Deconvolution of RNA-seq analysis of hyperbaric oxygen-treated mice lungs reveals mesenchymal cell subtype changes
Deconvolution of RNA-seq analysis of hyperbaric oxygen-treated mice lungs reveals mesenchymal cell subtype changes
Hyperbaric oxygen (HBO) is widely applied to treat several hypoxia-related diseases. Previous studies have focused on the immediate effect of HBO-exposure induced oxidative stress on the lungs, but knowledge regarding the chronic effects from repetitive HBO exposure is limited, especially at the gene expression level. We found that repetitive HBO exposure did not alter the morphology of murine lungs. However, by deconvolution of RNA-seq from those mice lungs using CIBERSORTx and the expression profile matrices of 8 mesenchymal cell subtypes obtained from bleomycin-treated mouse lungs, we identify several mesenchymal cell subtype changes. These include increases in Col13a1 matrix fibroblasts, mesenchymal progenitors and mesothelial cell populations and decreases in lipofibroblasts, endothelial and Pdgfrb high cell populations. Our data suggest that repetitive HBO exposure may affect biological processes in the lungs such as response to wounding, extracellular matrix, vasculature development and immune response.
CIBERSORTx, Hyperbaric oxygen, Lung, RNA-seq
1-19
Yuan, Yuan
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Zhou, Yilu
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Li, Yali
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Hill, Charlotte
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Ewing, Robert
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Jones, Mark
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Davies, Donna
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Jiang, Zhenglin
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Wang, Yihua
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18 February 2020
Yuan, Yuan
6e1cf6ff-c02d-472f-8b57-4c73801d457b
Zhou, Yilu
1878565d-39e6-467d-a027-7320bf4cdaf2
Li, Yali
066318a6-bd8e-4427-b6f0-24230ffc3986
Hill, Charlotte
6d1cfed3-11b1-48af-b171-b8726ab673eb
Ewing, Robert
022c5b04-da20-4e55-8088-44d0dc9935ae
Jones, Mark
a6fd492e-058e-4e84-a486-34c6035429c1
Davies, Donna
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Jiang, Zhenglin
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Wang, Yihua
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Yuan, Yuan, Zhou, Yilu, Li, Yali, Hill, Charlotte, Ewing, Robert, Jones, Mark, Davies, Donna, Jiang, Zhenglin and Wang, Yihua
(2020)
Deconvolution of RNA-seq analysis of hyperbaric oxygen-treated mice lungs reveals mesenchymal cell subtype changes.
International Journal of Molecular Sciences, 21 (4), , [1371].
(doi:10.3390/ijms21041371).
Abstract
Hyperbaric oxygen (HBO) is widely applied to treat several hypoxia-related diseases. Previous studies have focused on the immediate effect of HBO-exposure induced oxidative stress on the lungs, but knowledge regarding the chronic effects from repetitive HBO exposure is limited, especially at the gene expression level. We found that repetitive HBO exposure did not alter the morphology of murine lungs. However, by deconvolution of RNA-seq from those mice lungs using CIBERSORTx and the expression profile matrices of 8 mesenchymal cell subtypes obtained from bleomycin-treated mouse lungs, we identify several mesenchymal cell subtype changes. These include increases in Col13a1 matrix fibroblasts, mesenchymal progenitors and mesothelial cell populations and decreases in lipofibroblasts, endothelial and Pdgfrb high cell populations. Our data suggest that repetitive HBO exposure may affect biological processes in the lungs such as response to wounding, extracellular matrix, vasculature development and immune response.
Text
Deconvolution of RNA-seq analysis
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Accepted/In Press date: 16 February 2020
e-pub ahead of print date: 18 February 2020
Published date: 18 February 2020
Additional Information:
Funding Information:
Funding: This research was funded by Medical Research Council, grant number MR/S025480/1, an Academy of Medical Sciences/the Wellcome Trust Springboard Award, grant number SBF002\1038 and a Research Startup Fund of Nantong University. YZ was supported by an Institute for Life Sciences PhD Studentship. CH was supported by Gerald Kerkut Charitable Trust and University of Southampton Central VC Scholarship Scheme. YY was also supported by Natural Science Fund for Colleges and Universities in Jiangsu Province, grant number 19KJB320002, and ZJ was also supported by grants obtained from the National Natural Science Foundation of China, grant number 81372131, 81671859 and 81601639; Natural Science Foundation of Jiangsu Province, grant number BK20161282.
Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.
Keywords:
CIBERSORTx, Hyperbaric oxygen, Lung, RNA-seq
Identifiers
Local EPrints ID: 438154
URI: http://eprints.soton.ac.uk/id/eprint/438154
ISSN: 1422-0067
PURE UUID: 1d024cbc-4f5b-44cd-9cb8-6dd109c2cd21
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Date deposited: 03 Mar 2020 17:43
Last modified: 17 Mar 2024 03:39
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Author:
Yuan Yuan
Author:
Yali Li
Author:
Charlotte Hill
Author:
Zhenglin Jiang
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