Epigenome-wide DNA methylation profiling in aneurysmal subarachnoid hemorrhage and delayed ischemic neurologic deficit: a prospective observational study.

Background: The molecular mechanisms underlying aneurysmal subarachnoid hemorrhage (aSAH) and delayed ischemic neurologic deficit (DIND) remain poorly understood. We hereby present the study investigating epigenome-wide profile of DNA methylation in adults with aSAH and DIND.

Methods: A prospective observational epigenome-wide association study (EWAS) was conducted with DNA extracted from the peripheral whole blood of subjects with aSAH.

Changes of methylation at enhancers appear to be essential for HIV infection progression.

Background: We studied the influence of the European HIV-1 subtype B (most common in the Western and Central Europe) and subtype A6 (prevalent in Eastern Europe including Ukraine and Russia) on host methylome during infection progression and in virus-subtype-specific manner.

Results: Our results show that regardless of virus subtype, in the initial phase of the infection, HIV-related methylation changes more frequently affect parts of the genome with low expression activity including heterochromatin and quiescent regions. But, at stage four of the infection regions of the genome harboring HIV-related methylation changes are enhancers.

Evaluation of methylation changes in blood cells of COVID-19 patients as a biomarker of severity of the infection.

Background: A number of studies have shown that methylomes of blood cells of COVID-19 patients display infection-related methylation changes. Those methylation abnormalities were associated with clinical outcomes of the infection and, thus, can potentially be utilized as biomarkers in clinical COVID-19 management. However, a number of parameters need to be assessed, before a clinical use of a biomarker candidate is proposed, with the most important one being reproducible detection in independent target populations.

Methylation patterns at the adjacent CpG sites within enhancers are a part of cell identity.

Background: It is generally accepted that methylation status of CpG sites spaced up to 50 bp apart is correlated, and accumulation of locally disordered methylation at adjacent CpG sites is involved in neoplastic transformation, acting in similar way as stochastic accumulation of mutations.

Results: We used EPIC microarray data from 596 samples, representing 12 healthy tissue and cell types, as well as 572 blood cancer specimens to analyze methylation status of adjacent CpG sites across human genome, and subsequently validated our findings with NGS and Sanger sequencing. Our analysis showed that there is a subset of the adjacent CpG sites in human genome, with cytosine at one CpG site methylated and the other devoid of methyl group.

eDAVE - Extension of GDC data analysis, visualization, and exploration tools.

Publicly available repositories such as Genomic Data Commons or Gene Expression Omnibus are a valuable research resource useful for hypothesis driven research as well as validation of the results of new experiments. Frequently however, the use of those opulent resources is challenging because advanced computational skills are required to mine deposited data. To address this challenge, we have developed eDAVE, a user-friendly, web and desktop interface enabling intuitive and robust analysis of almost 12 000 methylomes and transcriptomes from over 200 types of cells and tissues deposited in the Genomic Data Commons repository.

Identified in blood diet-related methylation changes stratify liver biopsies of NAFLD patients according to fibrosis grade.

Background: High caloric diet and lack of physical activity are considered main causes of NAFLD, and a change in the diet is still the only effective treatment of this disease. However, molecular mechanism of the effectiveness of diet change in treatment of NAFLD is poorly understood. We aimed to assess the involvement of epigenetic mechanisms of gene expression regulation in treatment of NAFLD.

Epigenetic activation of antiviral sensors and effectors of interferon response pathways during SARS-CoV-2 infection.

Recent studies have shown that methylation changes identified in blood cells of COVID-19 patients have a potential to be used as biomarkers of SARS-CoV-2 infection outcomes. However, different studies have reported different subsets of epigenetic lesions that stratify patients according to the severity of infection symptoms, and more importantly, the significance of those epigenetic changes in the pathology of the infection is still not clear. We used methylomics and transcriptomics data from the largest so far cohort of COVID-19 patients from four geographically distant populations, to identify casual interactions of blood cells' methylome in pathology of the COVID-19 disease.

Methylation levels assessment with Methylation-Sensitive High-Resolution Melting (MS-HRM).

Testing for disease-related DNA methylation changes provides clinically relevant information in personalized patient care. Methylation-Sensitive High-Resolution Melting (MS-HRM) is a method used for measuring methylation changes and has already been used in diagnostic settings. This method utilizes one set of primers that initiate the amplification of both methylated and non-methylated templates.

Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells.

Bortezomib (BTZ) is proteasome inhibitor, effectively used in the treatment of multiple myeloma, but frequently discontinued due to peripheral neuropathy, which develops in patients after consecutive treatment cycles. The molecular mechanisms affected by BTZ in neuronal cells, which result in neuropathy, remain unknown. However, BTZ is unlikely to lead to permanent morphological nerve damage, because neuropathy reverses after discontinuation of treatment, and nerve cells have very limited renewal capacity.

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data.

The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.