Biology subjects

Mein, C. A.

Publications and source records attributed to Mein, C. A..

15 recordsLinked to original sources

bioRxiv2026

Transcriptome profiling of cell-free RNAs in prostate cancer patients on active surveillance

Active surveillance (AS) delays or avoids unnecessary treatment-related side effects for early localised non-aggressive prostate cancer (PCa) through monitoring with regular prostate-specific antigen (PSA) testing, digital rectal examination (DRE), magnetic resonance imaging (MRI) and prostate biopsy. Whilst baseline MRI has prognostic value and is increasingly used for disease monitoring, molecular biomarkers could be an adjunct to refine risk stratification and disease prognostication [2]. Unlike tissue-based genomic classifiers such as Decipher (Veracyte) and Prolaris CCP (Myriad), blood-based molecular testing for example cell-free RNA (cfRNA) offers minimally invasive real-time monitoring. Moreover, cfRNA may yield genetic information shed from different cell populations within the tumour microenvironment, as well as the host circulation, expanding the opportunities for biomarker discovery. Here, we test the feasibility of whole transcriptome profiling of cfRNAs from the blood of PCa patients under AS, exploring differences between patients with stable disease (SD), and progression to radical prostatectomy (RP).

cancer biology↗

bioRxiv2025

Maternal rejecting of newborns is epigenetic, intergenerationally transmitted and associated with altered miRNAs expression in owl monkeys.

Spontaneous maternal rejection of offspring is a considered a behavioural pathology affecting human and non-human primates, often with lethal consequences for newborns, yet it is widespread and pervasive across taxa, induced by stress or stress vulnerability. In some species, events of rejection can trigger chains of rejection which replicate themselves through generations. In this study we hypothesized that rejecting behaviours in owl monkeys are triggered and epigenetic in nature, transmitted to descendants, and their manifestation is associated with altered miRNA expression. Analysis of multi-generational records revealed that individuals who experienced rejection in infancy were 1.9 times more likely to reject their own offspring compared to controls, confirming its triggered nature. Transmission appears induced by experience rather than solely explained by genetic relatedness, as non-rejected full siblings showed no increased rejection tendency. Transcriptomic analysis identified distinct microRNA signatures associated with epigenetically induced rejecting behaviours. In rejected adults that become rejectors of their own offspring, mml-miR-1296, involved in lipid metabolism was significantly downregulated. In the naive daughters of rejected-rejectors, upregulated mml-miR-125b-5p, previously identified as biomarker in humans exposed to early life trauma that also suffered behavioural pathology, was identified. In summary, these findings confirm the epigenetic nature of spontaneous rejecting, with robust intergenerational transmission, and accompanied by alteration of epigenetic marks across generations in owl monkeys.

animal behavior and cognition↗

bioRxiv2025

Stress, Epigenetic Remodeling and FKBP51: Pathways to Chronic Pain Vulnerability

Stress is thought to contribute to the persistence of pain and comorbid anxiety, yet the underlying mechanisms remain unclear. In our pre-clinical model, sub-chronic stress exacerbated subsequently induced inflammatory pain and accelerated the development of comorbid anxiety. DNA methylation analysis of spinal cord tissue after stress exposure revealed hypomethylation in the Fkbp5 promoter site for the canonical FKBP51 transcript and other stress-related genes. However, most epigenetic changes in key regulatory regions did not correlate with changes in gene expression assessed by RNA sequencing, suggesting that stress exposure had remodeled the epigenome without altering gene activity and primed genes for hyper-responsiveness to future challenges. FKBP51 inhibition during stress exposure reduced the exacerbation of inflammatory pain by stress and reversed several stress-induced DNA methylation changes in promoter regions of genes associated with stress and nociception, including Rtn4, Cdk5 and Nrxn1, but not Fkbp5. These results indicate that sub-chronic stress leads to the hypomethylation of Fkbp5 and increased susceptibility to chronic pain driven by FKBP51, but reversing Fkbp5 hypomethylation is not necessary to prevent chronic pain vulnerability, which is likely driven by complex epigenetic regulation of multiple stress-regulated genes.

