A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients (original) (raw)
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COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
Nature
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure 1-4 , but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63 + intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments. The host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection ranges from asymptomatic infection to severe coronavirus disease 2019 (COVID-19) and death. The leading cause of mortality is acute lung injury and acute respiratory distress syndrome, or direct complications with multiple organ failure 1-4. Clinical deterioration in acute illness leads to ineffective viral clearance and collateral tissue damage 1-5. Severe COVID-19 is also accompanied by an inappropriate pro-inflammatory host immune response and a diminished antiviral interferon response 6-8. Many molecular and cellular questions related to COVID-19 pathophysiology remain unanswered, including how cell composition and gene programs shift, which cells are infected, and how associated genetic loci drive disease. Autopsies are crucial to understanding severe COVID-19 pathophysiology 9-12 , but comprehensive genomic studies are challenged by long post-mortem intervals (PMIs). Here, we developed a large cross-body COVID-19 autopsy biobank of 420 autopsy specimens, spanning 11 organs, and used it to generate a single-cell atlas of lung, kidney, liver and heart associated with COVID-19 and a lung spatial atlas, in a subset of 14-18 donors per organ. Our atlases provide crucial insights into the pathogenesis of severe COVID-19. A COVID-19 autopsy cohort and biobank We assembled an autopsy cohort of 20 male and 12 female donors, of various ages (>30->89 years), racial/ethnic backgrounds, intermittent mandatory ventilation (IMV) periods (0-30 days) and days from symptom start to death (Fig. 1a, Supplementary Table 1). A biobank was created with a subset of 17 donors. From most donors, we collected at least lung, heart and liver tissue (Fig. 1a, Extended Data Fig. 1a, Supplementary Methods), preserving specimens for single-cell and spatial analysis. We optimized single-cell and single-nucleus RNA sequencing (sc/snRNA-Seq) protocols for Biosafety Level 3 and NanoString GeoMx workflows to spatially profile RNA from different tissue compartments by cell composition or viral RNA (Supplementary Methods). A cell census of the COVID-19 lung Automatic annotation defined 28 subsets of parenchymal, endothelial and immune cells (Fig. 2a, Supplementary Table 2, Supplementary
2021
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients’ demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung,...
Despite intensive studies during the last 3 years, the pathology and underlying molecular mechanism of coronavirus disease 2019 (COVID-19) remain poorly defined. Here, we examined postmortem COVID-19 lung tissues by spatial single-cell transcriptome analysis (SSCTA). We identified 18 major parenchymal and immune cell types, all of which are infected by SARS-CoV-2. Compared to the non-COVID-19 control, COVID-19 lungs have reduced alveolar cells (ACs), and increased innate and adaptive immune cells. Additionally, 19 differentially expressed genes in both infected and uninfected cells across the tissues mirror the altered cellular compositions. Spatial analysis of local infection rates revealed regions with high infection rates that are correlated with high cell densities (HIHD). The HIHD regions express high levels of SARS-CoV-2 entry-related factors including ACE2, FURIN, TMPRSS2, and NRP1, and co-localized with organizing pneumonia (OP) and lymphocytic and immune infiltration that h...
