Multi-cohort cerebrospinal fluid proteomics identifies robust molecular signatures for asymptomatic and symptomatic Alzheimer's disease

Changes in Amyloid-β (A), hyperphosphorylated Tau (T) in brain and cerebrospinal fluid (CSF) precedes AD symptoms, making CSF proteome a potential avenue to understand the pathophysiology and facilitate reliable diagnostics and therapies. Using the AT framework and a three-stage study design (discovery, replication, and meta-analysis), we identified 2,173 proteins dysregulated in AD, that were further validated in a third totally independent cohort. Machine learning was implemented to create and validate highly accurate and replicable (AUC>0.90) models that predict AD biomarker positivity and clinical status. These models can also identify people that will convert to AD and those AD cases with faster progression. The associated proteins cluster in four different protein pseudo-trajectories groups spanning the AD continuum and were enrichment in specific pathways including neuronal death, apoptosis and tau phosphorylation (early stages), microglia dysregulation and endolysosomal dysfuncton(mid-stages), brain plasticity and longevity (mid-stages) and late microglia-neuron crosstalk (late stages).

Plasma proteomic associations with genetics and health in the UK Biobank

The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific pQTL mapping in non-European individuals. The study provides an updated characterization of the genetic architecture of the plasma proteome, contextualized with projected pQTL discovery rates as sample sizes and proteomic assay coverages increase over time. We offer extensive insights into trans pQTLs across multiple biological domains, highlight genetic influences on ligand-receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks, and illustrate long-range epistatic effects of ABO blood group and FUT2 secretor status on proteins with gastrointestinal tissue-enriched expression. We demonstrate the utility of these data for drug discovery by extending the genetic proxied effects of protein targets, such as PCSK9, on additional endpoints, and disentangle specific genes and proteins perturbed at loci associated with COVID-19 susceptibility. This public-private partnership provides the scientific community with an open-access proteomics resource of considerable breadth and depth to help to elucidate the biological mechanisms underlying proteo-genomic discoveries and accelerate the development of biomarkers, predictive models and therapeutics1.

Brain DNA Methylation Patterns in CLDN5 Associated With Cognitive Decline

BACKGROUND

Cognitive trajectory varies widely and can distinguish people who develop dementia from people who remain cognitively normal. Variation in cognitive trajectory is only partially explained by traditional neuropathologies. We sought to identify novel genes associated with cognitive trajectory using DNA methylation profiles from human postmortem brain.

METHODS

We performed a brain epigenome-wide association study of cognitive trajectory in 636 participants from the ROS (Religious Orders Study) and MAP (Rush Memory and Aging Project) using DNA methylation profiles of the dorsolateral prefrontal cortex. To maximize our power to detect epigenetic associations, we used the recently developed Gene Association with Multiple Traits test to analyze the 5 measured cognitive domains simultaneously.

RESULTS

We found an epigenome-wide association for differential methylation of sites in the CLDN5 locus and cognitive trajectory (p = 9.96 × 10^-7) that was robust to adjustment for cell type proportions (p = 8.52 × 10^-7). This association was primarily driven by association with declines in episodic (p = 4.65 × 10^-6) and working (p = 2.54 × 10^-7) memory. This association between methylation in CLDN5 and cognitive decline was significant even in participants with no or little signs of amyloid-β and neurofibrillary tangle pathology.

CONCLUSIONS

Differential methylation of CLDN5, a gene that encodes an important protein of the blood-brain barrier, is associated with cognitive trajectory beyond traditional Alzheimer's disease pathologies. The association between CLDN5 methylation and cognitive trajectory in people with low pathology suggests an early role for CLDN5 and blood-brain barrier dysfunction in cognitive decline and Alzheimer's disease.

