Biology subjects

Noble, W.

Publications and source records attributed to Noble, W..

At least 19 recordsLinked to original sources

bioRxiv2025

Proteomic Analysis Links Truncated Tau to Lysosome Motility, Autophagy and Endo-lysosomal Dysfunction

Tauopathies are characterized by the progressive accumulation of abnormal tau species, which disrupt the autophagy-lysosomal pathway (ALP), a critical system for degrading intracellular macromolecules and aggregated proteins, causing toxicity and cell death. This study investigates the impact of the N-terminally truncated Tau35 protein overexpression on proteolytic pathways, including effects on autophagy and endo-lysosomal processes. Using a Tau35 mouse model and SH-SY5Y cell lines stably expressing either the Tau35 fragment or full-length tau, we employed western blotting, proteomic analysis of lysosome-enriched brain fractions, proteolysis/endocytosis assays, and live-cell imaging with the lysotracker reporter to assess protein degradation and lysosomal function. Our findings identify early pathological changes in endo-lysosomal processes, including increased endocytosis, proteolytic dysfunction and lysosomal motility abnormalities, associated with Tau35-induced toxicity. This work extends previous research by providing new insights into the mechanisms of Tau35-induced neurotoxicity, offering a foundation for developing targeted therapeutic strategies to address tauopathies.

neuroscience↗

bioRxiv2024

Properties of Alzheimers disease brain-derived tau aggregates define tau processing by human astrocytes.

The templated misfolding of tau proteins accounts for tau pathology spread in Alzheimers disease (AD). Post-translational modifications, including phosphorylation at specific residues, are closely linked with tau seeding ability and clinical disease progression. Increasing evidence supports a contributing role for astrocytes in tau spread. This study demonstrates that tau aggregates from postmortem AD brain are internalized and processed by human astrocytes. Differences in the efficiency of tau internalization, clearance and/or seeding were noted, which may reflect molecular properties of tau. Notably, we observed a direct relationship between alterations in tau handling by astrocytes and astrocyte responses, which were evident in transcriptomic data. Dysregulated genes include several previously identified as upregulated in reactive astrocytes in AD brain, as well as being implicated in pathological tau clearance by autophagy and other pathways. The study provides new insights into the complex interplay between tau molecular diversity and astrocyte responses in AD.

neuroscience↗

bioRxiv2023

Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types

The human genome contains millions of candidate cis-regulatory elements (CREs) with cell-type-specific activities that shape both health and myriad disease states. However, we lack a functional understanding of the sequence features that control the activity and cell-type-specific features of these CREs. Here, we used lentivirus-based massively parallel reporter assays (lentiMPRAs) to test the regulatory activity of over 680,000 sequences, representing a nearly comprehensive set of all annotated CREs among three cell types (HepG2, K562, and WTC11), finding 41.7% to be functional. By testing sequences in both orientations, we find promoters to have significant strand orientation effects. We also observe that their 200 nucleotide cores function as non-cell-type-specific on switches providing similar expression levels to their associated gene. In contrast, enhancers have weaker orientation effects, but increased tissue-specific characteristics. Utilizing our lentiMPRA data, we develop sequence-based models to predict CRE function with high accuracy and delineate regulatory motifs. Testing an additional lentiMPRA library encompassing 60,000 CREs in all three cell types, we further identified factors that determine cell-type specificity. Collectively, our work provides an exhaustive catalog of functional CREs in three widely used cell lines, and showcases how large-scale functional measurements can be used to dissect regulatory grammar.

genomics↗

bioRxiv2023

Proteomics of the astrocyte secretome reveals changes in their response to soluble oligomeric Abeta

Astrocytes associate with amyloid plaques in Alzheimers disease (AD). Astrocytes react to changes in the brain environment, including to increasing concentrations of amyloid-{beta} (A{beta}). However, the precise response of astrocytes to soluble small A{beta} oligomers at concentrations similar to those present in the human brain has not been addressed. In this study, we exposed astrocytes to neuronal media containing soluble human A{beta} oligomers and used proteomics to investigate changes in the astrocyte secretome. Our data shows dysregulated secretion of astrocytic proteins involved in the extracellular matrix and cytoskeletal organization and increase secretion of proteins involved in oxidative stress responses and those with chaperone activity. Several of these proteins have been identified in previous transcriptomic and proteomic studies using brain tissue from human AD and cerebrospinal fluid (CSF). Our work highlights the relevance of studying astrocyte secretion to understand the brain response to AD pathology and the potential use of these proteins as biomarkers for the disease.

