The Role of Metabolism and Epigenetics in Regulating Cellular Plasticity

Eukaryotic cells encode genetic information in the form of DNA. However within our genetic code, only a subset of these genes are expressed in a given cell—giving rise to different cell types. The regulation of what genes are expressed is dictated by epigenetics. Epigenetics is the punctuation of our genetic code. It leaves unique marks that are read, written, and erased on DNA and on histone protein, which package our DNA. The writing and erasing of epigenetic marks requires metabolic products including but not limited to, acetyl-CoA, methionine, and NAD+. Consequently, cell metabolism, epigenetic regulation, and cell phenotype are tightly linked. The purpose of the work here is twofold. One, to propose that there are additional DNA epigenetic marks and pathways not previously described. Second, to describe the development and application of mass spectrometry techniques to monitor cell metabolism and its influence on epigenetics and cell phenotype. To accomplish this, we examined the activity of the human uracil DNA glycosylases (erasers) against all the possible substrates derived from oxidation and deamination of 5-methylcytosine—the primary epigenetic mark in DNA. Using an in vitro real-time kinetic assay, we identified that one of the best substrates for three of the four human glycosylases examined is 5-carboxyuracil (5caU). 5caU is the least likely product to form as it requires several sequential oxidations and deamination reactions of 5-methylcytosine. This raises additional questions as to its formation and what distinct role it plays. In the subsequent studies we describe the development of mass spectrometry techniques to measure metabolic pathways involved in providing key substrates for epigenetic writing. Specifically, we examined the role of the serine synthesis pathway in cancer cells and its role in one-carbon metabolism that contributes to both DNA and histone methylation. Finally, we describe the development of a technique that serves to combine the simultaneous measurement of metabolites, histone modifications, and proteomics that allow us to monitor cell metabolism, epigenetics, and plasticity, from the same sample.

Name thesis:degree_name

Pharmacology and Toxicology (Doctoral)

Discipline thesis:degree_discipline

Chemistry

Grantor

The University of Texas Medical Branch at Galveston

Year dc:date.issued

2023

Author dc:creator

• Sowers, Mark Lai

Advisor dc:contributor.advisor

• Zhang, Kangling

Committee members dc:contributor.committeemember

• Hatch, Sandra
• Laezza, Fernanda
• Fofanov, Yuriy
• Bossmann, Stefan

Handle dc:identifier.uri

https://hdl.handle.net/2152.3/12617

OAI identifier oai:identifier

oai:utmb-ir.tdl.org:2152.3/12617