Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease

Rationale: Persistent pulmonary sequelae are evident in many survivors of acute coronavirus disease 2019 (COVID-19) but the molecular mechanisms responsible are incompletely understood. Post-COVID radiological lung abnormalities comprise two broad categories, organising pneumonia and reticulation, interpreted as indicative of subacute inflammation and fibrosis, respectively. Whether these two patterns represent distinct pathologies, likely to require different treatment strategies is not known. Objectives: We sought to identify differences at molecular and cellular level, in the local immunopathology of post-COVID inflammation and fibrosis. Methods: We compared single-cell transcriptomic profiles and T cell receptor (TCR) repertoires of bronchoalveolar cells obtained from convalescent individuals with each radiological pattern of post-COVID lung disease (PCLD). Measurements and Main Results: Inflammatory and fibrotic PCLD single-cell transcriptomes closely resembled each other across all cell types. However, CD4 central memory T cells (TCM) and CD8 effector memory T cells (TEM) were significantly more abundant in inflammatory PCLD. A greater proportion of CD4 TCM also exhibited clonal expansion in inflammatory PCLD. High levels of clustering of similar TCRs from multiple donors was a striking feature of both PCLD phenotypes, consistent with tissue localised antigen-specific immune responses, but there was no enrichment for known SARS-CoV-2 reactive TCRs. Conclusions: There is no evidence that radiographic organising pneumonia and reticulation in post-COVID lung disease are associated with differential immmunopathological pathways. Inflammatory radiology is characterised by greater bronchoalveolar T cell accumulation. Both groups show evidence of shared antigen-specific T cell responses, but the antigenic target for these T cells remains to be identified. Comparison of bronchoalveolar cells from individuals with either inflammatory or fibrotic post-COVID lung disease.

研究背景：急性新型冠状病毒肺炎（Corona Virus Disease 2019, COVID-19）的多数幸存者会出现持续性肺部后遗症，但相关分子机制尚未完全阐明。新冠感染后肺部影像学异常可分为两大类，即机化性肺炎（organising pneumonia）与网状影（reticulation），二者分别被认为对应亚急性炎症与纤维化病变。目前尚不明确这两种影像学表现是否代表不同病理状态，是否需要采取差异化治疗策略。
研究目标：本研究旨在明确新冠感染后炎症与纤维化病变的局部免疫病理特征在分子与细胞层面的差异。
研究方法：我们对两种新冠感染后肺部疾病（post-COVID lung disease, PCLD）影像学表型的康复患者的支气管肺泡细胞，开展了单细胞转录组图谱与T细胞受体（T cell receptor, TCR）库的对比分析。
研究结果与主要发现：在所有细胞类型中，炎症型与纤维化型PCLD的单细胞转录组谱高度相似。但炎症型PCLD样本中，CD4+中枢记忆T细胞（CD4+ central memory T cells, TCM）与CD8+效应记忆T细胞（CD8+ effector memory T cells, TEM）的丰度显著更高；且炎症型PCLD样本中，更大比例的CD4+ TCM发生了克隆扩增。来自多个受试者的相似TCR发生高度聚集，是两种PCLD表型共有的显著特征，这与组织局部的抗原特异性免疫应答特征相符，但未检测到已知的严重急性呼吸综合征冠状病毒2（Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2）反应性TCR的富集。
研究结论：目前尚无证据表明，新冠感染后肺部疾病的影像学机化性肺炎与网状影表现对应不同的免疫病理通路。炎症型影像学表型以支气管肺泡T细胞浸润增多为特征。两组样本均存在共同的抗原特异性T细胞应答证据，但此类T细胞的抗原靶点仍有待明确。本研究对比了炎症型或纤维化型新冠感染后肺部疾病患者的支气管肺泡细胞。