neuroscience↗

bioRxiv2021

Astrocytic C-X-C motif chemokine ligand-1 mediates β-amyloid-induced tau mislocalization and synaptotoxicity

BackgroundPathological interactions between {beta}-amyloid (A{beta}) and tau drive the synapse loss that underlies neural circuit disruption and cognitive decline in Alzheimers disease (AD). Reactive astrocytes, displaying altered functions, are also a prominent feature of AD brain. This large and heterogeneous population of cells are increasingly recognised as contributing to early phases of disease. However, the contribution of astrocytes to detrimental A{beta}-tau interactions in AD is not well understood. MethodsMouse and human astrocyte cultures were stimulated with concentrations and species of human A{beta} that mimic those in human AD brain. Astrocyte conditioned medium was collected and immunodepleted of A{beta} before being added to rodent or human neuron cultures. Cytokines, identified in unbiased screens were also applied to neurons, including following the pre-treatment of neurons with chemokine receptor antagonists. Tau mislocalisation, synaptic markers and dendritic spine numbers were measured in cultured neurons and organotypic brain slice cultures. ResultsConditioned medium from astrocytes stimulated with A{beta} induces tau mislocalisation and exaggerated synaptotoxicity that is recapitulated following spiking of neuron culture medium with recombinant C-X-C motif chemokine ligand-1 (CXCL1), a chemokine we show to be upregulated in Alzheimers disease brain. Antagonism of neuronal C-X-C motif chemokine receptor 2 (CXCR2) prevented tau mislocalisation and synaptotoxicity in response to CXCL1 and A{beta}-stimulated astrocyte secretions. ConclusionsOur data indicate that astrocytes exacerbate tau mislocalisation and the synaptotoxic effects of A{beta} via interactions of astrocytic CXCL1 and neuronal CXCR2 receptors, highlighting this chemokine-receptor pair as a novel target for therapeutic intervention in AD.

neuroscience↗

bioRxiv2020

Synaptic dysfunction caused by truncated tau is associated with hyperpolarization-activated cyclic nucleotide-gated channelopathy

Progressive neurodegeneration in tauopathies is mediated through an elusive mechanism. Here, we show that hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are functionally linked to disease-associated abnormalities in tau. Selective rises in the proportion of HCN-positive neurons are detected both in post-mortem human brain from Alzheimers disease and in the Tau35 mouse model of tauopathy. Tau35 mice develop progressive abnormalities including increased phosphorylated tau, enhanced HCN channel expression and decreased dendritic branching, as well as reduced synapse density that is accompanied by vesicle clustering defects. Notably, altered spine density and increased HCN channel expression in Tau35 neurons correlates with functional abnormalities in network properties, including enhanced hyperpolarization-induced membrane voltage sag and changes in the frequency and kinetics of spontaneous excitatory postsynaptic currents. Our findings are consistent with pathological changes in tauopathies impacting on HCN channels to drive network-wide structural and functional synaptic deficits, providing new targets for therapeutic intervention.

