PXD007121

PXD007121 is an original dataset announced via ProteomeXchange.

Title	Long Non-coding RNA SNHG1 in Neuroblastoma
Description	Neuroblastoma (NB) is an embryonal tumor with various clinical presentations and behaviors. Several genomic alterations has been well-studied in NB, among which genomic amplification of MYCN oncogene, is a strong prognostic biomarker with worsens outcome. Long noncoding RNAs (lncRNAs), constitute major proportion of the cellular transcripts with no coding capacity. One of their function is to guide transcription factors to the target genes and facilitate gene expression. However, relative contribution of lncRNA and MYCN to the advanced NB has remained unclear. Herein, by applying a network-based integrative analysis on MYCN amplified and MYCN nonamplified lncRNA expression profile from both RNA-seq and microarray platform, we identified lncRNA, SNHG1 to be differentially expressed and strongly correlated with MYCN in MYCN-amplified NB. The expression of SNHG1 was validated by RT-qPCR in NB cell lines. Survival analysis revealed that higher expression of SNHG1 significantly associates with poor patient survival. Moreover, knockdown of MYCN in MYCN-amplified NB cell lines inhibited SNHG1 expression. Furthermore, to unravel the role of SNHG1 in NB, we extracted SNHG1-interacting proteins by RNA-protein pull down assay coupled with doi:10.6342/NTU201701980 ! ! VI liquid chromatography-tandem mass spectrometry (LC-MS/MS). We identified 27 SNHG1-interacting proteins in common from three NB cell lines. However, only three SNHG1-interacting proteins, MATR3, YBX1 and HHRNPL have binding site detected by DeepBind motif analysis. Western blot confirms interaction of MATR3 with SNHG1. Additionally, we further validated the direct interaction between MATR3 and SNHG1 by RNA-immunoprecipation (IP). MATR3 is known to be involved in RNA transport and stabilization. Therefore, we proposed that MATR3 after interacting with SNHG1 might help in SNHG1 transcription and stabilization. In conclusion, our study unveils that SNHG1 could be a prognostic marker for high-risk NB and possibly stabilized by MATR3. Our results might provide future directions for the development of therapeutic strategies against high-risk NB.
HostingRepository	PRIDE
AnnounceDate	2022-03-01
AnnouncementXML	Submission_2022-03-01_09:03:56.719.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tz-Wen Yang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-25 03:13:32	ID requested
⏵ 1	2022-03-01 09:03:57	announced

Yang TW, Sahu D, Chang YW, Hsu CL, Hsieh CH, Huang HC, Juan HF, RNA-Binding Proteomics Reveals MATR3 Interacting with lncRNA SNHG1 To Enhance Neuroblastoma Progression. J Proteome Res, 18(1):406-416(2019) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Neuroblastoma

MYCN

Long non-coding RNA

SNHG1

RNA-protein pull down assay

LC-MS/MS

RNA-immunoprecipation (IP)

MATR3

Hsueh-Fen Juan
contact affiliation	National Taiwan University, Institute of Molecular & Cellular Biology
contact email	yukijuan@gmail.com
lab head
Tz-Wen Yang
contact affiliation	National Taiwan University
contact email	r04b43006@ntu.edu.tw
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007121
     1. Label: PRIDE project
     2. Name: Long Non-coding RNA SNHG1 in Neuroblastoma