Biology subjects

Thalassinos, K.

Publications and source records attributed to Thalassinos, K..

18 recordsLinked to original sources

bioRxiv2026

Clathrin differentially adapts its trimerisation domain during mammalian evolution to traffic the insulin-responsive GLUT4 glucose transporter.

In humans, the CHC22 isoform of clathrin regulates glucose metabolism by trafficking the GLUT4 glucose transporter for intracellular storage in skeletal muscle and release following insulin signalling. Some vertebrate lineages have lost the gene encoding CHC22 but operate the same insulin-stimulated GLUT4 trafficking pathway. Here, we show that species lacking CHC22 exclusively produce an alternatively-spliced form of the universally expressed CHC17 clathrin isoform (CHC17-SAS) with a truncated C-terminus similar to CHC22, expressed predominantly in skeletal muscle. Through its trimerisation domain, CHC17-SAS binds the CHC22-specific adaptor SNX5 that enables CHC22's distinct intracellular function. The 2.3 [A] crystal structure of the CHC22 trimerisation domain demonstrates conservation of the core trimeric fold from CHC17 but differences in electrostatic surface charge that may account for their differential properties. Using GLUT4 translocation assays in HeLa cell models, we show that CHC17-SAS is a functional surrogate for CHC22. Identification of CHC17-SAS resolves the evolutionary conundrum posed by CHC22 absence in some vertebrate lineages, and reveals a common mechanism for mammalian GLUT4 trafficking.

cell biology↗

bioRxiv2026

Single-Cell Proteomics Reveals Heterogeneous and Bimodal Proteome Responses to DNA Damage

DNA damage response (DDR) involves coordinated activation of repair, checkpoint, and stress-adaptive signalling pathways following genomic toxicity. Bulk-cell proteomics, however, averages divergent responses across neighbouring cells, obscuring the characterisation of biologically meaningful proteome remodelling during genotoxic stress. This is particularly relevant to DDR, where a subset of cells undergo apoptosis, resulting in the sampling of dead cells that confound downstream biological interpretation. Here, we applied single-cell proteomics (SCP) to investigate the proteome response of U-2 OS cells to 6-thioguanine (6TG)-induced DNA damage. By filtering individual cells according to predefined morphological-, sampling- and biological-criteria, to ensure a matched comparison between control and DNA-damaged populations; 6TG treatment was found to activate canonical DDR, including mismatch repair and base excision repair, together with secondary stress responses linked to oxidative stress, mitochondrial dysfunction, inflammatory signalling and proteostasis. Using SCP, we were able to probe neighbouring cell-to-cell heterogeneity, revealing globally increased protein abundance variability following DNA-damage. Importantly, mismatch repair protein MSH3 exhibited amongst the largest abundance increases, concomitant with the greatest reduction in cell-to-cell abundance heterogeneity across all quantified proteins, highlighting it as the most robust and reproducible responder to 6TG-induced DNA damage. Furthermore, analysis of protein-abundance heterogeneity revealed proteins that exhibit bifurcated abundance states across neighbouring cells, with DNA damage inducing either the emergence or loss of these bimodal abundance distributions. Proteins linked to gene expression and protein synthesis were driven towards bifurcation into discrete high-low protein abundance states across neighbouring cells following DNA-damage. Conversely, 6TG abolished the intrinsic high-low abundance bimodality of several core-signalling, stress-signalling and trafficking proteins, suggesting their coordinated homogenisation in response to genotoxic stress. Collectively, these findings demonstrate the power of SCP to resolve the coordinated, yet heterogeneous, cellular response to DNA damage within a population of genetically identical cells.

cell biology↗

bioRxiv2026

The HMD domain of the PAF complex primes Rad6-Bre1 E3 ligase complexes for H2B ubiquitination

Mono-ubiquitination of histone H2B (H2Bub) is deposited by Bre1-type E3 ubiquitin ligase complexes during transcription elongation and is critical for chromatin organization, DNA repair, and transcription regulation. In S. pombe, this activity is carried out by HULC, a complex of the Bre1 homologs Brl1 and Brl2 with Rhp6 and Shf1. While H2Bub deposition depends on recruitment of HULC to RNA Pol II by the Paf1 complex (PAF1C), the molecular basis for how PAF1C activates HULC has remained unclear. Using AlphaFold modelling, biochemical reconstitution, and functional assays, we define the architecture of HULC as a flexible 1:1:1:1 assembly in which Shf1 stabilizes an elongated coiled-coil hairpin that brings the RING and Rad6-binding domains into proximity. However, for full stimulation of HULC activity, we find that the HMD domain of the PAF1C subunit Prf1 stimulates ubiquitin transfer through a RING-binding region (RBR) that repositions the RING domains adjacent to Rhp6 in a catalytically competent configuration. These findings reveal an activation mechanism in which transcription-associated Prf1 primes HULC for ubiquitin transfer through the Prf1RBR, revealing a critical regulatory interface for H2B ubiquitination.