A molecular single-cell lung atlas of lethal COVID-19
Nature, 2021
Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2 infection 1,2 , but the host response at the lung tissue level is poorly understood. Here we performed single-nucleus RNA sequencing of about 116,000 nuclei from the lungs of nineteen individuals who died of COVID-19 and underwent rapid autopsy and seven control individuals. Integrated analyses identified substantial alterations in cellular composition, transcriptional cell states, and cell-to-cell interactions, thereby providing insight into the biology of lethal COVID-19. The lungs from individuals with COVID-19 were highly inflamed, with dense infiltration of aberrantly activated monocyte-derived macrophages and alveolar macrophages, but had impaired T cell responses. Monocyte/macrophage-derived interleukin-1β and epithelial cell-derived interleukin-6 were unique features of SARS-CoV-2 infection compared to other viral and bacterial causes of pneumonia. Alveolar type 2 cells adopted an inflammationassociated transient progenitor cell state and failed to undergo full transition into alveolar type 1 cells, resulting in impaired lung regeneration. Furthermore, we identified expansion of recently described CTHRC1 + pathological fibroblasts 3 contributing to rapidly ensuing pulmonary fibrosis in COVID-19. Inference of protein activity and ligand-receptor interactions identified putative drug targets to disrupt deleterious circuits. This atlas enables the dissection of lethal COVID-19, may inform our understanding of long-term complications of COVID-19 survivors, and provides an important resource for therapeutic development. Globally, the pandemic of COVID-19, which results from infection with SARS-CoV-2, has led to more than 145 million cases (32 million in the USA) and 3.1 million deaths (570,000 in the USA; figures as of 26 April 2021) 1. Approximately 15% of infected individuals develop severe disease, which can manifest as acute respiratory distress syndrome (ARDS) and is associated with substantial morbidity and mortality 2,4. Previously, single-cell RNA sequencing (scRNA-seq) analyses of healthy individuals have revealed the tissue distribution of host receptors that are required for SARS-CoV-2 entry 5-7 , and examination of bronchoalveolar lavage fluid and blood from patients with COVID-19 of varying severity has identified the effects of SARS-CoV-2 infection on immune responses and cytokine dysregulation 8-12. However, owing to the practical limitations of accessing patient tissues, the effects of SARS-CoV-2 at the level of the lung tissue remain unclear. A series of autopsy studies that examined formalin-fixed, paraffin-embedded (FFPE) tissue sections from individuals who died of COVID-19 extended our understanding of virus organotropism, but these studies were limited in their discovery potential by low-plex assays (for example, immunohistochemistry) and/or prolonged post-mortem intervals (PMIs), which adversely affect RNA quality 13-15. We established a rapid autopsy program and, under Institutional Review Board approved protocols, collected snap-frozen organ specimens from individuals with COVID-19 within hours of death. We performed single-nucleus RNA-seq (snRNA-seq) on lung samples from individuals who died from COVID-19 and control individuals to build an atlas that provides insight into the pathophysiology of COVID-19 and provides a key resource for further investigation.
Molecular consequences of SARS-CoV-2 liver tropism
Nature Metabolism, 2022
Extrapulmonary manifestations of COVID-19 have gained attention due to their links to clinical outcomes and their potential long-term sequelae1. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) displays tropism towards several organs, including the heart and kidney. Whether it also directly affects the liver has been debated2,3. Here we provide clinical, histopathological, molecular and bioinformatic evidence for the hepatic tropism of SARS-CoV-2. We find that liver injury, indicated by a high frequency of abnormal liver function tests, is a common clinical feature of COVID-19 in two independent cohorts of patients with COVID-19 requiring hospitalization. Using autopsy samples obtained from a third patient cohort, we provide multiple levels of evidence for SARS-CoV-2 liver tropism, including viral RNA detection in 69% of autopsy liver specimens, and successful isolation of infectious SARS-CoV-2 from liver tissue postmortem. Furthermore, we identify transcription-, proteo...
2021
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression s...
