Biology subjects

Reilly, M.

Publications and source records attributed to Reilly, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Organelle Volume Facilitates Spindle Positioning During C. elegans Female Meiosis

Cortical positioning of oocyte meiotic spindles is required for reducing chromosome number by segregating chromosomes into polar bodies. In C. elegans, kinesin-1 transports membrane-bound organelles inward into a central ball that is hypothesized to push the meiotic spindle outward. Using focused ion beam scanning electron microscopy, we found that the percent volume occupied by membrane-bound organelles was 28% in a mature oocyte that has completed endocytosis of the yolk precursor, vitellogenin, compared to 17% in a less mature oocyte that has not yet endocytosed vitellogenin. We therefore hypothesized that blocking endocytosis of vitellogenin would reduce the size of the central ball of organelles packed inward by kinesin-1 and limit outward movement of the spindle. Depletion of vitellogenin or proteins required for endocytosis resulted in a smaller central volume of kinesin-coated organelles and defective spindle positioning. A computer simulation of a simple exclusion model faithfully recapitulated wildtype and mutant spindle position phenotypes. These results support a volume exclusion model for positioning acentriolar meiotic spindles.

cell biology↗

bioRxiv2026

Associations Between Plasma Lipoprotein(a) Levels and Circulating Monocyte Subsets Differ across Populations

BackgroundLipoprotein(a) [Lp(a)] is a causal risk factor for cardiovascular disease (CVD), with plasma concentrations higher in Black individuals than in White individuals. Published findings support a model in which high Lp(a), in part through oxidized phospholipid (oxPL)-mediated signaling, promotes a pro-inflammatory monocyte phenotype that may contribute to arterial wall inflammation and the development of CVD. Here, we examined the relationship between Lp(a) concentrations and isoform size and the distribution of circulating monocyte populations in Black and White individuals using single-cell RNA sequencing (scRNA-seq) data. MethodsUsing standardized assays, we measured plasma Lp(a) levels, isoform size, inflammatory markers, and oxidized phospholipids in stored plasma samples from our previously published cohort of 128 participants. After excluding smokers and individuals with type II diabetes, a total of 34 participants (20 Black participants, 14 White participants) were included in analyses. Participants were further stratified by plasma Lp(a) levels into normal Lp(a) [median 12.6 nmol/L, with 15 individuals (8 Black participants) and high Lp(a) (median 159 nmol/L, with 19 individuals (12 Black partcipants)]. Multivariable linear regression was used to assess the association between plasma Lp(a) levels, Lp(a)-oxPL, and the proportion of monocyte subsets. Across all participants, scRNA-seq data identified six classical monocyte subsets, one non-classical monocyte subset, one MHCIIhi monocyte subset, and one interferon (IFN)-responsive monocyte subset. ResultsThe distribution of monocyte subsets was similar in individuals with normal versus high Lp(a) levels. Despite the small study cohort, self resported race modified the assocation between plasma Lp(a) levels and the proportion of non-classical monocytes (P = 0.032), which was inversely associated in White participants (P = 0.028), but not in Black partcipatns (P = 0.470). OxPL bound to APO(a) showed a positive correlation with plasma Lp(a) levels (R2 = 0.84; P = 3.3x10-14), and non-classical monocytes (PWhites = 0.027; PBlacks = 0.275; PInteraction = 0.014). Race also modified the association between plasma Lp(a) levels and the proportion of classical 2 monocytes (P = 0.027). ConclusionsThese results underscore the importance of self reported race when analysing studies on Lp(a), monocytes and, cardiovascular related monocyte immune functions.

