Proteomic profiling and network biology of colorectal cancer liver metastasis

ABSTRACTIntroduction Tissue-based proteomic studies of colorectal cancer (CRC) metastasis have delivered fragmented results, with very few therapeutic targets and prognostic biomarkers moving beyond the discovery phase. This situation is likely due to the difficulties for obtaining and analyzing large numbers of patient-derived metastatic samples, the own heterogeneity of CRC and technical limitations in proteomics discovery. As an alternative, metastatic CRC cell lines provide a flexible framework to investigate the underlying mechanisms and network biology of metastasis for target discovery.Areas Covered In this perspective, we comment on different in-depth proteomic studies of metastatic versus non-metastatic CRC cell lines. Identified metastasis-related protein are introduced and discussed according to the spatial location in different cellular fractions, with special emphasis on membrane/adhesion proteins, secreted proteins and nuclear factors, including miRNAs associated to liver metastasis. Moreover, we analyze the biological significance and potential therapeutic applications of the identified liver metastasis-related proteins.Expert Opinion The combination of protein discovery and functional analysis is the only way to accelerate the progress to clinical translation of the proteomic-derived findings in a relatively fast pace. Patient-derived organoids represent a promising alternative to patient tissues and cell lines, but further optimizations are still required for achieving solid and reproducible results.KEYWORDS: Colorectal cancermetastasisQuantitative proteomicsInteractomicstherapeutic targetsDisclaimerAs a service to authors and researchers we are providing this version of an accepted manuscript (AM). Copyediting, typesetting, and review of the resulting proofs will be undertaken on this manuscript before final publication of the Version of Record (VoR). During production and pre-press, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal relate to these versions also. Article HighlightsDespite some known limitations, paired metastatic vs non metastatic cell lines still constitute the most suitable model for proteomic profiling and for deciphering molecular mechanisms underlying colorectal liver metastasis.The application of fractionation techniques to isolate the different cell compartments has significantly improved the amount and relevance of the deregulated proteins identified in metastatic cells.The proteomic analyses of cancer cell lines differing in their metastatic potential has demonstrated to be a rich source for the discovery of novel prognostic biomarkers and therapeutic targets against metastatic colorectal cancer.A number of relevant proteins in CRC liver metastasis: CDH17, IL13Rα2, SOSTDC1, ZG16B and SRSF3, among others, have been identified by proteomic analysis of metastatic cell lines, functionally characterized and tested for therapeutic targeting.Future advances in colorectal liver metastasis should rely in the optimization and massive use of patient-derived organoids biobanks for multi-omic characterization.Declaration of interestJI Casal has stock ownership of Protein Alternatives SL. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.Reviewer disclosuresPeer reviewers on this manuscript have no relevant financial or other relationships to disclose.1. Proteins and miRNAs are listed according to order of appearance. See manuscript for referencesFigure 1. Workflow of identification of potential therapeutic targets against CRC metastatic dissemination. The use of isogenic cell lines with different metastatic capacities enable the use of proteomics assays to identify proteins overexpressed in highly metastatic cells. Those assays can be carried out with prelytic labelling (as metabolic labelling or biotinylation of cell surface proteins), peptide labelling (as iTRAQ or TMT) or label-free. Subcellular fractionation, protein separation and HPLC (high-performance liquid chromatography) allow better resolution in complex samples. A first filter for overexpressed proteins is the validation in cell lysates and tumor samples. A second filter is the association with clinico-pathological data in CRC patients by in silico analysis. Potential target candidates overexpressed in highly metastatic cells and associated with metastatic stage or poor overall survival are analyzed by in vitro and in vivo assays using genetically modified cells (silenced for or overexpressing the studied protein). For poorly known proteins, interactomic assays (BioID, immunoprecipitation coupled to mass spectrometry) can shed light into their functions.Display full sizeFigure 2. Proteins involved in CRC metastasis. Proteins identified by proteomic assays in CRC cell lines are classified by cell location and the pro-metastatic process in which they are involved. Most proteins are cell receptors involved in cell adhesion or cell signaling leading to enhanced invasiveness, proliferation, stemness, survival, etc. through the activity of signaling proteins and transcription factors.Display full sizeAdditional informationFundingJI Casal was funded by grants PID2021-122227OB-I00, CPP2021-008337 and PDC2022-133056-I00 from the MCIN/AEI/10.13039/501100011033 and by the Next Generation EU/PRTR, and PMPTA22/00108 from the Instituto de Salud Carlos III.