Browsing by Subject "Epigenomics"

Now showing 1 - 5 of 5
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    Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin
    (Springer Nature, 2019-04-25) Zibetti, Cristina; Liu, Sheng; Wan, Jun; Qian, Jiang; Blackshaw, Seth; Medical and Molecular Genetics, School of Medicine
    Retinal neurogenesis occurs through partially overlapping temporal windows, driven by concerted actions of transcription factors which, in turn, may contribute to the establishment of divergent genetic programs in the developing retina by coordinating variations in chromatin landscapes. Here we comprehensively profile murine retinal progenitors by integrating next generation sequencing methods and interrogate changes in chromatin accessibility at embryonic and post-natal stages. An unbiased search for motifs in open chromatin regions identifies putative factors involved in the developmental progression of the epigenome in retinal progenitor cells. Among these factors, the transcription factor LHX2 exhibits a developmentally regulated cis-regulatory repertoire and stage-dependent motif instances. Using loss-of-function assays, we determine LHX2 coordinates variations in chromatin accessibility, by competition for nucleosome occupancy and secondary regulation of candidate pioneer factors.
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    In Vivo Dissection of Chamber-Selective Enhancers Reveals Estrogen-Related Receptor as a Regulator of Ventricular Cardiomyocyte Identity
    (Wolters Kluwer, 2023) Cao, Yangpo; Zhang, Xiaoran; Akerberg, Brynn N.; Yuan, Haiyun; Sakamoto, Tomoya; Xiao, Feng; VanDusen, Nathan J.; Zhou, Pingzhu; Sweat, Mason E.; Wang, Yi; Prondzynski, Maksymilian; Chen, Jian; Zhang, Yan; Wang, Peizhe; Kelly, Daniel P.; Pu, William T.; Pediatrics, School of Medicine
    Background: Cardiac chamber-selective transcriptional programs underpin the structural and functional differences between atrial and ventricular cardiomyocytes (aCMs and vCMs). The mechanisms responsible for these chamber-selective transcriptional programs remain largely undefined. Methods: We nominated candidate chamber-selective enhancers (CSEs) by determining the genome-wide occupancy of 7 key cardiac transcription factors (GATA4, MEF2A, MEF2C, NKX2-5, SRF, TBX5, TEAD1) and transcriptional coactivator P300 in atria and ventricles. Candidate enhancers were tested using an adeno-associated virus-mediated massively parallel reporter assay. Chromatin features of CSEs were evaluated by performing assay of transposase accessible chromatin sequencing and acetylation of histone H3 at lysine 27-HiChIP on aCMs and vCMs. CSE sequence requirements were determined by systematic tiling mutagenesis of 29 CSEs at 5 bp resolution. Estrogen-related receptor (ERR) function in cardiomyocytes was evaluated by Cre-loxP-mediated inactivation of ERRα and ERRγ in cardiomyocytes. Results: We identified 134 066 and 97 506 regions reproducibly occupied by at least 1 transcription factor or P300, in atria or ventricles, respectively. Enhancer activities of 2639 regions bound by transcription factors or P300 were tested in aCMs and vCMs by adeno-associated virus-mediated massively parallel reporter assay. This identified 1092 active enhancers in aCMs or vCMs. Several overlapped loci associated with cardiovascular disease through genome-wide association studies, and 229 exhibited chamber-selective activity in aCMs or vCMs. Many CSEs exhibited differential chromatin accessibility between aCMs and vCMs, and CSEs were enriched for aCM- or vCM-selective acetylation of histone H3 at lysine 27-anchored loops. Tiling mutagenesis of 29 CSEs identified the binding motif of ERRα/γ as important for ventricular enhancer activity. The requirement of ERRα/γ to activate ventricular CSEs and promote vCM identity was confirmed by loss of the vCM gene profile in ERRα/γ knockout vCMs. Conclusions: We identified 229 CSEs that could be useful research tools or direct therapeutic gene expression. We showed that chamber-selective multi-transcription factor, P300 occupancy, open chromatin, and chromatin looping are predictive features of CSEs. We found that ERRα/γ are essential for maintenance of ventricular identity. Finally, our gene expression, epigenetic, 3-dimensional genome, and enhancer activity atlas provide key resources for future studies of chamber-selective gene regulation.
