Biology subjects

Kapoor, M.

Publications and source records attributed to Kapoor, M..

At least 19 recordsLinked to original sources

bioRxiv2026

3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data

Light microscopy is routinely used to explore the cellular and molecular structure of tissues, but the scale and complexity of data remains a bottleneck for discovery. We introduce 3D-MAESTRO (3D-Microscopy Automation and Execution with Scalable Tools, Rendering, and Orchestration): an automated image processing workflow for large-scale microscopy data, built for scalable execution across cloud and local computing environments. 3D-MAESTRO orchestrates denoising, stitching of image tiles, atlas registration, and segmentation. Its modular architecture permits the integration and benchmarking of new packages, ensuring that performance evolves as more efficient or accurate algorithms emerge. We introduce a new 3D image template for automated registration of mouse brains cleared with aqueous reagents and an efficient method for detection of fluorescent cells. We apply 3D-MAESTRO to lightsheet images of whole mouse brains in the context of diverse anatomical and functional experiments, illustrating high-throughput and reproducible mapping of microscopic structures across the brain.

neuroscience↗

bioRxiv2026

A Robust and Scalable Workflow for the Production of Circular Single-Stranded DNA for Genome Engineering Applications

Circular single-stranded DNA (cssDNA) is a versatile biomolecule with applications spanning genome editing, DNA nanotechnology, synthetic biology, molecular diagnostics, and aptamer development. Compared with linear single-stranded DNA, cssDNA offers enhanced structural stability, resistance to in-cellulo degradation by exonucleases and enables the generation of long, sequence-defined DNA molecules that are difficult to obtain through conventional chemical synthesis methods. Despite its growing utility, widespread adoption of cssDNA has been limited by the lack of accessible, scalable, and cost-effective production methods, with many existing workflows relying on specialised reagents, extensive optimisation, or commercially synthesised DNA. Here, we present a streamlined, end-to-end protocol for the laboratory-scale production of high-purity cssDNA using an M13 phagemid-based system and standard molecular biology laboratory infrastructure. The workflow encompasses bacterial culture, phage amplification, nuclease treatment, phage precipitation, anion-exchange purification, and quality control, with practical optimisations to improve yield, reproducibility, and scalability. Using this approach, yields range from 120-195 {micro}g of purified cssDNA from 300 mL of culture supernatant. The protocol provides detailed guidance on critical process parameters, troubleshooting, and quality assessment, enabling reliable production of cssDNA suitable for a wide range of downstream molecular biology and genome engineering applications.

molecular biology↗

bioRxiv2026

Simulation of transcription factor clustering in nuclei from molecular kinetics

Transcription factors form clusters often described as condensates that exhibit emergent biophysical properties. Here we present a software package to simulate transcription factor spatial distributions from molecular diffusion and binding kinetics alone. The software simulates microscopy data and FRAP experiments and recapitulates the clustering behavior of experimentally characterized transcription factors. Our results demonstrate that condensate-like structures can emerge from molecular kinetics principles without invoking higher-order processes like phase separation.

biophysics↗

bioRxiv2025

A single-cell immune atlas of primary and secondary lymphoid organs in pigs

Single-cell RNA sequencing (scRNA-seq) has revolutionized understandings of cellular identities and functions due to the ability to study transcriptome-wide gene expression within individual cells. Multi-tissue scRNA-seq atlases have generated holistic understandings of body-wide cell dynamics and serve as key foundational resources for further scientific studies across a variety of species. Pigs are a valuable biomedical model, and pork is an essential global food source, but minimal understanding of immune cell identities and functions across anatomical locations limits agricultural and health advancements in pigs. To address current limitations, we apply scRNA-seq to create an atlas of immune cells recovered from key immune tissues including primary lymphoid organs (bone marrow and thymus) and secondary lymphoid organs (lymph node and spleen). Thymus data was compared to a previously published scRNA-seq dataset of pig thymus and shared a general consensus while also identifying several new thymic cell populations. Comparison of spleen to a human splenic scRNA-seq dataset also revealed conserved features, including two subsets of innate lymphoid cells conserved between pigs and humans. Spatial reconstruction of lymph node structure from scRNA-seq data revealed follicular organization with similar cell type distributions and cell signaling interactions to those in human lymph nodes. To expand accessibility of the scRNA-seq atlas for biological query, we deploy an interactive application and demonstrate its use for non-computational exploration of diverse cell populations recovered from bone marrow. Overall, results expand current foundational understandings of immune cell identities and functions in pig lymphoid organs and demonstrate pig-to-human immune similarities to consider for future research applications. Materials associated with this work are made readily accessible for others to investigate individual queries requiring foundational knowledge pertaining to pig immunity.

