Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes

To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n = 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6 months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.

Staining Hypoxic Areas of Frozen and FFPE Tissue Sections with Hypoxyprobe™

Hypoxia occurs due to inadequate levels of oxygen in tissue and has been implicated in numerous diseases such as cancer, diabetes, cardiovascular, and neurodegenerative diseases. Hypoxia activates hypoxia-inducible factors (HIF) which mediate the expression of several downstream genes. Within the context of cancer biology, these genes affect cellular processes including metabolism, proliferation, migration, invasion, and metastasis. Pimonidazole hydrochloride (HCl) is an exogenous marker that is reduced and binds to thiols under hypoxic conditions resulting in adducts that can be visualized using antibodies such as Hypoxyprobe™. This chapter describes a method for using Hypoxyprobe™ to detect hypoxic areas in frozen and FFPE mouse samples by immunofluorescence (IF) and immunohistochemistry (IHC) staining.

An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome

Hepatitis B virus (HBV) is one of the smallest human DNA viruses and its 3.2 Kb genome encodes multiple overlapping open reading frames, making its viral transcriptome challenging to dissect. Previous studies have combined quantitative PCR and Next Generation Sequencing to identify viral transcripts and splice junctions, however the fragmentation and selective amplification used in short read sequencing precludes the resolution of full length RNAs. Our study coupled an oligonucleotide enrichment protocol with state-of-the-art long read sequencing (PacBio) to identify the repertoire of HBV RNAs. This methodology provides sequencing libraries where up to 25 % of reads are of viral origin and enable the identification of canonical (unspliced), non-canonical (spliced) and chimeric viral-human transcripts. Sequencing RNA isolated from de novo HBV infected cells or those transfected with 1.3 × overlength HBV genomes allowed us to assess the viral transcriptome and to annotate 5' truncations and polyadenylation profiles. The two HBV model systems showed an excellent agreement in the pattern of major viral RNAs, however differences were noted in the abundance of spliced transcripts. Viral-host chimeric transcripts were identified and more commonly found in the transfected cells. Enrichment capture and PacBio sequencing allows the assignment of canonical and non-canonical HBV RNAs using an open-source analysis pipeline that enables the accurate mapping of the HBV transcriptome.

Therapeutic Targeting of Inflammation and Virus Simultaneously Ameliorates Influenza Pneumonia and Protects from Morbidity and Mortality

Influenza pneumonia is a severe complication caused by inflammation of the lungs following infection with seasonal and pandemic strains of influenza A virus (IAV), that can result in lung pathology, respiratory failure, and death. There is currently no treatment for severe disease and pneumonia caused by IAV. Antivirals are available but are only effective if treatment is initiated within 48 h of onset of symptoms. Influenza complications and mortality are often associated with high viral load and an excessive lung inflammatory cytokine response. Therefore, we simultaneously targeted the virus and inflammation. We used the antiviral oseltamivir and the anti-inflammatory drug etanercept to dampen TNF signaling after the onset of clinical signs to treat pneumonia in a mouse model of respiratory IAV infection. The combined treatment down-regulated the inflammatory cytokines TNF, IL-1β, IL-6, and IL-12p40, and the chemokines CCL2, CCL5, and CXCL10. Consequently, combined treatment with oseltamivir and a signal transducer and activator of transcription 3 (STAT3) inhibitor effectively reduced clinical disease and lung pathology. Combined treatment using etanercept or STAT3 inhibitor and oseltamivir dampened an overlapping set of cytokines. Thus, combined therapy targeting a specific cytokine or cytokine signaling pathway and an antiviral drug provide an effective treatment strategy for ameliorating IAV pneumonia. This approach might apply to treating pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Targeting ectromelia virus and TNF/NF-κB or STAT3 signaling for effective treatment of viral pneumonia