molecular biology↗

bioRxiv2026

Metformin promotes broad neuroprotection and proteostatic resilience via rngo/DDI2 stabilisation

Alzheimers disease (AD) is one of the most common age-related causes of death, with limited effective disease-modifying treatments. Although metformin shows promise as a disease-modifying agent for AD, its molecular mechanism--specifically how it confers neuroprotection despite potentially increasing amyloid-beta (A{beta}) load--remains obscure. Here, we demonstrate that metformin functions as a pharmacological activator of the ubiquitin-binding protease rngo/DDI2. Through a genetic screen in Drosophila, we identified rngo/DDI2 as a potent suppressor of A{beta} toxicity. We provide in silico and genetic evidence that metformin interacts with the conserved D257 residue of the rngo/DDI2 RVP domain, inducing homodimerisation and subsequent protein stabilisation. This activation boosts proteasome activity in the presence of A{beta} preferentially clearing highly abundant proteins to preserve proteostasis. Crucially, this intervention is broadly effective; rngo/DDI2 upregulation robustly suppresses toxicity in models of TDP-43 and C9orf72-repeat expansion pathology, indicating a generalised mechanism of neuroprotection. Supported by human iPSC data and evidence of DDI2 depletion in AD patient brains, our results identify rngo/DDI2 as a conserved regulator of neuronal resilience. We propose that directly targeting DDI2 stabilisation represents a novel, broadly applicable therapeutic strategy to counteract proteotoxic stress across a broad spectrum of neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Cysteine Glutathionylation as a Global Dynamic Regulator of Protein Active Site Accessibility and Protein Complex Formation

Protein-glutathionylation is traditionally viewed as a protective mechanism that shields cysteine-residues from irreversible oxidative damage. Its broader functional roles remain poorly understood, in part due to technical limitations in detecting this modification at scale. Here, we develop and leverage a new mass-spectrometry approach that preserves protein-glutathionylation, thereby revealing its widespread distribution across the proteome in cell models, worms, mice and human cardiac tissues. In all cases, we find that glutathionylation sites are enriched at both protein-protein interfaces and protein-active sites, and are highly conserved across species. We find that glutathionylation is dynamically redistributed in response to environmental challenges, thereby driving remodelling of cellular protein-protein interaction (PPI) networks, and access to protein active sites, with functional and phenotypic consequences. Finally, we show that glutathionylation accumulates on key cardiac-sarcomeric proteins in aged-mice and human cardiomyopathy biopsies, revealing its role in cardiovascular dysfunction. These findings reposition glutathionylation as a crucial regulatory PTM, akin to phosphorylation, that orchestrates adaptive cellular responses. This work redefines the role of glutathionylation, with broad implications for cell biology and disease.

molecular biology↗

bioRxiv2025

Enhanced Proteomics Analysis with a Novel Recombinant Chymotrypsin Analogue Engineered for High Cleavage Specificity

Chymotrypsin is widely used in shotgun proteomics owing to its orthogonal cleavage specificity relative to trypsin, which enhances sequence coverage of hydrophobic protein regions. However, commercial preparations often display variable cleavage specificity, trypsin contamination, and elevated missed-cleavage rates, which can collectively reduce proteome coverage and data reproducibility. To address these limitations, we present a novel recombinant chymotrypsin (rChymoSelect) engineered for improved cleavage specificity and robustness in proteomics workflows. Benchmarking against standard bovine chymotrypsin revealed 97 % C-terminal cleavages after tyrosine (Y), phenylalanine (F), and leucine (L) for rChymoSelect, compared with 72 % for the standard enzyme. This enhanced cleavage specificity reduced missed cleavages and increased peptide-spectrum matches across charge states. Across 3,638 identified proteins, rChymoSelect yielded 22.2 % unique identifications compared with 8.2 % for standard chymotrypsin, while maintaining similar peptide length, m/z, and hydrophobicity distributions. Notably, rChymoSelect showed enriched recovery of mitochondrial proteins, consistent with its improved digestion of hydrophobic targets. The enzyme remained active in up to 6 M urea and achieved near-maximal proteome coverage within 2 hours (only a 2.4 % gain after overnight digestion). Integration with data-independent acquisition (DIA) increased total protein identifications from approximately 2,200 (DDA) to 3,200 (DIA), a 45 % gain, with rChymoSelect outperforming standard chymotrypsin by 16.6-22.4 % in peptide-spectrum matches and 4.6-6.2 % in protein identifications. These results establish rChymoSelect as an advanced tool with improved cleavage specificity that reduces analytical complexity and enhances the reliability of proteomic analysis, while expanding chymotryptic digestion to hydrophobic and high-denaturant proteomics applications.

