Topic review

miRNA in Regulating CFTR

Subjects: Pathology & Pathobiology View times: 91
Submitted by: Nilay Mitash


The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a cAMP-activated ion channel that mediates transepithelial Cl- and HCO- secretion in fluid transporting epithelia. In the airway, a thin layer of fluid, known as the airway surface liquid (ASL), acts as a medium to facilitate ciliary function and allow for the overlying mucus layer to glide from the distal lung to the trachea where it can be expelled from the lung. CFTR gene mutations impair regulation of the transport of Cl-, HCO-, Na+, and water, and alter the volume and composition of the luminal contents of the airway, intestine, and biliary tree, leading to muco-obstructive disease cystic fibrosis (CF). Deletion of phenylalanine in position 508 (p.F508del) of the CFTR gene is present in at last 70% of CF patients.  We discuss the role of micro(mi)RNAs in regulating CFTR expression and function in health and disease.

1. Introduction

The expression of the CFTR gene is tightly regulated in a temporal and tissue-specific manner [1][2]. Gillen et al. first reported the role of miRNAs in CFTR expression [3]. The validated CFTR inhibitors miR-101, miR-145, and miR-384 play an essential role in the switch from a strong fetal to low postnatal CFTR expression [4]. Interestingly, miR-101 negatively regulated CFTR in the adult airway cell lines but did not affect CFTR in the fetal bronchial epithelial cells. These data demonstrate that miRNAs control the temporal expression of CFTR. In the postnatal airway, the CFTR protein is abundant in the submucosal serous gland cells, much less abundant in multi-ciliated surface epithelial cells, and highly expressed in the newly identified ionocytes [5][6][7]. The role of miRNAs in controlling the cell-type-specific expression of CFTR in the airway epithelium is practically unknown.

2. Role of miRNA in Regulating CFTR

Many miRNAs have been experimentally validated as CFTR inhibitors [3][4][8][9][10]. miR-101 and miR-494 markedly repressed CFTR expression alone and had a more substantial synergistic effect [11]. Other groups reported synergistic inhibitory effects on CFTR for the miR-145, miR-223, miR-384, miR-1246, and miR-494 or miR-509-3p together with miR-494 [3][8][9]. A reciprocal regulation was proposed that a decreased CFTR Cl channel activity may contribute to the overexpression of miR-145, miR-223, and miR-494 in the CF airway [3]. These data suggest that the severity of CF airway disease can be influenced by conditions that affect the active pools of the synergistically acting miRNAs. Enhancing the affinity of CFTR mRNA for miRNA binding is an exciting novel mechanism of CF that may explain why CFTR gene mutations are not identified in up to 10% CF alleles. Amato et al. reported a single nucleotide polymorphism (SNP) in the CFTR 3’UTR that increases the binding affinity of validated CFTR inhibitor miR-509-3p and reduces expression of CFTR protein, acting as a mild CFTR mutation [12]. Endale Ahanda et al. identified gene polymorphisms in the miR-99b/let-7e/miR-125a cluster that modulate the expression of these miRNAs [13]. Two of the polymorphisms in a cohort of p.F508del CF patients could modulate miRNA maturation and therefore impact the miR-99b/hsa-let-7e/hsa-miR-125a activity, acting as non-CFTR gene modifiers in CF. They may help to explain the variable severity of lung disease among CF patients with the same genotype.

