OMICS Analyses Unraveling Related Gene and Protein-Driven Molecular Mechanisms Underlying PACAP 38-Induced Neurite Outgrowth in PC12 Cells.

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Neurite projection elongation was suggested to be mediated via Pac1 receptor-mediated dephosphorylation of CRMP2, where GSK-3β, CDK5, and Rho/ROCK dephosphorylated CRMP2 within 3 h after addition of PACAP, but the dephosphorylation of CRMP2 by PACAP remained unclear. Thus, we attempted to identify the early factors in PACAP-induced neurite projection elongation via omics-based transcriptomic (whole genome DNA microarray) and proteomic (TMT-labeled liquid chromatography-tandem mass spectrometry) analyses of gene and protein expression profiles from 5-120 min after PACAP addition. The results revealed a number of key regulators involved in neurite outgrowth, including known ones, called 'Initial Early Factors', e.g., genes Inhba, Fst, Nr4a1,2,3, FAT4, Axin2, and proteins Mis12, Cdk13, Bcl91, CDC42, including categories of 'serotonergic synapse, neuropeptide and neurogenesis, and axon guidance'. cAMP signaling and PI3K-Akt signaling pathways and a calcium signaling pathway might be involved in CRMP2 dephosphorylation. Cross-referencing previous research, we tried to map these molecular components onto potential pathways, and we may provide important new information on molecular mechanisms of neuronal differentiation induced by PACAP. Gene and protein expression data are publicly available at NCBI GSE223333 and ProteomeXchange, identifier PXD039992.", "claims": [{"id": "claim-method", "statement": "Multiple sample test, controlled by the Benjamini–Hochberg FDR threshold of 0.05, was applied to identify the significant differences in the protein abundance (≥1.25- and ≥1.5-fold change).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36835581", "locator": "sections[24] \"3.3.4. Data Processing Using MaxQuant Software and Data Analysis Using Perseus and R Program\" paragraph 2", "quote": "Multiple sample test, controlled by the Benjamini–Hochberg FDR threshold of 0.05, was applied to identify the significant differences in the protein abundance (≥1.25- and ≥1.5-fold change)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this study are available in the article and submitted databases. 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PC12 cells cultured in 10 cm sterile culture dishes were incubated", "Materials and Methods 3.1. 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The categories mentioned in the di", "mote neurite outgrowth [63]. The present DNA microarray analysis showed that RGS2 expression tended"], "order_basis": "paper_text_order:709", "id": "assay:3"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ic (TMT-labeled liquid chromatography-tandem mass spectrometry) analyses of gene and protein expression pro", "abundance (≥1.25- and ≥1.5-fold change). The mass spectrometry proteomics data have been deposited to the P", "scriptomic (whole genome DNA microarray) and proteomic (TMT-labeled liquid chromatography-tandem ma", "n were used for total protein extraction for proteomic analysis [9,10,12]. 3.3.1. Protein Digestion"], "order_basis": "paper_text_order:725", "id": "assay:4"}]}