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Gene expression analysis of organoid model of human esophageal squamous cell carcinomas (ESCCs)

ABSTRACT: Gene expression analysis of organoid model of human esophageal squamous cell carcinomas (ESCCs)

PROVIDER: PRJNA1121932 | ENA |

REPOSITORIES: ENA

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Gene expression analysis of organoid model of human esophageal squamous cell carcinomas (ESCCs)

Project description:Esophageal squamous cell carcinoma (ESCC) is a serious cancer with a poor prognosis and a high recurrence rate after chemotherapy, which is a major clinical challenge. To elucidate the molecular basis of chemotherapy (chemo)-resistance and develop methods to effectively eliminate chemo-resistant tumor clones, we established a cancer organoid model from 24 ESCC patients of various stages, ages, and treatments. These ESCCOs recapitulated most oncogenic mutations of primary ESCC tissues and had tumorigenic properties upon xenografting. Each organoid line differs in its responsiveness to 5-fluorouracil (5-FU) and cisplatin (CDDP), chemotherapeutic agents commonly used to treat ESCC patients, with 7 lines exhibiting potent chemo-resistance. Importantly, these chemo-resistant ESCCOs had enhanced expression of genes involved in antioxidant stress response pathways and increased chromatin accessibility of their genomic loci, compared to chemo-sensitive ESCCOs, and these genes became useful biomarkers that can stratify chemo-resistant ESCC in histopathological specimens.

2025-02-25 | GSE269447 | GEO

A New Murine Esophageal Organoid Culture Method and Organoid-Driven Model of Esophageal Squamous Cell Neoplasia

Project description:A New Murine Esophageal Organoid Culture Method and Organoid-Driven Model of Esophageal Squamous Cell Neoplasia

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A New Murine Esophageal Organoid Culture Method and Organoid-Driven Model of Esophageal Squamous Cell Neoplasia

Project description:We sought to develop esophageal minimum essential organoid culture medium (E-MEOM) for culturing murine esophageal organoids (EOs) and establishing an early ESCC model. We formulated E-MEOM that is sufficient to grow EOs from a single cell with clonal expansion, maintenance, and passage. From the IHC and single cell RNA sequencing of EOs results, we found that EOs cultured in E-MEOM were histologically and functionally equivalent to the esophageal epithelium.

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MiRNA expression arrays from esophageal squamous cell carcinomas (ESCCs) and normal esophageal epithelia (Nes)

Project description:MiRNA expression arrays from esophageal squamous cell carcinomas (ESCCs) and normal esophageal epithelia (Nes)

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Human esophageal dysplasia (16 cases) vs. esophageal squamous cell carcinoma (59 cases)

Project description:Our aim is to identify frequent genomic aberrations both in ESCC and esophageal dysplasia, and to discover important copy number-driving genes and microRNAs in ESCC. We carried out array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR and immunohistochemistry (IHC). Integrated analysis was performed to identify genes or microRNAs with copy number-expression correlations. Two group experiment, esophageal dysplasia vs. esophageal squamous cell carcinoma. Biological replicates: 16 dysplasias vs. 59 carcinomas

2013-04-29 | E-GEOD-46452 | biostudies-arrayexpress

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.

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STAT3 expression, activity and functional consequences of STAT3 inhibition in esophageal squamous cell carcinomas and Barrett’s adenocarcinomas

Project description:Signal transducer and activator of transcription 3 (STAT3) is altered in several epithelial cancers and represents a potential therapeutic target. Here, STAT3 expression, activity and cellular functions were examined in two main histotypes of esophageal carcinomas. In situ, immunohistochemistry for STAT3 and STAT3-Tyr705 phosphorylation (P-STAT3) in esophageal squamous cell carcinomas (ESCC) and Barrett’s adenocarcinomas (BAC) revealed similar STAT3 expression in ESCCs and BACs, but preferentially activated P-STAT3 in ESCCs. In vitro, strong STAT3 activation was seen by EGF-stimulation in OE21 (ESCC) cells, whilst OE33 (BAC) cells showed constitutive weak STAT3 activation. STAT3 knockdown significantly reduced cell proliferation of OE21 and OE33 cells and reduced cell migration in OE33, but not in OE21 cells. Transcriptome analysis identified STAT3-knockdown associated down-regulation of cell cycle processes and the selective down-regulation of cyclins and cyclin dependent kinaes associated genes in both OE21 and OE33 cells. Moreover, the transcriptome response showed changes in cell migration/invasion related genes that correlated with the associated phenotype measurements. This study demonstrates the importance of STAT3 expression and activation in esophageal carcinomas, whereby the extent differs between ESCCs and BACs. STAT3 knockdown significantly reduces cell proliferation in both types of esophageal cancer cells and inhibits migration in BAC cells. Thus, STAT3 may be further exploited as potential novel therapeutic target for esophageal cancers.

2013-06-16 | GSE47763 | GEO

Expression data from esophageal squamous cell carcinomas and normal esophageal epithelia

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MAFB promotes the malignant phenotypes by IGFBP6 in esophageal squamous cell carcinomas

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Lung squamous cell carcinomas & papillary predominant adenocarcinomas

Project description:Protein Co-expression Network-based Profiles Revealed from Laser-microdissected Cancerous Cells of Lung Squamous-Cell Carcinomas

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