neuroscience↗

bioRxiv2024

Parental rejection is associated with intergenerational inheritance of reduced survival, altered behaviours and miRNAs in Owl Monkeys

Parental rejection in captive primates represents severe early-life stress, yet intergenerational effects remain poorly characterised. We investigated spontaneous rejection in owl monkeys (Aotus nancymaae) across two generations using demographic records (n=1,372), behavioural observations (n=65), and blood miRNA profiling (n=47). Rejected individuals showed 51% reduced lifespan, decreased probability of reaching reproductive age, and increased morbidity throughout life. Critically, well-reared offspring of rejected parents exhibited similar reductions in survival to reproductive age and lifespan. Rejected adults displayed heightened fearfulness and aggression with reduced paternal care; offspring showed decreased locomotion and altered stress responses. Blood miRNA analysis revealed significant upregulation of mml-miR-30a-5p in female offspring-a miRNA associated with early-life stress and behavioural disorders in humans. These findings demonstrate intergenerational transmission of rejection effects on fitness and behaviour, with preliminary evidence suggesting epigenetic mechanisms are associated with this transmission, though multiple pathways likely operate.

animal behavior and cognition↗

bioRxiv2023

Multi-parameter phenotyping of platelets and characterisation of the effects of agonists using machine learning

BackgroundPlatelets are crucial for thrombosis and haemostasis, with their function driven by the expression of specialised surface markers. The concept of distinct circulating sub-populations of platelets has emerged in recent years, but their exact nature remains debatable. We reasoned that a more comprehensive characterisation of surface marker changes at rest and upon activation would be valuable in determining this. ObjectiveTo use a full spectrum flow cytometry-based panel, together with parameters of physical properties, to describe surface marker changes in healthy platelets at rest and on activation, and to observe how these responses differ according to platelet age. MethodsA 14-marker flow cytometry panel was developed and applied to vehicle- or agonist-stimulated platelet-rich plasma samples obtained from healthy volunteers, or to platelets sorted according to SYTO-13 staining intensity as an indicator of platelet age. Data were analysed using both user-led and independent approaches incorporating novel machine learning-based algorithms. ResultsThe assay detected changes in marker expression in healthy platelets, at rest and on agonist activation, that are consistent with the literature. Machine learning identified stimulated populations of platelets with high accuracy (>80%). Similarly, differentiation between young and old platelet populations achieved 76% accuracy, primarily weighted by FSC-A, CD41, SSC-A, GPVI, CD61, and CD42b expression patterns. ConclusionsOur findings provide a novel assay to phenotype platelets coupled with a robust bioinformatics and machine learning workflow for deep analysis of the data. This could be valuable in characterising platelets in disease. (240 words) EssentialsO_LIPlatelet function is directed by the expression of specialised surface markers C_LIO_LICirculating platelet sub-populations are incompletely characterised C_LIO_LIMulti-parameter spectral flow cytometry allows robust and comprehensive phenotyping of platelets C_LIO_LICoupling multi-parameter spectral flow cytometry with machine learning offers a powerful method to determine platelet sub-populations C_LI

immunology↗

bioRxiv2023

Single cell sequencing data identify distinct B cell and fibroblast populations in stricturing Crohns disease

