title: Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient.
abstract: Compensatory signaling pathways in tumors confer resistance to targeted therapy, but the pathways and their mechanisms of activation remain largely unknown. We describe a procedure for quantitative proteomics and phosphoproteomics on snap-frozen biopsies of hepatocellular carcinoma (HCC) and matched nontumor liver tissue. We applied this procedure to monitor signaling pathways in serial biopsies taken from an HCC patient before and during treatment with the multikinase inhibitor sorafenib. At diagnosis, the patient had an advanced HCC. At the time of the second biopsy, abdominal imaging revealed progressive disease despite sorafenib treatment. Sorafenib was confirmed to inhibit MAPK signaling in the tumor, as measured by reduced ribosomal protein S6 kinase phosphorylation. Hierarchical clustering and enrichment analysis revealed pathways broadly implicated in tumor progression and resistance, such as epithelial-to-mesenchymal transition and cell adhesion pathways. Thus, we describe a protocol for quantitative analysis of oncogenic pathways in HCC biopsies and obtained first insights into the effect of sorafenib in vivo. This protocol will allow elucidation of mechanisms of resistance and enable precision medicine.
authors.affiliation: Biozentrum, University of Basel, 4056 Basel, Switzerland;
authors.forename: Eva
authors.initials: E
authors.lastname: Dazert
authors.affiliation: Biozentrum, University of Basel, 4056 Basel, Switzerland;
authors.forename: Marco
authors.initials: M
authors.lastname: Colombi
authors.affiliation: Department of Biomedicine, University Hospital Basel, 4031 Basel, Switzerland;
authors.forename: Tujana
authors.initials: T
authors.lastname: Boldanova
authors.affiliation: Biozentrum, University of Basel, 4056 Basel, Switzerland;
authors.forename: Suzette
authors.initials: S
authors.lastname: Moes
authors.affiliation: Department of Mathematics and Computer Science, University of Basel, 4051 Basel, Switzerland;
authors.forename: David
authors.initials: D
authors.lastname: Adametz
authors.affiliation: Molecular Pathology, University Hospital Basel, 4003 Basel, Switzerland.
authors.forename: Luca
authors.initials: L
authors.lastname: Quagliata
authors.affiliation: Department of Mathematics and Computer Science, University of Basel, 4051 Basel, Switzerland;
authors.forename: Volker
authors.initials: V
authors.lastname: Roth
authors.affiliation: Molecular Pathology, University Hospital Basel, 4003 Basel, Switzerland.
authors.forename: Luigi
authors.initials: L
authors.lastname: Terracciano
authors.affiliation: Department of Biomedicine, University Hospital Basel, 4031 Basel, Switzerland;
authors.forename: Markus H
authors.initials: MH
authors.lastname: Heim
authors.affiliation: Biozentrum, University of Basel, 4056 Basel, Switzerland;
authors.forename: Paul
authors.initials: P
authors.lastname: Jenoe
authors.affiliation: Biozentrum, University of Basel, 4056 Basel, Switzerland; m.hall@unibas.ch.
authors.forename: Michael N
authors.initials: MN
authors.lastname: Hall
mesh_terms: D000970:Antineoplastic Agents / Q000627:therapeutic use*; D001706:Biopsy; D006528:Carcinoma, Hepatocellular / Q000188:drug therapy / Q000378:metabolism* / Q000473:pathology; D006801:Humans; D008113:Liver Neoplasms / Q000188:drug therapy / Q000378:metabolism* / Q000473:pathology; D009536:Niacinamide / Q000031:analogs & derivatives* / Q000627:therapeutic use; D010671:Phenylurea Compounds / Q000627:therapeutic use*; D010750:Phosphoproteins / Q000378:metabolism*; D010766:Phosphorylation; D040901:Proteomics; D000077157:Sorafenib
chemical_list: D000970:Antineoplastic Agents; D010671:Phenylurea Compounds; D010750:Phosphoproteins; D009536:Niacinamide; D000077157:Sorafenib
keywords: EMT; MAPK; evasive resistance; liver; signal transduction