SARS-CoV-2 RNA elements share human sequence identity and upregulate hyaluronan via NamiRNA-enhancer network

Wei Li, Shuai Yang, Peng Xu, Dapeng Zhang, Ying Tong, Lu Chen, Ben Jia, Ang Li, Cheng Lian, Daoping Ru, Baolong Zhang, Mengxing Liu, Cancan Chen, Weihui Fu, Songhua Yuan, Chenjian Gu, Lu Wang, Wenxuan Li, Ying Liang, Zhicong Yang, Xiaoguang Ren, Shaoxuan Wang, Xiaoyan Zhang, Yuanlin Song, Youhua Xie, Hongzhou Lu, Jianqing Xu, Hailin Wang, Wenqiang Yu, Wei Li, Shuai Yang, Peng Xu, Dapeng Zhang, Ying Tong, Lu Chen, Ben Jia, Ang Li, Cheng Lian, Daoping Ru, Baolong Zhang, Mengxing Liu, Cancan Chen, Weihui Fu, Songhua Yuan, Chenjian Gu, Lu Wang, Wenxuan Li, Ying Liang, Zhicong Yang, Xiaoguang Ren, Shaoxuan Wang, Xiaoyan Zhang, Yuanlin Song, Youhua Xie, Hongzhou Lu, Jianqing Xu, Hailin Wang, Wenqiang Yu

Abstract

Background: Since late 2019, SARS-CoV-2 infection has resulted in COVID-19 accompanied by diverse clinical manifestations. However, the underlying mechanism of how SARS-CoV-2 interacts with host and develops multiple symptoms is largely unexplored.

Methods: Bioinformatics analysis determined the sequence similarity between SARS-CoV-2 and human genomes. Diverse fragments of SARS-CoV-2 genome containing Human Identical Sequences (HIS) were cloned into the lentiviral vector. HEK293T, MRC5 and HUVEC were infected with laboratory-packaged lentivirus or transfected with plasmids or antagomirs for HIS. Quantitative RT-PCR and chromatin immunoprecipitation assay detected gene expression and H3K27ac enrichment, respectively. UV-Vis spectroscopy assessed the interaction between HIS and their target locus. Enzyme-linked immunosorbent assay evaluated the hyaluronan (HA) levels of culture supernatant and plasma of COVID-19 patients.

Findings: Five short sequences (24-27 nt length) sharing identity between SARS-CoV-2 and human genome were identified. These RNA elements were highly conserved in primates. The genomic fragments containing HIS were predicted to form hairpin structures in silico similar to miRNA precursors. HIS may function through direct genomic interaction leading to activation of host enhancers, and upregulation of adjacent and distant genes, including cytokine genes and hyaluronan synthase 2 (HAS2). HIS antagomirs and Cas13d-mediated HIS degradation reduced HAS2 expression. Severe COVID-19 patients displayed decreased lymphocytes and elevated D-dimer, and C-reactive proteins, as well as increased plasma hyaluronan. Hymecromone inhibited hyaluronan production in vitro, and thus could be further investigated as a therapeutic option for preventing severe outcome in COVID-19 patients.

Interpretation: HIS of SARS-CoV-2 could promote COVID-19 progression by upregulating hyaluronan, providing novel targets for treatment.

Funding: The National Key R&D Program of China (2018YFC1005004), Major Special Projects of Basic Research of Shanghai Science and Technology Commission (18JC1411101), and the National Natural Science Foundation of China (31872814, 32000505).

Keywords: Human Identical Sequences; Hyaluronan; NamiRNA-enhancer network; SARS-CoV-2.

Conflict of interest statement

Declaration of interests Wenqiang Yu, Wei Li, Jianqing Xu, Hailin Wang, Cheng Lian, Peng Xu, Shuai Yang, and Daoping Ru are listed as inventors on patents' application related to this work; no other relationships or activities that could appear to have influenced the submitted work.

Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.

