Abstract 2704: Mass spectrometry-based profiling of lysine acetylation and arginine methylation for biomarker discovery in triple negative breast cancer
Authors: Schunter Alissa J. , Gu Hongbo , Ren Jian Min , Yang Vicky , Stokes Matthew P. 
Published: August 2018

(a) Introductory sentence

Antibody enrichment and liquid chromatography mass spectrometry (LC-MS) were used to profile lysine acetylation and arginine mono-methylation in triple negative breast cancer patient sera without prior immunodepletion of abundant proteins.

(b) Brief description of experiments

Triple negative breast cancer (TNBC) is the most aggressive type of breast tumor and there are currently no approved targeted therapies. Better biomarkers are needed for early detection and for therapeutically informative subtyping of this genetically heterogeneous disease. We recently reported a methodology to enrich post-translationally modified peptides from serum (Gu et al, Mol Cell Proteomics 2015) and found acetyl lysine (AcK) and mono-methyl arginine (RMe) to be some of the most abundant post-translational modifications (PTMs) in the sera of cancer patients. This method has the advantage of profiling serum samples without prior depletion of abundant serum proteins, a major limitation of current proteomic methods. To develop a biomarker signature of TNBC, these two PTMs were profiled in the sera of 10 patients with stage I-IIA TNBC and 10 healthy female controls. Serum proteins were trypsin digested prior to immunoaffinity enrichment of the modified peptides with PTM-specific antibodies. The enriched peptides were analyzed by LC-MS and relative abundance of peptides across samples was measured using label-free quantification.

(c) Summary of new, unpublished data

PTM enrichment quantified hundreds of AcK and RMe sites across samples. AcK levels decreased globally in patients compared to controls, suggestive of increased lysine deacetylase or decreased acetyltransferase activity. Of these, a number of sites were found significantly altered between TNBC patient samples and normal controls at the p&lt;0.05 level by two-sided t-tests, including novel sites not previously reported in the PhosphoSitePlus database or in previous publications. Some of the regulated sites reside on proteins with important immune functions and cancer-related pathways.

(d) Statement of conclusions

AcK and Rme peptide signatures were identified that correlate with disease status, tumor grade, and stage. Patient follow-up over time will allow for investigation of markers of treatment response and disease progression as well. AcK and Rme are known to affect gene transcription profiles in cancer. Drug molecules targeting multiple families of AcK interacting proteins, including KATs, HDACs, and BET proteins, have entered clinical trials for breast and other cancers. AcK was globally downregulated in the samples surveyed, which suggests that these tumors may be responsive to some of these drug classes. Further analysis will correlate the AcK and RMe profiles to identify a PTM signature of therapeutically vulnerable epigenetic regulators in TNBC.

Citation Format: Alissa J. Schunter, Hongbo Gu, Jian Min Ren, Vicky Yang, Matthew P. Stokes. Mass spectrometry-based profiling of lysine acetylation and arginine methylation for biomarker discovery in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2704.