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Genome-scale long noncoding RNA expression pattern in squamous cell lung cancer.

Wang Y, Qian CY, Li XP, Zhang Y, He H, Wang J, Chen J, Cui JJ, Liu R, Zhou H, Xiao L, Xu XJ, Zheng Y, Fu YL, Chen ZY, Chen X, Zhang W, Ye CC, Zhou HH, Yin JY, Liu ZQ - Sci Rep (2015)

Bottom Line: The expression level of genome-wide scale lncRNA and mRNA was determined by microarray. qRT-PCR was used to validate the lncRNA expression level in 47 patients.The annotation result of their co-expressed mRNAs showed that the most significantly related category of GO analysis was development and differentiation, while the most significantly related pathway was cell cycle.Our study indicated that clusters of lncRNAs were significantly and differentially expressed in SQCC compared with normal tissues in the same subject.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008; P. R. China; Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha 410078; P. R. China [2] The Affiliated Cancer Hospital of XiangYa School of Medicine, Central South University, Changsha, Hunan 410014, P. R. China.

ABSTRACT
In this study, we aimed to explore the long noncoding RNA expression pattern in squamous cell lung cancer (SQCC) on a genome-wide scale. Total RNAs were extracted from 16 lung SQCC patients' normal and matched lung cancer tissues by Trizol reagent. The expression level of genome-wide scale lncRNA and mRNA was determined by microarray. qRT-PCR was used to validate the lncRNA expression level in 47 patients. Data analyses were performed using R and Bioconductor. A total of 2,748 up and 852 down regulated probes were identified to be significantly and differentially expressed in tumor tissues. The annotation result of their co-expressed mRNAs showed that the most significantly related category of GO analysis was development and differentiation, while the most significantly related pathway was cell cycle. Subgroup analysis identified that 46 and 18 probes were specifically differentially expressed in smoking and moderately differentiated tumors, respectively. Our study indicated that clusters of lncRNAs were significantly and differentially expressed in SQCC compared with normal tissues in the same subject. They may exert a significant role in lung cancer development and could be potential targets for future treatment of SQCC.

No MeSH data available.


Related in: MedlinePlus

Significantly differentially expressed mRNAs in lung SQCC.(A) Volcano plot of the differential mRNA expression analysis. X-axis: log2 fold change (median tumor-median NTL); Y-axis: −1 × log10 (FDR p-value) for each probes; Vertical dotted lines: fold change ≥2 or ≤2; Horizontal dotted line: the significance cutoff (FDR p-value = 0.05). (B) Two-dimensional hierarchical clustering of the significant and differentially expressed mRNA probes in all samples (16 tumor tissues in gray vs. 16 NTL tissues in black). Probes are in rows; samples are in columns.
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f2: Significantly differentially expressed mRNAs in lung SQCC.(A) Volcano plot of the differential mRNA expression analysis. X-axis: log2 fold change (median tumor-median NTL); Y-axis: −1 × log10 (FDR p-value) for each probes; Vertical dotted lines: fold change ≥2 or ≤2; Horizontal dotted line: the significance cutoff (FDR p-value = 0.05). (B) Two-dimensional hierarchical clustering of the significant and differentially expressed mRNA probes in all samples (16 tumor tissues in gray vs. 16 NTL tissues in black). Probes are in rows; samples are in columns.

Mentions: For these 3,600 differentially expressed lncRNA probes, the function of most of them remains unknown. Therefore, we predicted their potential function via the annotation of their co-expressed mRNAs. Firstly, the genome wide mRNA expression profile of these 16 lung SQCC and matched NTL tissues were detected. Also, The criteria of corrected p-value < 0.05 and absolute fold change >2 were used to identify significantly and differentially expressed mRNAs. Among the 30,201 detected probes, a total of 5,253 probes were found to be significantly differentially expressed (Fig. 2A, Table S2). 2,593 probes were up regulated, and 2,660 probes were down regulated. These differentially expressed probes were used to generate a heatmap, as indicated in Fig. 2B, they were clearly segregated into tumor and NTL clusters. This result suggested that these mRNAs were substantially different between tumor and NTL tissues.