biochemistry↗

bioRxiv2025

Both terminal misfolding and polymerisation contribute to disease-relevant phenotypic changes in cell models of α1-antitrypsin deficiency-associated liver disease

Polymerisation of 1-antitrypsin within hepatocytes is considered central to the pathogenesis of 1-antitrypsin deficiency-associated liver fibrosis, most commonly in homozygotes for the Z (p.Glu342Lys) allele. Polymerisation proceeds via self-association of monomeric intermediate states. In parallel, >50% of synthesised Z 1-antitrypsin is instead recognized as terminally-misfolded and degraded. It is unclear whether this contributes to Z 1-antitrypsin deficiency-associated liver disease. We characterised the relationships between polymer formation, terminal misfolding and their cellular consequences, using label-free proteomics mass spectrometry (MS), light and electron microscopy, and cellular assays. Proteomic analyses of well-established CHO cell models of hepatocyte handling of 1-antitrypsin variants indicated that cellular responses to the Z mutation were surprisingly similar to those seen with the NullHongKong variant (NHK), which can only misfold terminally and cannot polymerise. A minor set of proteins showed increases associated with Z and not NHK 1-antitrypsin expression, consistent with a polymer-specific response, characterized by association with increased organellar organization and vesicle-mediated transport. Conversely, proteostatic and pro-fibrotic integrin-associated pathways increased with the degree of terminal misfolding of the expressed 1-antitrypsin variant. Bioenergetic pathway changes indicated concomitant switching from oxidative to glycolytic metabolism. Cell studies further correlated fibrosis-associated behaviours with terminal misfolding rather than polymerisation. Terminal misfolding, as well as polymerisation behaviour, may therefore be important for pro-fibrotic responses including metabolic reprogramming and senescence in Z 1-antitrypsin deficiency. Molecular therapies may prove most efficacious for associated liver disease if they address terminal misfolding as well as polymerisation.

cell biology↗

bioRxiv2025

TBK1 activity regulates the directionality of axonal transport of signalling endosomes

The polarised and complex morphology of neurons pose massive challenges for efficient cargo delivery between the axon and soma, a process termed axonal transport. We have previously shown that the retrograde axonal transport of pro-survival, neurotrophic signalling endosomes relies on Rab7 in motor neurons, and that their trafficking is impaired in the early stages of amyotrophic lateral sclerosis (ALS) pathogenesis. Here, we report the effect of Rab7 phosphorylation on the transport of these signalling endosomes. We show that the ALS-linked kinase TBK1 phosphorylates Rab7 at S72 in neurons, altering its binding to cytoplasmic dynein adaptors. Accordingly, both TBK1 knockdown and the expression of a loss-of-function Rab7 mutant (S72E) induce aberrant bidirectional movement of signalling endosomes without modifying neuronal polarity or endosomal sorting. This alteration is specific for signalling endosomes, as axonal transport of lysosomes and mitochondria remain unaffected. We have therefore discovered a new TBK1 function that ensures the unidirectional transport of signalling endosomes, suggesting that reduced TBK1 activity determines retrograde transport dysfunctions and long-range signalling impairments. SummarySignalling endosomes travel from the distal axon to the cell body, exerting pro-survival functions. TBK1, an ALS-linked kinase, governs the directionality of signalling endosome transport in motor neurons by phosphorylating Rab7. Thus, loss of TBK1 function results in long-range signalling impairment.

neuroscience↗

bioRxiv2025

NanoBondy reacting through NeissLock anhydride allows covalent immune cell decoration

