Search for a novel diagnostic marker for liver cancer.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE117361 | GEO | 2019/04/02
REPOSITORIES: GEO
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Project description:Analysis of the circular RNA expression profiles of tumor and normal tissue samples from Hepatocellular carcinoma (HCC).Find potential circular RNA to serve as diagnostic marker for liver cancer.
2020-10-09 | GSE159220 | GEO
Project description:Search for a novel diagnostic marker for liver cancer.
| PRJNA668068 | ENA
Project description:Search for a novel diagnostic marker for liver cancer.
| PRJNA481878 | ENA
Project description:In cancer management, early and accurate diagnosis of hepatocellular carcinoma (HCC) is important for enhancing survival rate of patients. Currently, serum alpha-fetoprotein (AFP) is the only one biomarker for detection of HCC. However, serum AFP is not satisfactory for diagnosis of HCC due to its low accuracy (about 60-70%). In this study, we collected 109 serum samples (discovery set) from healthy control (HC) and patients with chronic hepatitis B (CHB), liver cirrhosis (LC) and HCC, and analyzed them with custom lncRNA microarray. Profiling analysis shows 181 differentially expressed lncRNAs between HCs and patients with CHB, LC and HCC. Then a 48-lncRNA diagnostic signature was identified with 100% predictive accuracy for all subjects in the discovery set. This diagnostic signature was verified with a cross-validation analysis in the discovery set. To further corroborate the signature, we gathered another 66 serum samples (validation set) and also analyzed them with microarray. The result indicates that the same signature has similar diagnostic accuracy for HC (100%), CHB (73%), LC (88%) and HCC (95%), implying a reproducible diagnostic biomarker for HCC. Receiver operating characteristic (ROC) analysis exhibits that this signature has significantly higher diagnostic accuracy for HCC and non-cancerous subjects (area under curve [AUC]: 0.994) than AFP (AUC: 0.773) in the discovery set and this was also verified in the validation set (0.964 vs 0.792). More importantly, the signature detected small HCC (<3cm) with 100% (13/13) accuracy while AFP with only 61.5% (8/13). Altogether, this study demonstrates that the serum 48-lncRNA signature is not only a powerful and sensitive biomarker for diagnosis of HCC but also a potential biomarker for LC. ***************************************************************** Submitter declares these data are subject to patent number ZL 2016 1 0397094. *****************************************************************
2022-10-15 | GSE78160 | GEO
Project description:Dr. Kate Olson's Lab is interested to expand these analysis to comparisons between human normal lung tissue and human lung tumor tissue. In hopes that this will help in finding a diagnostic marker for lung cancer. Since there will be more variability between these samples, we would like to get preliminary data on ten normal lung tissue and ten lung tumor tissues from the same patient.
2011-06-14 | GSE29927 | GEO
Project description:Dr. Kate Olson's Lab is interested to expand these analysis to comparisons between human normal lung tissue and human lung tumor tissue. In hopes that this will help in finding a diagnostic marker for lung cancer. Since there will be more variability between these samples, we would like to get preliminary data on ten normal lung tissue and ten lung tumor tissues from the same patient. We have already analyzed 4 cell lines and we saw gene expression variability related to how metastatic the cell lines were. This has been written and submitted for publication. We would like to expand these analysis to comparisons between human normal lung tissue and human lung tumor tissue. We hope that this will help in finding a diagnostic marker for lung cancer. Since there will be more variability between these samples, we would like to get preliminary data on ten normal lung tissue and ten lung tumor tissues from the same patient. The samples were dissected by a pathologist prior to extraction to maximize the amount of normal tissue included in the tumor samples. RNA samples from non tumor and tumor lung cancer patients were received by Core E. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.
