MicroRNome analysis unravels the molecular basis of SARS infection in bronchoalveolar stem cells

Abstract

Severe acute respiratory syndrome (SARS), caused by the coronavirus SARS-CoV, is an acute infectious disease with significant mortality. A typical clinical feature associated with SARS is pulmonary fibrosis and associated lung failure. In the aftermath of the SARS epidemic, although significant progress towards understanding the underlying molecular mechanism of the infection has been made, a large gap still remains in our knowledge regarding how SARS-CoV interacts with the host cell at the onset of infection. The rapidly changing viral genome adds another variable to this equation. We have focused on a novel concept of microRNA (miRNA)-mediated host-virus interactions in bronchoalveolar stem cells (BASCs) at the onset of infection by correlating the "BASC-microRNome" with their targets within BASCs and viral genome. This work encompasses miRNA array data analysis, target prediction, and miRNA-mRNA enrichment analysis and develops a complex interaction map among disease-related factors, miRNAs, and BASCs in SARS pathway, which will provide some clues for diagnostic markers to view an overall interplay leading to disease progression. Our observation reveals the BASCs (Sca-1+ CD34+ CD45- Pecam-), a subset of Oct-4+ ACE2+ epithelial colony cells at the broncho-alveolar duct junction, to be the prime target cells of SARS-CoV infection. Upregulated BASC miRNAs-17*, -574-5p, and -214 are co-opted by SARS-CoV to suppress its own replication and evade immune elimination until successful transmission takes place. Viral Nucleocapsid and Spike protein targets seem to co-opt downregulated miR-223 and miR-98 respectively within BASCs to control the various stages of BASC differentiation, activation of inflammatory chemokines, and downregulation of ACE2. All these effectively accounts for a successful viral transmission and replication within BASCs causing continued deterioration of lung tissues and apparent loss of capacity for lung repair. Overall, this investigation reveals another mode of exploitation of cellular miRNA machinery by virus to their own advantage.

Figure 1. Lower respiratory tract focusing on bronchoalveolar duct junction (BADJ) of the lung.

Venn diagram represents an enlarged section of the BADJ showing up the different subsets of the distinct cellular population (Oct-4⁺ ACE2⁺) in this region of the lung. A subset of this cellular population is enriched in BASCs identified as Sca-1⁺ CD45⁻ Pecam⁻ CD34⁺, the other subset being Sca-1⁺ CD45⁻ Pecam⁻ CD34⁻. On differentiation Sca-1⁺ CD45⁻ Pecam⁻ CD34⁺ cells show positive for CCA and SP-C; Sca-1⁺ CD45⁻ Pecam⁻ CD34⁻ cells show positive for CCA, SP-C, and ciliated cells.

Figure 2. Fold change of the differentially expressed host miRNAs in BASC targeting host and virulent viral factors .

Figure 3. Sequence alignment between the common viral specific host miRNA mature sequences from 5′ to 3′ end.

The seed region (position 2 to 7) and the conserved positions (3^rd, 4^th, and 5^th) within the seed region are highlighted within boxes.

Figure 4. Modelled miRNA–mediated host–virus interaction within BASC in SARS-CoV pathogenesis.

Host miRNAs are central to viral pathogenesis. This figure illustrates how the host miRNA and SARS-CoV interactions can explain the features of SARS-CoV pathogenesis such as (A) entry of the virus in an undifferentiated BASC, (B) causing acute infection during the proliferative stage and onset of BASC differentiation, and (C) complete clearance of virus in a fully differentiated BASC.

Figure 5. miRNA–mRNA prediction pipelines.

This flow chart summarizes the steps followed and yields from BASCGAP consortium sequences to predict the miRNA-mRNA pairs involved in SARS pathogenesis.