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| Status |
Public on Jun 30, 2016 |
| Title |
Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer [Affymetrix] |
| Platform organism |
synthetic construct |
| Sample organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
|
| Summary |
Targeted cancer therapy for squamous cell carcinoma (SCC) has made little progress largely due to a lack of knowledge of the driving genomic alterations. Small non-coding RNAs (sncRNAs) as a potential biomarker and therapeutic target to SCC remain a challenge. We analyzed sncRNAs microarray in 108 fresh frozen specimens of esophageal squamous cell carcinoma (ESCC) as discovery set and assessed associations between sncRNAs and recurrence-free survival. SncRNA signature identified was externally validated in two independent cohorts. We investigated the functional consequences of sncRNA identified and its integrative analysis of complex cancer genomics. We identified 3 recurrence-associated sncRNAs (miR-223, miR-1269a and nc886) from discovery set and proved risk prediction model externally in high and low volume centers. We uncovered through in vitro experiment that nc886 was down-regulated by hypermethylation of its promoter region and influences splicing of pre-mRNAs with minor introns by regulating expression of minor spliceosomal small nuclear RNAs (snRNAs) such as RNU4atac. Integrative analysis from lung SCC data in The Cancer Genome Atlas revealed that patients with lower expression of nc886 had more genetic alterations of TP53, DNA damage response and cell cycle genes. nc886 inhibits minor splicing to suppress expression of certain oncogenes such as PARP1 and E2F family containing minor introns. We present risk prediction model with sncRNAs for ESCC. Among them, nc886 may contribute to complete minor splicing via regulation of minor spliceosomal snRNAs supporting the notion that aberrant alteration in minor splicing might be a key driver of ESCC.
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| |
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| Overall design |
Clinical study
ESCC tumor samples vs. ESCC normal samples
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| |
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| Contributor(s) |
Lee H, Lee Y, Lee J |
| Citation(s) |
27507904 |
| |
| Submission date |
Mar 13, 2014 |
| Last update date |
May 02, 2017 |
| Contact name |
Hyun-Sung Lee |
| E-mail(s) |
hyun-sung.lee@bcm.edu
|
| Phone |
7137988010
|
| Organization name |
BAYLOR COLLEGE OF MEDICINE
|
| Department |
Surgery
|
| Lab |
ABBR R651H
|
| Street address |
One Baylor Plaza
|
| City |
HOUSTON |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL14613 |
[miRNA-2] Affymetrix Multispecies miRNA-2 Array |
|
| Samples (216)
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| This SubSeries is part of SuperSeries: |
| GSE55857 |
Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer |
|
| Relations |
| BioProject |
PRJNA241158 |
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