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Comparison of wild type and HSPG2+/- hiPSC-CMs

ABSTRACT: Investigating the effect of perlecan haploinsufficiency on cardiomyocyte differentiation

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Alzbeta Chabronova

LAB HEAD: Mandy Peffers

PROVIDER: PXD046359 | Pride | 2025-02-26

REPOSITORIES: Pride

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			Action	DRS
	210923_MP_JS_S11.mgf	Mgf
	210923_MP_JS_S11.mzid.gz	Mzid
	210923_MP_JS_S11.raw	Raw
	210923_MP_JS_S12.mgf	Mgf
	210923_MP_JS_S12.mzid.gz	Mzid

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1 - 5 of 27

Publications

Perlecan (HSPG2) promotes structural, contractile, and metabolic development of human cardiomyocytes.

Johnson Benjamin B BB Cosson Marie-Victoire MV Tsansizi Lorenza I LI Holmes Terri L TL Gilmore Tegan T Hampton Katherine K Song Ok-Ryul OR Vo Nguyen T N NTN Nasir Aishah A Chabronova Alzbeta A Denning Chris C Peffers Mandy J MJ Merry Catherine L R CLR Whitelock John J Troeberg Linda L Rushworth Stuart A SA Bernardo Andreia S AS Smith James G W JGW

Cell reports 20240109 1

Perlecan (HSPG2), a heparan sulfate proteoglycan similar to agrin, is key for extracellular matrix (ECM) maturation and stabilization. Although crucial for cardiac development, its role remains elusive. We show that perlecan expression increases as cardiomyocytes mature in vivo and during human pluripotent stem cell differentiation to cardiomyocytes (hPSC-CMs). Perlecan-haploinsuffient hPSCs (HSPG2<sup>+/-</sup>) differentiate efficiently, but late-stage CMs have structural, contractile, metabol ...[more]

PMID: 38198277

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Mesenchymal Stromal Cell secretome is affected by tissue source and donor age.

Project description:Variation in Mesenchymal Stromal Cell (MSC) function depending on their origin is problematic, as it may confound clinical outcomes of MSC therapy. Current evidence suggests that the therapeutic benefits of MSCs is primarily attributed to secretion of various biologically active factors (secretome). However, the effect of donor characteristics on the MSC secretome composition remains largely unknown. Here, we examined the influence of donor age, sex and tissue source, on the protein profile of the equine MSC secretome. Initially, we used dynamic metabolic labelling with stable isotopes combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify secreted proteins in MSC conditioned media (CM). Seventy proteins were classified as classically-secreted based on the rate of isotope label incorporation into newly synthesised proteins released into the extracellular space. Next, we analysed CM of bone marrow- (n = 14) and adipose-derived MSCs (n = 16) with label-free LC-MS/MS proteomics. Clustering analysis of 314 proteins detected across all samples identified tissue source as the main factor driving variability in MSC CM proteomes. Linear modelling applied to the subset of 70 secreted proteins identified tissue-related difference in the abundance of 23 proteins. There was an age-related decrease in the abundance of two proteins (CTHRC1, LOX), which has been validated with western blot and enzymatic activity assay. There was limited evidence of sex-related differences in protein abundance. In conclusion, this study provides evidence that tissue source and donor age contribute to heterogeneity in the protein composition of MSC secretomes which may influence the effects of MSC-based cell therapy.

2024-01-26 | PXD039652 | Pride

Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimer’s disease

Project description:We performed a systems-level study of disease-associated proteome changes in human frontal cortex of Alzheimer’s disease (AD) patients using an integrated approach that combines mass spectrometry-based quantitative proteomics, differential expression analysis, and co-expression network analysis. Our analyses of 16 human brain tissues from AD patients and age-matched controls showed organization of the cortical proteome into a network of 24 biologically meaningful modules of co-expressed proteins. Of these, 5 modules are positively correlated to AD phenotypes with hub proteins that are up-regulated in AD, and 6 modules are negatively correlated to AD phenotypes with hub proteins that are down-regulated in AD.

2022-10-05 | PXD037133 | Pride

The first wave of the zygotic transcription is highly promiscuous and uncoupled from splicing and 3 prime end processing.

Project description:Initiation of zygotic transcription in mammals is poorly understood. In mice, zygotic transcription is first detected shortly after pronucleus formation in 1-cell embryos but the identity of the transcribed loci and mechanisms regulating their expression are not known. Using total RNA-seq we find that transcription in 1-cell embryos is highly promiscuous such that intergenic regions are extensively expressed and thousands of genes are transcribed at relatively low levels.

2015-03-19 | E-MTAB-2950 | biostudies-arrayexpress

FTIR, XPol, and LC-MS confirm endogenous collagen in Edmontosaurus fossil bone C4PR_LIV

Project description:Reports of proteins in fossilized bones have ignited an on-going debate because previously it was generally assumed that fossilization results in destruction of all organic components. We combine Attenuated Total Reflection (ATR) Fourier Transform InfraRed (FTIR) spectroscopy, cross-polarized light microscopy (XPol), and two variations of Liquid Chromatography Mass Spectrometry (LC-MS), to detect and verify endogenous collagen protein in fossilized bone. Data from an Edmontosaurus dinosaur excavated from Upper Cretaceous strata of the South Dakota Hell Creek Formation were compared with that from thermally decayed modern turkey (Meleagris) bone. The four methods show different evidence for collagen presence in the fossilized bone. ATR-FTIR spectra show a signal for carbonyl (C=O) groups, a repeat moiety in protein amino acid sequences. XPol shows the birefringence of collagen within Meleagris, as well as Edmontosaurus. LC-MS bottom-up proteomics showed m/z agreement between multiple ions from trypsin-digested samples and identified peptide sequences thus far only identified in a hadrosaur. Tandem LC-MS unambiguously identified hydroxyproline, a unique collagen-indicator amino acid, in acid-digested samples from the same.

