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Expression data from esophageal squamous cell carcinomas and normal esophageal epithelia

ABSTRACT: Preoperative chemoradiotherapy (CRT) followed by surgery has been proved to improve esophageal squamous cell carcinoma (ESCC) patients’ survival in comparison with surgery alone. However, the outcomes of CRT are heterogeneous, and no clinical or pathological method could predict CRT response. We aim to identify mRNA markers for ESCC CRT-response prediction through gene expression analyses.

ORGANISM(S): Homo sapiens

PROVIDER: GSE45670 | GEO | 2014/08/01

SECONDARY ACCESSION(S): PRJNA195583

REPOSITORIES: GEO

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Expression data from esophageal squamous cell carcinomas and normal esophageal epithelia

Project description:Preoperative chemoradiotherapy (CRT) followed by surgery has been proved to improve esophageal squamous cell carcinoma (ESCC) patientsM-bM-^@M-^Y survival in comparison with surgery alone. However, the outcomes of CRT are heterogeneous, and no clinical or pathological method could predict CRT response. We aim to identify mRNA markers for ESCC CRT-response prediction through gene expression analyses. Gene expression analyses were performed on pretreatment cancer biopsies from 28 ESCCs who received neoadjuvant CRT and surgery and 10 normal esophageal epithelia using Affymetrix U133 Plus 2.0 arrays.

2014-08-01 | E-GEOD-45670 | biostudies-arrayexpress

MiRNA expression arrays from esophageal squamous cell carcinomas with different neoadjuvant chemoradiotherapy response

2015-07-27 | GSE59974 | GEO

MiRNA expression arrays from esophageal squamous cell carcinomas with different neoadjuvant chemoradiotherapy response

Project description:Preoperative chemoradiotherapy (CRT) followed by surgery has been proved to improve esophageal squamous cell carcinoma (ESCC) patients’ survival in comparison with surgery alone. However, the outcomes of CRT are heterogeneous, and no clinical or pathological method could predict CRT response. We aim to identify miRNA markers for ESCC CRT-response prediction through miRNA expression analyses. MiRNA expression analyses were performed on pretreatment cancer biopsies from 28 ESCCs who received neoadjuvant CRT and surgery using Agilent human miRNA microarrays based on miRBase (release 18.0) GeneChip®.

2015-07-27 | E-GEOD-59974 | biostudies-arrayexpress

SNP data from genomic DNA in patient with rectal cancer

Project description:The identification of surrogate single nucleotide polymorphism (SNP) markers that can predict responses to preoperative chemoradiotherapy (CRT) in rectal cancer patients. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of tumor regression after CRT. We used Affymetrix’s SNP Array 6.0 to detail genetic polymorphism of patient’s group showing differential responsiveness to preoperative CRT and profiled SNP biomarkers.

2012-12-31 | GSE35282 | GEO

Proteome analysis of human serum from the esophageal cancer patient before preoperative chemoradiotherapy

Project description:To identify a biomarker that can predict the response of preoperative chemoradiotherapy (PCRT). Twenty-five serum samples from patents with esophageal cancer before PCRT (responder = 13, non-responder = 12) were analyzed by quantitative proteomics.

2020-02-21 | PXD012819 | JPOST Repository

Analysis of serum exosomal miRNAs associated with lymph node metastasis in esophageal squamous cell carcinoma

Project description:Preoperative prediction of lymph node (LN) metastasis is accepted as an important independent risk factor for treatment decision-making for esophageal squamous cell carcinoma (ESCC) patients. This study aimed to develop a non-invasive biomarker to identify LN metastasis preoperatively in ESCC patients with serum exosomal RNA-seq.

2020-07-30 | GSE155360 | GEO

MicroRNA profiling of plasma exosomes of ESCC patients

Project description:MiRNA arrays were performed for the plasma exosomes of ESCC patients before treatment. The tumor regression grade of the primary tumor (TRG-PT) was used to evaluate the therapeutic effect of chemoradiotherapy (CRT). Patients classified as Grade 3 were considered sensitive to CRT (n=4), while those classified as Grade 0 or 1a were considered resistant to CRT (n=4).

2022-02-03 | GSE195974 | GEO

Affymetrix SNP array data for esophageal squamous cell carcinoma samples

Project description:A proportion of superficial esophageal squamous cell carcinoma, a type of less invasive esophageal squamous cell carcinoma (ESCC), would have metastasis after esophagectomy or endoscopic resection with poor prognosis. The purpose of this study was to discover the whole-genome copy number alteration (CNA) profiles of superficial ESCC and compare the CNAs of superficial ESCC patients with and without metastasis after surgery. Thirty eight superficial ESCC cases, including 19 cases with metastasis and 19 cases without metastasis within 5 years after surgery, were analyzed CNAs by Affymetrix OncoScan™ FFPE Assay. A 39-gene signature was initially constructed to identify high risk of metastasis in superficial ESCC patients. In addition, amplification of 11q13.3 (FGF4) and deletion of 9p21.3 (CDKN2A) were identified as recurrent CNAs across all 38 superficial ESCC cases. And amplifications of 3p26.33 (SOX2-OT), 8q24.21 (MYC), 14q21.1 (FOXA1) and deletion of 3p12.1 (GBE1) were identified as recurrent CNAs among metastasis cases only. Our study provided a 39-gene signature tool to identified high risk metastasis in superficial ESCC and suggested that amplifications of SOX2-OT, MYC, FOXA1 genes and deletion of GBE1 gene might play a vital role in metastasis among superficial ESCC.

2017-06-10 | GSE78926 | GEO

Esophageal Cancer Project

Project description:Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC). Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases and additional 70 ESCC cases were subjected to array comparative genomic hybridization (a-CGH) analysis. We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases and additional 70 ESCC cases were subjected to array comparative genomic hybridization (a-CGH) analysis.

2014-03-11 | E-GEOD-54995 | biostudies-arrayexpress

T-cell receptor repertoire in rectal cancer

Project description:Emerging evidence suggests that an increased density of pre-treatment CD8+ tumor-infiltrating lymphocytes (TILs) is associated with good response to chemoradiotherapy (CRT) in patients with locally advanced rectal cancer. However, the significance of T-cell complexity in the clinical setting remains unknown. High-throughput T-cell receptor (TCR) β sequencing was applied to quantify the TCR repertoire of pre-treatment biopsies from 67 patients with advanced rectal cancer receiving preoperative CRT. Changes in TCR repertoire before and after CRT were also analysed in 23 patients.

2022-11-22 | GSE218181 | GEO

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