Loss of Adenosine Deaminase Acting on RNA 1 Induces Panoptosis and Immune Response in Ulcerative Colitis Gut Mucosa

Abstract

The gut virome is a complex community that exists in equilibrium with the host. Disruptions of this balance could drive the development of inflammatory diseases, such as inflammatory bowel disease (IBD). RNA editing, particularly A-to-I editing by ADAR1, prevents the excessive immune response to viral double strand (ds) RNA. Failure of RNA editing may sustain inflammation and this study explore the role of ADAR1 in IBD. ADAR1 was analyzed in IBD patients and healthy controls (CTR) using western blotting and qPCR. Colonic epithelial cells (HCEC-1CT), ex vivo organ cultures, and colonic organoids were treated poly I:C after ADAR1 silencing with an antisense oligonucleotide (AS). Inflammatory pathways and PANoptosome were measured by western blotting, flow cytometry, and ELISA. The role of ADAR1 was also studied in DSS-colitis model. ADAR1 was significantly reduced in the inflamed epithelium of ulcerative colitis (UC) gut samples. ADAR1 silencing in HCEC-1CT, ex vivo organ cultures or colonic organoids strongly increases the immune response to poly I:C and leads to activation of inflammatory pathways and PANoptosis. Inhibition of gut ADAR1 expression during DSS-colitis exacerbated gut inflammation. JAK inhibition or AhR activation mitigated the immune response that follows ADAR1 silencing. These data suggest that ADAR1 could be involved in IBD inflammation.

Keywords

adenosine deaminase acting on RNA 1 / inflammatory bowel disease / innate immunity / mucosal damage / panoptosis

References

[1] J. T. Chang, “Pathophysiology of Inflammatory Bowel Diseases,” New England Journal of Medicine 383, no. 27 (2020): 2652-2664.

[2] G. Roda, S. Chien Ng, P. G. Kotze, et al., “Crohn's Disease,” Nature Reviews Disease Primers 6, no. 1 (2020): 22.

[3] T. Kobayashi, B. Siegmund, C. Le Berre, et al., “Ulcerative Colitis,” Nature Reviews Disease Primers 6, no. 1 (2020): 74.

[4] S. C. Ng, H. Y. Shi, N. Hamidi, et al., “Worldwide Incidence and Prevalence of Inflammatory Bowel Disease in the 21st Century: A Systematic Review of Population-Based Studies,” Lancet 390, no. 10114 (2017): 2769-2778.

[5] M. Leppkes and M. F. Neurath, “Cytokines in Inflammatory Bowel Diseases—Update 2020,” Pharmacological Research 158 (2020): 104835.

[6] M. F. Neurath, “Cytokines in Inflammatory Bowel Disease,” Nature Reviews Immunology 14, no. 5 (2014): 329-342.

[7] T. T. MacDonald, I. Monteleone, M. C. Fantini, and G. Monteleone, “Regulation of Homeostasis and Inflammation in the Intestine,” Gastroenterology 140, no. 6 (2011): 1768-1775.

[8] M. Lee and E. B. Chang, “Inflammatory Bowel Diseases (IBD) and the Microbiome-Searching the Crime Scene for Clues,” Gastroenterology 160, no. 2 (2021): 524-537.

[9] Y. Shan, M. Lee, and E. B. Chang, “The Gut Microbiome and Inflammatory Bowel Diseases,” Annual Review of Medicine 73 (2022): 455-468.

[10] H. W. Virgin, “The Virome in Mammalian Physiology and Disease,” Cell 157, no. 1 (2014): 142-150.

[11] J. M. Norman, S. A. Handley, M. T. Baldridge, et al., “Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease,” Cell 160, no. 3 (2015): 447-460.

[12] F. Adiliaghdam, H. Amatullah, S. Digumarthi, et al., “Human Enteric Viruses Autonomously Shape Inflammatory Bowel Disease Phenotype Through Divergent Innate Immunomodulation,” Science Immunology 7, no. 70 (2022): eabn6660.

[13] L. Massimino, O. Palmieri, A. Facoetti, et al., “Gut Virome-Colonising Orthohepadnavirus Genus Is Associated With Ulcerative Colitis Pathogenesis and Induces Intestinal Inflammation In Vivo,” Gut 72, no. 10 (2023): 1838-1847.

