Biology subjects

Masters, C. L.

Publications and source records attributed to Masters, C. L..

8 recordsLinked to original sources

bioRxiv2024

Accurate estimation of SNP genotypes and genetic relatedness from DNA methylation data

Epigenome-wide association studies (EWAS) are susceptible to widespread confounding caused by population structure and genetic relatedness. Nevertheless, kinship estimation is challenging in EWAS without genotyping data. We propose MethylGenotyper, a method that for the first time enables accurate genotyping at thousands of SNPs directly from commercial DNA methylation microarrays. We model the intensities of methylation probes near SNPs with a mixture of three beta distributions corresponding to different genotypes and estimate parameters with an expectation-maximization algorithm. We conduct extensive simulations to demonstrate the performance of the method. When applying MethylGenotyper to Infinium EPIC array data of 4,662 Chinese, we obtain genotypes at 4,319 SNPs with a concordance rate of 98.26%, enabling the identification of 255 pairs of close relatedness. Furthermore, we show that MethylGenotyper allows for the estimation of both population structure and cryptic relatedness among 702 Australians of diverse ancestry. We have implemented MethylGenotyper in a publicly available R package to facilitate future large-scale EWAS.

bioinformatics↗

bioRxiv2024

Multi-omics characterization of highly enriched human plasma extracellular vesicles.

Extracellular vesicles (EVs) in blood plasma offer a valuable reservoir of intracellular cellular cargo, making them a promising source of liquid based biomarkers. The molecular cargo of small EVs (sEVs) is of particular interest because some EV subtypes encapsulate cargo from organelles including mitochondria, endosomes, and the autophagy pathways, which are implicated in multiple diseases. However, the complexity of plasma, with its abundance of non-EV particles and plasma proteins, presents challenges for their molecular characterization using mass spectrometry based omics technologies. Here, we optimised a rigorous method to isolate sEVs from human plasma based on both density and size. Following this, we analysed the protein and lipid content of sEVs from multiple individuals. We demonstrate the advantage of obtaining highly enriched sEVs from plasma for enhancing the detection of protein networks associated with mitochondria and the endosomal network, and also tissue types including the central nervous system. Some of the EV associated proteins reported here have not been detected in plasma, nor plasma sEVs, previously. We show that sphingomyelin lipids are the most abundant lipids in plasma sEVs (33.7 mol% total lipids) and provide the first report on cholesterol ester content. We demonstrate a 16-fold decrease in cholesterol ester lipids in sEVs compared to platelet free plasma and suggest that cholesterol ester content could serve as a valuable measure for assessing the effectiveness of plasma separation protocols or kits in enriching for sEVs. Our study highlights the benefit of reducing co-isolates from plasma sEV preparations to enable the detection of proteins and lipids with potential biomarker utility, and underscores the need for ongoing development of improved high throughput sEV isolation technologies.

biochemistry↗

bioRxiv2024

Single molecule fingerprinting reveals different growth mechanisms in seed amplification assays for different polymorphs of alpha Synuclein fibrils.

Alpha-synuclein (Syn) aggregates, detected in the biofluids of patients with Parkinsons disease, have the ability to catalyze their own aggregation, leading to an increase in the number and size of aggregates. This self-templated amplification is used by newly developed assays to diagnose Parkinsons disease and turned the presence of Syn aggregates into a biomarker of the disease. It has become evident that Syn can form fibrils with slightly different structures, called "strains" or polymorphs, but little is known about their differential reactivity in diagnostic assays. Here we compared the properties of two well-described Syn polymorphs. Using single molecule techniques, we observed that one of the polymorphs had an increased tendency to undergo secondary nucleation and we showed that this could explain the differences of reactivity observed in in vitro seed amplification assay and cellular assays. Simulations and high-resolution microscopy suggest that a 100-fold difference in apparent rate of growth can be generated by a surprisingly low number of secondary nucleation "points" (1 every 2,000 monomers added by elongation). When both strains are present in the same seeded reaction, secondary nucleation displaces proportions dramatically and causes a single strain to dominate the reaction as the major end-product.

