Differential RNA aptamer affinity profiling on plasma as a potential diagnostic tool for bladder cancer.
Søren FjelstrupDaniel M DupontClaus BusJan J EnghildJørgen B JensenKarin Birkenkamp-DemtröderLars DyrskjøtJørgen KjemsPublished in: NAR cancer (2022)
The molecular composition of blood is a signature of human health, reflected in the thousands of blood biomarkers known for human diseases. However, establishing robust disease markers is challenging due to the diversity of individual samples. New sequencing methods have simplified biomarker discovery for circulating DNA and RNA while protein profiling is still laborious and costly. To harness the power of high-throughput sequencing to profile the protein content of a biological sample, we developed a method termed APTASHAPE that uses oligonucleotide aptamers to recognize proteins in complex biofluids. We selected a large pool of 2'Fluoro protected RNA sequences to recognize proteins in human plasma and identified a set of 33 cancer-specific aptamers. Differential enrichment of these aptamers after selection against 1 μl of plasma from individual patients allowed us to differentiate between healthy controls and bladder cancer-diagnosed patients (91% accuracy) and between early non-invasive tumors and late stage tumors (83% accuracy). Affinity purification and mass spectrometry of proteins bound to the predictive aptamers showed the main target proteins to be C4b-binding protein, Complement C3, Fibrinogen, Complement factor H and IgG. The APTASHAPE method thus provides a general, automated and highly sensitive platform for discovering potential new disease biomarkers.
Keyphrases
- human health
- nucleic acid
- end stage renal disease
- binding protein
- mass spectrometry
- ejection fraction
- newly diagnosed
- risk assessment
- high throughput
- chronic kidney disease
- single cell
- prognostic factors
- squamous cell carcinoma
- amino acid
- capillary electrophoresis
- computed tomography
- ms ms
- patient reported outcomes
- single molecule
- young adults
- induced pluripotent stem cells
- cell free
- fluorescent probe
- living cells
- high performance liquid chromatography
- molecularly imprinted