immunology↗

bioRxiv2026

IgG Propels Atherosclerosis by Noncanonically Activating Macrophages

Despite being a central component of adaptive immunity and a highly abundant serum protein, the contribution of IgG to the milieu of atherosclerosis remains unappreciated. Here, we identify a pro-atherogenic role for IgG as it activates an innate immune cascade, independent of its classical antigen-neutralizing function. Analyses of human coronary artery plaques reveal a positive correlation between IgG and cardiovascular and cerebrovascular disease severity. Integrated single-cell plaque analyses localize IgG, coinciding with its recycling receptor FcRn, to pro-inflammatory and foamy macrophages. Genetic ablation of FcRn in myeloid cells prevents IgG from accumulating in mouse atherosclerotic lesions, diminishing plaque size and inflammation. Mechanistically, IgG acts as an endogenous ligand for TLR4, triggering NF-{kappa}B-NLRP3 inflammasome signaling without requiring its antigen-binding domain. Additionally, IgG accelerates macrophage foam cell formation through upregulation of downstream effector LCN2. Our work uncovers a role for previously overlooked adaptive immune molecules in the pathogenesis of atherosclerosis through a noncanonical mechanism linked with innate immunity.

immunology↗

bioRxiv2026

Toward Computationally Complete Spatial Omics

Multimodal spatial omics has transformed biology by mapping molecular complexity within intact tissues, yet current technologies remain limited in the number of modalities measured simultaneously and often produce lower-quality data than single-modality assays. We present COSIE, a computational framework that generates high-resolution, multilayered molecular landscapes across tissue sections, individuals, and platforms. COSIE integrates histology, epigenome, transcriptome, proteome, and metabolome into a unified representation. Applied to 12 datasets spanning 10 spatial technologies, eight modalities, and nine tissue types, ranging from thousands of spots to millions of cells, COSIE outperforms existing methods. It resolves tissue structures, enhances noisy measurements, predicts unmeasured modalities, and captures dynamic processes. In human tumors, COSIE identifies invasive subregions linked to clinical outcomes and predicts spatial gene expression in TCGA samples using only histology images. By transforming fragmented data into comprehensive spatial maps, COSIE advances computationally complete spatial omics and the creation of digital tissue twins for biomedicine.

genomics↗

bioRxiv2025

CRISPR-mediated transcriptional activation as a mutation-independent therapeutic strategy for SYNGAP1-related intellectual disability

Synaptic Ras GTPase-activating protein (SynGAP) regulates synaptic strength and neuronal signaling, with essential roles in cortical development and synaptic plasticity. Heterozygous loss-of-function variants in SYNGAP1 cause SYNGAP1-related intellectual disability (SRID), a severe neurodevelopmental disorder characterized by epilepsy, developmental delay, and autism. SYNGAP1 mutations often result in haploinsufficiency, providing a strong rationale for gene-targeted therapies. However, no treatment currently addresses the underlying genetic cause of SRID. Here, we developed a CRISPR-mediated transcriptional activation (CRISPRa) approach to upregulate the functional Syngap1 allele in a SRID mouse model. CRISPRa activated Syngap1, normalized SynGAP protein expression and downstream signaling, and rescued working memory deficits. We validated the translational potential of this strategy in human induced pluripotent stem cell (hiPSC)-derived excitatory cortical neurons. CRISPRa rescued SYNGAP1 in two distinct loss-of-function variant lines. Together, these findings demonstrate the feasibility of mutation-independent transcriptional activation as a therapeutic approach for SRID and its broader applicability to haploinsufficiency disorders.

neuroscience↗

bioRxiv2025

Bi-allelic mutations in KCTD11 cause a new form of autosomal recessive intermediate Charcot-Marie-Tooth disease

