Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Prolonged lung pathology has been associated with COVID-19, yet the cellular and molecular mechanisms behind this chronic inflammatory disease are poorly understood. In this study, we combine advanced imaging and spatial transcriptomics to shed light on the local immune response in severe COVID-19. We show that activated adventitial niches are crucial microenvironments contributing to the orchestration of prolonged lung immunopathology. Up-regulation of the chemokines CCL21 and CCL18 associates to endothelial-to-mesenchymal transition and tissue fibrosis within these niches. CCL21 over-expression additionally links to the local accumulation of T cells expressing the cognate receptor CCR7. These T cells are imprinted with an exhausted phenotype and form lymphoid aggregates that can organize in ectopic lymphoid structures. Our work proposes immune-stromal interaction mechanisms promoting a self-sustained and non-resolving local immune response that extends beyond active viral infection and perpetuates tissue remodeling.
Article activity feed
-
-
SciScore for 10.1101/2022.03.24.22272768: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was conducted in accordance with the declaration of Helsinki and with the approval of the Ethics Committee of the Charité (EA 1/144/927 13, EA2/066/20 and EA1/317/20) and the Charité - BIH COVID-19 research board.
Consent: Autopsy consent was obtained from the families of the patients.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources The following antibodies were used for staining: anti-Collagen I-PE, anti-Collagen IV-FITC anti-Collagen I-PE, anti-Collagen IV-FITCsuggested: Noneanti-Collagensuggested: NoneWe used following antibodies and dilutions for staining: … SciScore for 10.1101/2022.03.24.22272768: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was conducted in accordance with the declaration of Helsinki and with the approval of the Ethics Committee of the Charité (EA 1/144/927 13, EA2/066/20 and EA1/317/20) and the Charité - BIH COVID-19 research board.
Consent: Autopsy consent was obtained from the families of the patients.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources The following antibodies were used for staining: anti-Collagen I-PE, anti-Collagen IV-FITC anti-Collagen I-PE, anti-Collagen IV-FITCsuggested: Noneanti-Collagensuggested: NoneWe used following antibodies and dilutions for staining: Sytox-AF488 (1:40.000, Thermo Fisher), ER-TR7-AF546 (1st 1:200/2nd 1:100, Santa Cruz Biotechnology) or near-infrared (NIR) CD3-iFluor790 (1:50 ER-TR7-AF546suggested: None1stsuggested: NoneCD3-iFluor790suggested: NoneSoftware and Algorithms Sentences Resources The ImageCycler is a robotic microscopic system with 3 main components:(1) an inverted widefield (epi)fluorescence microscope Leica DM IRE2 equipped with a CMOS camera and a motor-controlled XY-stage, (2) CAVRO XL3000 Pipette/Diluter ImageCyclersuggested: NoneImages were then normalized in Fiji, where a rolling ball algorithm was used for background estimation, edges were removed (accounting for the maximum allowed shift during the autofocus procedure) and fluorescence intensities were scaled to the full intensity range (16 bit => 216). Fijisuggested: (Fiji, RRID:SCR_002285)Cell segmentation and single-cell feature extraction: Segmentation was performed in a two-step process as previously described 17, a signal-classification step using Ilastik 1.3.2 62 and an object-recognition step using CellProfiler 3.1.8 63. Ilastiksuggested: (Ilastik, RRID:SCR_015246)CellProfilersuggested: NoneSeurat package 4.0.0 64 was used in R (R Core Team (2021, 2021) (https://www.R-project.org/) to perform mean centering and scaling, followed by principal component analysis (PCA), and reduced the dimensions of the data to the top 11 principal components in the lung and 10 principal components in the lung dLNs. Seuratsuggested: (SEURAT, RRID:SCR_007322)Frames around the capture area on the Visium slide were aligned manually and spots covering the tissue were manually selected based on the immunofluorescence staining, using Loupe Browser 5.1.0 software (10x Genomics). Loupe Browsersuggested: (Loupe Browser, RRID:SCR_018555)Image processing: We separately acquired 16-bit grayscale TIFF images for each channel by light sheet microscopy with the ImSpector software (LaVision Biotec) ImSpectorsuggested: (Imspector, RRID:SCR_018863)Tiff stacks were converted (ImarisConverterx64) into Imaris files (.ims) and stitched by Imaris Stitcher. Imarissuggested: (Imaris, RRID:SCR_007370)Quantification and statistical analysis: Statistical analysis was performed with GraphPad Prism® 9.2.0 (Graph Pad Software, LA Jolla, CA, USA). GraphPad Prism®suggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Despite the non-negligible limitations of post-mortem studies, we think the mechanisms described here might also help to shed light into the pathophysiology of the Long-COVID syndrome. By combining advanced microscopy approaches coupled to single-cell computational analysis with ST techniques in autopsy tissues, we delineated the fibrovascular niche, as a site where a dysregulated immune response leads to tissue repurposing in prolonged COVID-19 disease. In line with the idea that endothelial dysfunction is a key pathogenic mechanism in COVID-19 13,14 and that endothelial cells are major participants in and regulators of inflammatory reactions 34, we identify EndMT as a mechanism driving fibrosis. When activated endothelial cells undergo EndMT, they are transcriptionally reprogrammed, their tight cellular junctions are disrupted and they turn into fibroblast-like cells. Consequently, they lose the expression of cell adhesion proteins, such as CD31, while mesenchyme-specific factors, including α-SMA, are upregulated 35. All these features are evident in our samples (Fig. 2A-C, Fig. 3A-C, Fig. S4C). In addition, we find that fibroblasts in COVID-19 lung fibrovascular niches express the chemokine receptor CCR8 (Fig. 3C). Its ligand, CCL18, has previously been linked to pulmonary inflammation and fibrosis 36 and it is the biomarker most consistently associated with negative outcomes in IPF 37. It was previously reported to be enriched in SARS-CoV-2 RNA+ myeloid cells in the lungs...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
