Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase acting on RNA (ADAR) enzymes, is important in the epitranscriptomic regulation of RNA metabolism. However, the role of A-to-I RNA editing in vascular disease is unknown. Here we show that cathepsin S mRNA (CTSS), which encodes a cysteine protease associated with angiogenesis and atherosclerosis, is highly edited in human endothelial cells. The 3′ untranslated region (3′ UTR) of the CTSS transcript contains two inverted repeats, the AluJo and AluSx+ regions, which form a long stem–loop structure that is recognized by ADAR1 as a substrate for editing. RNA editing enables the recruitment of the stabilizing RNA-binding protein human antigen R (HuR; encoded by ELAVL1) to the 3′ UTR of the CTSS transcript, thereby controlling CTSS mRNA stability and expression. In endothelial cells, ADAR1 overexpression or treatment of cells with hypoxia or with the inflammatory cytokines interferon-γ and tumor-necrosis-factor-α induces CTSS RNA editing and consequently increases cathepsin S expression. ADAR1 levels and the extent of CTSS RNA editing are associated with changes in cathepsin S levels in patients with atherosclerotic vascular diseases, including subclinical atherosclerosis, coronary artery disease, aortic aneurysms and advanced carotid atherosclerotic disease. These results reveal a previously unrecognized role of RNA editing in gene expression in human atherosclerotic vascular diseases.
Subscribe to Journal
Get full journal access for 1 year
only $17.42 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Welti, J., Loges, S., Dimmeler, S. & Carmeliet, P. Recent molecular discoveries in angiogenesis and anti-angiogenic therapies in cancer. J. Clin. Invest. 123, 3190–3200 (2013).
Weber, C. & Noels, H. Atherosclerosis: current pathogenesis and therapeutic options. Nat. Med. 17, 1410–1422 (2011).
Stamatelopoulos, K. et al. Amyloid-β (1–40) and the risk of death from cardiovascular causes in patients with coronary heart disease. J. Am. Coll. Cardiol. 65, 904–916 (2015).
Hansson, G.K. Inflammation, atherosclerosis and coronary artery disease. N. Engl. J. Med. 352, 1685–1695 (2005).
Hoopengardner, B., Bhalla, T., Staber, C. & Reenan, R. Nervous system targets of RNA editing identified by comparative genomics. Science 301, 832–836 (2003).
Eggington, J.M., Greene, T. & Bass, B.L. Predicting sites of ADAR editing in double-stranded RNA. Nat. Commun. 2, 319 (2011).
Nishikura, K. Editor meets silencer: cross-talk between RNA editing and RNA interference. Nat. Rev. Mol. Cell Biol. 7, 919–931 (2006).
Wulff, B.E., Sakurai, M. & Nishikura, K. Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing. Nat. Rev. Genet. 12, 81–85 (2011).
Nishikura, K. A-to-I editing of coding and noncoding RNAs by ADARs. Nat. Rev. Mol. Cell Biol. 17, 83–96 (2016).
Bass, B.L. et al. A standardized nomenclature for adenosine deaminases that act on RNA. RNA 3, 947–949 (1997).
Park, E., Williams, B., Wold, B.J. & Mortazavi, A. RNA editing in the human ENCODE RNA-seq data. Genome Res. 22, 1626–1633 (2012).
Levanon, E.Y. et al. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22, 1001–1005 (2004).
Athanasiadis, A., Rich, A. & Maas, S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2, e391 (2004).
Daniel, C., Silberberg, G., Behm, M. & Öhman, M. Alu elements shape the primate transcriptome by cis-regulation of RNA editing. Genome Biol. 15, R28 (2014).
Bazak, L., Levanon, E.Y. & Eisenberg, E. Genome-wide analysis of Alu editability. Nucleic Acids Res. 42, 6876–6884 (2014).
Barak, M. et al. Evidence for large diversity in the human transcriptome created by Alu RNA editing. Nucleic Acids Res. 37, 6905–6915 (2009).
Häsler, J. & Strub, K. Alu elements as regulators of gene expression. Nucleic Acids Res. 34, 5491–5497 (2006).
Hung, T. et al. The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. Science 350, 455–459 (2015).
Holdt, L.M. et al. Alu elements in ANRIL noncoding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet. 9, e1003588 (2013).
Ramaswami, G. et al. Identifying RNA editing sites using RNA sequencing data alone. Nat. Methods 10, 128–132 (2013).
Kim, D.D. et al. Widespread RNA editing of embedded Alu elements in the human transcriptome. Genome Res. 14, 1719–1725 (2004).
Shi, G.P. et al. Deficiency of the cysteine protease cathepsin S impairs microvessel growth. Circ. Res. 92, 493–500 (2003).
Wang, B. et al. Cathepsin S controls angiogenesis and tumor growth via matrix-derived angiogenic factors. J. Biol. Chem. 281, 6020–6029 (2006).
