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Affymetrix SNP array data for nasopharyngeal carcinoma samples

ABSTRACT: Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. We determined the genomic landscape of 52 NPC cases with SNP-array analysis. This approach identified multiple recurrent SCNVs, with the most frequent deletion peak spanning the CDKN2A gene on 9p21. Additional SCNVs involving established cancer genes including CCND1, AKT2, MYC and TP53 were observed. Notably, we identified that one component of the SWI/SNF complex, ARID1A, was frequently deleted in NPC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57100 | GEO | 2014/05/01

SECONDARY ACCESSION(S): PRJNA245424

REPOSITORIES: GEO

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Affymetrix SNP array data for nasopharyngeal carcinoma samples

Project description:Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. We determined the genomic landscape of 52 NPC cases with SNP-array analysis. This approach identified multiple recurrent SCNVs, with the most frequent deletion peak spanning the CDKN2A gene on 9p21. Additional SCNVs involving established cancer genes including CCND1, AKT2, MYC and TP53 were observed. Notably, we identified that one component of the SWI/SNF complex, ARID1A, was frequently deleted in NPC. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen nasopharyngeal carcinoma biopsy tissues Copy number analysis of Affymetrix 250K SNP arrays was performed for 52 nasopharyngeal carcinoma samples. Please note that the sample characteristics 'primary tumor size, metastasis, and regional lymph node' represents T, M and N in WHO TNM staging of nasopharyngeal cancer (according to American Joint Committee on Cancer (AJCC)), respectively.

2014-05-01 | E-GEOD-57100 | biostudies-arrayexpress

The genomic landscape of nasopharyngeal carcinoma

Project description:Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. Here we determined the mutational landscape of 128 cases with NPC using whole-exome and targeted deep sequencing, as well as SNP array analysis. These approaches revealed a distinct mutational signature and nine significantly mutated genes, many of which have not been implicated previously in NPC. Notably, integrated analysis showed enrichment of genetic lesions affecting several important cellular processes and pathways, including chromatin modification, ERBB-PI3K signaling and autophagy machinery. Further functional studies suggested the biological relevance of these lesions to the NPC malignant phenotype. In addition, we uncovered a number of new druggable candidates because of their genomic alterations. Together our study provides a molecular basis for a comprehensive understanding of, and exploring new therapies for, NPC Examination of mRNA expression levels in 4 individuals dignosed for Nasopharyngeal Carcinoma using RNA sequencing.

2014-11-18 | E-GEOD-63381 | biostudies-arrayexpress

The genomic landscape of nasopharyngeal carcinoma

Project description:Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. Here we determined the mutational landscape of 128 cases with NPC using whole-exome and targeted deep sequencing, as well as SNP array analysis. These approaches revealed a distinct mutational signature and nine significantly mutated genes, many of which have not been implicated previously in NPC. Notably, integrated analysis showed enrichment of genetic lesions affecting several important cellular processes and pathways, including chromatin modification, ERBB-PI3K signaling and autophagy machinery. Further functional studies suggested the biological relevance of these lesions to the NPC malignant phenotype. In addition, we uncovered a number of new druggable candidates because of their genomic alterations. Together our study provides a molecular basis for a comprehensive understanding of, and exploring new therapies for, NPC

2014-11-18 | GSE63381 | GEO

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

Project description:Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with extremely skewed ethnic and geographic distributions. Increasing evidence indicates that targeting the tumour microenvironment (TME) represents a promising therapeutic approach in NPC, highlighting an urgent need to deepen the understanding of the complex NPC TME. Here, we generated single-cell transcriptome profiles for 7,581 malignant cells and 40,285 immune cells from 15 primary NPC tumours and one normal sample. We revealed malignant signatures capturing intratumoural transcriptional heterogeneity and predicting aggressiveness of malignant cells. Diverse immune cell subtypes were identified, including novel subtypes such as CLEC9A+ dendritic cells (DCs). We further revealed transcriptional regulators underlying immune cell diversity, and cell-cell interaction analyses highlighted promising immunotherapeutic targets in NPC. Moreover, we established the immune subtype-specific signatures, and demonstrated that the signatures of macrophages, plasmacytoid dendritic cells (pDCs), CLEC9A+ DCs, natural killer (NK) cells, and plasma cells were significantly associated with improved survival outcomes in NPC. Taken together, our findings represent a unique resource providing in-depth insights into the cellular heterogeneity of NPC TME and highlight potential biomarkers for anticancer treatment and risk stratification, laying a new foundation for the precision therapies in NPC.

