CircRNA sequencing analysis of PTMC with lateral lymph node metastases and related clinical value studies of circRNA.
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ABSTRACT:
PROVIDER: PRJNA847254 | ENA |
REPOSITORIES: ENA
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Project description:High-throughput sequencing was used to detect the expression profile of circRNA in PTMC of lymph node metastasis in lateral cervical region, and RT-qPCR was used to detect the expression of circRNA in cancer tissues and normal tissues adjacent to cancer. The receiver operating characteristic (ROC) curve and the area under ROC curve (AUC) were used to evaluate whether CircRNAs could be used as a biomarker for the diagnosis of thyroid cancer. Bioinformatics was used to predict the PTMC-related ceRNA mechanism of lateral cervical lymph node metastasis.
2023-06-08 | GSE205733 | GEO
Project description:Different aspects of intra-tumor heterogeneity (ITH), which are associated with development of cancer and its response to treatment, have postulated prognostic value. Here we searched for the potential association between phenotypic ITH analyzed by mass spectrometry imaging (MSI) and the prognosis of head and neck cancer. The study involved tissue specimens resected from 77 patients with locally advanced oral squamous cell carcinoma, including 37 patients where matched samples of primary tumor and synchronous lymph node metastases were analyzed. A 3-year follow-up was available for all patients that enabled their separation into two groups: with no evidence of disease (NED, n=41) and with progressive disease (PD, n=36). After the on-tissue trypsin digestion, peptide maps of all cancer regions were segmented using an unsupervised approach to reveal their intrinsic heterogeneity. We found that intra-tumor similarity of spectra was higher in the PD group and diversity of clusters identified during image segmentation was higher in the NED group, which indicated a higher level of ITH in patients with more favorable outcomes. Furthermore, signature of molecular components that correlated with long-term outcomes could be associated with proteins involved in the immune functions. Hence, we proposed that a higher level of ITH revealed by MSI in cancers with a better prognosis could reflect the presence of heterotypic components of tumor microenvironment such as infiltrating immune cells enhancing the response to the treatment. LC-MALDI-MS/MS data deposited in this repository originate from protein lysates obtained from FFPE sections consecutive to sections dedicated to MSI measurements. The hypothetical identity of the MSI components was established by assignment of a component location on the m/z scale for the measured masses of tryptic peptides identified by LC-MALDI-MS/MS allowing ±0.05% mass tolerance.
2022-10-13 | PXD034958 | Pride
Project description:To identify the lymph node (LN) metastasis-associated genes in primary ESCC tumors, gene expression profiling assay (GEP) was performed to identify the differences in gene expression profiles between primary ESCC tumors that were with LN metastases (N+) and those without LN metastases (N-).
2018-08-14 | GSE118493 | GEO
Project description:We performed oligonucleotide microarray analysis to assess the genetic expression alteration wich affected on lateral neck node metastasis of thyroid papillary microcarcinoma(PTMC). We performed microarray analysis in three PTMCs without cervical lymph-node metastases (N0), and five PTMCs with lateral neck-node metastasis (N1b) at initial diagnosis, using an Illumina HumanHT-12 v4.0 Expression BeadChip.
2019-11-12 | GSE129562 | GEO
Project description:Lymph Node Metastases in Colon Cancer are Polyclonal
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Project description:Samples were taken from colorectal cancers in surgically resected specimens in 89 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting lymph node metastases. Keywords: disease state analysis
2010-08-31 | GSE4459 | GEO
Project description:Skin melanomas are highly aggressive and metastatic. Omomyc is the best MYC inhibitor currently available. We analysed the effect of Omomyc expression in a transgenic and inducible (upon Doxycycline addition) manner in spontaneous lymph node metastases from SkMel147 (mutated in NRAS) melanoma cells in vivo. We used microarrays to detail the change in the gene expression programs induced by Omomyc on day 2.
2023-04-09 | GSE227843 | GEO
Project description:CONTEXT:Most papillary microcarcinomas (PMCs) are indolent and subclinical. However, as many as 10% can present with clinically significant nodal metastases. OBJECTIVE AND DESIGN:Characterization of the genomic and transcriptomic landscape of PMCs presenting with or without clinically important lymph node metastases. SUBJECTS AND SAMPLES:Formalin-fixed paraffin-embedded PMC samples from 40 patients with lateral neck nodal metastases (pN1b) and 71 patients with PMC with documented absence of nodal disease (pN0). OUTCOME MEASURES:To interrogate DNA alterations in 410 genes commonly mutated in cancer and test for differential gene expression using a custom NanoString panel of 248 genes selected primarily based on their association with tumor size and nodal disease in the papillary thyroid cancer TCGA project. RESULTS:The genomic landscapes of PMC with or without pN1b were similar. Mutations in TERT promoter (3%) and TP53 (1%) were exclusive to N1b cases. Transcriptomic analysis revealed differential expression of 43 genes in PMCs with pN1b compared with pN0. A random forest machine learning-based molecular classifier developed to predict regional lymph node metastasis demonstrated a negative predictive value of 0.98 and a positive predictive value of 0.72 at a prevalence of 10% pN1b disease. CONCLUSIONS:The genomic landscape of tumors with pN1b and pN0 disease was similar, whereas 43 genes selected primarily by mining the TCGA RNAseq data were differentially expressed. This bioinformatics-driven approach to the development of a custom transcriptomic assay provides a basis for a molecular classifier for pN1b risk stratification in PMC.
| S-EPMC6733494 | biostudies-literature
Project description:In order to clarify the gene expression and identify genes involved in tumor progression, gene expression profiling was performed on tumor specimens. Samples comprised 18 primary tumors, 17 lymph node (LN) metastases and 7 liver metastases. Patients were grouped according to clinical data and histopathology into indolent or progressive course. RNA was subjected to a spotted oligo microarray and B-statistics were performed. Differentially expressed genes were verified using quantitative RT-PCR. Self-organising maps demonstrated three clusters. Eleven primary tumors separated in one cluster, 5 LN metastases in another whereas all liver metastases, 7 primary and 12 LN metastases, formed a third cluster. There was no correlation between indolent and progressive behaviour. The primary tumors with Ki67 > 5%, with low frequency of the carcinoid syndrome and a tendency towards shorter survival grouped together. Primary tumors differed in expression profile from their associated LN metastases. ACTG2, GREM2, REG3A, TUSC2, RUNX1, TPH1, TGFBR2 and CDH6 were differentially expressed between clusters and subgroups of tumors. The expression profile that assembles tumors as being genetically similar on the RNA expression level may not be concordant with the clinical disease course. This study reveals different gene expression profiles and novel genes not previously known to be involved in neuroendocrine tumorigenesis, and which may be of importance for tumor progression. Gene expression comparisons between 18 primary tumors, 17 lymph node metastases and 7 liver metastases.
2011-02-10 | E-GEOD-27162 | biostudies-arrayexpress
Project description:Samples were taken from colorectal cancers in surgically resected specimens in 89 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting lymph node metastases. Keywords: disease state analysis Eighty-nine colorectal cancer patients were studied. Samples from 89 patients were divided into a training set (69 samples) and a testing set (20 samples).
2010-08-31 | E-GEOD-4459 | biostudies-arrayexpress