neuroscience↗

bioRxiv2022

Neuroimaging within the Dominantly Inherited Alzheimer's Network (DIAN): PET and MRI

The Dominantly Inherited Alzheimer Network (DIAN) Observational Study is an international collaboration studying autosomal dominant Alzheimer disease (ADAD). This rare form of Alzheimer disease (AD) is caused by mutations in the presenilin 1 (PSEN1), presenilin 2 (PSEN2), or amyloid precursor protein (APP) genes. As individuals from these families have a 50% chance of inheriting the familial mutation, this provides researchers with a well-matched cohort of carriers vs non-carriers for case-control studies. An important trait of ADAD is that the age at symptom onset is highly predictable and consistent for each specific mutation, allowing researchers to estimate an individuals point in their disease time course prior to symptom onset. Although ADAD represents only a small proportion (approximately 0.1%) of all AD cases, studying this form of AD allows researchers to investigate preclinical AD and the progression of changes that occur within the brain prior to AD symptom onset. Furthermore, the young age at symptom onset (typically 30-60 years) means age-related comorbidities are much less prevalent than in sporadic AD, thereby allowing AD pathophysiology to be studied independent of these confounds. A major goal of the DIAN Observational Study is to create a global resource for AD researchers. To that end, the current manuscript provides an overview of the DIAN magnetic resonance imaging (MRI) and positron emission tomography (PET) protocols and highlights the key imaging results of this study to date.

neuroscience↗

bioRxiv2022

Impact of APOE e3 and e4 genotypes on plasma proteome signatures in Alzheimer's disease

The {varepsilon}4 allele of the apolipoprotein E (APOE) gene is a high-risk factor for Alzheimers disease (AD). However, approximately 25%-40% of patients with AD do not carry the APOE{varepsilon}4 allele, and the pathophysiological mechanisms underlying AD are less evident in these individuals. The main objective of this study was to understand better the changes in plasma that may contribute to disease pathogenesis in AD and how APOE{varepsilon}3 and APOE{varepsilon}4 contribute to biomarker profiles in AD. We conducted an in-depth plasma proteomics analysis using intensive depletion of high-abundant plasma proteins using the Agilent multiple affinity removal liquid chromatography (LC) column-Human 14 (Hu14) followed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS PAGE) technique. In this study, we identified a high number of protein expression alterations in plasma which were found uniquely in APOE{varepsilon}3 and APOE{varepsilon}4 carriers. These differentially expressed proteins (DEPs) were associated with several molecular functions, including complement cascade, glycolysis, metabolism, plasma lipoprotein assembly, remodelling, and clearance. In addition to unique changes in both APOE genotypes, many proteins were also dysregulated in the presence of both APOE{varepsilon}3 and APOE{varepsilon}4 genotypes depicting the involvement of these proteins in the pathogenesis of AD regardless of the APOE genotypes. We also compared the plasma proteomes of{varepsilon} 4 and{varepsilon} 3 carriers in normal controls, which provided insight into factors that may provide protection from progression to AD despite the presence of the{varepsilon} 4 allele. Furthermore, our findings also identified some proteins previously discovered in AD CSF and brain proteomics signatures that could provide clinically meaningful information.