2011-06-14 | E-GEOD-29927 | biostudies-arrayexpress
Project description:Purpose: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. Although the molecular mechanisms underpinning HCC are unknown, gene copy number and associated mRNA expression changes are frequently reported. Experimental Design: Comparative genomic hybridization arrays spotted with 4,041 bacterial artificial chromosome clones were used to assess copy number changes in 45 HCC tissues to identify chromosomal regions associated with the pathogenesis of HCC. Seventy more HCC tissues were used to validate candidate genes by using western blots and immunohistochemistry. Results: A total of 259 clones were associated with copy number changes that significantly differed between normal liver and HCC samples. The chromosomal region 1q32.1 containing the nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) gene was associated with tumor vascular invasion. Western blot analysis demonstrated that NUCKS1 was up-regulated in 37 of 70 (52.8%) HCC tissues compared with adjacent non-tumor tissues, and over-expressed in a vast majority of HCCs (44/52, 84.6%) as determined by immunohistochemical staining. Furthermore, immunostaining of both NUCKS1 and glypican-3 improved the diagnostic prediction of HCC. Knock-down of NUCKS1 by siRNA decreased the cell viability of the Hep3B cell line and reduced tumor formation in a xenograft mouse model. Functional enrichment analysis revealed the association of NUCKS1 with signal transduction, immunity and defense, and nucleotide metabolism pathways. Conclusions: NUCKS1 was identified as a potential oncogene at chromosomal 1q32.1 in patients with HCC, and it might be a valuable immunodiagnostic marker for HCC. Comparative genomic hybridization arrays spotted with 4,041 bacterial artificial chromosome clones were used to assess copy number changes in 45 HCC tissues and 25 normal liver tissues to identify chromosomal regions associated with the pathogenesis of HCC
2015-01-24 | E-GEOD-65237 | biostudies-arrayexpress
Project description:Saliva is rich in proteins, DNA, RNA and microorganisms, and can be regarded as a biomarker library. In order to explore a noninvasive and simple means of early screening for liver cancer, proteomics was used to screen salivary markers of hepatitis B associated liver cancer. We used mass spectrometry coupled isobaric tags for relative and absolute quantitation (iTRAQ)-technology to identify differentially expressed proteins (DEPs). Western blot, immunohistochemistry and enzyme linked immunosorbent assay were used to detect marker expression of in tissues and saliva. Statistical analysis was used to analyze the diagnostic efficacy of the markers was analyzed through statistical analyses. By comparing the hepatocellular carcinoma (HCC) group with non-HCC groups, we screened out 152 salivary DEPs. We found orosomucoid 1(ORM1) had significantly higher expression in saliva of HCC patients compared with non-HCC groups (p<0.001) and the expression of ORM1 in liver cancer tissues was significantly higher than that in adjacent normal tissues(p<0.001). The combination of salivary ORM1 and alpha-fetoprotein (AFP) showed reasonable specificities and sensitivities for detecting HCC. In a word, salivary ORM1 as a new biomarker of hepatitis B associated hepatocellular carcinoma, combination of salivary ORM1 and AFP as an improved diagnostic tool for hepatocellular carcinoma.
2022-07-13 | PXD033752 | Pride
Project description:Purpose: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. Although the molecular mechanisms underpinning HCC are unknown, gene copy number and associated mRNA expression changes are frequently reported. Experimental Design: Comparative genomic hybridization arrays spotted with 4,041 bacterial artificial chromosome clones were used to assess copy number changes in 45 HCC tissues to identify chromosomal regions associated with the pathogenesis of HCC. Seventy more HCC tissues were used to validate candidate genes by using western blots and immunohistochemistry. Results: A total of 259 clones were associated with copy number changes that significantly differed between normal liver and HCC samples. The chromosomal region 1q32.1 containing the nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) gene was associated with tumor vascular invasion. Western blot analysis demonstrated that NUCKS1 was up-regulated in 37 of 70 (52.8%) HCC tissues compared with adjacent non-tumor tissues, and over-expressed in a vast majority of HCCs (44/52, 84.6%) as determined by immunohistochemical staining. Furthermore, immunostaining of both NUCKS1 and glypican-3 improved the diagnostic prediction of HCC. Knock-down of NUCKS1 by siRNA decreased the cell viability of the Hep3B cell line and reduced tumor formation in a xenograft mouse model. Functional enrichment analysis revealed the association of NUCKS1 with signal transduction, immunity and defense, and nucleotide metabolism pathways. Conclusions: NUCKS1 was identified as a potential oncogene at chromosomal 1q32.1 in patients with HCC, and it might be a valuable immunodiagnostic marker for HCC.
2015-01-24 | GSE65237 | GEO
Project description:Genome wide DNA methylation profiling of blood samples collected from patients after diagnosis with hepatocellular carcinoma (HCC) (cases) vs. blood samples collected from healthy individuals without family history of cancer (controls). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human samples corresponding to cases (post-diagnostic HCC) and controls. Samples included 24 cases and 24 controls. Cases were matched with controls on gender, age, ethnicity, hepatitis C infection, and diabetes. The presence or absence of HCC in our study was determined based on the AASLD criteria.
2022-01-31 | GSE113409 | GEO