neuroscience↗

bioRxiv2020

Tau accumulates in Crohn's disease gut

A sizeable body of evidence has recently emerged to suggest that gastrointestinal inflammation might be involved in the development of Parkinsons disease. There is now strong epidemiological and genetical evidence linking Parkinsons disease to inflammatory bowel diseases and we recently demonstrated that the neuronal protein alpha-synuclein, which is critically involved in Parkinsons disease pathophysiology, is upregulated in inflamed segments of Crohns colon. The microtubule associated protein tau is another neuronal protein critically involved in neurodegenerative disorders but, in contrast to alpha-synuclein, no data are available about its expression and phosphorylation patterns in inflammatory bowel diseases. Here, we examined the expression levels of tau isoforms, their phosphorylation profile and truncation in colon biopsy specimens from 16 Crohns disease and 6 ulcerative colitis patients and compared them to samples from 16 controls. Additional experiments were performed in full thickness segments of colon of 5 Crohns disease and 5 control subjects, in primary cultures of rat enteric neurons and in Nrf2 knockout mice. Our results show the upregulation of two main human tau isoforms in the enteric nervous system in Crohns disease but not in ulcerative colitis. This upregulation was not transcriptionally regulated but instead likely resulted from a decrease in protein clearance via an Nrf2 pathway. Our findings, which provide the first detailed characterization of tau in Crohns disease, suggest that the key proteins involved in neurodegenerative disorders such as alpha-synuclein and tau, might also play a role in Crohns disease.

neuroscience↗

bioRxiv2019

Measuring significant changes in chromatin conformation with ACCOST

Chromatin conformation assays such as Hi-C cannot directly measure differences in 3D architecture between cell types or cell states. For this purpose, two or more Hi-C experiments must be carried out, but direct comparison of the resulting Hi-C matrices is confounded by several features of Hi-C data. Most notably, the genomic distance effect, whereby contacts between pairs of genomic loci that are proximal along the chromosome exhibit many more Hi-C contacts that distal pairs of loci, dominates every Hi-C matrix. Furthermore, the form that this distance effect takes often varies between different Hi-C experiments, even between replicate experiments. Thus, a statistical confidence measure designed to identify differential Hi-C contacts must accurately account for the genomic distance effect or risk being misled by large-scale but artifactual differences. ACCOST (Altered Chromatin Conformation STatistics) accomplishes this goal by extending the statistical model employed by DEseq, re-purposing the \"size factors,\" which were originally developed to account for differences in read depth between samples, to instead model the genomic distance effect. We show via analysis of simulated and real data that ACCOST provides unbiased statistical confidence estimates that compare favorably with competing methods such as diffHiC, FIND, and HiCcompare. ACCOST is freely available with an Apache license at https://bitbucket.org/noblelab/accost.

genomics↗

bioRxiv2019

Loss of the Alzheimer’s-linked bridging integrator 1 (BIN1) protein affects synaptic structure and disrupts tau localisation and release

BackgroundPost-translational modifications of tau modify its interaction with binding partners and cause tau mislocalisation and altered tau function in Alzheimers disease (AD). The AD risk gene BIN1, is a binding partner for tau, however the mechanism by which BIN1 influences tau function is not fully understood. We hypothesised that BIN1 modulates AD risk by causing damaging tau mis-sorting to the synapse.\n\nMethodsTau and BIN1 levels, distribution and interactions were assessed in post-mortem control and AD brain and in primary neurons. In primary neurons, tau was further examined using structured illumination microscopy and immunoblotting following BIN1 knockdown, BIN1-tau interactions were examined using proximity ligation assays and tau release from neurons was measured by sensitive sandwich ELISA.\n\nResultsProline 216 in tau was identified as critical for tau interaction with the BIN1-SH3 domain, and tau phosphorylation at serine/threonine residues disrupted this interaction. Subcellular fractionation showed that BIN1 is lost from the cytoplasm of AD brain and this correlated with the mislocalisation of phosphorylated tau to synapses. Mimicking BIN1 loss in AD by knockdown of the protein in primary neurons altered the structure of dendritic spines, caused phosphorylated tau to mis-sort to synapses and reduced the physiological release of predominantly dephosphorylated tau.\n\nConclusionsThese data suggest that BIN1 loss in AD allows phosphorylated tau to be mis-sorted to synapses which likely alters the integrity of the post-synapse, alongside reducing the functionally important release of physiological forms of tau.

