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

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. 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.

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.

A longstanding interest as indicated above, in the archer lab are the mechanisms by which the hormone-stimulated glucocorticoid receptor (GR) modulates transcription by interacting with thousands of enhancers and GR binding sites (GBSs) throughout the genome. In recently published work we examined the effects of GR binding on enhancer dynamics and investigated the contributions of individual GBSs to the hormone response. Hormone treatment resulted in genome-wide reorganization of the enhancer landscape in breast cancer cells. Upstream of the DDIT4 oncogene, GR bound to four sites constituting a hormone-dependent super enhancer. Three GBSs were required as hormone-dependent enhancers that differentially promoted histone acetylation, transcription frequency, and burst size. Conversely, the fourth site suppressed transcription and hormone treatment alleviated this suppression. GR binding within the super enhancer promoted a loop-switching mechanism that allowed interaction of the DDIT4 TSS with the active GBSs. The unique functions of each GR binding site contribute to hormone-induced transcriptional heterogeneity and demonstrate the potential for targeted modulation of oncogene expression. Consequently, this highly successful project that resulted in the elucidation of an elegant molecular mechanism of GR transcriptional regulation. (Hoffman et al., Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response. Mol Cell, 2022 Feb 17;82(4):803-815.e5. doi: 10.1016/j.molcel.2021.12.035. Epub 2022 Jan 24. PMID: 35077705 PMCID: PMC8897972)

We contributed to studies in the Anchang lab at NIEHS that examined a major topic of debate in developmental biology centers on whether development is continuous, discontinuous, or a mixture of both. They presented a data-driven framework that addresses these limitations with temporal single-cell data collected at discrete time points as inputs and a mixture of dependent minimum spanning trees (MSTs) as outputs, denoted as dynamic spanning forest mixtures (DSFMix). DSFMix uses decision-tree models to select genes that account for variations in multimodality, skewness and time. The genes are subsequently used to build the forest using tree agglomerative hierarchical clustering and dynamic branch cutting. These results indicate that the expression of genes during normal development exhibits a high proportion of non-uniformly distributed profiles that are mostly right-skewed and multimodal; the latter being a characteristic of major steady states during development. Consequently this study also identifies and validates gene signatures driving complex dynamic processes during somatic or germline differentiation.(Anchang, et al., 2022 Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures Brief Bioinform. 2022 Mar 10;23(2):bbac017. doi: 10.1093/bib/bbac017.)

In studies with the Zannas lab at the University of North Carolina, we examined mechanisms by which chronic environmental stress can profoundly impact cell and body function. While the underlying mechanisms are poorly understood, epigenetics has emerged as a key link between environment and health. The genomic effects of stress are thought to be mediated by the action of glucocorticoid stress hormones, primarily cortisol in humans, which act via the glucocorticoid receptor (GR). To dissect how naturalistic GR activation influences epigenetic and cell states, human fibroblasts underwent prolonged exposure to physiological stress levels of cortisol and/or a selective GR antagonist. Cortisol was found to drive robust changes in cell proliferation, migration, and morphology, which were abrogated by concomitant GR blockade. These GR-driven phenotypes were accompanied by widespread, yet genomic context-dependent, changes in DNA methylation and mRNA expression involving genes with known roles in cell proliferation and migration. These findings provide novel insights into how chronic stress-driven functional epigenomic patterns become established to shape key cell phenotypes.(Leung, et al., 2022, Chronic stress-driven glucocorticoid receptor activation programs key cell phenotypes and functional epigenomic patterns in human fibroblasts ISCIENCE-D-22-01259R4 (in press)