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Cell-free RNA as a Novel Biomarker for Response to Therapy in Head & Neck Cancer

ABSTRACT: Cell-free RNA as a Novel Biomarker for Response to Therapy in Head & Neck Cancer

PROVIDER: PRJNA803144 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17871132.fastq.gz	Fastqsanger.gz
	SRR17871133.fastq.gz	Fastqsanger.gz
	SRR17871134.fastq.gz	Fastqsanger.gz
	SRR17871135.fastq.gz	Fastqsanger.gz
	SRR17871136.fastq.gz	Fastqsanger.gz

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Cell-free RNA as a Novel Biomarker for Response to Therapy in Head & Neck Cancer

Project description:Liquid biopsies are gaining more traction as non-invasive tools for the diagnosis and monitoring of cancer. A new class of cancer therapeutics, synergistic botanical drug combinations (APG-157) can target multiple pathways and provide a durable response and safety. Monitoring the efficacy of such drugs involves assessing multiple molecules and cellular events simultaneously. We report a methodology using plasma cell-free RNA (cfRNA) as an indicator of patient response during drug treatment. Plasma was collected from six patients with head and neck cancer (HNC) and four controls receiving APG-157 or placebo through an oral mucosal route, before treatment and on multiple points post-dosing. Circulating cfRNA was extracted from plasma at 0-, 3- and 24-hours post-treatment, followed by RNA sequencing. Analysis of the circulating transcriptome pointed to significant perturbations following APG-157 treatment. Transcripts associated with inflammatory response and leukocyte activation were upregulated upon treatment with APG-157 in cancer patients, but not in controls or placebo-treated patients. A platelet-related transcriptional signature could be detected in patients but not in controls, indicating a platelet-centric pathway in HNC. These results from a Phase 1 study are a proof of principle of the utility of cfRNAs as non-invasive biomarkers for monitoring the efficacy of APG-157 in HNC.

2022-04-05 | GSE196038 | GEO

TCAB1M-oM-<M-^ZA Potential Target for Diagnosis and Therapy in Head and Neck Cancers

Project description:Previous studies indicated TCAB1, also known as WRAP53, had oncogenic feature in a certain extend. However, there is none direct study on the function of TCAB1 in tumorigenesis and development of head and neck cancers. First of all, we verified the function of TCAB1 in head and neck cancers. Knockdown TCAB1 would inhibit cell proliferation in Vitro as well as in Vivo, meanwhile, depletion TCAB1 would decrease the invasion potential of OSCC Cal-27 cells. cDNA microarray analysis showed many pathways and factors associated with occurrence and development of carcinomas were implicated in this process. Our study indicated TCAB1 might be a potential target for prognosis and therapy in head and neck cancers. Immunohistochemistry assay and western blot showed TCAB1 was overexpressed in clinical nasopharyngeal carcinoma and head and neck cell lines. Depletion endogenous TCAB1 by shRNA lentivirus in Cal-27 would verify the function of TCAB1 in cells proliferation and invasion. Furthermore, cDNA microarray was performed to detect some pathways or factors involved in the process.

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Project description:These are the Visium spatial transcriptomic data (10x Genomics) from 9 patients with Head and Neck Squamous Cell Carcinoma (oral cavity) treated in Gustave Roussy. Patients are stratified by their tumoral density of multinucleated giant cells (MGC) : 6 patients have high MGC density (patients 1, 2, 3, 4, 5, 8) and 3 have low MGC density (patients 6, 7, 9). There is one data file for each patient, except for one patient that has 3 data files (patient 1). Accordingly, there are 9 patients but 11 samples. The source code of the is available on GitHub (https://github.com/AhmedAmineAnzali/MGC_Paper_Analysis). The results are published in the paper untitled : Trem2-expressing multinucleated giant macrophages are a biomarker of good prognosis in head and neck squamous cell carcinoma (Gessain et al., 2024, Cancer Discovery). Please contact the corresponding author for more information.

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Project description:Sage performed on microdissection of Head and Neck tumor, and Head and Neck normal tissue comparative analysis of gene expression profiles of head and neck squamous cell carcinoma and Head and Neck normal tissue

2008-09-30 | E-GEOD-11986 | biostudies-arrayexpress

Gene expression profiles of head and neck squamous cell carcinoma

Project description:Sage performed on microdissection of Head and Neck tumor, and Head and Neck normal tissue

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Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue

Project description:Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas. The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples. Bisulphite-converted DNA from the 18 normal head and neck samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

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