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Series GSE158127 Query DataSets for GSE158127
Status Public on Oct 28, 2020
Title Lung transplantation for patients with severe COVID-19
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Lung transplantation can potentially be a life-saving treatment for patients with non-resolving COVID-19-associated respiratory failure. Concerns limiting transplant include recurrence of SARS-CoV-2 infection in the allograft, technical challenges imposed by viral-mediated injury to the native lung, and potential risk for allograft infection by pathogens associated with ventilator-associated pneumonia in the native lung. Most importantly, the native lung might recover, resulting in long-term outcomes preferable to transplant. Here, we report results of the first successful lung transplantation procedures in patients with non-resolving COVID-19-associated respiratory failure in the United States. We performed sm-FISH to detect both positive and negative strands of SARS-CoV-2 RNA in the explanted lung tissue, extracellular matrix imaging using SHIELD tissue clearance, and single cell RNA-Seq on explant and warm post-mortem lung biopsies from patients who died from severe COVID-19 pneumonia. Lungs from patients with prolonged COVID-19 were free of virus but pathology showed extensive evidence of injury and fibrosis which resembled end-stage pulmonary fibrosis. We used a machine learning approach to project single cell RNA-Seq data from patients with late stage COVID-19 onto a single cell atlas of pulmonary fibrosis, revealing similarities across cell lineages. There was no recurrence of SARS-CoV-2 or pathogens associated with pre-transplant ventilator associated pneumonias following transplantation. Our findings suggest that some patients with severe COVID-19 develop fibrotic lung disease for which lung transplantation is the only option for survival.
Overall design Distal lung biopsies were obtained from the explanted lung and donor lung from Case 1, and the two post-mortem biopsies. In addition, a biopsy that included the main left bronchus and distal parenchyma from the upper lobe was obtained from another donor lung that was not placed for transplant. Single-cell suspensions from the biopsies were incubated with CD31 beads, and the positive fraction was selected for single-cell. The negative fraction was FACS-sorted for macrophages, epithelial and stromal cells. Single-cell libraries were prepared with 10x Genomics 3' V3 chemistry. Libraries were pooled and sequenced on Illumina HiSeq 4000 or NovaSeq 6000. Gene expression matrices were generated with 10x cellranger v3.1.0 software using custom reference genome of GRCh38.93 and SARS-CoV-2 (NC_045512.2).
****RNA-Seq raw data will be made available through dbGaP (controlled access) due to patient privacy concerns.
Contributor(s) Bharat A, Querrey M, Markov NS, Kim S, Kurihara C, Garza-Castillon R, Manerikar A, Shilatifard A, Tomic R, Politanska Y, Abdala-Valencia H, Yeldandi AV, Lomasney JW, Misharin AV, Budinger GS
Citation(s) 33257409
Submission date Sep 17, 2020
Last update date Jan 27, 2021
Contact name Alexander V Misharin
Organization name Northwestern University
Street address 303 E Superior
City Chicago
State/province Illinois
ZIP/Postal code 60611
Country USA
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (22)
GSM4792459 Donor1_1
GSM4792460 Donor1_2
GSM4792461 Donor1_3
BioProject PRJNA664057

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE158127_01epithelial-metadata.csv.gz 1.6 Mb (ftp)(http) CSV
GSE158127_01epithelial.h5ad.gz 677.3 Mb (ftp)(http) H5AD
GSE158127_02immune-metadata.csv.gz 2.3 Mb (ftp)(http) CSV
GSE158127_02immune.h5ad.gz 911.2 Mb (ftp)(http) H5AD
GSE158127_03stromal-metadata.csv.gz 851.6 Kb (ftp)(http) CSV
GSE158127_03stromal.h5ad.gz 292.8 Mb (ftp)(http) H5AD
GSE158127_04all-lineages-metadata.csv.gz 6.1 Mb (ftp)(http) CSV
GSE158127_04all-lineages.h5ad.gz 1.1 Gb (ftp)(http) H5AD
GSE158127_RAW.tar 3.8 Gb (http)(custom) TAR (of H5)
Raw data not provided for this record
Processed data provided as supplementary file

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