Whole blood transcriptional profiling of pulmonary functional sequelae in ARDS- secondary to SARS-CoV-2 infection

Up to 80% of patients surviving acute respiratory distress syndrome (ARDS) secondary to SARS-CoV-2 infection present persistent anomalies in pulmonary function after hospital discharge. There is a limited understanding of the mechanistic pathways linked to post-acute pulmonary sequelae. Our main goal was to identify the molecular underpinnings associated with severe lung diffusion involvement in survivors of SARS-CoV-2-induced ARDS. Survivors attended to a complete pulmonary evaluation 3 months after hospital discharge. RNA sequencing (RNA-seq) was performed using Illumina technology in whole-blood samples from 50 patients with moderate to severe diffusion impairment (DLCO<60%) and age- and sex-matched individuals with mild-normal lung function (DLCO≥60%). A transcriptomic signature for optimal classification was constructed using random forest. Transcriptomic data were analyzed for biological pathway enrichment, cellular deconvolution, cell/tissue-specific gene expression and candidate drugs. RNA-seq identified 1357 differentially expressed transcripts. A model composed of 14 mRNAs allowed the optimal discrimination of survivors with severe diffusion impairment (AUC=0.979). Hallmarks of lung sequelae involved cell death signaling, cytoskeleton reorganization, cell growth and differentiation and the immune response. Resting natural killer (NK) cells were the most important immune cell subtype for the prediction of severe diffusion impairment. Components of the signature correlated with neutrophil, lymphocyte and monocyte counts. A variable expression profile of the transcripts was observed in lung cell subtypes and bodily tissues. One upregulated gene, TUBB4A, constitutes a target for FDA-approved drugs. This work defines the transcriptional programme associated with post-acute pulmonary sequelae and provides novel insights for targeted interventions and biomarker development. Comparative gene expression profiling analysis of RNAseq data from whole blood from survivors of COVID-19-driven ARDS with moderate-to-severe functional pulmonary sequelae (DLCO<60% of predicted; group of study) and with mild or absence of functional pulmonary sequelae (DLCO≥60% of predicted; control group).约80%的严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）感染继发急性呼吸窘迫综合征（ARDS）的存活患者，在出院后仍存在持续的肺功能异常。目前学界对急性感染后肺后遗症相关的分子机制通路的认知仍较为有限。本研究的核心目标为，明确SARS-CoV-2感染诱发ARDS的存活患者中，与重度肺弥散功能受损相关的分子基础。所有存活患者均在出院后3个月接受了全面的肺功能评估。本研究采用Illumina测序技术，对50名存在中至重度肺弥散功能受损（肺一氧化碳弥散量DLCO<60%预测值）的患者，以及年龄、性别匹配的肺功能轻度至正常（DLCO≥60%预测值）个体的全血样本进行了RNA测序（RNA-seq）。采用随机森林算法构建了用于最优分类的转录组特征模型。对转录组数据开展了生物通路富集分析、细胞反卷积分析、细胞/组织特异性基因表达分析以及候选药物筛选。RNA-seq共鉴定出1357个差异表达转录本。由14个mRNA组成的模型可最优区分重度弥散功能受损的存活患者（曲线下面积AUC=0.979）。肺后遗症的核心特征涉及细胞死亡信号通路、细胞骨架重排、细胞增殖与分化以及免疫应答过程。静息自然杀伤（NK）细胞是预测重度弥散功能受损的最重要免疫细胞亚型。该转录组特征的相关组分与中性粒细胞、淋巴细胞及单核细胞计数存在相关性。上述转录本在肺细胞亚型及人体各组织中呈现出差异化的表达谱。其中一个上调基因TUBB4A可作为美国食品药品监督管理局（FDA）获批药物的作用靶点。本研究明确了与急性感染后肺后遗症相关的转录调控程序，为靶向干预手段开发以及生物标志物研发提供了全新的研究视角。本数据集为对比基因表达谱分析数据，源自新型冠状病毒肺炎（COVID-19）诱发ARDS的存活患者的全血RNA测序结果：其中研究组为存在中至重度肺功能后遗症（DLCO<预测值60%）的患者，对照组为肺功能后遗症轻微或缺如（DLCO≥预测值60%）的个体。