Biology subjects

Nicholson, M.

Publications and source records attributed to Nicholson, M..

7 recordsLinked to original sources

bioRxiv2025

Fecal Microbial and Metabolic Signatures in VEO-IBD: Implications for Unique Pathophysiology

Background and AimsVery early onset inflammatory bowel disease (VEO-IBD) is a clinically distinct form of IBD manifesting in children before the age of six years. Disease in these children is especially severe and often refractory to treatment. While previous studies have investigated changes in the fecal microbiome and metabolome in adult and pediatric IBD, insights in VEO-IBD remain limited. This multi-omics analysis reveals changes in the fecal microbiome and metabolome in VEO-IBD compared with healthy controls. MethodsFecal samples were collected from children diagnosed with VEO-IBD and age- and sex-matched healthy controls. Both the fecal metabolome and microbiome were profiled in each sample, using untargeted liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and 16S rRNA gene amplicon sequencing. ResultsFecal microbial and metabolic profiles in VEO-IBD were significantly different from healthy controls. Untargeted metabolomics analysis identified a depletion of short-chain N-acyl lipids and an enrichment of dipeptides, tripeptides, and oxo bile acids in VEO-IBD patients. Differential abundance analysis of the gut microbiome showed lower abundance of beneficial bacteria such as Bifidobacterium and Blautia, and higher abundance of Lachnospira, Veillonella, and Bacteroides in VEO-IBD. The joint analysis suggested a clear association between the altered gut microbiome composition and metabolic dysregulation, specifically for the N-acyl lipids. ConclusionsThis study offers unique insight into fecal microbial and metabolic signatures in VEO-IBD, paving the way for a better understanding of disease patterns and thereby more effective treatment strategies.

microbiology↗

bioRxiv2025

The Gut Microbiome and Butyrate Differentiate Clostridioides difficile Colonization and Infection in Children

Background and AimsSymptomatic Clostridioides difficile infection (CDI) can cause significant morbidity and mortality. Conversely, patients can be colonized with toxigenic C. difficile in the absence of symptoms, termed asymptomatic colonization. We previously demonstrated that the presence and function of C. difficile toxins do not differentiate between asymptomatic colonization and CDI in children, suggesting the influence of other factors. This study aimed to interrogate the intestinal microbiome and butyrate in stool samples from children with CDI and asymptomatic colonization. MethodsDesign: Case-control study Setting: Tertiary care childrens hospital Participants and measures: Asymptomatic children had stool tested for C. difficile by nucleic-acid amplification-based testing (NAAT) and were considered colonized if positive (N=50). Residual stool was also obtained from symptomatic children who tested positive for C. difficile by NAAT (N=55). The microbiome was assessed via 16S rRNA sequencing and butyrate via liquid chromatography-mass spectrometry. ResultsCompared to clinical co-variates and comorbidities, C. difficile symptom status (i.e., asymptomatic colonization versus symptomatic CDI) demonstrated the strongest differential abundance association on gut microbes. Symptomatic CDI was associated with increased abundance of Escherichia/Shigella (Benjamini-Hochberg adjusted q=3.94x10-5), Haemophilus (q=0.022), and Gemella (q=0.085), and depleted abundance of gut commensals such as Faecalibacterium (q=0.041), Blautia (q=0.041), and Bifidobacterium (q=0.063). We also observed depletion in the abundance of microbial butyrate producers and fecal butyrate in participants with symptomatic CDI versus asymptomatic colonization. ConclusionThe gut microbiota and butyrate differ between participants with asymptomatic C. difficile colonization and symptomatic CDI, suggesting their potential role in symptom development.

microbiology↗

bioRxiv2024

AMH regulates ovary size by counteracting ovarian follicle cluster effects.

Serum anti-Mullerian hormone (AMH) is the primary clinical indicator of mature oocyte counts in the ovaries, but its biological role remains poorly understood. Mammalian ovaries have a finite lifetime of oocytes that are slowly depleted as the dormant follicles housing the oocytes initiate maturation. Less than 0.1% of these follicles will reach maturity and ovulate an oocyte. Recent studies suggest that AMH is a key regulator that removes most of these follicles at early stages of follicle maturation. Most AMH is secreted as an inactive precursor protein, and we show that the required activating-enzymes are largely present outside the follicle. We then measured AMH concentrations in ovarian stroma with microdialysis showing that activity is confined to a short range from the site of secretion. To examine short-range interactions between follicles, we reconstructed the ovarian follicle positions from sheep ovaries in 3D space. This showed that most early follicles develop in proximity to more advanced follicles. Active immunisation of sheep against AMH to inhibit signalling, greatly expanded early follicle numbers, but almost entirely in proximity to large follicles. Large follicle proximity appears to greatly enhance early follicle survival, and AMH appears to attenuate this effect to prevent follicle overgrowth beyond sustainable limits.

physiology↗

bioRxiv2024

Quantifying "just-right" APC inactivation for colorectal cancer initiation

Dysregulation of the tumour suppressor gene Adenomatous Polyposis Coli (APC) is a canonical step in colorectal cancer development. Curiously, most colorectal tumours carry biallelic mutations that result in only partial loss of APC function, suggesting that a just-right level of APC inactivation, and hence Wnt signalling, provides the optimal conditions for tumorigenesis. Mutational processes act variably across the APC gene, which could contribute to the bias against complete APC inactivation. Thus the selective consequences of partial APC loss are unclear. Here we propose a mathematical model to quantify the tumorigenic effect of biallelic APC genotypes, controlling for somatic mutational processes. Analysing sequence data from >2500 colorectal cancers, we find that APC genotypes resulting in partial protein function confer about 50 times higher probability of progressing to cancer compared to complete APC inactivation. The optimal inactivation level varies with anatomical location and additional mutations of Wnt pathway regulators. We use this context dependency to assess the regulatory effect of secondary Wnt drivers in combination with APC in vivo, and provide evidence that mutant AMER1 combines with APC genotypes that lead to relatively low Wnt. The fitness landscape of APC inactivation is consistent across microsatellite unstable and POLE-deficient colorectal cancers and tumours in patients with Familial Adenomatous Polyposis suggesting a general just-right optimum, and pointing to Wnt hyperactivation as a potential cancer vulnerability.