Viral causes of pneumonia pose constant threats to global public health, but there are no specific treatments currently available for the condition. Antivirals are ineffective when administered late after the onset of symptoms. Pneumonia is caused by an exaggerated inflammatory cytokine response to infection, but tissue necrosis and damage caused by virus also contribute to lung pathology. We hypothesized that viral pneumonia can be treated effectively if both virus and inflammation are simultaneously targeted. Combined treatment with the antiviral drug cidofovir and etanercept, which targets tumor necrosis factor (TNF), down-regulated nuclear factor kappa B-signaling and effectively reduced morbidity and mortality during respiratory ectromelia virus (ECTV) infection in mice even when treatment was initiated after onset of clinical signs. Treatment with cidofovir alone reduced viral load, but animals died from severe lung pathology. Treatment with etanercept had no effect on viral load but diminished levels of inflammatory cytokines and chemokines including TNF, IL-6, IL-1β, IL-12p40, TGF-β, and CCL5 and dampened activation of the STAT3 cytokine-signaling pathway, which transduces signals from multiple cytokines implicated in lung pathology. Consequently, combined treatment with a STAT3 inhibitor and cidofovir was effective in improving clinical disease and lung pathology in ECTV-infected mice. Thus, the simultaneous targeting of virus and a specific inflammatory cytokine or cytokine-signaling pathway is effective in the treatment of pneumonia. This approach might be applicable to pneumonia caused by emerging and re-emerging viruses, like seasonal and pandemic influenza A virus strains and severe acute respiratory syndrome coronavirus 2.

Blood copper and risk of cardiometabolic diseases-A Mendelian randomization study

Observational evidence links higher blood levels of copper with higher risk of cardiovascular diseases. However, whether those associations reflect causal links or can be attributed to confounding is still not fully clear. We investigated causal effects of copper on the risk of cardiometabolic endpoints (stroke, coronary artery disease [CAD] and type 2 diabetes) and cardiometabolic risk factors in two-sample Mendelian randomization (MR) studies. The selection of genetic instruments for blood copper levels relied on meta-analysis of genome-wide association studies in three independent studies (European Prospective Investigation into Cancer and Nutrition-Potsdam study, Prospective investigation of the Vasculature in Uppsala Seniors study, Queensland Institute of Medical Research studies). For the selected instruments, outcome associations were drawn from large public genetic consortia on the respective disease endpoints (MEGASTROKE, Cardiogram, DIAGRAM) and cardiometabolic risk factors. MR results indicate an inverse association for genetically higher copper levels with risk of CAD (odds ratio [95% confidence interval] = 0.92 [0.86–0.99], P = 0.022) and systolic blood pressure (beta [standard error (SE)] = −0.238 [0.121]; P = 0.049). Multivariable MR incorporating copper and systolic blood pressure into one model suggested systolic blood pressure as mediating factor between copper and CAD risk. In contrast to previous observational evidence establishing higher blood copper levels as risk-increasing factor for cardiometabolic diseases, this study suggests that higher levels of genetically predicted copper might play a protective role for the development of CAD and systolic blood pressure.

Probiotic therapy for periodontal and peri-implant health - silver bullet or sham?

Probiotics are thought to be beneficial microbes that influence health-related outcomes through host immunomodulation and modulation of the bacteriome. Its reported success in the treatment of gastrointestinal disorders has led to further research on its potential applicability within the dental field due to similarities such as a polymicrobial aetiology and disease associated microbial-shifts. Although the literature is replete with studies demonstrating its efficacy, the use of probiotics in dentistry continues to polarise opinion. Here, we explore the evidence for probiotics and its effect on periodontal and peri-implant health. MEDLINE, EMBASE, and CENTRAL were systemically searched from June 2010 to June 2020 based on a formulated search strategy. Of 1,956 potentially relevant articles, we selected 27 double-blinded randomised clinical trials in the areas of gingivitis, periodontitis, residual pockets during supportive periodontal therapy, and peri-implant diseases, and reviewed their efficacy in these clinical situations. We observed substantial variation in treatment results and protocols between studies. Overall, the evidence for probiotic therapy for periodontal and peri-implant health appears unconvincing. The scarcity of trials with adequate power and follow-up precludes any meaningful clinical recommendations. Thus, the routine use of probiotics for these purposes are currently unsubstantiated. Further multi-centre trials encompassing a standardised investigation on the most promising strains and administration methods, with longer observation times are required to confirm the benefits of probiotic therapy for these applications.

Utility of ultrasound assessment in management of pregnancies with preterm prelabor rupture of membranes

OBJECTIVES

To evaluate the utility of ultrasound markers in the management of pregnancies complicated by preterm prelabor rupture of membranes (PPROM) between 23 + 0 and 33 + 6 weeks' gestation, and to assess the ability of ultrasound markers to predict adverse neonatal outcomes.

