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Use of RNA Sequencing to Perform Comprehensive Analysis of Long Noncoding RNA Expression Profiles in Macrophages Infected with Trichosporon asahii

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Abstract

Trichosporon asahii (T. asahii) is a clinically important opportunistic pathogenic fungus capable of causing systemic lethal infection in immunosuppressive and immunodeficient hosts. However, the mechanism of the host immune response upon T. asahii infection has not been elucidated. Recent evidence has shown that long noncoding RNAs (lncRNAs) play key roles in regulating the immune response to resist microbial infections. In this study, we analyzed the expression profiles of lncRNAs at 12 and 24 h post-infection (hpi) in THP-1 cells infected with T. asahii using RNA sequencing (RNA-Seq). A total of 64 and 160 lncRNAs displayed significant differentially expressed (DE) at 12 h and 24 hpi, respectively. Among these lncRNAs, 18 lncRNAs were continuous DE at two time points. The DE of eight candidate lncRNAs were verified by real time quantitative polymerase chain reaction (RT-qPCR). Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to analyze the cis-target genes of 18 DE lncRNAs. The results showed that they were enriched in signaling pathways related to the host immune response, indicating that these lncRNAs might play important roles in fungi–host interactions. Finally, we explored the function of lncRNA NEAT1 and found that the expression of TNF-α and IL-1β declined after NEAT1 knockdown in T. asahii-infected THP-1 cells. To our knowledge, this is the first report of a expression analysis of lncRNAs in macrophages infected with T. asahii. Our study helps to elucidate the role of lncRNAs in the host immune response to early infection by T. asahii.

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The data used to support the findings of this study are included within the supplementary files.

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Acknowledgements

The authors express their gratitude to all of the laboratory members for their assistance.

Funding

This work was supported by the National Natural Science Foundation of China (Grant: 81571972, 82002120 and 82073466) and the National Science Foundation of Beijing, China (Grant: 7202201 and 7212105).

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Author notes

  1. Mingwang Zhang and Zhikuan Xia: Co-first author.

Authors and Affiliations

  1. Department of Dermatology, Southwest Hospital, Army Medical University, Chongqing, 400038, China

    Mingwang Zhang

  2. Department of Dermatology, The Seventh Medical Center of PLA General Hospital, Beijing, 100700, China

    Mingwang Zhang, Zhikuan Xia, Xin Yang, Junhong Ao & Rongya Yang

  3. The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510280, Guangdong, China

    Zhikuan Xia, Xin Yang & Rongya Yang

  4. Department of Dermatology, Clinic of Political Work Department of PLA, Beijing, 10000, China

    Dequan Zhang

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Contributions

MZ and ZX conducted the experiments and wrote the manuscript. DZ and XY collected and analyzed the data. RY and JA supervised the project. All authors read and approved the final manuscript.

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Correspondence to Junhong Ao or Rongya Yang.

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Zhang, M., Xia, Z., Zhang, D. et al. Use of RNA Sequencing to Perform Comprehensive Analysis of Long Noncoding RNA Expression Profiles in Macrophages Infected with Trichosporon asahii. Mycopathologia 186, 355–365 (2021). https://doi.org/10.1007/s11046-021-00552-2

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