immunology↗

bioRxiv2025

Metabolomics Ex/GWAS in the Amish reveals novel insights into cardiometabolic disease pathways

We conducted an exome and genome-wide association study (Ex/GWAS) of 1,015 metabolites in serum samples from 5,981 Amish adults. We identified 149 functional or likely functional genetic variants, based on CADD scores significantly associated (P < 5.8 x 10-8) with 519 metabolite levels, 69 of which were >10-fold enriched in the Amish versus Europeans in gnomAD. We discovered novel associations involving a PCK2 splice-donor variant (rs138881435) and metabolites important for energy metabolism and mitochondrial function. In UK Biobank participants, this variant was associated with increased longitudinal relaxation time (T1) values on liver MRI suggesting increased inflammation and fibrosis. Furthermore, we found novel associations involving ENPEP stop-gain variant (rs33966350) and peptide and amino acid metabolite levels, implicating ENPEPs roles in blood pressure regulation. Additional known and novel genetic variant-metabolite associations were identified including genes involved in Amish-enriched Mendelian diseases and cardiometabolic traits, providing insights into underlying mechanisms of these disorders.

genomics↗

bioRxiv2025

A cell atlas of human and mouse synovium from early and advanced stages of knee osteoarthritis: BHLHE40 regulates fibroblast activation

Osteoarthritis (OA) is a destructive joint disease affecting multiple tissues, including synovium. Previous studies have identified some distinct fibroblast subtypes within synovium; however, the characterization of fibroblast subsets during distinct stages of knee (K)OA disease, and their contributions to the endogenous mechanisms that drive synovial fibrosis during KOA, are not well characterized. Here we profile synovium from early- (KL I) and advanced- (KL III/IV) stages of radiographic KOA. First, bulk-RNA sequencing of early- and advanced-staged KOA synovial tissue revealed transcriptomic differences between the two disease stages. Using single-nuclei RNA sequencing (snRNA-seq) and flow cytometry, we identified distinct fibroblast subsets and uncovered an endotypic shift in fibroblast subsets during KOA pathogenesis, transitioning from DPP4+ in early-stage to ITGB8+ in advanced-stages. SnRNA-seq of synovium from mice with experimental KOA revealed analogous populations of Dpp4+ and Itgb8+ fibroblasts in tissue from early and advanced model stages. Human advanced-stage KOA synovial tissue had stronger expression of matrisome-annotated genes compared to early-stage tissue. BHLHE40, a crucial transcriptional regulator of ECM related genes, was identified as upregulated in ITGB8+ fibroblasts compared to DPP4+ fibroblasts. Using primary human OA fibroblasts in vitro, and conditional knock out mice in vivo, we found that fibroblast-intrinsic loss of BHLHE40 increased fibrosis-related gene expression, enhanced fibroblast activation and induced severe synovial fibrosis in vivo. In contrast, overexpression of BHLHE40 in vitro was able to suppress TGF-{beta}-induced fibroblast activation. Overall, this study provides a comprehensive cellular atlas of KOA synovium and has identified BHLHE40 as a crucial regulator of fibroblast-mediated synovial fibrosis.

molecular biology↗

bioRxiv2025

A cluster of RNA Polymerase II molecules is stably associated with an active gene

In eukaryotic nuclei, transcription is associated with the clustering of RNA Polymerase II (RNAPII) molecules. The mechanisms underlying cluster formation, their interactions with genes, and their impact on transcriptional activity remain heavily debated. Here, we take advantage of the naturally occurring increase in transcriptional activity during Zygotic Genome Activation (ZGA) in Drosophila melanogaster embryos to characterize the functional roles of RNAPII clusters in a developmental context. Using single-molecule tracking and lattice light-sheet microscopy, we find that RNAPII cluster formation depends on transcription initiation, and that cluster lifetimes depend on transcriptional activity when not constrained by interphase duration. We show that single clusters are stably associated with active gene loci during transcription and that cluster intensities are strongly correlated with transcriptional output. Collectively, our data and simulations on cluster formation kinetics show that RNAPII clusters reflect local accumulations of transcriptionally engaged polymerases and do not form through higher-order mechanisms such as phase separation.