2020-07-20 | GSE150430 | GEO

microRNA profile of human nasopharyngeal tissues: nasopharyngeal carcinoma tissues vs. normal nasopharyngeal tissues

Project description:MicroRNAs are biomarkers of prognosis and survival for many types of cancer. We evaluated whether microRNAs can predict the survival and efficacy of concurrent chemotherapy in nasopharyngeal carcinoma (NPC) patients. We retrospectively analyzed microRNA expression in 312 paraffin-embedded NPC specimens and 18 normal nasopharyngeal tissues using microarray. We found Forty-one microRNAs are differentially expressed between NPC and normal tissues, and a five-microRNA signature can predict survival independent of stage. NPC patients with the low-risk microRNA signature have a favorable response to concurrent chemotherapy. microRNA profiling of nasopharyngeal carcinoma tissues vs. normal nasopharyngeal tissues 312 paraffin-embedded nasopharyngeal carcinoma tissues and 18 paraffin-embedded normal nasopharyngeal tissues

2012-06-30 | E-GEOD-32960 | biostudies-arrayexpress

Novel murine primary and orthotopically nasopharyngeal cancer models reveal LMP1 as a driver of metastasis

Project description:Current NPC models cannot reproduce the process of NPC tumorigenesis, which is critical for investigating the functions and mechanisms of the disease-associated factors in this malignancy.So,we aimed to generate primary and orthotopic NPC models from normal nasopharyngeal epithelium with NPC related genetic drivers. For this purpose, we cultured normal mouse nasopharyngeal organoids and induced Trp53 and Cdkn2a mutations by CRISPR/cas9 editing, together with Myc overexpression. We showed that these organoids could initiate primary NPC once transplanted into recipient mice subcutaneously or orthotopically. And we also tested the functions of LMP1 in these models and found that it dramatically promoted NPC metastases.

2022-08-15 | GSE182284 | GEO

nasopharyngeal carcinoma versus nasopharyngeal phlogistic tissue reference

Project description:Nasopharyngeal carcinoma (NPC) remains a majoy health problem worldwide, specially in Southeast China. In order to find the new candidate genes and molecular markers that are associated with nasopharyngeal carcinoma (NPC), this study focused on the screening NPC relative genes by gene expression profile. Keywords: disease state analysis 23 NPC biopsies and 15 nasopharynx chronic phlogistic biopsies were used to screen NPC relative genes by BioStarH-141s (2004) profile gene chips which contained 14112 points of full length human genes. The tumor samples were labeled with Cy5-dUTP.The nasopharyngeal phlogistic tissues were labeled with Cy3-dUTP. Biostatistics and bioinformatics were also used to analyse the differently expressed genes.

2009-04-21 | E-GEOD-11219 | biostudies-arrayexpress

nasopharyngeal carcinoma versus nasopharyngeal phlogistic tissue reference

2009-04-21 | GSE11219 | GEO

Human nasopharyngeal carcinoma

Project description:To uncover the oncogenic pathways of nasopharyngeal carcinoma, gene expression profiles of primary NPC cell strains and NPC-derived cell lines were conducted and analyzed in depth. Keywords: Oncogenesis Gene expression profiles of 9 primary NPC cell strains and 5 NPC-derived cell lines were analyzed. Forty Î¼g total RNA from one NPC sample was needed for a dye-swap experiment. Total RNA from 32 normal nasopharyngeal epithelial cell strains was pooled to serve as a universal reference.

2010-05-15 | E-GEOD-14262 | biostudies-arrayexpress

Genome-wide expressing profiling of nasopharyngeal carcinoma primary tumors versus non-cancerous nasopharyngeal tissues.

Project description:To explore differentially expressed genes between nasopharyngeal carcinoma (NPC) primary tumors and non-cancerous nasopharyngeal tissues, 18 NPC tissue samples versus 18 control samples were utilized to perform genome-wide expressing profiling. Consequently, 2992 genes were found to be differentially expressed in NPC tissues relative to the control (FC>2, P<0.05). Among these 2992 genes, uPA was ranked as the top one in all upregulated genes sorted by ascending order of P-value. Moreover, expression of uPAR was also upregulated in NPC tissues with FC=3.34 and P=7.52M-CM-^W105. 18 nasopharyngeal carcinoma primary tumors and 18 non-cancerous nasopharyngeal tissues were used to perform genome-wide expressing profiling. The median ages of patients were 46 (range, 19-77) for NPC patients and 45 (range, 18-78) for the non-cancerous cohort. Almost one third of patients were female. All samples were collected before any anti-cancer treatment.

2014-01-05 | E-GEOD-53819 | biostudies-arrayexpress

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