A machine learning approach to brain epigenetic analysis reveals kinases associated with Alzheimer's disease

Alzheimer's disease (AD) is influenced by both genetic and environmental factors; thus, brain epigenomic alterations may provide insights into AD pathogenesis. Multiple array-based Epigenome-Wide Association Studies (EWASs) have identified robust brain methylation changes in AD; however, array-based assays only test about 2% of all CpG sites in the genome. Here, we develop EWASplus, a computational method that uses a supervised machine learning strategy to extend EWAS coverage to the entire genome. Application to six AD-related traits predicts hundreds of new significant brain CpGs associated with AD, some of which are further validated experimentally. EWASplus also performs well on data collected from independent cohorts and different brain regions. Genes found near top EWASplus loci are enriched for kinases and for genes with evidence for physical interactions with known AD genes. In this work, we show that EWASplus implicates additional epigenetic loci for AD that are not found using array-based AD EWASs.

Genetic control of the human brain proteome

We generated an online brain pQTL resource for 7,376 proteins through the analysis of genetic and proteomic data derived from post-mortem samples of the dorsolateral prefrontal cortex of 330 older adults. The identified pQTLs tend to be non-synonymous variation, are over-represented among variants associated with brain diseases, and replicate well (77%) in an independent brain dataset. Comparison to a large study of brain eQTLs revealed that about 75% of pQTLs are also eQTLs. In contrast, about 40% of eQTLs were identified as pQTLs. These results are consistent with lower pQTL mapping power and greater evolutionary constraint on protein abundance. The latter is additionally supported by observations of pQTLs with large effects' tending to be rare, deleterious, and associated with proteins that have evidence for fewer protein-protein interactions. Mediation analyses using matched transcriptomic and proteomic data provided additional evidence that pQTL effects are often, but not always, mediated by mRNA. Specifically, we identified roughly 1.6 times more mRNA-mediated pQTLs than mRNA-independent pQTLs (550 versus 341). Our pQTL resource provides insight into the functional consequences of genetic variation in the human brain and a basis for novel investigations of genetics and disease.

Association between DNA methylation levels in brain tissue and late-life depression in community-based participants

OBJECTIVE

Major depressive disorder (MDD) arises from a combination of genetic and environmental risk factors and DNA methylation is one of the molecular mechanisms through which these factors can manifest. However, little is known about the epigenetic signature of MDD in brain tissue. This study aimed to investigate associations between brain tissue-based DNA methylation and late-life MDD.

METHODS

We performed a brain epigenome-wide association study (EWAS) of late-life MDD in 608 participants from the Religious Order Study and the Rush Memory and Aging Project (ROS/MAP) using DNA methylation profiles of the dorsal lateral prefrontal cortex generated using the Illumina HumanMethylation450 Beadchip array. We also conducted an EWAS of MDD in each sex separately.

RESULTS

We found epigenome-wide significant associations between brain tissue-based DNA methylation and late-life MDD. The most significant and robust association was found with altered methylation levels in the YOD1 locus (cg25594636, p value = 2.55 × 10-11; cg03899372, p value = 3.12 × 10-09; cg12796440, p value = 1.51 × 10-08, cg23982678, p value = 7.94 × 10-08). Analysis of differentially methylated regions (p value = 5.06 × 10-10) further confirmed this locus. Other significant loci include UGT8 (cg18921206, p value = 1.75 × 10-08), FNDC3B (cg20367479, p value = 4.97 × 10-08) and SLIT2 (cg10946669, p value = 8.01 × 10-08). Notably, brain tissue-based methylation levels were strongly associated with late-life MDD in men more than in women.

CONCLUSIONS

We identified altered methylation in the YOD1, UGT8, FNDC3B, and SLIT2 loci as new epigenetic factors associated with late-life MDD. Furthermore, our study highlights the sex-specific molecular heterogeneity of MDD.

0987 Characterizing Scratch And Limb Movements In Atopic Dermatitis During Sleep

Introduction

Children with atopic dermatitis (AD) experience significant sleep disruption due to nocturnal scratching. Our group has found distinct patterns of limb movements in contrast to control and PLMD patients. To expand on previous findings, our objective was to characterize timing and duration of scratch v. non-scratch movement in children with AD coincidentally undergoing polysomnography (PSG).

Methods

Retrospective chart review of PSG, video footage was synchronized with the EEG and limb electrode readings using a time/date generator and was then operationally classified as either scratching or non-scratching movement. Analysis of data was done using SPSS and groups were compared using an ANOVA.