biophysics↗

bioRxiv2024

microRNA-544a as a new modulator of the Wnt-signalling network in the articular cartilage and osteoarthritis

ObjectiveDetermining the effect of microRNA-544a (miR-544a) in articular chondrocytes isolated from patients affected by osteoarthritis (OA) and its role in the modulation of the Wnt signalling. MethodsArticular chondrocytes were isolated from patients undergoing joint replacement because of OA. Expression levels of miR-544a were measured by PCR and by in situ hybridization. Putative targets of miR-544a were confirmed by reporter assay and by qPCR in cells stimulated with a miR-544a mimic. The effect of miR-544a on chondrocyte metabolism was monitored by qPCR for phenotypic markers, protein expression levels of aggrecan neoepitopes/MMP-13 and modulation of alcian blue content in micromass cultures, upon stimulation with a miR-544a mimic. The expression levels of MMP-13 and Aggrecan neoepitopes in response to miR-544a stimulation was also measured in co-stimulation with Xav-939 and KN93, which are respectively {beta}-catenin and CaMKII inhibitors. ResultsOur results suggest that miR-544a enhances the activation of the Wnt-signalling in the articular chondrocytes, by downregulating the expression of components of the Wnt/{beta}-catenin destruction complex. The expression of miR-544a is higher in chondrocytes isolated from damaged areas of the articular cartilage removed from OA patients, and can be upregulated by pro-inflammatory and pro-fibrotic cytokines. miR-544a exerts a pro-catabolic effect of articular chondrocytes, which is rescued both by the inhibition of the Wnt/{beta}-catenin and Wnt/CaMKII signalling pathways. Conclusionour results point to miR-544a as a new, important modulator of the Wnt signalling network within the articular cartilage suggesting a key role for microRNAs in regulating how the multiple branches of the network and their interaction modulate cartilage homeostasis.

pharmacology and toxicology↗

bioRxiv2024

Identification of Ephrin type-B receptor 4 as a critical mediator of tissue fibrosis

Pulmonary fibrosis (PF) is a pathology associated with interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF). Fibrosis promotes continual secretion of extracellular matrix (ECM), producing non-functional scar tissue and causing organ failure. This study investigated the tyrosine kinase receptor Ephrin type-B receptor 4 (EphB4) as a mediator of PF. To this end, we generated mice with conditional Col1a2-driven deletion of Ephb4 and used a preclinical mouse model of PF, total and single nuclei RNA (snRNA) sequencing, NanoString, previously published single cell data, computational analysis, and functional assays of mouse and human healthy control and IPF lung fibroblasts. Col1a2-CreERT-driven Ephb4 deletion, or EphB4 inhibition via NVP-BHG712, markedly protected against bleomycin-induced PF. Total RNA-sequencing of fibroblasts isolated from Ephb4-deficient fibrotic mouse lungs exhibited reduced expression of ECM, ER Cargo, and protein trafficking-related genes. NVP-BHG712 reduced expression of these identified genes in mouse lung fibroblasts under fibrotic conditions in vitro. SnRNA sequencing of mouse lungs treated with NVP-BHG712 identified transcriptomic changes of ECM genes in specific fibroblast subpopulations. RNA sequencing, computational, and functional assays using mouse and human IPF fibroblasts identified elastin as a key mediator involved in EphB4 signaling. Combined, our data show that EphB4 is a crucial mediator of PF.

pathology↗

bioRxiv2024

Integrative genomics approach identifies glial transcriptomic dysregulation and risk in the cortex of individuals with Alcohol Use Disorder

