Biology subjects

Page, K.

Publications and source records attributed to Page, K..

8 recordsLinked to original sources

bioRxiv2026

ARMC1 regulates mitochondrial fatty acid oxidation through theinsertase/scramblase MTCH2

MTCH2 (mitochondrial carrier homolog 2) is a noncanonical member of the solute carrier family with five transmembrane (TM) helices, localized to the mitochondrial outer membrane. MTCH2's atypical topology creates a membrane-accessible hydrophilic groove, predicted to be necessary for its protein insertase and lipid scramblase activities. MTCH2 is linked to lipid metabolism and obesity and is required for starvation-induced mitochondrial hyperfusion. Here, we show that MTCH2 is a stable component of a complex containing the Armadillo (ARM) repeat-containing protein, ARMC1, and the DnaJ/Hsp40 chaperone protein, DNAJC11. Protein crosslinking, protein structural modeling, and molecular dynamics simulations demonstrate that the ARMC1 alpha-helical C-terminal domain (CTD) inserts into and stably interacts with the MTCH2 hydrophilic groove and blocks its lipid scramblase activity. We observe that starvation-induced mitochondrial fatty acid oxidation (FAO) is negatively regulated by the ARMC1-MTCH2 interaction. In ARMC1-deficient cells, FAO is stimulated compared to wild-type cells and lipid droplet abundance is significantly reduced. The altered lipid phenotype of ARMC1-/- cells is strictly dependent on MTCH2 and is reversed by ARMC1 expression in a manner dependent on its CTD. Beyond this metabolic axis, we also identify a function for ARMC1 in regulating lysosomal distribution and autophagic flux that is independent of its CTD and interaction with MTCH2. Thus, our data support a model in which the MTCH2-ARMC1 interaction functions as a metabolic switch during starvation to regulate the balance between fat storage and fat burning.

cell biology↗

bioRxiv2025

NETSseq Reveals Inflammatory and Aging Mechanisms in Distinct Cell Types Driving Cerebellar Decline in Ataxia Telangiectasia

The cellular and molecular changes driving the neurological abnormalities associated with ataxia - telangiectasia (A-T) are not well understood. Here, we applied our proprietary Nuclear Enriched Transcript Sort sequencing (NETSseq) platform to investigate changes in cell type composition and gene expression in human cerebellar post-mortem tissue from A-T and control donors. Compared to single-nuclei technologies, NETSseq provided a more robust detection of genes with low abundance, a higher cell type specific expression pattern, and significantly lower levels of cross-contamination. We found dysregulation in neurotransmitter signaling in granule neurons, potentially underlying the impaired motor coordination in A-T. Astrocytes and microglia have evidence of accelerated aging, with astrocytes being characterized by neurotoxic signatures, while microglia showed activation of DNA damage response pathways. These findings highlight the importance of NETSseq as a resource for investigating mechanisms and biological processes associated with disease, providing high-sensitivity, cell-specific insights to advance targeted therapies for neurodegenerative diseases.

neuroscience↗

bioRxiv2023

The Genetic Architecture of Dietary Iron Overload and Associated Pathology in Mice

Tissue iron overload is a frequent pathologic finding in multiple disease states including non-alcoholic fatty liver disease (NAFLD), neurodegenerative disorders, cardiomyopathy, diabetes, and some forms of cancer. The role of iron, as a cause or consequence of disease progression and observed phenotypic manifestations, remains controversial. In addition, the impact of genetic variation on iron overload related phenotypes is unclear, and the identification of genetic modifiers is incomplete. Here, we used the Hybrid Mouse Diversity Panel (HMDP), consisting of over 100 genetically distinct mouse strains optimized for genome-wide association studies and systems genetics, to characterize the genetic architecture of dietary iron overload and pathology. Dietary iron overload was induced by feeding male mice (114 strains, 6-7 mice per strain on average) a high iron diet for six weeks, and then tissues were collected at 10-11 weeks of age. Liver metal levels and gene expression were measured by ICP-MS/ICP-AES and RNASeq, and lipids were measured by colorimetric assays. FaST-LMM was used for genetic mapping, and Metascape, WGCNA, and Mergeomics were used for pathway, module, and key driver bioinformatics analyses. Mice on the high iron diet accumulated iron in the liver, with a 6.5 fold difference across strain means. The iron loaded diet also led to a spectrum of copper deficiency and anemia, with liver copper levels highly positively correlated with red blood cell count, hemoglobin, and hematocrit. Hepatic steatosis of various severity was observed histologically, with 52.5 fold variation in triglyceride levels across the strains. Liver triglyceride and iron mapped most significantly to an overlapping locus on chromosome 7 that has not been previously associated with either trait. Based on network modeling, significant key drivers for both iron and triglyceride accumulation are involved in cholesterol biosynthesis and oxidative stress management. To make the full data set accessible and useable by others, we have made our data and analyses available on a resource website. Author summaryThe response to a high iron diet is determined in part by genetic factors. We now report the responses to such a diet in a diverse set of inbred strains of mice, known as the Hybrid Mouse Diversity Panel, that enables high resolution genetic mapping and systems genetics analyses. The levels of iron in the liver varied about >5 fold across the strains, with genetic variation explaining up to 74% of the variation in liver iron. Pathologies included copper deficiency, anemia, and fatty liver, with liver triglycerides varying over 50 fold among the strains. Genetic mapping and network modeling identified significant genetic loci and pathways underlying the response to diet.