2025-03-24 | PXD048810 | Pride

Genotype-specific responses in hepatic lipid metabolism to complete dietary fish oil replacement by vegetable oil in Atlantic salmon

Project description:As part of a study investigating the effects of genotype on responses to sustainable feeds in Atlantic salmon, a microarray analysis of the liver transcriptome of two family groups, identified as 'Lean' or 'Fat' (based on flesh lipid content), which were fed a diet containing either 100% fish oil (FO) or 100% vegetable oil (VO) was undertaken. Cholesterol and lipoprotein metabolism pathways that were differentially affected by diet depending on the genetic background of the fish were identified.<br><br>The TRAITS/SGP (v.2.1) salmon 17k cDNA microarray was used in this experiment. A dual-labelled experimental design was employed for the microarray hybridisations. aRNA from each experimental sample (Cy3 labelled) was competitively hybridised against a common pooled-reference sample (Cy5 labelled), which comprised equal amounts of aRNA from each of the samples used in the study. This design permits valid statistical comparisons across all treatments to be made. The entire experiment comprised 24 hybridisations - 2 lipid phenotypes (Lean/Fat) × 2 diets (FO/VO) × 6 biological replicates.

2011-01-04 | E-TABM-1089 | biostudies-arrayexpress

O-GlcNAc pattern of sOGT regulates its substrate selectivity and function

Project description:O-GlcNAcylation occurs on thousands of proteins involved in various cellular events. O-GlcNAc transferase (OGT), one of the enzymes responsible for protein O-GlcNAcylation, is known to be auto-O-GlcNAcylated at multiple sites. However, the role of O-GlcNAcylation on OGT is still unknown. Here, we report the role of O-GlcNAcylation on short form OGT (sOGT). By LC-ETD-MS analysis and western blot, we show that sOGT was mainly O-GlcNAcylated in the tetratricopeptide repeat (TPR) motifs with T12 and S56 being two “key” sites. T12 was a predominant O-GlcNAcylation site and the absence of S56 O-GlcNAcylation enhanced sOGT O-GlcNAcylation level. We found that O-GlcNAcylation of sOGT did not affect the enzyme activity but increased its binding to substrate proteins. S56A bound to and hence glycosylated more proteins, while T12A associated with fewer substrates. Proteomic studies combined with cell proliferation/cell cycle analyses indicated that S56A substantially enhanced cell proliferation, while T12A reduced it, and T12A led to a G2/M cell cycle arrest, due to O-GlcNAcylation of diverse proteins. These findings demonstrate that the O-GlcNAc pattern on sOGT modulates its function in cells by targeting different proteins.

2019-09-16 | PXD010173 | Pride

Genotype-specific responses in intestinal lipid metabolism to complete dietary fish oil replacement by vegetable oil in Atlantic salmon

Project description:As part of a study investigating the effects of genotype on responses to sustainable feeds in Atlantic salmon, a microarray analysis of the intestine transcriptome of two family groups, identified as 'Lean' or 'Fat' (based on flesh lipid content), which were fed a diet containing either 100% fish oil (FO) or 100% vegetable oil (VO) was undertaken.

2012-03-01 | E-TABM-1173 | biostudies-arrayexpress

NGLY1 mutations cause protein aggregation in human neurons

Project description:Biallelic mutations in the gene that encodes the enzyme N-glycanase 1 (NGLY1) cause a rare disease with multi-symptomatic features including developmental delay, intellectual disability, neuropathy and seizures. NGLY1’s activity in human neural cells is currently not well understood. To understand how NGLY1 gene loss leads to the specific phenotypes of NGLY1 deficiency, we employed direct conversion of NGLY1 patient-derived induced pluripotent stem cells (iPSCs) to functional cortical neurons. Transcriptomic, proteomic, and functional studies of iPSC-derived neurons lacking NGLY1 function revealed several major cellular processes that were altered, including protein aggregate-clearing functionality, mitochondrial homeostasis, and synaptic dysfunctions. These phenotypes were rescued by introduction of a functional NGLY1 gene and were observed in iPSC-derived mature neurons, but not astrocytes. Finally, laser capture microscopy followed by mass spectrometry provided detailed characterization of the composition of protein aggregates specific to NGLY1-deficient neurons. Future studies will harness this knowledge for therapeutic development.

2024-05-23 | PXD031091 | Pride

MOV10 is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation Along 3' UTRs (PAR-CLIP)

Project description:RNA helicases are important regulators of gene expression that act by remodeling RNA secondary structures and as RNA-protein interactions. Here, we demonstrate that MOV10 has an ATP-dependent 5' to 3' in vitro RNA unwinding activity and determine the RNA-binding sites of MOV10 and its helicase mutants using PAR-CLIP. We find that MOV10 predominantly binds to 3' UTRs upstream of regions predicted to form local secondary structures and provide evidence that MOV10 helicase mutants are impaired in their ability to translocate 5' to 3' on their mRNA targets. MOV10 interacts with UPF1, the key component of the nonsense-mediated mRNA decay pathway. PAR-CLIP of UPF1 reveals that MOV10 and UPF1 bind to RNA in close proximity. Knockdown of MOV10 resulted in increased mRNA half-lives of MOV10-bound as well as UPF1-regulated transcripts, suggesting that MOV10 functions in UPF1-mediated mRNA degradation as an RNA clearance factor to resolve structures and displace proteins from 3' UTRs. Flp-In T-REx HEK293 cells expressing FLAG/HA-tagged MOV10 WT, MOV10 K530A, MOV10 D645N and UPF1 were sequenced. mRNA half-life data under GSE56751.

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