Homo sapiens
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PROVIDER: PRJNA255856 | ENA |
REPOSITORIES: ENA
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Project description:Background: MicroRNA (miRNA) is an emerging subclass of small non-coding RNAs that regulates gene expression and has a pivotal role for many physiological processes including cancer development. Recent reports revealed the role of miRNAs as ideal biomarkers and therapeutic targets due to their tissue- or disease-specific nature. Head and neck cancer (HNC) is a major cause of cancer-related mortality and morbidity, and laryngeal cancer has the highest incidence in it. However, the molecular mechanisms involved in laryngeal cancer development remain to be known and highly sensitive biomarkers and novel promising therapy is necessary. Methodology/Principal Findings: To explore laryngeal cancer-specific miRNAs, RNA from 5 laryngeal surgical specimens including cancer and non-cancer tissues were hybridized to microarray carrying 723 human miRNAs. The resultant differentially expressed miRNAs were further tested by using quantitative real time PCR (qRT-PCR) on 43 laryngeal tissue samples including cancers, noncancerous counterparts, benign diseases and precancerous dysplasias. Significant expressional differences between matched pairs were reproduced in miR-133b, miR-455-5p, and miR-196a, among which miR-196a being the most promising cancer biomarker as validated by qRT-PCR analyses on additional 84 tissue samples. Deep sequencing analysis revealed both quantitative and qualitative deviation of miR-196a isomiR expression in laryngeal cancer. In situ hybridization confirmed laryngeal cancer-specific expression of miR-196a in both cancer and cancer stroma cells. Finally, inhibition of miR-196a counteracted cancer cell proliferation in both laryngeal cancer-derived cells and mouse xenograft model. Conclusions/Significance: Our study provided the possibilities that miR-196a might be very useful in diagnosing and treating laryngeal cancer.
2013-06-04 | GSE47610 | GEO
Project description:Background: MicroRNA (miRNA) is an emerging subclass of small non-coding RNAs that regulates gene expression and has a pivotal role for many physiological processes including cancer development. Recent reports revealed the role of miRNAs as ideal biomarkers and therapeutic targets due to their tissue- or disease-specific nature. Head and neck cancer (HNC) is a major cause of cancer-related mortality and morbidity, and laryngeal cancer has the highest incidence in it. However, the molecular mechanisms involved in laryngeal cancer development remain to be known and highly sensitive biomarkers and novel promising therapy is necessary. Methodology/Principal Findings: To explore laryngeal cancer-specific miRNAs, RNA from 5 laryngeal surgical specimens including cancer and non-cancer tissues were hybridized to microarray carrying 723 human miRNAs. The resultant differentially expressed miRNAs were further tested by using quantitative real time PCR (qRT-PCR) on 43 laryngeal tissue samples including cancers, noncancerous counterparts, benign diseases and precancerous dysplasias. Significant expressional differences between matched pairs were reproduced in miR-133b, miR-455-5p, and miR-196a, among which miR-196a being the most promising cancer biomarker as validated by qRT-PCR analyses on additional 84 tissue samples. Deep sequencing analysis revealed both quantitative and qualitative deviation of miR-196a isomiR expression in laryngeal cancer. In situ hybridization confirmed laryngeal cancer-specific expression of miR-196a in both cancer and cancer stroma cells. Finally, inhibition of miR-196a counteracted cancer cell proliferation in both laryngeal cancer-derived cells and mouse xenograft model. Conclusions/Significance: Our study provided the possibilities that miR-196a might be very useful in diagnosing and treating laryngeal cancer. To explore laryngeal cancer-specific miRNAs, RNA from 5 laryngeal surgical specimens including cancer and non-cancer tissues were hybridized to microarray carrying 723 human miRNAs. Total RNA including low molecular weight RNA from tissue samples was isolated using the mirVanaTM miRNA Isolation Kit (Ambion) according to the manufacturer's instructions. The quality of the RNA samples was assessed using an Agilent 2100 Bioanalyzer, and only the samples meeting the criteria of 28S/18S > 1 and RNA Integrity Number (RIN) M-bM-^IM-% 7.5 were used for all analyses. For microarray analysis, we used the Human miRNA Microarray Kit V2 (Agilent Technologies, Santa Clara, CA), which contains 20-40 features targeting each of 723 human miRNAs (Agilent design ID 019118) as annotated in the Sanger miRBase, release 10.1. Labeling and hybridization of total RNA samples were performed according to the manufacturer's protocol. One hundred ng of total RNA was used as an input into the labeling reaction, and the entire reaction was hybridized to each array for 20 hours at 55M-BM-0C. The results were analyzed using Agilent GeneSpring GX7.3. Normal controls and cancer samples were compared using Welch's t-test (p<0.05) and differentially expressed miRNAs with at least a 2-fold change in expression were considered to be potential biomarkers.
