Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide analysis of miRNA levels in colon cancer

ABSTRACT: Analysis of miRNA levels found in tissue obtained from proficient mismatch repair (pMMR) TNM stage 2|3|4 colon tumor, deficient MMR (dMMR) colon tumor, and normal colon. miRNA levels obtained from macrodissected colon tumors with > 70% H&E staining were compared with normal colon tissue. Additional comparisons based on mismatch repair status identified by loss of hMLH1 protein and microsattelite instability assay and TNM stage were carried out. This submission provides access to the data discussed in our paper. The supplementary file 'GSE18392_non-normalized_data.txt' file contains non-normalized data for Samples GSM458618-GSM458762.

ORGANISM(S): Homo sapiens

SUBMITTER: Aaron Sarver

PROVIDER: E-GEOD-18392 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states.

Sarver Aaron L AL French Amy J AJ Borralho Pedro M PM Thayanithy Venugopal V Oberg Ann L AL Silverstein Kevin A T KA Morlan Bruce W BW Riska Shaun M SM Boardman Lisa A LA Cunningham Julie M JM Subramanian Subbaya S Wang Liang L Smyrk Tom C TC Rodrigues Cecilia M P CM Thibodeau Stephen N SN Steer Clifford J CJ

BMC cancer 20091118

<h4>Background</h4>Colon cancer arises from the accumulation of multiple genetic and epigenetic alterations to normal colonic tissue. microRNAs (miRNAs) are small, non-coding regulatory RNAs that post-transcriptionally regulate gene expression. Differential miRNA expression in cancer versus normal tissue is a common event and may be pivotal for tumor onset and progression.<h4>Methods</h4>To identify miRNAs that are differentially expressed in tumors and tumor subtypes, we carried out highly sens ...[more]

PMID: 19922656

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Project description:Long non-coding RNAs (lncRNAs) are recently characterized players that are involved in the regulatory circuitry of self-renewal in human embryonic stem cells (hESCs). However, the specific roles of lncRNAs in this circuitry are poorly understood. Here, we determined that growth-arrest-specific transcript 5 (GAS5), which is a known tumor suppressor and growth arrest gene, is abundantly expressed in the cytoplasm of hESCs and essential for hESC self-renewal. GAS5 depletion in hESCs significantly impaired their pluripotency and self-renewal ability, whereas GAS5 overexpression in hESCs accelerated the cell cycle, enhanced their colony formation ability and increased pluripotency marker expression. By RNA sequencing and bioinformatics analysis, we determined that GAS5 activates NODAL-SMAD2/3 signaling by sustaining the expression of NODAL, which plays a key role in hESC self-renewal but not in somatic cell growth. Further studies indicated that GAS5 functions as a competing endogenous RNA (ceRNA) to protect NODAL mRNA against degradation and that GAS5 transcription is directly controlled by the core pluripotency transcriptional factors (TFs). Taken together, we suggest that the core TFs, GAS5 and NODAL-SMAD2/3 form a feed-forward loop to maintain the hESC self-renewal process. These findings are specific to ESCs and did not occur in the somatic cell lines we tested; therefore, our findings also provide evidence that the functions of lncRNAs vary in different biological contexts. We analyzed long non-coding RNAs in two hESC cell lines (X-01 and H1), and found GAS5 is highly expressed and functional in maintaining hESC self-renewal. We generate stable overexpressed or knockdown hESC cell lines using lentiviral approach. We transfected cells initialy after passage, and lentiviruses are added with daily medium change for three days (at a final concentration of 10^5 IU/ml). Puromycin is added for selection and supplied with daily medium change. Stable cell lines are established after two passages and verified under fluorescence scope. Total RNAs and miRNAs are extracted separately of all three cell lines (LV-NC, LV-GAS5 and LV-shGAS5) and put to sequencing.

Dataset Information

Genome-wide analysis of miRNA levels in colon cancer

Publications

Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states.

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