Alcohol use disorder (AUD) is a prevalent neuropsychiatric disorder that is a major global health concern, affecting millions of people worldwide. Past molecular studies of AUD used underpowered single cell analysis or bulk homogenates of postmortem brain tissue, which obscures gene expression changes in specific cell types. Here we performed single nuclei RNA-sequencing analysis of 73 post-mortem samples from individuals with AUD (N=36, Nnuclei= 248,873) and neurotypical controls (N=37, Nnuclei= 210,573) in both sexes across two institutional sites. We identified 32 clusters and found widespread cell type-specific transcriptomic changes across the cortex in AUD, particularly affecting glia. We found the greatest dysregulation in novel microglial and astrocytic subtypes that accounted for the majority of differential gene expression and co-expression modules linked to AUD. Analysis for cell type-specific enrichment of aggregate genetic risk for AUD identified subtypes of microglia and astrocytes as potential key players not only affected by but causally linked to the progression of AUD. These results highlight the importance of cell-type specific molecular changes in AUD and offer opportunities to identify novel targets for treatment.

neuroscience↗

bioRxiv2024

Manipulating the EphB4-ephrinB2 axis to reduce metastasis in HSNCC

The EphB4-ephrinB2 signaling axis has been heavily implicated in metastasis across numerous cancer types. Our emerging understanding of the dichotomous roles that EphB4 and ephrinB2 play in head and neck squamous cell carcinoma (HNSCC) poses a significant challenge to rational drug design. We find that EphB4 knockdown in cancer cells enhances metastasis in preclinical HNSCC models by augmenting immunosuppressive cells like T regulatory cells (Tregs) within the tumor microenvironment. EphB4 inhibition in cancer cells also amplifies their ability to metastasize through increased expression of genes associated with epithelial mesenchymal transition and hallmark pathways of metastasis. In contrast, vascular ephrinB2 knockout coupled with radiation therapy (RT) enhances anti-tumor immunity, reduces Treg accumulation into the tumor, and decreases metastasis. Notably, targeting the EphB4-ephrinB2 signaling axis with the engineered EphB4 ligands EFNB2-Fc-His and Fc-TNYL-RAW-GS reduces local tumor growth and distant metastasis in a preclinical model of HNSCC. Our data suggest that targeted inhibition of vascular ephrinB2 while avoiding inhibition of EphB4 in cancer cells could be a promising strategy to mitigate HNSCC metastasis.

cancer biology↗

bioRxiv2024

Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis

ObjectivesIn this study, we employ a multi-omic approach to identify major cell types and subsets, and their transcriptomic profiles within the infrapatellar fat pad (IFP), and to determine differences in the IFP based on knee osteoarthritis (KOA), sex, and obesity status. MethodsSingle-nucleus RNA sequencing of 82,924 nuclei from 21 IFPs (n=6 healthy control and n=15 KOA donors), spatial transcriptomics and bioinformatic analysis were used to identify contributions of the IFP to KOA. We mapped cell subclusters from other white adipose tissues using publicly available literature. The diversity of fibroblasts within the IFP was investigated by bioinformatic analyses, comparing by KOA, sex, and obesity status. Metabolomics was used to further explore differences in fibroblasts by obesity status. ResultsWe identified multiple subclusters of fibroblasts, macrophages, adipocytes, and endothelial cells with unique transcriptomic profiles. Using spatial transcriptomics, we resolved distributions of cell types and their transcriptomic profiles, and computationally identified putative cell-cell communication networks. Furthermore, we identified transcriptomic differences in fibroblasts from KOA versus healthy control donor IFPs, female versus male KOA-IFPs, and obese versus normal body mass index (BMI) KOA-IFPs. Finally, using metabolomics, we defined differences in metabolite levels in supernatants of naive, profibrotic- and proinflammatory stimuli-treated fibroblasts from obese compared to normal BMI KOA-IFP. ConclusionsOverall, by employing a multi-omic approach, this study provides the first comprehensive map of cellular and transcriptomic diversity of human IFP and identifies IFP fibroblasts as a key cell type contributing to transcriptomic and metabolic differences related to KOA disease, sex, or obesity.

cell biology↗

bioRxiv2023

A deep catalog of protein-coding variation in 985,830 individuals

Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.

genetics↗

bioRxiv2022

Insights into β-manno-oligosaccharide uptake and metabolism in Bifidobacterium adolescentis DSMZ 20083 from whole-genome microarray analysis

