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Gene expression profiles of cervical cancers for novel molecular classification

ABSTRACT: Cervical cancers is the second most malignancy in women. It has been clinically important histological variants such as squamous cell carcinoma (SCC) and adenocarcinoma (AC) and adenosquamous carcinomas (ASC). It has been postulated that AC and ASC has a worse prognosis than pure SCC. However, many of the mixed or other types confuses its diagnosis and aggressive/resistant behavior of some tumors has resulted in debate for prognostic role of empirical pathological classification. In addition, the prognosis of adenosquamous carcinoma is still under debate. To establish a novel molecular classification of cervical cancer, we investigated intrinsic characteristics using expression profile.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20167 | GEO | 2010/09/28

SECONDARY ACCESSION(S): PRJNA125629

REPOSITORIES: GEO

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Gene expression profiles of cervical cancers for novel molecular classification

Project description:Cervical cancers is the second most malignancy in women. It has been clinically important histological variants such as squamous cell carcinoma (SCC) and adenocarcinoma (AC) and adenosquamous carcinomas (ASC). It has been postulated that AC and ASC has a worse prognosis than pure SCC. However, many of the mixed or other types confuses its diagnosis and aggressive/resistant behavior of some tumors has resulted in debate for prognostic role of empirical pathological classification. In addition, the prognosis of adenosquamous carcinoma is still under debate. To establish a novel molecular classification of cervical cancer, we investigated intrinsic characteristics using expression profile. A total of 80 cevical cancer samples of following histology were included in this study: 54 SCC, 18 ASC, 6 AC, and 2 others. Replicate number: 2. No control/no reference sample was included. One-color.

2010-09-28 | E-GEOD-20167 | biostudies-arrayexpress

Comprehensive profile and contrastive analysis of circular RNA in cervical squamous carcinoma and adenocarcinoma

Project description:To contrastively analyze the expression pattern of circRNAs in cervical squamous carcinoma, adenocarcinoma and adenosquamous carcinoma variants. CircRNAs expression in cervical squamous carcinoma, adenocarcinoma and adenosquamous carcinoma tissues together with the adjacent normal tissues were profiled by high-throughput RNA sequencing.

2022-12-31 | GSE208089 | GEO

Exon-array profiling of squamous cell carcinoma and adenocarcinoma in human cervical FFPE samples

2011-02-17 | GSE27388 | GEO

Exon-array profiling of squamous cell carcinoma and adenocarcinoma in human cervical FFPE samples

Project description:Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. In this study, we investigated the feasibility of gene expression signature generation from archival FFPE materials. Nineteen cervical squamous cell carcinoma (SCC) and nine adenocarcinoma (AC) 10~16-year-old FFPE samples were profiled using Affymetrix Exon 1.0 ST arrays. A comparison of the global gene expression changes between SCC and AC revealed 1217 differentially expressed genes. Of these, 1062 showed significantly higher expression levels in SCC relative to AC, and 155 genes were found to be specifically upregulated in AC. When the 1217-gene signature was tested on a fresh-frozen human non-small cell lung cancer (NSCLC) series, it correctly separated the 58 NSCLC samples into SCC and AC. In conclusion, our results showed that clinically and biologically relevant gene expression profiles can be derived from FFPE samples with Exon array profiling. The study population contains 28 FFPE human cervix samples (19 SCC and 9 AC). Histopathology assessment and p63 IHC were performed on all samples to confirm their histological subtypes. Total RNA was extracted and hybridised to Affymetrix Human Exon 1.0 ST arrays. Expression values were normalised using RMA. Only exonic probesets that were flagged as present (DABG< 0.01) in at least three samples were retained for further analysis. LIMMA was used to identify probesets that were differentially expressed between SCC and AC subtypes, using FDR ≤ 0.01 and absolute fold-change ≥ 2 as cutoff.

2011-02-17 | E-GEOD-27388 | biostudies-arrayexpress

SBV - Gene Expression Profiles of Lung Cancer Tumors - Adenocarcinomas and Squamous Cell Carcinomas

