Epigenetic and Transcriptional Functions of Nuclear Receptors and Chromatin Remodeling Proteins in Stem and Cancer Cells

National Institute Of Environmental Health Sciences

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Abstract

The elegant organization of nucleic acids, predominantly DNA, into chromatin serves essential structural and regulatory roles in eukaryotic cells. This beautiful architecture allows for an expansion of the underlying genetic information by overlaying a spectrum of epigenetic controls. The interplay between genome accessibility, chromatin posttranslational modifications and transcriptional activity is a critical hub of gene expression regulation. Fundamental to many disease processes is a dysregulation of transcription that underlies the critical role regulated gene transcription plays in normal development physiology and homeostasis. A major focus, of the Archer group has been an understanding of how epigenetic enzymes, including chromatin remodeling proteins such as the SWI/SNF complex, work with transcription factors, such as the glucocorticoid receptor, to respond to environmental cues, both internal and external. Many of our studies have utilize the glucocorticoid receptor, a ligand-activated transcription factor that has important functions in many aspects of mammalian physiology including development, reproduction, immune response, cardiac function, and energy metabolism. Consistent with the broad physiological functions, dysregulation of GR activity is a major factor in health and disease. In this way we hope to understand the function of both the receptor and the requirement for chromatin remodeling and other epigenetic enzymes in these processes. The organization of DNA as chromatin, and its assembly around four core histones, as well as a linker histone, H1, provides a platform for studying mechanisms of gene transcription that relate to environmental responses as well as developmental cues important in determining prepotency of embryonic stem cells. The advent of both embryonic stem cells as well as induced pluripotency stem cells (iPSCs) have opened a significant avenue of experimental approaches to understand both normal and disease states in humans. Many of the studies with pluripotent stem cells have affirmed a major determinant of a role for epigenetics as a mechanism by which the DNA residing in all cells can have specific features of pluripotency. Research pursued in the chromatin and gene expression group within the ESCBL aligns with the NIEHS strategic plan themes one, two and three and multiple goals within those three themes particularly with respect to basic biological research, outreach communications and engagement, environmental health disparities and environmental justice, the professional pipeline, and greater workforce diversity and training in capacity building in global health. Together these studies allow us to fulfill the mission of the NIEHS to improve an understanding of environmental impact on human health and development. Examples of our recently completed studies include data showing that individual heterogeneity, or genetic variability among samples, can substantially affect reprogramming of induced pluripotent stem cells (iPSCs).Indeed it is well established that iPSCs can be derived from differentiated cells, enabling the generation of personalized disease models by differentiating patient-derived iPSCs into disease-relevant cell lines. While genetic variability between different iPSC lines affects differentiation potential, how this variability in somatic cells affects pluripotent potential is less understood. We generated and compared transcriptomic data from 72 dermal fibroblast-iPSC pairs with consistent variation in reprogramming efficiency. By considering equal numbers of samples from self-reported African Americans and White Americans, we identified both ancestry-dependent and ancestry-independent transcripts associated with reprogramming efficiency, suggesting that transcriptomic heterogeneity can substantially affect reprogramming. Moreover, reprogramming efficiency-associated genes are involved in diverse dynamic biological processes, including cancer and wound healing, and are predictive of 5-year breast cancer survival in an independent cohort. Candidate genes may provide insight into mechanisms of ancestry-dependent regulation of cell fate transitions and motivate additional studies for improvement of reprogramming. (Bisogno LS, et al., 2020. Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes. Sci Adv; 2020 Nov 20;6(47): 10.1126/sciadv.abc3851 . In collaboration with the Grant laboratory at NCCU we investigated the role of EGF on the expression of these enzymes since it interacts with signaling pathways to also affect prostate tumor progression and is additionally associated with decreased DNA methylation. The expression of UGT2B15, UGT2B17, de novo methyltransferases, DNMT3A and DNMT3B was assessed in prostate cancer cells (LNCaP) treated with EGF, an EGFR inhibitor PD16893, and the methyltransferase inhibitor, 5-azacytidine, respectively. The results showed that EGF treatment decreased levels of expression of all four genes and that their expression was reversed by PD16893. Treatment with 5-azacytidine, markedly decreased expression of UGT2B15 and UGT2B17 over 85% as well as significantly decreased expression of DNMT3B, but not the expression of DNMT3A. DNMT3B siRNA treated LNCaP cells had decreased expression of UGT2B15 and UGT2B17, while DNMT3A siRNA treated cells had only moderately decreased UGT2B15 expression. Treatment with DNMT methyltransferase inhibitor, RG108, significantly decreased UGT2B17 expression. Additionally, methylation differences between prostate cancer samples and benign prostate samples from an Illumina 450K Methylation Array study were assessed. The results taken together suggest that hypomethylation of the UGT2B15 and UGT2B17 genes contributes to increased risk of prostate cancer and may provide a putative biomarker or epigenetic target for chemotherapeutics. (Shafiee-Kermani F, et al., 2021 Expression of UDP Glucuronosyltransferases 2B15 and 2B17 is associated with methylation status in prostate cancer cells. Epigenetics. 2021 Mar;16(3):289-299. doi: 10.1080/15592294.2020.1795601.)