DNA methylation levels change with age. Recent studies have identified biomarkers of chronological age based on DNA methylation levels. It is not yet known whether DNA methylation age captures ...aspects of biological age.
Here we test whether differences between people's chronological ages and estimated ages, DNA methylation age, predict all-cause mortality in later life. The difference between DNA methylation age and chronological age (Δage) was calculated in four longitudinal cohorts of older people. Meta-analysis of proportional hazards models from the four cohorts was used to determine the association between Δage and mortality. A 5-year higher Δage is associated with a 21% higher mortality risk, adjusting for age and sex. After further adjustments for childhood IQ, education, social class, hypertension, diabetes, cardiovascular disease, and APOE e4 status, there is a 16% increased mortality risk for those with a 5-year higher Δage. A pedigree-based heritability analysis of Δage was conducted in a separate cohort. The heritability of Δage was 0.43.
DNA methylation-derived measures of accelerated aging are heritable traits that predict mortality independently of health status, lifestyle factors, and known genetic factors.
The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain.
We conducted an association study of body mass index (BMI) and differential ...methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants. We examined variations in whole blood gene expression and conducted Mendelian randomization analyses to investigate the functional and clinical relevance of the findings. We identified novel and previously reported BMI-related differential methylation at 83 CpGs that replicated across cohorts; BMI-related differential methylation was associated with concurrent changes in the expression of genes in lipid metabolism pathways. Genetic instrumental variable analysis of alterations in methylation at one of the 83 replicated CpGs, cg11024682 (intronic to sterol regulatory element binding transcription factor 1 SREBF1), demonstrated links to BMI, adiposity-related traits, and coronary artery disease. Independent genetic instruments for expression of SREBF1 supported the findings linking methylation to adiposity and cardiometabolic disease. Methylation at a substantial proportion (16 of 83) of the identified loci was found to be secondary to differences in BMI. However, the cross-sectional nature of the data limits definitive causal determination.
We present robust associations of BMI with differential DNA methylation at numerous loci in blood cells. BMI-related DNA methylation and gene expression provide mechanistic insights into the relationship between DNA methylation, obesity, and adiposity-related diseases.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
DNA methylation plays an important role in the regulation of transcription. Genetic control of DNA methylation is a potential candidate for explaining the many identified SNP associations with ...disease that are not found in coding regions. We replicated 52,916 cis and 2,025 trans DNA methylation quantitative trait loci (mQTL) using methylation from whole blood measured on Illumina HumanMethylation450 arrays in the Brisbane Systems Genetics Study (n = 614 from 177 families) and the Lothian Birth Cohorts of 1921 and 1936 (combined n = 1366). The trans mQTL SNPs were found to be over-represented in 1 Mbp subtelomeric regions, and on chromosomes 16 and 19. There was a significant increase in trans mQTL DNA methylation sites in upstream and 5' UTR regions. The genetic heritability of a number of complex traits and diseases was partitioned into components due to mQTL and the remainder of the genome. Significant enrichment was observed for height (p = 2.1 × 10
), ulcerative colitis (p = 2 × 10
), Crohn's disease (p = 6 × 10
) and coronary artery disease (p = 5.5 × 10
) when compared to a random sample of SNPs with matched minor allele frequency, although this enrichment is explained by the genomic location of the mQTL SNPs.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Detailed laboratory characterization of Escherichia coli O157 is essential to inform epidemiological investigations. This study assessed the utility of whole-genome sequencing (WGS) for outbreak ...detection and epidemiological surveillance of E. coli O157, and the data were used to identify discernible associations between genotypes and clinical outcomes. One hundred five E. coli O157 strains isolated over a 5-year period from human fecal samples in Lothian, Scotland, were sequenced with the Ion Torrent Personal Genome Machine. A total of 8,721 variable sites in the core genome were identified among the 105 isolates; 47% of the single nucleotide polymorphisms (SNPs) were attributable to six "atypical" E. coli O157 strains and included recombinant regions. Phylogenetic analyses showed that WGS correlated well with the epidemiological data. Epidemiological links existed between cases whose isolates differed by three or fewer SNPs. WGS also correlated well with multilocus variable-number tandem repeat analysis (MLVA) typing data, with only three discordant results observed, all among isolates from cases not known to be epidemiologically related. WGS produced a better-supported, higher-resolution phylogeny than MLVA, confirming that the method is more suitable for epidemiological surveillance of E. coli O157. A combination of in silico analyses (VirulenceFinder, ResFinder, and local BLAST searches) were used to determine stx subtypes, multilocus sequence types (15 loci), and the presence of virulence and acquired antimicrobial resistance genes. There was a high level of correlation between the WGS data and our routine typing methods, although some discordant results were observed, mostly related to the limitation of short sequence read assembly. The data were used to identify sublineages and clades of E. coli O157, and when they were correlated with the clinical outcome data, they showed that one clade, Ic3, was significantly associated with severe disease. Together, the results show that WGS data can provide higher resolution of the relationships between E. coli O157 isolates than that provided by MLVA. The method has the potential to streamline the laboratory workflow and provide detailed information for the clinical management of patients and public health interventions.