neuroscience↗

bioRxiv2019

Inferring diploid 3D chromatin structures from Hi-C data

The 3D organization of the genome plays a key role in many cellular processes, such as gene regulation, differentiation, and replication. Assays like Hi-C measure DNA-DNA contacts in a high-throughput fashion, and inferring accurate 3D models of chromosomes can yield insights hidden in the raw data. For example, structural inference can account for noise in the data, disambiguate the distinct structures of homologous chromosomes, orient genomic regions relative to nuclear landmarks, and serve as a framework for integrating other data types. Although many methods exist to infer the 3D structure of haploid genomes, inferring a diploid structure from Hi-C data is still an open problem. Indeed, the diploid case is very challenging, because Hi-C data typically does not distinguish between homologous chromosomes. We propose a method to infer 3D diploid genomes from Hi-C data. We demonstrate the accuarcy of the method on simulated data, and we also use the method to infer 3D structures for mouse chromosome X, confirming that the active homolog exhibits a bipartite structure, whereas the active homolog does not.

bioinformatics↗

bioRxiv2019

Jointly embedding multiple single-cell omics measurements

Many single-cell sequencing technologies are now available, but it is still difficult to apply multiple sequencing technologies to the same single cell. In this paper, we propose an unsupervised manifold alignment algorithm, MMD-MA, for integrating multiple measurements carried out on disjoint aliquots of a given population of cells. Effectively, MMD-MA performs an in silico co-assay by embedding cells measured in different ways into a learned latent space. In the MMD-MA algorithm, single-cell data points from multiple domains are aligned by optimizing an objective function with three components: (1) a maximum mean discrepancy (MMD) term to encourage the differently measured points to have similar distributions in the latent space, (2) a distortion term to preserve the structure of the data between the input space and the latent space, and (3) a penalty term to avoid collapse to a trivial solution. Notably, MMD-MA does not require any correspondence information across data modalities, either between the cells or between the features. Furthermore, MMD-MAs weak distributional requirements for the domains to be aligned allow the algorithm to integrate heterogeneous types of single cell measures, such as gene expression, DNA accessibility, chromatin organization, methylation, and imaging data. We demonstrate the utility of MMD-MA in simulation experiments and using a real data set involving single-cell gene expression and methylation data.

bioinformatics↗

bioRxiv2019

Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

MotivationRecent efforts to describe the human epigenome have yielded thousands of uniformly processed epigenomic and transcriptomic data sets. These data sets characterize a rich variety of biological activity in hundreds of human cell lines and tissues ("biosamples"). Understanding these data sets, and specifically how they differ across biosamples, can help explain many cellular mechanisms, particularly those driving development and disease. However, due primarily to cost, the total number of assays that can be performed is limited. Previously described imputation approaches, such as Avocado, have sought to overcome this limitation by predicting genome-wide epigenomics experiments using learned associations among available epigenomic data sets. However, these previous imputations have focused primarily on measurements of histone modification and chromatin accessibility, despite other biological activity being crucially important. ResultsWe applied Avocado to a data set of 3,814 tracks of data derived from the ENCODE compendium, spanning 400 human biosamples and 84 assays. The resulting imputations cover measurements of chromatin accessibility, histone modification, transcription, and protein binding. We demonstrate the quality of these imputations by comprehensively evaluating the models predictions and by showing significant improvements in protein binding performance compared to the top models in an ENCODE-DREAM challenge. Additionally, we show that the Avocado model allows for efficient addition of new assays and biosamples to a pre-trained model, achieving high accuracy at predicting protein binding, even with only a single track of training data. AvailabilityTutorials and source code are available under an Apache 2.0 license at https://github.com/jmschrei/avocado. Contactwilliam-noble@uw.edu or jmschr@cs.washington.edu

bioinformatics↗

bioRxiv2018

Detecting modifications in proteomics experiments with Param-Medic

Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in re-analysis of public data sets, this experimental metadata may be missing or inaccurate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling, tandem mass tags, and phosphorylation, directly from a given set of mass spectra. We demonstrate the sensitivity and specificity of the proposed approach, and we provide open source Python and C++ implementations in a new version of the software tool Param-Medic.

bioinformatics↗

bioRxiv2018

An averaging strategy to reduce variability in target-decoy estimates of false discovery rate

Decoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR) associated with spectrum identifications from shotgun proteomics data. However, the procedure can yield different results for a fixed dataset analyzed with different decoy databases, and this decoy-induced variability is particularly problematic for smaller FDR thresholds, datasets or databases. In such cases, the nominal FDR might be 1% but the true proportion of false discoveries might be 10%. The averaged TDC protocol combats this problem by exploiting multiple independently shuffled decoy databases to provide an FDR estimate with reduced variability. We provide a tutorial introduction to aTDC, describe an improved variant of the protocol that offers increased statistical power, and discuss how to deploy aTDC in practice using the Crux software toolkit.

