Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Long noncoding RNA expression profile analysis of colorectal cancer and metastatic lymph node based on microarray data.

ABSTRACT: Long noncoding RNAs (lncRNAs) are emerging as an important part of biological progress in cancers, yet the aberrant lncRNAs implicated in colorectal cancer (CRC) with lymph node metastasis remain unknown. In this study, a total of 390 lncRNA transcripts and 508 mRNA transcripts were dysregulated in tumor tissues compared with paired metastatic lymph nodes. Functional prediction showed that lots of lncRNAs might be involved in biological pathways related to CRC metastasis by cis-regulation and trans-regulation of coexpressed genes. As a representative, ENST00000430471 was associated with cell proliferation and invasion of CRC cells. These results provided support for further investigations of the metastatic pathogenesis of CRC.

SUBMITTER: Yang P

PROVIDER: S-EPMC4853163 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Long noncoding RNA expression profile analysis of colorectal cancer and metastatic lymph node based on microarray data.

Yang Peng P Xu Zi-Peng ZP Chen Tao T He Zhen-Yu ZY

OncoTargets and therapy 20160426

Long noncoding RNAs (lncRNAs) are emerging as an important part of biological progress in cancers, yet the aberrant lncRNAs implicated in colorectal cancer (CRC) with lymph node metastasis remain unknown. In this study, a total of 390 lncRNA transcripts and 508 mRNA transcripts were dysregulated in tumor tissues compared with paired metastatic lymph nodes. Functional prediction showed that lots of lncRNAs might be involved in biological pathways related to CRC metastasis by cis-regulation and tr ...[more]

PMID: 27217770

Similar Datasets

The long noncoding RNA expression profile of hepatocellular carcinoma identified by microarray analysis.

Project description:BackgroundThousands of long noncoding RNAs (lncRNAs) have been reported in mammalian genomes. These RNAs represent an important subset of pervasive genes involved in a broad range of biological functions. Aberrant expression of lncRNAs is associated with many types of cancers. Here, in order to explore the potential lncRNAs involved in hepatocellular carcinoma (HCC) oncogenesis, we performed lncRNA gene expression profile analysis in 3 pairs of human HCC and adjacent non-tumor (NT) tissues by microarray.MethodologyDifferentially expressed lncRNAs and mRNAs were detected by human lncRNA microarray containing 33,045 lncRNAs and 30,215 coding transcripts. Bioinformatic analyses (gene ontology, pathway and network analysis) were applied for further study of these differentially expressed mRNAs. By qRT-PCR analysis in nineteen pairs of HCC and adjacent normal tissues, we found that eight lncRNAs were aberrantly expressed in HCC compared with adjacent NT tissues, which is consistent with microarray data.ConclusionsWe identified 214 lncRNAs and 338 mRNAs abnormally expressed in all three HCC tissues (Fold Change ≥2.0, P<0.05 and FDR <0.05) with the genome-wide lncRNAs and mRNAs expression profile analysis. The lncRNA-mRNA co-expression network was constructed, which may be used for predicting target genes of lncRNAs. Furthermore, we demonstrated for the first time that BC017743, ENST00000395084, NR_026591, NR_015378 and NR_024284 were up-regulated, whereas NR_027151, AK056988 and uc003yqb.1 were down-regulated in nineteen pairs of HCC samples compared with adjacent NT samples. Expression of seven lncRNAs was significantly correlated to their nearby coding genes. In conclusion, our results indicated that the lncRNA expression profile in HCC was significantly changed, and we identified a series of new hepatocarcinoma associated lncRNAs. These results provide important insights about the lncRNAs in HCC pathogenesis.

| S-EPMC4099127 | biostudies-literature

Microarray Profile of Long Noncoding RNA and Messenger RNA Expression in a Model of Alzheimer's Disease.