2013-06-04 | E-GEOD-47610 | biostudies-arrayexpress
Project description:We used NCode Human Long Non-coding RNA microarray to study differential expression of noncoding RNAs in tumor samples from patients with ovarian cancer. Normal ovarian tissue samples were used as controls.
2015-12-30 | GSE74448 | GEO
Project description:Although many protein-coding genes have been identified to be aberrantly expressed in cervical cancer, the mechanisms of development and progression of cervical cancer remain unclear. In recent years, non-coding RNAs, especially including microRNAs and long non-coding RNAs, have been shown to play important regulatory roles in mammalian cell biology. In our study, we investigated the whole genome gene expression level changes by human transcriptome array in tumor tissues and paired adjacent non-tumor tissue of patients with cervical cancer. The functions of different expression microRNAs, long non-coding RNAs and mRNAs were further analyzed in vitro and in vivo using loss-of-function and gain-of-function approaches. A ten chip study using total RNA recovered from five separate cervical cancer tissues and five paired adjacent non-tumor samples.
2014-10-27 | E-GEOD-55940 | biostudies-arrayexpress
Project description:Background Despite improvement in diagnostic and therapeutic techniques, a significant percentage of patients with early stage laryngeal cancer still recur after treatment. Gene expression models prognostic of recurrence risk could suggest which patients with early stage laryngeal cancer would be more appropriate for testing adjuvant strategies. Patients and Methods Expression profiling using whole genome DASL arrays was performed on 56 formalin-fixed paraffin-embedded tumor samples of patients with early stage laryngeal cancer, treated with surgery or radiation therapy. We split the samples into a training set and a validation set. Using the supervised principal components survival analysis in the first cohort, we identified multiple gene expression profiles that predict the risk of recurrence. These profiles were then validated in the second independent cohort. Results Gene models comprising different number of genes (40-100) identified a subgroup of patients who were at high risk of recurrence. Of these, the best prognostic model distinguished between a high- and a low-risk group (median DFS: 92 and 123 months, log rank p<0.005, permutation p<0.05), Hazard Ratio (HR): 8.51 (95% CI, 1.01 to 71.77; p<0.05). These models performed similarly in the independent cohort of our study (median DFS: 38 vs 161 months, log rank p=0.018), HR=5.19 (95% CI, 1.14 to 23.57; p<0.05). Conclusions We have identified gene expression prognostic models which can refine the estimation of a patient’s risk of recurrence. These findings, if further validated, should aid in patient stratification for testing adjuvant treatment strategies. 56 patients with early stage laryngeal cancer were included in this study.
2011-11-26 | E-GEOD-25727 | biostudies-arrayexpress
Project description:Long non-coding RNAs show highly tissue and disease specific expression profiles. We analyzed prostate cancer and normal adjacent prostate samples to identify cancer-specific transcripts and found 334 candidates, of which 15 were validated by RT-PCR.
2015-03-02 | GSE59745 | GEO
Project description:Oral epithelial dysplasias are believed to progress through a series of histopathological stages; from mild to severe dysplasia, to carcinoma in situ, and finally to invasive OSCC. Underlying this change in histopathological grade are gross chromosome alterations and changes in gene expression of both protein-coding genes and non-coding RNAs. Recent papers have described associations of aberrant expression of microRNAs, one class of non-coding RNAs, with oral cancer. However, expression profiling of long non-coding RNAs (lncRNAs) has not been reported. Long non-coding RNAs are a novel class of mRNA-like transcripts with no protein coding capacity, but with a variety of functions including roles in epigenetics and gene regulation. In recent reports, the aberrant expression of lncRNAs has been associated with human cancers, suggesting a critical role in tumorigenesis. Here, we present the first long non-coding RNA expression map for the human oral mucosa. We describe the expression of 325 long non-coding RNAs, suggesting lncRNA expression contributes significantly to the oral transcriptome. Intriguingly, 60% of the detected lncRNAs show aberrant expression in oral premalignant lesions. A number of these lncRNAs have been previously associated with other human cancers. A total of six normal oral samples and ten oral premalignant lesions were used to construct SAGE libraries which were then queried for long non-coding RNA expression profiles. The six normal oral samples were previously deposited as GSE8127.
2011-08-14 | E-GEOD-31021 | biostudies-arrayexpress
Project description:RNAseq analysis of 12 human macrophage samples was performed using ribosomal-depleted total RNA to analyze long non-coding RNA and coding transcript expression profiles comparing macrophage in vitro subtypes (M2, M1 and TAM) obtained from peripheral blood normal monocytes.
2022-06-23 | GSE135491 | GEO
Project description:CircRNA expression profiles for 6 human samples derived from patients with gastric cancer
| PRJNA350394 | ENA
Project description:LncRNA expression profiles for 6 human samples derived from patients with gastric cancer
| PRJNA208084 | ENA