Summary
Although the exact etiology of inflammatory bowel disease (IBD) remains unclear, exaggerated immune response in genetically predisposed individuals has been reported. Th1 and Th17 cells mediate IBD development. Macrophages produce IL-12 and IL-23 that share p40 subunit encoded by IL12B gene as heteromer partner to drive Th1 and Th17 differentiation. The available animal and human data strongly support the pathogenic role of IL-12/IL-23 in IBD development and suggest that blocking p40 might be the potential strategy for IBD treatment. Furthermore, aberrant alteration of some cytokines expression via epigenetic mechanisms is involved in pathogenesis of IBD. In this study, we analyzed core promoter region of IL12B gene and investigated whether IL12B expression could be regulated through targeted epigenetic modification with gene editing technology. Transcription activator-like effectors (TALEs) are widely used in the field of genome editing and can specifically target DNA sequence in the host genome. We synthesized the TALE DNA-binding domains that target the promoter of human IL12B gene and fused it with the functional catalytic domains of epigenetic enzymes. Transient expression of these engineered enzymes demonstrated that the TALE-DNMT3A targeted the selected IL12B promoter region, induced loci-specific DNA methylation, and down-regulated IL-12B expression in various human cell lines. Collectively, our data suggested that epigenetic editing of IL12B through methylating DNA on its promoter might be developed as a potential therapeutic strategy for IBD treatment.
Similar content being viewed by others
Change history
11 January 2021
Prof. Mei YE works in the Department of Gastroenterology, Zhongnan Hospital, Wuhan University, and Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, as shown above. Her affiliation was incorrectly indicated in the article.
References
Baumgart DC, Sandborn WJ. Crohn’s disease. Lancet, 2012,380(9853):1590–1605
Campos N, Magro F, Castro AR, et al. Macrophages from IBD patients exhibit defective tumour necrosis factor-alpha secretion but otherwise normal or augmented pro-inflammatory responses to infection. Immunobiology, 2011,216(8):961–970
Hibi T, Ogata H. Novel pathophysiological concepts of inflammatory bowel disease. J Gastroenterol, 2006,41(1):10–16
Parronchi P, Romagnani P, Annunziato F, et al. Type 1 T-helper cell predominance and interleukin-12 expression in the gut of patients with Crohn’s disease. Am J Pathol, 1997,150(3):823–832
Sakuraba A, Sato T, Kamada N, et al. Th1/Th17 Immune Response Is Induced by Mesenteric Lymph Node Dendritic Cells in Crohn’s Disease. Gastroenterology, 2009,137(5):1736–1745
Strober W, Fuss IJ. Proinflammatory Cytokines in the Pathogenesis of Inflammatory Bowel Diseases. Gastroenterology, 2011,140(6):1756–1767
Mcgeachy MJ, Cua DJ. Th17 cell differentiation: the long and winding road. Immunity, 2008,28(4):445–453
Schmidt C, Giese T, Ludwig B, et al. Expression of interleukin-12-related cytokine transcripts in inflammatory bowel disease: elevated interleukin-23p19 and interleukin-27p28 in Crohn’s disease but not in ulcerative colitis. Inflamm Bowel Dis, 2005,11(1):16–23
Rovedatti L, Kudo T, Biancheri P, et al. Differential regulation of interleukin 17 and interferon gamma production in inflammatory bowel disease. Gut, 2009,58(12):1629–1636
Mcgovern D, Powrie F. The IL23 axis plays a key role in the pathogenesis of IBD. Gut, 2007,56(10):1333–1336
Feagan BG, Sandborn WJ, Gasink C, et al. Ustekinumab as Induction and Maintenance Therapy for Crohn’s Disease. N Engl J Med, 2016,375(20):1946–1960
Lamb YN, Duggan ST. Ustekinumab: A Review in Moderate to Severe Crohn’s Disease. Drugs, 2017,77(10):1105–1114