Objective The identification of new causal risk factors has the potential to improve cardiovascular disease (CVD) risk prediction and the development of new treatments to reduce CVD deaths. In the ...general population, we sought to determine whether cortisol is a causal risk factor for CVD and coronary heart disease (CHD). Design and methods Three approaches were adopted to investigate the association between cortisol and CVD/CHD. First, we used multivariable regression in two prospective nested case-control studies (total 798 participants, 313 incident CVD/CHD with complete data). Second, a random-effects meta-analysis of these data and previously published prospective associations was performed (total 6680 controls, 696 incident CVD/CHD). Finally, one- and two-sample Mendelian randomization analyses were performed (122,737 CHD cases, 547,261 controls for two-sample analyses). Results In the two prospective nested case–control studies, logistic regression adjusting for sex, age, BMI, smoking and time of sampling, demonstrated a positive association between morning plasma cortisol and incident CVD (OR: 1.28 per 1 SD higher cortisol, 95% CI: 1.06–1.54). In the meta-analysis of prospective studies, the equivalent result was OR: 1.18, 95% CI: 1.06–1.31. Results from the two-sample Mendelian randomization were consistent with these positive associations: OR: 1.06, 95% CI: 0.98–1.15. Conclusions All three approaches demonstrated a positive association between morning plasma cortisol and incident CVD. Together, these findings suggest that elevated morning cortisol is a causal risk factor for CVD. The current data suggest strategies targeted at lowering cortisol action should be evaluated for their effects on CVD.
The epidemiology of unplanned extubations (UEs) and associated adverse outcomes in pediatric cardiac ICUs (CICU).
Registry data (August 2014 to October 2020).
Forty-five Pediatric Cardiac Critical ...Care Consortium hospitals.
Patients receiving mechanical ventilation (MV) via endotracheal tube (ETT).
None.
Fifty-six thousand five hundred eight MV courses occurred in 36,696 patients, with a crude UE rate of 2.8%. In cardiac surgical patients, UE was associated with longer duration of MV, but we failed to find such association in medical patients. In both cohorts, UE was associated with younger age, being underweight, and airway anomaly. In multivariable logistic regression, airway anomaly was associated with UE in all patients. Younger age, higher Society of Thoracic Surgeons-European Association for Cardio-Thoracic Surgery score category, longer duration of MV, and initial oral rather than nasal ETT are associated with UE in the surgical group, but we failed to find such associations in the medical group. UE was associated with a higher reintubation rate compared with elective extubation (26.8 vs 4.8%; odds ratio OR, 7.35; 95% CI, 6.44-8.39; p < 0.0001) within 1 day of event. After excluding patients having redirection of care, UE was associated with at least three-fold greater odds for each of ventilator-associated pneumonia (VAP), cardiac arrest, and use of mechanical circulatory support (MCS). However, we failed to identify an association between UE and greater odds of mortality (1.2 vs 0.8%; OR, 1.48; 95% CI, 0.86-2.54; p = 0.15), but uncertainty remains.
