Tumor Biology

, Volume 36, Issue 9, pp 7175–7183 | Cite as

Long non-coding RNA LINC01296 is a potential prognostic biomarker in patients with colorectal cancer

Research Article

Abstract

Colorectal cancer (CRC), one of the most malignant cancers, is currently the fourth leading cause of cancer deaths worldwide. Recent studies indicated that long non-coding RNAs (lncRNAs) could be robust molecular prognostic biomarkers that can refine the conventional tumor-node-metastasis staging system to predict the outcomes of CRC patients. In this study, the lncRNA expression profiles were analyzed in five datasets (GSE24549, GSE24550, GSE35834, GSE50421, and GSE31737) by probe set reannotation and an lncRNA classification pipeline. Twenty-five lncRNAs were differentially expressed between CRC tissue and tumor-adjacent normal tissue samples. In these 25 lncRNAs, patients with higher expression of LINC01296, LINC00152, and FIRRE showed significantly better overall survival than those with lower expression (P < 0.05), suggesting that these lncRNAs might be associated with prognosis. Multivariate analysis indicated that LINC01296 overexpression was an independent predictor for patients’ prognosis in the test datasets (GSE24549, GSE24550) (P = 0.001) and an independent validation series (GSE39582) (P = 0.027). Our results suggest that LINC01296 could be a novel prognosis biomarker for the diagnosis of CRC.

Keywords

Colorectal cancer lncRNA Biomarker LINC01296 

Supplementary material

13277_2015_3448_Fig4_ESM.gif (51 kb)
Fig. S1

Validation of 45 differentially expressed lncRNAs using an independent dataset (GSE50421). In HCA (A), the x axis represents the samples, and lncRNAs are shown on the y axis. Red spots represent upregulated genes, and green spots represent downregulated genes. The sample types are shown with bar colors in the dendrogram; blue stripes represent tumor-adjacent normal samples, and red stripes are tumor samples. In PCA (B), green dots represent tumor-adjacent normal tissue samples, and red dots represent tumor tissue samples. In GSE50421, CRC samples can be distinguished from tumor-adjacent normal tissues by HCA and PCA (GIF 51 kb)

13277_2015_3448_MOESM1_ESM.tif (5 mb)
High resolution image (TIFF 5137 kb)
13277_2015_3448_Fig5_ESM.gif (48 kb)
Fig. S2

Validation of 38 differentially expressed lncRNAs using an independent dataset (GSE35834). In HCA (A), the x axis represents the samples, and lncRNAs are shown on the y axis. Red spots represent upregulated genes, and green spots represent downregulated genes. The sample types are shown with bar colors in the dendrogram; blue stripes represent tumor-adjacent normal samples, and red stripes are tumor samples. In PCA (B), green dots represent tumor-adjacent normal tissue samples, and red dots represent tumor tissue samples. In GSE35834, CRC samples can be distinguished from tumor-adjacent normal tissues by HCA and PCA (GIF 48 kb)

13277_2015_3448_MOESM2_ESM.tif (4.6 mb)
High resolution image (TIFF 4678 kb)
13277_2015_3448_Fig6_ESM.gif (67 kb)
Fig. S3

Validation of 48 differentially expressed lncRNAs using an independent dataset (GSE24549). In HCA (A), the x axis represents the samples, and lncRNAs are shown on the y axis. Red spots represent upregulated genes, and green spots represent downregulated genes. The sample types are shown with bar colors in the dendrogram; blue stripes represent tumor-adjacent normal samples, and red stripes are tumor samples. In PCA (B), green dots represent tumor-adjacent normal tissue samples, and red dots represent tumor tissue samples. In GSE24549, CRC samples can be distinguished from tumor-adjacent normal tissues by HCA and PCA (GIF 67 kb)

13277_2015_3448_MOESM3_ESM.tif (3.1 mb)
High resolution image (TIFF 3164 kb)
13277_2015_3448_Fig7_ESM.gif (62 kb)
Fig. S4

Validation of 45 differentially expressed lncRNAs using an independent dataset (GSE24550). In HCA (A), the x axis represents the samples, and lncRNAs are shown on the y axis. Red spots represent upregulated genes, and green spots represent downregulated genes. The sample types are shown with bar colors in the dendrogram; blue stripes represent tumor-adjacent normal samples, and red stripes are tumor samples. In PCA (B), green dots represent tumor-adjacent normal tissue samples, and red dots represent tumor tissue samples. In GSE24550, CRC samples can be distinguished from tumor-adjacent normal tissues by HCA and PCA (GIF 61 kb)

13277_2015_3448_MOESM4_ESM.tif (3.6 mb)
High resolution image (TIFF 3693 kb)
13277_2015_3448_MOESM5_ESM.doc (28 kb)
ESM 5(DOC 28 kb)
13277_2015_3448_MOESM6_ESM.doc (14 kb)
ESM 6(DOC 13 kb)
13277_2015_3448_MOESM7_ESM.doc (74 kb)
ESM 7(DOC 73 kb)

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Copyright information

© International Society of Oncology and BioMarkers (ISOBM) 2015

Authors and Affiliations

  1. 1.Shanghai Children’s Hospital, Shanghai Institute of Medical GeneticsShanghai Jiao Tong University School of MedicineShanghaiChina
  2. 2.Key Laboratory of Embryo Molecular BiologyMinistry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction EngineeringShanghaiChina
  3. 3.State Key Laboratory of Biocherapy/Collaborative Innovation Center for Biotherapy, West China HospitalSichuan UniversityChengduChina

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