Browsing by Subject "Epigenome"

Now showing 1 - 6 of 6
  • Thumbnail Image
    Item
    Chronic cAMP activation induces adipocyte browning through discordant biphasic remodeling of transcriptome and chromatin accessibility
    (Elsevier, 2022) So, Jisun; Taleb, Solaema; Wann, Jamie; Strobel, Olivia; Kim, Kyungchan; Roh, Hyun Cheol; Biochemistry and Molecular Biology, School of Medicine
    Objective: Adipose tissue thermogenesis has been suggested as a new therapeutic target to promote energy metabolism for obesity and metabolic disease. Cold-inducible thermogenic adipocytes, called beige adipocytes, have attracted significant attention for their potent anti-obesity activity in adult humans. In this study, we identified the mechanisms underlying beige adipocyte recruitment, so-called adipocyte browning, by different stimuli. Methods: We generated a new adipocyte cell line with enhanced browning potentials and determined its transcriptomic and epigenomic responses following cAMP (forskolin, FSK) versus PPARγ activation (rosiglitazone). We performed time-course RNA-seq and compared the treatments and in vivo adipocyte browning. We also developed an improved protocol for Assay for Transposase Accessible Chromatin-sequencing (ATAC-seq) and defined changes in chromatin accessibility in a time course. The RNA-seq and ATAC-seq data were integrated to determine the kinetics of their coordinated regulation and to identify a transcription factor that drives these processes. We conducted functional studies using pharmacological and genetic approaches with specific inhibitors and shRNA-mediated knockdown, respectively. Results: FSK, not rosiglitazone, resulted in a biphasic transcriptomic response, resembling the kinetics of in vivo cold-induced browning. FSK promoted tissue remodeling first and subsequently shifted energy metabolism, concluding with a transcriptomic profile similar to that induced by rosiglitazone. The thermogenic effects of FSK were abolished by PPARγ antagonists, indicating PPARγ as a converging point. ATAC-seq uncovered that FSK leads to a significant chromatin remodeling that precedes or persists beyond transcriptomic changes, whereas rosiglitazone induces minimal changes. Motif analysis identified nuclear factor, interleukin 3 regulated (NFIL3) as a transcriptional regulator connecting the biphasic response of FSK-induced browning, as indicated by disrupted thermogenesis with NFIL3 knockdown. Conclusions: Our findings elucidated unique dynamics of the transcriptomic and epigenomic remodeling in adipocyte browning, providing new mechanistic insights into adipose thermogenesis and molecular targets for obesity treatment.
  • Thumbnail Image
    Item
    Combinatorial Inhibition of Epigenetic Regulators to Treat Glioblastoma
    (2022-07-29) Burket, Noah; Koenig, Jenna; Saratsis, Amanda
    Glioblastoma (GBM) is a deadly primary brain cancer that affects 12,000 patients in the US annually with a median survival time of 15 months. Temozolomide is the standard-of-care chemotherapy for GBM; however, many tumors are resistant, necessitating the expansion of therapeutic options. EZH2 and JMJD3 are two proteins responsible for epigenetic regulation of the genome via histone methylation, with EZH2 also affecting non-histone targets. Prior studies showed that inhibition of these proteins decreased cell counts and induced radiosensitivity in GBM cells. Thus, we investigated combined use of EZH2 inhibitor, EPZ6438, and JMJD3 inhibitor, GSK-J4, in the treatment of temozolomide-resistant GBM10 cells. Non-irradiated cells were treated with both drugs singly and combined, and counted at 24-, 48-, and 72-hour intervals. Irradiated cells were pre-treated with each drug and combination therapy for three days, irradiated, and then counted at 24-, 48-, and 72-hour intervals. Western blot was used to investigate dsDNA damage biomarker y-H2AX, gene-silencing modification H3K27me3, tumor suppressor p53, EZH2, and JMJD3 expression in non-irradiated and irradiated cells following drug treatment. Single EPZ-6438 and GSK-J4 treatments reduced cell counts with increasing concentration and time. GSK-J4 appears to reduce cell counts more than EPZ-6438 alone, and combinatorial use reduces this further. Western blot reveals increased H3K27me3 expression with GSK-J4 treatment following radiation, but not with EPZ-6438. y-H2AX expression is increased after EPZ-6438 treatment but is not further increased with radiation. Meanwhile, GSK-J4 increased y-H2AX, but only after irradiation. Reduced cell counts following treatment with GSK-J4 may be due to its effects on gene silencing from inhibition of H3K27 demethylation. Additionally, increased dsDNA breaks seen in EPZ-6438 and GSK-J4 supports their roles in radiosensitizing GBM cells. This study highlights the importance of further investigation into GSK-J4 and EPZ-6438 combination therapy in temozolomide-resistant GBM tumors.
