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Series GSE130688 Query DataSets for GSE130688
Status Public on May 18, 2022
Title Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Transcriptome analysis of pancreatic ductal adenocarcinoma (PDAC) has been useful to identify gene expression changes that sustain malignant phenotypes. Yet, most studies examined only tumor tissues and focused on protein-coding genes, leaving long non-coding RNAs (lncRNAs) largely underexplored.

Methods: We generated total RNA-Seq data from patient-matched tumor and nonmalignant pancreatic tissues and implemented a computational pipeline to survey known and novel lncRNAs. siRNA-mediated knockdown in tumor cell lines was performed to assess the contribution of PDAC-associated lncRNAs to malignant phenotypes. Gene co-expression network and functional enrichment analyses were used to assign deregulated lncRNAs to biological processes and molecular pathways.

Results: We detected 9,032 GENCODE lncRNAs as well as 523 unannotated lncRNAs, including transcripts significantly associated with patient outcome. Aberrant expression of a subset of novel and known lncRNAs was confirmed in patient samples and cell lines. siRNA-mediated knockdown of a subset of these lncRNAs (LINC01559, LINC01133, CCAT1, LINC00920 and UCA1) reduced cell proliferation, migration and invasion. Gene co-expression network analysis associated PDAC-deregulated lncRNAs with diverse biological processes, such as cell adhesion, protein glycosylation and DNA repair. Furthermore, UCA1 knockdown was shown to specifically deregulate co-expressed genes involved in DNA repair and to negatively impact DNA repair following damage induced by ionizing radiation.

Conclusions: Our study expands the repertoire of lncRNAs deregulated in PDAC, thereby revealing novel candidate biomarkers for patient risk stratification. It also provides a roadmap for functional assays aimed to characterize novel mechanisms of action of lncRNAs in pancreatic cancer, which could be explored for therapeutic development.

 
Overall design Strand-oriented total RNA-seq libraries from 15 paired samples (tumor and non-tumor adjacent pancreatic tissue) were sequenced using Illumina HiSeq 1500/2500 platform
 
Contributor(s) Reis EM, Sosa O
Citation(s) 35567709
Submission date May 03, 2019
Last update date May 22, 2022
Contact name Eduardo Moraes Reis
E-mail(s) emreis@iq.usp.br
Phone +55-11-30912173
Organization name University of São Paulo
Department Biochemistry
Street address Av. Prof. Lineu Prestes, 748
City São Paulo
State/province SP
ZIP/Postal code 05508-900
Country Brazil
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (30)
GSM3747758 Non-tumor 1N
GSM3747759 Tumor 1T
GSM3747760 Non-tumor 2N
Relations
BioProject PRJNA540989
SRA SRP194936

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE130688_RAW.tar 62.4 Mb (http)(custom) TAR (of TXT)
GSE130688_pdac_assembly.fa.gz 81.2 Mb (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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