AimsTo determine the ability of adult-associated B. adolescentis DSMZ 20083 to utilize dietary {beta}-manno-oligosaccharides and understand the underlying molecular mechanism. Methods and ResultsIn-vitro fermentation and TLC were used to determine the ability of B. adolescentis DSMZ 20083 to utilize {beta}-manno-oligosaccharides from guar gum, locust bean gum, konjac and copra meal. Further, Whole-genome transcriptome analysis, q-RT-PCR and molecular docking were employed to reconstruct copra meal {beta}-manno-oligosaccharides (CM-{beta}-MOS) utilization pathway in B. adolescentis DSMZ 20083. B. adolescentis DSMZ 20083 grew appreciably (A600nm up to 0.8) on all tested {beta}-manno-oligosaccharides but maximally on CM-{beta}-MOS. Transcriptome analysis revealed differential up-regulation of three distinct gene clusters encoding, ABC transporter cassette (ESBPs and permeases), MFS transporter, GH1 {beta}-glucosidase and, GH32 {beta}-fructofuranosidases. ABC and MFS possibly transported majorly DP[≥]2 and DP[≥]3 CM-{beta}-MOS, respectively. Sugar absorption and utilization pathways; ABC transport system, pyruvate metabolism, glycolysis/gluconeogenesis, pentose, and glucouronate inter-conversions were also up-regulated. ConclusionsB. adolescentis DSMZ 20083 possibly utilizes ABC & MFS transporters to internalise and GH1 {beta}-glucosidase, and GH32 {beta}-fructofuranosidase to deconstruct CM-{beta}-MOS. Significance and Impact of the StudyFirst study reporting possible molecular determinants used by B. adolescentis DSMZ 20083 to utilize {beta}-manno-oligosaccharides and thus, can prove resourceful in precision microbiome modulation.

microbiology↗

bioRxiv2020

Multi-omics integration analysis identifies novel genes for alcoholism with potential link to neurodegenerative diseases

SignificanceIdentification of causal variants and genes underlying genome-wide association study (GWAS) loci is essential to understanding the biology of alcohol use disorder (AUD). MethodsIntegration of "multi-omics" data is often necessary to nominate candidate causal variants and genes and prioritize them for follow up studies. Here, we used Mendelian randomization to integrate AUD and drinks per week (DPW) GWAS summary statistics with the gene expression and methylation quantitative trait loci (eQTLs and mQTLs) in the largest brain and myeloid datasets. We also used AUD-related single cell epigenetic data to nominate candidate causal variants and genes associated with DPW and AUD. ResultsOur multi-omics integration analyses prioritized unique as well as shared genes and pathways among AUD and DPW. The GWAS variants associated with both AUD and DPW showed significant enrichment in the promoter regions of fetal and adult brains. The integration of GWAS SNPs with mQTLs from fetal brain prioritized variants on chromosome 11 in both AUD and DPW GWASs. The co-localized variants were found to be overlapping with promoter marks for SPI1, specifically in human microglia, the myeloid cells of the brain. The co-localized SNPs were also strongly associated with SPI1 mRNA expression in myeloid cells from peripheral blood. The prioritized variant at this locus is predicted to alter the binding site for a transcription factor, RXRA, a key player in the regulation of myeloid cell function. Our analysis also identified MAPT as a candidate causal gene specifically associated with DPW. mRNA expression of MAPT was also correlated with daily amounts of alcohol intake in post-mortem brains (frontal cortex) from alcoholics and controls (N = 92). Results may be queried and visualized in an online public resource of these integrative analysis (https://lcad.shinyapps.io/alc_multiomics/). These results highlight overlap between causal genes for neurodegenerative diseases, alcohol use disorder and alcohol consumption. In conclusionintegrating GWAS summary statistics with multi-omics datasets from multiple sources identified biological similarities and differences between typical alcohol intake and disordered drinking highlighting molecular heterogeneity that might inform future targeted functional and cross-species studies. Interestingly, overlap was also observed with causal genes for neurodegenerative diseases.

genomics↗

bioRxiv2020

Epigenetic memory as a time integral over prior history of Polycomb phase separation

