Manuscript Detail

Title: Longitudinal transcriptome analyses show robust T cell immunity during recovery from COVID-19

Authors: Zheng, Hong-Yi et al

Abstract: Understanding the processes of immune regulation in patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for improving treatment. Here, we performed longitudinal whole-transcriptome RNA sequencing on peripheral blood mononuclear cell (PBMC) samples from 18 patients with coronavirus disease 2019 (COVID-19) during their treatment, convalescence, and rehabilitation. After analyzing the regulatory networks of differentially expressed messenger RNAs (mRNAs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) between the different clinical stages, we found that humoral immunity and type I interferon response were significantly downregulated, while robust T-cell activation and differentiation at the whole transcriptome level constituted the main events that occurred during recovery from COVID-19. The formation of this T cell immune response might be driven by the activation of activating protein-1 (AP-1) related signaling pathway and was weakly affected by other clinical features. These findings uncovered the dynamic pattern of immune responses and indicated the key role of T cell immunity in the creation of immune protection against this disease.

Journal: Signal Transduct Target Ther

Curator: Hancock Lab

Reviewer: Aris Floratos

Author-provided data:

paper: Zheng, H., Xu, M., Yang, C., Tian, R., Zhang, M., Li, J., Wang, X., Ding, Z., Li, G., Li, X., He, Y., Dong, X., Yao, Y. and Zheng, Y. (2020). Longitudinal transcriptome analyses show robust T cell immunity during recovery from COVID-19. Signal Transduct Target Ther https://doi.org/10.1038/s41392-020-00457-4
contributor: Yong-Tang Zheng
contributor_organization: University of Chinese Academy of Sciences
contributor_email: zhengyt@mail.kiz.ac.cn

- description: up-regulated genes in PBMC samples from patients with COVID-19 during the recovery.
- exact_source: Figure 2
- tissue: PBMC
- immune_exposure: COVID-19 infection
- cohort: Children and adults(3.5-69 years old)
- comparison: Comparison among treatment, convalescence and rehabilitation stages
- repository_id: GSE157859
- platform: Ensembl_gene_ID
- response_components: ENSG00000006652, ENSG00000050344, ENSG00000076826, ENSG00000089723, ENSG00000090971, ENSG00000099860, ENSG00000099985, ENSG00000100906, ENSG00000104804, ENSG00000106328, ENSG00000107968, ENSG00000108375, ENSG00000109321, ENSG00000110848, ENSG00000111537, ENSG00000112149, ENSG00000113369, ENSG00000118298, ENSG00000119508, ENSG00000119986, ENSG00000121101, ENSG00000121764, ENSG00000121966, ENSG00000123358, ENSG00000123689, ENSG00000124575, ENSG00000125462, ENSG00000126262, ENSG00000132002, ENSG00000133316, ENSG00000139438, ENSG00000141682, ENSG00000143443, ENSG00000143878, ENSG00000144749, ENSG00000145632, ENSG00000145675, ENSG00000149243, ENSG00000149646, ENSG00000153234, ENSG00000154640, ENSG00000154764, ENSG00000154920, ENSG00000155307, ENSG00000155719, ENSG00000156232, ENSG00000156966, ENSG00000158050, ENSG00000161835, ENSG00000162783, ENSG00000163141, ENSG00000163874, ENSG00000164099, ENSG00000166444, ENSG00000168026, ENSG00000168298, ENSG00000171757, ENSG00000172803, ENSG00000177606, ENSG00000179029, ENSG00000183598, ENSG00000184545, ENSG00000184557, ENSG00000184588, ENSG00000185338, ENSG00000187837, ENSG00000188163, ENSG00000188886, ENSG00000197019, ENSG00000197837, ENSG00000204186, ENSG00000205189, ENSG00000205710, ENSG00000213085, ENSG00000213386, ENSG00000218281, ENSG00000224796, ENSG00000225808, ENSG00000231461, ENSG00000232810, ENSG00000234816, ENSG00000235618, ENSG00000249884, ENSG00000251682, ENSG00000255040, ENSG00000255274, ENSG00000256683, ENSG00000257838, ENSG00000259950, ENSG00000270276, ENSG00000270903, ENSG00000273802, ENSG00000274997, ENSG00000275714, ENSG00000275993, ENSG00000276410, ENSG00000277632, ENSG00000278463
- response_behavior: up
  - - description: down-regulated genes in PBMC samples from patients with COVID-19 during the recovery.
    - exact_source: Figure 2
    - tissue: PBMC
    - immune_exposure: COVID-19 infection
    - cohort: Children and adults(3.5-69 years old)
    - comparison: Comparison among treatment, convalescence and rehabilitation stages
    - repository_id: GSE157859
    - platform: Ensembl_gene_ID
    - response_components: ENSG00000004799, ENSG00000047457, ENSG00000047597, ENSG00000048342, ENSG00000065618, ENSG00000079385, ENSG00000096060, ENSG00000100154, ENSG00000102230, ENSG00000114737, ENSG00000116675, ENSG00000116962, ENSG00000117009, ENSG00000118276, ENSG00000122025, ENSG00000125735, ENSG00000133216, ENSG00000134061, ENSG00000136842, ENSG00000139318, ENSG00000141469, ENSG00000143476, ENSG00000145945, ENSG00000146858, ENSG00000148346, ENSG00000149798, ENSG00000156194, ENSG00000157890, ENSG00000160097, ENSG00000163823, ENSG00000163885, ENSG00000164023, ENSG00000164077, ENSG00000165949, ENSG00000170476, ENSG00000171049, ENSG00000171115, ENSG00000173334, ENSG00000178726, ENSG00000180535, ENSG00000180549, ENSG00000180871, ENSG00000185909, ENSG00000187808, ENSG00000196296, ENSG00000196565, ENSG00000197520, ENSG00000198848, ENSG00000204323, ENSG00000211592, ENSG00000211598, ENSG00000211637, ENSG00000211640, ENSG00000211644, ENSG00000211648, ENSG00000211651, ENSG00000211653, ENSG00000211659, ENSG00000211662, ENSG00000211663, ENSG00000211666, ENSG00000211669, ENSG00000211673, ENSG00000211679, ENSG00000211896, ENSG00000211897, ENSG00000211933, ENSG00000211937, ENSG00000211941, ENSG00000211947, ENSG00000211951, ENSG00000211956, ENSG00000211959, ENSG00000211964, ENSG00000211965, ENSG00000211966, ENSG00000211976, ENSG00000224373, ENSG00000239264, ENSG00000239951, ENSG00000241294, ENSG00000241351, ENSG00000242076, ENSG00000243290, ENSG00000243414, ENSG00000244116, ENSG00000244437, ENSG00000244575, ENSG00000251546, ENSG00000253998, ENSG00000259581, ENSG00000270550, ENSG00000274576, ENSG00000275111, ENSG00000276566, ENSG00000280411, ENSG00000280852
    - response_behavior: down