The TGF-β1 gene is a known non-CFTR modifier in p.F508del CF patients. Two SNPs present in ~40% of F508del homozygous patients, increase TGF-β1 protein levels, correlate with more severe lung disease, and exacerbate the damaging effects of secondhand smoke in CF patients [14][15]. Besides, Pseudomonas aeruginosa infection and reduced nutrition increase TGF-β1 levels in p.F508del homozygous patients [16][17][18][19]. Independent of the underlying cause, high TGF-β1 levels are strongly associated with poor outcomes [20][21][22][23][24][25]. Thus, TGF-β1 may represent a prevalent ASL inhibitor and an antagonist limiting the residual and corrected CFTR activity in CF patients. TGF-β1 inhibits CFTR mRNA level and reduces the full beneficial effects of CFTR correctors in human airway epithelial cells [26][27][28]. Although TGF-β1 is a transcriptional regulator, current data show that its inhibitory effect on CFTR is mediated post-transcriptionally via miRNAs, including miR-145 and miR-143 [29][30][10][31]. TGF-β1 changes the expression of many miRNAs, including those validated as CFTR inhibitors [29][31][32]. However, the total cellular miRNA level does not correlate with the inhibitory effect on a target gene. In agreement with this view, we have recently shown that TGF-β1 recruits specific miRNA to RISC, independently of how it affects their total cellular levels [29]. Only the miRNAs validated as CFTR inhibitors and recruited by TGF-β1 to RISC, including miR-143 and miR-145, would mediate the TGF-β1 inhibition of CFTR mRNA. This study provides another novel observation that the cellular environment of chronic lung disease, including CF, contains additional factor(s) required for the TGF-β1-mediated decay of CFTR mRNA [29]. Data showing that TGF-β1 did not inhibit CFTR mRNA in primary human airway epithelial cells from lungs without chronic disease despite recruiting miR-145 to RISC and increasing the total cellular miR-145 levels support the conclusion. These data emphasize the complexity of the TGF-β1-miRNA axis and its context-specific effects. TGF-β1 plays a significant role in the pathogenesis of other forms of lung disease, including chronic obstructive pulmonary disease (COPD), the third leading cause of death in the US, where it causes acquired CFTR dysfunction by cigarettes smoke exposure [25][33][34][35][36][37]. Environmental pollutants, including cigarette smoke, also increase TGF-β1 levels and raise the risk of sinopulmonary disease in carriers of the CFTR gene mutations (15,000,000 people in the US), compared to the general population [38]. The SNPs associated with high TGF-β1 levels may also contribute to the acquired CFTR dysfunction. We have shown that TGF-β1 inhibits CFTR mRNA in human bronchial epithelial cells from COPD and idiopathic pulmonary fibrosis (IPF) lungs [29]. These data suggest that miRNAs may also carry out the TGF-β1 repression in these conditions. Dutta et al. provided evidence for the role of TGF-β1 and miR-145 in cigarette smoke-induced acquired CFTR dysfunction [31]. Cigarette smoke exposure is associated with a specific signature comprised of a network of miRNAs and proinflammatory signaling cascades, leading to decreased pulmonary function [39]. Avoiding cigarette smoke exposure is the only valid measure known to date to prevent the harmful effects mediated by these miRNAs.

Some miRNAs induce CFTR expression by targeting transcriptional repressors. For example, the miR-138 mimic restored the p.F508del-CFTR expression and function by downregulating the expression of the highly conserved transcriptional repressor SIN3A [40]. Although miR-138 may have a positive effect on CFTR protein abundance and the CFTR Cl channel function, overexpression of other genes would be expected as a result of the miR-138-mediated inhibition of SIN3A. Thus, miR-138-based therapy for CF is not feasible. By contrast, blockade of the MRE in CFTR 3’UTR by TSBs can precisely restore the CFTR Cl channel activity in CF bronchial epithelial cells. De Santi et al. recently showed that TSBs directed against the miR-223-3p and miR-145-5p MREs in the CFTR 3’UTR, encapsulated in poly-lactic-co-glycolic acid (PLGA) nanoparticles and delivered to the airway in an aerosolized form, increased CFTR expression and function in CF bronchial epithelial cells [32]. Thus, TSBs emerge as potential therapeutics precisely and specifically eliminating the inhibitory effects of miRNA on CFTR, allowing the full potential of the FDA-approved CFTR modulators in the CF airway. Moreover, the prevention of the hypoxic milieu of the muco-obstructive airway disease in CF may enhance the efficacy of CFTR correctors by preventing miRNA-200b from directly targeting the CFTR mRNA [41].