Genome-scale long noncoding RNA expression pattern in squamous cell lung cancer.

Wang Y, Qian CY, Li XP, Zhang Y, He H, Wang J, Chen J, Cui JJ, Liu R, Zhou H, Xiao L, Xu XJ, Zheng Y, Fu YL, Chen ZY, Chen X, Zhang W, Ye CC, Zhou HH, Yin JY, Liu ZQ - Sci Rep (2015)

Significantly differentially expressed mRNAs in lung SQCC.(A) Volcano plot of the differential mRNA expression analysis. X-axis: log2 fold change (median tumor-median NTL); Y-axis: −1 × log10 (FDR p-value) for each probes; Vertical dotted lines: fold change ≥2 or ≤2; Horizontal dotted line: the significance cutoff (FDR p-value = 0.05). (B) Two-dimensional hierarchical clustering of the significant and differentially expressed mRNA probes in all samples (16 tumor tissues in gray vs. 16 NTL tissues in black). Probes are in rows; samples are in columns.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4498179&req=5

f2: Significantly differentially expressed mRNAs in lung SQCC.(A) Volcano plot of the differential mRNA expression analysis. X-axis: log2 fold change (median tumor-median NTL); Y-axis: −1 × log10 (FDR p-value) for each probes; Vertical dotted lines: fold change ≥2 or ≤2; Horizontal dotted line: the significance cutoff (FDR p-value = 0.05). (B) Two-dimensional hierarchical clustering of the significant and differentially expressed mRNA probes in all samples (16 tumor tissues in gray vs. 16 NTL tissues in black). Probes are in rows; samples are in columns.
Mentions: For these 3,600 differentially expressed lncRNA probes, the function of most of them remains unknown. Therefore, we predicted their potential function via the annotation of their co-expressed mRNAs. Firstly, the genome wide mRNA expression profile of these 16 lung SQCC and matched NTL tissues were detected. Also, The criteria of corrected p-value < 0.05 and absolute fold change >2 were used to identify significantly and differentially expressed mRNAs. Among the 30,201 detected probes, a total of 5,253 probes were found to be significantly differentially expressed (Fig. 2A, Table S2). 2,593 probes were up regulated, and 2,660 probes were down regulated. These differentially expressed probes were used to generate a heatmap, as indicated in Fig. 2B, they were clearly segregated into tumor and NTL clusters. This result suggested that these mRNAs were substantially different between tumor and NTL tissues.

Bottom Line: The expression level of genome-wide scale lncRNA and mRNA was determined by microarray. qRT-PCR was used to validate the lncRNA expression level in 47 patients.The annotation result of their co-expressed mRNAs showed that the most significantly related category of GO analysis was development and differentiation, while the most significantly related pathway was cell cycle.Our study indicated that clusters of lncRNAs were significantly and differentially expressed in SQCC compared with normal tissues in the same subject.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008; P. R. China; Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha 410078; P. R. China [2] The Affiliated Cancer Hospital of XiangYa School of Medicine, Central South University, Changsha, Hunan 410014, P. R. China.

ABSTRACT
In this study, we aimed to explore the long noncoding RNA expression pattern in squamous cell lung cancer (SQCC) on a genome-wide scale. Total RNAs were extracted from 16 lung SQCC patients' normal and matched lung cancer tissues by Trizol reagent. The expression level of genome-wide scale lncRNA and mRNA was determined by microarray. qRT-PCR was used to validate the lncRNA expression level in 47 patients. Data analyses were performed using R and Bioconductor. A total of 2,748 up and 852 down regulated probes were identified to be significantly and differentially expressed in tumor tissues. The annotation result of their co-expressed mRNAs showed that the most significantly related category of GO analysis was development and differentiation, while the most significantly related pathway was cell cycle. Subgroup analysis identified that 46 and 18 probes were specifically differentially expressed in smoking and moderately differentiated tumors, respectively. Our study indicated that clusters of lncRNAs were significantly and differentially expressed in SQCC compared with normal tissues in the same subject. They may exert a significant role in lung cancer development and could be potential targets for future treatment of SQCC.

No MeSH data available.


Related in: MedlinePlus