PHARM Medicinal Chemistry
College of Pharmacy
College of Pharmacy
Proteomics Studies of DNA-Protein Cross-Links and Epigenetics and DNA Epigenetics Marks Sequencing
This research consists of three projects:
- Cytosine methylation (5-methylcytosine (MeC)) regulates gene expression in a tissue-specific manner. These methylation marks are introduced by DNA methyltransferases (DNMTs), which catalyze de novo methylation of CpG sites and maintain DNA methylation patterns to allow for activation and inactivation of specific genes. Cytosine methylation patterns are stable in normal somatic tissues, but are significantly altered in many diseases including cancer, asthma, and autism. Ten-eleven translocation proteins 1-3 (Tet) catalyze α-ketoglutarate dependent oxidation of MeC to 5-hydroxymethyl-cytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC). These oxidized forms of MeC are not recognized by DNMTs and are removed via base excision mechanism, leading to gene reactivation. Furthermore, studies in the brain have shown that hmC, fC, and caC can be recognized by specific protein readers and may have their own function in human cells. Many key questions remain in regard to the biological roles of Tet proteins and the oxidized forms of MeC in normal cells and in human disease. This project employes quantitative proteomics to establish the biological functions of Tet proteins and oxidized forms of MeC in the lung. These studies will identify protein readers of MeC, hmC, fC, and caC in human bronchial epithelial cells using quantitative proteomics. This will contribute to basic understanding of epigenetic regulation in human cells and will help identify novel targets for therapeutic interventions.
- Exposure to common antitumor drugs, environmental toxins, transition metals, UV light, ionizing radiation, and free radical-generating systems can result in cellular proteins becoming covalently trapped on DNA. The resulting DNA-protein cross-links (DPCs) are hypothesized to be toxic and mutagenic. DPCs are known to progressively accumulate with the heart and brain tissues with age. This project employs mass spectrometry based proteomics to detect and characterize DPCs in cells and tissues. These tools are now being employed to characterize DPC formation in the heart following a myocardial infarction. The researchers hypothesize that DPCs play an important role in cardiotoxicity which follows myocardial infarctions. This information should aid in the development of novel protective agents which could be utilized to prevent cardiac tissue damage following a heart attack.
- DNA methylation can regulate nearby gene expression by recruting specific protein readers. Preliminary studies in this lab have found a global alteration of DNA methylation after triggering inflammation. In addition, inflammation is found to be a high risk factor of lung cancer development. Therefore, the researchers hypothesize that this epigenetic mechanism could serve as a bridge between inflammation and lung cancer. This project compares epigenomics (DNA methylation/hydroxymethylation), transcriptomics, and proteomics changes in A/J mice treated with cigarette smoke (CS), inflammatory agent LPS, and tobacco carcinogen NNK. Integration of these -omics datasets will provide a complete view of inflammation induced changes at the molecular level and be a guide for therapy development in the future.
Dr. Juan Abrahante - Llorens
Shin Young Park
Dr. Aaron Sarver
Professor Natalia Tretyakova