genetics↗

bioRxiv2022

Meta-Analyzed Atopic Dermatitis Transcriptome (MAADT) defines a strong correlation to disease activity and consistent to therapeutic effect

BackgroundAtopic Dermatitis (AD) is a persistent inflammatory disease of the skin to which a few novel treatment options have recently become available. Multiple published datasets, from RNA sequencing (RNA-seq) and microarray experiments performed on lesional (LS) and non-lesional (NL) skin biopsies collected from AD patients, provide a useful resource to better define an AD gene signature and evaluate therapeutic effects. MethodsWe evaluated 22 datasets using defined selection criteria and leave-one-out analysis and then carried out a meta-analysis (M-A) to combine 4 RNA-seq datasets and 5 microarray datasets to define a disease gene signature for AD skin tissue. We used this gene signature to evaluate its correlation to disease activity in published AD datasets, as well as the treatment effect of some of the existing and experimental therapies. ResultsWe report the AD gene signatures developed separately from the RNA-seq or the microarray datasets, as well as a gene signature from datasets combined across these two technologies; all 3 gene signatures showed a strong correlation to the disease activity score (SCORAD) - microarray: Pearsons{rho} = 0.651, p-value < 0.01, RNA-seq:{rho} = 0.640, p-value < 0.01, combined:{rho} = 0.649, p-value < 0.01. The gene signature improvement (GSI) of two existing effective therapies, Dupilumab and Cyclosporine, as well as that of other experimental treatments, is consistent with their reported cohort level efficacy from the associated clinical trials. ConclusionsThe M-A derived AD gene signature provides an evolution of an important resource to correlate gene expression to disease activity and will be helpful for evaluating potential treatment effects for novel therapies.

bioinformatics↗

bioRxiv2021

Structure modeling hints at a granular organization of the Vertebrate Golgi ribbon

Vertebrate cells display a specific Golgi apparatus architecture, known as the "ribbon", where the functional subunits, the mini-stacks, are linked into a tridimensional network. The importance of the ribbon architecture is underscored by evidence of its disruption in a host of diseases, but just how it relates to the biological Golgi functions remains unclear. Are all the connections between mini-stacks functionally equal? Is the local structure of the ribbon of functional importance? These are difficult questions to address, due to the lack of a secretory cargo providing a quantifiable readout of the functional output of ribbon-embedded mini-stacks. Endothelial cells produce rod-shaped secretory granules, the Weibel-Palade bodies (WPB), whose von Willebrand Factor (VWF) cargo is central to hemostasis. In these cells, the Golgi apparatus exerts a dual control on WPB size at both mini-stack and ribbon levels. Mini-stack dimensions delimit the size of VWF boluses" while the ribbon architecture allows their linear co-packaging at the trans-Golgi network generating WPBs of different lengths. This Golgi/WPB size relationship lends itself to mathematical analysis. Here, different ribbon structures were modeled and their predicted effects on WPB size distribution compared to the ground truth of experimental data. Strikingly, the best-fitting model describes a Golgi ribbon made by linked subunits corresponding to differentially functioning monomer and dimer ministacks. These results raise the intriguing possibility that the fine-grained structure of the Golgi ribbon is more complex than previously thought.

cell biology↗

bioRxiv2020

Genomic evaluation of circulating proteins for drug target characterisation and precision medicine

Circulating proteins are vital in human health and disease and are frequently used as biomarkers for clinical decision-making or as targets for pharmacological intervention. By mapping and replicating protein quantitative trait loci (pQTL) for 90 cardiovascular proteins in over 30,000 individuals, we identified 467 pQTLs for 85 proteins. The pQTLs were used in combination with other sources of information to evaluate known drug targets, and suggest new target candidates or repositioning opportunities, underpinned by a) causality assessment using Mendelian randomization, b) pathway mapping using trans-pQTL gene assignments, and c) protein-centric polygenic risk scores enabling matching of plausible target mechanisms to sub-groups of individuals enabling precision medicine.

genetics↗

bioRxiv2020

Longitudinal whole-exome sequencing of cell-free DNA unravels the metastatic evolutionary dynamics of BRCA2 mutated breast cancer

Little is known about the metastatic evolutionary dynamics of BRCA2-mutated cancers. Here, we applied whole-exome sequencing (WES) of primary tumor (PT), local relapse (LR) and eight serial plasma cfDNA samples collected from disease progression to depict the 12 years evolutionary trajectory of a metastatic BRCA2-mutated breast cancer. While longitudinal WES-cfDNA recapitulated clonal and subclonal mutations and copy number profiles detected in LR, emergence of plasma-exclusive mutations in TSC2 and HDAC9 cancer-related genes and loss of HLA loci as an immune escape mechanism were also detected. Lastly, mutation signature 3, associated with homologous recombination deficiency and response to platinum-based therapy raised profoundly from 19% in PT to 60% in late stage disease. In conclusion, we show for the first time that longitudinal WES-cfDNA enables the evolutionary trajectory of advanced cancer to be uncovered and that increment of MS3 and loss of HLA are key players in this BRCA2-mutated breast metastasis.

cancer biology↗

bioRxiv2019

Neuronal differentiation affects tissue mechanics and progenitor arrangement in the vertebrate neuroepithelium

Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube where neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we use experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates inter-kinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube.

developmental biology↗