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| Status |
Public on Feb 12, 2022 |
| Title |
The alterations of gene expression profiling induced by ts-ARFGEF1 knockdown in MCF-7 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Analysis of high-throughput transcriptome sequencing (RNA-seq) data often observed numerous 'non-co-linear' (NCL) transcripts, which may originate from genetic rearrangements (gene fusion) indicated the importance of fusion events and circRNAs in carcinogenesis; however, the role of ts-RNAs remains largely uninvestigated. Here we developed a hybrid sequencing pipeline ("NCLscan-hybrid"), which integrated different types of short (Illumina-based) and extra-long (PacBio-based) RNA-seq data to eliminate potential false positives from experimental artifacts, fusion events, and circRNAs. We applied NCLscan-hybrid to investigate of ts-RNAs in human breast cancer, the most malignant tumors diagnosed in women worldwide. Through multiple experimental validation steps, we confirmed that the intragenic ts-RNA, ts-ARFGEF1, was highly expressed in breast cancer cells but absent in normal breast cells. Furthermore, we experimentally validated that ts-ARGEF1 can contribute to cell proliferation and apoptosis. Analysis of xenograft in nude mice showed that disruption of ts-ARFGEF1 expression can significantly attenuate tumor growth. Microarray analysis revealed that ts-ARFGEF1 knockdown could trigger PERK/ATF4/CHOP signaling pathway, implying the function of ts-ARFGEF1 in ER homeostasis. Taken together, our findings provide an in-depth view of the true complexity of intragenic NCL events and, for the first time, show further insight into the potential roles of intragenic ts-RNAs in tumor cell development.
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| Overall design |
We performed knockdown ts-ARFGEF1 in MCF-7 cells.
The microarray results were used to screen gene expression changes by ts-ARFGEF1
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| Contributor(s) |
Chuang T |
| Citation missing |
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| Submission date |
Feb 10, 2022 |
| Last update date |
Feb 23, 2022 |
| Contact name |
Trees-Juen Chuang |
| E-mail(s) |
trees@gate.sinica.edu.tw
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| Organization name |
Academic Sinica
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| Department |
Genomics Research Center
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| Street address |
128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan
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| City |
Taipei |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
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| Platforms (1) |
| GPL23126 |
[Clariom_D_Human] Affymetrix Human Clariom D Assay [transcript (gene) version] |
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| Samples (6)
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| GSM5889155 |
MCF-7 cells, negative control for knockdown of ts-ARFGEF1, rep1 |
| GSM5889156 |
MCF-7 cells, negative control for knockdown of ts-ARFGEF1, rep2 |
| GSM5889157 |
MCF-7 cells, negative control for knockdown of ts-ARFGEF1, rep3 |
| GSM5889158 |
MCF-7 cells, knockdown of ts-ARFGEF1, rep1 |
| GSM5889159 |
MCF-7 cells, knockdown of ts-ARFGEF1, rep2 |
| GSM5889160 |
MCF-7 cells, knockdown of ts-ARFGEF1, rep3 |
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| Relations |
| BioProject |
PRJNA805506 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE196514_RAW.tar |
128.3 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE196514_comparison_of_ASO_vs_Scr.txt.gz |
4.6 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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