Cell-surface conjugation has enormous therapeutic and research potential. Existing technologies for cell-surface modification are usually reversible, non-specific, or rely on genetic editing of target cells. Here we present the NanoBondy, a nanobody modified for covalent ligation to an endogenous protein target at the cell-surface. The NanoBondy utilizes the 20 naturally occurring amino acids, harnessing NeissLock chemistry engineered from Neisseria meningitidis. We evaluated binding and specificity of a panel of nanobodies to CD45, a long-lived surface marker of nucleated hematopoietic cells. We demonstrated conversion of existing nanobodies to covalently reacting NanoBondies using a disulfide clamp to position the self-processing module of FrpA close to the nanobody antigen-binding site. Addition of calcium induces anhydride formation at the NanoBondy C-terminus and proximity-directed ligation to surface amines on CD45. We optimized NanoBondy reaction by fine-tuning linkers and disulfide clamp sites to modulate anhydride positioning. Tandem mass spectrometry mapped reaction sites between the NanoBondy and CD45. NanoBondy ligation was robust to buffer, pH and temperature and was detected within 2 minutes. We established reaction specificity of NanoBondies to endogenous CD45 at the surface of NK cells and T cells. NanoBondy technology provides a modular approach for targeted, inducible and covalent cell-surface modification of immune cells.

synthetic biology↗

bioRxiv2024

Laminin 111 triggers cell quiescence and long-term survival by inducing IQGAP1-mediated cytosolic scaffolding of ERK and BAD inactivation

In an adult human body, only a minority ([~]1%) of cells are dividing; all others are either quiescent, senescent or terminally differentiated. Cellular quiescence, also called G0, is a reversible non-proliferative state in which cells, such as adult stem cells, exist until stimuli trigger their re-entry into the cell cycle. Quiescent cells are known to reside within microenvironment niches of specific extracellular matrix (ECM) composition, but the molecular mechanisms that control their entry and maintenance into G0 and their long-term survival are poorly understood. Here, using a reproducible and homogenous in vitro model of quiescence, ex vivo tissue histology, phosphoproteomics, and molecular cell biological assays, we revealed that Laminin 111 was sufficient to trigger i) reversible cell cycle exit into G0; ii) sustained and elevated MAPK/ERK signaling; and iii) long-term survival. We found that ERK was activated through the Rap1-BRAF-MEK arm underneath Laminin-binding Integrin 3{beta}1. Activated pERK was scaffolded into the cytoplasm by IQGAP1, thereby blocking its translocation into the nucleus and the activation of proliferative transcription factors. Instead, cytoplasmic pERK inhibited pro-apoptotic protein BAD, which mediated the survival of quiescent cells even in absence of mitogen stimuli. Importantly, we confirmed that pERK was elevated and retained in the cytoplasm of Lgr5+ stem cells when they were located within Laminin 1-positive niches in porcine intestine. These findings uncovered a molecular mechanism that may explain how quiescent cell pools, such as dormant adult stem cells, can survive many years despite low mitogen stimuli and be resistant to apoptotic challenges, including chemotherapy. HIGHLIGHTSO_LILaminin 111 is sufficient to induce cellular quiescence (G0) and long-term survival. C_LIO_LILaminin 111 triggers the sustained and elevated activation of ERK during G0. C_LIO_LIERK is activated not by growth factor receptors but through the Rap1-BRAF-MEK arm underneath Laminin-binding Integrin 3{beta}1. C_LIO_LIActive, phosphorylated ERK (pERK) is scaffolded by IQGAP1, which prevents it from translocating into the nucleus and activating proliferative transcription factors. C_LIO_LIInstead, cytoplasmic pERK mediates the phosphorylation, and thus inhibition, of BAD, thereby raising the threshold at which G0 cells enter apoptosis. C_LI

cell biology↗

bioRxiv2024

Aging-associated long non-coding RNA boosts longevity and reduces the ribosome content of non-dividing fission yeast cells

Genomes produce widespread long non-coding RNAs (lncRNAs) of largely unknown functions. We characterize aal1 (aging-associated lncRNA) which is induced in quiescent cells of fission yeast. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression of aal1 prolongs their lifespan, indicating that this lncRNA acts in trans. The overexpression of aal1 leads to the repression of ribosomal protein genes and inhibition of cell growth, and aal1 genetically interacts with coding genes functioning in protein translation. The aal1 RNA localizes to the cytoplasm and associates with ribosomes. Notably, aal1 deletion or overexpression is sufficient to increase or decrease the cellular ribosome content. The rpl1901 mRNA, encoding a ribosomal protein, is a binding target of aal1. The levels of rpl1901 are reduced [~]2-fold by aal1, which is critical and sufficient to extend the lifespan. Remarkably, the expression of aal1 lncRNA in Drosophila triggers an extension of fly lifespan. We propose that aal1 reduces the ribosome content by decreasing the levels of Rpl1901, thus attenuating protein translation and promoting longevity. Although the aal1 lncRNA itself is not conserved, its effect in flies raises the possibility that animals feature related mechanisms that modulate aging, based on the conserved translational machinery.

