Using liquid biopsy to understand organ injury in critical illness

“液体活检”，包括分析无细胞核酸(CfNA)，已经作为一种非侵入性的诊断和精确医学方法被开创(Lo等人，2021年)。在健康和疾病状态下，在体液中发现无细胞DNA(CfDNA)和无细胞RNA(CfRNA)，代表细胞死亡的碎屑。最近发展起来的分子和计算方法可以检测血浆cfDNA和cfRNA的组织来源，以告知疾病状态(Sadeh等人，2021，Sevahn等人，2022)，并扩大液体活检的临床潜力。在危重疾病中，患者经常出现由各种病理导致的多器官衰竭。该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。破译病理生理学受到不能直接和同时活检相关组织的限制。“液体活检”提供了一种了解危重疾病病理生理学机制的方法。使用血浆cfDNA染色质免疫沉淀和修饰组蛋白的测序(CHIP-SEQ)，可以获得关于组织起源和基因转录的基因组规模信息(Sadeh等人，2021)。这是基于识别组织特异性基因调控的组蛋白甲基化标记(Biddie等人，2010年)。同样，循环中的血浆cfRNA已被证明包含来自多个器官的成熟转录本，并可以通过计算去卷积映射到起源的组织以告知疾病状态(Sevahn等人，2022)。因此，cfNAs的干预可以提供对危重疾病的机械性洞察。检测多个组织信号的可能性提供了整个患者水平的非侵入性活组织检查，以了解与多器官衰竭相关的危重疾病。危重患者将被招募为LICUID(急性疾病危重不适液体活检)研究的一部分(PI：Simon Biddie博士)。将从重症监护患者的血浆样本中收集cfDNA和cfRNA，这些患者患有各种潜在的急性疾病，包括心肌梗死和肾脏损伤。血浆样本将用于生成cfDNA芯片序列和cfRNA-序列图。CfNA‘组学’方法与临床信息的结合将揭示病理生理学机制，目标是识别精确医学的新生物标记物和治疗靶点。目的1.从cfNAs中识别组织特异性转录和表观基因组特征作为一种非侵入性方法来确定危重疾病的病理机制。从cfNA转录和表观基因组数据集中识别疾病特异性基因，以发现危重疾病的新机制和治疗靶点。从cfNAs中检测疾病特异性转录或表观遗传标记，以告知危重患者队列中潜在的诊断和/或预后生物标记。参考Biddie等，核受体作用的基因组范围机制。趋势内分泌代谢。2010；21(1)：3-9Lo等人，表观遗传学，片段组学，液体活检中无细胞DNA的拓扑结构。科学。2021；372(6538)：Eaaw3616Sadeh等人，无核小体血浆细胞芯片序列识别起源细胞的基因表达程序。纳特生物科技公司。2021；39(5)：586-598 Sevahn等人，无细胞转录组起源的细胞类型。纳特生物科技公司。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