cancer biology↗

bioRxiv2022

Early microglial response, myelin deterioration and lethality in mice deficient for very long chain ceramide synthesis in oligodendrocytes

The sphingolipids galactosylceramide (GalCer), sulfatide (ST) and sphingomyelin (SM) are essential for myelin stability and function. GalCer and ST are synthesized mostly from C22-C24 ceramides, generated by Ceramide Synthase 2 (CerS2). To clarify the requirement for C22-C24 sphingolipid synthesis in myelin lipid biosynthesis and stability, we generated mice lacking CerS2 specifically in myelinating cells (CerS2{Delta}O/{Delta}O). At 6 weeks of age, normal-appearing myelin had formed in CerS2{Delta}O/{Delta}O mice, however there was a reduction in myelin thickness and the percentage of myelinated axons. Pronounced loss of C22-C24 sphingolipids in myelin of CerS2{Delta}O/{Delta}O mice was compensated by greatly increased levels of C18 sphingolipids. A distinct microglial population expressing high levels of activation and phagocytic markers such as CD64, CD11c, MHC class II, and CD68 was apparent at 6 weeks of age in CerS2{Delta}O/{Delta}O mice, and had increased by 10 weeks. Increased staining for denatured myelin basic protein was also apparent in 6-week-old CerS2{Delta}O/{Delta}O mice. By 16 weeks, CerS2{Delta}O/{Delta}O mice showed pronounced myelin atrophy, motor deficits, and axon beading, a hallmark of axon stress. 90% of CerS2{Delta}O/{Delta}O mice died between 16 and 26 weeks of age. This study highlights the importance of sphingolipid acyl chain length for the structural integrity of myelin, demonstrating how a modest reduction in lipid chain length causes exposure of a denatured myelin protein epitope and expansion of phagocytic microglia, followed by axon pathology, myelin degeneration, and motor deficits. Understanding the molecular trigger for microglial activation should aid the development of therapeutics for demyelinating and neurodegenerative diseases. Main PointsO_LIOligodendrocytes lacking CerS2 produce myelin using sphingolipids with C16/C18 instead of C22/C24 N-acyl chains C_LIO_LIC22/C24 myelin sphingolipids are essential for myelin stability, microglial quiescence, and survival beyond young adulthood C_LI Table of Contents Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/493337v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1125540org.highwire.dtl.DTLVardef@9aeebdorg.highwire.dtl.DTLVardef@1afbeb4org.highwire.dtl.DTLVardef@11156c2_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria

Superspreading events shape the COVID-19 pandemic. Here we provide a national-scale analysis of SARS-CoV-2 outbreaks in Austria, a country that played a major role for virus transmission across Europe and beyond. Capitalizing on a national epidemiological surveillance system, we performed deep whole-genome sequencing of virus isolates from 576 samples to cover major Austrian SARS-CoV-2 clusters. Our data chart a map of early viral spreading in Europe, including the path from low-frequency mutations to fixation. Detailed epidemiological surveys enabled us to calculate the effective SARS-CoV-2 population bottlenecks during transmission and unveil time-resolved intra-patient viral quasispecies dynamics. This study demonstrates the power of integrating deep viral genome sequencing and epidemiological data to better understand how SARS-CoV-2 spreads through populations. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

microbiology↗

bioRxiv2020

Remodeling of pre-existing myelinated axons and oligodendrocytes is stimulated by environmental enrichment in the young adult brain

Oligodendrocyte production and central nervous system (CNS) myelination is a protracted process, extending into adulthood. While stimulation of neuronal circuits has been shown to enhance oligodendrocyte production and myelination during development, the extent to which physiological stimuli induces activity-dependent plasticity within oligodendrocytes and myelin is unclear, particularly in the adult CNS. Here, we find that using environmental enrichment (EE) to physiologically stimulate neuronal activity for 6-weeks during young adulthood in C57Bl/6 mice results in an enlargement of callosal axon diameters, with a corresponding increase in thickness of pre-existing myelin sheaths. Additionally, EE uniformly promotes the direct differentiation of pre-existing oligodendroglia in both corpus callosum and somatosensory cortex, while differentially impeding OPC homeostasis in these regions. Furthermore, results of this study indicate that physiologically relevant stimulation in young adulthood exerts little influence upon the de novo generation of new myelin sheaths on previously unmyelinated segments and does not enhance OPC proliferation. Rather in this context, activity-dependent plasticity involves the coincident structural remodeling of axons and pre-existing myelin sheaths and increases the direct differentiation of pre-existing oligodendroglia, implying constraints on maximal de novo production in the adult CNS. Together, our findings of myelinated axon remodeling and increased pre-existing oligodendroglial differentiation constitute a previously undescribed form of adaptive myelination that likely contributes to neuronal circuit maturation and the maintenance of optimum cognitive function in the young adult CNS. Main pointsO_LIEnvironmental enrichment induces the plasticity of myelinated axons, resulting in axon caliber enlargement and increased thickness of pre-existing myelin sheaths C_LIO_LIEnvironmental enrichment increases the direct differentiation of pre-existing oligodendroglia C_LIO_LIEnvironmental enrichment alters OPC homeostasis C_LI

neuroscience↗