METHODS

This was a retrospective cohort study of all patients with PPROM between 23 + 0 and 33 + 6 weeks' gestation and latency period (PPROM to delivery) > 48 h, who delivered before 34 weeks' gestation at a tertiary referral center between 2005 and 2017. All patients underwent a non-stress test daily and an ultrasound scan twice a week for assessment of amniotic fluid volume, biophysical profile (BPP) and umbilical artery (UA) pulsatility index (PI). In patients with suspected fetal growth restriction, fetal middle cerebral artery (MCA)-PI was also assessed and the cerebroplacental ratio (CPR) calculated. The last ultrasound examination performed prior to delivery was analyzed. We compared the characteristics and outcomes between women who were delivered owing to clinical suspicion of chorioamnionitis and those who were not delivered for this indication. The primary objective was to evaluate the utility of ultrasound in the management of patients with PPROM. The secondary objective was to assess the diagnostic performance of ultrasound markers (BPP score < 6, oligohydramnios, UA-PI > 95^th percentile, MCA-PI < 5^th percentile, CPR < 5^th percentile) for the prediction of composite adverse neonatal outcome, which was defined as the presence of one or more of: perinatal death, respiratory distress syndrome, periventricular leukomalacia, intraventricular hemorrhage Grade 3 or 4, necrotizing enterocolitis, hypoxic ischemic encephalopathy, neonatal sepsis or neonatal seizures.

RESULTS

A total of 504 women were included in the study, comprising 120 with suspected chorioamnionitis and 384 without. Women with suspected chorioamnionitis, compared with those without, were less likely to be nulliparous (34.2% vs 45.3%; P = 0.03) and more likely to have fever (50.8% vs 2.6%; P < 0.001) and be delivered by Cesarean section (69.2% vs 42.4%; P < 0.001), mainly owing to a history of previous Cesarean section (18.3% vs 9.1%; P = 0.005) and to having non-reassuring fetal heart rate tracings (32.5% vs 14.6%; P < 0.001). No significant differences were found between the two groups with regard to the median amniotic fluid volume, overall BPP score, BPP score < 6, MCA-PI or CPR. Median UA-PI was slightly higher in the suspected-chorioamnionitis group, yet the incidence of UA-PI > 95^th percentile was similar between the two groups. There was a higher incidence of composite adverse neonatal outcome in the group with suspected chorioamnionitis than in the group without (78.3% vs 64.3%, respectively; P = 0.004). However, on logistic regression analysis, none of the ultrasound markers evaluated was found to be associated with chorioamnionitis or composite adverse neonatal outcome, and they all had a poor diagnostic performance for the prediction of chorioamnionitis and composite adverse neonatal outcome.

CONCLUSIONS

Commonly used ultrasound markers in pregnancies complicated by PPROM were similar between women delivered for suspected chorioamnionitis and those delivered for other indications, and performed poorly in predicting composite adverse neonatal outcome. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Chronic stress, depression and personality type in patients with myasthenia gravis

BACKGROUND AND PURPOSE

Stress is a known risk factor for the onset and modulation of disease activity in autoimmune disorders. The aim of this cross-sectional study was to determine any associations between myasthenia gravis (MG) severity and chronic stress, depression and personality type.

METHODS

In all, 179 consecutive adult patients with confirmed MG attending the Neuromuscular Clinic between March 2017 and December 2017 were included. At baseline, patients were assessed clinically and they completed self-administered scales for disease severity, perceived stress, depression and personality type.

RESULTS

Higher disease severity [Myasthenia Gravis Impairment Index (MGII)] showed a moderate correlation with depression score (Beck's Depression Inventory, Second Edition, r = 0.52, P < 0.001) and a lower correlation with chronic stress (Trier Inventory for Assessment of Chronic Stress, r = 0.28, P = 0.001). Chronic stress scores were different according to personality types (anova, P = 0.02). The linear regression model with MGII score as the dependent variable showed R² = 0.34, likelihood ratio chi-squared 74.55, with P < 0.0001. The only variables that predicted disease severity were depression scores (P < 0.0001) and female sex (P = 0.003).

CONCLUSIONS

A significant association of MG severity with depression and chronic stress was found, as well as with female gender. These findings should raise awareness that the long-term management of MG should address depression and potential stress and consider behavioural management to prevent stress-related immune imbalance.

