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Expression analysis of cancer of unknown primary (CUP) 1

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE42392 | GEO | 2012/11/20

SECONDARY ACCESSION(S): PRJNA181270

REPOSITORIES: GEO

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Expression analysis of cancer of unknown primary (CUP) 2

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

Expression analysis of cancer of unknown primary (CUP)

2012-11-20 | E-GEOD-42392 | biostudies-arrayexpress

Cancers of unknown primary (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin.

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

Expression analysis of cancer of unknown primary (CUP)

Project description:Expression analysis of cancer of unknown primary (CUP)

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DNA methylation profiles of lymph node tissue of head and neck cancer of unknown primary

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

Expression analysis of cancer of unknown primary (CUP) 2

Project description:Expression analysis of cancer of unknown primary (CUP) 2

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Comparative genomic profiling by array of human carcinomas of unknown primary compared to classical secondary metastases

Project description:Carcinomas of unknown primary (CUP) are characterized by early metastatic dissemination in the absence of a detectable primary tumor. This disease accounts for about 3% of all malignant tumors. Most CUPs are poorly responsive to chemotherapy and have a rapid fatal evolution. The biological mechanisms supporting metastatic growth in various sites combined with regression or absence of growth in the primary site are still poorly understood. The aim of this project was to investigate structural genome alterations specifically detected by CGH-array in CUP but not in classical secondary metastases. The design of the project was as follows : 5 samples representative of CUPs were compared to 3 samples representative of classical secondary metastases. The CUP samples were : a) 3 fresh biopsies containing more than 60 % malignant cells on tissue sections adjacent to the tumor fragment used for DNA extraction (Gal., Pro., Gag.); b) 2 fragment derived from 2 xenografted CUP tumor lines, Capi 1 and Capi 3 respectively. The samples derived from classical secondary metastases were : a) one fresh biopsy fragment derived from the secondary metastasis of a rectal adenocarcinoma (Vuc.); b) fragments of a tumor resulting from a xenograft of Capan 1, an in vitro cell line derived from a pancreatic adenocarcinoma secondary metastasis; 3) fragments of a xenografted tumor derived from a lung adenocarcinoma metastasis called IC14 (NSCLC).

2011-08-04 | E-TABM-1057 | biostudies-arrayexpress

Transcription profiling by array of human carcinomas of unknown primary

Project description:Carcinomas of unknown primary (CUP) are characterized by early metastatic dissemination in the absence of a detectable primary tumor. This disease accounts for about 3% of all malignant tumors. Most CUPs are poorly responsive to chemotherapy and have a rapid fatal evolution. The biological mechanisms supporting metastatic growth in various sites combined with regression or absence of growth in the primary site are still poorly understood. The aim of this project was to investigate characteristics of gene expression profile specific of CUPs with special attention to genes overexpressed or silenced in CUPs but not in classical secondary metastases. Three series of experiments were performed in 2006 and 2007. In all experiments, the mRNA used as a reference was obtained from diploid untransformed human fibroblasts (MRC5). The CUP samples were 2 xenografted CUP tumors (Capi1 and Capi3) and 4 CUP biopsies including a squamous carcinoma (Aud) and 3 adenocarcinomas (Gal, Pro, Gag). Samples representative of secondary metastases were xenografted tumors derived from metastases of nasopharyngeal carcinoma (C17), lung adenocarcinoma (IC14) and pancreatic adenocarcinoma (xenografted Capan 1 cell line) and one biopsy from a breast carcinoma (Vuc).

2011-08-04 | E-TABM-1058 | biostudies-arrayexpress

Expression analysis of cancer of unknown primary (CUP)

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-01-31 | GSE125915 | GEO

Molecular characterisation and liquid biomarkers in Carcinoma of Unknown Primary (CUP): taking the 'U' out of 'CUP'.

Project description: Not available

| S-EPMC6342985 | biostudies-literature