Results

We analyzed four previously completed sleep studies in children with atopic dermatitis (1 female and 3 males), mean age years±SD 11.3±1.0, mean BMI±SD 21.9±7.1, mean AHI±SD 2.3±0.8. Average scratch duration was not significantly different by sleep stage, N1v.N2v.N3v.REM (mean scratch duration in seconds±SD= 9.0±1.5 v 6.3±3.2 v. 11.9±11.8 v. 6.3±7.3, respectively p=0.65). However, frequency of scratching events were more common during N2v.N1v.N3v.REM (mean scratching events±SD= 9.3±3.9 v 3.8±1.7 v. 4.3±4.3 v. 1.3±1.9, respectively p=0.02). Yet, given the duration of total time spent in sleep stages, minutes of scratching events occupied the largest percentage of N1v.N2v.N3v.REM (mean% ±SD= 3.9±0.9 v. 0.6±0.4 v. 0.4±0.2 v. 0.3±0.5, respectively, p&lt0.01). Interestingly, non-scratch related movements were not significantly different between sleep stages (p=0.2). However, non-scratch related movements trended to occupy the largest percentage of N1v.N2v.N3v.REM (mean% ±SD= 9.3±7.7 v. 2.1±1.6 v. 1.5±0.8 v. 1.9±1.4, respectively, p=0.05).

Conclusion

Our results suggest that scratching episodes in children with AD occur most commonly during N2 sleep, but occupy the largest % of N1 sleep. Future work will include comparing these limb movements to age and gender-matched allergic rhinitis patients.

Support

This study was unfunded.

Determination of antimony and barium in UK air quality samples as indicators of non-exhaust traffic emissions

The aim of this study was to determine concentrations of antimony and barium in air quality samples and assess the potential suitability of these metals as tracer elements for non-exhaust traffic emissions sources. Air quality filters sampled at monitoring sites around the UK for the purposes of the UK Heavy Metals Monitoring Network were subjected to microwave digestion in hydrogen peroxide and nitric acid, then analysed by ICP-MS for a suite of metals including antimony and barium. The average antimony concentration found across all the network sites was 1.84 ng m^-3; the average barium concentration was 6.33 ng m^-3. The range of antimony concentrations observed was 0.13-8.02 ng m^-3; barium concentrations ranged from levels below the detection limit of 0.18 to 39.9 ng m^-3. There are no legislative limits for antimony and barium in ambient air, but the maximum concentrations found are well below the Workplace Exposure Limits specified by the UK Health and Safety Executive. The highest concentrations were found at roadside sites situated to monitor traffic environments, supporting the suitability of antimony and barium to be considered tracer elements for traffic emissions sources. Strong correlations were observed between antimony, barium and copper, indicating they share a common traffic-related source. Based on the strong correlation with copper at urban and traffic locations, indicative annual UK atmospheric emission estimates for antimony and barium in brake and tyre wear were calculated as 6 and 19 tonnes respectively.

An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

Background

Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome.

Results

We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), > 50% are distal (> 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P < 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60–70% of occurrences and are enriched for annotated gene promoters and enhancers (P < 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control.

Conclusions

This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4842-3) contains supplementary material, which is available to authorized users.

A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells

Long-distance intracellular transport of organelles, mRNA, and proteins ("cargo") occurs along the microtubule cytoskeleton by the action of kinesin and dynein motor proteins, but the vast network of factors involved in regulating intracellular cargo transport are still unknown. We capitalize on the Drosophila melanogaster S2 model cell system to monitor lysosome transport along microtubule bundles, which require enzymatically active kinesin-1 motor protein for their formation. We use an automated tracking program and a naive Bayesian classifier for the multivariate motility data to analyze 15,683 gene phenotypes and find 98 proteins involved in regulating lysosome motility along microtubules and 48 involved in the formation of microtubule filled processes in S2 cells. We identify innate immunity genes, ion channels, and signaling proteins having a role in lysosome motility regulation and find an unexpected relationship between the dynein motor, Rab7a, and lysosome motility regulation.