[14] N. M. Mannion, S. M. Greenwood, R. Young, et al., “The RNA-Editing Enzyme ADAR1 Controls Innate Immune Responses to RNA,” Cell Reports 9, no. 4 (2014): 1482-1494.

[15] S. Maas, Y. Kawahara, K. M. Tamburro, and K. Nishikura, “A-to-I RNA Editing and Human Disease,” RNA Biology 3, no. 1 (2006): 1-9.

[16] S. Al Wardat, L. Frassinelli, E. Orecchini, et al., “Characterization of the Molecular Dysfunctions Occurring in Aicardi-Goutieres Syndrome Patients With Mutations in ADAR1,” Genes & Diseases 11, no. 3 (2024): 101028.

[17] Q. Li, M. J. Gloudemans, J. M. Geisinger, et al., “RNA Editing Underlies Genetic Risk of Common Inflammatory Diseases,” Nature 608, no. 7923 (2022): 569-577.

[18] W. Qiu, X. Wang, M. Buchanan, et al., “ADAR1 is Essential for Intestinal Homeostasis and Stem Cell Maintenance,” Cell Death & Disease 4, no. 4 (2013): e599.

[19] K. Pestal, C. C. Funk, J. M. Snyder, N. D. Price, P. M. Treuting, and D. B. Stetson, “Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-Organ Development,” Immunity 43, no. 5 (2015): 933-944.

[20] D. Di Fusco, M. T. Segreto, A. Iannucci, et al., “An Essential Role of Adenosine Deaminase Acting on RNA 1 in Coeliac Disease Mucosa,” Frontiers in Immunology 14 (2023): 1175348.

[21] R. Karki, B. Sundaram, B. R. Sharma, et al., “ADAR1 Restricts ZBP1-Mediated Immune Response and PANoptosis to Promote Tumorigenesis,” Cell Reports 37, no. 3 (2021): 109858.

[22] R. Karki and T. D. Kanneganti, “ADAR1 and ZBP1 in Innate Immunity, Cell Death, and Disease,” Trends in Immunology 44, no. 3 (2023): 201-216.

[23] J. V. Patankar and C. Becker, “Cell Death in the Gut Epithelium and Implications for Chronic Inflammation,” Nature Reviews Gastroenterology & Hepatology 17, no. 9 (2020): 543-556.

[24] M. F. Neurath, “Strategies for Targeting Cytokines in Inflammatory Bowel Disease,” Nature Reviews Immunology 24, no. 8 (2024): 559-576.

[25] I. Rauluseviciute, R. Riudavets-Puig, R. Blanc-Mathieu, et al., “JASPAR 2024: 20th Anniversary of the Open-Access Database of Transcription Factor Binding Profiles,” Nucleic Acids Research 52, no. D1 (2024): D174-D182.

[26] I. Monteleone, A. Rizzo, M. Sarra, et al., “Aryl Hydrocarbon Receptor-Induced Signals Up-Regulate IL-22 Production and Inhibit Inflammation in the Gastrointestinal Tract,” Gastroenterology 141, no. 1 (2011): 237-248.

[27] I. Monteleone, F. Pallone, and G. Monteleone, “Aryl Hydrocarbon Receptor and Colitis,” Seminars in Immunopathology 35, no. 6 (2013): 671-675.

[28] S. Oki, T. Ohta, G. Shioi, et al., “ChIP-Atlas: A Data-Mining Suite Powered by Full Integration of Public ChIP-Seq Data,” EMBO Reports 19, no. 12 (2018): e46255.

[29] Z. Zou, T. Ohta, F. Miura, and S. Oki, “ChIP-Atlas 2021 Update: A Data-Mining Suite for Exploring Epigenomic Landscapes by Fully Integrating ChIP-Seq, ATAC-Seq and Bisulfite-Seq Data,” Nucleic Acids Research 50, no. W1 (2022): W175-W182.

[30] U. E. Knebel, S. Peleg, C. Dai, et al., “Disrupted RNA Editing in Beta Cells Mimics Early-Stage Type 1 Diabetes,” Cell Metabolism 36, no. 1 (2024): 48-61.

[31] L. Shallev, E. Kopel, A. Feiglin, et al., “Decreased A-to-I RNA Editing as a Source of Keratinocytes' dsRNA in Psoriasis,” Rna 24, no. 6 (2018): 828-840.

[32] A. Gatsiou and K. Stellos, “RNA Modifications in Cardiovascular Health and Disease,” Nature Reviews Cardiology 20, no. 5 (2023): 325-346.