Project description:This dataset encompassing the profiles of 150 lung cancer tumors was developed to serve as test dataset in the SBV IMPROVER Diagnostic Signature Challenge (sbvimprover.com). The aim of this subchallenge was to verify that it is possible to extract a robust diagnostic signature from gene expression data that can identify stages of different types of lung cancer. Participants were asked to develop and submit a classifier that can stratify lung cancer patients in one of four groups M-bM-^@M-^S Stage 1 of Adenocarcinoma (AC Stage 1), Stage 2 of Adenocarcinoma (AC Stage 2), Stage 1 of Squamous cell carcinoma (SCC Stage 1) or Stage 2 of Squamous cell carcinoma (SCC Stage 2). The classifier could be built by using any publicly available gene expression data with related histopathological information and was tested on the independent dataset described here. 150 non-small cell lung cancer tumors (adenocarcinoma, AC and squamous cell carcinoma, SCC) of stages I and II were collected by surgical resection from patients who have provided consent. Adenosquamous and large cell tumor samples were excluded. The number of smokers and non-smokers was balanced: there were 41 AC1 (adenocarcinoma stage I), 36 AC2, 34 SCC1, and 39 SCC2 samples. Study pathologists at each of the seven sites (Lebanon, Republic of Moldova, Romania, Russian Federation, Ukraine, Vietnam and United States of America) reviewed both the tumor permanent sections and the frozen sections of the samples. Clinical information was also collected about tumor staging, history of prior cancers, lymph node involvement by lymph node sampling/dissection, smoking history, age, gender.

2013-10-18 | E-GEOD-43580 | biostudies-arrayexpress

The expression profile of lung sqaumous cell carcinoma (SCC) and adenosquamous carcninoma (ASC) of CCSPiCreLkb1f/fPtenf/f mice

Project description:Lung cancer, majorly divided into non-small cell lung cancer (80-85%) and small cell lung cancer (15-20%), is the leading cause of cancer death in USA. Squamous Cell Carcinoma (SCC) is one of major subtypes of non-small cell lung cancer. Although genomic analysis of tumors from SSC patients have identified frequently mutated genes in these tumors, it’s still largely unknown which genes determine SCC development. Now we found that ablation of Lkb1 and Pten could induce SCC and ASC around 3 months of age. Therefore, transcriptome analysis of lung SCC and ASC of CCSPiCreLkb1f/f mice will help us understand how Lkb1 and Pten regulate the development of lung SCC and ASC.

2019-03-01 | GSE111335 | GEO

Transcription profiling of human non-small cell lung cancer adenocarcinoma and squamous cell carcinoma subtypes

Project description:Non-small cell lung cancer (NSCLC) can be classified into the major subtypes adenocarcinoma (AC) and squamous cell carcinoma (SCC) subtypes. Although explicit molecular, histological and clinical characteristics have been reported for both subtypes, no specific therapy exists so far. However, the characterization of suitable molecular targets holds great promises to develop novel therapies in NSCLC. In the present study, global gene expression profiling of 58 human high grade NSCLC specimens revealed large transcriptomic differences between AC and SCC subtypes: More than 1.700 genes were found to be differentially expressed. Experiment Overall Design: The NSCLC patient collective was composed of the histological subtype adenocarcinoma (n=40) and squamous cell carcinoma (n=18). We subjected gene expression profiles of 40 AC and 18 SCC samples into further analysis. Unsupervised hierarchical clustering of all 58 NSCLC tumors using the 500 most variably expressed transcripts revealed two different clusters, which were strongly associated with the histological subtypes AC and SCC of NSCLC. Our result indicated that the major impact on global transcriptional changes was due to the NSCLC histology.

2009-10-11 | E-GEOD-10245 | biostudies-arrayexpress

The expression profile of lung sqaumous cell carcinoma (SCC) and adenosquamous carcninoma (ASC) of CCSPiCreLkb1f/fPtenf/f mice

Project description:The expression profile of lung sqaumous cell carcinoma (SCC) and adenosquamous carcninoma (ASC) of CCSPiCreLkb1f/fPtenf/f mice

| PRJNA436647 | ENA

Lkb1 inactivation drives lung cancer lineage switching governed by Polycomb Repressive Complex 2

Project description:Adenosquamous lung tumors may result from cellular plasticity. We demonstrate lineage switching of KRAS+ lung adenocarcinomas (ADC) to squamous cell carcinoma (SCC) through deletion of Lkb1 (Stk11) in autochthonous and transplant models. Chromatin analysis reveals loss of H3K27me3 and gain of H3K27ac and H3K4me3 at squamous lineage genes, included Sox2, ΔNp63 and Ngfr. SCC lesions have higher levels of the H3K27 methyltransferase EZH2 than the ADC lesions, but there is a clear lack of the essential Polycomb Repressive Complex 2 (PRC2) subunit EED in the SCC lesions.

2017-02-02 | GSE94365 | GEO

microRNA profile in the cervical mucus of the cervical neoplasia

Project description:Cervical mucus was collected from 86 patients with a normal cervix, cervical intraepithelial neoplasia (CIN), squamous cell carcinoma (SCC), or adenocarcinoma (AD). 76 candidates of miRNAs were selected according to criteria such as absolute value of the signal intensity included more than 20 and the ratio of the SCC/normal or AD/normal included more than four.

2018-05-09 | GSE105409 | GEO

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