Riese, R.J. et al. Cathepsin S activity regulates antigen presentation and immunity. J. Clin. Invest. 101, 2351–2363 (1998).
Sukhova, G.K. et al. Deficiency of cathepsin S reduces atherosclerosis in LDL-receptor-deficient mice. J. Clin. Invest. 111, 897–906 (2003).
Peng, S.S., Chen, C.Y., Xu, N. & Shyu, A.B. RNA stabilization by the AU-rich-element-binding protein, HuR, an ELAV protein. EMBO J. 17, 3461–3470 (1998).
Reiser, J., Adair, B. & Reinheckel, T. Specialized roles for cysteine cathepsins in health and disease. J. Clin. Invest. 120, 3421–3431 (2010).
Xu, J. et al. Proteolytic exposure of a cryptic site within collagen type IV is required for angiogenesis and tumor growth in vivo. J. Cell Biol. 154, 1069–1079 (2001).
Jobs, E. et al. Association between serum cathepsin S and mortality in older adults. J. Am. Med. Assoc. 306, 1113–1121 (2011).
Wu, Y. et al. Adenosine deaminase that acts on RNA 1 p150 in alveolar macrophage is involved in LPS-induced lung injury. Shock 31, 410–415 (2009).
Folkersen, L. et al. Unraveling divergent gene expression profiles in bicuspid and tricuspid aortic valve patients with thoracic aortic dilatation: the ASAP study. Mol. Med. 17, 1365–1373 (2011).
Perisic, L. et al. Gene expression signatures, pathways and networks in carotid atherosclerosis. J. Intern. Med. 279, 293–308 (2016).
Rueter, S.M., Dawson, T.R. & Emeson, R.B. Regulation of alternative splicing by RNA editing. Nature 399, 75–80 (1999).
Ota, H. et al. ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing. Cell 153, 575–589 (2013).
Kawahara, Y. et al. Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315, 1137–1140 (2007).
Hartner, J.C., Walkley, C.R., Lu, J. & Orkin, S.H. ADAR1 is essential for the maintenance of hematopoiesis and suppression of interferon signaling. Nat. Immunol. 10, 109–115 (2009).
Wang, Q. et al. Stress-induced apoptosis associated with null mutation of ADAR1 RNA editing deaminase gene. J. Biol. Chem. 279, 4952–4961 (2004).
Hartner, J.C. et al. Liver disintegration in the mouse embryo caused by deficiency in the RNA-editing enzyme ADAR1. J. Biol. Chem. 279, 4894–4902 (2004).
Qiu, W. et al. ADAR1 is essential for intestinal homeostasis and stem cell maintenance. Cell Death Dis. 4, e599 (2013).
Mannion, N.M. et al. The RNA-editing enzyme ADAR1 controls innate immune responses to RNA. Cell Rep. 9, 1482–1494 (2014).
Rice, G.I. et al. Mutations in ADAR1 cause Aicardi–Goutières syndrome associated with a type I interferon signature. Nat. Genet. 44, 1243–1248 (2012).
Gandy, S.Z. et al. RNA editing of the human herpesvirus 8 kaposin transcript eliminates its transforming activity and is induced during lytic replication. J. Virol. 81, 13544–13551 (2007).
Rabinovici, R. et al. ADAR1 is involved in the development of microvascular lung injury. Circ. Res. 88, 1066–1071 (2001).
Yang, J.H. et al. Widespread inosine-containing mRNA in lymphocytes regulated by ADAR1 in response to inflammation. Immunology 109, 15–23 (2003).
Jiang, Q. et al. ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia. Proc. Natl. Acad. Sci. USA 110, 1041–1046 (2013).
Chen, L. et al. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat. Med. 19, 209–216 (2013).
Nemlich, Y. et al. MicroRNA-mediated loss of ADAR1 in metastatic melanoma promotes tumor growth. J. Clin. Invest. 123, 2703–2718 (2013).
Nevo-Caspi, Y., Amariglio, N., Rechavi, G. & Paret, G. A-to-I RNA editing is induced upon hypoxia. Shock 35, 585–589 (2011).
Levy, N.S., Chung, S., Furneaux, H. & Levy, A.P. Hypoxic stabilization of vascular endothelial growth factor mRNA by the RNA-binding protein HuR. J. Biol. Chem. 273, 6417–6423 (1998).
Chang, S.H. et al. Antagonistic function of the RNA-binding protein HuR and miR-200b in post-transcriptional regulation of vascular endothelial growth factor–A expression and angiogenesis. J. Biol. Chem. 288, 4908–4921 (2013).
Lin, F.Y. et al. The role of human antigen R, an RNA-binding protein, in mediating the stabilization of toll-like receptor 4 mRNA induced by endotoxin: a novel mechanism involved in vascular inflammation. Arterioscler. Thromb. Vasc. Biol. 26, 2622–2629 (2006).