UE in CICU patients is associated with greater odds of cardiac arrest, VAP, and MCS. Cardiac medical and surgical patients in the CICU appear to have different explanatory factors associated with UE, and perhaps these may be modifiable and tested in future collaborative population research.
High-throughput transcriptomics has matured into a very well established and widely utilised research tool over the last two decades. Clinical datasets generated on a range of different platforms ...continue to be deposited in public repositories provide an ever-growing, valuable resource for reanalysis. Cost and tissue availability normally preclude processing samples across multiple technologies, making it challenging to directly evaluate performance and whether data from different platforms can be reliably compared or integrated.
This study describes our experiences of nine new and established mRNA profiling techniques including Lexogen QuantSeq, Qiagen QiaSeq, BioSpyder TempO-Seq, Ion AmpliSeq, Nanostring, Affymetrix Clariom S or U133A, Illumina BeadChip and RNA-seq of formalin-fixed paraffin embedded (FFPE) and fresh frozen (FF) sequential patient-matched breast tumour samples.
The number of genes represented and reliability varied between the platforms, but overall all methods provided data which were largely comparable. Crucially we found that it is possible to integrate data for combined analyses across FFPE/FF and platforms using established batch correction methods as required to increase cohort sizes. However, some platforms appear to be better suited to FFPE samples, particularly archival material.
Overall, we illustrate that technology selection is a balance between required resolution, sample quality, availability and cost.
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Paediatric cardiac critical care continues to become more sub-specialised, and many institutions have transitioned to dedicated cardiac ICUs. Literature regarding the effects of these changes on ...paediatric critical care medicine fellowship training is limited.
To describe the current landscape of cardiac critical care education during paediatric critical care medicine fellowship in the United States and demonstrate its variability.
A review of publicly available information in 2021 was completed. A supplemental REDCap survey focusing on cardiac ICU experiences during paediatric critical care medicine fellowships was e-mailed to all United States Accreditation Council of Graduate Medical Education-accredited paediatric critical care medicine fellowship programme coordinators/directors. Results are reported using inferential statistics.
Data from 71 paediatric critical care medicine fellowship programme websites and 41 leadership responses were included. Median fellow complement was 8 (interquartile range: 6, 12). The majority (76%, 31/41) of programmes had a designated cardiac ICU. Median percentage of paediatric critical care medicine attending physicians with cardiac training was 25% (interquartile range: 0%, 69%). Mandatory cardiac ICU time was 16 weeks (interquartile range: 13, 20) with variability in night coverage and number of other learners present. A minority of programmes (29%, 12/41) mandated other cardiac experiences. Median CHD surgical cases per year were 215 (interquartile range: 132, 338). When considering the number of annual cases per fellow, programmes with higher case volume were not always associated with the highest case number per fellow.
There is a continued trend toward dedicated cardiac ICUs in the United States, with significant variability in cardiac training during paediatric critical care medicine fellowship. As the trend toward dedicated cardiac ICUs continues and practices become more standardised, so should the education.
The aberrant gain of DNA methylation at CpG islands is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these ...CpG islands are targeted by de novo DNA methyltransferases in a sequence-specific manner, but this has not been tested. Using ectopically integrated CpG islands, here we find that aberrantly methylated CpG islands are subject to low levels of de novo DNA methylation activity in colorectal cancer cells. By delineating DNA methyltransferase targets, we find that instead de novo DNA methylation activity is targeted primarily to CpG islands marked by the histone modification H3K36me3, a mark associated with transcriptional elongation. These H3K36me3 marked CpG islands are heavily methylated in colorectal tumours and the normal colon suggesting that de novo DNA methyltransferase activity at CpG islands in colorectal cancer is focused on similar targets to normal tissues and not greatly remodelled by tumourigenesis.
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