extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma

Supplementary Information Supplementary Figs 1-3; Supplementary tables 1-10 Supplementary tables (separate files): Supplementary Table Contains clinical information on samples used from microdissection and the proteomic analysis (A) and samples used for IHC staining (B) Supplementary Table Contains information on all identified peptides in the analysis of the clinical samples (normal, cancer, and metastasis) Supplementary Table Contains information on all identified proteins in the analysis of the clinical samples (normal, cancer, and metastasis) Supplementary Table Lists all quantified proteins with rations observed between cancer and normal and, cancer and metastasis Supplementary Table Lists all proteins with significantly changed protein abundances Supplementary Table List of proteins quantified in the analysis of the CaCo-2 cells Supplementary Table Lists proteins with their observed copy numbers in normal mucosa, adenocarcinoma, HeLa and Caco-2 cells Supplementary Table Contains data used for creation of Figure 8A comparing transcriptomic data summarized in the reference (Cardoso et al., 2007) with results of the proteomic analysis described in this manuscript Supplementary Table Contains data comparing transcriptomic data on transcripts changed in cancer and metastasis vs normal tissue summarized in the reference (Nambiar et al., 2010) with results of the proteomic analysis described in this manuscript Supplementary Table 10 Contains data used for creation of Figure 8B comparing proteomic data summarized in the reference (Jimenez et al., 2010) with results of the analysis described in this manuscript Supplementary Figures (below) Supplementary Figure (page: 2) Supplementary Figure (page: 11) Supplementary Figure (page: 22) Supplementary Figure (8 Patient matched samples) Microdissection of samples Panels ‘Hematoxylin’: Hematoxylin-Eosin stained slices; Panels ‘Before -’ and ‘after microdissection’: Hematoxylin stained sections according to the microdissection protocol [Wiśniewski et al (2011) J Proteome Res 10, 3040-3049] Sample Hematoxylin Normal Adenocarcinoma Metastasis to node Before microdissection After microdissection Sample Hematoxylin Normal Adenocarcinoma Metastasis to node Before microdissection After microdissection Sample Hematoxylin Normal Adenocarcinoma Before microdissection After microdissection Sample Hematoxylin Normal Adenocarcinoma Metastasis to node Before microdissection After microdissection Sample Hematoxylin Normal Adenocarcinoma Metastasis to node Before microdissection After microdissection Sample Hematoxylin Normal Adenocarcinoma Metastasis to node Before microdissection After microdissection Sample Hematoxylin Normal Adenocarcinoma Metastasis to node Before microdissection After microdissection Sample Hematoxylin Normal Adenocarcinoma Metastasis to node Before microdissection After microdissection Supplementary Figure 2: Canonical Pathways Identified proteins are key members in a number of canonical pathways including a) apoptosis signaling, b) EIF2 signaling, c) ERK/MAPK signaling, d) IL8 signaling, e) insulin receptor signaling, f) mTOR signaling, g) oxidative phosphorylation, h) p53 signaling, i) PI3K/AKT signaling, and j) VEGF signaling Quantitative changes are reflected in green (higher protein expression in normal tissue) and red (higher protein expression in cancer) The pathway images were generated with IPA (Ingenuity Systems, www.ingenuity.com) a)  Apoptosis  Signaling   b)  EIF2  Signaling   c)  ERK/MAPK  Signaling   d)  IL8  Signaling   e)  Insulin  Receptor  Signaling   f)  mTOR  Signaling   g)  OxidaDve  PhosphorylaDon   h)  p53  Signaling   i)  PI3K/AKT  Signaling   j)  VEGF  Signaling   Supplementary Figure Copy number variability in colon cancer vs normal tissue (black circles) and un- vs differentiated CaCo-2 cells (red circles) The plots show copy numbers calculated for individual measurements The black lines connect the clinical sample pairs Red lines are between the average values measured for CaCo-2 cells  ... colon cancer vs normal tissue (black circles) and un- vs differentiated CaCo-2 cells (red circles) The plots show copy numbers calculated for individual measurements The black lines connect the. .. PI3K/AKT signaling, and j) VEGF signaling Quantitative changes are reflected in green (higher protein expression in normal tissue) and red (higher protein expression in cancer) The pathway images... et al (2011) J Proteome Res 10, 3040-3049] Sample Hematoxylin Normal Adenocarcinoma Metastasis to node Before microdissection After microdissection Sample Hematoxylin Normal Adenocarcinoma Metastasis