Zika virus infection in a cell culture model reflects the transcriptomic signatures in patients

Abstract

Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection.

Activation of ATF3 via the Integrated Stress Response Pathway Regulates Innate Immune Response to Restrict Zika Virus

“…Together, these data indicated that peak viral protein and RNA expression coincided with ATF3 RNA and protein expression. Moreover, the induction of ATF3 expression during ZIKV infection is consistent with increased ATF3 levels in two biologically relevant systems to ZIKV infection namely SH-SY5Y neuronal cells and peripheral blood mononuclear cells (PBMCs) isolated from ZIKV-infected patients (39,40).…”

“…In a previous gene expression study, we observed that ZIKV PRVABC59 (ZIKV PR ) infection in a neuronal cell line (SH-SY5Y) stimulated immune and stress response genes such as ATF3 and CHOP (39). Moreover, in a reanalysis of RNA-seq data collected from peripheral blood mononuclear cells from patients in early- and late-acute and convalescent stages of ZIKV infection, we determined that ATF3 levels were increased (40). To determine when ATF3 was stimulated during ZIKV infection, we infected cells with ZIKV and examined viral and cellular proteins and RNA levels at different timepoints following infection.…”

“…Conversely this stress-induced transcription factor may benefit the virus by dampening the expression of genes necessary for virus restriction and/or resolution of virusinduced stress (36)(37)(38)74). We previously showed that ATF3 was upregulated during ZIKV infection of SH-SY5Y cells and PMBC isolated from early acute ZIKV-infected patients (39,40), however the upstream effector proteins inducing ATF3 expression and the impact of ATF3 activation on ZIKV gene expression was unknown.…”

“…To determine when ATF3 was stimulated during ZIKV infection, we infected cells with ZIKV and examined viral and cellular proteins and RNA levels at different timepoints following infection. In this research we used the human A549 lung adenocarcinoma cell line as these cells support robust ZIKV infection (41)(42)(43)(44), can induce an immune response upon viral infection (42,44), and are a tractable cell culture system to investigate foundational molecular mechanisms and cellular pathways influencing ZIKV infections (40). The highest level of the ZIKV nonstructural protein NS1 was observed at 24 hours post-infection and correlated with peak ATF3 protein expression (Fig 1A).…”