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 po-tential 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. We identified a subset of methylation changes that is uniformly present in all COVID-19 patients regardless of symptoms. Those changes are not present in patients suffering from upper respiratory tract infections with symptoms similar to COVID-19. Most importantly, the identified epigenetic changes affect the expression of genes involved in interferon response pathways and the expression of those genes differs be-tween patients admitted to intensive care units and only hospitalized. In conclusion, the DNA methylation changes involved in pathophysiology of SARS-CoV-2 infection, which are specific to COVID-19 patients, can not only be utilized as biomarkers in the disease management but also present a potential treatment target

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. The application is implemented in Python, supported for major browsers and available at: https://edave.pum.edu.pl

Relationship between toll-like receptor 2 R753Q and T16934A polymorphisms and Staphylococcus aureus nasal carriage

BACKGROUND: The association among specific single-nucleotide polymorphisms (SNPs) in TLR2 R753Q (rs5743708) and T16934A (rs4696480) and the nasal carriage of Staphylococcus aureus was studied in adults before CABG. METHODS: The TLR2 polymorphisms were genotyped in 299 consecutive patients prepared for a CABG operation. Genotyping was performed using restriction fragment length polymorphism (RFLP) analysis of PCR-amplified fragments. Two nasal swab cultures were taken within 2 weeks before the operation. Subjects were classified as Staphylococcus aureus carriers if at least one culture was positive while those patients with both cultures found to be negative were classified as non-carriers. RESULTS: The prevalence of nasal S. aureus carriage in the final cohort was 22.1% (66/299), while no MRSA was detected in our study group. No significant differences in the TLR2 polymorphisms were observed between the study and the control groups. No associations were found between TLR2 haplotypes and the covariates of age, sex, NYHA, weight, height, BMI, CAD, smoking status and ESlog score. No differences were found between carriers and noncarriers regarding the allelic distribution of the TLR2 T-16934A SNP. Almost 93% of the patients who were screened for the presence of the TLR2 Arg753Gln (rs5743708) were GG wild type homozygous. Twenty one subjects from the study group (7.1%) were GA heterozygous, while no patient in either group was homozygous for the TLR2 Arg753Gln (rs5743708) mutation. TLR2 Arg753Gln genotyping showed that GA heterozygous patients were detected more frequently in the group of Staphylococcus aureus nasal carriers than in non-carrier adults. CONCLUSION: Our results suggest that the carrier status for the GA variant of the TLR2 Arg753Gln (rs5743708) polymorphism may be a risk factor for Staphylococcus aureus carriage.  BACKGROUND: The association among specific single-nucleotide polymorphisms (SNPs) in TLR2 R753Q (rs5743708) and T16934A (rs4696480) and the nasal carriage of Staphylococcus aureus was studied in adults before CABG. METHODS: The TLR2 polymorphisms were genotyped in 299 consecutive patients prepared for a CABG operation. Genotyping was performed using restriction fragment length polymorphism (RFLP) analysis of PCR-amplified fragments. Two nasal swab cultures were taken within 2 weeks before the operation. Subjects were classified as Staphylococcus aureus carriers if at least one culture was positive while those patients with both cultures found to be negative were classified as non-carriers. RESULTS: The prevalence of nasal S. aureus carriage in the final cohort was 22.1% (66/299), while no MRSA was detected in our study group. No significant differences in the TLR2 polymorphisms were observed between the study and the control groups. No associations were found between TLR2 haplotypes and the covariates of age, sex, NYHA, weight, height, BMI, CAD, smoking status and ESlog score. No differences were found between carriers and noncarriers regarding the allelic distribution of the TLR2 T-16934A SNP. Almost 93% of the patients who were screened for the presence of the TLR2 Arg753Gln (rs5743708) were GG wild type homozygous. Twenty one subjects from the study group (7.1%) were GA heterozygous, while no patient in either group was homozygous for the TLR2 Arg753Gln (rs5743708) mutation. TLR2 Arg753Gln genotyping showed that GA heterozygous patients were detected more frequently in the group of Staphylococcus aureus nasal carriers than in non-carrier adults. CONCLUSION: Our results suggest that the carrier status for the GA variant of the TLR2 Arg753Gln (rs5743708) polymorphism may be a risk factor for Staphylococcus aureus carriage