Project description:Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by a deficiency in cognitive skills. Although long noncoding RNAs (lncRNAs) have been proposed as associated with AD, the aberrant lncRNAs expression and the co-expression of lncRNAs-mRNAs network in AD remains unclear. Therefore, in this study, lncRNA microarray was performed on the brain of APP/PS1 mice at different age, widely used as an AD mouse model, and on age-matched wide-type controls. Our results identified a total of 3306 lncRNAs and 2458 mRNAs as aberrantly expressed among AD mice at different age and their age-matched control. Gene Ontology and pathway analysis of the AD-related lncRNAs and mRNAs indicated that neuroinflammation-related and synaptic transmission signaling pathways represented the main enriched pathways. An lncRNA-mRNA-miRNA network between the differentially expressed transcripts was constructed. Moreover, an mRNA-miRNA network between both significantly dysregulated and highly conserved genes was also constructed, and among this network, the IGF1, P2RX7, TSPO, SERPINE1, EGFR, HMOX1, and NFE212 genes were predicted to play a role in the development of AD. In conclusion, this study illustrated the prognostic value of lncRNAs and mRNAs associated to AD pathology by microarray analysis and might provide potential novel biomarkers in the diagnosis and treatment of AD.

| S-EPMC7281340 | biostudies-literature

Plasma long noncoding RNA expression profile identified by microarray in patients with Crohn's disease.

Project description:AimTo investigate the expression pattern of plasma long noncoding RNAs (lncRNAs) in Chrohn's disease (CD) patients.MethodsMicroarray screening and qRT-PCR verification of lncRNAs and mRNAs were performed in CD and control subjects, followed by hierarchy clustering, GO and KEGG pathway analyses. Significantly dysregulated lncRNAs were categorized into subgroups of antisense lncRNAs, enhancer lncRNAs and lincRNAs. To predict the regulatory effect of lncRNAs on mRNAs, a CNC network analysis was performed and cross linked with significantly changed lncRNAs. The overlapping lncRNAs were randomly selected and verified by qRT-PCR in a larger cohort.ResultsInitially, there were 1211 up-regulated and 777 down-regulated lncRNAs as well as 1020 up-regulated and 953 down-regulated mRNAs after microarray analysis; a heat map based on these results showed good categorization into the CD and control groups. GUSBP2 and AF113016 had the highest fold change of the up- and down-regulated lncRNAs, whereas TBC1D17 and CCL3L3 had the highest fold change of the up- and down-regulated mRNAs. Six (SNX1, CYFIP2, CD6, CMTM8, STAT4 and IGFBP7) of 10 mRNAs and 8 (NR_033913, NR_038218, NR_036512, NR_049759, NR_033951, NR_045408, NR_038377 and NR_039976) of 14 lncRNAs showed the same change trends on the microarray and qRT-PCR results with statistical significance. Based on the qRT-PCR verified mRNAs, 1358 potential lncRNAs with 2697 positive correlations and 2287 negative correlations were predicted by the CNC network.ConclusionThe plasma lncRNAs profiles provide preliminary data for the non-invasive diagnosis of CD and a resource for further specific lncRNA-mRNA pathway exploration.

| S-EPMC4870078 | biostudies-literature

Synchronous Resectable Metastatic Colorectal Cancer: Lymph Node Involvement Predicts Poor Outcome.

Project description:To evaluate the value of lymph node status of primary tumors in predicting the prognosis of synchronous resectable metastatic colorectal cancer (mCRC).The characteristics of resectable mCRC are substantially different from other cancers, and the prognostic factors of resectable mCRC are still controversial.The data of 2007 patients with mCRC who received resection of the primary tumors and metastatic lesions synchronously were reviewed from the Surveillance, Epidemiology and End-Result database. The Kaplan-Meier method was used to evaluate the capacity of different prognostic factors. Univariate and multivariate logistic regression models were used to evaluate the relationship between the lymph node status and other factors. The mRNA profiles of primary resectable mCRC tumors were obtained by microarray at our center.The median survival times were 50, 36, 32, 27, and 19 months in the N0-stage, N1a-stage, N1b-stage, N2a-stage, and N2b-stage subgroups according to the 7th American Joint Committee on Cancer (AJCC) Tumor Lymph Node Metastasis (TNM) N-classification (P = 0.000), and 40, 29, 22, and 15 months in patients with metastatic lymph node ratio (LNR) <0.25, 0.25-0.49, 0.5-0.74, and ≥0.75 subgroups (P = 0.000). In the COX model, the 7th AJCC TNM N-stage and LNR were independent prognostic factors. The mRNA profile was not associated with lymph node involvement.Both the N-stage according to the 7th AJCC TNM staging system and LNR had the capacity to subclassify synchronous resectable mCRC with different prognoses. The lymph node might be integrated into the AJCC staging system as a diagnose-delay prognostic factor for stage IV disease.

