Microarray Analysis of Serum mRNA in Patients with Head and Neck Squamous Cell Carcinoma at Whole-Genome Scale

Čapková, Markéta; Šáchová, Jana; Strnad, Hynek; Kolář, Michal; Hroudová, Miluše; Chovanec, Martin; Čada, Zdeněk; Šteffl, Martin; Valach, Jaroslav; Kastner, Jan; Vlček, Čestmı́r; Smetana, Karel; Plzák, Jan

doi:10.1155/2014/408683

Cited by 6 publications

(3 citation statements)

References 59 publications

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“…Nowadays, the method is also used for rapid and high throughput detection and quantification of miRNAs and lncRNAs. Since it is based on hybridization methodology and does not involve PCR amplification of the sample, it has lower sensitivity than RNA-Seq, but microarrays are not prone to PCR-introduced errors and bias [ 130 , 131 , 132 ]. Recently, the NanoString nCounter System—a hybridization-based digital count technology—was also introduced.…”

Section: Cf-na Detectionmentioning

confidence: 99%

Circulating Cell-Free Nucleic Acids: Main Characteristics and Clinical Application

Szilágyi

Pös

Márton

et al. 2020

IJMS

149

108

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Liquid biopsy recently became a very promising diagnostic method that has several advantages over conventional invasive methods. Liquid biopsy may serve as a source of several important biomarkers including cell-free nucleic acids (cf-NAs). Cf-DNA is widely used in prenatal testing in order to characterize fetal genetic disorders. Analysis of cf-DNA may provide information about the mutation profile of tumor cells, while cell-free non-coding RNAs are promising biomarker candidates in the diagnosis and prognosis of cancer. Many of these markers have the potential to help clinicians in therapy selection and in the follow-up of patients. Thus, cf-NA-based diagnostics represent a new path in personalized medicine. Although several reviews are available in the field, most of them focus on a limited number of cf-NA types. In this review, we give an overview about all known cf-NAs including cf-DNA, cf-mtDNA and cell-free non-coding RNA (miRNA, lncRNA, circRNA, piRNA, YRNA, and vtRNA) by discussing their biogenesis, biological function and potential as biomarker candidates in liquid biopsy. We also outline possible future directions in the field.

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Section: Cf-na Detectionmentioning

confidence: 99%

Circulating Cell-Free Nucleic Acids: Main Characteristics and Clinical Application

Szilágyi

Pös

Márton

et al. 2020

IJMS

149

108

View full text Add to dashboard Cite

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“…High throughput molecular profiling using techniques that catalog the differences at the whole genome, transcriptome [ 3 ] [ 4 ] [ 5 ] and proteome [ 6 ] levels have been carried out in HNSCC. These studies have catalogued markers of progression [ 7 ] [ 8 ] and response to treatment [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Meta-Analyses of Microarray Datasets Identifies ANO1 and FADD as Prognostic Markers of Head and Neck Cancer

et al. 2016

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The head and neck squamous cell carcinoma (HNSCC) transcriptome has been profiled extensively, nevertheless, identifying biomarkers that are clinically relevant and thereby with translational benefit, has been a major challenge. The objective of this study was to use a meta-analysis based approach to catalog candidate biomarkers with high potential for clinical application in HNSCC. Data from publically available microarray series (N = 20) profiled using Agilent (4X44K G4112F) and Affymetrix (HGU133A, U133A_2, U133Plus 2) platforms was downloaded and analyzed in a platform/chip-specific manner (GeneSpring software v12.5, Agilent, USA). Principal Component Analysis (PCA) and clustering analysis was carried out iteratively for segregating outliers; 140 normal and 277 tumor samples from 15 series were included in the final analysis. The analyses identified 181 differentially expressed, concordant and statistically significant genes; STRING analysis revealed interactions between 122 of them, with two major gene clusters connected by multiple nodes (MYC, FOS and HSPA4). Validation in the HNSCC-specific database (N = 528) in The Cancer Genome Atlas (TCGA) identified a panel (ECT2, ANO1, TP63, FADD, EXT1, NCBP2) that was altered in 30% of the samples. Validation in treatment naïve (Group I; N = 12) and post treatment (Group II; N = 12) patients identified 8 genes significantly associated with the disease (Area under curve>0.6). Correlation with recurrence/re-recurrence showed ANO1 had highest efficacy (sensitivity: 0.8, specificity: 0.6) to predict failure in Group I. UBE2V2, PLAC8, FADD and TTK showed high sensitivity (1.00) in Group I while UBE2V2 and CRYM were highly sensitive (>0.8) in predicting re-recurrence in Group II. Further, TCGA analysis showed that ANO1 and FADD, located at 11q13, were co-expressed at transcript level and significantly associated with overall and disease-free survival (p<0.05). The meta-analysis approach adopted in this study has identified candidate markers correlated with disease outcome in HNSCC; further validation in a larger cohort of patients will establish their clinical relevance.

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“…In addition to different analyte types, the number of methods to study and evaluate these analytes has rocketed. Next to standard techniques available in most diagnostics laboratories, innovative high-end exploratory methods have been used, including microarray analysis and (single-cell) sequencing and proteomic approaches [ 16 , 17 , 18 , 19 , 20 , 21 ]. The power and utility of liquid biopsies for HNSCC have recently been shown, capturing the complex and dynamic features of the disease.…”

Section: Introductionmentioning

confidence: 99%

Tracking the Molecular Fingerprint of Head and Neck Cancer for Recurrence Detection in Liquid Biopsies

Diez-Fraile

Ceulaer

Derpoorter

et al. 2022

IJMS

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The 5-year relative survival for patients with head and neck cancer, the seventh most common form of cancer worldwide, was reported as 67% in developed countries in the second decade of the new millennium. Although surgery, radiotherapy, chemotherapy, or combined treatment often elicits an initial satisfactory response, relapses are frequently observed within two years. Current surveillance methods, including clinical exams and imaging evaluations, have not unambiguously demonstrated a survival benefit, most probably due to a lack of sensitivity in detecting very early recurrence. Recently, liquid biopsy monitoring of the molecular fingerprint of head and neck squamous cell carcinoma has been proposed and investigated as a strategy for longitudinal patient care. These innovative methods offer rapid, safe, and highly informative genetic analysis that can identify small tumors not yet visible by advanced imaging techniques, thus potentially shortening the time to treatment and improving survival outcomes. In this review, we provide insights into the available evidence that the molecular tumor fingerprint can be used in the surveillance of head and neck squamous cell carcinoma. Challenges to overcome, prior to clinical implementation, are also discussed.

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Microarray Analysis of Serum mRNA in Patients with Head and Neck Squamous Cell Carcinoma at Whole-Genome Scale

Cited by 6 publications

References 59 publications

Circulating Cell-Free Nucleic Acids: Main Characteristics and Clinical Application

Circulating Cell-Free Nucleic Acids: Main Characteristics and Clinical Application

Meta-Analyses of Microarray Datasets Identifies ANO1 and FADD as Prognostic Markers of Head and Neck Cancer

Tracking the Molecular Fingerprint of Head and Neck Cancer for Recurrence Detection in Liquid Biopsies

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