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Phosphoproteomics analysis of PC-12 cells stimulated with IGF-1 for 30 minutes

ABSTRACT: For this study, we stimulated neuronal differentiated pheochromocytoma (PC-12) cells with IGF-1 or vehicle for 30 minutes before extracting protein and subjecting each replicate to tandem mass tag (TMT)-labeled quantitative mass spectrometric phosphoproteomics analysis. Peptides were analyzed on the Orbitrap Eclipse Tribrid mass spectrometer.

INSTRUMENT(S):

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Adrenal Gland

SUBMITTER: Morgan Rothschadl

LAB HEAD: Samuel Sathyanesan

PROVIDER: PXD067358 | Pride | 2026-02-02

REPOSITORIES: Pride

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Source:

			Action	DRS
	Experiment_MaxQuant_lysate_from_SathyanesanS_012324_Lysate_SF01__17_others.mgf	Mgf
	Experiment_MaxQuant_lysate_from_SathyanesanS_012324_Lysate_SF01__17_others.mzid	Mzid
	Experiment_MaxQuant_phospho_from_SathyanesanS_012324_phos_SF01__17_others.mgf	Mgf
	Experiment_MaxQuant_phospho_from_SathyanesanS_012324_phos_SF01__17_others.mzid	Mzid
	SathyanesanS_012324_Lysate_SF01.raw	Raw

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Project description:Conserved Oligomeric Golgi (COG) is an octameric protein complex that orchestrates intra-Golgi trafficking of glycosylation enzymes. Over a hundred individuals with 31 different COG mutations have been identified until now. The cellular phenotypes and clinical presentations of COG-CDGs are heterogeneous, and patients primarily represent neurological, skeletal, and hepatic abnormalities. The establishment of a cellular COG disease model will benefit the molecular study of the disease, explaining the detailed sequence of the interplay between the COG complex and the trafficking machinery. Moreover, patient fibroblasts are not a good representative of all the organ systems and cell types that are affected by COG mutations. We developed and characterized cellular models for human COG4 mutations specifically in RPE1 and HEK293T cell lines. Using a combination of CRISPR/Cas9 and lentiviral transduction technologies, both myc-tagged wild-type and mutant (G516R and R729W) COG4 proteins were expressed under the endogenous COG4 promoter. Constructed isogenic cell lines were comprehensively characterized using biochemical, microscopy (superresolution and electron), and proteomics approaches. The analysis revealed similar stability and localization of COG complex subunits, wild-type cell growth, and normal Golgi morphology in all three cell lines. Importantly, COG4-G516R cells demonstrated increased HPA-647 binding to the plasma membrane glycoconjugates, while COG4-R729W cells revealed high GNL-647 binding, indicating specific defects in O- and N-glycosylation. Both mutant cell lines express elevated level of heparin sulfate proteoglycans. Moreover, a quantitative mass-spectrometry analysis of proteins secreted by COG-deficient cell lines revealed abnormal secretion of SIL1 and ERGIC-53 proteins by COG4-G516R cells. Interestingly, the clinical phenotype of patients with congenital mutations in SIL1 gene (Marinesco-Sjogren syndrome) overlaps with the phenotype of COG4-G516R patients (Saul-Wilson syndrome). Our work is the first compressive study involving the creation of different COG mutations in different cell lines other than patient’s fibroblast. It may help to address the underlying cause of the phenotypic defects leading to the discovery of a proper treatment guideline for COG-CDGs.

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Phosphoproteomics analysis of PC-12 cells stimulated with IGF-1 for 30 minutes

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