| S-EPMC4554134 | biostudies-literature

Aberrant Expression Profile of Long Noncoding RNA in Human Sinonasal Squamous Cell Carcinoma by Microarray Analysis.

Project description:Objectives. This study aimed to identify aberrantly expressed long noncoding RNAs (lncRNAs) profile of sinonasal squamous cell carcinoma (SSCC) and explore their potential functions. Methods. We investigated lncRNA and mRNA expression in SSCC and paired adjacent noncancerous tissues obtained from 6 patients with microarrays. Gene ontology (GO) analysis and pathway analysis were utilized to investigate the gene function. Gene signal-network and lncRNA-mRNA network were depicted. Quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to validate 5 lncRNAs in a second set of paired SSCC and adjacent noncancerous tissues obtained from 22 additional patients. Results. We identified significantly differentially expressed lncRNAs (n = 3146) and mRNAs (n = 2208) in SSCC relative to noncancerous tissues. The GO annotation indicated that there are some core gene products that may be attributed to the progress of SSCC. The pathway analysis identified many pathways associated with cancer. The results of lncRNA-mRNA network and gene signal-network implied some core lncRNAs/mRNAs might play important roles in SSCC pathogenesis. The results of qRT-PCR showed that all of the 5 lncRNAs were differentially expressed and consistent with the microarray results. Conclusion. Our study is the first screening and analysis of lncRNAs expression profile in SSCC and may offer new insights into pathogenesis of this disease.

| S-EPMC5156798 | biostudies-literature

Integrated analysis of long noncoding RNA and mRNA expression profile in children with obesity by microarray analysis.

Project description:Long noncoding RNAs (lncRNAs) have an important role in adipose tissue function and energy metabolism homeostasis, and abnormalities may lead to obesity. To investigate whether lncRNAs are involved in childhood obesity, we investigated the differential expression profile of lncRNAs in obese children compared with non-obese children. A total number of 1268 differentially expressed lncRNAs and 1085 differentially expressed mRNAs were identified. Gene Ontology (GO) and pathway analysis revealed that these lncRNAs were involved in varied biological processes, including the inflammatory response, lipid metabolic process, osteoclast differentiation and fatty acid metabolism. In addition, the lncRNA-mRNA co-expression network and the protein-protein interaction (PPI) network were constructed to identify hub regulatory lncRNAs and genes based on the microarray expression profiles. This study for the first time identifies an expression profile of differentially expressed lncRNAs in obese children and indicated hub lncRNA RP11-20G13.3 attenuated adipogenesis of preadipocytes, which is conducive to the search for new diagnostic and therapeutic strategies of childhood obesity.

| S-EPMC5993825 | biostudies-literature

Altered long noncoding RNA profile after intracerebral hemorrhage.