Retrospective mutational analysis of NPHS1, NPHS2, WT1 and LAMB2 in children with steroid-resistant focal segmental glomerulosclerosis – a single-centre experience

The aim of our study was to examine NPHS1, NPHS2, WT1 and LAMB2 mutations, previously reported in two thirds of patients with nephrotic syndrome with onset before the age of one year old. Genomic DNA samples from Polish children (n=33) with Steroid-ResistantNephrotic Syndrome (SRNS) due to focal segmental glomerulosclerosis (FSGS), manifesting before the age of 13 years old, underwent retrospective analysis of NPHS1, NPHS2, WT1 (exons 8, 9 and adjacent exon/intron boundaries) and LAMB2. No pathogenic NPHS1 or LAMB2 mutations were found in our FSGS cohort. SRNS-causing mutations of NPHS2 and WT1 were detected in 7 of 33 patients (21%), including those with nephrotic syndrome manifesting before one year old: five of seven patients. Four patients had homozygous c.413G>A (p.Arg138Gln) NPHS2 mutations; one subject was homozygous for c.868G>A (p.Val290Met) NPHS2. A phenotypic female had C>T transition at position +4 of the WT1 intron 9 (c.1432+4C>T) splice-donor site, and another phenotypic female was heterozygous for G>A transition at position +5 (c.1432+5G>A). Genotyping revealed a female genotypic gender (46, XX) for the first subject and male (46, XY) for the latter. In addition, one patient was heterozygous for c.104dup (p.Arg36Profs*34) NPHS2; two patients carried a c.686G>A (p.Arg229Gln) NPHS2 non-neutral variant. Results indicate possible clustering of causative NPHS2 mutations in FSGS-proven SRNS with onset before age one year old, and provide additional evidence that patients with childhood steroid-resistant nephrotic syndrome due to focal segmentalglomerulosclerosis should first undergo analysis of NPHS2 coding sequence and WT1 exons 8 and 9 and surrounding exon/intron boundary sequences, followed by gender genotyping

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

Altres ajuts: Polish National Agency for Academic Exchange grant number: PPN/PPO/2018/1/00088/U; European Regional Development Fund of the West Pomeranian Province 2014-2020, PROTO_LAB/K1/2020/U/18Recent 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. We identified a subset of methylation changes that is uniformly present in all COVID-19 patients regardless of symptoms. Those changes are not present in patients suffering from upper respiratory tract infections with symptoms similar to COVID-19. Most importantly, the identified epigenetic changes affect the expression of genes involved in interferon response pathways and the expression of those genes differs between patients admitted to intensive care units and only hospitalized. In conclusion, the DNA methylation changes involved in pathophysiology of SARS-CoV-2 infection, which are specific to COVID-19 patients, can not only be utilized as biomarkers in the disease management but also present a potential treatment target

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. We have previously shown that BTZ induces methylation changes in SH-SY5Y cells, which take part in the development of treatment resistance. Here, we hypothesized that BTZ affects the methylomes of mature neurons, and these changes are associated with BTZ neurotoxicity. Thus, we studied methylomes of neuronal cells, differentiated from the LUHMES cell line, after cycles of treatment with BTZ. Our results show that BTZ induces specific methylation changes in mature neurons, which are not present in SH-SY5Y cells after BTZ treatment. These changes appear to affect genes involved in morphogenesis, neurogenesis, and neurotransmission. Furthermore, identified methylation changes are significantly enriched within binding sites of transcription factors previously linked to neuron physiology, including EBF, PAX, DLX, LHX, and HNF family members. Altogether, our results indicate that methylation changes are likely to be involved in BTZ neurotoxicity