Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Poly(GR) Drives Intra-Condensate Demixing and Pathological Aggregation of TDP-43

ABSTRACT: TAR DNA-binding protein 43 (TDP-43) pathology and C9orf72 hexanucleotide repeat expansions are two major pathological features of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). Growing evidence indicates that dipeptide repeat proteins produced from C9orf72 repeats, particularly glycine–arginine (poly(GR)), promote TDP-43 aggregation, but the underlying mechanism remains unclear. Here we show that poly(GR) enhances liquid–liquid phase separation (LLPS) of TDP-43 and induces phase demixing within the resulting condensates. Demixed condensates contain regions with high local TDP-43 concentration that progressively solidify and undergo conformational changes from dynamic assemblies into oligomeric and fibrillar species rich in β-sheet structure, which promote the formation of toxic TDP-43 aggregates in cellular assays. Together, these findings support a mechanism in which phase separation enables poly(GR) to promote pathological TDP-43 aggregation and highlight condensate demixing and conformational conversion, constituting a key pathway for TDP-43 aggregation and a potential target for therapeutic intervention.

ORGANISM(S): Homo Sapiens

SUBMITTER: Chun Tang

PROVIDER: PXD074330 | iProX | Wed Feb 11 00:00:00 GMT 2026

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Noncoding RNAs induce TDP43 pathology in the ALS-iPSC models

Project description:Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron (MN) degenerative disease with a major pathological feature of cytoplasmic TDP-43 aggregation. However, the mechanisms underlying TDP-43 proteinopathy are still largely unknown. We performed in vitro differentiation of ALS-induced pluripotent stem cells (ALS-iPSCs; carrying the TDP-43M337V mutation) and isogenic controls and found upregulation of paraspeckle-associated lncRNA NEAT1 isoforms in the ALS-iPSC-derived MNs (ALS-iPSC-MNs). Intriguingly, the upregulated NEAT1 isoforms were mislocalized to the cytoplasm of ALS-iPSC-MNs, and the cytoplasmic NEAT1 provoked TDP-43 and TDP-43M337V liquid-liquid phase separation, generating long-lived protein condensates. These condensates had reduced mobility and were converted into aggregates, finally co-aggregating with phospho-TDP-43. Disruption of NEAT1 expression reduced its cytoplasmic levels and also reduced the levels of TDP-43/TDP-43M337V condensates. In 3D neuromuscular organoids with the TDP-43M337V mutation, treatment with NEAT1-antisense oligonucleotides (NEAT1-ASO) promoted neuromuscular junction formation and function, as well as muscle contractility. Furthermore, treatment of TDP-43Q331K mice with Neat1-ASO attenuated TDP-43 pathology in spinal cord and preserved motor function. These findings suggest that NEAT1 plays an important role in TDP-43-associated pathology, and NEAT1-ASO may attenuate pathological TDP-43 aggregation to prevent motor neuron degeneration and muscle weakness in ALS.

2024-11-24 | GSE189470 | GEO

Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

Project description:An intronic GGGGCC repeat expansion in C9orf72 is a common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. The repeats are transcribed in both sense and antisense directions to generate distinct dipeptide repeat proteins, of which poly(GA), poly(GR) and poly(PR) have been implicated in contributing to neurodegeneration. Poly(PR) binding to RNA may contribute to toxicity, but analysis of poly(PR)-RNA binding on a transcriptome-wide scale has not yet been carried out. We therefore performed crosslinking and immunoprecipitation (CLIP) analysis in human cells to identify the RNA binding sites of poly(PR). We found that poly(PR) binds to nearly 600 RNAs, with the sequence GAAGA enriched at the binding sites. In vitro experiments showed that poly(GAAGA) RNA binds poly(PR) with higher affinity than control RNA and induces phase-separation of poly(PR) into condensates. These data indicate that poly(PR) preferentially binds to poly(GAAGA)-containing RNAs, which may have physiological consequences.