We used human full thickness Crohns disease (CD) small bowel resection specimens and single cell RNA sequencing to identify potential therapeutic targets for stricturing (S)CD. Using an unbiased approach, 16 cell lineages were assigned within 14,539 sequenced cells from patient-matched SCD and non-stricturing (NSCD) preparations. SCD and NSCD contained identical cell types. Amongst immune cells, B cells and plasma cells were selectively increased in SCD samples. B cell subsets suggested formation of tertiary lymphoid tissue in SCD and compared with NSCD there was an increase in IgG, and a decrease in IgA plasma cells, consistent with their potential role in CD fibrosis. Two Lumican-positive fibroblast subtypes were identified and subclassified based on expression of selectively enriched genes as fibroblast clusters (C)12 and C9. Cells within these clusters expressed the profibrotic genes Decorin (C12) and JUN (C9). C9 cells expressed ACTA2; ECM genes COL4A1, COL4A2, COL15A1, COL6A3, COL18A1 and ADAMDEC1; LAMB1 and GREM1. GO and KEGG Biological terms showed extracellular matrix, stricture organisation and regulation of WNT pathway genes are associated with the C12 and C9 gene sets. Trajectory and differential gene analysis of C12 and C9 identified four sub-clusters. Intra sub-cluster gene analysis detected co-regulated gene modules that aligned along predicted pseudotime trajectories and identified CXCL14 and ADAMDEC1 as key module markers. Our findings support further investigation of fibroblast heterogeneity and interactions with local and circulating immune cells at earlier time points in fibrosis progression. Breaking these interactions by targeting one or other population may improve therapeutic management for SCD.

genomics↗

bioRxiv2022

Using the DNA methylation profile of the stress driver gene FKBP5 for chronic pain diagnosis

Epigenetic changes can bring insight into gene regulatory mechanisms associated with disease pathogenicity, including chronicity and increased vulnerability. To date, we are yet to identify genes sensitive to epigenetic regulation that contribute to the maintenance of chronic pain and with an epigenetic landscape indicative of the susceptibility to persistent pain. Such genes would provide a novel opportunity for better pain management, as their epigenetic profile could be targeted for the treatment of chronic pain or used as an indication of vulnerability for prevention strategies. Here, we investigated the epigenetic profile of the gene FKBP5 for this potential, using targeted bisulphite sequencing in rodent pre-clinical models of chronic and latent hypersensitive states. The FKBP5 promoter DNA methylation (DNAm) signature in the CNS was significantly different between models of persistent pain and there was a significant correlation between CNS and peripheral blood FKBP5 DNAm, indicating that further exploration of FKBP5 promoter DNAm as a biomarker of chronic pain pathogenic origin is warranted. We also found that maternal separation, which promotes the persistency of inflammatory pain in adulthood, was accompanied by long-lasting reduction in FKBP5 DNAm, suggesting that FKPB5 DNAm profile may indicate the increased vulnerability to chronic pain in individuals exposed to trauma in early life. Overall, our data demonstrate that the FKBP5 promoter DNAm landscape brings novel insight into the differing pathogenic origins of chronic pain, may be able to diagnose and stratify patients, and predict the susceptibility to chronic pain.

neuroscience↗

bioRxiv2021

Glyphosate and its formulations Roundup Bioflow and RangerPro alter bacterial and fungal community composition in the rat caecum microbiome

The potential health consequences of glyphosate-induced gut microbiome alterations have become a matter of intense debate. As part of a multifaceted study investigating toxicity, carcinogenicity and multigenerational effects of glyphosate and its commercial herbicide formulations, we assessed changes in bacterial and fungal populations in the caecum microbiota of rats exposed prenatally until adulthood (13 weeks after weaning) to three doses of glyphosate (0.5, 5, 50 mg/kg body weight/day), or to the formulated herbicide products Roundup Bioflow and RangerPro at the same glyphosate-equivalent doses. Caecum bacterial microbiota were evaluated by 16S rRNA sequencing whilst the fungal population was determined by ITS2 amplicon sequencing. Results showed that both fungal and bacterial diversity were affected by the Roundup formulations in a dose-dependent manner, whilst glyphosate alone significantly altered only bacterial diversity. At taxa level, a reduction in Bacteroidota abundance, marked by alterations in the levels of Alloprevotella, Prevotella and Prevotellaceae UCG-003, was concomitant to increased levels of Firmicutes (e.g., Romboutsia, Dubosiella, Eubacterium brachy group or Christensenellaceae) and Actinobacteria (e.g., Enterorhabdus, Adlercreutzia, or Asaccharobacter). Treponema and Mycoplasma also had their levels reduced by the pesticide treatments. Analysis of fungal composition indicated that the abundance of the rat gut commensal Ascomycota Kazachstania was reduced while the abundance of Gibberella, Penicillium, Claviceps, Cornuvesica, Candida, Trichoderma and Sarocladium were increased by exposure to the Roundup formulations, but not to glyphosate. Altogether, our data suggest that glyphosate and its Roundup RangerPro and Bioflow caused profound changes in caecum microbiome composition by affecting the fitness of major commensals, which in turn reduced competition and allowed opportunistic fungi to grow in the gut, in particular in animals exposed to the herbicide formulations. This further indicates that changes in gut microbiome composition might influence the long-term toxicity, carcinogenicity and multigenerational effects of glyphosate-based herbicides.

