Genome-wide profiling of host-encoded circular RNAs highlights their potential role during the Japanese encephalitis virus-induced neuroinflammatory response

Abstract

Background: Japanese encephalitis virus (JEV) is one of the common causes of acute encephalitis in humans. Japanese encephalitis is characterized by the uncontrolled release of inflammatory cytokines, which ultimately results in neuronal cell damage. In recent years, with the advancement of high-throughput sequencing technology, studies have shown that circRNAs, by competing with endogenous miRNAs, play a vital role in the pathology of CNS diseases. However, it is unknown whether circRNAs participate in JEV-induced neuroinflammation. Results: By employing Illumina RNA-sequencing, we identified 180 circRNAs and 58 miRNAs that showed significant differential expression in JEV-infected mice brain tissues. The functional enrichment analyses revealed that these differentially regulated circRNAs were predominantly related to neurotransmission, histone modifications, transcription misregulation, and inflammation-associated calcium signaling pathway. Our established competing endogenous RNA (ceRNA) interaction network suggested the correlation of several circRNAs, miRNAs, and mRNAs in regulating the inflammatory response during JEV infection. Among the predicted interactions, the correlation between circ_0000220, miR-326-3p, and BCL3/MK2/TRIM25 mRNAs was experimentally validated by knockdown or overexpression of the non-coding RNA entities in cultured mouse microglia. The knockdown of circ_0000220 or overexpression of miR-326-3p caused a lower production of JEV-induced inflammatory cytokines. Conclusions: Conclusively, our study provides new insights into the host response to JEV infection and proposes the circRNA-targeting therapeutic interventions to rein in Japanese encephalitis.

Insights into the multifaceted role of circular RNAs: implications for Parkinson’s disease pathogenesis and diagnosis

“…In Japanese encephalitis, characterized by the uncontrolled release of inflammatory cytokines in the brain, HTS identified 180 DE circRNAs in JEV-infected murine brains. Gene ontology and KEGG enrichment analyses revealed that the circRNA parental genes were related to neurotransmission, histone modifications, transcription misregulation, and inflammation-associated calcium signaling 99 . Additional analysis of one of the DE circRNAs, circ-0000220, revealed that either knockdown of this circRNA or overexpression of its target miR-326-3p in BV-2 microglia cells lowered the production of inflammatory cytokines 99 .…”

Pathogenicity and virulence of Japanese encephalitis virus: Neuroinflammation and neuronal cell damage

“…RNA sequence analyses of JEV-infected mice brain tissues have also unveiled widespread alterations in the expression of other non-coding RNAs that include long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). Functional enrichment analysis of differentially expressed lncRNAs and circRNAs exhibit a strong relationship with cellular processes related to innate immunity, inflammation, neurotransmission, and transcription dysregulation [ 42 , 43 ]. The siRNA-mediated silencing of lncRNAs E52329 and N54010 caused dephosphorylation of JNK and MKK4 proteins in cultured mouse microglia infected with JEV, resulting in the deactivation of JNK/MKK4 pathway and reduced inflammatory cytokines release [ 42 ].…”

“…The siRNA-mediated silencing of lncRNAs E52329 and N54010 caused dephosphorylation of JNK and MKK4 proteins in cultured mouse microglia infected with JEV, resulting in the deactivation of JNK/MKK4 pathway and reduced inflammatory cytokines release [ 42 ]. Since circRNAs regulate mRNA expression via sponging miRNAs, the overexpression or knockdown of one of JEV-triggered circRNAs, circRNA-0000220, ameliorated inflammatory response in mouse microglial cells, which might have regulated through sponging the miR-326-3p and subsequently modulating the stability of miR-326-3p-target mRNAs, viz ., MK2, Bcl-3, and TRIM25 [ 43 ]. Further studies providing deeper mechanistic insights into the functions of lncRNAs or circRNAs in mediating the neuroinflammatory response during JEV infection are required which may highlight potential therapeutic targets to treat JE.…”

The role of circular RNA circ_0008285 in gestational diabetes mellitus by regulating the biological functions of trophoblasts

“…The 3′ and 5′ ends of circRNA are connected to form a unique and complete circular covalent closed structure, which are resistant to RNA exonuclease and possess higher biological stability than that of linear RNA [ 8 , 10 ]. With the development of high-throughput sequencing technology, increasing numbers of circRNAs have been discovered and their biological characteristics and regulatory functions have been revealed [ 9 , 11 ]. Specific circRNAs can be used as miRNA sponges to regulate the transcription and post-transcription of miRNA-targeted genes, which play the role in several physiological and pathological processes, including proliferation, migration, and invasion [ 10 , 12 ].…”

“…Termed as “microRNA sponges,” these competitive inhibitors are transcripts that are expressed from strong promoters and contain multiple, tandem- binding sites to a microRNA of interest [ 13 ]. circRNAs have close clinical relevance to human diseases such as tumors, diabetes, and cardiovascular diseases [ 11 , 14 – 16 ]. For example, hsa_circ_0008285 has been reported to inhibit colorectal cancer cell proliferation and metastasis through sponging with miR-382-5p, promote the cervical cancer progression through sponging with miR-211-5p, and promote breast cancer progress through sponging with miR-1275 [ 17 – 19 ].…”