Deep learning-assisted lactylprotein mining (DeepLaM) identifies potential pan-cancer biomarkers

The study of the functionality of lactylation, a recently discovered post-translational modification (PTM), has been emerging lately. However, its role in cancer progression remains to be elucidated. Previously, we found a lactylated lysine-derived cyclic immonium (cycIm) ion and demonstrated that its presence can signify true lysine lactylation (Klac) and identify novel Klac sites from unriched proteomic datasets. Here, we advanced this data mining strategy to DeepLaM, which involves the use of artificial intelligence (AI) algorithms to predict true Klac sites after training with the largest Klac-bearing peptide library to date. With DeepLaM, we efficiently identied several Klac sites that are consistently present in multiple cancer types, including lung adenocarcinoma, colon cancer, pancreatic ductal adenocarcinoma, squamous lung cancer, and small cell lung cancer by searching public data collected by the Clinical Proteomic Tumor Analysis Consortium (CPTAC). This finding implies these Klac sites as potential pan-cancer biomarkers and their association with cancer progression. Interestingly, these Klac-modified protein substrates converge in their involvement in NADPH-dependent reductase catalysis.

To further evaluate the potential of these novel Klac sites as cancer biomarkers and even drivers of cancer progression, we performed Klac proteome profiling and detected their upregulation in our collected lung adenocarcinoma samples. Their functionality was elucidated in vitro using genetic codon expansion (GCE). We site-specifically engineered the discovered Klac proteins in lung cancer cell lines, and demonstrated that these proteins modulate the redox homeostasis in cancer cells and contribute to cell growth and migration. Together, by integrating AI-based spectral learning and prediction, Klac proteome profiling and GCE, we are expanding our ability to efficiently discover cancer biomarkers and uncover their contribution to cancer. Such knowledge deepens our understanding in lactylation and cancer biology, and may provide novel target proteins for cancer prognosis and treatment.