pharmacology and toxicology↗

bioRxiv2021

TREM2 impacts brain microglia, oligodendrocytes and endothelial co-expression modules revealing genes and pathways important in Alzheimer s disease

A microglia response to pathogenic signals in diseases such as Alzheimers disease (AD) has long been recognised, but recent genetic findings have cemented their direct causal contribution to AD and thus the potential to target them or their effector pathways as a possible treatment strategy. TREM2 is a highly penetrant microglia risk gene for AD, which appears central to the coordination of the damage response by microglia in AD. Its absence has a negative impact on Tau and amyloid symptoms and pathologies. Full knowledge of its pathway and relationships with other brain cells in AD has not been fully characterised, but will be essential to fully evaluate the impact of manipulating this pathway for treatment development and to establish the best targets for achieving this. We used whole genome RNA sequencing of hippocampus and cortical brain samples from control, AD, and AD TREM2 risk carriers to identify TREM2-dependent genes driving changes in pathways, processes and cell types in AD. Through highly influential intra and intermodular hub genes and overall changes in the levels of gene expression, TREM2-DAP12 was found to strongly influence a number of other microglia, oligodendrocyte and endothelial genes, notably those involved in complement and Fc{gamma} receptor function, microglia-associated ribosomal genes and oligodendrocyte genes, particularly proteosomal subunits. These strong TREM2 centred co-expression relationships were significantly disrupted in AD cases with a TREM2 risk variant, revealing for the first time genes and pathways directly impacted by TREM2 in the brains of AD patients. Consistent with its function as a lipid sensor, our data supports a role for TREM2 in mediating oligodendrocyte and/or myelin clearance in AD which may be essential not only for preserving healthy tissue homeostasis but may also serve to minimise the persistence of antigenic peptides and lipids which may lead to detrimental pro-inflammatory sequelae. Further work should expand our knowledge of TREM2 on complement and Fc{gamma} receptor function and its impact on oligodendcrotye and myelin integrity and further evaluate the genes and pathways we have identified as possible treatment targets for AD.

neuroscience↗

bioRxiv2021

In-depth comparative toxicogenomics of glyphosate and Roundup herbicides: histopathology, transcriptome and epigenome signatures, and DNA damage

Whether glyphosate-based herbicides (GBHs) are more potent than glyphosate alone at activating cellular mechanisms, which drive carcinogenesis remains controversial. As GBHs are more cytotoxic that glyphosate, we reasoned they may also be more capable of activating carcinogenic pathways. We tested this hypothesis by comparing the effects of glyphosate with Roundup GBHs both in vitro and in vivo. First, glyphosate was compared with representative GBHs namely MON 52276 (EU), MON 76473 (UK) and MON 76207 (USA) using the mammalian stem cell-based ToxTracker system. Here, MON 52276 and MON 76473, but not glyphosate and MON 76207, activated oxidative stress and unfolded protein responses. Second, molecular profiling of liver was performed in female Sprague-Dawley rats exposed to glyphosate or MON 52276 (both at 0.5, 50, 175 mg/kg bw/day glyphosate) for 90 days. MON 52276 but not glyphosate increased hepatic steatosis and necrosis. MON 52276 and glyphosate altered the expression of genes in liver reflecting TP53 activation by DNA damage and circadian rhythm regulation. Genes most affected in liver were similarly altered in kidneys. Small RNA profiling in liver showed decreased amounts of miR-22 and miR-17 from MON 52276 ingestion. Glyphosate decreased mir-30 while miR-10 levels were increased. DNA methylation profiling of liver revealed 5,727 and 4,496 differentially methylated CpG sites between the control and glyphosate and MON 52276 exposed animals respectively. Apurinic/apyrimidinic DNA damage formation in liver was increased with glyphosate exposure. Altogether, our results show that Roundup formulations cause more biological changes linked with carcinogenesis than glyphosate.

