GEO DataSets

(Submitter supplied) It has been postulated that a high number of mutations resulting in the expression of neoantigens promotes T-cell-mediated inflammation and, as a consequence leads to the activation of immune checkpoints Hence, we determined if high tumor mutational burden (TMB) was associated with a distinct immune expression signature. For this analysis, 37 cases with tumor material for nanoString mRNA expression analysis were available. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23249

37 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

28 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL5175 GPL6801

201 Samples

Download data: CEL, CHP

(Submitter supplied) In order to identify biomarkers that contribute to genetic causes of OSCC, we attempt to identify copy number variation regions (CNV) in patients with OSCC. We identified and confirmed the clinical significance of amplification regions scattered from 8q22.2 to 8q24.3.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL6801

122 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Intratumoral CD8+ T-cell infiltration in squamous cell carcinoma of the head and neck (HNSCC) has previously been linked to the efficacy of chemoradiation (CRTX) and immune checkpoint inhibitor (ICI) monotherapy. Further detailed characterization of the tumor immune-micromilieu and its influence on outcome may suggest rational CRTX-ICI combinations. In this study, the complex interaction of the tumor immune microenvironment with the efficacy of CRTX in HNSCC was analyzed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23249

100 Samples

Download data: TXT

(Submitter supplied) First line chemotherapy with platinum and cetuximab is usually offered to RM-HNSCC pts. In the Extreme trial a median progression free survival (PFS) time of 5.6 months was reported. However, a small fraction of pts achieves a prolonged PFS (> than 12 months). Till now, no recognized predictive biological factor has been identified.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14951

40 Samples

Download data: TXT

(Submitter supplied) Objectives: Phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) is commonly altered in many human tumors, leading to the activation of p110α enzymatic activity that stimulates growth factor-independent cell growth. PIK3CA alterations such as mutation, gene amplification and overexpression are common in head and neck squamous cell carcinoma (HNSCC) and. We aim to explore how these alterations and clinical outcome are associated, as well as the molecular mechanisms involved. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

31 Samples

Download data: CEL

(Submitter supplied) While mutation-derived neoantigens are well recognized in generating anti-tumor T cell responses, increasing evidences highlight the complex association between tumor mutation burden (TMB) and tumor infiltrating lymphocytes (TILs). We examined this relationship across nine major cancer types to identify non-TMB determinants of immune responses within the tumor microenvironment. TMB overall correlated poorly with both TILs and exhausted CD8+ T cells (Tex) as an indicator of tumor-specific T cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

11 Samples

Download data: MTX, TSV

(Submitter supplied) ER+ breast cancer is an immune cold cancer. We utilized single-cell RNA-sequencing to learn the cell heterogeneity in ER+ breast tumor microenvironment.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: MTX, TSV

(Submitter supplied) We identify subsets of BC tumors infiltrated by CD8+ T cells with characteristic features of exhausted T cells (TEX). Tumors with abundant CD8+ TEX exhibit a distinct tumor microenvironment marked by amplified interferon-γ signaling related pathways and higher PD-L1 expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL19965

36 Samples

Download data: RCC, TXT

(Submitter supplied) The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

13 Samples

Download data: VCF

(Submitter supplied) (Objectives) The goal of this study is to investigate paracrine effect of Peripheral Blood Mononuclear Cells (PBMCs) on Head and Neck cancer cell lines. (Method) Transcription profiles of PBMCs (control) and PBMCs co-cultured with Head and Neck cancer cell lines (treatment) were generated by deep sequencing, in triplicate for HN17 and duplicate for HN4, using Illumina HiSeq 4000. (Results and conclusion) Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with HN cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

63 Samples

Download data: MTX, TSV

(Submitter supplied) This work demonstrates the potential of soluble Semaphorin 4D (sSema4D) as an immune biomarker in plasma of patients with head and neck squamous cell carcinoma (HNSCC) that can read the histological immune subtype (HIS) and IFN-γ signature of the paired tumor tissue. Advanced analysis of 10 HNSCC tumor tissue using the IO-360 nanoString platform, showed that tumors with high sSema4D in plasma (HsS4D) clustered as negative IFN-γ immune signature and were most of histologically immune Excluded (HIS‐IE). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL28781

10 Samples

Download data: RCC

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL11154 GPL18900 GPL19699

108 Samples

Download data: IDAT

(Submitter supplied) Purpose: There is substantial heterogeneity within the human papillomavirus (HPV) positive head and neck cancer (HNC) tumors that predispose them to different outcomes, however this subgroup is poorly characterized due to various historical reasons. Experimental Design: we perform unsupervised gene expression clustering on well-annotated HPV(+) HNC samples from two cohorts ( 84 total primary tumors), as well as 18 HPV(-) HNCs, to discover subtypes, and begin to characterize the differences between the subtypes in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number variations and mutation frequencies. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL18900 GPL19699

72 Samples

Download data: IDAT, TXT

(Submitter supplied) Purpose: There is substantial heterogeneity within the human papillomavirus (HPV) positive head and neck cancer (HNC) tumors that predispose them to different outcomes, however this subgroup is poorly characterized due to various historical reasons. Experimental Design: we perform unsupervised gene expression clustering on well-annotated HPV(+) HNC samples from two cohorts ( 84 total primary tumors), as well as 18 HPV(-) HNCs, to discover subtypes, and begin to characterize the differences between the subtypes in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number variations and mutation frequencies. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: TXT

(Submitter supplied) Despite the promise of immune checkpoint inhibition (ICI), therapeutic responses remain limited. This raises the possibility that standard of care treatments delivered in concert may compromise the tumor response. To address this, we employed tobacco-signature HNSCC murine models in which we mapped tumor-draining lymphatics and developed models for regional lymphablation with surgery or radiation. Remarkably, we found that lymphablation eliminates the tumor ICI response, significantly worsening overall survival and repolarizing the tumor- and peripheral- immune compartments. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

15 Samples

Download data: TXT

(Submitter supplied) This study correlated miR expression with predicted targets to determine those miRs that both downregulated a subset of their predicted targets and showed differential expression in cancer samples compared to controls

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL8786

69 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

synthetic construct; Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array; Genome variation profiling by SNP array; Non-coding RNA profiling by array

4 related Platforms

284 Samples

Download data: CEL