Charcot-Marie-Tooth disease (CMT) is the most common inherited neuromuscular disorder, characterized by progressive, length-dependent degeneration of peripheral nerves, resulting in distal muscle atrophy and weakness, foot and hand deformities, and sensory deficits. The disease is clinically and genetically heterogeneous, with over 125 disease-causing genes identified to date. Here, genetic studies in ten patients from 5 unrelated families of diverse ethnic background, led to the identification of KCTD11 as a novel CMT gene, responsible for a new autosomal recessive intermediate CMT subtype, RI-CMTE. The variants identified are loss of function. KCTD11 encodes KCTD11/REN, a protein of yet unknown function in the Peripheral Nervous System, known to regulate HDAC1, {beta}-catenin, and mTORC1, key regulators of myelination and neuronal differentiation in the PNS. To explore KCTD11s role in the PNS, we used a constitutive Kctd11-/- mouse model and the derived in vitro myelin model of sensory neuron and Schwann cell co-culture (DRGN/SC), to mimic the loss-of-function induced by patient mutations. We first demonstrate that the loss of KCTD11 is due to enhanced degradation of the mutated protein via autophagy. Both in vitro and in vivo, we demonstrate abnormal myelination in vivo and altered myelination dynamics in vitro. These defects were associated with dysregulation of the expression of key transcription factors in Schwann cells, such as Egr2 and Sox10, along with other myelin-related genes, as revealed by mRNA-sequencing data. Regarding pathophysiological mechanisms, we identified dysregulation of HDAC1 expression, as well as alterations in the Wnt/{beta}-catenin, Sonic Hedgehog and Hippo/YAP signaling pathways. The deregulation of these pathways seem to converge to altered autophagy and altered balance between proliferation, differentiation and apoptosis, at least in Schwann cells. These mechanisms remain to be explored in axons from PNS neurons. Altogether, our results identify KCTD11 as a novel gene defective in autosomal recessive intermediate RI-CMTE and highlight the key role of KCTD11 in maintaining myelin homeostasis through regulation of HDAC1 and phosphorylated {beta}-catenin levels, thereby preventing late-onset myelin abnormalities and degradation.

genetics↗

bioRxiv2025

Comprehensive Multimodal Profiling of Atherosclerosis Reveals Bhlhe40 as a Potential Regulator of Vascular Smooth Muscle Cell Phenotypic Modulation

BackgroundVascular smooth muscle cells (VSMCs) play a central role in atherosclerosis by undergoing phenotypic modulation from a quiescent, contractile state to a range of synthetic phenotypes, including fibroblast-like, macrophage-like, and lipid-laden foam cell-like states. However, a comprehensive multimodal characterization and understanding of the transcriptional programs driving these transitions remain incomplete. MethodsTo comprehensively define the phenotypic diversity of VSMCs during atherosclerosis progression, we performed in-depth profiling using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and bulk RNA sequencing in a VSMC lineage-tracing atherosclerotic mouse model. Insights from these datasets guided the design of targeted in vitro experiments to investigate candidate regulatory mechanisms. ResultsSingle-cell multi-omics revealed extensive cellular heterogeneity within atherosclerotic plaques, including a rare population of VSMC-derived macrophage-like cells, whose presence was confirmed by histological analysis. These studies also identified a substantial population of VSMC-derived foam cells, comprising approximately 70% of all foam cells in the lesions. These cells exhibited activation of gene programs associated with lipid metabolism, proliferation, and tumor-like features. The transcription factor Bhlhe40 emerged as a key regulator of this phenotypic transition, with elevated expression in VSMC-derived foam cells during disease progression. Functional knockdown of Bhlhe40 suppressed VSMC phenotypic switching and foam cell characteristics, underscoring its potential role as a driver of VSMC modulation. ConclusionsThese findings advance our understanding of VSMC phenotypic modulation in atherosclerosis and highlight Bhlhe40 as a key regulator of this process. Elucidating the mechanisms governing VSMC plasticity may offer new therapeutic opportunities to reduce cardiovascular risk by targeting disease-driving cellular transitions.

molecular biology↗

bioRxiv2025

Single cell spatial transcriptomics integration deciphers the morphological heterogeneity of atherosclerotic carotid arteries

