SARS-CoV-2 infection severity and mortality is modulated by repeat-mediated regulation of alternative splicing

Abstract

Like single-stranded RNA viruses, SARS-CoV-2 hijacks the host transcriptional machinery for its own replication. Numerous traditional differential gene expression-based investigations have examined the diverse clinical symptoms caused by SARS-CoV-2 infection. The virus, on the other hand, also affects the host splicing machinery, causing host transcriptional dysregulation, which can lead to diverse clinical outcomes. Hence, in this study, we performed host transcriptome sequencing of 125 hospital-admitted COVID-19 patients to understand the transcriptomic differences between the severity sub-phenotypes of mild, moderate, severe, and mortality. We performed transcript-level differential expression analysis, investigated differential isoform usage, looked at the splicing patterns within the differentially expressed transcripts (DET), and elucidated the possible genome regulatory features. Our DTE analysis showed evidence of diminished transcript length and diversity as well as altered promoter site usage in the differentially expressed protein-coding transcripts in the COVID-19 mortality patients. We also investigated the potential mechanisms driving the alternate splicing and discovered a compelling differential enrichment of repeats in the promoter region and a specific enrichment of SINE (Alu) near the splicing sites of differentially expressed transcripts. These findings suggested a repeat-mediated plausible regulation of alternative splicing as a potential modulator of COVID-19 disease severity. In this work, we emphasize the role of scarcely elucidated functional role of alternative splicing in influencing COVID-19 disease severity sub-phenotypes, clinical outcomes, and its putative mechanism. IMPORTANCE The wide range of clinical symptoms reported during the COVID-19 pandemic inherently highlights the numerous factors that influence the progression and prognosis of SARS-CoV-2 infection. While several studies have investigated the host response and discovered immunological dysregulation during severe infection, most of them have the common theme of focusing only up to the gene level. Viruses, especially RNA viruses, are renowned for hijacking the host splicing machinery for their own proliferation, which inadvertently puts pressure on the host transcriptome, exposing another side of the host response to the pathogen challenge. Therefore, in this study, we examine host response at the transcript-level to discover a transcriptional difference that culminates in differential gene-level expression. Importantly, this study highlights diminished transcript diversity and possible regulation of transcription by differentially abundant repeat elements near the promoter region and splicing sites in COVID-19 mortality patients, which together with differentially expressed isoforms hold the potential to elaborate disease severity and outcome.

Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing

“…In addition, we noted a decrease in transcript length, particularly in the coding sequence (CDS), in the severe patients, between significant DTEs compared with the DIs ( P = 0.008 ). These findings suggest a reduction in the length of transcript isoforms associated with severe dengue similar to our previous study on SARS-CoV-2 differential disease severity ( Fig S1G–I ) ( 27 ). The decreased number of exons observed in severe dengue aligns with the diminished length of transcript isoforms that exhibit differential expression (DTEs) in these individuals.…”

“…This implies that dengue severity is closely linked to enrichment of transcripts with non-functional biotypes such as NMD and retained intron, accompanied by a simultaneous reduction in protein-coding transcripts. The lower number of exons and shorter CDS length in the severe group align with our earlier findings in severe COVID-19 patients, indicating consistent transcript length patterns ( 27 ). However, unlike our previous observations, severe dengue patients showed increased transcript diversity, characterised by a rise in non-canonical transcripts and a decrease in protein-coding isoforms.…”

“…Our previous investigation identified preferential enrichment of repeat elements, specifically short interspersed nuclear elements (SINEs), near the splicing sites of differentially expressed transcripts in the COVID-19 patients ( 27 ). This observation prompted us to investigate the overall presence of repeat elements, specifically within 200 bases downstream of 5′ splice sites (5′ss) and upstream of 3′ splice sites (3′ss) of DTEs across dengue severity ( Fig 4A ).…”

“…The observed changes in the distribution of splicing events indicate potential alterations in transcript isoform diversity, likely influencing the functional repertoire of transcripts associated with severe disease. Our previous investigation identified preferential enrichment of repeat elements, specifically short interspersed nuclear elements (SINEs), near the splicing sites of differentially expressed transcripts in the COVID-19 patients (27). This observation prompted us to investigate the overall presence of repeat elements, specifically within 200 bases downstream of 59 splice sites (59ss) and upstream of 39 splice sites (39ss) of DTEs across dengue severity (Fig 4A).…”

Suppressed transcript diversity and immune response in COVID-19 ICU patients: a longitudinal study

“…However, the observed decrease in transcriptome diversity in our study adds a novel aspect to our understanding of the disease and its impact on transcriptional processes. In our previous study, we also noted a similar decrease in transcript diversity among COVID-19 patients, further emphasizing the association between transcript diversity and disease severity (P-value 0.032) (Fig S3A) (51). This finding suggests a potential role of transcriptome dysregulation in the development of severe COVID-19 outcomes.…”