Novel Prognostic Markers in Triple-Negative Breast Cancer Discovered by MALDI-Mass Spectrometry Imaging

Abstract

There are no widely-accepted prognostic markers currently available to predict outcomes in patients with triple-negative breast cancer (TNBC), and no targeted therapies with confirmed benefit. We have used MALDI mass spectrometry imaging (MSI) of tryptic peptides to compare regions of cancer and benign tissue in 10 formalin-fixed, paraffin-embedded sections of TNBC tumors. Proteins were identified by reference to a peptide library constructed by LC-MALDI-MS/MS analyses of the same tissues. The prognostic significance of proteins that distinguished between cancer and benign regions was estimated by Kaplan-Meier analysis of their gene expression from public databases. Among peptides that distinguished between cancer and benign tissue in at least 3 tissues with a ROC area under the curve >0.7, 14 represented proteins identified from the reference library, including proteins not previously associated with breast cancer. Initial network analysis using the STRING database showed no obvious functional relationships except among collagen subunits COL1A1, COL1A2, and COL63A, but manual curation, including the addition of EGFR to the analysis, revealed a unique network connecting 10 of the 14 proteins. Kaplan-Meier survival analysis to examine the relationship between tumor expression of genes encoding the 14 proteins, and recurrence-free survival (RFS) in patients with basal-like TNBC showed that, compared to low expression, high expression of nine of the genes was associated with significantly worse RFS, most with hazard ratios >2. In contrast, in estrogen receptor-positive tumors, high expression of these genes showed only low, or no, association with worse RFS. These proteins are proposed as putative markers of RFS in TNBC, and some may also be considered as possible targets for future therapies.

Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes

“…The protein product of the COL1A1 gene forms part of the type I collagen protein complex, which has previously been identified as up-regulated in mesenchymal MpBCs when compared to adjacent normal tissue [27]. Further, high expression of the COL1A1 gene and protein has been associated with shorter recurrence free and overall survival in breast cancer, as well as with response to cisplatin [28, 29]. Additionally, we identified increased HAS2 in MpBC samples.…”

Imaging Mass Spectrometry Is an Accurate Tool in Differentiating Clear Cell Renal Cell Carcinoma and Chromophobe Renal Cell Carcinoma: A Proof-of-concept Study

“…4 It has recently been used in studying triple negative breast cancer, thyroid tumors, ovarian cancer, and malignant pleural and peritoneal effusion. 15,17-20 IMS has the advantage of profiling a large number of biomarkers simultaneously. 21 It also requires only a small amount of tumor tissue (0.018 mm 2 per ROI; ~0.35 mm 2 in total on a single 6 µm slide, per case, in our study).…”

Implementation of MALDI Mass Spectrometry Imaging in Cancer Proteomics Research: Applications and Challenges

“…Extensive proteomic research with MALDI MSI was performed by Casadonte et al [ 36 ] on pancreatic ductal adenocarcinoma and pancreatic neuroendocrine tumor tissues, leading to the development of a class prediction model to differentiate between both entities with high accuracy, essential for the appropriate treatment modality. MALDI MSI proteomic analyses has also proven their relevance in triple-negative breast cancer in the search for putative markers for recurrence-free survival: Phillips et al [ 37 ] identified nine proteins, not previously associated with breast cancer, that were significantly associated with worse recurrence-free survival when these proteins were highly expressed. Meding et al [ 38 ] demonstrated that MALDI MSI can be used to classify six different tumor entities in different organ sites with high confidence, based on 117 m / z species in the average imaging spectra.…”