[33] G. I. Rice, P. R. Kasher, G. M. Forte, et al., “Mutations in ADAR1 Cause Aicardi-Goutieres Syndrome Associated With a Type I Interferon Signature,” Nature Genetics 44, no. 11 (2012): 1243-1248.

[34] I. Marafini, I. Monteleone, F. Laudisi, and G. Monteleone, “Aryl Hydrocarbon Receptor Signalling in the Control of Gut Inflammation,” International Journal of Molecular Sciences 25, no. 8 (2024): 4527.

[35] N. I. Vlachogiannis, A. Gatsiou, D. A. Silvestris, et al., “Increased Adenosine-to-Inosine RNA Editing in Rheumatoid Arthritis,” Journal of Autoimmunity 106 (2020): 102329.

[36] K. Takahashi, K. Shigeyasu, Y. Kondo, et al., “RNA Editing Is a Valuable Biomarker for Predicting Carcinogenesis in Ulcerative Colitis,” Journal of Crohn's and Colitis 17, no. 5 (2023): 754-766.

[37] J. M. Wang, J. Yang, W. Y. Xia, et al., “Comprehensive Analysis of PANoptosis-Related Gene Signature of Ulcerative Colitis,” International Journal of Molecular Sciences 25, no. 1 (2023): 348.

[38] K. K. Jena, J. Mambu, D. Boehmer, et al., “Type III Interferons Induce Pyroptosis in Gut Epithelial Cells and Impair Mucosal Repair,” Cell 187, no. 26 (2024): 7533-7550.

[39] T. Zhang, C. Yin, A. Fedorov, et al., “ADAR1 Masks the Cancer Immunotherapeutic Promise of ZBP1-Driven Necroptosis,” Nature 606, no. 7914 (2022): 594-602.

[40] H. Yang, S. Xu, X. Hong, et al., “ADAR1 Prevents ZBP1-Dependent PANoptosis via A-to-I RNA Editing in Developmental Sevoflurane Neurotoxicity,” Cell Biology and Toxicology 40, no. 1 (2024): 57.

[41] Y. J. Crow, D. S. Chase, J. Lowenstein Schmidt, et al., “Characterization of Human Disease Phenotypes Associated With Mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, and IFIH1,” American Journal of Medical Genetics Part A 167, no. 2 (2015): 296-312.

[42] M. Boirivant, F. Pallone, C. Di Giacinto, et al., “Inhibition of Smad7 With a Specific Antisense Oligonucleotide Facilitates TGF-Beta1-Mediated Suppression of Colitis,” Gastroenterology 131, no. 6 (2006): 1786-1798.

[43] P. Flood, A. Fanning, J. A. Woznicki, et al., “DNA Sensor-Associated Type I Interferon Signaling Is Increased in Ulcerative Colitis and Induces JAK-Dependent Inflammatory Cell Death in Colonic Organoids,” American Journal of Physiology Gastrointestinal and Liver Physiology 323, no. 5 (2022): G439-G460.

[44] K. W. Schroeder, W. J. Tremaine, and D. M. Ilstrup, “Coated Oral 5-Aminosalicylic Acid Therapy for Mildly to Moderately Active Ulcerative Colitis. A Randomized Study,” New England Journal of Medicine 317, no. 26 (1987): 1625-1629.

[45] I. Monteleone, M. Federici, M. Sarra, et al., “Tissue Inhibitor of Metalloproteinase-3 Regulates Inflammation in Human and Mouse Intestine,” Gastroenterology 143, no. 5 (2012): 1277-1287.

[46] M. Jihad, G. Mucciolo, W. Li, et al., “Protocol for the Characterization of the Pancreatic Tumor Microenvironment Using Organoid-Derived Mouse Models and Single-Nuclei RNA Sequencing,” STAR Protocols 5, no. 3 (2024): 103203.

[47] M. Colella, A. Iannucci, C. Maresca, et al., “SMAD7 Sustains XIAP Expression and Migration of Colorectal Carcinoma Cells,” Cancers 16, no. 13 (2024): 2370.

[48] D. Di Fusco, A. Di Grazia, G. Di Maggio, et al., “A Novel Tumour Enhancer Function of Insulin-Like Growth Factor II mRNA-Binding Protein 3 in Colorectal Cancer,” Cell Death & Disease 14, no. 4 (2023): 243.

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