Table_2_The Neat Dance of COVID-19: NEAT1, DANCR, and Co-Modulated Cholinergic RNAs Link to Inflammation.xlsx

The COVID-19 pandemic exerts inflammation-related parasympathetic complications and post-infection manifestations with major inter-individual variability. To seek the corresponding transcriptomic origins for the impact of COVID-19 infection and its aftermath consequences, we sought the relevance of long and short non-coding RNAs (ncRNAs) for susceptibility to COVID-19 infection. We selected inflammation-prone men and women of diverse ages among the cohort of Genome Tissue expression (GTEx) by mining RNA-seq datasets from their lung, and blood tissues, followed by quantitative qRT-PCR, bioinformatics-based network analyses and thorough statistics compared to brain cell culture and infection tests with COVID-19 and H1N1 viruses. In lung tissues from 57 inflammation-prone, but not other GTEx donors, we discovered sharp declines of the lung pathology-associated ncRNA DANCR and the nuclear paraspeckles forming neuroprotective ncRNA NEAT1. Accompanying increases in the acetylcholine-regulating transcripts capable of controlling inflammation co-appeared in SARS-CoV-2 infected but not H1N1 influenza infected lung cells. The lung cells-characteristic DANCR and NEAT1 association with inflammation-controlling transcripts could not be observed in blood cells, weakened with age and presented sex-dependent links in GTEx lung RNA-seq dataset. Supporting active involvement in the inflammatory risks accompanying COVID-19, DANCR’s decline associated with decrease of the COVID-19-related cellular transcript ACE2 and with sex-related increases in coding transcripts potentiating acetylcholine signaling. Furthermore, transcription factors (TFs) in lung, brain and cultured infected cells created networks with the candidate transcripts, indicating tissue-specific expression patterns. Supporting links of post-infection inflammatory and cognitive damages with cholinergic mal-functioning, man and woman-originated cultured cholinergic neurons presented differentiation-related increases of DANCR and NEAT1 targeting microRNAs. Briefly, changes in ncRNAs and TFs from inflammation-prone human lung tissues, SARS-CoV-2-infected lung cells and man and woman-derived differentiated cholinergic neurons reflected the inflammatory pathobiology related to COVID-19. By shifting ncRNA differences into comparative diagnostic and therapeutic profiles, our RNA-sequencing based Resource can identify ncRNA regulating candidates for COVID-19 and its associated immediate and predicted long-term inflammation and neurological complications, and sex-related therapeutics thereof. Our findings encourage diagnostics of involved tissue, and further investigation of NEAT1-inducing statins and anti-cholinergic medications in the COVID-19 context.

新冠疫情可引发炎症相关副交感神经系统并发症及感染后后遗症，且此类病症存在显著的个体间异质性。为探究新冠病毒感染及其后续影响的转录组学根源，本研究旨在明确长、短链非编码RNA（non-coding RNAs, ncRNAs）与新冠病毒感染易感性之间的关联。我们从基因型-组织表达（Genotype-Tissue Expression, GTEx）数据库队列中筛选了不同年龄段的炎症易感个体，对其肺组织与血液组织的RNA测序（RNA-seq）数据集进行挖掘，并开展实时定量荧光PCR（qRT-PCR）、基于生物信息学的网络分析及严谨的统计学检验，同时以脑细胞培养及新冠病毒、H1N1流感病毒感染实验作为对照。在57名炎症易感者的肺组织（而非其他GTEx捐赠者的肺组织）中，我们发现与肺病理相关的非编码RNA DANCR以及构成核散斑的神经保护性非编码RNA NEAT1均出现显著下调。可调控炎症的乙酰胆碱相关转录本在严重急性呼吸综合征冠状病毒2（SARS-CoV-2）感染的肺细胞中同步上调，但在感染H1N1流感病毒的肺细胞中未观察到此现象。在血细胞中未检测到肺细胞特有的DANCR、NEAT1与炎症调控转录本的关联；该关联随年龄增长而减弱，并在GTEx肺组织RNA测序数据集中呈现出性别依赖性特征。DANCR的下调与新冠病毒相关细胞转录本血管紧张素转换酶2（ACE2）的表达降低相关，同时与增强胆碱能信号的编码转录本的性别特异性上调相关，这进一步证实了其在新冠相关炎症风险中的关键作用。此外，肺组织、脑组织及感染培养细胞中的转录因子（transcription factors, TFs）与候选转录本构建了调控网络，提示其存在组织特异性表达模式。针对感染后炎症与认知损伤和胆碱能功能障碍的关联，来自不同性别的培养胆碱能神经元中，靶向微小RNA的DANCR与NEAT1均出现了分化相关的表达上调。简言之，源自炎症易感人群肺组织、SARS-CoV-2感染肺细胞以及不同性别分化胆碱能神经元的ncRNAs与TFs的表达变化，反映了与新冠病毒感染相关的炎症病理生物学特征。本研究基于RNA测序构建的数据集资源，可通过对比分析非编码RNA的表达差异开发诊断与治疗方案，能够筛选出调控新冠病毒感染及其相关即时、潜在长期炎症与神经系统并发症的非编码RNA靶点，以及对应的性别特异性治疗策略。本研究结果为相关受累组织的临床诊断提供了理论依据，并推动了在新冠疫情背景下针对NEAT1的他汀类药物及抗胆碱能药物的进一步研究。