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Liquid Biopsy: Examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for molecular tumor markers

ABSTRACT: Liquid Biopsy: Examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for molecular tumor markers

PROVIDER: PRJNA658334 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12483610.fastq.gz	Fastqsanger.gz
	SRR12483611.fastq.gz	Fastqsanger.gz
	SRR12483612.fastq.gz	Fastqsanger.gz
	SRR12483613.fastq.gz	Fastqsanger.gz
	SRR12483614.fastq.gz	Fastqsanger.gz

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Similar Datasets

Liquid Biopsy: Examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for molecular tumor markers

Project description:The present study aims to clarify whether patients suffering from head and neck squamous cell carcinoma (HNSCC) could be recognized based on platelet mRNA sequencing (RNAseq). Sequencing analysis of RNA derived from platelets of tumor patients and healthy donors revealed significantly differentially expressed RNA encoding 618 genes. Among them, we identified RNA coding for 49 genes characteristically expressed in epithelial cells. Additionally, in tumor patient’s platelets we observed RNA coding for genes involved in tumor progression by contributing to proliferation, metastasis or angiogenesis. Furthermore, 41 non-coding RNAs involved in transcription and translation have been identified. Results were verified by quantitative RT-PCR on platelet RNA derived from a second tumor patient / healthy donor cohort. However, in order to identify a combination of a certain set of genes allowing the identification of HNSCC based on platelet RNAseq further research is necessary.

2023-07-19 | GSE156554 | GEO

Liquid biopsy: an examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for predictive molecular tumor markers.

Project description:AimRecently, a tumor cell-platelet interaction was identified in different tumor entities, resulting in a transfer of tumor-derived RNA into platelets, named further "tumor-educated platelets (TEP)". The present pilot study aims to investigate whether such a tumor-platelet transfer of RNA occurs also in patients suffering from head and neck squamous cell carcinoma (HNSCC).MethodsSequencing analysis of RNA derived from platelets of tumor patients (TPs) and healthy donors (HDs) were performed. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used for verification of differentially expressed genes in platelets from TPs and HDs in a second cohort of patients and HDs. Data were analyzed by applying bioinformatic tools.ResultsSequencing of RNA derived from the tumor as well as from platelets of TPs and HDs revealed 426 significantly differentially existing RNA, at which 406 RNA were more and 20 RNA less abundant in platelets from TPs in comparison to that of HDs. In TPs' platelets, abundantly existing RNA coding for 49 genes were detected, characteristically expressed in epithelial cells and RNA, the products of which are involved in tumor progression. Applying bioinformatic tools and verification on a second TP/HD cohort, collagen type I alpha 1 chain (COL1A1) and zinc finger protein 750 (ZNF750) were identified as the strongest potentially platelet-RNA-sequencing (RNA-seq)-based biomarkers for HNSCC.ConclusionsThese results indicate a transfer of tumor-derived messenger RNA (mRNA) into platelets of HNSCC patients. Therefore, analyses of a patient's platelet RNA could be an efficient option for liquid biopsy in order to diagnose HNSCC or to monitor tumorigenesis as well as therapeutic responses at any time and in real time.

| S-EPMC10344902 | biostudies-literature

Multi-parametric liquid biopsy approach

Project description:Multi-parametric liquid biopsy approach

| PRJEB39331 | ENA

Retinoblastoma Aqueous Humor Liquid Biopsy Repository

Project description:Retinoblastoma Aqueous Humor Liquid Biopsy Repository

| PRJNA887892 | ENA

Retinoblastoma Aqueous Humor Liquid Biopsy Repository

Project description:Retinoblastoma Aqueous Humor Liquid Biopsy Repository

| PRJNA887893 | ENA

PiRNA Obtained through Liquid Biopsy as a Possible Cancer Biomarker.

Project description:In recent years PIWI-interacting RNAs (piRNAs) have gained the interest of scientists, mainly because of their possible implications in cancer. Many kinds of research showed how their expression can be linked to malignant diseases. However, most of them evaluated the expression of piRNAs in tumor tissues. It was shown how these non-coding RNAs can interfere with many signaling pathways involved in the regulation of proliferation or apoptosis. A comparison of piRNA expression in tumor tissue and adjacent healthy tissues has demonstrated they can be used as biomarkers. However, this way of obtaining samples has a significant drawback, which is the invasiveness of such a procedure. Liquid biopsy is an alternative for acquiring biological material with little to no harm to a patient. Several different piRNAs in various types of cancer were shown to be expressed in bodily fluids such as blood or urine. Furthermore, their expression significantly differed between cancer patients and healthy individuals. Hence, this review aimed to assess the possible use of liquid biopsy for cancer diagnosis with piRNAs as biomarkers.

| S-EPMC10252662 | biostudies-literature

Tumor-educated platelet RNA for the detection and (pseudo)progression monitoring of glioblastoma

Project description:We report RNA-sequencing data of 805 blood platelet samples, including 240 tumor-educated platelet (TEP) samples collected from patients with glioblastoma and 126 TEP samples collected from patients with brain metastases. In addition, we report RNA-sequencing data of blood platelets isolated from 353 asymptomatic controls and 86 individuals with multiple sclerosis. This dataset highlights the ability of TEP RNA-based 'liquid biopsy' diagnostics for the detection and (pseudo)progression monitoring of glioblastoma.

2020-10-22 | GSE156902 | GEO

Diagnostic accuracy of liquid biopsy in endometrial cancer

Project description:Diagnostic accuracy of liquid biopsy in endometrial cancer

| PRJNA767010 | ENA

HSD17B13 liquid-liquid phase separation activates autocrine platelet-activating factor signaling in NASH

Project description:Loss-of-function variants in 17-beta hydroxysteroid dehydrogenase 13 (HSD17B13) are associated with decreased inflammation in human chronic liver disease. The underlying mechanism by which HSD17B13 promotes liver inflammation remains largely elusive. Here we find that HSD17B13 undergoes liquid-liquid phase separation (LLPS) around lipid droplets (LDs) in the liver of NASH patients. Dimerization of HSD17B13 drives LLPS formation and regulates its enzyme activity. HSD17B13 LLPS promotes leukocyte adhesion and fibrinogen expression in hepatocytes via activating autocrine platelet activating factor (PAF) signaling. Importantly, adeno-associated viral (AAV)-mediated xeno-expression of human HSD17B13 promotes liver inflammation in Hsd17b13-/- mice induced by high fat diet/carbon tetrachloride treatment. In conclusion, HSD17B13 LLPS triggers liver inflammation via promoting PAF-mediated leukocyte adhesion. Targeting HSD17B13 phase transition would be a promising approach to treat liver inflammation in chronic liver disease.

2024-12-19 | GSE238060 | GEO

Platelet microRNA-mRNA Co-Expression Profiles Correlate with Platelet Reactivity

Project description:MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'UTRs of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5 and miR-107:CLOCK) were selected from this list and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets. Total RNA from the platelets of 19 donors was harvested and labeled with Hy3. Reference RNA (a pool of all samples) was labeled with Hy5. This submission represents the miRNA expression component of the study.

2011-09-26 | E-GEOD-27917 | biostudies-arrayexpress

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