Structural organization of the genome into transcriptionally active euchromatin and silenced heterochromatin is essential for eukaryotic cell function. Heterochromatin is a more compact form of chromatin, and is associated with characteristic post-translational histone modifications and chromatin binding proteins. Phase-separation has recently been suggested as a mechanism for heterochromatin formation, through condensation of heterochromatin associated proteins. However, it is unclear how phase-separated condensates can contribute to stable and robust repression, particularly for heritable epigenetic changes. The Polycomb complex PRC1 is known to be key for heterochromatin formation, but the multitude of Polycomb proteins has hindered our understanding of their collective contribution to chromatin repression. Here, we take a quantitative live cell imaging approach to show that PRC1 proteins form multicomponent condensates through hetero-oligomerization. They preferentially seed at H3K27me3 marks, and subsequently write H2AK119Ub marks. Using optogenetics to nucleate local Polycomb condensates, we show that Polycomb phase separation can induce chromatin compaction, but phase separation is dispensable for maintenance of the compacted state. Our data are consistent with a model in which the time integral of historical Polycomb phase separation is progressively recorded in repressive histone marks, which subsequently drive chromatin compaction. These findings link the equilibrium thermodynamics of phase separation with the fundamentally non-equilibrium concept of epigenetic memory.

biophysics↗

bioRxiv2020

Evaluation of in vitro activity of manogepix against multidrug-resistant and pan-resistant Candida auris from the New York Outbreak

An ongoing Candida auris outbreak in the New York metropolitan area is the largest recorded to date in North America. Laboratory surveillance revealed NY C. auris isolates are resistant to fluconazole, with variable resistance to other currently used broad-spectrum antifungal drugs, and that several isolates are pan-resistant. Thus, there is an urgent need for new drugs with a novel mechanism of action to combat the resistance challenge. Manogepix (MGX) is a first-in-class agent that targets the fungal Gwt1 enzyme. The prodrug, fosmanogepix, is currently in Phase 2 clinical development for the treatment of fungal infections. We evaluated the susceptibility of 200 New York C. auris isolates to MGX and 10 comparator drugs using CLSI methodology. MGX demonstrated lower MICs than comparators (MIC50 and MIC90 0.03 mg/L; range 0.004-0.06 mg/L). The MGX epidemiological cutoff value (ECV, 99% cutoff) for the tested C. auris isolates was 0.06 mg/L. MGX was 8-32-fold more active than the echinocandins, 16-64-fold more active than the azoles, and 64-fold more active than amphotericin B. No differences were found in the MGX or comparators MIC50, MIC90, or GEOMEAN values when subsets of clinical, surveillance, and environmental isolates were evaluated. The range of MGX MIC values for six C. auris pan-resistant isolates was 0.008-0.015 mg/L, and the median and mode MIC values were 0.015 mg/L, demonstrating that MGX retains activity against these isolates. These data support further clinical evaluation of fosmanogepix for the treatment of C. auris infections, including highly resistant isolates.

microbiology↗

bioRxiv2019

Cholesterol and matrisome pathways dysregulated in human APOE ε4 glia

Apolipoprotein E (APOE) {varepsilon}4 is the strongest genetic risk factor for Alzheimers disease (AD). Although its association with AD is well-established, the impact of APOE {varepsilon}4 on human brain cell function remains unclear. Here we investigated the effects of APOE {varepsilon}4 on several brain cell types derived from human induced pluripotent stem cells and human APOE targeted replacement mice. Gene set enrichment and pathway analyses of whole transcriptome profiles showed that APOE {varepsilon}4 is associated with dysregulation of cholesterol homeostasis in human but not mouse astrocytes and microglia. Elevated matrisome signaling associated with chemotaxis, glial activation and lipid biosynthesis in APOE {varepsilon}4 mixed neuron/astrocyte cultures parallels altered pathways uncovered in cell-type deconvoluted transcriptomic data from APOE {varepsilon}4 glia and AD post-mortem brains. Experimental validation of the transcriptomic findings showed that isogenic APOE {varepsilon}4 is associated with increased lysosomal cholesterol levels and decreased cholesterol efflux, demonstrating decoupled lipid metabolism. APOE {varepsilon}4 glia also secrete higher levels of proinflammatory chemokines, cytokines and growth factors, indicative of glial activation. Thus, APOE {varepsilon}4 induces human glia-specific dysregulation that may initiate AD risk.

neuroscience↗