Gene expression profiling analysis of laryngeal cancer
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA894710 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22060457_1.fastq.gz | Fastqsanger.gz | |||
| SRR22060457_2.fastq.gz | Fastqsanger.gz | |||
| SRR22060458_1.fastq.gz | Fastqsanger.gz | |||
| SRR22060458_2.fastq.gz | Fastqsanger.gz | |||
| SRR22060459_1.fastq.gz | Fastqsanger.gz |
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Project description:To investigate the metabolic mechanisms of laryngeal cancer. We then performed gene expression profiling analysis using data obtained from ten tumor tissue samples and ten nontumor tissue samples.
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Project description:The pathophysiology of recurrent laryngeal nerve (RLN) transection injury is rare in that it is characteristically followed by a high degree of spontaneous reinnervation, with reinnervation of the laryngeal adductor complex (AC) preceding that of the abducting posterior cricoarytenoid (PCA) muscle. Here, we aim to elucidate the differentially expressed myogenic factors following RLN injury that may be at least partially responsible for the spontaneous reinnervation. F344 male rats underwent RLN injury or sham surgery (n=12). One week after RLN injury, larynges were harvested following euthanasia. mRNA was extracted from PCA and AC muscles bilaterally, and microarray analysis was performed using a full rat genome array. Microarray analysis of denervated AC and PCA muscles demonstrated dramatic differences in gene expression profiles, with 205 individual probes that were differentially expressed between the denervated AC and PCA muscles, and only 14 genes with similar expression patterns. The differential expression patterns of the AC and PCA suggest different mechanisms of reinnervation. The PCA showed the gene patterns of Wallerian degeneration, while the AC expressed the gene patterns of reinnervation by adjacent axonal sprouting. This finding may reveal important therapeutic targets applicable to RLN and other peripheral nerve injuries. Compare mRNA expression from injured tissue (recurrent laryngeal nerve transection injury) to normal tissue from two tissues laryngeal adductor complex and posterior cricoarytenoid muscles.
2016-07-01 | E-GEOD-72361 | biostudies-arrayexpress
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:To understanding the miRNA expression profiling of cancer stem cells of laryngeal squamous carcinoma, the total RNA of CD133+CD44+ laryngeal cancer stem cells (isolated from LSCC cell line TU-177, named TDP), CD133-CD44- cells (TDN) and parental TU-177 (unsorted TU-177 cells, named TPT) was extracted, followed by miRNA sequencing. Differentially expressed miRNAs were identified.
2018-10-27 | GSE106280 | GEO
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:In this study, we aimed to explore the role of miR-145, which is downregulated in LSCC, on cancer stem cell potency of laryngeal cancer cells. Using microRNA expression profiling and experimental follow-up studies, we demonstrated the regulatory role of miR-145 in stem cell characteristics of Hep-2 cells. Based on these results, we propose that mir-145 might carry crucial roles in LSCC tumorigenesis, prognosis, metastasis, chemoresistance and recurrence through regulating stem cell properties of tumor cells.
2015-11-10 | GSE70289 | GEO
Project description:To understand the gene expression profiling of cancer stem cells of laryngeal squamous carcinoma, the total RNA of CD133+CD44+ laryngeal cancer stem cells (isolated from LSCC cell line TU-177, named TDP), CD133-CD44- cells (TDN) and parental TU-177 (unsorted TU-177 cells, named TPT) was extracted, followed by RNA sequencing. Differentially expression of lncRNA, mRNA, and circRNA was identified.
2018-10-27 | GSE106283 | GEO
Project description:In this study, we aimed to explore the role of miR-145, which is downregulated in LSCC, on cancer stem cell potency of laryngeal cancer cells. Using microRNA expression profiling and experimental follow-up studies, we demonstrated the regulatory role of miR-145 in stem cell characteristics of Hep-2 cells. Based on these results, we propose that mir-145 might carry crucial roles in LSCC tumorigenesis, prognosis, metastasis, chemoresistance and recurrence through regulating stem cell properties of tumor cells. LSCC tissue samples and normal tissues were profiled for microRNA expression; cancer tissue profiles were compared with normal tissue profiles.
2015-11-10 | E-GEOD-70289 | biostudies-arrayexpress