neuroscience↗

bioRxiv2022

A snapshot of brain and cognition in healthy mid-life and older adults

Deficits in memory are seen as a canonical sign of ageing and a prodrome to dementia in older adults. However, the nature of cognitive and brain changes across a wider aperture of adulthood is not well known. We quantify the relationship between cognitive function and brain morphology from mid-life to older adulthood, and the influence of age, sex, amyloid and genetic risk for dementia. We analyzed three observational cohorts (PISA, AIBL, ADNI) with cognitive, genetic and neuroimaging measures comprising a total of 1570 healthy mid-life and older adults (mean age 72, range 49-90 years, 1330 males) and 1365 age- and sex-matched adults with mild cognitive impairment or Alzheimers disease. Among healthy adults, we find robust modes of co-variation between regional sulcal width and multidomain cognitive function that change from mid-life to the older age range. The most prominent cortical changes in mid-life are predominantly associated with changes in executive functions, whereas they are most strongly associated with poorer memory function in older age. These cognitive changes are accompanied by an age-dependent pattern of sulcal widening. Amyloid exerts a weak, but significant, influence on cognition, but not on sulcal width. The APOE {varepsilon}4 allele also exerts a weak influence on cognition, but only significantly in the (larger and older) AIBL cohort. These findings provide new insights into brain and cognition in mid-life and older adults, suggesting that cognitive screening in mid-life cohorts should encompass executive functions as well as memory.

neuroscience↗

bioRxiv2020

Characterization of Brain-Derived Extracellular Vesicle Lipids in Alzheimer's Disease

Lipid dyshomeostasis is associated with the most common form of dementia, Alzheimers disease (AD). Substantial progress has been made in identifying positron emission tomography (PET) and cerebrospinal fluid (CSF) biomarkers for AD, but they have limited use as front-line, non-invasive diagnostic tools. Small extracellular vesicles (EVs) are released by all cell types and contain an enriched subset of their parental cell molecular composition, including lipids. EVs are released from the brain into the periphery, providing a potential source of tissue and disease specific lipid biomarkers. However, the EV lipidome of the central nervous system (CNS) is currently unknown and the potential of brain-derived EVs (BDEVs) to inform on lipid dyshomeostasis in AD remains unclear. The aim of this study was to reveal the lipid composition of BDEVs in human frontal cortex tissue, and to determine whether BDEVs in AD have altered lipid profiles compared to age-matched neurological controls (NC). Here, using semi-quantitative mass spectrometry, we describe the BDEV lipidome, covering 4 lipid categories, 17 lipid classes and 692 lipid molecules. Frontal cortex-derived BDEVs were enriched in glycerophosphoserine (PS) lipids, a characteristic of small EVs. Here we report that BDEVs are enriched in ether-containing PS lipids. A novel finding that further establishes ether lipids as a feature of EVs. While no significant changes were detected in the frontal cortex in AD, the lipid profile of the BDEVs from this tissue exhibited disease related differences. AD BDEVs had altered glycerophospholipid (GP) and sphingolipid (SP) levels, specifically increased plasmalogen glycerophosphoethanolamine (PE-P) and decreased polyunsaturated fatty acyl containing lipids (PUFAs), and altered amide-linked acyl chain content in sphingomyelin (SM) and ceramide (Cer) lipids relative to vesicles from neurological control subjects. The most prominent alteration being a two-fold decrease in lipid species containing docosahexaenoic acid (DHA). The in-depth lipidome analysis provided in this study highlights the advantage of EVs over more complex tissues for improved detection of dysregulated lipids that may serve as potential biomarkers in the periphery.

molecular biology↗

bioRxiv2019

Harmonization of large multi-site imaging datasets: Application to 10,232 MRIs for the analysis of imaging patterns of structural brain change throughout the lifespan

As medical imaging enters its information era and presents rapidly increasing needs for big data analytics, robust pooling and harmonization of imaging data across diverse cohorts with varying acquisition protocols have become critical. We describe a comprehensive effort that merges and harmonizes a large-scale dataset of 10,232 structural brain MRI scans from participants without known neuropsychiatric disorder from 18 different studies that represent geographic diversity. We use this dataset and multi-atlas-based image processing methods to obtain a hierarchical partition of the brain from larger anatomical regions to individual cortical and deep structures and derive normative age trends of brain structure through the lifespan (3 to 96 years old). Critically, we present and validate a methodology for harmonizing this pooled dataset in the presence of nonlinear age trends. We provide a web-based visualization interface to generate and present the resulting age trends, enabling future studies of brain structure to compare their data with this normative reference of brain development and aging, and to examine deviations from normative ranges, potentially related to disease.

bioinformatics↗