Differentially expressed genes in HNSCC tissues, normal oral epithelial tissues and CAFs
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE172120 | GEO | 2021/05/01
REPOSITORIES: GEO
Similar Datasets
Project description:Next generation sequencing was perfomed to identify differentially expressed micro-RNA in HNSCC tissues, normal oral epithelial tissues and CAFs.
2021-10-02 | GSE184991 | GEO
Project description:Differentially expressed genes in HNSCC tissues, normal oral epithelial tissues and CAFs
| PRJNA722177 | ENA
Project description:Differentially expressed micro-RNA in head and neck squamous cell cancer (HNSCC) tissues, normal oral epithelial tissues and CAFs
| PRJNA767333 | ENA
Project description:This study aims to identify genes differentially expressed in oral CAFs with respect to their normal counterparts, i.e. oral NFs. We collected oral normal mucosal tissues and oral squamous cell carcinoma (OSCC) tissues from 12 healthy people and 12 OSCC patients, respectively, at West China Hospital of Stomatology, Sichuang University, P. R. China. The tissues were isolated, cultured and purified using standard protocols to obtain oral NFs and CAFs. Agilent 4×44K Whole Genome Oligo Microarrays were used to measure the gene expression profiles of the samples. Sample preparation and hybrid reactions were performed according to the manufacture’s instructions. RNA samples from NFs and CAFs were pooled respectively before hybridization. The chips were scanned and visualized using the Agilent DNA microarray scanner. Probe set intensities were measured using Agilent Feature Extraction software (version 10.5.1.1). Raw data were normalized in the Agilent GeneSpring GX software (version 11.0) using the Agilent FE one-color scenario (mainly median normalization). Oral NFs and CAFs were obtained from tissues derived from 12 healthy people undergoing plastic surgery and 12 OSCC patiens undergoing surgical resection. RNA samples from NFs and CAFs were pooled respectively before hybridization.
2012-01-26 | E-GEOD-35356 | biostudies-arrayexpress
Project description:This study aims to identify genes differentially expressed in oral CAFs with respect to their normal counterparts, i.e. oral NFs. We collected oral normal mucosal tissues and oral squamous cell carcinoma (OSCC) tissues from 12 healthy people and 12 OSCC patients, respectively, at West China Hospital of Stomatology, Sichuang University, P. R. China. The tissues were isolated, cultured and purified using standard protocols to obtain oral NFs and CAFs. Agilent 4×44K Whole Genome Oligo Microarrays were used to measure the gene expression profiles of the samples. Sample preparation and hybrid reactions were performed according to the manufacture’s instructions. RNA samples from NFs and CAFs were pooled respectively before hybridization. The chips were scanned and visualized using the Agilent DNA microarray scanner. Probe set intensities were measured using Agilent Feature Extraction software (version 10.5.1.1). Raw data were normalized in the Agilent GeneSpring GX software (version 11.0) using the Agilent FE one-color scenario (mainly median normalization).
2012-01-26 | GSE35356 | GEO
Project description:Cancer associated fibroblasts (CAFs) are the major cellular component of the tumor microenvironment and they have been shown to stimulate tumor growth, epithelial-to-mesenchymal transition (EMT), invasion and radio-resistance. We used microarrays to investigate the influence of CAFs on the gene expression profile of HNSCC cells in 2D co-cultures
2021-06-15 | GSE178153 | GEO
Project description:Cancer associated fibroblasts (CAFs) are the major cellular component of the tumor microenvironment and they have been shown to stimulate tumor growth, epithelial-to-mesenchymal transition (EMT), invasion and radio-resistance. We used microarrays to investigate the influence of CAFs on the gene expression profile of HNSCC cells in 3D co-cultures
2021-06-15 | GSE178154 | GEO
Project description:Oral carcinogenesis is a multi-step process involving normal mucosa progressing to oral precancerous lesions and finally to oral squamous cell carcinoma (OSCC). This complex process encompasses various molecules, including non-coding RNAs (ncRNAs). In this study, we performed whole-transcriptome analyses on adjacent normal tissues, oral leukoplakia tissues, and OSCC tissues, with the goal of identifying key differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs associated with different stages of oral carcinogenesis. In our study, numerous differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs were identified in adjacent normal, oral leukoplakia, and OSCC tissues. Subsequently, we constructed two regulatory competitive endogenous RNA (ceRNA) networks and identified some potential critical molecules involved in oral carcinogenesis. In conclusion, based on the whole-transcriptome analyses, we mapped the molecular feathers at RNA level during the process of oral carcinogenesis and revealed certain ncRNAs with great research potential.
