Expanding the landscape of lysine acetylation stoichiometry and clinical impact

Lysine acetylation, once viewed primarily as a histone mark, is now recognized as a widespread regulator of protein function. Recent breakthroughs in chemical labeling, isotopic tagging workflows, and data-independent acquisition mass spectrometry enable precise, site-specific quantification of acetylation stoichiometry. This quantitative “acetylomics” approach reveals a “rheostat” model, where most acetylation sites exhibit low occupancy, acting as subtle modulators, while a subset of highly acetylated lysines (e.g., p53 C-terminus, AKT1, histones) serve as pivotal regulatory switches in gene expression, metabolism, and cell fate. Site-specific occupancy changes (e.g., p53, PKM2) increasingly serve as robust biomarkers for cancer diagnosis, prognosis, and therapeutic monitoring, often surpassing mRNA or total protein levels. Quantitative acetylation data now guide the development of targeted epigenetic therapies, including HDAC and p300/CBP inhibitors. Beyond oncology, acetylomics can pinpoint metabolic bottlenecks in heart failure, epigenetic deficits in neurodegenerative conditions, and inflammatory signaling nodes. With advances in high-throughput workflows, FFPE and liquid biopsy compatibility, and microfluidic platforms, acetylation stoichiometry is poised for clinical translation. We highlight both the promise and challenges of this emerging dimension of precision medicine, emphasizing the need for integrated multi-omics approaches and robust clinical validation to fully realize the potential of quantitative acetylomics in disease diagnosis and therapy.

Significance

Understanding the extent of acetylation occupancy in proteins, beyond simply determining presence or absence of acetylation, has profound implications for biology and medicine. This review emphasizes the importance of acetylation stoichiometry, connecting advanced proteomic technologies with translational science. We emphasize that quantifying site occupancy reveals which acetylation events truly modulate enzyme function. For instance, it can identify which acetylation events truly modulate enzyme activity or gene expression. Additionally, it can highlight molecular changes in diseases like cancer that are not apparent through qualitative analyses. These quantitative insights pave the way for clinical innovations, including novel biomarkers that stratify patients based on their acetylation profiles and targeted therapies that modulate acetylation levels. In summary, this work highlights the evolving landscape of protein acetylation research over the past two decades and its increasing influence on translational proteomics, celebrating milestones achieved by the global research community.