Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pharmacologic inhibition of PCBP2 biomolecular condensates relieves Alzheimer’s disease

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE306042 | GEO | 2025/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Microproteomics of PCBP2 biomolecular condensates

Project description:PCBP2 condensates were isolated by FAPS. To identify the PCBP2 condensates signature, we performed a mass spectrometry analysis and compared the pre-sorted and post-sorted fractions.For each sorting experiment, cells were cultured to approximately 80-90% confluence in three 15-cm dishes. Cells were pelleted in PBS by centrifugation at 1,000 × g for 3 min at RT and immediately flash-frozen in liquid nitrogen overnight. Unless otherwise stated, the following steps were conducted at 4°C or on ice. Cell pellets were resuspended in lysis buffer (50 mM Tris [pH 7.4], 1 mM EDTA, 150 mM NaCl, 0.2% Triton X-100), containing 65 U/mL RNase inhibitor and EDTA-free protease inhibitor cocktail. To facilitate lysis, the extracts were passed 20 times through a 25G syringe needle, with a total incubation time of 20 min. Lysates were spun at 200 x g for 5 min to remove nuclei. To digest remaining DNA contaminants, the supernatants were treated with RQ1 RNase-free DNase for 30 min at RT, and then centrifuged at 10,000 x g for 7 min. The resulting pellets were resuspended in 2 mL of lysis buffer, and the organelle-enriched fraction obtained at 10,000 x g was designated as the pre-sorted fraction. From this fraction, PCBP2-biomolecular condensates were sorted on a cell sorter (Bigfoot, Invitrogen) equipped with a 100 μm nozzle and operating at a pressure of 30 psi. Particles were identified based on their forward-scattered light (FSC) and mCherry fluorescence, utilizing a 561 nm excitation laser and a 615/24 nm bandpass filter. The sorting window for PCBP2-biomolecular condensates was specifically set to exclude mCherry-SH-SY5Y fluorescent particles while retaining mCherry-labeled PCBP2 condensates. The mCherry-PCBP2 fraction represented 8-10% of total events and was subsequently collected. These fractions were centrifuged at 10,000 × g for 7 min, and the pellets were then analyzed as the post-sorted fractions.

| PXD055459 |

Synthetic biomolecular condensates enhance translation from a target mRNA in living cells

Project description:Biomolecular condensates composed of proteins and RNA are one approach by which cells regulate post-transcriptional gene expression. Their formation typically involves the phase separation of intrinsically disordered proteins with a target mRNA, sequestering the mRNA into a liquid condensate. This sequestration regulates gene expression by modulating translation or facilitating RNA processing. Here, we engineer synthetic condensates using a fusion of an RNA-binding protein, the human Pumilio2 homology domain, and a synthetic intrinsically disordered protein, an elastin-like polypeptide, that can bind and sequester a target mRNA transcript. In protocells, sequestration of a target mRNA largely limits its translation. Conversely, in E. Coli, sequestration of the same target mRNA increases its translation. We characterize the Pum2-ELP condensate system using microscopy, biophysical and biochemical assays, and RNA-seq. This approach enables modulation of cell function via the formation of synthetic biomolecular condensates that upregulate the expression of a target protein.

2024-11-30 | GSE277409 | GEO

High-Throughput and Proteome-wide Discovery of Endogenous Biomolecular Condensates

Project description:Phase separation inside mammalian cells regulates the formation of biomolecular condensates that are related to gene expression, signalling, development, and diseases. However, a large population of endogenous condensates and their candidate phase separating proteins have yet to be discovered in a quantitative and high-throughput manner. Here, we demonstrate that endogenously-expressed biomolecular condensates can be identified across a cell's proteome by sorting proteins across varying oligomeric states. We employ volumetric compression to modulate the concentrations of intracellular proteins and the degree of crowdedness, which are physical regulators of cellular biomolecular condensates. The changes in degree of the partition of proteins into condensates or phase separation lead to varying oligomeric states of the proteins, which can be detected by coupling density gradient ultracentrifugation and quantitative mass spectrometry. In total, we identified 1,518 endogenous-expression condensate proteins, of which 538 have not been reported before. Furthermore, we demonstrate that our strategy can identify condensate proteins that respond to specific biological processes.

2024-03-18 | PXD048218 | Pride

Material properties of biomolecular condensates regulates RNA splicing and tumorigenesis

Project description:It remains largely unclear how material properties of biomolecular condensates impact physiological and pathological processes such as cancer. Here we show that AKAP95, a nuclear protein involved in gene regulation, plays an important role in tumorigenesis through directly regulating mRNA splicing. We show that AKAP95, through an intrinsic disordered region (IDR), forms liquid-like droplets in vitro and dynamic foci in nucleus. We have also identified key residues in IDR whose mutations to different residues perturb AKAP95 condensation in opposite directions. Importantly, the biological activity of AKAP95 in splice regulation is affected by either disruption of liquid condensation or enhancing the gelation of the assembly. We then show that the ability of AKAP95 in overcoming oncogene-induced senescence requires AKAP95 in an appropriate window of liquidity. These results thus link phase separation to tumorigenesis and uncover an important role of regulating the material property of protein condensates in disease including cancer.