2023-10-26 | GSE246050 | GEO
Project description:To study of differential effect on cancer-associated fibroblasts of HNSCC, we have employed microarray expression profiling. The critical effect of the tumor microenvironment to caner progression is well recognized. Recent research suggests that the cancer-promoting properties of the tumor stroma may attributed to fibroblasts. However, little is known about fibroblasts that inhibit cancer progression. From the immunohistochemical analysis of cancer tissues from head and neck squamous cell carcinoma (HNSCC) patients, we divided cancer-associated fibroblast (CAF) into two groups depending on whether the boundary between epithelial cancer cells and the surrounding extracellular matrix (ECM) is clear and smooth or not. Therefore, we tried to evaluate whether there is a difference between these two CAFs in HNSCC progression. CAF was primary cultured, followed by co-culture with HNSCC cell to observe the effect on Matrigel invasion. The mRNA expression patterns between these two CAF groups were compared by DNA microarray analysis. FaDu cell and primary CAF from each group was co-transplanted into the oral mucosa of mice, and the tumorigenesis was compared. The CAF group (CAF-Promote, CAF-P) from cancer tissues which have unclear boundary between ECM and epithelial cancer cells showed a tendency to stimulate in vitro Matrigel invasion of HNSCC cell. On the contrary, the CAF group (CAF-Defense, CAF-D) from cancer tissues, which have clear boundary with epithelial cancer cell caused no remarkable increase of Matrigel invasion. In addition, CAF-D reduced the tumorigenicity of FaDu compared to CAF-P in the in vivo mice model. In DNA microarray analysis, COL3A1, COL6A6, COL25A1, and COL26A1 were particularly highly expressed in CAF-D group. In this study, these collagen proteins derived from cancer stroma were found to have a function of inhibiting the progression of HNSCC. It is expected to provide important information for predicting the prognosis of HNSCC and development of drug target in the future.
2021-02-18 | GSE160919 | GEO
Project description:Oral squamous cell carcinoma (OSCC) is a main reason of oral cancer mortality and morbidity. Cancer of oral cavity in central south Asia, ranks among third most common kinds of cancer. The discovery of candidate markers to differentiate normal from malignant cells in clinical diagnosis of OSCC would be of critical importance because this malignancy has poor prognosis. To improve the clinical outcome in OSCC patients, the present study was aimed at identifying robust candidate biomarkers for early OSCC diagnosis and to enhance understanding of the mechanisms of disease progression and pathogenesis. Of particular interest are proteins that can be found in tissue lysates of OSCC tumor vs normal adjacent mucosa samples and secreted in cell line Secretomes of HNSCC for non-invasive detection. We analysed 17 paired human malignant OSCC tissues and normal adjacent tissue in addition to secretomes of 9 HNSCC cell lines. The proteome dataset of OSCC and normal tissues consisted of 5,123 protein groups, including 299 proteins with strong differential expression (p-value <0.01, fold change barrier to ˃+2 and <-2, 205 upregulated and 94 down regulated) and 134 common proteins were also found out of total dataset of 4473 identified proteins of HNSCC cell line secretomes. Functional data analysis revealed that these differential proteins were significantly associated with multiple biological processes. Myogenesis, Fatty Acid Metabolism and KRAS Signaling DN were associated with the proteins downregulated in cancer tissues, while Protein Secretion, Unfolded Protein Response, Spliceosomal complex assembly, Protein localization to endosome and Interferon Gamma Response were enriched in the set of upregulated proteins and these regulated proteins may be classically or non-classically secreted. Furthermore, we found differential enrichment of Creb3L1, ESRRA, YY, ELF2, STAT1 and XBP transcription factors potentially regulating these major pathways.
2022-04-04 | PXD025701 | Pride