LungMAP Data Explorer

Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

Updated October 20, 2023

Respiratory failure associated with COVID-19 has placed focus on the lungs. Here, we present single-nucleus accessible chromatin profiles of 90,980 nuclei and matched single-nucleus transcriptomes of 46,500 nuclei in non-diseased lungs from donors of ~30 weeks gestation,~3 years and ~30 years. We mapped candidate cis-regulatory elements (cCREs) and linked them to putative target genes. We identified distal cCREs with age-increased activity linked to SARS-CoV-2 host entry gene TMPRSS2 in alveolar type 2 cells, which had immune regulatory signatures and harbored variants associated with respiratory traits. At the 3p21.31 COVID-19 risk locus, a candidate variant overlapped a distal cCRE linked to SLC6A20, a gene expressed in alveolar cells and with known functional association with the SARS-CoV-2 receptor ACE2. Our findings provide insight into regulatory logic underlying genes implicated in COVID-19 in individual lung cell types across age. More broadly, these datasets will facilitate interpretation of risk loci for lung diseases.

Xin SunUniversity of California, San Diegoxinsun@health.ucsd.edu
Xin Sun (Principle Investigator)1
1University of California, San Diego
None

To reference this project, please use the following link:

https://data-browser.lungmap.net/projects/20037472-ea1d-4ddb-9cd3-56a11a6f0f76
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Analysis Portals

LGEALGEA
LungMAP AppsLungMAP Apps
ShinyShiny
ToppCellToppCell

Project Label

Human_Multiome-Lung-Lifespan-UCSD1

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

Lung

Organ Part

middle lobe of right lung

Selected Cell Types

Unspecified

Disease Status (Specimen)

Unspecified

Disease Status (Donor)

2 disease statuses

Development Stage

6 development stages

Library Construction Method

10x 3' v3 sequencing

Nucleic Acid Source

single nucleus

Paired End

true

Analysis Protocol

0b4eeed3-20be-4bd6-9a4f-0a6c3fe0fb25, c9d53f42-2afb-4b4f-baeb-fd881a51489e

File Format

7 file formats

Cell Count Estimate

Unspecified

Donor Count

10
barcodes11 file(s)fastq.gz56 file(s)h5ad1 file(s)mtx.gz11 file(s)regions11 file(s)tsv.gz1 file(s)txt.gz1 file(s)