PXD010221-2

PXD010221 is an original dataset announced via ProteomeXchange.

Title	Proteomics analysis of DUX4-expressing myoblasts
Description	DUX4 is a double homeodomain transcription factor whose misexpression in the muscle causes facioscapulohumeral muscular dystrophy (FSHD). The transcriptional activity of DUX4 has been extensively characterized, and is thought to be the primary driver of FSHD pathogenesis. Yet, DUX4 expression lowers the protein level of an RNA quality control factor, UPF1, without affecting its transcript level, hinting at post-transcriptional regulatory activity downstream of DUX4 expression. How extensive the post-transcriptional activity of DUX4 is, and how relevant it is to FSHD pathogenesis, is unknown. In order to gain insight into DUX4-induced post-transcriptional gene regulation, we measured transcript and protein levels in DUX4 expressing cells via RNA-seq and SILAC-based quantitative mass spectrometry, respectively. We show that DUX4 transcriptional targets are robustly translated, including those genes previously identified as potential FSHD biomarkers. However, comparing the overall pattern of gene expression changes for RNA versus protein reveals striking differences in the most highly activated pathways, with the former showing changes in RNA processing and splicing, and the latter affecting the humoral immune response, proteolysis and exocytosis, among other pathways. Consistent with a misregulation of exocytosis, fluorescence imaging shows fragmented golgi apparatus in DUX4-expressing cells. Of the genes that showed discordant RNA and protein expression levels, post-transcriptional buffering was particularly evident for genes involved in stress response and may explain why DUX4-expressing cells succumb to toxicity despite robust transcriptional activation of stress response genes. Moreover, several genes involved in RNA decay including UPF1, UPF3B, SMG6 and XRN1 showed downregulation at the protein level, which may explain the massive inhibition of RNA quality control in DUX4-expressing cells. These results highlight the importance of considering post-transcriptional gene regulation in DUX4-expressing cells in order to fully understand the FSHD disease process.
HostingRepository	PRIDE
AnnounceDate	2022-03-14
AnnouncementXML	Submission_2022-03-14_05:53:45.535.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Philip Gafken
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-26 01:56:45	ID requested
1	2019-01-21 04:47:01	announced
⏵ 2	2022-03-14 05:53:46	announced	2022-03-14: Updated project metadata.
3	2024-10-22 04:46:21	announced	2024-10-22: Updated project metadata.

Jagannathan S, Ogata Y, Gafken PR, Tapscott SJ, Bradley RK, Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of facioscapulohumeral muscular dystrophy. Elife, 8():(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: myoblasts, SILAC,Dux4, FSHD, gelc-ms

Sujatha Jagannathan
contact affiliation	University of Colorado School of Medicine Biochemistry and Molecular Genetics Denver, CO
contact email	sujatha.jagannathan@ucdenver.edu
lab head
Philip Gafken
contact affiliation	Fred Hutchinson Cancer Research Center
contact email	pgafken@fhcrc.org
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/2019/01/PXD010221

PRIDE project URI

• PRIDE
  1. PXD010221
     1. Label: PRIDE project
     2. Name: Proteomics analysis of DUX4-expressing myoblasts