 cytoplasmic vesicle GO:0031982 vesicle GO:0043209 myelin sheath GO:0005743 mitochondrial inner membrane GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II GO:0000902 cell morphogenesis GO:0019866 organelle inner membrane GO 0042613 GO:0042613 MHC class l II protein t i complex l GO:0000904 cell morphogenesis involved in differentiation GO:0048468 cell development GO:0044255 cellular lipid metabolic process GO:0006629 lipid metabolic process GO:0030529 ribonucleoprotein complex GO:0005770 late endosome GO:0060348 bone development GO:0007399 nervous system development GO 0005794 GO:0005794 G Golgi l i apparatus t GO:0022008 neurogenesis GO:0045177 apical part of cell GO:0044433 cytoplasmic vesicle part GO:0005741 mitochondrial outer membrane GO:0007409 axonogenesis GO:0032438 melanosome organization GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II GO:0030100 regulation of endocytosis GO:0048753 pigment granule organization GO:0005975 carbohydrate metabolic process GO:0051593 response to folic acid GO:0006091 generation of precursor metabolites and energy GO:0030173 integral to Golgi membrane GO:0006396 RNA processing GO:0031228 intrinsic to Golgi membrane GO:0030424 axon GO:0033273 response to vitamin GO:0022010 central nervous system myelination GO:0015904 tetracycline transport GO:0006643 membrane lipid metabolic process GO:0051384 response to glucocorticoid stimulus GO:0001503 ossification GO:0006664 glycolipid metabolic process

Term size 212 179 179 44 813 17 18 468 825 105 27 61 324 341 469 450 10 535 565 23 266

Term size in genome 271 224 224 32 1128 9 10 599 1033 95 19 46 396 424 539 519 4 643 675 14 315

FDR adj_pvalue 6.66E-10 1.00E-08 1.00E-08 1.57E-07 1.44E-06 3.70E-06 3.70E-06 4.76E-06 5.37E-06 8.17E-06 1.77E-05 3.04E-05 4.89E-05 4.89E-05 8.02E-05 8.08E-05 1.25E-04 3.65E-04 3.65E-04 4.56E-04 4.68E-04

32 391 282 23 288 784 642 747 431 57 198 940 694 533 172 160 82 222 14

78 435 336 105 305 921 784 949 660 54 202 1136 893 617 174 162 86 234 8

4.99E-04 6.79E-04 1.06E-03 1 62E 03 1.62E-03 2.43E-03 2.43E-03 4.22E-03 4.22E-03 6.56E-03 7.16E-03 7.21E-03 1.13E-02 1 14E 02 1.14E-02 1.14E-02 1.47E-02 1.53E-02 1.55E-02 1.71E-02 1.71E-02

23 67 15 526 12 358 48 433 51 167 94 6 27 79 100 192 43

21 59 9 676 5 403 45 595 48 167 72 3 32 85 91 195 32

1.91E-02 2 00E 02 2.00E-02 2.00E-02 2.23E-02 2.37E-02 2.42E-02 2.58E-02 2.85E-02 2.97E-02 3.01E-02 3 43E-02 3.43E-02 3.44E-02 3.44E-02 3.44E-02 3.44E-02 3.44E-02 3.57E-02

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Table S1, related to Figure 1. GO-“CELLULAR COMPONENT” and “BIOLOGICAL PROCESSES“ selectively enriched in melanoma (continuation)

GO -Term and Description GO:0032400 GO:0006665 GO:0006790 GO:0006644 GO:0016044 GO:0019882 GO:0016471 GO:0005774 GO:0019867 GO:0034045 GO:0005594 GO:0042891 GO:0031960 GO:0009101 GO:0034341 GO:0000307 GO:0046469

melanosome localization sphingolipid metabolic process sulfur compound metabolic process phospholipid metabolic process cellular membrane organization antigen processing and presentation vacuolar proton-transporting V-type ATPase complex vacuolar membrane outer membrane pre-autophagosomal structure membrane collagen type IX antibiotic transport response to corticosteroid stimulus glycoprotein biosynthetic process response to interferon-gamma cyclin-dependent protein kinase holoenzyme complex platelet activating factor metabolic process

Term size 18 76 119 178 378 78 13 52 104 10 10 30 106 155 17 19 11

Term size in genome 12 79 121 220 409 237 16 57 105 3 3 35 97 171 9 11 5

FDR adj_pvalue 3.89E-02 4.01E-02 4.01E-02 4.01E-02 4.01E-02 4.06E-02 4.12E-02 4.12E-02 4.12E-02 4.27E-02 4.27E-02 4.66E-02 4.66E-02 4.66E-02 4.67E-02 4.69E-02 4.98E-02

Results from Gene Set Enrichment Analysis (GSEA) in the multi-cancer NCI-60 cell line dataset (GSE5720GO) showing GO terms in the indicated categories that are selectively enriched in the melanoma samples (FDR