Biology subjects

McKay, M. J.

Publications and source records attributed to McKay, M. J..

4 recordsLinked to original sources

bioRxiv2024

RNA mis-splicing in children with myotonic dystrophy is associated with physical function

ObjectivesDysregulated RNA alternative splicing is the hallmark of myotonic dystrophy type 1 (DM1). However, the association between RNA mis-splicing and physical function in children with the most severe form of disease, congenital myotonic dystrophy (CDM), is unknown. Methods82 participants (42 DM1 adults & 40 CDM children) with muscle biopsies and measures of myotonia, motor function, and strength were combined from five observational studies. Data were normalized and correlated with an aggregate measure of alternative splicing dysregulation, [MBNL]inferred in skeletal muscle biopsies. Multiple linear regression analysis was performed to predict [MBNL]inferred using clinical outcome measures alone. Similar analyses were performed to predict 12-month physical function using baseline metrics. ResultsMyotonia (measured via vHOT) was significantly correlated with RNA mis-splicing in our cross-sectional population of all DM1 individuals; CDM participants alone displayed no myotonia despite a similar range of RNA mis-splicing. Measures of motor performance and muscle strength were significantly associated with [MBNL]inferred in our cohort of all DM1 individuals and when assessing CDM children independently. Multiple linear regression analyses yielded two models capable of predicting [MBNL]inferred from select clinical outcome assessments alone in all subjects (adjusted R2 = 0.6723) or exclusively in CDM children (adjusted R2 = 0.5875). InterpretationOur findings establish significant correlations between skeletal muscle performance and a composite measure of alternative splicing dysregulation, [MBNL]inferred, in DM1. The strength of these correlations and the development of the predictive models will assist in designing efficacious clinical trials for individuals with DM1, particularly CDM.

genetics↗

bioRxiv2021

Patterns of gene expression in pollen of cotton (Gossypium hirsutum) indicate down-regulation as a feature of thermotolerance

Reproductive performance in plants is impaired as maximum temperatures consistently approach 40{degrees}C. However, the timing of heatwaves critically affects their impact. We studied the molecular responses of cotton male reproductive stages, to investigate the vulnerability of maturing pollen to high temperature. Tetrads, uninucleate and binucleate microspores, and mature pollen were subjected to SWATH-MS and RNA-seq analyses after exposure to 38/28{degrees}C (day/night) for 5 days. The results indicated that molecular signatures were down-regulated over developmental stages in response to heat. This was more evident in leaves where three-quarters of differentially changed proteins were decreased in abundance. Functional analysis showed that translation of genes increased in tetrads after exposure to heat; however, the reverse pattern was observed in mature pollen and leaves. Proteins involved in transport were highly abundant in tetrads, whereas in later stages of development and leaves, heat suppressed cell-to-cell communication. Moreover, a large number of heat shock proteins (HSPs) were identified in heat-affected tetrads, but these proteins were less abundant in mature pollen and leaves. We speculate that the sensitivity of tetrad cells to heat is related to increased activity of translation involved in non-essential pathways. Molecular signatures during pollen development after heatwaves provide markers for future genetic improvement.

plant biology↗

bioRxiv2020

A Recombinant Protein Biomarker DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins

Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). Here, we employed a mixture of recombinant proteins in DDA libraries to subsequently detect cancer-associated low abundance plasma proteins using SWATH/DIA. The exemplar DDA recombinant protein spectral library (rPSL) was derived from tryptic digestion of 36 human recombinant proteins that had been previously implicated as possible cancer biomarkers in both our own and other studies. The rPSL was then used to identify proteins from non-depleted colorectal cancer (CRC) plasmas by SWATH-MS. Most (32/36) of the proteins in the rPSL were reliably identified in plasma samples, including 8 proteins (BTC, CXCL10, IL1B, IL6, ITGB6, TGF, TNF, TP53) not previously detected using high-stringency MS in human plasmas according to PeptideAtlas. The rPSL SWATH-MS protocol was compared to DDA-MS using MARS-depleted and post-digestion peptide fractionated plasmas (here referred to as a human plasma DDA library). Of the 32 proteins identified using rPSL SWATH, only 12 were identified using DDA-MS. The 20 additional proteins exclusively identified by using the rPSL approach with SWATH were mostly lower abundance (i.e., <10ng/ml) plasma proteins. To mitigate FDR concerns, and replicating a more typical approach, the DDA rPSL was also merged into a human plasma DDA library. When SWATH identification was repeated using this merged library, the majority (33/36) of low abundance plasma proteins from the rPSL could still be identified using high-stringency HPP Guidelines v3.0 protein inference criteria.

biochemistry↗

bioRxiv2020

Experimental glaucoma retinal proteomics identifies mutually exclusive and overlapping molecular characteristics with human glaucoma

Current evidence suggests that exposure to chronically induced intraocular pressure (IOP) leads to neurodegenerative changes in the inner retina. This study aimed to determine retinal proteomic alterations in a rat model of glaucoma and compared findings with human retinal proteomics changes in glaucoma reported previously. We developed an experimental glaucoma rat model by subjecting the rats to increased IOP (9.3{+/-}0.1 vs 20.8{+/-}1.6 mm Hg) by weekly microbead injections into the eye (8 weeks). The retinal tissues were harvested from control and glaucomatous eyes and protein expression changes analysed using multiplexed quantitative proteomics approach. Immunofluorescence was performed for selected protein markers for data validation. Our study identified 4304 proteins in the rat retinas. Out of these, 139 proteins were downregulated ([≤]0.83) while expression of 109 proteins was upregulated ([≥]1.2-fold change) under glaucoma conditions (p[≤]0.05). Computational analysis revealed reduced expression of proteins associated with glutathione metabolism, mitochondrial dysfunction/oxidative phosphorylation, cytoskeleton and actin filament organisation, along with increased expression coagulation cascade, apoptosis, oxidative stress and RNA processing markers. Further functional network analysis highlighted the differential modulation of nuclear receptor signalling, cellular survival, protein synthesis, transport and cellular assembly pathways. Alterations in crystallin family, glutathione metabolism and mitochondrial dysfunction associated proteins shared similarities between the animal model of glaucoma and the human disease condition. In contrast, the activation of the classical complement pathway and upregulation of cholesterol transport proteins, were exclusive to the human glaucoma. These findings provide insights into the neurodegenerative mechanisms that are specifically affected in the retina in response to chronically elevated IOP.

neuroscience↗