Observational evidence of a long-term increase in precipitation due to urbanization effects and its implications for sustainable urban living

Although projected precipitation increases in East Asia due to future climate change have aroused concern, less attention has been paid by the scientific community and public to the potential long-term increase in precipitation due to rapid urbanization. A ten-year precipitation dataset was analysed for both a rapidly urbanized megacity and nearby suburban/rural stations in southern China. Rapid urbanization in the megacity was evident from satellite observations. A statistically significant, long-term, increasing trend of precipitation existed only at the megacity station (45.6mm per decade) and not at the other stations. The increase was attributed to thermal and dynamical modifications of the tropospheric boundary layer related to urbanization, which was confirmed by the results of our WRF-SLUCM simulations. The results also suggested that a long-term regional increase in precipitation, caused by greenhouse gas-induced climate change, for instance, was not evident within the study period. The urbanization-induced increase was found to be higher than the precipitation increase (18.3mm per decade) expected from future climate change. The direct climate impacts due to rapid urbanization is highlighted with strong implications for urban sustainable development and the planning of effective adaptation strategies for issues such as coastal defenses, mosquito-borne disease spread and heat stress mortality.

Genetic and methylation variation in the CYP2B6 gene is related to circulating p,p'-dde levels in a population-based sample

OBJECTIVES

Since the metabolism of the organochlorine pesticide dichlorodiphenyltrichloroethane (DDT) is not fully known in humans, we evaluated if circulating levels of a major breakdown product of DDT, p,p'-DDE, were related to genome-wide genetic and methylation variation in a population-based sample.

METHODS

In the population-based Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study (1016 subjects all aged 70), circulating levels of p,p'-DDE were analyzed by high-resolution chromatography coupled to high-resolution mass spectrometry (HRGC/HRMS). Genetic variants were genotyped and imputed (1000 Genomes reference, March 2012 release). Methylation sites were assayed using the Illumina HumanMethylation450 array in whole blood. A genome-wide association study (GWAS) approach was applied.

RESULTS

Evidence for genome-wide significant association with p,p'-DDE levels was observed only for a locus at chromosome 19 corresponding to the CYP2B6 gene (lead SNP rs7260538). Subjects being homozygote for the G allele showed a median level of 472ng/g lipid, while the corresponding level for those being homozygote for the T allele was 192ng/g lipid (p=1.5×10^-31). An analysis conditioned on the lead SNP disclosed a distinct signal in the same gene (rs7255374, position chr19:41520351; p=2.2×10^-8). A whole-genome methylation analysis showed one significant relationship vs. p,p'-DDE levels (p=6.2×10^-9) located 7kb downstream the CYP2B6 gene (cg27089200, position chr19:41531976). This CpG-site was also related to the lead SNP (p=3.8×10^-35), but mediated only 4% of the effect of the lead SNP on p,p'-DDE levels.

CONCLUSION

Circulating levels of p,p'-DDE were related to genetic variation in the CYP2B6 gene in the general elderly population. DNA methylation in this gene is not closely linked to the p,p'-DDE levels.

Location! Location! Location! The Impact of Single-Room Design on Neurodevelopment of Preterm Infants

BACKGROUND: The impact of neonatal intensive care unit (NICU) design on neurodevelopmental outcomes of preterm infants is uncertain. Although single room design (SRD) reduces nosocomial infections and improves breastfeeding rates and parental satisfaction, recent data suggests that SRD may be associated with language delays and alterations in cortical development.

OBJECTIVES: To compare neurodevelopmental outcomes of preterm infants who received care in a contemporary SRD environment compared with a similar cohort who received care during an earlier period with an open bay design (OBD).

DESIGN/METHODS: Retrospective single-centre cohort study comparing the neurodevelopmental outcomes of all surviving extremely low birth weight (ELBW) i nfants admitted within 24 hours of birth in 2009 (OBD epoch) and 2011 (SRD epoch). The primary outcome was moderate or severe neurodevelopmental impairment using the Bayley Scales of Infant Development, third edition (BSID-III) at 18 months corrected age. Secondary outcomes included severe NDI and BSID-III scores. Multivariable logistic regression (MLR) analysis was used to evaluate the independent association between NICU design and outcomes.

