Expression analysis of cancer of unknown primary (CUP)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Yoshihiko Fujita
PROVIDER: E-GEOD-42392 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Biopsies (lymph nodes, ascites or hydrothorax) from 60 patients with cancer of unknown primary origin were analyzed. Results provide insight into the molecular pathogenesis of CUP.
2019-01-31 | GSE125908 | GEO
Project description:Biopsies (lymph nodes, ascites or hydrothorax) from 60 patients with cancer of unknown primary origin were analyzed. Results provide insight into the molecular pathogenesis of CUP.
2012-11-20 | GSE42392 | GEO
Project description:Employing genome wide transcriptome analysis,Linear Discriminant Analysis (LDA) and Quadratic Discriminant Analysis (QDA), we created a successful classification model to identify the putative origin of a CUP. Using the classifications of the CUPs enable the comparison of transcriptome profiles from CUPs to the equivalent normal metastasis across the different carcinoma types. Gene Set Enrichment Analysis (GSEA) and Pathway analysis were used to reveal the common biological features characterizing CUPs. The classifier was build using 2208 samples of normal tissue, known primary tumors, metastasis of known origin and tested on 60 CUP samples. 130 of these samples were collected and analyzed as part of the project and submitted to ArrayExpress. The analyses show that CUPs are distinct from metastases of known origin. CUPs exhibit inconsistent expression of conventional cancer biomarkers and QDA derived outlier scores show that CUPs are more distantly related to their primary tumor class than corresponding metastases of known origin. Gene set enrichment analysis showed that CUPs display increased expression of genes involved in DNA damage repair and by employing signatures of chromosome instability (CIN), we found that CUPs are chromosome unstable compared to metastases of known origin.
2015-05-31 | E-MTAB-3222 | biostudies-arrayexpress
Project description:Expression analysis of cancer of unknown primary (CUP)
| PRJNA517939 | ENA
Project description:Expression analysis of cancer of unknown primary (CUP) 2
| PRJNA517938 | ENA
Project description:Background: Cervical lymph node metastasis is a potent prognostic factor in oral squamous cell carcinoma (OSCC). However, lymph nodes resected by sentinel node biopsy or neck dissection are usually diagnosed by examining only one or two sections of the maximal cut surface. Accurate diagnosis of the metastasis in lymph nodes is important but depends on a heavy workload of the pathologist. In this study, we have attempted to identify novel molecular markers to find the harboring cancer cells in the lymph node and establish rapid detection method. Methods: We determined the gene expression profiles of 7 metastatic lymph nodes from patients with OSCC and 1 normal lymph node and 5 salivary glands from non-cancerous patients by microarray analysis. We found the overexpression genes in all metastatic lymph nodes. Subsequently, we examined the expression of these genes in newly 23 metastatic lymph nodes and 9 normal lymph nodes by real-time quantitative RT-PCR (qRT-PCR) assay. Moreover, the rapid detection of lymph node metastasis by these genes was examined using the reverse transcription loop-mediated isothermal amplification (RT-LAMP) method. Result: Among the 4 genes identified by microarray analysis, annexin A8 (ANXA8) and desmoglein 3 (DSG3) were detected in all metastatic lymph nodes at a much higher level but not in normal lymph nodes at all by qRT-PCR. Furthermore, RT-LAMP method targeting ANXA8 rapidly detected almost lymph nodes with metastasis. Conclusions: ANXA8 could be a useful marker for detecting lymph node metastasis in OSCC. Using AB1700 system, we determined the gene expression profiles of lymph nodes with metastasis of OSCC. Normal lymph node and salivary gland tissues were used as control samples.