Dixon, D.A. et al. Expression of COX-2 in platelet–monocyte interactions occurs via combinatorial regulation involving adhesion and cytokine signaling. J. Clin. Invest. 116, 2727–2738 (2006).
Korff, T. & Augustin, H.G. Integration of endothelial cells in multicellular spheroids prevents apoptosis and induces differentiation. J. Cell Biol. 143, 1341–1352 (1998).
Diehl, F., Rössig, L., Zeiher, A.M., Dimmeler, S. & Urbich, C. The histone methyltransferase MLL is an upstream regulator of endothelial-cell sprout formation. Blood 109, 1472–1478 (2007).
Ramaswami, G. et al. Accurate identification of human Alu and non-Alu RNA editing sites. Nat. Methods 9, 579–581 (2012).
Dabiri, G.A., Lai, F., Drakas, R.A. & Nishikura, K. Editing of the GLURB ion channel RNA in vitro by recombinant double-stranded RNA adenosine deaminase. EMBO J. 15, 34–45 (1996).
Lai, F., Chen, C.X., Carter, K.C. & Nishikura, K. Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases. Mol. Cell. Biol. 17, 2413–2424 (1997).
Raitskin, O., Cho, D.S., Sperling, J., Nishikura, K. & Sperling, R. RNA editing activity is associated with splicing factors in lnRNP particles: the nuclear pre-mRNA processing machinery. Proc. Natl. Acad. Sci. USA 98, 6571–6576 (2001).
König, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual-nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909–915 (2010).
Georgiopoulos, G.A. et al. Prolactin and preclinical atherosclerosis in menopausal women with cardiovascular risk factors. Hypertension 54, 98–105 (2009).
Stamatelopoulos, K.S. et al. Atherosclerosis in rheumatoid arthritis versus diabetes: a comparative study. Arterioscler. Thromb. Vasc. Biol. 29, 1702–1708 (2009).
Naylor, A.R., Rothwell, P.M. & Bell, P.R. Overview of the principal results and secondary analyses from the European and North American randomized trials of endarterectomy for symptomatic carotid stenosis. Eur. J. Vasc. Endovasc. Surg. 26, 115–129 (2003).
Halliday, A. et al. 10-year stroke prevention after successful carotid endarterectomy for asymptomatic stenosis (ACST-1): a multicenter randomized trial. Lancet 376, 1074–1084 (2010).
This work was funded by the 'FFF–Innovation 2012' program of the J.W. Goethe University Frankfurt (K. Stellos), the August–Scheidel Stiftung (K. Stellos), the Excellence Cluster Cardio-Pulmonary System (ECCPS) (K. Stellos), the Else Kröner–Fresenius–Stiftung (K. Stellos), the LOEWE Center for Cell and Gene Therapy (State of Hessen) (K. Stellos), the German Center for Cardiovascular Research (DZHK) (K. Stellos) and the German Cardiac Society (K. Stellos). H.S. and S.D. are members of the cluster of excellence 'macromolecular complexes'. B.F., H.S. and S.D. are supported by DFG SFB902. The BiKE study (U.H.) was conducted with support from the Swedish Heart and Lung Foundation, the Swedish Research Council, Uppdrag Besegra Stroke, the Strategic Cardiovascular Programs of Karolinska Institutet and the Stockholm County Council, the Foundation for Strategic Research and the European Commission (CarTarDis, AtheroRemo, VIA and AtheroFlux projects). L.P.M. was supported by the Swedish Society for Medical Research (SSMF). The thoracic aortic aneurysm study (P.E.) was supported by the Swedish Research Council, the Swedish Heart–Lung Foundation and a donation by F. Lundberg. O.R. is supported by the LOEWE program 'Medical RNomics' (State of Hessen). The authors would like to thank I. Dikic (Goethe University Frankfurt) for providing us with the HeLa cells, A. Knau for expert technical support, G. Georgiopoulos for statistical consulting, R. Achangwa and M. Sachse for proofreading, M. Karakitsou for technical assistance in subclinical atherosclerosis assessment, and A. Mareti, C. Kritsioti and A. Kotsogianni for helping with the recruitment of patients of the PBMC cohort.
The authors declare no competing financial interests.
About this article
Cite this article
Stellos, K., Gatsiou, A., Stamatelopoulos, K. et al. Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation. Nat Med 22, 1140–1150 (2016). https://doi.org/10.1038/nm.4172
Usefulness of Cathepsin S to Predict Risk for Obstructive Sleep Apnea among Patients with Type 2 Diabetes
Disease Markers (2020)
Cellular and Molecular Life Sciences (2020)
Journal of Autoimmunity (2020)
ADAR1 Transcriptome editing promotes breast cancer progression through the regulation of cell cycle and DNA damage response
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research (2020)
Adenosine-to-Inosine Editing of Vasoactive MicroRNAs Alters Their Targetome and Function in Ischemia
Molecular Therapy - Nucleic Acids (2020)