RESULTS: The study included 100 ELBW infants in 2009, and 98 in 2011. The 2 epochs were similar in follow-up rates (80% in 2009; 82% in 2011) and infant characteristics (including those lost to follow up). Mortality was 7.9% in 2009 and 6.1% in 2011. BSID-III language scores (median [interquartile range]) were similar for infants in the OBD and SRD epochs (86 [71,100] vs. 81 [71,94], p=NS). On MLR analysis, NICU design was not associated with significant differences in NDI or BSID-III language score less than 80 after adjustment for antenatal and perinatal confounders. (Table1)

CONCLUSION: There was no significant difference in NDI between cohorts of ELBW infants cared for in an SRD compared with an OBD NICU design environment. The contrast in findings from earlier studies may be attributable to the local context of government-supported parental leave and strong promotion of parental presence in the NICU.

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Assessing the Risk Factors of Cyber and Mobile Phone Bullying Victimization in a Nationally Representative Sample of Singapore Youth

This study utilized routine activity theory to examine the relationships between online behaviors, target suitability, and cyber and mobile phone-based bullying victimization in a nationally representative sample of youth from nine schools across Singapore. Key measures in all three categories-access to technology, online routine behaviors, and target suitability-were significant predictors of both forms of bullying victimization. In particular, females and victims of physical bullying were more likely to experience both forms of victimization. Access to technology and online routine behaviors predicted cyber and mobile phone-based bullying victimization differently. These findings demonstrate that routine activity theory is a viable framework to understand online bullying in non-Western nations, consistent with the existing literature on Western nations.

Papular acantholytic dyskeratosis of the vulva associated with familial Hailey-Hailey disease

Papular acantholytic dyskeratosis (PAD) of the vulva is a rare, chronic disorder first described in 1984. It presents in young women as white to skin-coloured smooth papules over the vulva, which are persistent but asymptomatic. Histologically, there is hyperkeratosis and focal parakeratosis with acantholytic and dyskeratotic cells forming corps ronds and grains, placing PAD within Ackerman's spectrum of focal acantholytic dyskeratoses with Hailey-Hailey disease (HHD) and Darier disease. There have been 17 previous reports of PAD of the vulva, to our knowledge. Only one demonstrated a familial pattern, and none of the cases was associated with a family history of HHD. This is the first report of PAD and HHD in a single family, suggesting that PAD and HHD lie on a spectrum of disease and are genetically linked.

Genomic modulators of gene expression in human neutrophils

Neutrophils form the most abundant leukocyte subset and are central to many disease processes. Technical challenges in transcriptomic profiling have prohibited genomic approaches to date. Here we map expression quantitative trait loci (eQTL) in peripheral blood CD16+ neutrophils from 101 healthy European adults. We identify cis-eQTL for 3281 neutrophil-expressed genes including many implicated in neutrophil function, with 450 of these not previously observed in myeloid or lymphoid cells. Paired comparison with monocyte eQTL demonstrates nuanced conditioning of genetic regulation of gene expression by cellular context, which relates to cell-type-specific DNA methylation and histone modifications. Neutrophil eQTL are markedly enriched for trait-associated variants particularly autoimmune, allergy and infectious disease. We further demonstrate how eQTL in PADI4 and NOD2 delineate risk variant function in rheumatoid arthritis, leprosy and Crohn's disease. Taken together, these data help advance understanding of the genetics of gene expression, neutrophil biology and immune-related diseases.

Association of unit size, resource utilization and occupancy with outcomes of preterm infants

OBJECTIVE

Assess association of NICU size, and occupancy rate and resource utilization at admission with neonatal outcome.

STUDY DESIGN

Retrospective cohort study of 9978 infants born at 23-32 weeks gestation and admitted to 23 tertiary-level Canadian NICUs during 2010-2012. Adjusted odds ratios (AOR) were estimated for a composite outcome of mortality/any major morbidity with respect to NICU size, occupancy rate and intensity of resource utilization at admission.

RESULTS

A total of 2889 (29%) infants developed the composite outcome, the odds of which were higher for 16-29, 30-36 and >36-bed NICUs compared with <16-bed NICUs (AOR (95% CI): 1.47 (1.25-1.73); 1.49 (1.25-1.78); 1.55 (1.29-1.87), respectively) and for NICUs with higher resource utilization at admission (AOR: 1.30 (1.08-1.56), Q4 vs Q1) but not different according to NICU occupancy.

CONCLUSION

Larger NICUs and more intense resource utilization at admission are associated with higher odds of a composite adverse outcome in very preterm infants.