The process of arterial atherosclerosis is characterised by accumulation of lipids and fibrous material with accompanying inflammation. As plaques progress, they restrict blood flow and cause rupture, which results in life threatening organ ischemia and dysfunction. Although extensively studied, a clear understanding of plaque heterogeneity and mechanisms that trigger their destabilization remains elusive. Our study reveals the molecular microarchitecture of human carotid artery plaques, using bulk and single-cell RNA sequencing combined with single cell spatial transcriptomics, for which we present optimized cell segmentation algorithms. We identified distinct plaque morphologies linked to different cell type compositions, impacting early and advanced lesion formation, as well as destabilization. Spatial transcriptomics enabled us further to determine an inflammatory smooth muscle cell subtype, localize regions of neovascularization, and assign hotspots for macrophage activity within distinct cellular neighbourhoods across lesions. For different macrophage substates, we propose gradual and locally contained transdifferentiation of subluminal inflammatory HMOX1+ macrophages into a lipid-handling TREM2+ phenotype within border zones of the fibrous cap and necrotic core. Our findings provide insight into the complex heterogeneity of human atherosclerosis by unravelling location and proximity of different mural and immune cell substates involved in plaque progression and vulnerability.

cell biology↗

bioRxiv2025

PRDM16 controls smooth muscle cell fate in atherosclerosis

Vascular smooth muscle cells (SMCs) normally exist in a contractile state but can undergo fate switching to produce various cell phenotypes in response to pathologic stimuli1-3. In atherosclerosis, these phenotypically modulated SMCs regulate plaque composition and influence the risk of major adverse cardiovascular events4,5. We found that PRDM16, a transcription factor that is genetically associated with cardiovascular disease, is highly expressed in arterial SMCs and downregulated during SMC fate switching in human and mouse atherosclerosis. Loss of Prdm16 in SMCs of mice activates a synthetic modulation program under homeostatic conditions. Single cell analyses show that loss of Prdm16 drives a synthetic program in all SMC populations. Upon exposure to atherogenic stimuli, SMC-selective Prdm16 deficient mice develop SMC-rich, fibroproliferative plaques that contain few foam cells. Acute loss of Prdm16 results in the formation of collagen-rich lesions with thick fibrous caps. Reciprocally, increasing PRDM16 expression in SMCs blocks synthetic processes, including migration, proliferation, and fibrosis. Mechanistically, PRDM16 binds to chromatin and decreases activating histone marks at synthetic genes. Altogether, these results define PRDM16 as a critical determinant of SMC identity and atherosclerotic lesion composition.

molecular biology↗

bioRxiv2025

Single-Cell Multimodal Profiling Reveals a Novel CD26+ Fibroblast Subpopulation in Atherosclerosis

BackgroundAtherosclerosis involves complex interactions between lipids, immune cells, vascular smooth muscle cells (VSMCs), and fibroblasts within the arterial wall. While significant advances in single-cell technologies have shed light on the roles of immune cells and VSMCs in plaque development, fibroblasts remain underexplored, leaving critical gaps in understanding their contributions to disease progression and plaque stability. Comprehensive characterization of fibroblast phenotypes in atherosclerosis is essential to unravel their diverse functions and to distinguish between subsets that may play protective versus pathogenic roles in the disease process. MethodsHere, we utilized CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) to comprehensively profile fibroblast diversity in a mouse model of atherosclerosis. Mice were fed an atherogenic diet for 0, 8, 19, and 26 weeks, representing distinct stages of disease progression, enabling a detailed phenotypic characterization of fibroblasts throughout the course of atherosclerosis development. ResultsWe identified four distinct fibroblast subpopulations, including a myofibroblast population closely resembling VSMC-derived chondromyocytes. The proportions of these fibroblast subsets exhibited a modest decline as atherosclerosis progressed. Through multimodal analysis, we identified CD26 as a highly expressed and specific marker for one of these fibroblast subpopulations, distinguishing it from other subsets. Using a combination of flow cytometry and immunohistochemistry, we demonstrated that CD26+ fibroblasts predominantly reside in the adventitia of healthy arteries. During atherosclerosis progression, these cells expand into the intima and primarily localize within the fibrous cap of the lesion. ConclusionsOur multi-omic analysis highlights the phenotypic diversity and dynamic changes of fibroblasts during atherosclerosis progression. Among these, CD26+ fibroblasts emerge as a distinct subpopulation that expands within atherosclerotic lesions and may play a critical role in promoting plaque stability through their migration into the fibrous cap.

