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Series GSE114772 Query DataSets for GSE114772
Status Public on Dec 03, 2018
Title KLF4, a gene regulating prostate stem cell homeostasis, is a barrier to malignant progression and predictor of a good prognosis in prostate cancer
Organism Mus musculus
Experiment type Expression profiling by genome tiling array
Genome binding/occupancy profiling by high throughput sequencing
Summary We propose that genes that control adult stem cell homeostasis in slowly turning over organs, such as prostate, control cancer fate. One such gene, KLF4, highly expressed in murine prostate stem cells, regulates their homeostasis, blocks malignant transformation and controls the self-renewal of tumor initiating cells. KLF4 loss induces molecular features of aggressive cancer and converts PIN lesions to invasive sarcomatoid carcinomas; its re-expression in vivo reverses this process. Bioinformatic analysis links these changes to human cancer. KLF4 and its signature containing downstream targets identify indolent tumors and predict recurrence-free survival in 2 prostate cancer cohorts. Thus, the link between normal stem cells and cancer control provides new approaches to improve prognosis and for identifying therapeutic targets for advanced cancer.
Overall design The Akt transformed prostate stem cell line was infected with shKlf4 (shKlf4) or non-silencing control (shCon) lentivirus. After 48 hr cells were selected by puromycin for 2 days and passaged for 10 days to allow cells to undergo EMT. The infected shCon and shKlf4 cells were collected for RNA extraction. Another cohort of shKlf4 cells was infected with BFP tagged Doxycycline inducible human KLF4 (shKlf4+KLF4) or BFP tagged Doxycycline inducible empty vector (shKlf4+EV) lentivirus. After 3 days, 100 ng/ml of Dox was added to cultures of shKlf4+KLF4 and shKlf4+BFP cells to induce KLF4 expression while companion cultures (shKlf4+KLF4 and shKlf4+EV cells) received no Dox. Two days later, all shKlf4+KLF4 and shKlf4+EV cells with or without Dox treatment were collected for RNA extraction. Total RNA was extracted using an RNeasy mini kit (Qiagen, CA). RNA-seq libraries were prepared with the TruSeq sample preparation kit (Illumina, CA).
Contributor(s) Xiong X, Khodadadi-Jamayran A, Zhou H, Tsirigos A, Wilson EL
Citation(s) 30540935
Submission date May 22, 2018
Last update date Mar 21, 2019
Contact name Alireza Khodadadi-Jamayran
Organization name New York University, NYU Langone Medical Center
Department Division of Advanced Research Technologies (DART)
Lab Applied Bioinformatics Laboratories (ABL)
Street address 550 1st Ave, MSB 304
City New York City
State/province NY
ZIP/Postal code 10016
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (14)
GSM3149970 input_IgG
GSM3149971 Klf4_Ab
GSM3149972 RHS_1
BioProject PRJNA472603
SRA SRP148691

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

Supplementary file Size Download File type/resource
GSE114772_RAW.tar 2.5 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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