genetics↗

bioRxiv2023

Modeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry

We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2, and conformer selection using XL-MS data. For conformer selection, we developed two scores - the monolink probability score (MP) and the crosslink probability score (XLP), both of which are based on residue depth. We benchmarked MP and XLP on a large dataset of decoy protein structures, and showed that our scores outperform previously developed scores. We then tested our methodology on three proteins having an open and closed conformation in the Protein Data Bank: Complement component 3 (C3), luciferase, and glutamine-binding periplasmic protein (QBP), first generating ensembles using AF2, which were then screened for the open and closed conformations using experimental XL-MS data. In five out of six cases, the most accurate model within the AF2 ensembles - or a conformation within 1 [A] of this model - was identified using crosslinks, as assessed through the XLP score. In the remaining case, only the monolinks (assessed through the MP score) successfully identified the open conformation of QBP. This serves as a compelling proof-of-concept for the effectiveness of monolinks. In contrast, the AF2 assessment score (pTM) was only able to identify the most accurate conformation in two out of six cases. Our results highlight the complementarity of AF2 with experimental methods like XL-MS, with the MP and XLP scores providing reliable metrics to assess the quality of the predicted models.

biochemistry↗

bioRxiv2023

Structural basis of substrate progression through the chaperonin cycle

The bacterial chaperonin GroEL-GroES promotes protein folding through ATP-regulated cycles of substrate protein binding, encapsulation, and release. Here, we have used cryoEM to determine structures of GroEL, GroEL-ADP{middle dot}BeF3, and GroEL-ADP{middle dot}AlF3-GroES all complexed with the model substrate Rubisco. Our structures provide a series of snapshots that show how the conformation and interactions of non-native Rubisco change as it proceeds through the GroEL-GroES reaction cycle. We observe specific charged and hydrophobic GroEL residues forming strong initial contacts with non-native Rubisco. Binding of ATP or ADP{middle dot}BeF3 to GroEL-Rubisco results in the formation of an intermediate GroEL complex displaying striking asymmetry in the ATP/ADP{middle dot}BeF3-bound ring. In this ring, four GroEL subunits bind Rubisco and the other three are in the GroES-accepting conformation, explaining how GroEL can recruit GroES without releasing bound substrate. Our cryoEM structures of stalled GroEL-ADP{middle dot}AlF3-Rubisco-GroES complexes show Rubisco folding intermediates interacting with GroEL-GroES via different sets of residues.

biophysics↗

bioRxiv2021

The ataxia protein sacsin is required for integrin trafficking and synaptic organization

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is caused by mutations in SACS, which manifest as a childhood-onset cerebellar ataxia. Cellular ARSACS phenotypes include mitochondrial dysfunction, intermediate filament (IF) disorganization, and loss of Purkinje neurons. It is unclear how the loss of SACS causes these deficits, or why they manifest as cerebellar ataxia. We employed a multi-omics approach to characterize molecular and cellular deficiencies in SACS knockout (KO) cells. We identified alterations in microtubule structure and dynamics, protein trafficking, and mislocalization of synaptic and focal adhesion proteins. Targeting PTEN, a negative regulator of focal adhesions, rescued several cellular phenotypes in SACS KO cells. We found sacsin interacts with proteins implicated in vesicle transport, including HSP proteins, and interactions between structural and cell adhesion proteins were diminished in SACS KO cells. In all, this study suggests that trafficking and localization of synaptic adhesion proteins is a causal molecular deficiency in ARSACS.

