Multi-level Proteomics Identifies CT45 as a Chemosensitivity Mediator and Immunotherapy Target in Ovarian Cancer

Abstract

SUMMARY Most high-grade serous ovarian cancer (HGSOC) patients develop resistance to platinum-based chemotherapy and recur, but 15% remain disease free over a decade. To discover drivers of long-term survival, we quantitatively analyzed the proteomes of platinum-resistant and -sensitive HGSOC patients from minute amounts of formalin-fixed, paraffin-embedded tumors. This revealed cancer/testis antigen 45 (CT45) as an independent prognostic factor associated with a doubling of disease-free survival in advanced-stage HGSOC. Phospho- and interaction proteomics tied CT45 to DNA damage pathways through direct interaction with the PP4 phosphatase complex. In vitro, CT45 regulated PP4 activity, and its high expression led to increased DNA damage and platinum sensitivity. CT45-derived HLA class I peptides, identified by immunopeptidomics, activate patient-derived cytotoxic T cells and promote tumor cell killing. This study highlights the power of clinical cancer proteomics to identify targets for chemo- and immunotherapy and illuminate their biological roles.

Efficient mitotic checkpoint signaling depends on integrated activities of Bub1 and the RZZ complex

“…This was done essentially as in Coscia et al (2018). MS raw files were processed with the MaxQuant software (Cox & Mann, 2008;version 1.5.0.38).…”

A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis

“…This work was supported by the Max Planck Society for the Advancement of Science and by the Novo Nordisk Foundation (grant agreement NNF14CC0001 and NNF15CC0001), European Union's Horizon 2020 research and innovation program under grant agreement 686547 (MSmed Project) and the University of Chicago Cancer Center Support Grant P30CA014599. OvCa [29], FFPE OvCa [12]. E) Comparison of lysine methylation rates between SDS-and TFE-based protocols.…”

“…We first macro-dissected similar tumor areas (~5 x 5 mm) by scraping from two consecutive 10 µm thick sections of the same high-grade serous ovarian cancer (OvCa) specimen. We then processed the collected tissues with our organic solvent (Methods) or SDS based workflow as described previously for in-depth proteomic profiling of FFPE biobank samples [12]. We noticed that long boiling (90 min) in the SDS buffer fully resolved FFPE tissue in contrast to the TFE-based lysis.…”

“…As a result, in-depth proteomic analysis of FFPE tissues in a clinical context has now become feasible. Using MSbased proteomics on archived FFPE tissues, we recently profiled more than 9,000 protein groups from metastatic ovarian cancer (OvCa) FFPE tissues and identified a novel prognostic disease biomarker, 'CT45', causally linked to patient long-term survival [12]. In another study, we stratified breast cancer patients into distinct proteomic subtypes based on newly discovered classification markers, some of which were not reflected at the mRNA level [13].…”

Limited Environmental Serine Confers Sensitivity to PHGDH Inhibition in Brain Metastasis

“…To gain insight into the molecular events underlying brain metastasis, we analyzed both the peptide mixtures and labeling of central carbon metabolites from parental, aggressive, and indolent TNBC brain metastatic cells. [41][42][43][44][45] Comparative proteomic expression profiling of TNBC cells that differ in their capacity to colonize the brain or lung using an optimized, high-sensitivity, label-free protein expression profiling workflow quantified ~7,000 proteins per sample with excellent reproducibility. [44][45][46][47] Our analysis yielded protein expression profiles of the parental, indolent, and aggressive brain metastatic cells that segregated independently by principal component analysis, indicating that each population is phenotypically distinct (Fig.…”