Spatial Proteomic Analysis of Isogenic Metastatic Colorectal Cancer Cells Reveals Key Dysregulated Proteins Associated with Lymph Node, Liver and Lung Metastasis

ABSTRACT: Liver, lung and lymph nodes are the most common metatastic sites of colorectal cancer (CRC) cells. Here, we aimed to analyze by quantitative spatial proteomics the isogenic KM12 cell system (non-metastatic KM12C cells, liver metastatic KM12SM cells and liver and lung metastatic KM12L4a cells), and the isogenic non-metastatic SW480 and lymph nodes metastatic SW620 cells to study CRC metastasis. Cells were fractionated to study by proteomics five subcellular fractions corresponding to cytoplasm (CEB), membrane (MEB), nucleus (NEB), chromatin-bound proteins (NEB-CBP), and cytoskeletal proteins (PEB), and the secretome. Protein extracts were trypsin digested, labeled with TMT 11-plex and fractionated prior to proteomics analysis on a Q Exactive. We provide data on protein abundance and localization of 4031 proteins in their different subcellular fractions, depicting dysregulation of proteins in abundance and/or localization in the most common sites of CRC metastasis. Alterations in abundance and localization for selected proteins were validated via WB, IF, IHC and ELISA using CRC cells and patients’ tissue and plasma samples. These results supported the relevance of the proteomics results in a real-life scenario of CRC metastasis.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Colon Cancer

SUBMITTER: Ana Montero Calle  

LAB HEAD: Rodrigo Barderas

PROVIDER: PXD030671 | Pride | 2022-02-22

REPOSITORIES: Pride