Tighe D, Hall B, Jeyarajah SK, et al. One-Year Clinical Outcomes in an IBD Cohort Who Have Previously Had Anti-TNFa Trough and Antibody Levels Assessed. Inflamm Bowel Dis, 2017,23(7):1154–1159
Amiot A, Serrero M, Peyrin-Biroulet L, et al. One-year effectiveness and safety of vedolizumab therapy for inflammatory bowel disease: a prospective multicentre cohort study. Aliment Pharmacol Ther, 2017,46(3):310–321
Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature, 2012,491(7422):119–124
Ellinghaus D, Bethune J, Petersen BS, et al. The genetics of Crohn’s disease and ulcerative colitis—status quo and beyond. Scand J Gastroenterol, 2015,50(1):13–23
Gonsky R, Fleshner P, Deem RL, et al. Association of Ribonuclease T2 Gene Polymorphisms with Decreased Expression and Clinical Characteristics of Severity in Crohn’s Disease. Gastroenterology, 2017,153(1):219–232
Bai AH, Wu WK, Xu L, et al. Dysregulated Lysine Acetyltransferase 2B Promotes Inflammatory Bowel Disease Pathogenesis Through Transcriptional Repression of Interleukin-10. J Crohns Colitis, 2016,10(6):726–734
Dawson MA, Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell, 2012,150(1):12–27
Liu Y, Peng J, Sun T, et al. Epithelial EZH2 serves as an epigenetic determinant in experimental colitis by inhibiting TNFalpha-mediated inflammation and apoptosis. Proc Natl Acad Sci USA, 2017,114(19):E3796–E3805
Ghadimi D, Helwig U, Schrezenmeir J, et al. Epigenetic imprinting by commensal probiotics inhibits the IL-23/IL-17 axis in an in vitro model of the intestinal mucosal immune system. J Leukoc Biol, 2012,92(4):895–911
Adamik J, Henkel M, Ray A, et al. The IL17A and IL17F loci have divergent histone modifications and are differentially regulated by prostaglandin E2 in Th17 cells. Cytokine, 2013,64(1):404–412
Pfister SX, Ashworth A. Marked for death: targeting epigenetic changes in cancer. Nat Rev Drug Discov, 2017,16(4):241–263
Heerboth S, Lapinska K, Snyder N, et al.. Use of epigenetic drugs in disease: an overview. Genet Epigenet, 2014,6:9–19
Moscou MJ, Bogdanove AJ. A simple cipher governs DNA recognition by TAL effectors. Science, 2009, 326(5959):1501
Kim Y, Kweon J, Kim A, et al. A library of TAL effector nucleases spanning the human genome. Nat Biotechnol, 2013,31(3):251–258
Miller JC, Tan S, Qiao G, et al. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol, 2011,29(2):143–148
Maeder ML, Angstman JF, Richardson ME, et al. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat Biotechnol, 2013,31(12):1137–1142
Mendenhall EM, Williamson KE, Reyon D, et al. Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol, 2013,31(12):1133–1136
Bernstein DL, Le Lay JE, Ruano EG, et al. TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts. J Clin Invest, 2015,125(5):1998–2006
Bakshi C, Vijayvergiya R, Dhawan V. Aberrant DNA methylation of M1-macrophage genes in coronary artery disease. Sci Rep, 2019,9(1):1429
Wichnieski C, Maheshwari K, Souza LC, et al. DNA methylation profiles of immune response-related genes in apical periodontitis. Int Endod J, 2019,52(1):5–12
Chanput W, Mes JJ, Wichers HJ. THP-1 cell line: an in vitro cell model for immune modulation approach. Int Immunopharmacol, 2014,23(1):37–45
Kobayashi T, Okamoto S, Hisamatsu T, et al. IL23 differentially regulates the Th1/Th17 balance in ulcerative colitis and Crohn’s disease. Gut, 2008,57(12):1682–1689
Rutgeerts P, Gasink C, Chan D, et al. Efficacy of Ustekinumab for Inducing Endoscopic Healing in Patients With Crohn’s Disease. Gastroenterology, 2018,155(4):1045–1058