pharmacology and toxicology↗

bioRxiv2020

Multi-omics phenotyping of the gut-liver axis allows health risk predictability from in vivo subchronic toxicity tests of a low-dose pesticide mixture

Human health effects from chronic exposure to mixtures of pesticide residues are little investigated. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in an in vivo subchronic toxicity test of a mixture of six pesticide active ingredients frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole). Sprague-Dawley rats were administered with the pesticide mixture with each ingredient at its regulatory permitted acceptable daily intake. Analysis of water and feed consumption, body weight, histopathology and serum biochemistry showed little or no physiological effects from exposure to the pesticide mixture. In marked contrast, analysis of the host-gut microbiome axis using serum and caecum metabolomics revealed that nicotinamide and tryptophan metabolism were affected, which suggested the initiation of a cell danger response, including adaptation to oxidative stress. Only limited effects were detected on the caecum microbiota by shotgun metagenomics. Further analyses of in vitro bacterial cultures showed that growth of Lactobacillus rhamnosus and Escherichia coli strains was negatively impacted by the pesticide mixture at concentrations that were not inhibitory when exposure was to a single agent. Transcriptomics of the liver showed that 257 genes had their expression changed. Gene functions affected included those involved in the regulation of response to hormones and correlated with previously reported transcriptome changes following administration of nicotinamide. Genome-wide DNA methylation analysis of the same liver samples showed that 4255 CpG sites were differentially methylated (> 10% difference). Overall, we demonstrated that unlike standard blood biochemical and organ histological analysis, in-depth molecular profiling using a combination of high-throughput -omics methods in laboratory animals exposed to low concentrations of pesticides reveals metabolic effects on the gut-liver axis, which can potentially be used as biomarkers for the prediction of future negative health outcomes. Our data suggest that adoption of multi-omics as part of regulatory risk assessment procedures will result in more accurate outcome measures, with positive public health implications.

pharmacology and toxicology↗

bioRxiv2020

Areca catechu-(Betel-nut)-induced whole transcriptome changes associated with diabetes, obesity and metabolic syndrome in a human monocyte cell line

Betel-nut consumption is the fourth most common addictive habit globally and there is good evidence to link it with obesity, type 2 diabetes and the metabolic syndrome. We adopted a genome-wide transcriptomic approach in a human monocyte cell line incubated with arecoline and its nitrosated products to identify gene expression changes relevant to obesity, type 2 diabetes and the metabolic syndrome. The THP1 monocyte cell line was incubated separately with arecoline and 3-methylnitrosaminopropionaldehyde (MNPA) in triplicate for 24 hours and pooled cDNA indexed paired-end libraries were sequenced (Illumina NextSeq 500). After incubation with arecoline and MNPA, 15 and 39 genes respectively had significant changes in their expression (q<0.05, log fold change 1.5). Eighteen of those genes have reported associations with type 2 diabetes and obesity in humans; of these genes there was strong evidence to implicate CLEC10A, MAPK8IP1, NEGR1, NQ01 and INHBE. In summary, these pilot studies have identified a large number of genes whose expression was changed significantly in human TPH1 cells following incubation with arecoline or with 3-methylnitrosaminopropionaldehyde. These findings suggest that further investigation of these genes in betel-quid chewers with obesity and/or type 2 diabetes is warranted.