genomics↗

bioRxiv2024

Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology

Cryptococcus neoformans is the most common cause of fungal meningitis and the top-ranked W.H.O. priority fungal pathogen. Only distantly related to model fungi, C. neoformans is also a powerful experimental system for exploring conserved eukaryotic mechanisms lost from specialist model yeast lineages. To decipher its biology globally, we constructed 4328 gene deletions and measured--with exceptional precision--the fitness of each mutant under 141 diverse growth-limiting in vitro conditions and during murine infection. We defined functional modules by clustering genes based on their phenotypic signatures. In-depth studies leveraged these data in two ways. First, we defined and investigated new components of key signaling pathways, which revealed animal-like pathways/components not predicted from studies of model yeasts. Second, we identified environmental adaptation mechanisms repurposed to promote mammalian virulence by C. neoformans, which lacks a known animal reservoir. Our work provides an unprecedented resource for deciphering a deadly human pathogen.

microbiology↗

bioRxiv2024

Single-cell multimodal profiling of monocytes reveals diverse phenotypes and alterations linked to cardiovascular disease risks

Monocytes are a critical innate immune system cell type that serves homeostatic and immunoregulatory functions. The Cell surface expression of CD14 and CD16 has historically identified them, however, recent single-cell studies have uncovered that they are much more heterogeneous than previously realized. We utilized cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-cell RNA sequencing (scRNA-seq) to describe the comprehensive transcriptional and phenotypic landscape of 437,126 monocytes. This high-dimensional multimodal approach identified vast phenotypic diversity and functionally distinct subsets, including IFN-responsive, MHCIIhi, monocyte-platelet aggregates, and non-classical, as well as several subpopulations of classical monocytes. Using flow cytometry, we validated the existence of MHCII+CD275+ MHCIIhi, CD42b+ monocyte-platelet aggregates, CD16+CD99- non-classical monocytes, and CD99+ classical monocytes. Each subpopulation exhibited unique functions, developmental trajectories, transcriptional regulation, and tissue distribution. Moreover, we revealed alterations associated with cardiovascular disease (CVD) risk factors, including race, smoking, and hyperlipidemia, and the effect of hyperlipidemia was recapitulated in mouse models of elevated cholesterol. This integrative and cross-species comparative analysis provides a unique resource to compare alterations in monocytes in pathological conditions and offers insights into monocyte-driven mechanisms in CVD and the potential for targeted therapies. SummaryMultimodal profiling provides a comprehensive phenotypic and transcriptional understanding of monocytes in health and cardiovascular disease risk states.

genomics↗

bioRxiv2023

Hypoxic volatile metabolic markers in the MDA-MB-231 breast cancer cell line

Hypoxia in disease describes persistent low oxygen conditions, observed in a range of pathologies, including cancer. In the discovery of biomarkers in biological models, pathophysiological traits present a source of translatable metabolic products for the diagnosis of disease in humans. Part of the metabolome is represented by its volatile, gaseous fraction; the volatilome. Human volatile profiles, such as those found in breath, are able to diagnose disease, however accurate volatile biomarker discovery is required to target reliable biomarkers to develop new diagnostic tools. Using custom chambers to control oxygen levels and facilitate headspace sampling, the MDA-MB-231 breast cancer cell line was exposed to hypoxia (1% oxygen) for 24 hours. The maintenance of hypoxic conditions in the system was successfully validated over this time period. Targeting and non-targeting gas chromatography mass spectrometry approaches revealed four significantly altered volatile organic compounds when compared to control cells. Three compounds were actively consumed by cells: methyl chloride, acetone and n-Hexane. Cells under hypoxia also produced significant amounts of styrene. This work presents a novel methodology for identification of volatile metabolisms under controlled gas conditions with novel observations of volatile metabolisms by breast cancer cells.

