Longwise Cluster Analysis for the Prediction of COVID-19 Severity within 72 h of Admission: COVID-DATA-SAVE-LIFES Cohort by Rodrigo San-Cristobal, Roberto Martín-Hernández, Omar Ramos-Lopez, Diego Martinez-Urbistondo, Víctor Micó, Gonzalo Colmenarejo, Paula Villares Fernandez, Lidia Daimiel, Jose Alfredo Martínez

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Uncovering the gene regulatory network of type 2 diabetes through multi-omic data integration by Jiachen Liu, Shenghua Liu, Zhaomei Yu, Xiaorui Qiu, Rundong Jiang, Weizheng Li

“…Methods The datasets used in the experiments comprise three groups: (1) genomic (2) transcriptomic, and (3) epigenomic categories. Then, a series of bioinformatics technologies including Marker set enrichment analysis (MSEA), weighted key driver analysis (wKDA) was performed to identify key drivers. …”
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DNA methylation-based classifier and gene expression signatures detect BRCAness in osteosarcoma by Maxim Barenboim, Michal Kovac, Baptiste Ameline, David T. W. Jones, Olaf Witt, Stefan Bielack, Stefan Burdach, Daniel Baumhoer, Michaela Nathrath

“…Machine-learning and gene expression approaches add new epigenomic and transcriptomic aspects to already established genomic methods for evaluation of BRCAness in osteosarcoma and can be extended to cancers characterized by genome instability. …”
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DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA by Laura J. Smyth, Christopher C. Patterson, Elizabeth J. Swan, Alexander P. Maxwell, Alexander P. Maxwell, Amy Jayne McKnight

“…Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.…”
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VWA3A-derived ependyma promoter drives increased therapeutic protein secretion into the CSF by Ellie M. Carrell, Yong Hong Chen, Paul T. Ranum, Stephanie L. Coffin, Larry N. Singh, Luis Tecedor, Megan S. Keiser, Eloise Hudry, Bradley T. Hyman, Beverly L. Davidson

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Leveraging Multilayered “Omics” Data for Atopic Dermatitis: A Road Map to Precision Medicine by Debajyoti Ghosh, Jonathan A. Bernstein, Gurjit K. Khurana Hershey, Marc E. Rothenberg, Tesfaye B. Mersha

“…Integrating omics layers (e.g., genome, epigenome, transcriptome, proteome, metabolome, lipidome, exposome, microbiome), which often have complementary and synergistic effects, might provide the opportunity to capture the flow of information underlying AD disease manifestation. …”
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Elucidating disease-associated mechanisms triggered by pollutants via the epigenetic landscape using large-scale ChIP-Seq data by Zhaonan Zou, Yuka Yoshimura, Yoshihiro Yamanishi, Shinya Oki

“…Methods Large-scale public ChIP-Seq data (human, n = 15,155; mouse, n = 13,156) were used to predict TFs that are enriched in the pollutant-induced differentially accessible genomic regions (DARs) obtained from epigenome analyses (ATAC-Seq). The resultant pollutant–TF matrices were then cross-referenced to a repository of TF–disorder associations to account for pollutant modes of action. …”
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A comparison of DNA methylation in newborn blood samples from infants with and without orofacial clefts by Zongli Xu, Rolv T. Lie, Allen J. Wilcox, Ola Didrik Saugstad, Jack A. Taylor

“…Methods In blood samples from 2- to 3-day-old infants (n = 747) collected in a nationwide population-based study of orofacial clefts in Norway, we measured DNA methylation profiles for more than 450,000 CpGs and then conducted epigenome-wide association analyses (EWAS). We tested methylation profile difference at each CpG between controls (n = 436) and each of the cleft subtypes (92 cleft lip only, CLO; 84 cleft palate only, CPO; 132 cleft lip and palate, CLP). …”
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Testicular cancer in mice: interplay between stem cells and endocrine insults by Ankita Kaushik, Deepa Bhartiya

“…T2GCT initiates from tissue-resident, pluripotent VSELs due to their altered epigenome. Neonatal exposure to DES blocks differentiation (spermatogenesis) and VSELs get transformed into CD166 positive cancer stem cells that undergo excessive self-renewal and initiate cancer in adult life challenging existing concept of fetal origin of T2GCT.…”
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HDAC1 is Involved in Neuroinflammation and Blood-Brain Barrier Damage in Stroke Pathogenesis by Wang HK, Su YT, Ho YC, Lee YK, Chu TH, Chen KT, Wu CC

“…Histone deacetylase 1 (HDAC1) is a repressor of epigenomic gene transcription and participates in DNA damage and cell cycle regulation. …”
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Accelerated epigenetic aging in women with emotionally unstable personality disorder and a history of suicide attempts by Adrian Desai E. Boström, Peter Andersson, Esmail Jamshidi, Alexander Wilczek, Åsa Nilsonne, Mathias Rask-Andersen, Marie Åsberg, Jussi Jokinen