2023-07-10 | GSE212761 | GEO

Aberrant phase separation of transcription factors in human developmental disorders

Project description:Components of the transcription machinery can undergo liquid-liquid phase separation, but the functional importance of phase-separated condensates in transcriptional control is not well understood. Here we report that disease-causing mutations in several transcription factors (TFs) alter the phase separation capacity of those TFs. We first demonstrate that the Hoxd13 TF, and its intrinsically disordered N-terminus form phase-separated condensates. Expansions of a polyalanine repeat, which cause hereditary synpolydactyly in humans, facilitate phase separation of Hoxd13, and alter the transcriptional program of several cell types in a cell-specific manner in vivo. Disease-associated expansions of aminoacid repeats in intrinsically disordered regions of other TFs were similarly found to alter phase separation. These results suggest that aberrant phase separation of transcriptional regulators may underlie a spectrum of human pathologies. The paper is available at https://doi.org/10.1016/j.cell.2020.04.018

2020-05-07 | GSE128818 | GEO

Pharmacologic inhibition of PCBP2 biomolecular condensates relieves Alzheimer’s disease

Project description:Biomolecular condensates are involved in a variety of neurodegenerations. These condensates are formed through phase separation mechanism. However, how they may be functional in the pathophysiology of Alzheimer’s disease (AD) remains poorly understood. Here, we report that in the brain of AD patients and animal models, an elevation of poly(C)-binding protein 2 (PCBP2) correlates with biomolecular condensation that involves phase separation. These condensates sequester large numbers of mitochondrial and mRNA-binding proteins, leading to the outside impairment of mitochondrial morphology and function, and BACE1 mRNA decay relative to amyloid deposition. We then identify a small molecule CN-0928 that inhibits the condensates by reducing PCBP2 protein level and mitigates AD pathology and cognitive decline, in which CN-0928 binding to a target protein integrator complex subunit 1 (INTS1) allows to regulate PCBP2 expression. Our findings place PCBP2 condensates as a key player that cooperates the seemingly disparate but important pathways, and show pharmacological modulation of PCBP2 as an effective approach for treating AD.

2025-09-30 | GSE306042 | GEO

Identification of TDP-43 - TAU interactions by XL-MS

Project description:Identification of TDP-43 - TAU interactions by XL-MS (DSS). The interactions were identified in for equimolar amount of TDP-43 - TAU and, as control, TDP-43 and MBP. After 30 minutes from the induction of phase separation, samples were either analyzed (bulk condition) or subjected to centrifugation (10min at 21’000g) to pellet the formed condensates.

2025-08-25 | PXD063858 | Pride

Disparate Leukemia Mutations Converge on Nuclear Phase-Separated Condensates

Project description:During cancer development, mutations promote gene expression changes that cause transformation. Leukemia is frequently associated with aberrant HOXA expression driven by translocations in nucleoporin genes or KMT2A, and mutations in NPM1. How disparate mutations converge on this regulatory pathway is not understood. Here we demonstrate that mutant NPM1 (NPM1c) forms nuclear condensates in multiple human cell lines, mouse models, and primary patient samples. We show NPM1c phase separation is necessary and sufficient to recruit NUP98 and KMT2A to condensates. Through extensive mutagenesis and pharmacological destabilization of phase separation, we find that NPM1c condensates are necessary for regulating gene expression, promoting in vivo expansion, and maintaining the undifferentiated leukemic state. Finally, we show that nucleoporin and KMT2A fusion proteins form condensates that are biophysically indistinguishable from NPM1c condensates. Together, these data define a new condensate underlying leukemias that we term coordinating bodies (C-bodies), and propose C-bodies as a therapeutic vulnerability.

2025-11-04 | GSE306285 | GEO

YAP maintains the dynamics of TDP-43 condensates and antagonizes TDP-43 pathology

