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Homo sapiens

ABSTRACT: Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)

PROVIDER: PRJNA288722 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2084810.fastq.gz	Fastqsanger.gz
	SRR2084807.fastq.gz	Fastqsanger.gz
	SRR2084808.fastq.gz	Fastqsanger.gz
	SRR2084809.fastq.gz	Fastqsanger.gz

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Integration of p16/HPV DNA status with a 24-miRNA-defined molecular phenotype improves clinically relevant stratification of head and neck cancer patients

Project description:Head and neck squamous cell carcinomas (HNSCC) driven by human papillomavirus (HPV) generally have a more favourable prognosis. We hypothesized that HPV-positive HNSCC may be identified based on a miRNA signature according to their specific molecular pathogenesis and are characterized by a unique transcriptome compared to HPV-negative HNSCC. We characterized the miRNA-expression patterns of the tumors from 229 head and neck squamous cell carcinoma patients by Agilent miRNA microarrays in order to define a HPV-predicting miRNA signature.

2023-05-10 | GSE175509 | GEO

Multi-omics analysis to uncover the molecular basis of tumor budding in head and neck squamous cell carcinoma

Project description:Tumor budding (TB) is a well-established prognostic biomarker in HPV-negative head and neck squamous cell carcinoma (HNSCC) and an emerging prognostic biomarker in HPV-positive HNSCC. The molecular determinants and mechanisms underlying TB are incompletely understood. Here, we profile an in-house cohort of HPV-negative HNSCCs by MS-based proteomics to uncovered molecular correlates of TB in HNSCC.

2025-03-09 | PXD058014 | Pride

Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)

Project description:We report the first RNA-Seq experiments profiling the effects of DEK loss in HNSCC. Our data also incorporates HPV+ and HPV- tumors to idenfity HPV-dependent and -independent gene signatures. RNA-Seq of DEK-dependent gene signatures in HNSCC cell lines

2016-02-05 | E-GEOD-70462 | biostudies-arrayexpress

Label-free Proteomics of Exosomes and Cell Lines from HPV-positive and HPV-negative HNSCC

Project description:This study investigates the influence of human papillomavirus (HPV) on the proteomic content of exosomes derived from head and neck squamous cell carcinoma (HNSCC) cell lines. Label-free quantitative proteomics was used to analyze exosomes and parental cells from HPV16-positive (93VU147T, UDSCC2) and HPV-negative (OCT-1) HNSCC cell lines. Raw LC-MS/MS data were acquired to study differentially exported proteins, with emphasis on exosomal cargo variation and its functional implications.

2026-07-06 | PXD067001 | Pride

miRNA expression in head and neck squamous cell carcinoma (HNSCC)

Project description:The involvement of microRNAs (miRNAs) in cancer and their potential as biomarkers of diagnosis, prognosis and response to therapy is becoming increasingly appreciated. The etiology of head and neck squamous cell carcinoma (HNSCC) is predominantly associated with the synergistic effects of tobacco and alcohol use, as well as Human Papilloma Virus (HPV) infection, which embodies a distinct clinical and biological phenotype. We sought to examine whether the profile of miRNAs in HNSCC varies based on HPV status, and to identify specific miRNAs altered in head and neck carcinogenesis. Total RNA was isolated from 16 HNSCC fresh frozen primary tumors, 5 fresh frozen non-diseased head and neck epithelial tissues, and 2 HNSCC cell lines. The miRNA profile of 662 individual miRNAs in these tissues was examined by microarray. 18 miRNAs are significantly altered in their expression between normal tissues and HNSCC tumors and 5 miRNAs are identified as significantly differentially expressed between HPV-positive (HPV+) and HPV-negative (HPV-) tumors. A striking difference in expression pattern of miRNA was also observed between primary tissues and cell lines. These data suggest that the pattern of miRNA expression may be reflective of disease etiology, and may be useful in the realm of diagnostic biomarkers defining broadly responsive prevention and treatment strategies for HNSCC. These data also suggest that cultured tumor cell lines may be inappropriate for novel miRNA biomarker identification. Keywords: miRNA; Disease-state analysis Expression of 662 individual miRNA was assessed in16 HNSCC fresh frozen primary tumors, 5 fresh frozen non-diseased head and neck epithelial tissues, and 2 HNSCC cell lines were arrayed

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Deciphering head and neck cancer microenvironment: Single‐cell and spatial transcriptomics reveals human papillomavirus‐associated differences

Project description:Human papillomavirus (HPV) is a major causative factor of head and neck squamous cell carcinoma (HNSCC), and the incidence of HPV-associated HNSCC is increasing. The role of tumor microenvironment (TME) in viral infection and metastasis needs to be explored further. Thus we studied the molecular characteristics of primary tumors (PTs) and lymph node metastatic tumors (LNMTs) by stratifying them based on their HPV status using spatial transcriptomics.