bioRxiv (Cold Spring Harbor Laboratory), 2023
Acute kidney injury (AKI) in COVID-19 patients is associated with high mortality and morbidity. Critically ill COVID-19 patients are at twice the risk of in-hospital mortality compared to non-COVID AKI patients. We know little about the cell-specific mechanism in the kidney that contributes to worse clinical outcomes in these patients. New generation single cell technologies have the potential to provide insights into physiological states and molecular mechanisms in COVID-AKI. One of the key limitations is that these patients are severely ill posing significant risks in procuring additional biopsy tissue. We recently generated single nucleus RNAsequencing data using COVID-AKI patient biopsy tissue as part of the human kidney atlas. Here we describe this approach in detail and report deeper comparative analysis of snRNAseq of 4 COVID-AKI, 4 reference, and 6 non-COVID-AKI biopsies. We also generated and analyzed urine transcriptomics data to find overlapping COVID-AKI-enriched genes and their corresponding cell types in the kidney from snRNA-seq data. We identified all major and minor cell types and states by using by using less than a few cubic millimeters of leftover tissue after pathological workup in our approach. Differential expression analysis of COVID-AKI biopsies showed pathways enriched in viral response, WNT signaling, kidney development, and cytokines in several nephron epithelial cells. COVID-AKI profiles showed a much higher proportion of altered TAL cells than non-COVID AKI and the reference samples. In addition to kidney injury and fibrosis markers indicating robust remodeling we found that, 17 genes overlap between urine cell COVID-AKI transcriptome and the snRNA-seq data from COVID-AKI biopsies. A key feature was that several of the distal nephron and collecting system cell types express these markers. Some of these markers have been previously observed in COVID-19 studies suggesting a common mechanism of injury and potentially the kidney as one of the sources of soluble factors with a potential role in disease progression.
2020
SummaryThe recent pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 was first reported in China (December 2019) and now prevalent in ∼170 countries across the globe. Entry of SARS-CoV-2 into mammalian cells require the binding of viral Spike (S) proteins to the ACE2 (angiotensin converting enzyme 2) receptor. Once entered the S protein is primed by a specialised serine protease, TMPRSS2 (Transmembrane Serine Protease 2) in the host cell. Importantly, beside respiratory symptoms, consistent with other common respiratory virus infection when patients become viraemic, a significant number of COVID-19 patients also develop liver comorbidities. We explored if specific target cell-type in the mammalian liver, could be implicated in disease pathophysiology other than the general deleterious response to cytokine storms. Here we employed single-cell RNA-seq (scRNA-seq) to survey the human liver and identified p...
Unveiling SARS-COV-2 associated Organ Specific Cell Types and Corresponding Pathways Connectivity
2020
The novel coronavirus or 2019-nCoV has originated from Wuhan city, China and became pandemic. It is evidenced that Angiotensin Converting Enzyme 2 (ACE2) plays a key role in the host cells as a receptor of Spike I Glycoprotein of SARS-COV-2 which causes final infection. ACE2 is highly expressed in Bladder, Ileum, Kidney, and Liver, comparing with ACE2 expression in the Lung specific Pulmonary Alveolar Type 1 cells. In this study, the single-cell RNA-Seq data of the five tissues from different humans are curated and cell-types with the high expressions of ACE2 are identified. Subsequently, the Protein-protein interaction networks have been established. From the network, potential biomarkers which can form functional hubs, are selected based on K-means Network Clustering. It is observed that Angiotensin, PPAR family proteins show important roles in the functional hubs. To understand the functions of the potential markers, corresponding pathways have been researched thoroughly through the ...
SARS-CoV-2 induced hepatic injuries and liver complications
Frontiers in Cellular and Infection Microbiology
BackgroundCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is resilient, highly pathogenic, and rapidly transmissible. COVID-19 patients have been reported to have underlying chronic liver abnormalities linked to hepatic dysfunction.DiscussionViral RNAs are detectable in fecal samples by RT-PCR even after negative respiratory samples, which suggests that SARS-CoV-2 can affect the gastrointestinal tract and the liver. The case fatality rates are higher among the elderly and those with underlying comorbidities such as hypertension, diabetes, liver abnormality, and heart disease. There is insufficient research on signaling pathways. Identification of molecular mechanisms involved in SARS-CoV-2-induced damages to hepatocytes is challenging. Herein, we demonstrated the multifactorial effects of SARS-CoV-2 on liver injury such as psychological stress, immunopathogenesis, systemic inflammation, ischemia and hypoxia, drug t...