“…Abstract Emotional unstable personality disorder (EUPD; previously borderline personality disorder, BPD) is associated with excess natural-cause mortality, comorbid medical conditions, poor health habits and stress related epigenomic alterations. Previous studies demonstrated that GrimAge – a state-of-the-art epigenetic age (EA) estimator – strongly predicts mortality risk and physiological dysregulation. …”
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Cold stress induces rapid gene-specific changes in the levels of H3K4me3 and H3K27me3 in Arabidopsis thaliana by Léa Faivre, Nathalie-Francesca Kinscher, Ana Belén Kuhlmann, Xiaocai Xu, Kerstin Kaufmann, Daniel Schubert

“…In this study, we offer an epigenome profiling of H3K27me3 and its antagonistic active mark H3K4me3 during short-term cold exposure. …”
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Promyelocytic Leukemia Protein (PML) Controls <italic toggle="yes">Listeria monocytogenes</italic> Infection by David Ribet, Valérie Lallemand-Breitenbach, Omar Ferhi, Marie-Anne Nahori, Hugo Varet, Hugues de Thé, Pascale Cossart

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The effects of a motorized passive simulated jogging device on descent of the arterial pulse waveform dicrotic notch: A single arm placebo‐controlled cross‐over trial by Jose A. Adams, Jose R. Lopez, Vinay Nadkarni, Zarazuela Zolkipli‐Cunningham, Harry Ischiropoulos, Marvin A. Sackner

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Heat Shock Protein 90 Regulates the Activity of Histone Deacetylase Sir2 in Plasmodium falciparum by Wahida Tabassum, Mrinnanda Bhattacharya, Sayan Bakshi, Mrinal Kanti Bhattacharyya

“…Here, we uncover that the molecular chaperone PfHsp90 regulates the abundance and activity of the histone-deacetylase PfSir2, a prominent regulator of Plasmodium epigenome. Given that PfSir2 controls both virulence and multiplicity of the parasite, and that PfHsp90 is an essential chaperone involved in diverse cellular processes, our findings argue that the PfHsp90-PfSir2 axis could be targeted to curb malaria.…”
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A Novel Framework for the Identification of Reference DNA Methylation Libraries for Reference-Based Deconvolution of Cellular Mixtures by Shelby Bell-Glenn, Jeffrey A. Thompson, Lucas A. Salas, Devin C. Koestler

“…Additionally, reference libraries constructed using RESET resulted in cellular composition estimates that explained more variation in DNAm as compared to the Legacy approach when evaluated in the context of epigenome-wide association studies (EWAS) of several publicly available data sets. …”
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Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity by Yu, V, Yong, F, Marta, A, Khadayate, S, Osakwe, A, Bhattacharya, S, Varghese, SS, Chabosseau, P, Tabibi, SM, Chen, K, Georgiadou, E, Parveen, N, Suleiman, M, Stamoulis, Z, Marselli, L, De Luca, C, Tesi, M, Ostinelli, G, Delgadillo-Silva, L, Wu, X, Hatanaka, Y, Montoya, A, Elliott, J, Patel, B

“…Changes at the level of the epigenome provide one such possibility, which we explore here by focusing on the imprinted gene Nnat (encoding neuronatin [NNAT]), which is required for normal insulin synthesis and secretion. …”

Histone lysine and DNA methylation: dynamic marks in the chromatin by Belle, R

“…TET enzymes play an essential role in shaping the epigenome and loss of TET2’s function has frequently been described in haematopoietic malignancies with notable examples being myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). …”

Genome-wide analysis of DNA methylation and risk of cardiovascular disease in a Chinese population by Yan Gao, Huifang Pang, Bowang Chen, ChaoQun Wu, Yanping Wang, Libo Hou, Siming Wang, Dianjianyi Sun, Xin Zheng

“…Methods We performed an epigenome-wide association study (EWAS) to identify CpGs related to CVD development in a Chinese population.We adopted a nested case–control design based on data from China PEACE Million Persons Project. …”
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Developmental exposure to the organochlorine pesticide dieldrin causes male-specific exacerbation of α-synuclein-preformed fibril-induced toxicity and motor deficits by Aysegul O. Gezer, Joseph Kochmanski, Sarah E. VanOeveren, Allyson Cole-Strauss, Christopher J. Kemp, Joseph R. Patterson, Kathryn M. Miller, Nathan C. Kuhn, Danielle E. Herman, Alyssa McIntire, Jack W. Lipton, Kelvin C. Luk, Sheila M. Fleming, Caryl E. Sortwell, Alison I. Bernstein

“…This sex-specific result is consistent with both previous work in the MPTP model, our previously reported sex-specific effects of this exposure paradigm on the male and female epigenome, and the higher prevalence and more severe course of PD in males. …”
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