Genome-wide association study of plasma levels of polychlorinated biphenyls disclose an association with the CYP2B6 gene in a population-based sample

BACKGROUND

Polychlorinated biphenyls (PCBs) are a group of man-made environmental pollutants which accumulate in humans with adverse health effects. To date, very little effort has been devoted to the study of the metabolism of PCBs on a genome-wide level.

OBJECTIVES

Here, we conducted a genome-wide association study (GWAS) to identify genomic regions involved in the metabolism of PCBs.

METHODS

Plasma levels of 16 PCBs ascertained in a cohort of elderly individuals from Sweden (n=1016) were measured using gas chromatography-high resolution mass spectrophotometry (GC-HRMS). DNA samples were genotyped on the Infinium Omni Express bead microarray, and imputed up to reference panels from the 1000 Genomes Project. Association testing was performed in a linear regression framework under an additive model.

RESULTS

Plasma levels of PCB-99 demonstrated genome-wide significant association with single nucleotide polymorphisms (SNPs) mapping to chromosome 19q13.2. The SNP with the strongest association was rs8109848 (p=3.7×10(-13)), mapping to an intronic region of CYP2B6. Moreover, when all PCBs were conditioned on PCB-99, further signals were revealed for PCBs -74, -105 and -118, mapping to the same genomic region. The lead SNPs were rs8109848 (p=3.8×10(-12)) for PCB-118, rs4802104 (p=1.4×10(-9)) for PCB-74 and rs4803413 (p=2.5×10(-9)) for PCB-105, all of which map to CYP2B6.

CONCLUSIONS

In our study, we found plasma levels of four lower-chlorinated PCBs to be significantly associated with the genetic region mapping to the CYP2B6 locus. These findings show that CYP2B6 is of importance for the metabolism of PCBs in humans, and may help to identify individuals who may be susceptible to PCB toxicity.

Genome-wide association study of toxic metals and trace elements reveals novel associations

The accumulation of toxic metals in the human body is influenced by exposure and mechanisms involved in metabolism, some of which may be under genetic control. This is the first genome-wide association study to investigate variants associated with whole blood levels of a range of toxic metals. Eleven toxic metals and trace elements (aluminium, cadmium, cobalt, copper, chromium, mercury, manganese, molybdenum, nickel, lead and zinc) were assayed in a cohort of 949 individuals using mass spectrometry. DNA samples were genotyped on the Infinium Omni Express bead microarray and imputed up to reference panels from the 1000 Genomes Project. Analyses revealed two regions associated with manganese level at genome-wide significance, mapping to 4q24 and 1q41. The lead single nucleotide polymorphism (SNP) in the 4q24 locus was rs13107325 (P-value = 5.1 × 10⁻¹¹, β = −0.77), located in an exon of SLC39A8, which encodes a protein involved in manganese and zinc transport. The lead SNP in the 1q41 locus is rs1776029 (P-value = 2.2 × 10⁻¹⁴, β = −0.46). The SNP lies within the intronic region of SLC30A10, another transporter protein. Among other metals, the loci 6q14.1 and 3q26.32 were associated with cadmium and mercury levels (P = 1.4 × 10⁻¹⁰, β = −1.2 and P = 1.8 × 10⁻⁹, β = −1.8, respectively). Whole blood measurements of toxic metals are associated with genetic variants in metal transporter genes and others. This is relevant in inferring metabolic pathways of metals and identifying subsets of individuals who may be more susceptible to metal toxicity.

Diabetic retinopathy: pathogenesis, clinical grading, management and future developments

Decades of research into the pathophysiology and management of diabetic retinopathy have revolutionized our understanding of the disease process. Diabetic retinopathy is now more accurately defined as a neurovascular rather than a microvascular disease as neurodegenerative disease precedes and coexists with microvascular changes. However, the complexities of the pathways involved in different stages of disease severity continue to remain a challenging issue for drug discovery. Currently, laser photocoagulation is the mainstay of treatment for proliferative diabetic retinopathy, but is gradually being superseded for diabetic macular oedema. However, it is destructive and at best results in a gradual but modest improvement in vision in the long term. So, diabetic retinopathy remains the most prevalent cause of visual impairment in the working-age population despite established screening programmes, early diagnosis and treatment of the condition. The recent discovery of inhibitors of vascular endothelial growth factor is revolutionizing the management of diabetic retinopathy, particularly diabetic macular oedema. However, not all patients respond to anti-vascular endothelial growth factor agents, reinforcing the fact that diabetic retinopathy is a multifactorial disease. Studies are still required to improve our understanding of how retinal structure correlates with visual function. It is hoped that these will lead to better characterization of the disease phenotype based on treatment responses to different agents and allow an algorithm to be developed that will guide the management of diabetic retinopathy and diabetic macular oedema at different stages of severity.

