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Gene expression in normal and tumor samples from patients with HNSCC

ABSTRACT: Tissue samples were collected from patients diagnosed with HNSCC (oropharynx, hypopharynx, larynx). Samples were taken from the tumor site (tumor samples) and from a site distant to the tumor (normal samples) prior to therapy. The study goals were to 1) compare the expression of microRNAs in tumor and normal samples from individual patients and 2) determine whether the differences in expression of microRNAs is associated with patient survival outcomes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE58911 | GEO | 2014/07/07

SECONDARY ACCESSION(S): PRJNA254524

REPOSITORIES: GEO

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Gene expression in normal and tumor samples from patients with HNSCC

Project description:Tissue samples were collected from patients diagnosed with HNSCC (oropharynx, hypopharynx, larynx). Samples were taken from the tumor site (tumor samples) and from a site distant to the tumor (normal samples) prior to therapy. The study goals were to 1) compare the expression of microRNAs in tumor and normal samples from individual patients and 2) determine whether the differences in expression of microRNAs is associated with patient survival outcomes. Fifteen paired normal and tumor samples from individual patients were analyzed (a total of 30 samples).

2014-07-07 | E-GEOD-58911 | biostudies-arrayexpress

Gene expression profile in relapsed or metastatic HNSCC patients treated with cetuximab and platinum therapy

Project description:First line chemotherapy with platinum and cetuximab is usually offered to RM-HNSCC pts. In the Extreme trial a median progression free survival (PFS) time of 5.6 months was reported. However, a small fraction of pts achieves a prolonged PFS (> than 12 months). Till now, no recognized predictive biological factor has been identified. A group of 14 cases treated with a first line platinum and cetuximab with a PFS exceeding 12 months (long PFS) and a group of 26 pts with a PFS less than 5.6 months (short PFS) were selected. The 2 groups were well balanced in regard to recognized prognostic factors (performance status, weight loss, prior radiotherapy, tumor grade, site of primary tumor, residual disease at primary tumor site). Tumor specimens of the recurrence or, if not available, of the primary tumor were collected. In order to identify molecular profiles deregulated between the 2 groups, a gene expression microarray analysis was performed using the Whole-Genome DASL assay and HumanHT-12_v4 BeadArray chips (lllumina). Gender: male=0; female=1. Age: years at diagnosis Site of primary: oral cavity=0; oropharynx=1; hypopharynx=2; larynx=3. Stage of T at first diagnosis according to AJCC 8th edition Grading according to WHO: well differentiated=1; moderately differentiated=2; scarcely differentiated=3. Radiotherapy (RT) prior to recurrence: No=0; Yes=1. Progression Free Survival (PFS): Long (>12 months); Short(<5 months).

2016-08-01 | E-GEOD-65021 | biostudies-arrayexpress

Hypopharyngeal_cancer_transcriptome

Project description:Gene expression analysis of a unique HNSCC (Head and Neck Squamous Cell Carcinoma) localization, the hypopharynx. Four normal and 34 tumor samples were analysed using Affymetrix HG-U95A microarrays containing probe sets representing ~12650 distinct transcription features. Keywords = HNSCC Hypopharynx Keywords: ordered

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Comparison between HPV+ / p16+ versus the HPV-/p16- from HNSCC patients

Project description:Head and neck squamous cell carcinomas are heterogeneous neoplasms that show clinical and biological differences in association with the human papillomavirus (HPV). To provide adequate therapeutic strategies, biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. Reports on HNSCC are scarce in Mexico, thus in the present study, we analyze 414 cases of HNSCC, including those of the oropharynx (OPSCC), larynx (LASCC), and oral cavity (OCSCC). We determined the presence of HPV and p16 expression. Global expression profiles were analyzed with Affymetrix HTA 2.0 microarray in 25 selected cases HPV+/p16+ versus HPV-/p16-. In our study we analyze 25 samples derived from HNSCC patients. 18 samples were HPV-/p16- and 7 HPV+/p16+. We compared the HPV-/p16- versus the HPV+/p16+ and identified differentially expressed RNAs with a fold change greater than 1.5 or less than -1.5. These data were used to obtain 98 genes that are differentially expressed in absence of HPV. The present study offers information regarding clinical and molecular characteristics of HNSCC, both associated and unassociated with HPV, in Mexican patients.

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Gene Expression Profiles of Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumors

Project description:60 fresh frozen HNSCC from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. 55 tumor samples were collected from the primary tumor and five tumor samples were collected from a local recurrence at the primary site; one tumor also had a sample of the primary tumor and an associated lymph node metastasis . In addition, we profiled three normal tonsillar epithelium samples that were collected from three pediatric patients following routine tonsillectomy and four HNSCC tumor derived cell lines (UNC7, UMSCCA1, CAL27 and JHU022). Each experimental sample (tumor, normal or cell line) was assayed versus a “common reference” sample that was a pool of total RNA derived from 30 of the HNSCC samples. This tumor pool reference strategy has been successfully used in another profiling study. In total, 78 experiments were performed, which utilized three separate preparations of the common reference pool. Keywords = Head and neck cancer Keywords = gene expression profiles Keywords = microarray Keywords: parallel sample

2004-03-24 | GSE686 | GEO

Gene Expression Profiles of Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumors

Project description:60 fresh frozen HNSCC from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. 55 tumor samples were collected from the primary tumor and five tumor samples were collected from a local recurrence at the primary site; one tumor also had a sample of the primary tumor and an associated lymph node metastasis . In addition, we profiled three normal tonsillar epithelium samples that were collected from three pediatric patients following routine tonsillectomy and four HNSCC tumor derived cell lines (UNC7, UMSCCA1, CAL27 and JHU022). Each experimental sample (tumor, normal or cell line) was assayed versus a â??common referenceâ?? sample that was a pool of total RNA derived from 30 of the HNSCC samples. This tumor pool reference strategy has been successfully used in another profiling study. In total, 78 experiments were performed, which utilized three separate preparations of the common reference pool. Keywords = Head and neck cancer Keywords = gene expression profiles Keywords = microarray

2010-06-09 | E-GEOD-686 | biostudies-arrayexpress

Transcription profiling of human hypopharyngeal cancer samples

2007-08-25 | E-GEOD-2379 | biostudies-arrayexpress

HNSCC samples vs. normal tonsil samples: reference design

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HNSCC samples vs. normal tonsil samples: self-self hybridization design

Project description:transcription profiling of human head and neck squamous cell carcinoma (HNSCC) samples vs. normal tonsil samples using a self-self hybridization experimental design on two-color arrays. Used to identify differentially expressed genes in tumor/normal samples, and compare the result to that of the same samples using the reference design experimental setting. Keywords: tumor/normal comparison

2009-01-22 | GSE13397 | GEO

HNSCC samples vs. normal tonsil samples: reference design

Project description:transcription profiling of human head and neck squamous cell carcinoma (HNSCC) samples vs. normal tonsil samples using a two-color reference design experimental setting. Used to identify differentially expressed genes in tumor/normal samples, and compare the result to that of the same samples using the self-self hybridization experimental setting. Keywords: tumor/normal comparison 8 HNSCC tumor samples and 8 normal tonsil samples. One sample per array. Two-color reference design with a common reference sample (a modified version of the Stratagene Human Universal Reference) on each array.

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