737eb2b0-8d30-440f-8f6c-f0f3627dd60c - samples
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ABSTRACT:
PROVIDER: EGAD00001005719 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Low-coverage whole genome sequencing data of 37 HPV-negative HNSCC specimens from patients treated at The Netherlands Cancer Institute. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for WGS to a depth of approx. 0.5X.
| EGAD00001005718 | EGA
Project description:RNA-Seq data of 55 HPV-negative HNSCC specimens from patients treated at the VU medical Centre, Amsterdam, The Netherlands. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.
| EGAD00001005716 | EGA
Project description:RNA-Seq data of 28 HPV-negative HNSCC specimens from patients treated at the Netherlands Cancer Institute (Amsterdam), VU Medical Centre (Amsterdam) or MAASTRO Clinic (Maastricht) in The Netherlands. HNSCC biopsy samples were obtained prior to treatment (chemo-radiotherapy) for the prospective study within the DESIGN project and used for polyA mRNA sequencing.
| EGAD00001005722 | EGA
Project description:RNA-Seq data of 36 HPV-negative HNSCC specimens from patients treated at The Netherlands Cancer Institute, Amsterdam. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.
| EGAD00001005715 | EGA
Project description:RNA-Seq data of 17 HPV-negative HNSCC specimens from patients treated at the MAASTRO clinic, Maastricht, The Netherlands. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.
| EGAD00001005717 | EGA
Project description:RNA-Seq data of 25 HNSCC specimens from patients treated at The Netherlands Cancer Institute, Amsterdam and enrolled in the ARTFORCE trial. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.
| EGAD00001005721 | EGA
Project description:Radiotherapy is a key treatment for head and neck squamous cell carcinoma (HNSCC) especially in patients with human papilloma virus-negative (HPV-) HNSCC. Our studies identify polo-like kinase 1 (PLK1) as a promising target for HNSCC. PLK1 inhibition with onvansertib reduces cell viability and spheroid growth of HPV- HNSCC cells. PLK1 inhibition combined with radiation increases G2/M arrest, decreases colony formation of HPV- HNSCC cells, and reduces tumor growth in vivo. RNA-sequencing demonstrates radiation increases MMP10 expression but PLK1 inhibition reverses this effect in HPV- HNSCC cells. PLK1 inhibition also reduces MMP10 activity in HPV- HNSCC cells. These findings suggest that combining PLK1 inhibition with radiation may improve therapeutic response for HPV- HNSCC via MMP10, offering a novel approach to overcome radiation resistance.
2025-10-15 | GSE306710 | GEO
Project description:Human papillomavirus (HPV) positive HNSCC patients generally have a favorable survival and promising responsiveness to radiotherapy, chemoradiotherapy and checkpoint blockades. However, HPV negative patients, the majority of HNSCC patients, have been largely overlooked. Cell death has been involved in the therapeutic resistance of cancers. We constructed a cell death index (CDI), based on autophagy, apoptosis and pyroptosis related genes, to predict the prognosis for HNSCC using TCGA dataset, and validated in a cohort from Qilu Hospital of Shandong University. We performed RNA sequencing of 28 paraffin-embedded tissue from HNSCC patients and determined HPV status by immunohistochemistry of p16. We found that CDI was an independent prognostic indicator for overall survival. Notably, the prognostic value of CDI was more profound in HPV negative HNSCC patients compared with those with HPV positivity.
2023-02-07 | GSE208576 | GEO
Project description:Background: Oropharynx squamous cell carcinoma (OPSCC) is a subtype of HNSCC, arising from the base of tongue, lingual tonsil, tonsil, oropharynx, pharynx. The majority of OPSCC positive for HPV infection is associated with better prognosis, but a fraction of them, similarly to HPV-negative ones, is resistant to therapy and has poor prognosis. A deep molecular study of OPSCC is mandatory to identify either prognostic markers or targets for therapy, in particular in patients with worse prognosis. Methods: 14 HPV-positive and 15 HPV-negative Italian OPSCC (n=29) with complete clinical information and follow-up of more than 5 years were molecularly characterized by gene expression profiling and compared to three cohorts of OPSCC extracted from public HNSCC datasets. AKR1C3 emerged as robust marker overexpressed in HPV-negative OPSCC and in HPV-positive lesions with worse prognosis. Fadu and Cal-27 OPSCC cell lines were treated with AKR1C3 inhibitors, alone or in combination with Cisplatin. Results: Gene set enrichment analysis revealed that up-regulated genes in HPV-positive samples are involved in immune system, muscle related processes, response to stimuli, actin organization, tissue development and adhesion, while down-regulated genes participated in glutathione derivative biosynthetic and xenobiotic metabolic processes, hypoxia and oxidative stress. AKR1C3, coding for an enzyme involved in chemio-radioresistance, is in the top10 genes with higher upregulation in HPV-negative samples. Pre-treatment with a selective AKR1C3 inhibitor potentiated the effect of Cisplatin in cells with higher basal level of the enzyme. Conclusions: We identified a druggable target, AKR1C3, associated with survival in subgroups of OPSCC patients either positive or negative for HPV infection and to resistance to chemo-radiotherapy in HNSCC. Pretreatment of OPSCC cell lines expressing this enzyme with a selective AKR1C3 inhibitor is able to enhance Cisplatin efficacy.
2021-07-30 | GSE142583 | GEO
Project description:ABSTRACT Two major subgroups of head and neck squamous cell carcinomas (HNSCC) are currently distinguished based on etiology and pattern of genetic alterations; tumors with biologically active human papillomavirus (HPV) and tumors without. It is at present unclear whether additional genetically distinct subgroups exist within HPV-negative HNSCC. Aim of this study is to genetically classify HNSCC without HPV involvement and to correlate the genetically defined classes to tumor and patient characteristics. By means of array comparative genomic hybridization (aCGH) we determined DNA copy number variation in thirty-nine HPV-negative, but further unselected HNSCC. Unsupervised analysis of aCGH data distinguished two genetic groups in HPV-negative HNSCC, one characterized by a low level of chromosomal alterations (N=9), and another by a high level of chromosomal alterations (N=30). Absence of chromosomal aberrations was significantly associated with wild-type TP53, a low level of alcohol consumption, a female gender and a better prognosis. The tumors were negative for microsatellite instability. The discovery of this new class of HNSCC with unique genetic and clinical characteristics has important consequences for future basic and clinical studies. All DNAs are isolated from fresh frozen HNSCC specimen. All tissue specimens were microdissected to obtain at least 90% tumor DNA. All sampels are hybridized against a pool of reference DNA of normal individuals of the opposite gender.
2009-03-11 | E-GEOD-11929 | biostudies-arrayexpress