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    Increased epigenetic age in normal breast tissue from luminal breast cancer patients
    (Biomed Central, 2018-08-29) Hofstatter, Erin W.; Horvath, Steve; Dalela, Disha; Gupta, Piyush; Chagpar, Anees B.; Wali, Vikram B.; Bossuyt, Veerle; Storniolo, Anna Maria; Hatzis, Christos; Patwardhan, Gauri; Von Wahlde, Marie-Kristin; Butler, Meghan; Epstein, Lianne; Stavris, Karen; Sturrock, Tracy; Au, Alexander; Kwei, Stephanie; Pusztai, Lajos; Medicine, School of Medicine
    BACKGROUND: Age is one of the most important risk factors for developing breast cancer. However, age-related changes in normal breast tissue that potentially lead to breast cancer are incompletely understood. Quantifying tissue-level DNA methylation can contribute to understanding these processes. We hypothesized that occurrence of breast cancer should be associated with an acceleration of epigenetic aging in normal breast tissue. RESULTS: Ninety-six normal breast tissue samples were obtained from 88 subjects (breast cancer = 35 subjects/40 samples, unaffected = 53 subjects/53 samples). Normal tissue samples from breast cancer patients were obtained from distant non-tumor sites of primary mastectomy specimens, while samples from unaffected women were obtained from the Komen Tissue Bank (n = 25) and from non-cancer-related breast surgery specimens (n = 28). Patients were further stratified into four cohorts: age < 50 years with and without breast cancer and age ≥ 50 with and without breast cancer. The Illumina HumanMethylation450k BeadChip microarray was used to generate methylation profiles from extracted DNA samples. Data was analyzed using the "Epigenetic Clock," a published biomarker of aging based on a defined set of 353 CpGs in the human genome. The resulting age estimate, DNA methylation age, was related to chronological age and to breast cancer status. The DNAmAge of normal breast tissue was strongly correlated with chronological age (r = 0.712, p < 0.001). Compared to unaffected peers, breast cancer patients exhibited significant age acceleration in their normal breast tissue (p = 0.002). Multivariate analysis revealed that epigenetic age acceleration in the normal breast tissue of subjects with cancer remained significant after adjusting for clinical and demographic variables. Additionally, smoking was found to be positively correlated with epigenetic aging in normal breast tissue (p = 0.012). CONCLUSIONS: Women with luminal breast cancer exhibit significant epigenetic age acceleration in normal adjacent breast tissue, which is consistent with an analogous finding in malignant breast tissue. Smoking is also associated with epigenetic age acceleration in normal breast tissue. Further studies are needed to determine whether epigenetic age acceleration in normal breast tissue is predictive of incident breast cancer and whether this mediates the risk of chronological age on breast cancer risk.
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    Integrative Co-methylation Network Analysis Identifies Novel DNA Methylation Signatures and Their Target Genes in Alzheimer's Disease
    (Elsevier, 2023) Kim, Jun Pyo; Kim, Bo-Hyun; Bice, Paula J.; Seo, Sang Won; Bennett, David A.; Saykin, Andrew J.; Nho, Kwangsik; Radiology and Imaging Sciences, School of Medicine
    Background: DNA methylation is a key epigenetic marker, and its alternations may be involved in Alzheimer's disease (AD). CpGs sharing similar biological functions or pathways tend to be co-methylated. Methods: We performed an integrative network-based DNA methylation analysis on 2 independent cohorts (N = 941) using brain DNA methylation profiles and RNA-sequencing as well as AD pathology data. Results: Weighted co-methylation network analysis identified 6 modules as significantly associated with neuritic plaque burden. In total, 15 hub CpGs including 3 novel CpGs were identified and replicated as being significantly associated with AD pathology. Furthermore, we identified and replicated 4 target genes (ATP6V1G2, VCP, RAD52, and LST1) as significantly regulated by DNA methylation at hub CpGs. In particular, VCP gene expression was also associated with AD pathology in both cohorts. Conclusions: This integrative network-based multiomics study provides compelling evidence for a potential role of DNA methylation alternations and their target genes in AD.
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    Multi-omics Investigation into Alzheimer's Disease: Functional Mechanism and Early Detection
    (2024-08) Pugalenthi, Pradeep Varathan; Yan, Jingwen; Janga, Sarath Chandra; Nho, Kwangsik; Wang, Juexin
    Alzheimer’s disease (AD), a multi-factorial and highly heritable condition, stands as the foremost contributor to dementia. Despite its early discovery and extensive studies, the underlying pathogenesis of AD remains incomplete. This thesis addresses critical aspects of AD through multi-omics approach for improved understanding of underlying functional mechanisms and for improved precision in early detection. Multi-omics integration allows us to explore a wide spectrum of AD-related changes at different biological levels including genomics and metabolomics and how they associate with the biomarkers. In the first aim, I performed an integrative analysis of summary statistics from genome-wide association study (GWAS) and expression quantitative trait loci (eQTL) analysis. Results of this study confirmed the potential of integrative GWAS and eQTL analysis in estimating the transcriptomic changes when lack of tissue-specific expression data, and provided important insights into tissue-specific downstream biology of observed GWAS associations in AD. In the second aim, I took a step further and hypothesized the epistatic effect of GWAS findings and neighboring variants on the downstream functional mechanism. Leveraging the recent advances in sequence-based genome annotation, I investigated the tissue-specific effects of top AD GWAS variants on the chromatin profiles. With in-silico mutagenesis, GWAS variants were found to function via either lead effect or epistatic effect, pinpointing the limitation of existing focus on single-variant-based function annotation. In the last aim, I built a comprehensive bioinformatics pipeline to investigate the potential of metabolic age as an early indicator for AD progression, in which we also observed significant difference between sex groups. We identified strong associations of metabolic age with longitudinal changes of current diagnostic metrics in the ATN framework, suggesting the potential of metabolic age as early biomarkers. Collectively, results from these aims contribute to advancing our understanding of AD and provide valuable insights for future research and clinical applications.