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| Status |
Public on Feb 02, 2021 |
| Title |
LncRNA ASTILCS as an important regulator of liver carcinoma cell survival [non-coding RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Extensive genomic studies have significantly improved our understanding of hepatocellular carcinoma (HCC) biology and have led to the discovery of multiple protein-coding genes driving hepatocarcinogenesis. In addition, these studies have identified thousands of new non-coding transcripts deregulated in HCC, suggesting these transcripts are important for disease progression. Long non-coding RNA is a large class of non-coding transcripts which participate in the regulation of virtually all cellular functions. However, a majority of lncRNAs remain dramatically understudied. Here, we applied a pooled shRNA-based screen to identify lncRNAs essential for HCC cell survival. We validated our screening results using RNAi, CRISPRi, and antisense oligonucleotides. We found a lncRNA, termed ASTILCS, is critical for HCC cell growth and is overexpressed in tumors from HCC patients. We demonstrated that HCC cell death upon ASTILCS knockdown is associated with apoptosis induction and downregulation of a neighboring gene, Protein Tyrosine Kinase 2 (PTK2), a crucial protein for HCC cell survival. Taken together, our study describes a novel regulator of HCC progression providing valuable insight in HCC biology.
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| Overall design |
RNA-Seq of Huh7 liver cell line RNA
Sample title "H" and "L" are internal nomenclature and do not represent variables used in analysis.
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| Contributor(s) |
Rybakova Y, Gonzalez JT, Bogorad R, Chauhan VP, Dong YL, Whittaker CA, Kotelianski V, Anderson DG |
| Citation(s) |
33589614 |
| Submission date |
Jun 17, 2020 |
| Last update date |
May 04, 2021 |
| Contact name |
Charles Arthur Whittaker |
| E-mail(s) |
charliew@mit.edu
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| Organization name |
Koch Institute
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| Street address |
77 Mass Ave 76-189
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02152 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE152651 |
LncRNA ASTILCS as an important regulator of liver carcinoma cell survival |
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| Relations |
| BioProject |
PRJNA639970 |
| SRA |
SRP267629 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE152650_hg19_GRCh37_68_noncoding.fa.gz |
4.4 Mb |
(ftp)(http) |
FA |
| GSE152650_rybkayu_fpkm.txt.gz |
169.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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