cell biology↗

bioRxiv2021

Intermittent bulk release of human cytomegalovirus through multivesicular bodies

Human Cytomegalovirus (HCMV) can infect a variety of cell types by using virions of varying glycoprotein compositions. It is still unclear how this diversity is generated, but spatio-temporally separated envelopment and egress pathways might play a role. So far, one egress pathway has been described in which HCMV particles are individually enveloped into small vesicles and are subsequently exocytosed continuously. However, some studies have also found enveloped virus particles inside multivesicular structures but could not link them to productive egress or degradation pathways. We used a novel 3D-CLEM workflow allowing us to investigate these structures in HCMV morphogenesis and egress at high spatio-temporal resolution. We found that multiple envelopment events occurred at individual vesicles leading to multiviral bodies (MViBs), which subsequently traversed the cytoplasm to release virions as intermittent bulk pulses at the plasma membrane to form extracellular virus accumulations (EVAs). Our data support the existence of a novel bona fide HCMV egress pathway, which opens the gate to evaluate divergent egress pathways in generating virion diversity.

microbiology↗

bioRxiv2020

Cdk5 and GSK3β inhibit Fast Endophilin-Mediated Endocytosis

Endocytosis mediates the cellular uptake of micronutrients and cell surface proteins. Parallel to Clathrin-mediated endocytosis, additional Clathrin-independent endocytic routes exist, including fast Endophilin-mediated endocytosis (FEME). The latter is not constitutively active but requires the activation of selected receptors. In cell culture, however, the high levels of growth factors in the regular culture media induce spontaneous FEME, which can be suppressed upon serum starvation. Thus, we predicted a role for protein kinases in this growth factor receptor-mediated regulation of the pathway. Using chemical and genetic inhibition, we found that Cdk5 and GSK3{beta} are negative regulators of FEME. Their inhibition was sufficient to activate FEME promptly in resting cells and boosted the production of endocytic carriers containing {beta} 1-adrenergic receptor, following dobutamine addition. We established that the kinases suppress FEME at several levels. They control Dynamin-1 and Dynein recruitment and sorting of cargo receptors such as Plexin A1 and ROBO1 into FEME carriers. They do so by antagonizing the binding of Endophilin to Dynamin-1 as well as to Collapsin response mediator protein 4 (CRMP4), a Plexin A1 adaptor. Cdk5 and GSK3{beta} also hamper the binding and recruitment of Dynein onto FEME carriers by Bin1. Interestingly, we found that GSK3{beta} binds to Endophilin, thus imposing a local regulation of FEME. Collectively, these findings place the two kinases as key regulators of FEME, licensing cells for rapid uptake by the pathway only upon when Cdk5 and GSK3{beta} activity is low.

cell biology↗

bioRxiv2020

Combining Information from Crosslinks and Monolinks in the Modelling of Protein Structures

Monolinks are produced in a Chemical Crosslinking Mass Spectrometry experiment and are more abundant than crosslinks. They convey residue exposure information, but so far have not been used in the modelling of protein structures. Here we present the Monolink Depth Score (MoDS), for assessing structural models based on the depth of monolinked residues, corresponding to their distance to the nearest bulk water. Using simulated and reprocessed experimental data from the Proteomic Identification Database, we compare the performance of MoDS to MNXL - our previously-developed score for assessing models based on crosslinking data. Our results show that MoDS can be used to effectively score model structures based on monolinks, and that combining it with MNXL leads to overall higher scoring performance. The work strongly supports the use of monolink data in the context of integrative structure determination. We also present XLM-Tools, a programme to assist in this effort, available at: https://github.com/Topf-Lab/XLM-Tools.

bioinformatics↗

bioRxiv2018

Tracking dynamic changes in Alzheimer’s disease brain proteome reveals ageing-independent damage in Drosophila

Alzheimers disease (AD), the most prevalent form of dementia, is a progressive and devastating neurodegenerative condition for which there are no effective treatments. Understanding the molecular pathology of AD during disease progression may identify new ways to reduce neuronal damage. Here, we present a longitudinal study tracking dynamic proteomic alterations in the brains of an inducible Drosophila melanogaster model of AD expressing the Arctic mutant A{beta}42 gene. We identified 3093 proteins from flies that were induced to express A{beta}42 and age-matched healthy controls using label-free quantitative ion-mobility data independent analysis mass spectrometry. Of these, 228 proteins were significantly altered by A{beta}42 accumulation and were enriched for AD-associated processes. Network analyses further revealed that these proteins have distinct hub and bottleneck properties in the brain protein interaction network, suggesting that several may have significant effects on brain function. Our unbiased analysis provides useful insights into the key processes governing the progression of amyloid toxicity and forms a basis for further functional analyses in model organisms and translation to mammalian systems.

biochemistry↗