Spinal Cord Injury regulates circular RNA expression in axons

Siddiq, M. M.; Toro, C. A.; Johnson, N. P.; Hansen, J.; Xiong, Y.; Mellado, W.; Tolentino, R. E.; Johnson, K.; Jayaraman, G.; Suhail, Z.; Harlow, L.; Beaumont, K. G.; Sebra, R. G.; Willis, D. E.; Cardozo, C. P.; Iyengar, R.

doi:10.1101/2023.04.26.538466

bioRxiv · 10.1101/2023.04.26.538466

Spinal Cord Injury regulates circular RNA expression in axons

Siddiq, M. M.·Toro, C. A.·Johnson, N. P.·Hansen, J.·Xiong, Y.·Mellado, W.·Tolentino, R. E.·Johnson, K.·Jayaraman, G.·Suhail, Z.·Harlow, L.·Beaumont, K. G.·Sebra, R. G.·Willis, D. E.·Cardozo, C. P.·Iyengar, R.

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Abstract

IntroductionNeurons transport mRNA and translational machinery to axons for local translation. After spinal cord injury (SCI), de novo translation is assumed to enable neurorepair. Knowledge of the identity of axonal mRNAs that participate in neurorepair after SCI is limited. We sought to identify and understand how axonal RNAs play a role in axonal regeneration. MethodsWe obtained preparations enriched in axonal mRNAs from control and SCI rats by digesting spinal cord tissue with cold-active protease (CAP). The digested samples were then centrifuged to obtain a supernatant that were then sequenced. We used bioinformatics analyses to identify DEGS and map them to various biological processes. We validated the DEGs by RT-qPCR and RNA-scope. ResultsThe supernatant fraction was highly enriched for axonal mRNA. Using Gene Ontology, the second most significant pathway for all differentially expressed genes (DEGs) was axonogenesis. Among the DEGs was Rims2, which is predominately a circular RNA (circRNA) in the CNS. We show that Rims2 RNA within spinal cord axons is circular. We found an additional 200 putative circRNAs in the axonal-enriched fraction. Knockdown in primary rat cortical neurons of the RNA editing enzyme ADAR1, which inhibits formation of circRNAs, significantly increased axonal outgrowth. Focusing on Rims2 we used Circular RNA Interactome to predict that several of the miRNAs that bind to circRims2 also bind to the 3UTR of GAP-43, PTEN or CREB1, all known regulators of axonal outgrowth. Axonally-translated GAP-43 supports axonal elongation and we detect GAP-43 mRNA in the rat axons by RNAscope. DiscussionBy using our method for enrichment of axonal RNA, we detect SCI induced DEGs, including circRNA such as Rims2. Ablation of ADAR1, the enzyme that regulates circRNA formation, promotes axonal outgrowth of cortical neurons. We developed a pathway model using Circular RNA Interactome that indicates that Rims2 through miRNAs can regulate the axonal translation GAP-43 a known regulator of axonal regeneration indicating that axonal mRNA contribute to regeneration.

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Siddiq, M. M., Toro, C. A., Johnson, N. P., Hansen, J., Xiong, Y., Mellado, W., Tolentino, R. E., Johnson, K., Jayaraman, G., Suhail, Z., Harlow, L., Beaumont, K. G., Sebra, R. G., Willis, D. E., Cardozo, C. P., Iyengar, R.. 2023-04-27. Spinal Cord Injury regulates circular RNA expression in axons. https://doi.org/10.1101/2023.04.26.538466

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