cell biology↗

bioRxiv2022

Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte

BackgroundHuman heart failure is characterized by global alterations in the myocardial DNA methylation profile, yet little is known about epigenetic regulation of non-coding transcripts and potential reversibility of DNA methylation with left ventricular assist device (LVAD) support. MethodGenome-wide mapping of myocardial DNA methylation was performed in 36 patients with end-stage heart failure at the time of LVAD implant, 8 patients at the time of LVAD explant, and 7 non-failing controls using high-density bead array platform. Transcriptomic and functional studies were performed in human induced pluripotent stem cell derived cardiomyocytes (iPSCs). ResultsEtiology-specific analysis revealed 2079 differentially methylated positions (DMPs) in ischemic cardiomyopathy (ICM) and 261 DMPs in non-ischemic cardiomyopathy (NICM). 192 DMPs were common to ICM and NICM. Analysis of paired samples before and after LVAD support demonstrated reverse methylation of only 3.2% of HF-specific DMPs. Methylation-expression correlation analysis yielded several protein-coding genes that are hypomethylated and upregulated (HTRA1, FAM65A, FBXO16, EFCAB13, AKAP13, RPTOR) or hypermethylated and downregulated (TBX3) in ICM and NICM patients. A novel cardiac-specific super-enhancer lncRNA (LINC00881) is hypermethylated and downregulated in the failing human heart. LINC00881 is an upstream regulator of sarcomere and calcium channel gene expression including MYH6, CACNA1C, and RYR2. LINC00881 knockdown significantly reduced peak calcium amplitude in the beating human iPSCs. ConclusionsFailing human heart exhibits etiology-specific changes in DNA methylation including coding and non-coding regions, which are minimally reversible with mechanical unloading. Epigenetic reprogramming may be necessary to achieve transcriptional normalization and sustained clinical recovery from heart failure.

genomics↗

bioRxiv2021

A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation

cAMP signaling pathways are critical for both oncogenesis and tumor suppression. cAMP signaling is localized to multiple spatially distinct microdomains, but the role of cAMP microdomains in cancer cell biology is poorly understood. We developed a tunable genetic system that allows us to activate cAMP signaling in specific microdomains. We uncovered a previously unappreciated nuclear cAMP microdomain that functionally activates a tumor suppressive pathway in a broad range of cancers by inhibiting YAP, a key effector protein of the Hippo pathway, inside the nucleus. We show that nuclear cAMP induces a LATS-dependent pathway leading to phosphorylation of nuclear YAP solely at serine 397, export of YAP from the nucleus, without YAP protein degradation. Thus, nuclear cAMP inhibition of nuclear YAP is distinct from other known mechanisms of Hippo regulation. Pharmacologic targeting of specific cAMP microdomains remains an untapped therapeutic approach for cancer, and since Hippo pathway deregulation can lead to oncogenesis and chemotherapeutic resistance, drugs directed at the nuclear cAMP microdomain may provide new avenues for the treatment of cancer.

cancer biology↗

bioRxiv2021

Bisphenol S and bisphenol F are less disruptive to cardiac electrophysiology and potentially safer for use in medical products, as compared to bisphenol A

BackgroundBisphenol A (BPA) is a high-production volume chemical that is commonly used to manufacture consumer and medical-grade plastic products. Due to its ubiquity, the general population can incur daily environmental exposure to BPA, while heightened BPA exposure has been reported in intensive care patients and industrial workers. Due to health concerns, structural analogues are being explored as replacements for BPA. ObjectiveThis study aimed to examine the direct nongenomic effects of BPA on cardiac electrophysiology and compare its safety profile to recently developed alternatives, including BPS (bisphenol S) and BPF (bisphenol F). MethodsWhole-cell voltage-clamp recordings were performed on cell lines transfected with Nav1.5, hERG, or Cav1.2. Results of single channel experiments were validated by conducting electrophysiology studies on human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) and intact, whole heart preparations. ResultsOf the chemicals tested, BPA was the most potent inhibitor of both fast (INa-P) and late (INa-L) sodium channel (IC50 = 55.3 and 23.6 M, respectively), L-type calcium channel (IC50 = 30.8 M) and hERG channel current (IC50 = 127 M). The inhibitory effects of BPA and BPF on L-type calcium channels were supported by microelectrode array recordings, which revealed shortening of the extracellular field potential (akin to QT interval). Further, BPA and BPF exposure impaired atrioventricular conduction in intact, whole heart experiments. BPS did not alter any of the cardiac electrophysiology parameters tested. DiscussionResults of this study demonstrate that BPA and BPF exert an immediate inhibitory effect on cardiac ion channels, and that BPS may be a safer alternative. Intracellular signaling or genomic effects of bisphenol analogues were not investigated; therefore, additional mechanistic studies are necessary to fully elucidate the safety profile of bisphenol analogues on the heart.