Figures

Figure 1
Figure 1
Identification of human identical sequences in SARS-CoV-2. (a) The sequences of five HIS identified in SARS-CoV-2. Numbers in parentheses indicate the location of HIS in the corresponding genomes. (b) The location of the identical sequence of HIS-SARS2-1 and HIS-SARS2-2 in human chromosome 3 and their surrounding genes. All genes within ± 500 kb of these loci are listed. Among them, inflammation- or immunity- related genes are written in red, which are defined by text mining (search combining keywords "gene name + inflammation" or "gene name + immunity") in PubMed and Google Scholar. (c) The distribution of enhancer marker H3K27 acetylation (H3K27ac) across the identical sequence of HIS-SARS2-1 in human genome in seven human cell lines. The location of the identical sequence of HIS-SARS2-1 is marked in red line and black block, respectively. (d) KEGG pathway enrichment analysis of genes within ± 500 kb of the identical sequences of HIS-SARS2 in human genomes.
Figure 2
Figure 2
The distribution and conservation of HIS. (a) Number of HIS identified in seven known HCoVs. (b) The sequence conservation of HIS-SARS2-1 in 19 species. The color of bases represents the conservation degree, dark blue represents the fully conserved, while light blue represents the mismatched base, single line (-) indicates no bases in the aligned species. (c) The predicted RNA secondary structures of HIS-SARS2-1 and its adjunct bases (defined as pre-HIS-SARS2-1) by the algorithm of minimum free energy. The sequence in red represents HIS-SARS2-1 RNA.
Figure 3
Figure 3
HIS-SARS2 activates genes related to COVID-19 pathology. (a–c) The relative mRNA expression of the neighboring genes FBXO15, TIMM21, and CYB5A after HIS-SARS2-4 vector transfected in HEK293T cells (a), MRC5 cells (b), and HUVEC cells (c). (d–f) The relative mRNA expression of the distant gene EPN1, MYL9, and ISOC2 after HIS-SARS2-3 vector transfected in HEK293T cells (d), MRC5 cells (e), and HUVEC cells (f). (g–i) The relative mRNA expression of HSA2 after five HIS-SARS2 vectors transfected in HEK293T cells, MRC5 cells, and HUVEC cells. (k) The enrichment of enhancer marker H3K27ac after HIS-SARS-1, HIS-SARS2-1, HIS-SARS2-3, and HIS-SARS2-4 transfection. Data are represented as mean ± SEM (n = 3). P-values were calculated using the unpaired, two-tailed Student's t test by GraphPad Prism 7.0. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ns, not significant.
Figure 4
Figure 4
Loss-of-function of HIS abolishes the upregulation of their targeted genes. (a) The relative mRNA expression of HIS-SARS2-1 targeted gene KALRN in HEK293T cells after Cas13d knocked down HIS-SARS2-1. (b) The relative mRNA expression of HIS-SARS2-3 targeted genes HAS2 and MYL9 in HEK293T cells after Cas13d knocked down HIS-SARS2-3. (c) The relative mRNA expression of HIS-SARS2-4 targeted genes HAS2, FBXO15, and TIMM21 in HEK293T cells after Cas13d knocked down HIS-SARS2-4. (d–f) The relative mRNA expression of the targeted gene KALRN (d), MYL9 (e), HAS2, FBXO15, and TIMM21 (f) after transfection of antagomirs of HIS-SARS2-1, HIS-SARS2-3, and HIS-SARS2-4, respectively. Data are represented as mean ± SEM (n = 3). In all figures, P-values were calculated using the unpaired, two-tailed Student's t test by GraphPad Prism 7.0. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ns, not significant.
Figure 5
Figure 5
HIS-SARS2 RNA binds to homologous sequence of human genome for gene activation. (a) The UV absorption spectra of 2 μM HIS-SARS2-1 DNA (red curve a), 2 μM HIS-SARS2-1 RNA (blue curve b), mixed HIS-SARS2-1 DNA and RNA (dark cyan curve), hybridized mixture of HIS-SARS2-1 (magenta curve), and the simple sum of curve a and b (dark yellow dotted curve). (b) The relative absorbance changes of 2 μM hybridized mixture of HIS-SARS2-1 and the complementary RNA-HIS-SARS2-1(black square) or HIS-SARS2-1 and the complementary ssDNA (red circle) at 260 nm versus temperature. (c) Gel showing of 25 nM 5′Cy5-HIS-SARS2-1 in the presence of increasing concentrations of hAGO2. (d) Gel showing of 25 nM 5′Cy5-HIS-SARS2-1 DNA duplex in the presence of increasing concentrations of hAGO2. (e) Gel showing of 25 nM 5′Cy5-HIS-SARS2-1 DNA-RNA hybrid in the presence of increasing concentrations of hAGO2. (f) Gel showing 25 nM 5′Cy5-HIS-SARS2-1 (lane 1, 2), 5′Cy5-HIS-SARS2-1 DNA-RNA hybrid (lane 3, 4), 5′Cy5-HIS-SARS2-1 DNA duplex (lane 5, 6) in the absence and presence of 100 nM hAGO2. (g) The bound fraction of 5′Cy5-HIS-SARS2-1 (blue triangle), 5′Cy5-HIS-SARS2-1 DNA-RNA hybrid (black square) and 5′Cy5-HIS-SARS2-1 DNA duplex (red circle) probes in the presence of different concentration of hAGO2.
Figure 6
Figure 6
Hyaluronan can serve as a potential therapeutic target for COVID-19. (a) Hyaluronan released in cell culture supernatants of Mock, HIS-SARS-1, HIS-SARS2-3, and HIS-SARS2-4 overexpressed in HEK293T cell. (b) Hyaluronan in mild patients (n = 37) and severe patients (n = 100). (c-e) HA level (10 ng/mL) functions as a discriminator for patients’ lymphocytes number (c), D-Dimer level (d), and CRP level (e). (f) Represented CT images of pulmonary lesions in mice treated with hyaluronan were presented (n = 5 / group). (g) HA released in cell culture supernatants of Mock, HIS-SARS-1, HIS-SARS2-3, or HIS-SARS2-4 overexpressed in HEK293T after treated with 500 µM 4-MU and DMSO as control. (h) HA released in cell culture supernatants of Mock, HIS-SARS-1, HIS-SARS2-3, and HIS-SARS2-4 overexpressed in HEK293T after treated with 200 µg/ml hymecromone and DMSO as control. Data are represented as mean ± SEM (n = 3). In (a, g-h), P-values were calculated using the unpaired, two-tailed Student's t-test; in (b–e), P-values were calculated using the two-tailed nonparametric Mann–Whitney test by GraphPad Prism 7.0. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

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