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BMC Med Genomics
. 2023 Oct 18;16(1):249.
doi: 10.1186/s12920-023-01693-7. Exploring the global immune landscape of peripheral blood mononuclear cells in H5N6-infected patient with single-cell transcriptomics
Jiamin Gao # 1 , Jing Wei # 2 , Simei Qin 3 , Sheng Liu 2 , Shuangyan Mo 3 , Qian Long 4 , Shiji Tan 2 , Ning Lu 2 , Zhouhua Xie 5 6 , Jianyan Lin 7
Affiliations
Background: Avian influenza viruses (AIV), particularly H5N6, have risen in infection frequency, prompting major concerns. Single-cell RNA sequencing (scRNA-seq) can illustrate the immune cell landscape present in the peripheral circulation of influenza H5N6-infected individuals at the single-cell level. This study attempted to employ scRNA-seq technology to map the potentially hidden single cell landscape of influenza H5N6.
Methods: High-quality transcriptomes were generated from scRNA-seq data of peripheral blood mononuclear cells (PBMCs), which were taken from a critically-ill child diagnosed with H5N6 avian influenza infection and one healthy control donor. Cluster analysis was then performed on the scRNA-seq data to identify the different cell types. The pathways, pseudotime developmental trajectories and gene regulatory networks involved in different cell subpopulations were also explored.
Results: In total, 3,248 single cell transcriptomes were captured by scRNA-seq from PBMC of the child infected with H5N6 avian influenza and the healthy control donor and further identified seven immune microenvironment cell types. In addition, a subsequent subpopulation analysis of innate lymphoid cells (ILC) and CD4+ T cells revealed that subpopulations of ILC and CD4+ T cells were involved in cytokine and inflammation-related pathways and had significant involvement in the biological processes of oxidative stress and cell death.
Conclusion: In conclusion, characterizing the overall immune cell composition of H5N6-infected individuals by assessing the immune cell landscape in the peripheral circulation of H5N6 avian influenza-infected and healthy control donors at single-cell resolution provides key information for understanding H5N6 pathogenesis.
Keywords: Avian influenza virus; Cell death; H5N6; Immune cells; Oxidative stress; Single cell RNA sequencing.
. 2023 Oct 18;16(1):249.
doi: 10.1186/s12920-023-01693-7. Exploring the global immune landscape of peripheral blood mononuclear cells in H5N6-infected patient with single-cell transcriptomics
Jiamin Gao # 1 , Jing Wei # 2 , Simei Qin 3 , Sheng Liu 2 , Shuangyan Mo 3 , Qian Long 4 , Shiji Tan 2 , Ning Lu 2 , Zhouhua Xie 5 6 , Jianyan Lin 7
Affiliations
- PMID: 37853397
- PMCID: PMC10585775
- DOI: 10.1186/s12920-023-01693-7
Background: Avian influenza viruses (AIV), particularly H5N6, have risen in infection frequency, prompting major concerns. Single-cell RNA sequencing (scRNA-seq) can illustrate the immune cell landscape present in the peripheral circulation of influenza H5N6-infected individuals at the single-cell level. This study attempted to employ scRNA-seq technology to map the potentially hidden single cell landscape of influenza H5N6.
Methods: High-quality transcriptomes were generated from scRNA-seq data of peripheral blood mononuclear cells (PBMCs), which were taken from a critically-ill child diagnosed with H5N6 avian influenza infection and one healthy control donor. Cluster analysis was then performed on the scRNA-seq data to identify the different cell types. The pathways, pseudotime developmental trajectories and gene regulatory networks involved in different cell subpopulations were also explored.
Results: In total, 3,248 single cell transcriptomes were captured by scRNA-seq from PBMC of the child infected with H5N6 avian influenza and the healthy control donor and further identified seven immune microenvironment cell types. In addition, a subsequent subpopulation analysis of innate lymphoid cells (ILC) and CD4+ T cells revealed that subpopulations of ILC and CD4+ T cells were involved in cytokine and inflammation-related pathways and had significant involvement in the biological processes of oxidative stress and cell death.
Conclusion: In conclusion, characterizing the overall immune cell composition of H5N6-infected individuals by assessing the immune cell landscape in the peripheral circulation of H5N6 avian influenza-infected and healthy control donors at single-cell resolution provides key information for understanding H5N6 pathogenesis.
Keywords: Avian influenza virus; Cell death; H5N6; Immune cells; Oxidative stress; Single cell RNA sequencing.