Project description:OBJECTIVE:We investigated the expression pattern of long noncoding RNAs (lncRNA) and messenger RNAs (mRNA) from two different intracerebral hemorrhage (ICH) rat models, and performed gene ontology and gene/protein interaction analyses. METHODS:We harvested hemorrhagic brain 1, 3, and 7 days after ICH induction by stereotactic collagenase injection. We performed microarray analyses with Agilent array platform to compare the expression of lncRNA and mRNAs from hemorrhagic and normal brains. The RNA expression patterns were also examined from the autologous blood injection ICH model at days 1 and 3, and significantly altered lncRNAs from two ICH models were validated by quantitative reverse transcriptase-polymerase chain reaction. Gene ontology analysis and pathway analysis were performed with differentially expressed mRNAs after ICH. Gene and protein interaction analysis was performed to elucidate the functional role of upregulated lncRNA in neuronal damage. RESULTS:Among the 13,661 lncRNAs studied, 83, 289, and 401 lncRNAs were significantly elevated after 1, 3, and 7 days after collagenase-induced ICH, respectively. NR_027324, or H19, was the most upregulated lncRNA after 1 day from the two ICH models and its elevation persisted until the 7th day. Gene ontology analysis revealed that immune-related biological processes such as immune response, immune system process, and defense response were upregulated from both ICH models. Gene and protein interaction study demonstrated that NR_027324 was closely related to the type I interferon signaling pathway. INTERPRETATION:This study illustrates the dynamic expression pattern of the lncRNA profile following ICH, and that H19 is the most consistently upregulated lncRNA after ICH.

| S-EPMC6801204 | biostudies-literature

Long noncoding RNA ANRIL as a novel biomarker of lymph node metastasis and prognosis in human cancer: a meta-analysis.

Project description:Dysregulation of the long noncoding RNA antisense noncoding RNA in the INK4 locus (ANRIL) has been reported in various solid tumors. We performed a synthetic analysis to clarify the clinical value of ANRIL as a prognostic indicator in malignant tumors. Article collection was conducted using several electronic databases, including PubMed, Web of Science, Medline, OVID and Embase (up to July 14 2017). Thirteen original studies and 1172 total patients were included in the meta-analysis. There was a significant positive association between the high expression level of ANRIL and lymph node metastasis (OR = 4.77, 95% CI: 2.30-9.91, P < 0.001) by a random effects model (I2 = 73.2, P = 0.001) and negative association with poor grade cancer (OR = 3.44, 95% CI: 1.68-7.08) by a random-effects model (I2 = 77.9, P = 0.000). The results of the meta-analysis showed that overexpression of ANRIL is positively related to poor overall survival (OS) (pooled HR = 2.12, 95% CI: 1.78-2.53, P < 0.0001) by a fixed-effects model (I2 = 0%, P = 0.654) and poor disease-free survival (DFS) (HR = 2.10, 95% CI: 1.51-2.92, P < 0.001) by a fixed-effects model (I2 = 13.3%, P = 0.315) in human solid cancers. Statistically significant associations were also found with cancer type, analysis method, sample size, and follow-up time. In conclusion, ANRIL may serve as a novel biomarker for indicating lymph node metastasis and prognosis in human cancer.

| S-EPMC5865693 | biostudies-literature

Limited effect of lymph node status on the metastatic pattern in colorectal cancer.

Project description:Regional lymph node metastases in colorectal cancer (CRC) decrease outcome. Whether nodal metastases function as a biomarker, i.e. as a sign of advanced disease, or are in fact involved in the metastatic process is unclear. We evaluated metastatic patterns of CRC according to the lymph node status of the primary tumor.A retrospective review of 1393 patients with metastatic CRC who underwent autopsy in the Netherlands was performed. Metastatic patterns of regional lymph node positive and negative CRC were compared and validated by population-based data from the Eindhoven Cancer Registry (ECR).Patients with regional lymph node positive CRC more often developed peritoneal metastases (28% vs. 21%, p=0.003) and distant lymph node metastases (25% vs. 15%, p <0.001). Incidences of liver and lung metastases were comparable. Data from the ECR confirmed our findings regarding peritoneal (22.4% vs. 17.0%, p=0.003) and distant lymph node metastases (15.8% vs. 9.7%, p <0.001).Regional lymph node positive CRC show a slightly different dissemination pattern, with higher rates of peritoneal and distant lymph nodes metastases. Comparable incidences of liver and lung metastases support the hypothesis that dissemination to distant organs occurs independently of lymphatic spread.

| S-EPMC5077970 | biostudies-literature

Cancer histology in metastatic lymph node predicts prognosis in patients with node-positive stage IV colorectal cancer

Project description: Not available

| S-EPMC11243965 | biostudies-literature