Asian Zika virus isolate significantly changes the transcriptional profile and alternative RNA splicing events in a neuroblastoma cell line

Abstract

Alternative splicing of pre-mRNAs expands a single genetic blueprint to encode multiple functionally diverse protein isoforms. Viruses have previously been shown to interact with, depend on, and alter host splicing machinery. The consequences however incited by viral infection on the global alternative slicing (AS) landscape are under appreciated. Here we investigated the transcriptional and alternative splicing profile of neuronal cells infected with a contemporary Puerto Rican Zika virus (ZIKV PR ) isolate, the prototypical Ugandan ZIKV (ZIKV MR ) isolate and dengue virus 2 (DENV2). Our analyses revealed that ZIKV PR induced significantly more differential changes in expressed genes compared to ZIKV MR or DENV2, despite all three viruses showing equivalent infectivity and viral RNA levels. Consistent with the transcriptional profile, ZIKV PR induced a higher number of alternative splicing events compared to ZIKV MR or DENV2, and gene ontology analyses highlighted alternative splicing changes in genes associated with mRNA splicing. All three viruses modulated alternative splicing with ZIKV PR having the largest impact on splicing. ZIKV alteration of the transcriptomic landscape during infection caused changes in cellular RNA homeostasis, which might dysregulate neurodevelopment and function leading to neuropathologies such as microcephaly and Guillain-Barré syndrome associated with the ZIKV infection. IntroductionZika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that is classified within the Flaviviridae family. Other notable flaviviruses include Dengue virus (DENV), Yellow Fever virus (YFV), West Nile virus (WNV) and Tick-borne encephalitis virus, all of which are primarily transmitted via the bite of an infected mosquito or tick [1]. Flavivirus infections rarely result in death and common symptoms include maculopapular rash, fever, and achy joints [2]. Until the early 2000s, only 13 confirmed ZIKV infections in humans were reported [3-6]. The first major outbreak of ZIKV occurred in 2007 on Yap Island [7], followed by a 2010 outbreak in Cambodia [8], and an outbreak in French Polynesia in 2013 which resulted in more than 29,000 human infections [9]. This Asian lineage of ZIKV expanded west and in 2015 efforts were redirected towards understanding the link between ZIKV infection and the associated neurological pathologies that are now termed Congenital Zika Syndrome (CZS) [10,11]. To date there are no antivirals or a licensed vaccine to prevent ZIKV infection. Therefore, to develop effective therapies and thus limit the dreadful symptoms associated with ZIKV infection it is critical to understand viral-host interactions and ZIKV pathogenesis.The striking feature of the recent ZIKV outbreak in the America's was the correlation between intrauterine ZIKV infection and the devastating consequences to fetal brain development resulting in microcephaly, cortical malformations and intracranial calcifications [12][13][14][15] and the increased number of cases of Guillain-Barré syndrome in adults [16][17][18][...

Deciphering the molecular pathogenesis behind neurological manifestations of SARS-CoV-2 and drug repurposing, a systems biology approach

“…DDIT3 is also dysregulated in other viral infections such as the Zika virus (ZIKV), Tick-borne encephalitis virus (TBEV), and West Nile virus (WNV). The three viral infections can progress to the CNS and cause encephalitis or meningitis in severe cases (Selinger, Wilkie et al 2017, Huang, West et al 2019, Ojha, Rodriguez et al 2019, Bonenfant, Meng et al 2020). Bcl2l2 (Bcl-w) is an Anti-apoptotic member of The B-cell lymphoma-2 (BCL-2) family (Hartman and Czyz 2020).…”

Integrative transcriptomic and proteomic meta-analysis of Zika viral infection reveals potential mechanisms for oncolytic therapy in neuroblastoma

“…We identify the PRVABC59 Asian, Uganda #976 African and MR766 African strains as the top three candidates (Table 2). Interestingly, the PRVABC59 Asian strain induces significantly more DEGs and splice events in SH-SY5Y cells compared to the African MR766 strain; including more immune and inflammatory response genes (22). Brain metastases develop in 5-11% of neuroblastoma patients and are correlated with poor prognosis (23).…”

“…ZIKV likely upregulates GADD34 to combat ER stress-induced translational repression, as fresh virions require de novo protein synthesis. CHOP (DDIT3) is a pro-apoptotic protein downstream of the PERK UPR pathway that others have observed to be significantly upregulated in SH-SY5Y and SK-N-SH cells in response to ZIKV infection (36)(37)(38). CHOP induces apoptotic markers, including Caspase 3, leading to cell death.…”