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Series GSE212912 Query DataSets for GSE212912
Status Public on Oct 18, 2022
Title Selective Regulation of Tuft Cell-Like Small Cell Lung Cancer by Novel Transcriptional Co-activators C11orf53 and COLCA2
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The DepMap project has generated a huge resource for investigating selectively essential genes, which represent potential cancer therapeutic targets. However, manually sorting out which of the hundreds of selectively essential genes is understudied and warrants investigations is time-consuming and probably not practical. To efficiently identify uncharacterized, selectively essential genes, we collected and ranked the 347 selectively essential genes from the DepMap dataset by their PubMed publication counts, based on the assumption that genes with low publication counts are un-studied or under-studied. We successfully validated two of the top candidates in our ranking system, C11orf53 and COLCA2, as new vulnerabilities that are selectively essential in the class II POU domain transcription factor POU2F3-dependent tuft cell-like small cell lung cancer (SCLC) cell lines. Importantly, we found that the sequence motif, which mediates physical interactions of the transcriptional co-activator POU2AF1 with two of the class II POU domain-containing family of transcription factors (POU2F1 and POU2F2), is also present in the N-terminal regions of C11orf53 and COLCA2. We further confirmed that 1) COLCA2 physically interacts with POU2F3 through this conserved sequence motif; 2) this interaction is important for COLCA2 to regulate tuft cell-like SCLC cell growth, and 3) both C11orf53 and COLCA2 contain transcriptional co-activator domains. Consistently, we find similar transcriptomic changes in response to the loss of COLCA2 or POU2F3 in SCLC cells. In summary, our analysis pipeline enables identification and prioritization of understudied but important, selectively essential genes, leading to the identification of two new transcriptional co-activators for the class II POU domain transcription factors. Disruption of this important physical interaction is predicted to be a potential therapeutic strategy to selectively inhibit tuft cell-like SCLCs.
Overall design We performed RNA-sequencing for NCI-H1048 cells treated with COLCA2 gRNA (2 samples were treated with different COLCA2 gRNAs), POU2F3 gRNA or non-targeting gRNA.
Web link
Contributor(s) Zhou C
Citation(s) 36253350
Submission date Sep 08, 2022
Last update date Oct 21, 2022
Contact name Yang Shi
Organization name Ludwig Institute for Cancer Research, University of Oxford
Street address Old Road Campus Research Building, Roosevelt Drive
City Oxford
ZIP/Postal code OX3 7DQ
Country United Kingdom
Platforms (1)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (4)
GSM6560964 NCIH1048_COLCA2_gRNA_1
GSM6560965 NCIH1048_COLCA2_gRNA_2
GSM6560966 NCIH1048_POU2F3_gRNA
BioProject PRJNA878253

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Supplementary file Size Download File type/resource
GSE212912_RAW.tar 1.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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