Unbiased plasma profiling using pre-selected RNA aptamer pools predicts mortality in COVID-19 and identifies protein risk factors

Asger Givskov Jørgensen; Daniel Miotto Dupont; Søren Fjelstrup; Claus Bus; Cecilie Bo Hansen; Thomas Benfield; Peter Garred; Peter M H Heegaard; Jørgen Kjems

doi:10.1016/j.omtn.2024.102253

Unbiased plasma profiling using pre-selected RNA aptamer pools predicts mortality in COVID-19 and identifies protein risk factors

Mol Ther Nucleic Acids. 2024 Jun 15;35(3):102253. doi: 10.1016/j.omtn.2024.102253. eCollection 2024 Sep 10.

Authors

Asger Givskov Jørgensen¹, Daniel Miotto Dupont¹, Søren Fjelstrup¹, Claus Bus¹, Cecilie Bo Hansen², Thomas Benfield³, Peter Garred², Peter M H Heegaard⁴, Jørgen Kjems¹

Affiliations

¹ Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.
² Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark.
³ Department of Infectious Diseases, Copenhagen University Hospital - Amager and Hvidovre, 2650 Hvidovre, Denmark.
⁴ Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.

Abstract

The impact of the COVID-19 pandemic demands effective prognostic tools for precise risk evaluation and timely intervention. This study utilized the APTASHAPE technology to profile plasma proteins in COVID-19 patient samples. Employing a highly diverse 2'-fluoro-protected RNA aptamer pool enriched toward proteins in the plasma samples from COVID-19 patients, we performed a single round of parallel selection on the derivation cohort and identified 93 discriminatory aptamers capable of distinguishing COVID-19 and healthy plasma samples. A subset of these aptamers was then used to predict 30-day mortality with high sensitivity and specificity in a validation cohort of 165 patients. We predicted 30-day mortality with areas under the curve (AUCs) of 0.91 in females and 0.68 in males. Affinity purification coupled with mass spectrometry analysis of the aptamer-targeted proteins identified potential biomarkers associated with disease severity, including complement system components. The study demonstrates the APTASHAPE technology as an unbiased approach that not only aids in predicting disease outcomes but also offers insights into gender-specific differences, shedding light on the nuanced aspects of COVID-19 pathophysiology. In conclusion, the findings highlight the promise of APTASHAPE as a valuable tool for estimating risk factors in COVID-19 patients and enabling stratification for personalized treatment management.

Keywords: MT: Oligonucleotides: Diagnostics and Biosensors; NGS; RNA aptamers; biomarker discovery; blood analysis; high-throughput screening; nanotechnology; next-generation sequencing; precision medicine; prognostic applications; protein biomarkers; proteomics.