Using liquid biopsy to understand organ injury in critical illness

包括无细胞核酸（cfNA）分析的“液体活组织检查”已被开创为用于诊断和精确医学的非侵入性方法（Lo等人，2021年）。在健康和疾病状态下，体液中存在游离DNA（cfDNA）和游离RNA（cfRNA），代表细胞死亡的碎屑。最近开发的分子和计算方法可以检测血浆cfDNA和cfRNA的起源组织以告知疾病状态（Sadeh等人，2021，Sevahn等人，2022），并扩大了“液体活检”的临床潜力。在危重病中，患者经常出现由各种病理引起的多器官衰竭。这种疾病的急性和严重性质往往造成诊断、治疗和预后方面的挑战。由于无法直接和同时对相关组织进行活检，因此对病理生理学的解读受到限制。使用血浆cfDNA染色质免疫沉淀结合修饰的组蛋白的测序（ChIP-seq），可以获得关于起源组织和基因转录的基因组规模的信息（Sadeh等人，2021年）。这是基于鉴定组织特异性基因调控的组蛋白甲基化标记（Biddie et al.，2010年）。类似地，已显示循环血浆cfRNA含有源自多个器官的成熟转录物，并且可以通过计算去卷积映射到起源组织以告知疾病状态（Sevahn et al. 2022).因此，询问cfNA可以提供对危重疾病的机械见解。检测多个组织信号的可能性提供了一个整体患者水平的非侵入性“活检”，以了解与多器官功能衰竭相关的危重病。危重病患者将被招募作为LicuiD（急性疾病危重不适液体活检）研究的一部分（PI：Dr Simon Biddie）。将从患有各种基础急性疾病（包括心肌梗死和肾损伤）的重症监护重症患者中采集血浆样本用于cfDNA和cfRNA。血浆样本将用于生成cfDNA ChIP-seq和cfRNA-seq图谱。cfNA“组学”方法与临床信息的整合将揭示病理生理学机制，目标是鉴定新的生物标志物和治疗靶点，以实现精准医学。目标1.从cfNAs中鉴定组织特异性转录组和表观基因组特征作为确定危重疾病病理机制的非侵入性方法。从cfNA转录组和表观基因组数据集中识别疾病特异性基因，以发现危重病中的新机制和治疗靶点。从cfNA中检测疾病特异性转录或表观遗传标志物，以告知重症队列中的潜在诊断和/或预后生物标志物。核受体作用的全基因组机制。内分泌代谢趋势2010; 21（1）：3- 9 Lo等人，液体活检中游离DNA的表观遗传学、片段组学和拓扑学。科学2021; 372（6538）：eaaw 3616 Sadeh等人，无浆细胞核小体的ChIP-seq鉴定起源细胞的基因表达程序。Nat Biotechnol. 2021; 39（5）：586- 598 Sevahn等人，无细胞转录组起源的细胞类型。Nat Biotechnol. 2022; 40（6）：855-861

'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. Aims1. 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.ReferencesBiddie et al., Genome-wide mechanisms of nuclear receptor action. Trends Endocrinol Metab. 2010; 21(1): 3-9Lo et al., Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science. 2021; 372(6538): eaaw3616Sadeh et al., ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. Nat Biotechnol. 2021; 39(5): 586-598Sevahn et al., Cell types of origin of the cell-free transcriptome. Nat Biotechnol. 2022; 40(6): 855-861