  • Thumbnail Image
    Item
    Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies
    (Springer Nature, 2024-01-05) Reho, Paolo; Saez-Atienzar, Sara; Ruffo, Paola; Solaiman, Sultana; Shah, Zalak; Chia, Ruth; Kaivola, Karri; Traynor, Bryan J.; Tilley, Bension S.; Gentleman, Steve M.; Hodges, Angela K.; Aarsland, Dag; Monuki, Edwin S.; Newell, Kathy L.; Woltjer, Randy; Albert, Marilyn S.; Dawson, Ted M.; Rosenthal, Liana S.; Troncoso, Juan C.; Pletnikova, Olga; Serrano, Geidy E.; Beach, Thomas G.; Easwaran, Hariharan P.; Scholz, Sonja W.; Pathology and Laboratory Medicine, School of Medicine
    Dementia with Lewy bodies (DLB) is a common form of dementia in the elderly population. We performed genome-wide DNA methylation mapping of cerebellar tissue from pathologically confirmed DLB cases and controls to study the epigenetic profile of this understudied disease. After quality control filtering, 728,197 CpG-sites in 278 cases and 172 controls were available for the analysis. We undertook an epigenome-wide association study, which found a differential methylation signature in DLB cases. Our analysis identified seven differentially methylated probes and three regions associated with DLB. The most significant CpGs were located in ARSB (cg16086807), LINC00173 (cg18800161), and MGRN1 (cg16250093). Functional enrichment evaluations found widespread epigenetic dysregulation in genes associated with neuron-to-neuron synapse, postsynaptic specialization, postsynaptic density, and CTCF-mediated synaptic plasticity. In conclusion, our study highlights the potential importance of epigenetic alterations in the pathogenesis of DLB and provides insights into the modified genes, regions and pathways that may guide therapeutic developments.
  • Thumbnail Image
    Item
    DNA methylation program during development
    (Frontiers Media, 2012) Zhou, Feng C.; Anatomy, Cell Biology and Physiology, School of Medicine
    DNA methylation is a key epigenetic mark when occurring in the promoter and enhancer regions regulates the accessibility of the binding protein and gene transcription. DNA methylation is inheritable and can be de novo-synthesized, erased and reinstated, making it arguably one of the most dynamic upstream regulators for gene expression and the most influential pacer for development. Recent progress has demonstrated that two forms of cytosine methylation and two pathways for demethylation constitute ample complexity for an instructional program for orchestrated gene expression and development. The forum of the current discussion and review are whether there is such a program, if so what the DNA methylation program entails, and what environment can change the DNA methylation program. The translational implication of the DNA methylation program is also proposed.
  • Thumbnail Image
    Item
    Lysine Methylation Regulators Moonlighting outside the Epigenome
    (Elsevier, 2019-09-19) Cornett, Evan M.; Ferry, Laure; Defossez, Pierre-Antoine; Rothbart, Scott B.; Biochemistry and Molecular Biology, School of Medicine
    Landmark discoveries made nearly two decades ago identified known transcriptional regulators as histone lysine methyltransferases; since then the field of lysine methylation signaling has been dominated by studies of how this small chemical posttranslational modification regulates gene expression and other chromatin-based processes. However, recent advances in mass spectrometry-based proteomics have revealed that histones are just a subset of the thousands of eukaryotic proteins marked by lysine methylation. As the writers, erasers, and readers of histone lysine methylation are emerging as a promising therapeutic target class for cancer and other diseases, a key challenge for the field is to define the full spectrum of activities for these proteins. Here we summarize recent discoveries implicating non-histone lysine methylation as a major regulator of diverse cellular processes. We further discuss recent technological innovations that are enabling the expanded study of lysine methylation signaling. Collectively, these findings are shaping our understanding of the fundamental mechanisms of non-histone protein regulation through this dynamic and multi-functional posttranslational modification.
  • Thumbnail Image
    Item
    Role of Polycomb Group Protein Mel18 in Hematopoietic Stem Cell Maintenance
    (2025-05) Cai, Wenjie; Wek, Ronald; Zhang, Ji; Capitano, Maegan; Wan, Jun; Ren, Hongxia; Liu, Yan
    Polycomb group (PcG) proteins are epigenetic gene silencers that have been implicated in stem cell maintenance and cancer development. Genetic and biochemical studies indicate that Polycomb group proteins exist in at least two protein complexes, Polycomb repressive complex 2 (PRC2) and Polycomb repressive complex 1 (PRC1). PRC2 complex deposits the mono-, di-, and tri- methylation on histone 3 lysine 27, whereas PRC1 introduces mono-ubiquitination on histone 2A lysine 119 (H2AK119ub1). PRC1 can also regulate 3D chromatin structure. Bmi1 (PCGF4) and Mel18 (PCGF2) are two major homologs of the PCGF subunit within the canonical PRC1 complex. While Bmi1 is a positive regulator of hematopoietic stem cells (HSCs) and leukemia stem cells (LSCs) self-renewal, the role of Mel18 in normal and malignant hematopoiesis is not fully understood. Based upon our previous studies and the literature, I hypothesized that Mel18 inhibits HSC self-renewal and proliferation but promotes HSC senescence. To test my hypothesis, I examined HSC behavior in Mel18 conditional knockout mice (Mel18f/f-Mx1Cre+). I found that acute deletion of Mel18 enhances the repopulating potential of HSCs and increases the number of functional HSCs, without affecting HSC homing. Loss of Mel18 decreased hematopoietic stem and progenitor cell (HSPCs) senescence. In addition, loss of Mel18 promotes cell cycle progression in HSPCs. Therefore, I demonstrated that loss of Mel18 enhances the repopulating potential of HSCs, promotes cell cycle progression in HSCs, but reduces HSC senescence. Mechanistically, loss of Mel18 increases the chromatin accessibility to genes important for HSC self-renewal and ex vivo expansion such as homeobox gene Hoxb4. CUT&RUN sequencing assays revealed that loss of Mel18 reduces the H2AK119ub1 enrichment at the promoter regions of Cdk4 and Cdk6, leading to their enhanced expression in HSPCs. Furthermore, I identified a Mel18-specific chromatin loop at the S100a9 locus, a gene important for senescence and inflammation, using Hi-C assays, Collectively, these findings demonstrated that Mel18 plays an important role in hematopoietic stem cell maintenance. Mel18 inhibits HSC self-renewal and proliferation but promotes HSC senescence through modulating histone modifications, chromatin accessibility, and 3D chromatin structure in HSCs.