Using liquid biopsy to understand organ injury in critical illness

'Liquid biopsy', which includes the analysis of cell-free nucleic acids (cfNA), has been pioneered as a noninvasive method for diagnostics and precision medicine (Lo et al., 2021). In healthy and disease states, cell-free DNA (cfDNA) and cell-free RNA (cfRNA), are found in body fluids, representing the detritus of cell death. Recently developed molecular and computational methods can detect the tissue-of-origin of plasma cfDNA and cfRNA to inform disease states (Sadeh et al., 2021, Sevahn et al., 2022) and expand the clinical potential of 'liquid biopsies'.
In critical illness, patients frequently present in multiple organ failure caused by a variety of pathologies. The acute and severe nature of the illness often causes diagnostic, therapeutic and prognostic challenges. Deciphering the pathophysiology is limited by inability to directly and contemporaneously biopsy relevant tissues. 'Liquid biopsies' offers a method to understand pathophysiology mechanisms in critical illness.
Using plasma cfDNA chromatin immunoprecipitation with sequencing (ChIP-seq) of modified histones, genome-scale information on tissue-of-origin and gene transcription can be obtained (Sadeh et al., 2021). This is based on histone methylation marks that identify tissue-specific gene regulation (Biddie et al., 2010). Similarly, circulating plasma cfRNA have been shown to contain mature transcripts that originate from multiple organs, and can be mapped to tissue-of-origin through computational deconvolution to inform disease states (Sevahn et al., 2022).
Interrogation of cfNAs can therefore provide mechanistic insight into critical illness. The possibility of detecting multiple tissue signals provides a whole-patient level of noninvasive 'biopsy' to understand critical illness associated with multiple organ failure.
Critically ill patients will be recruited as part of the LicuiD (Liquid biopsy In the Critically Unwell wIth acute Disease) study (PI: Dr Simon Biddie). Plasma samples will be collected for cfDNA and cfRNA from critically ill patients in intensive care with a variety of underlying acute illnesses, including myocardial infarct and kidney injury. Plasma samples will be used to generate cfDNA ChIP-seq and cfRNA-seq profiles. The integration of cfNA 'omics' approaches with clinical information will uncover pathophysiology mechanisms, with a goal to identify novel biomarkers and therapeutic targets towards precision medicine.
Aims
1. Identify tissue-specific transcriptomic and epigenomic signatures from cfNAs as a noninvasive method to determine pathological mechanisms in critical illness.
2. Identify disease-specific genes from cfNA transcriptomic and epigenomic datasets to discover novel mechanistic and therapeutic targets in critical illness.
3. Detect disease-specific transcription or epigenetic markers from cfNAs to inform potential diagnostic and / or prognostic biomarkers in critically ill cohorts.
References
Biddie et al., Genome-wide mechanisms of nuclear receptor action. Trends Endocrinol Metab. 2010; 21(1): 3-9
Lo et al., Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science. 2021; 372(6538): eaaw3616
Sadeh et al., ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. Nat Biotechnol. 2021; 39(5): 586-598
Sevahn et al., Cell types of origin of the cell-free transcriptome. Nat Biotechnol. 2022; 40(6): 855-861