2015-12-21 | E-GEOD-70604 | biostudies-arrayexpress
Project description:Background. The unknown tissue of origin in head and neck cancer of unknown primary (hnCUP) leads to invasive diagnostic procedures and unspecific and potentially inefficient treatment options for patients. The most common histological subtype, squamous cell carcinoma, can stem from various tumor primary sites, including the oral cavity, oropharynx, larynx, head and neck skin, lungs, and esophagus. DNA methylation profiles are highly tissue-specific and have been successfully used to classify tissue origin. We therefore developed a support vector machine (SVM) classifier trained with publicly available DNA methylation profiles of commonly cervically metastasizing squamous cell carcinomas (n = 1,103) in order to identify the primary tissue of origin of our own cohort of squamous cell hnCUP patient’s samples (n = 28). Methylation analysis was performed with Infinium MethylationEPIC v1.0 BeadChip by Illumina. Results. The SVM algorithm achieved the highest overall accuracy of tested classifiers, with 87%. Squamous cell hnCUP samples on DNA methylation level resembled squamous cell carcinomas commonly metastasizing into cervical lymph nodes. The most frequently predicted cancer localization was the oral cavity in 11 cases (39%), followed by the oropharynx and larynx (both 7, 25%), skin (2, 7%), and esophagus (1, 4%). These frequencies concord with the expected distribution of lymph node metastases in epidemiological studies. Conclusions. On DNA methylation level, hnCUP is comparable to primary tumor tissue cancer types that commonly metastasize to cervical lymph nodes. Our SVM-based classifier can accurately predict these cancers’ tissues of origin and could significantly reduce the invasiveness of hnCUP diagnostics and enable a more precise therapy after clinical validation.
2024-03-04 | GSE256413 | GEO
Project description:ANGPTL4 regulates plasma triglyceride levels by inhibiting lipoprotein lipase. Inactivation of ANGPTL4 decreases plasma triglycerides and reduces risk of coronary artery disease. Unfortunately, targeting ANGPTL4 for the therapeutic management of dyslipidemia and atherosclerosis is hampered by the observation that mice and monkeys in which ANGPTL4 is inactivated exhibit lipid accumulation in mesenteric lymph nodes. In mice these pathological events exclusively unfold upon feeding a high saturated fatty acid diet and are followed by an ultimately lethal pro-inflammatory response and chylous ascites. Here we show that Angptl4-/- mice fed a diet rich in trans fatty acids develop numerous lipid-filled giant cells in their mesenteric lymph nodes, yet do not have elevated serum amyloid and haptoglobin, do not exhibit ascites, and survive, unlike Angptl4-/- mice fed a saturated fatty acid-rich diet. In RAW264.7 macrophages the saturated fatty acid palmitate markedly increases markers of inflammation and the unfolded protein response, whereas the trans-unsaturated elaidate and the cis-unsaturated oleate have the opposite effect. In conclusion, trans and saturated fatty acids have very distinct biological effects. Furthermore, lipid accumulation in mesenteric lymph nodes is uncoupled from activation of an acute-phase response and chylous ascites, suggesting that ANGPTL4 should not be fully dismissed as target for dyslipidemia.
2017-04-27 | GSE98303 | GEO
Project description:Identification of genes expressed in a preferential manner in the developing ciliary body/iris will provide a starting point for future functional analyses. To identify candidate genes expressed in a variety of ocular tissues during development, we have profiled single cells from the developing eye. Post hoc identification of the origin of these cells showed that they included cells from the periphery of the developing optic cup. By comparing the expression profiles of these cells to many retinal cell types, candidate genes for preferential expression in the periphery were identified.
2009-05-01 | GSE15566 | GEO
Project description:The dermal sheath cup is the peribulbar component of the hair follicle dermal sheath, and has hair inductive potential similar to the dermal papilla. To characterize it in comparison with other mesenchymal follicle tissuesparts, we performed gene expression profiling of intact dermal sheath cups, which were separated from hair follicles by microdissection. Gene expression profiles of the dermal sheath cup, dermal papilla and upper dermal sheath were compared. We identified a dermal sheath cup signature composed of 32 upregulated genes, which included extracellular matrix components and BMP binding mollecules, while dermal papilla signature included a number of dermal papilla signature genes which had already reported. Analyses of upstream regulators showed that TGF- b1 is a putative regulator of these genes. These results suggest some of molecular mechanism that contributes to human dermal sheath cup properties, which could be useful for hair follicle bioengineering.
2020-02-22 | GSE95219 | GEO