Early cancer detection using cell-free RNA in blood
Description: Cancer is the leading cause of mortality worldwide and presents a significant challenge in its management and treatment. A key area of focus is the early detection of cancer, as tumor staging strongly predicts the overall survival of cancer patients. This is particularly true for head and neck squamous cell carcinoma (HNSCC), which is the sixth most common cancer worldwide, with 890’000 new cases and 450’00 deaths in 2018. Most patients are diagnosed with advanced-stage disease, a stage where fewer than 50% of patients survive beyond five years. Thus, there is a clear unmet need for early detection of HNSCC.Liquid biopsies have the potential to revolutionize cancer detection. The cell-free transcriptome in liquid biopsies has recently emerged as an exciting new frontier and holds great promise to non-invasively detect and molecularly classify HNSCC in the population. Cell-free RNA has several major advantages to cell-free DNA due to its ability to detect cancer without the necessity of pre-existing knowledge about potential DNA mutations. This attribute offers a broader scope for early non-invasive HNSCC detection in the Swiss population. However, a prerequisite to implementing the detection of cell-free RNA in liquid biopsies for HNSCC patient care is a systematic understanding of the role of cell-free RNA in cancer patients. Translating the cell-free transcriptome to patient care requires the development of a platform to detect and bioinformatically deconvolve cell-free RNA to allow the inference of HNSCC cell types.Here, we propose to develop a framework to exploit the cell-free transcriptome of HNSCC for cancer detection. First, we will determine the single-cell transcriptomic landscape of HNSCC. The comprehensive single-cell atlas will provide insights into HNSCC biology at high resolution and serve as a reference for detecting cell-free RNA in liquid biopsies. Second, we plan to isolate and sequence cell-free RNA in the blood of healthy and HNSCC patients to systematically assess the potential of the cell-free transcriptome in HNSCC detection. Finally, we aim to establish a bioinformatic deconvolution pipeline to map the cell-free transcriptome to our single-cell RNA sequencing atlas. Together, our pilot study will test the potential cell-free RNA in the blood to establish a platform for the detection of cell- free RNA in HNSCC patients and will form the basis for future investigations into whether the cell-free transcriptome in liquid biopsies can be translated to clinical patient care.
Amount: CHF 99,600
Funding type: grant
Funder scheme: Spark
Start date: 2026-01-01
End date: 2026-12-31
Investigator: Weber, Ramona
Institution: University of Zurich – ZH
Subfield: Molecular Biology
Domain: Life Sciences
Funded outputs count: 1
Funder award ID: 237816
OpenAlex ID: G7484877321