2020-05-06 | GSE122308 | GEO

Selective RNA sequestration in biomolecular condensates directs cell fate transitions

Project description:Recent studies have emphasized the significance of biomolecular condensates in modulating gene expression through RNA processing and translational control. However, the functional roles of RNA condensates in cell fate specification remains poorly understood. Here, we profiled the coding and non-coding transcriptome within intact biomolecular condensates, specifically P-bodies, in diverse developmental contexts, spanning multiple vertebrate species. Our analyses revealed the conserved, cell type-specific sequestration of untranslated RNAs encoding key cell fate regulators. Notably, P-body contents did not directly reflect active gene expression profiles for a given cell type, but rather were enriched for translationally repressed transcripts characteristic of the preceding developmental stage. Mechanistically, microRNAs (miRNAs) direct the selective sequestration of RNAs into P-bodies in a context-dependent manner, and perturbing AGO2 or alternative polyadenylation profoundly reshapes P-body RNA content. Building on these mechanistic insights, we demonstrate that modulating P-body assembly or miRNA activity dramatically enhances both activation of a totipotency transcriptional program in naïve pluripotent stem cells as well as the programming of primed human embryonic cells towards the germ cell lineage. Collectively, our findings establish a direct link between biomolecular condensates and cell fate decisions across vertebrate species and provide a novel framework for harnessing condensate biology to expand clinically relevant cell populations.

2025-09-30 | GSE302363 | GEO

The Poly(C) binding protein Pcbp2, and its retrotransposed derivative Pcbp1, are independently essential to mouse development

Project description:RNA-binding proteins participate in a complex array of post-transcriptional controls essential to cell-type specification and somatic development. Despite their detailed biochemical characterizations, the degree to which each RNA-binding protein impacts on mammalian embryonic development remains incompletely defined and the level of functional redundancy among subsets of these proteins remains open to question. The poly-(C) binding proteins, Pcbp's (aCPs, hnRNPEs), are encoded by a highly conserved and broadly expressed gene family. The two major Pcbp isoforms, Pcbp2 and Pcbp1, are robustly expressed in a wide range of tissues and exert both nuclear and cytoplasmic controls over gene expression. Here we report that Pcbp1-null embryos are rendered nonviable in the peri-implantation stage. In contrast, Pcbp2-null embryos survive until mid-gestation at which time they undergo a loss in viability associated with cardiovascular and hematopoietic abnormalities. Adult mice heterozygous for either Pcbp1 or Pcbp2 null alleles display a mild and non-disruptive growth defect. These data reveal that Pcbp1 and Pcbp2 are individually essential for mouse embryonic development and post-natal growth, reveal a non-redundant in vivo role for Pcpb2 in hematopoiesis, and provide direct evidence that Pcbp1, a retrotransposed derivative of Pcpb2, has evolved essential function(s) in the mammalian genome. mRNA-seq on fetal liver tissue from 12.5 days post coitum. 4 replicates of WT and 3 replicates of PCBP2 Knockout

2015-11-05 | E-GEOD-72491 | biostudies-arrayexpress

mRNA sequencing of human AC16 cells expressing PCBP1, PCBP2, or both

Project description:To explore potential functional implications of isoform usage shifts, we examined the effect of PCBP1/PCBP2 expression in human AC16 cardiac cells. PCBP1/PCBP2 are KH-domain-containing RNA-binding proteins (RBP) that have been implicated in transcriptional, post-transcriptional and translational regulations. How PCBP1 and PCBP2 are functionally differentiated remains a subject of interest and few reports have outlined their function in cardiac cells. The two paralogs share close homology (~85% identical sequences) and partially overlapping RNA binding targets, suggesting they may form mutually regulatory relationships. Human and mouse PCBP1 sequences share 100.0% identity, whereas human and mouse PCBP2 are identical except in 5 positions; therefore we expressed the human/mouse PCBP1 and human PCBP2 coding sequences in human AC16 cardiac cells. Immunofluorescence imaging confirms broad cytonuclear localization of both paralogs under overexpression. The cells were then subjected to RNA sequencing to determine the effects of PCBP1/2 on gene expression.

2025-07-25 | GSE303619 | GEO

Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production

Project description:Biomolecular condensates play important roles in diverse biological processes. Many viruses form biomolecular condensates which have been implicated in various functions critical for productive infection of host cells. The adenovirus L1-52/55 kilodalton protein (52K) was recently shown to form viral biomolecular condensates that coordinate viral genome packaging and capsid assembly. Although critical for packaging, we do not know how viral condensates are regulated during adenovirus infection. Here we show that phosphorylation of serine residues 28 and 75 within the N-terminal intrinsically disordered region of 52K modulates viral condensates in vitro and in cells, promoting liquid-like properties over condensate hardening. Furthermore, we demonstrate that phosphorylation of 52K promotes viral genome packaging and production of infectious progeny particles. Collectively, our findings provide insights into how viral condensate properties are regulated and maintained in a state conducive to their function in viral progeny production. In addition, our findings have implications for antiviral strategies aimed at targeting the regulation of viral biomolecular condensates to limit viral multiplication.

2023-12-06 | PXD046971 | Pride

Material properties of biomolecular condensates regulates RNA splicing and tumorigenesis

Project description:Material properties of biomolecular condensates regulates RNA splicing and tumorigenesis

| PRJNA504562 | ENA

Human glioma cell line T98G: BAP-PCBP2 RIP vs. BAP-GFP RIP (Control)

Project description:RIP-Chip analysis of PCBP2 and identification of preferentially associated mRNAs. T98G cells were transfected transiently with BAP-tagged constructs. BAP-tagged proteins were biotinylated in vivo by the co-transfected hBirA enzyme. RNPs were recovered via precipitation with Steptavidin-sepharose beads. Finally, RNAs were purified and analyzed on microarrays. BAP-GFP as control was used in three independent sets of experiments. Two-condition experiment, BAP-PCBP2 vs. BAP-GFP cells. Biological replicates: 3 BAP-PCBP2 replicates, 3 BAP-GFP (Control) replicates

2013-07-24 | E-GEOD-44048 | biostudies-arrayexpress

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