Variables associated with corneal confocal microscopy parameters in healthy volunteers: implications for diabetic neuropathy screening

AIM

Corneal confocal microscopy is a promising screening method for diabetic neuropathy. Although much research in this field has been accomplished, we aimed to determine and confirm the known clinical and eyewear variables associated with the parameters of corneal confocal microscopy specifically in healthy volunteers, in particular associations with corneal nerve fibre length.

METHODS

Clinical characteristics, electrophysiological examination and a general clinical eye history were collected from 64 healthy volunteers. Corneal confocal microscopy was performed to determine corneal nerve fibre length, corneal nerve branch density, corneal nerve fibre density and tortuosity coefficient. Univariate and multivariate linear regression analysis was used to determine clinical variables associated with corneal nerve fibre length parameters.

RESULTS

We observed that corneal nerve fibre length has a broad distribution in healthy volunteers (18 ± 4 mm/mm(2), 95% confidence interval, 12.3-25.7 mm/mm(2)). Multivariate regression analysis demonstrated that HbA(1c) was the only independent clinical factor to account for variations in corneal nerve fibre length, independent of age and status of contact lens wear.

CONCLUSIONS

This study does not provide convincing evidence that corneal nerve fibre length is independently associated with age or the wearing of contact lenses, and that these factors are therefore unlikely to hinder valid screening for polyneuropathies such as diabetic neuropathy. Furthermore, the strong inverse association of corneal nerve fibre length with glycaemic exposure may support the use of this parameter to detect subclinical pre-diabetic nerve injury.

The Excess Financial Burden of Multidrug Resistance in Severe Gram-negative Infections in Singaporean Hospitals

Introduction: Multidrug-resistant (MDR) Gram-negative healthcare-associated infections are prevalent in Singaporean hospitals. An accurate assessment of the socioeconomic impact of these infections is necessary in order to facilitate appropriate resource allocation, and to judge the cost-effectiveness of targeted interventions. Materials and Methods: A retrospective cohort study involving inpatients with healthcare-associated Gram-negative bacteraemia at 2 large Singaporean hospitals was conducted to determine the hospitalisation costs attributed to multidrug resistance, and to elucidate factors affecting the financial impact of these infections. Data were obtained from hospital administrative, clinical and financial records, and analysed using a multivariate linear regression model. Results: There were 525 survivors of healthcare-associated Gram-negative bacteraemia in the study cohort, with 224 MDR cases. MDR bacteraemia, concomitant skin and soft tissue infection, higher APACHE II score, ICU stay, and appropriate definitive antibiotic therapy were independently associated with higher total hospitalisation costs, whereas higher Charlson comorbidity index and concomitant urinary tract infection were associated with lower costs. The excess hospitalisation costs attributed to MDR infection was $8638.58. In the study cohort, on average, 62.3% of the excess cost attributed to MDR infection was paid for by government subvention. Conclusion: Multidrug resistance in healthcare-associated Gram-negative bacteraemia is associated with higher financial costs—a significant proportion of which are subsidised by public funding in the form of governmental subvention. More active interventions aimed at controlling antimicrobial resistance are warranted, and the results of our study also provide possible benchmarks against which the cost-effectiveness of such interventions can be assessed. Key words: Antimicrobial resistance, Cohort study, Gram-negative bacteraemia, Healthcare costs

The excess financial burden of multidrug resistance in severe gram-negative infections in Singaporean hospitals

INTRODUCTION

Multidrug-resistant (MDR) Gram-negative healthcare-associated infections are prevalent in Singaporean hospitals. An accurate assessment of the socioeconomic impact of these infections is necessary in order to facilitate appropriate resource allocation, and to judge the costeffectiveness of targeted interventions.

MATERIALS AND METHODS

A retrospective cohort study involving inpatients with healthcare-associated Gram-negative bacteraemia at 2 large Singaporean hospitals was conducted to determine the hospitalisation costs attributed to multidrug resistance, and to elucidate factors affecting the financial impact of these infections. Data were obtained from hospital administrative, clinical and financial records, and analysed using a multivariate linear regression model.

