Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Cancer hotspot mutation sequencing of patient derived xenografts of head and neck cancer

PROVIDER: PRJNA381909 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5422800_1.fastq.gz	Fastqsanger.gz
	SRR5422800_2.fastq.gz	Fastqsanger.gz
	SRR5422791_1.fastq.gz	Fastqsanger.gz
	SRR5422791_2.fastq.gz	Fastqsanger.gz
	SRR5422801_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Homo sapiens

Project description:Gene expression data from head and neck cancer patient derived xenografts

| PRJNA330908 | ENA

Transcriptomic Characterization of HPV+ and HPV- Head and Neck Cancer Patient-Derived Xenografts

Project description:Transcriptomic Characterization of HPV+ and HPV- Head and Neck Cancer Patient-Derived Xenografts

| PRJNA854080 | ENA

The dual pathway inhibitor rigosertib is effective in direct-patient tumor xenografts of head and neck squamous cell carcinomas

Project description:Rigosertib treatment of head and neck squamous cell cancer The dual pathway inhibitor rigosertib inhibits phosphoinositide 3-kinase (PI3K) pathway activation as well as polo-like kinase 1 (PLK1) activity across a broad spectrum of cancer cell lines. The importance of PIK3CA alterations in head and neck squamous cell cancer (HNSCC) has raised interest in exploring agents targeting PI3K, the product of PIK3CA. The genetic and molecular basis of rigosertib treatment response was investigated in a panel of 16 HNSCC cell lines, and direct patient tumor xenografts from 8 HNSCC patients (4 HPV16-positive). HNSCC cell lines and xenografts were characterized by pathway enrichment gene expression analysis, exon sequencing, gene copy number, western blotting, and IHC. Rigosertib had potent antiproliferative effects on 11 of the 16 HPV- HNSCC cell lines. Treatment sensitivity was confirmed in two cell lines using an orthotopic in vivo xenograft model. Growth reduction after rigosertib treatment was observed in 3/8 HNSCC direct patient tumor lines. The responsive tumor lines carried a combination of a PI3KCA activating event (amplification or mutation) and a p53 inactivating event (either HPV16-mediated or mutation-mediated TP53 inactivation). In this study, we evaluated the in vitro and in vivo efficacy of rigosertib in both HPV+ and HPV- HNSCCs focusing on inhibition of the PI3K pathway. Although consistent inhibition of the PI3K pathway was not evident in HNSCC, we identified a combination of PI3K/TP53 events necessary, but not sufficient for rigosertib-sensitivity. Sixteen HNSCC lines data were profiled at baseline to find differentially expressed genes and pathways sensitive to rigosertib.

2013-06-13 | E-GEOD-47864 | biostudies-arrayexpress

Caveolin-1 and Sox-2 are Predictive Biomarkers of Cetuximab Response in Head and Neck Cancer

Project description:Expression analysis (RNA-seq) and RPPA data (see publication) of head and neck cancer patient-derived xenographs (PDXs) revealed Sox-2 and Cav-1 expression to be biomarker determinants of head and neck cancer patient tumor response to cetuximab (EGFR inhibitor) treatment.

2021-10-12 | GSE183881 | GEO

The dual pathway inhibitor rigosertib is effective in direct-patient tumor xenografts of head and neck squamous cell carcinomas

2013-06-13 | GSE47864 | GEO

Integrated Genomics Approach to Identify Biologically Relevant Alterations in Fewer Samples.

Project description:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.

2015-11-27 | E-MTAB-3961 | biostudies-arrayexpress

Whole exome sequencing and transcription profiling of a patient cohort of oral cavity squamous cell carcinomas

Project description:Oral cavity Squamous Cell Carcinoma (OCSCC) is a common form of head and neck cancer through the developed and developing world. However, the etiology of OCSCC is still unclear. To explore whether smoking, HPV and/or other underlying genetic and transcriptomic changes could be responsible for the oncogenesis events for OCSCC. A prospective observational study of fresh tissue biopsy from 45 participants with OCSCC collected from Brisbane Head and Neck Clinics between 2013 to 2015. Exploration of the genetic and transcriptomic landscape was performed using RNA sequencing and whole exome sequencing. Identification of HPV was to be performed using DNA PCR genotyping and RNA sequencing. Patient medical records were retrieved and the patient demographics were used to correlate with genomic and transcriptomics analyses, including the location of the tumor within the oral cavity, smoking and alcohol histories.

2018-09-28 | E-MTAB-6448 | biostudies-arrayexpress

4219ec5f-9f86-4486-943c-9e45f29df918 - samples

Project description:patient-derived head and neck cancer organoids

| EGAD00001010134 | EGA

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (ChIP-Seq)

Project description:Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV+) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis.

2018-03-20 | GSE112021 | GEO

ChIP-seq profiles of primary, metastatic, drug-resistant and drug-holiday cells

Project description:We employed ChIP-seq to detect poised and active chromatin regions in cisplatin sensitive and resistant head neck squamous cell carcinoma patient derived primary and lymph node cell lines.

2018-11-22 | GSE120634 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data