Project description:Recent studies exploring the underlying pathomechanisms of amyotrophic lateral sclerosis (ALS), a fatal motor neuron disorder, have focused on biomolecular condensates, such as stress granules (SGs) and TDP-43 condensates. Our comprehension of the physicochemical processes that control the behavior of these condensates is still evolving. In this work, we reveal an unexpected function for YAP, a central component of the Hippo pathway, in regulating the dynamic behavior of SGs and TDP-43 condensates, a role that is independent of its transcriptional activity in Hippo pathway. We found that YAP can directly bind to the TB domain of TDP-43 through its N-terminal domain. This interaction promotes the homotypic multimerization and phase separation of TDP-43, while inhibiting its hyper- phosphorylation and solidification under stress conditions. Remarkably, YAP, whose mRNA level is reduced in ALS patients, is found to co-localize with pathological pTDP-43 aggregates in the cytoplasmic foci of ALS patient brains. Additionally, elevating YAP/Yorkie expression substantially reduces neurotoxicity in a TDP-43 transgenic fly model of ALS. Our findings highlight an unexpected chaperone-like role of YAP in managing ALS-associated biomolecular condensates, presenting significant implications for potential ALS treatments.

2024-02-24 | PXD050122 |

Molecular Basis and Cellular Effects of Janus-Class–Driven Cytoplasmic PYK2 Coacervates

Project description:Kinase activity is increasingly associated with biomolecular phase separation. Focal adhesion kinase (FAK) forms membrane-associated condensates with paxillin to promote adhesion. Here we show that its paralogue, proline-rich tyrosine kinase 2 (PYK2), undergoes phase separation via a distinct mechanism. PYK2 forms cytoplasmic condensates primarily driven by its kinase–FAT linker (KFL) region. Overexpression of PYK2 induces condensates enriched in its autophosphorylated form, which sequester paxillin from focal adhesions and impair cell adhesion. We uncover an autoregulatory mechanism involving the KFL, linking self-association, autophosphorylation, and condensation. Uncommon among known phase separation drivers, KFL condensation is phosphorylation-independent and its sequence belongs to the “Janus” class. Using a transformer-based protein language model, we identified non-homologous sequences with similar features, many from adhesion and cytoskeletal regulators. We validated the phase-separating potential of several of these sequences in cells. These findings reveal a mechanism linking phase separation with kinase activation, and demonstrate distinct condensation behavior in homologues. Our results also highlight how protein concentration modulates condensate function, with implications for disease, and expand the landscape of phase separation drivers.

2026-01-11 | PXD072123 | Pride

Phase separation of RNA-binding protein promotes polymerase binding and transcription

Project description:An RNA-involved phase-separation model has been proposed for transcription control. Yet, the molecular links that connect RNA to the transcription machinery remain missing. Here we find RNA-binding proteins (RBPs) constitute half of the chromatin proteome in embryonic stem cells (ESCs), and some are colocalized with RNA polymerase (Pol) II at promoters and enhancers. Biochemical analyses of representative RBPs show that the paraspeckle protein PSPC1 inhibits the RNA-induced premature release of Pol II, and makes use of RNA as multivalent molecules to enhance the formation of transcription condensates and subsequent phosphorylation and release of Pol II. This synergistic interplay enhances polymerase engagement and activity via the RNA-binding and phase-separation activities of PSPC1. In ESCs, auxin-induced acute degradation of PSPC1 leads to genome-wide defects in Pol II binding and nascent transcription. We propose that promoter-associated RNAs and their binding proteins synergize the phase separation of polymerase condensates to promote active transcription.

2020-05-12 | GSE150399 | GEO

HspB8 controls hardening and molecular aging of FUS condensates by domain-specific protein interactions Part 1

Project description:Biomolecular condensates formed by phase separation offer a confined space where protein-protein interactions (PPIs) facilitate distinct biochemical reactions. As their aberrant behavior is increasingly associated with disease, it is crucial to understand the molecular organization of PPIs within condensates. Using quantitative and time-resolved crosslinkingmass spectrometry we directly and specifically monitor PPIs and protein dynamics of fused in sarcoma (FUS) condensates and identify its RNA recognition motif (RRM) as a key player of condensate-specific PPIs and aging. We find that the chaperone HspB8, but not a disease-associated mutant, prevents FUS aging. The disordered region of HspB8 directs its α-crystallin domain (αCD) into FUS condensates. Here, RRM unfolding drives aggregation but binding of HspB8 via a droplet-specific αCD – RRM interface significantly delays the onset of aging. We propose that chaperones such as HspB8 prevent aberrant phase transitions by stabilizing aggregation prone RNA binding domains in times of cellular stress.

2021-10-12 | PXD021114 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data