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Fei X, Zhu M, Li X. Characterization of Cell Type Abundance and Gene Expression Timeline from Burned Skin Bulk Transcriptomics by Deconvolution. J Burn Care Res 2024; 45:205-215. [PMID: 37956340 DOI: 10.1093/jbcr/irad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Indexed: 11/15/2023]
Abstract
Currently, no timeline of cell heterogeneity in thermally injured skin has been reported. In this study, we proposed an approach to deconvoluting cell type abundance and expression from skin bulk transcriptomics with cell type signature matrix constructed by combining independent normal skin and peripheral blood scRNA-seq datasets. Using CIBERSORTx group mode deconvolution, we identified perturbed cell type fractions and cell type-specific gene expression in three stages postthermal injury. We found an increase in cell proportions and cell type-specific gene expression perturbation of neutrophils, macrophages, and endothelial cells and a decrease in CD4+ T cells, keratinocytes, melanocyte, and fibroblast cells, and cell type-specific gene expression perturbation postburn injury. Keratinocyte, fibroblast, and macrophage up regulated genes were dynamically enriched in overlapping and distinct Gene Ontology biological processes including acute phase response, leukocyte migration, metabolic, morphogenesis, and development process. Down-regulated genes were enriched in Wnt signaling, mesenchymal cell differentiation, gland and axon development, epidermal morphogenesis, and fatty acid and glucose metabolic process. We noticed an increase in the expression of CCL7, CCL2, CCL20, CCR1, CCR5, CCXL8, CXCL2, CXCL3, MMP1, MMP8, MMP3, IL24, IL6, IL1B, IL18R1, and TGFBR1 and a decrease in expression of CCL27, CCR10, CCR6, CCR8, CXCL9, IL37, IL17, IL7, IL11R, IL17R, TGFBR3, FGFR1-4, and IGFR1 in keratinocytes and/or fibroblasts. The inferred timeline of wound healing and CC and CXC genes in keratinocyte was validated on independent dataset GSE174661 of purified keratinocytes. The timeline of different cell types postburn may facilitate therapeutic timing.
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Affiliation(s)
- Xiaoyi Fei
- School of Biomedical Engineering, Anhui Medical University, Hefei, Anhui 230009, People's Republic of China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, People's Republic of China
- Oncology Translational Medicine Research Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, People's Republic of China
| | - Min Zhu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, People's Republic of China
- Oncology Translational Medicine Research Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, People's Republic of China
- School of Mathematics and Computer Science, Tongling University, Tongling, Anhui 244061, People's Republic of China
| | - Xueling Li
- School of Biomedical Engineering, Anhui Medical University, Hefei, Anhui 230009, People's Republic of China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, People's Republic of China
- Oncology Translational Medicine Research Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, People's Republic of China
- School of Mathematics and Computer Science, Tongling University, Tongling, Anhui 244061, People's Republic of China
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