genomics↗

bioRxiv2019

The Genomic Loci of Specific Human tRNA Genes Exhibit Ageing-Related DNA Hypermethylation

The epigenome deteriorates with age, potentially impacting on ageing-related disease. Here, we interrogate the DNA methylation state of the genomic loci of human tRNA. Whilst arising from only ~46kb (<0.002% genome), this information transfer machinery is the second most abundant cellular transcript. tRNAs also control metabolic processes known to affect ageing, through core translational and additional regulatory roles. We identified a genomic enrichment for age-related DNA hypermethylation at tRNA loci. Analysis in 4,350 MeDIP-seq peripheral-blood DNA methylomes (16-82 years), classified 44 and 21 hypermethylating specific tRNAs at study- and genome-wide significance, respectively, contrasting with 0 hypomethylating. Validation and replication (450k array & independent targeted Bisuphite-sequencing) supported thehypermethylation of this functional unit. The strongest consistent signals, also independent of major cell-type change, occur in tRNA-iMet-CAT-1-4 and tRNA-Ser-AGA-2-6. This study is this first comprehensive evaluation of the genomic DNA methylation state of human tRNA genes and reveals a discreet hypermethylation with advancing age.

genomics↗

bioRxiv2018

Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126

Chemical pollutant exposure is a risk factor contributing to the growing epidemic of nonalcoholic fatty liver disease (NAFLD) affecting human populations that consume a Western diet. Although it is recognized that intoxication by chemical pollutants can lead to NAFLD, there is limited information available regarding the mechanism by which typical environmental levels of exposure can contribute to the onset of this disease. Here we describe the alterations in gene expression profiles and metabolite levels in the human hepatocyte HepaRG cell line, a validated model for cellular steatosis, exposed to the polychlorinated biphenyl (PCB) 126, one of the most potent chemical pollutants that can induce NAFLD. Sparse partial least squares classification of the molecular profiles revealed that exposure to PCB 126 provoked a decrease in polyunsaturated fatty acids as well as an increase in sphingolipid levels, concomitant with a decrease in the activity of genes involved in lipid metabolism. This was associated with an increased oxidative stress reflected by marked disturbances in taurine metabolism. A gene ontology analysis showed hallmarks of an activation of the AhR receptor by dioxin-like compounds. These changes in metabolome and transcriptome profiles were observed even at the lowest concentration (100 pM) of PCB 126 tested. A decrease in docosatrienoate levels was the most sensitive biomarker. Overall, our integrated multi-omics analysis provides mechanistic insight into how this class of chemical pollutant can cause NAFLD. Our study lays the foundation for the development of molecular signatures of toxic effects of chemicals causing fatty liver diseases to move away from a chemical risk assessment based on in vivo animal experiments.

pharmacology and toxicology↗

bioRxiv2018

Loss of Trem2 in microglia leads to widespread disruption of cell co-expression networks in mouse brain

Rare heterozygous coding variants in the Triggering Receptor Expressed in Myeloid cells 2 (TREM2) gene, conferring increased risk of developing late-onset Alzheimer's disease, have been identified. We examined the transcriptional consequences of the loss of Trem2 in mouse brain to better understand its role in disease using differential expression and coexpression network analysis of Trem2 knockout and wild-type mice. We generated RNA-Seq data from cortex and hippocampus sampled at 4 and 8 months. Using brain cell type markers and ontology enrichment, we found subnetworks with cell type and/or functional identity. We primarily discovered changes in an endothelial-gene enriched subnetwork at 4 months, including a shift towards a more central role for the Amyloid Precursor Protein (App) gene, coupled with widespread disruption of other cell-type subnetworks, including a subnetwork with neuronal identity. We reveal an unexpected potential role of Trem2 in the homeostasis of endothelial cells that goes beyond its known functions as a microglial receptor and signalling hub, suggesting an underlying link between immune response and vascular disease in dementia.

systems biology↗