A phase IB safety and pharmacokinetic (PK) study of recombinant human Apo2L/TRAIL in combination with rituximab in patients with low-grade non-Hodgkin lymphoma

8078

Background: Recombinant human Apo2L/TRAIL (rhApo2L/TRAIL) induces apoptosis (programmed cell death) through binding to the pro-apoptotic receptors DR4 and DR5. Preclinical studies show that rhApo2L/TRAIL selectively induces apoptosis in many cancer cell lines derived from various malignancies including NHL, while sparing most normal cells. In vivo, rhApo2L/TRAIL and Rituximab cooperate to shrink or attenuate the growth of various NHL tumor xenografts in SCID mice. RhApo2L/TRAIL is being co-developed by Genentech and Amgen as a targeted therapy for solid tumors and hematologic malignancies. Methods: Subjects were eligible to participate if they had CD20+ follicular NHL or small lymphocytic lymphoma or marginal zone B-cell lymphoma that had progressed following stable disease or an objective response lasting > 6 months duration to the most recent rituximab-contain regimen. RhApo2L/TRAIL is administered intravenously over 1 hour for 5 consecutive days every three weeks up to 4 cycles at dose levels of 4 and 8 mg/kg. Rituximab is administered intravenously at 375 mg/m2 weekly for up to eight doses. Results: Six subjects with low grade NHL (4 with follicular NHL and 2 with small cell NHL) have been enrolled and treated with 4 mg/kg rhApo2L/TRAIL and rituximab, and one subject (with follicular NHL) has been enrolled and treated with 8 mg/kg rhApo2L/TRAIL and rituximab. The enrolled subjects range in age from 39–82 years; there are 6 male and 1 females. The number of prior therapies for NHL range from 1–8. Four subjects have received all protocol specified therapy. There have been no DLTs or SAEs or Grade 3/4 adverse events reported to date. To date, five subjects have undergone tumor response assessment: there have been 2 patients with complete response, 1 with partial response and 2 with stable disease. Conclusion: The combination of rhApo2L/TRAIL at 4 mg/kg/day and rituximab appears safe and shows evidence of activity in subjects with low grade NHL that has relapsed following previous rituximab-containing therapy. Enrollment is continuing to test rhApo2L/TRAIL at 8 mg/kg plus rituximab for expanded safety data and further dose optimization.

No significant financial relationships to disclose.

Survey of the use of thromboprophylaxis for medical patients at Christchurch Hospital

AIM

To determine the level of utilisation of thromboprophylaxis in relation to risk factors for medical patients at Christchurch Hospital.

METHODS

All medical wards were surveyed three times over a 12-week period from January 1998. Patients currently under investigation for venous thromboembolism were excluded, as were those currently receiving anticoagulant treatment for unrelated disorders. Primary prophylaxis was defined as the use of low-dose heparins or elastic stockings in asymptomatic patients. Patients with two or more risk factors were defined as being at high risk.

RESULTS

Three hundred and eighty-seven patients were interviewed, of whom 80% were considered to be potentially eligible for primary prophylaxis. One hundred and one patients (33%) were at high risk, of whom 20 (20%) were given primary prophylaxis. Cancer, confinement to bed, recent surgery and heart failure were the most common risk factors. Elastic stockings and low-dose heparin were employed in the same proportion of high risk cases but no patient received both. Patients with cancer were less likely to receive thromboprophylaxis than those with the other risk factors. Overall, only about 7% of high-risk patients received thromboprophylaxis for more than 75% of the duration of their stay in hospital.

CONCLUSION

Thromboprophylaxis is underutilised at Christchurch Hospital. Guidelines are required and audits of compliance are indicated.

Dysfunctional attitudes in depressed patients before and after clinical treatment and in normal control subjects

To evaluate the role of maladaptive thinking patterns in depression, the authors administered the Dysfunctional Attitude Scale to 112 depressed patients before and after 3-6 weeks of treatment with antidepressants or placebo. Twenty-two normal subjects were also assessed twice. Depressed patients had a significantly higher initial mean score than control subjects, but during treatment their score significantly decreased, and the posttreatment score of those with complete recoveries was nearly as low as the control subjects' final score. The higher the initial dysfunctional attitude score the poorer the response to treatment. Patients with endogenous depression had significantly lower scores than nonendogenously depressed patients.