PXD039945

PXD039945 is an original dataset announced via ProteomeXchange.

Title	Effects of pro-opiomelanocortin neuropeptides on immunological pathways mediated by the melanocortin 3 receptor revealed by label-free quantitative thermal proteome profiling
Description	In a thermal proteome profiling experiment we have identified 300 unique proteins that become thermally stabilized or destabilized downstream of signal activation of the melanocortin 3 receptor (MC3R) when expressed in HEK293 cells. Upon stimulation with either one of the endogenous MC3R-agonists ACTH, alpha-, or gamma-MSH, derived from the pro-opiomelanocortin (POMC) prohormone, we found that the majority of these thermally affected proteins is related to immunoregulatory processes including signaling cascades up- and downstream of the key transcription factors IRF, STAT and NFkappaB. Here, we have developed a computational pipeline that allows assessment of thermal melting curves from data obtained with label-free quantitation from ion-mobility enhanced LC-MS data. It enables differential expression analysis within the data obtained from a thermal proteome profiling experiment, since all relative abundance information is retained. We found with principal component analysis that the three POMC-peptides act in very distinguished ways on the expression pattern in the MC3R-expressing HEK293 cells. This is consistent with our findings from thermal proteome profiling analysis where we identified 142, 107 and 95 proteins to be thermally affected by ACTH, alpha- and gamma-MSH, respectively, with only 4 proteins identified across all three agonists, and an additional 36 proteins shared pairwise between the agonists. Interestingly, we found proteins involved in immune responses to be enriched according to gene set enrichment analysis with Reactome pathways. As a result of these findings, we inferred transcription factor activities of the involved thermally affected transcription factors using Bayesian analysis based on differential expression data. Our findings on transcription factor activity were validated with patterns of peptide phosphorylation abundance analysis. These combined efforts revealed that all three agonists act via the cAMP-PKA-CREB pathway but that there are differences in the further downstream affected pathways and the identities of the thermally affected pathways proteins in particular kinases.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:13:43.360.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD039945
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Erik Jansson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	amidated residue; acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-08 02:07:16	ID requested
1	2023-10-25 09:39:34	announced
⏵ 2	2023-11-14 09:13:50	announced	2023-11-14: Updated project metadata.

10.6019/PXD039945;

Sandbaumh, ü, ter FA, Nezhyva M, Andr, é, n PE, Jansson ET, Label-Free Quantitative Thermal Proteome Profiling Reveals Target Transcription Factors with Activities Modulated by MC3R Signaling. Anal Chem, 95(41):15400-15408(2023) [pubmed]

submitter keyword: MC3R, TPP, label-free quantitation, POMC

Erik Jansson
contact affiliation	Department of Pharmaceutical Biosciences, Uppsala University
contact email	erik.jansson@farmbio.uu.se
lab head
Erik Jansson
contact affiliation	Uppsala University
contact email	erik.jansson@farmbio.uu.se
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/10/PXD039945

PRIDE project URI

• PRIDE
  1. PXD039945
     1. Label: PRIDE project
     2. Name: Effects of pro-opiomelanocortin neuropeptides on immunological pathways mediated by the melanocortin 3 receptor revealed by label-free quantitative thermal proteome profiling