Kim JS, Kim SY, Lee M, et al. Radioresistance in a human laryngeal squamous cell carcinoma cell line is associated with DNA methylation changes and topoisomerase II alpha. Cancer Biol Ther, 2015,16(4):558–566
Kim SY, Shin DY, Kim SM, et al.. Aberrant DNA methylation-induced gene inactivation is associated with the diagnosis and/or therapy of T-cell leukemias. Leuk Res, 2016,47:116–122
Li K, Pang J, Cheng H, et al. Manipulation of prostate cancer metastasis by locus-specific modification of the CRMP4 promoter region using chimeric TALE DNA methyltransferase and demethylase. Oncotarget, 2015,6(12):10030–10044
Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA, 1996,93(3):1156–1160
Snowden AW, Gregory PD, Case CC, et al. Gene-specific targeting of H3K9 methylation is sufficient for initiating repression in vivo. Curr Biol, 2002,12(24):2159–2166
Chen H, Kazemier HG, de Groote ML, et al. Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res, 2014,42(3):1563–1574
Siddique AN, Nunna S, Rajavelu A, et al. Targeted methylation and gene silencing of VEGF-A in human cells by using a designed Dnmt3a-Dnmt3L single-chain fusion protein with increased DNA methylation activity. J Mol Biol, 2013,425(3):479–491
Grimmer MR, Stolzenburg S, Ford E, et al. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Res, 2014,42(16):10856–10868
Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 2012,337(6096):816–821
Persikov AV, Osada R, Singh M. Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics, 2009,25(1):22–29
Zhang M, Wang F, Li S, et al. TALE: a tale of genome editing. Prog Biophys Mol Biol, 2014,114(1):25–32
Vora S, Tuttle M, Cheng J, et al. Next stop for the CRISPR revolution: RNA-guided epigenetic regulators. Febs J, 2016,283(17):3181–3193
Vojta A, Dobrinic P, Tadic V, et al. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res, 2016,44(12):5615–5628
Amabile A, Migliara A, Capasso P, et al. Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing. Cell, 2016,167(1):219–232
Mlambo T, Nitsch S, Hildenbeutel M, et al. Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells. Nucleic Acids Res, 2018,46(9):4456–4468
Pattanayak V, Lin S, Guilinger JP, et al. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol, 2013,31(9):839–843
Wu Y, Liang D, Wang Y, et al. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell, 2013,13(6):659–662
Fu Y, Foden JA, Khayter C, et al. High-frequency offtarget mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol, 2013,31(9):822–826
Shin J, Jiang F, Liu JJ, et al. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv, 2017,3(7):e1701620
Hu JH, Miller SM, Geurts MH, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature, 2018,556(7699):57–63
Fu Y, Sander JD, Reyon D, et al. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol, 2014,32(3):279–284
Lin L, Liu Y, Xu F, et al. Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience, 2018,7(3):1–19
Ke Q, Li W, Lai X, et al. TALEN-based generation of a cynomolgus monkey disease model for human microcephaly. Cell Res, 2016,26(9):1048–1061
Author information
Authors and Affiliations
Corresponding author
Additional information
The study was supported by the National Natural Science Foundation of China (No. 81270468).
Conflict of Interest Statement
The authors declare that there is no conflict of interest with any financial organization or corporation or individual that can inappropriately influence this work.
Rights and permissions
About this article
Cite this article
Chen, M., Zhu, H., Mao, Yj. et al. Regulation of IL12B Expression in Human Macrophages by TALEN-mediated Epigenome Editing. CURR MED SCI 40, 900–909 (2020). https://doi.org/10.1007/s11596-020-2249-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11596-020-2249-2