Human long noncoding RNA, VILMIR, is induced by major respiratory viral infections and modulates the host interferon response

Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic datasets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus inducible lncRNA modulator of interferon response (VILMIR), that was consistently upregulated after in vitro influenza infection across multiple human epithelial cell lines and influenza A virus subtypes. VILMIR was also upregulated after SARS-CoV-2 and RSV infections in vitro. We experimentally confirmed the response of VILMIR to influenza infection and interferon-beta (IFN-β) treatment in the A549 human epithelial cell line and found the expression of VILMIR was robustly induced by IFN-β treatment in a dose and time-specific manner. Single cell RNA-seq analysis of bronchoalveolar lavage fluid (BALF) samples from COVID-19 patients uncovered that VILMIR was upregulated across various cell types including at least five immune cells. The upregulation of VILMIR in immune cells was further confirmed in the human T cell and monocyte cell lines, SUP-T1 and THP-1, after IFN-β treatment. Finally, we found that knockdown of VILMIR expression reduced the magnitude of host transcriptional responses to both IFN-β treatment and influenza A virus infection in A549 cells. Together, our results show that VILMIR is a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation. To investigate the functional role of VILMIR during the human antiviral response, VILMIR expression was repressed using CRISPR interference. A549 cells expressing dCas9-KRAB and GFP were transduced with two guide RNAs (gRNAs) targeting the 5’ end of VILMIR (VILMIRg1 and VILMIRg2) along with a negative control gRNA targeting GFP expression (Ctrl). In addition, a STAT1 knockdown cell line (STAT1g1) was included for comparison, as STAT1 is well-known to impact the host interferon and antiviral response. All cell lines were treated with or without influenza A virus California/04/2009 (H1N1) for 18 hours in triplicate. RNA-sequencing and differential expression analysis was then performed to identify the impact of VILMIR knockdown on the host transcriptional response to H1N1 infection.