2024-11-20 | GSE281978 | GEO

Extracellular matrix-myCAF signatures correlate with resistance to neoadjuvant aPD-L1 immune checkpoint inhibition with durvalumab + metformin in HPV+ HNSCC

Project description:In HPV-positive head and neck squamous cell carcinoma (HNSCC), early resistance to neoadjuvant durvalumab plus metformin therapy is associated with baseline enrichment of extracellular matrix–associated myofibroblastic cancer-associated fibroblasts (ECM-myCAF) within the tumor compartment. In contrast, treatment responders exhibit a distinct tumor microenvironment marked by baseline enrichment of Langerhans-like dendritic cells and post-treatment upregulation of antigen presentation pathways. These findings highlight the tumor-stroma interface as a key determinant of immunotherapy response and provide a foundation for biomarker-driven patient selection. Identifying stromal and immune signatures predictive of response to neoadjuvant aPD-L1 therapy supports future strategies targeting the tumor microenvironment to improve outcomes in HNSCC.

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Gene expression analysis of TIL rich HPV driven head and neck tumours reveals a distinct B-cell signature when compared to HPV independent tumours.

Project description:Purpose: Human papilloma virus (HPV) associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than HPV(-) negative cancer. This may be due, in part, to the higher number of tumour infiltrating lymphocytes (TIL) in HPV(+) tumours. We used RNAseq to evaluate whether these differences in clinical behaviour could be explained simply by a numerical difference in TILs or whether there was a fundamental difference between TILs in these two settings. Patients and methods: Twenty-three consecutive HNSCC cases with high and moderate TIL density were subjected to RNAseq analysis. Differentially expressed genes (DEG) between 10 HPV(+) and 13 HPV(-) tumours were identified with EdgeR. Immune subset analysis was performed using, FAIME (Functional Analysis of Individual Microarray Expression) and Immune gene transcript count analysis. Results: 1634 genes were differentially expressed. There was a dominant immune signature in HPV(+) tumours. After normalizing expression profiles for numerical differences in T cells and B cells, 437 significantly DEGs still remained. A B-cell associated signature emerged, which segregated HPV(+) from HPV(-) cancers and included CD200, STAG3, GGA2, SPIB and ADAM28. Differential expression of these genes was confirmed by real-time quantitative PCR and immunohistochemistry. Conclusion: In our dataset, the difference associated with T-cells between patients with HPV(+) and (-) HNSCC was predominantly numerical. However, when TIL numbers are corrected, a distinct differential B-cell signature was revealed. mRNA profiles of 10 HPV driven (HPV+) and 13 HPV independant (HPV-) head and neck squamous cell carcinoma (HNSCC) tumours were generated by RNA-Seq, using Illumina HiSeq 2000.

2016-09-01 | E-GEOD-72536 | biostudies-arrayexpress

Genome-wide Scan for Methylation Profiles in head and Neck Cancer

Project description:Genome wide DNA methylation profiling of HPV positive and HPV negative head and neck squamous cell cancer (HNSCC) samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across approximately 485577 CpGs in 4 HPV positive and 4 HPV negative HNSCC tumors

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Immune landscape of viral- and carcinogen-drived head and neck cancer

Project description:Head and neck squamous cell carcinoma (HNSCC) arises through exposure to environmental carcinogens or malignant transformation by human papillomavirus (HPV). Here, we assessed the transcriptional profiles of 131,224 single cells from peripheral and intra-tumoral CD45+ immune populations from HPV– and HPV+ HNSCC and healthy donors. A spectrum of transcriptional signatures in immune lineages ranging from similar to highly divergent was present in the tumor microenvironments (TME) in HPV– and HPV+ HNSCC. CD8+ and regulatory CD4+ T cells were similar in HPV– and HPV+ HNSCC, compared to significant differences between helper CD4+ T cells, B cells and myeloid cells. Further dissection of the major immune lineages identified unique cell states and differentiation trajectories. We contextualized our results by performing multispectral immunofluorescence and evaluating putative cell-cell communication based on spatial proximity, and found longer progression free survival in patients with enrichment of a CD4+ T follicular helper cell signature.

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