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Series GSE129951 Query DataSets for GSE129951
Status Public on Jan 22, 2020
Title Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Aberrant expression of HOXC6 and HOXC4 is commonly detected in prostate cancer. The high expression of these transcription factors is associated with aggressive prostate cancer and can predict cancer recurrence after treatment. Thus, HOXC4 and HOXC6 are clinically relevant biomarkers of aggressive prostate cancer. However, the molecular mechanisms by which these HOXC genes contribute to prostate cancer is not yet understood. To begin to address the role of HOXC4 and HOXC6 in prostate cancer, we performed RNA-seq analyses before and after siRNA-mediated knockdown of HOXC4 and/or HOXC6 and also performed ChIP-seq to identify genomic binding sites for both of these transcription factors. Our studies demonstrate that HOXC4 and HOXC6 co-localize with HOXB13, FOXA1 and AR, three transcription factors previously shown to contribute to the development of prostate cancer. We suggest that the aberrantly upregulated HOXC4 and HOXC6 proteins may compete with HOXB13 for binding sites, thus altering the prostate transcriptome. This competition model may be applicable to many different human cancers that display increased expression of a HOX transcription factor.
Overall design Examination of HOXC6 binding sites in human prostate cancer 22Rv1 cell line. HOXC4 and HOXC6 were knockdown by siRNA the transcriptomic changes were investigated by RNA_seq.
Contributor(s) Luo Z, Farnham PJ
Citation(s) 32012197
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 CA136924 Prostate Cancer Risk Enhancers UNIVERSITY OF SOUTHERN CALIFORNIA PEGGY J Farnham
Submission date Apr 17, 2019
Last update date Feb 24, 2020
Contact name Zhifei Luo
Organization name University of Southern California
Street address 1450 Biggy Street, NRT 6514
City Los Angeles
State/province CA
ZIP/Postal code 90089-9601
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (28)
GSM3728501 siControl_rep1
GSM3728502 siControl_rep2
GSM3728503 siControl_rep3
BioProject PRJNA533284
SRA SRP192852

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Supplementary file Size Download File type/resource
GSE129951_HOXB13.narrowPeak.gz 152.4 Kb (ftp)(http) NARROWPEAK
GSE129951_HOXC4.narrowPeak.gz 222.2 Kb (ftp)(http) NARROWPEAK
GSE129951_IDR.FOXA1.narrowPeak.gz 555.3 Kb (ftp)(http) NARROWPEAK
GSE129951_IDR.HOXC6.22Rv1.narrowPeak.gz 636.1 Kb (ftp)(http) NARROWPEAK
GSE129951_raw_read_counts.txt.gz 1.3 Mb (ftp)(http) TXT
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Processed data are available on Series record

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