bioinformatics↗

bioRxiv2018

Predicting gene expression in the human malaria parasite Plasmodium falciparum

Empirical evidence suggests that the malaria parasite Plasmodium falciparum employs a broad range of mechanisms to regulate gene transcription throughout the organisms complex life cycle. To better understand this regulatory machinery, we assembled a rich collection of genomic and epigenomic data sets, including information about transcription factor (TF) binding motifs, patterns of covalent histone modifications, nucleosome occupancy, GC content, and global 3D genome architecture. We used these data to train machine learning models to discriminate between high-expression and low-expression genes, focusing on three distinct stages of the red blood cell phase of the Plasmodium life cycle. Our results highlight the importance of histone modifications and 3D chromatin architecture and suggest a relatively small role for TF binding in Plasmodium transcriptional regulation.

genomics↗

bioRxiv2018

Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data

To achieve accurate assignment of peptide sequences to observed fragmentation spectra, a shotgun proteomics database search tool must make good use of the very high resolution information produced by state-of-the-art mass spectrometers. However, making use of this information while also ensuring that the search engines scores are well calibrated--i.e., that the score assigned to one spectrum can be meaningfully compared to the score assigned to a different spectrum--has proven to be challenging. Here, we describe a database search score function, the \"residue evidence\" (res-ev) score, that achieves both of these goals simultaneously. We also demonstrate how to combine calibrated res-ev scores with calibrated XCorr scores to produce a \"combined p-value\" score function. We provide a benchmark consisting of four mass spectrometry data sets, which we use to compare the combined p-value to the score functions used by several existing search engines. Our results suggest that the combined p-value achieves state-of-the-art performance, generally outperforming MS Amanda and Morpheus and performing comparably to MS-GF+. The res-ev and combined p-value score functions are freely available as part of the Tide search engine in the Crux mass spectrometry toolkit (http://crux.ms).

bioinformatics↗

bioRxiv2018

Unsupervised embedding of single-cell Hi-C data

Single-cell Hi-C (scHi-C) data promises to enable scientists to interrogate the 3D architecture of DNA in the nucleus of the cell, studying how this structure varies stochastically or along developmental or cell cycle axes. However, Hi-C data analysis requires methods that take into account the unique characteristics of this type of data. In this work, we explore whether methods that have been developed previously for the analysis of bulk Hi-C data can be applied to scHi-C data. In this work, we apply methods designed for analysis of bulk Hi-C data to scHi-C data in conjunction with unsupervised embedding. We find that one of these methods, HiCRep, when used in conjunction with multidimensional scaling (MDS), strongly outperforms three other methods, including a technique that has been used previously for scHi-C analysis. We also provide evidence that the HiCRep/MDS method is robust to extremely low per-cell sequencing depth, that this robustness is improved even further when high-coverage and low-coverage cells are projected together, and that the method can be used to jointly embed cells from multiple published datasets.

bioinformatics↗

bioRxiv2018

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages

The development of malaria parasites throughout their various life cycle stages is controlled by coordinated changes in gene expression. We previously showed that the three-dimensional organization of the P. falciparum genome is strongly associated with gene expression during its replication cycle inside red blood cells. Here, we analyzed genome organization in the P. falciparum and P. vivax transmission stages. Major changes occurred in the localization and interactions of genes involved in pathogenesis and immune evasion, erythrocyte and liver cell invasion, sexual differentiation and master regulation of gene expression. In addition, we observed reorganization of subtelomeric heterochromatin around genes involved in host cell remodeling. Depletion of heterochromatin protein 1 (PfHP1) resulted in loss of interactions between virulence genes, confirming that PfHP1 is essential for maintenance of the repressive center. Overall, our results suggest that the three-dimensional genome structure is strongly connected with transcriptional activity of specific gene families throughout the life cycle of human malaria parasites.

systems biology↗