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Role of epigenetics in the clinical evolution of COVID-19 disease. Epigenome-wide association study identifies markers of severe outcome.

ABSTRACT: We performed a whole-genome DNA methylation analysis using EPIC Illumina BeadArrays on a cohort of 187 “Italian” COVID-19 patients (123 mild and 64 severe) to identify epigenetic markers underlying the worst evolution of the disease (death or Intensive Care Unit admission for mechanical ventilation support).

ORGANISM(S): Homo sapiens

PROVIDER: GSE199591 | GEO | 2023/02/22

REPOSITORIES: GEO

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Multiomic chromatin accessibility and gene expression in peripheral blood predicts future decompensation in hospitalized adults with COVID-19

Project description:To elucidate host response elements that define impending decompensation during SARS-CoV-2 infection, we enrolled subjects hospitalized with COVID-19 who were matched for disease severity and comorbidities at the time of admission and initial sampling. We then performed combined single-cell RNA sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) on peripheral blood mononuclear cells (PBMCs) from the time of admission and compared subjects who improved from their initial low-level oxygen requirement (no change from initial WHO Ordinal category 4/5) to those who later clinically decompensated and required invasive mechanical ventilation or died (WHO Ordinal score 7/8). Chromatin accessibility and transcriptomic immune profiles were markedly altered at admission in patients who will go on to develop critical illness. The greatest immunologic signals were seen in CD4+ T cells, inflammatory T cells, dendritic cells, and NK cell subsets, where an aggregate multiomic signature score calculated at admission offered strong prediction of future clinical deterioration (area under the receiver operating characteristic curve (auROC) 0.91). Epigenetic and transcriptional changes in PBMCs reveal unique, early, and conserved aspects of the immune response before typical clinical signals of decompensation are apparent and thus provide novel biomarkers that can predict future disease severity.

2023-10-17 | GSE215915 | GEO

Melanoma epigenetics: novel mechanisms, markers, and medicines.

Project description: Not available

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Inflammasome-regulated cytokines are critical mediators of lung injury in humans.

Project description:A microarray analysis involving whole blood samples isolated from critically ill patients in the medical intensive care unit at Brigham and Women's Hospital. Four groups of intubated subjects undergoing mechanical ventilation were recruited for the study: those with sepsis alone (Sepsis), those with sepsis + ARDS (se/ARDS), those with SIRS (SIRS), and those whithout sepsis, SIRS, or ARDS (untreated). Blood was obtained from patients on the day of admission (day 0) and 7 days later. RNA was isolated from the whole blood samples and microarrays were prepared to determine differential gene expression between the four groups. Total RNA obtained from whole blood samples of critically ill patients

2012-07-10 | E-GEOD-32707 | biostudies-arrayexpress

Inflammasome-regulated cytokines are critical mediators of lung injury in humans.

2012-07-11 | GSE32707 | GEO

Epigenetics of Yakutia and Central Russia regions

Project description:Lobachevsky University DNAm dataset. Whole blood DNA Methylation (EPIC) profiles from healthy samples from two regions: central Russia (131 samples) and Yakutia (114 samples) obtained in the Laboratory of System Medicine for Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Russia Dataset contains DNAm data from 245 healthy control samples from two regions: central Russia (131) and Yakutia (114). The following characteristics are available for all samples: sex, age, region. Healthy participants in the central Russia region were recruited in 2019–2022. Yakutian participants we recruited in 2022. All measurements were performed at the Laboratory of System Medicine for Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Russia.

2023-12-14 | GSE234461 | GEO

Methylome analyses of three glioblastoma cohorts reveal chemotherapy sensitivity markers within DDR genes [EORTC 26101 cohort]

Project description:The data contains Illumina 450k/EPIC array methylation files from 298 glioblastoma patients from the EORTC 26101 study

2020-11-18 | GSE143755 | GEO

Integrative multi-omic analyses of malignant pleural mesothelioma

Project description:Multi-omic data (whole-genome sequencing, RNA-seq, EPIC 850K methylation arrays) for 123 samples from the MESOMICS project, the French project of molecular characterization of malignant pleural mesothelioma

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Markers as mediators: A review and synthesis of epigenetics literature.

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EPIGENETICS OF ALM

Project description:Epigenetic signatures of alm and assoication with outcome. Background: Acral melanoma (AM) is a rare, aggressive type of cutaneous melanoma (CM) with a distinct genetic profile for which comprehensive genome-wide methylation analysis (GWMA) is lacking. We aimed to identify a methylome signature distinguishing primary acral lentiginous melanoma (PALM) from primary non-lentiginous AM involving the acral sites (NALM), metastatic ALM (MALM), primary non-acral CM (PCM), and acral nevus (AN). Methods: A total of 22 PALM, 9 NALM, 10 MALM, 9 PCM, and 3 AN cases were subjected to GWMA using the Illumina Infinium Methylation EPIC array interrogating 866,562 CpG sites, and their methylomes were compared. Results: A prominent finding was that the methylation profiles of PALM and NALM were distinct, although both are considered canonical AMs. Four of the genes most differentially methylated between PALM and NALM or PALM and MALM were HHEX, DIPK2A (formerly C3orf58), NELFB (formerly COBRA1), and TEF. However, when primary AMs (PALM+NALM) were compared with MALM, IFITM1 and SIK3 were the most differentially methylated, highlighting their pivotal role in the metastatic potential of AMs. Patients with NALM had significantly worse disease-specific (DSS) and overall survival than patients with PALM. Aberrant methylation was significantly associated with aggressive clinicopathologic parameters, including greater Breslow thickness, ulceration, increased mitotic rate, and lymph node metastasis, and with worse DSS. Conclusion: Our study emphasizes the importance of distinguishing the two epigenetically distinct subtypes of AM. We also identified novel epigenetic prognostic biomarkers that may serve to risk-stratify patients with AM. These epigenetic alterations may be leveraged for development of targeted therapies.

2020-02-03 | GSE133395 | GEO

Methylome analyses of three glioblastoma cohorts reveal chemotherapy sensitivity markers within DDR genes [Heidelberg cohort part 2]

Project description:The data contains Illumina 450k/EPIC array methylation files from 18 patients with diffuse IDH wild-type glioma from the Heidelberg Neuro-Oncology center

2020-11-18 | GSE143842 | GEO

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