RESULTS

There were 525 survivors of healthcare-associated Gram-negative bacteraemia in the study cohort, with 224 MDR cases. MDR bacteraemia, concomitant skin and soft tissue infection, higher APACHE II score, ICU stay, and appropriate definitive antibiotic therapy were independently associated with higher total hospitalisation costs, whereas higher Charlson comorbidity index and concomitant urinary tract infection were associated with lower costs. The excess hospitalisation costs attributed to MDR infection was $8638.58. In the study cohort, on average, 62.3% of the excess cost attributed to MDR infection was paid for by government subvention.

CONCLUSION

Multidrug resistance in healthcare-associated Gram-negative bacteraemia is associated with higher financial costs--a significant proportion of which are subsidised by public funding in the form of governmental subvention. More active interventions aimed at controlling antimicrobial resistance are warranted, and the results of our study also provide possible benchmarks against which the cost-effectiveness of such interventions can be assessed.

The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer

Aberrant DNA methylation is an important cancer hallmark, yet the dynamics of DNA methylation changes in human carcinogenesis remain largely unexplored. Moreover, the role of DNA methylation for prediction of clinical outcome is still uncertain and confined to specific cancers. Here we perform the most comprehensive study of DNA methylation changes throughout human carcinogenesis, analysing 27,578 CpGs in each of 1,475 samples, ranging from normal cells in advance of non-invasive neoplastic transformation to non-invasive and invasive cancers and metastatic tissue. We demonstrate that hypermethylation at stem cell PolyComb Group Target genes (PCGTs) occurs in cytologically normal cells three years in advance of the first morphological neoplastic changes, while hypomethylation occurs preferentially at CpGs which are heavily Methylated in Embryonic Stem Cells (MESCs) and increases significantly with cancer invasion in both the epithelial and stromal tumour compartments. In contrast to PCGT hypermethylation, MESC hypomethylation progresses significantly from primary to metastatic cancer and defines a poor prognostic signature in four different gynaecological cancers. Finally, we associate expression of TET enzymes, which are involved in active DNA demethylation, to MESC hypomethylation in cancer. These findings have major implications for cancer and embryonic stem cell biology and establish the importance of systemic DNA hypomethylation for predicting prognosis in a wide range of different cancers.

Reproducibility of in vivo corneal confocal microscopy as a novel screening test for early diabetic sensorimotor polyneuropathy

AIM

With the goal of identifying a valid biomarker of early diabetic sensorimotor polyneuropathy, we aimed to identify the most reliable in vivo corneal confocal microscopy (CCM) parameter for detection of abnormality of small nerve fibre morphology.

METHODS

Cross-sectional examination of 46 subjects (26 with Type 1 diabetes and 20 healthy volunteers) examined by corneal confocal microscopy for intra- and interobserver reproducibility by the intraclass correlation coefficient method. Corneal nerve fibre density, nerve branch density, nerve fibre length and tortuosity were measured on the same day that subjects underwent clinical and electrophysiological examination.

RESULTS

The 26 subjects with Type 1 diabetes had mean age and diabetes duration 42.8 ± 16.9 and 22.7 ± 16.4 years, respectively. Twelve of those subjects (46%) did not meet criteria for diabetic sensorimotor polyneuropathy, while five (19%) had mild, three (12%) had moderate and six (23%) had severe diabetic sensorimotor polyneuropathy. None of the healthy volunteers (mean age 41.4 ± 17.3 years) had polyneuropathy. Re-examination of selected corneal confocal microscopy images or sets of 40 images yielded very good to excellent intraclass correlation coefficients for all parameters. However, only one parameter (corneal nerve fibre length) emerged with consistently very good reproducibility using a clinically relevant 'study-level' protocol of subject re-examination (intra-observer intraclass correlation coefficient 0.72; interobserver intraclass correlation coefficient 0.73). Despite no differences in intraclass correlation coefficient between subgroups, corneal nerve fibre length was significantly lower (14.76 vs. 16.15 mm/mm(2), P = 0.04) in those with diabetes.

CONCLUSIONS

Development of corneal confocal microscopy may need to focus on the measurement of corneal nerve fibre length, as it appears to have superior reliability in comparison with other parameters, and as evidence exists for its potential as a clinical biomarker of early diabetic sensorimotor polyneuropathy.