pharmacology and toxicology↗

bioRxiv2020

Brazilin Removes Toxic alpha-Synuclein and Seeding Competent Assemblies from Parkinson Brain by Altering Conformational Equilibrium

Alpha-synuclein (-syn) fibrils, a major constituent of the neurotoxic Lewy Bodies in Parkinsons disease, form via nucleation dependent polymerization and can replicate by a seeding mechanism. Brazilin, a small molecule derived from red cedarwood trees in Brazil, has been shown to inhibit the fibrillogenesis of amyloid-beta (A{beta}) and -syn, prompting our inquiry in its mechanism of action. Here we test the effects of Brazilin on both seeded and unseeded -syn fibril formation and show that the natural polyphenol inhibits fibrillogenesis of -syn by a unique mechanism that is distinct from other polyphenols and is also distinct from its effect on A{beta}. Brazilin preserves the natively unfolded state of -syn by stabilizing the compact conformation of the -syn monomer over the aggregation-competent extended conformation. Molecular docking of Brazilin shows the molecule to interact both with unfolded -syn monomers and with the cross-{beta} sheet structure of -syn fibrils. Brazilin eliminates seeding competence of -syn assemblies from Parkinsons disease patient brain tissue, and treatment of pre-formed fibril assemblies with Brazilin significantly reduces their toxicity in primary neurons. Our findings suggest that Brazilin has substantial potential as a neuroprotective and therapeutic agent for Parkinsons Disease. Highlights- The natural polyphenol Brazilin binds to monomeric, oligomeric and fibrillar -syn - Brazilin shifts the equilibrium away from aggregation-competent monomer conformations - Brazilin inactivates seeding-competent -syn isolated from Parkinson patients brains - Brazilin detoxifies -syn aggregation intermediates and stabilizes mature amyloid fibrils Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=117 HEIGHT=200 SRC="FIGDIR/small/318220v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@447629org.highwire.dtl.DTLVardef@a9871dorg.highwire.dtl.DTLVardef@1e5a83dorg.highwire.dtl.DTLVardef@8843eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

A Joint Deep Learning Model for Simultaneous Batch Effect Correction, Denoising and Clustering in Single-Cell Transcriptomics

Recent development of single-cell RNA-seq (scRNA-seq) technologies has led to enormous biological discoveries. As the scale of scRNA-seq studies increases, a major challenge in analysis is batch effect, which is inevitable in studies involving human tissues. Most existing methods remove batch effect in a low-dimensional embedding space. Although useful for clustering, batch effect is still present in the gene expression space, leaving downstream gene-level analysis susceptible to batch effect. Recent studies have shown that batch effect correction in the gene expression space is much harder than in the embedding space. Popular methods such as Seurat3.0 rely on the mutual nearest neighbor (MNN) approach to remove batch effect in the gene expression space, but MNN can only analyze two batches at a time and it becomes computationally infeasible when the number of batches is large. Here we present CarDEC, a joint deep learning model that simultaneously clusters and denoises scRNA-seq data, while correcting batch effect both in the embedding and the gene expression space. Comprehensive evaluations spanning different species and tissues showed that CarDEC consistently outperforms scVI, DCA, and MNN. With CarDEC denoising, those non-highly variable genes offer as much signal for clustering as the highly variable genes, suggesting that CarDEC substantially boosted information content in scRNA-seq. We also showed that trajectory analysis using CarDECs denoised and batch corrected expression as input revealed marker genes and transcription factors that are otherwise obscured in the presence of batch effect. CarDEC is computationally fast, making it a desirable tool for large-scale scRNA-seq studies.

bioinformatics↗