The entry is from 10.3390/ijms21113848


  1. Tizzano, E.F.; O’Brodovich, H.; Chitayat, D.; Benichou, J.C.; Buchwald, M. Regional expression of CFTR in developing human respiratory tissues. Am. J. Respir. Cell Mol. Biol. 1994, 10, 355–362.
  2. Tizzano, E.F.; Chitayat, D.; Buchwald, M. Cell-specific localization of CFTR mRNA shows developmentally regulated expression in human fetal tissues. Hum. Mol. Genet. 1993, 2, 219–224.
  3. Gillen, A.E.; Gosalia, N.; Leir, S.H.; Harris, A. MicroRNA regulation of expression of the cystic fibrosis transmembrane conductance regulator gene. Biochem. J. 2011, 438, 25–32.
  4. Viart, V.; Bergougnoux, A.; Bonini, J.; Varilh, J.; Chiron, R.; Tabary, O.; Molinari, N.; Claustres, M.; Taulan-Cadars, M. Transcription factors and miRNAs that regulate fetal to adult CFTR expression change are new targets for cystic fibrosis. Eur. Respir. J. 2015, 45, 116–128.
  5. Jiang, Q.; Engelhardt, J.F. Cellular heterogeneity of CFTR expression and function in the lung: Implications for gene therapy of cystic fibrosis. Eur. J. Hum. Genet. 1998, 6, 12–31.
  6. Montoro, D.T.; Haber, A.L.; Biton, M.; Vinarsky, V.; Lin, B.; Birket, S.E.; Yuan, F.; Chen, S.; Leung, H.M.; Villoria, J.; et al. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 2018, 560, 319–324.
  7. Plasschaert, L.W.; Žilionis, R.; Choo-Wing, R.; Savova, V.; Knehr, J.; Roma, G.; Klein, A.M.; Jaffe, A.B. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 2018, 560, 377–381.
  8. Oglesby, I.K.; Chotirmall, S.H.; McElvaney, N.G.; Greene, C.M. Regulation of cystic fibrosis transmembrane conductance regulator by microRNA-145, -223, and -494 is altered in DeltaF508 cystic fibrosis airway epithelium. J. Immunol. 2013, 190, 3354–3362.
  9. Ramachandran, S.; Karp, P.H.; Osterhaus, S.R.; Jiang, P.; Wohlford-Lenane, C.; Lennox, K.A.; Jacobi, A.M.; Praekh, K.; Rose, S.D.; Behlke, M.A.; et al. Post-transcriptional regulation of cystic fibrosis transmembrane conductance regulator expression and function by microRNAs. Am. J. Respir. Cell. Mol. Biol. 2013, 49, 544–551.
  10. De Santi, C.; Gadi, S.; Swiatecka-Urban, A.; Greene, C.M. Identification of a novel functional miR-143-5p recognition element in the Cystic Fibrosis Transmembrane Conductance Regulator 3’UTR. AIMS Genet. 2018, 5, 53–62.
  11. Megiorni, F.; Cialfi, S.; Dominici, C.; Quattrucci, S.; Pizzuti, A. Synergistic post-transcriptional regulation of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) by miR-101 and miR-494 specific binding. PLoS ONE 2011, 6, e26601.
  12. Amato, F.; Seia, M.; Giordano, S.; Elce, A.; Zarrilli, F.; Castaldo, G.; Tomaiuolo, R. Gene mutation in microRNA target sites of CFTR gene: A novel pathogenetic mechanism in cystic fibrosis? PLoS ONE 2013, 8, e60448.
  13. Endale Ahanda, M.L.; Bienvenu, T.; Sermet-Gaudelus, I.; Mazzolini, L.; Edelman, A.; Zoorob, R.; Davezac, N. The hsa-miR-125a/hsa-let-7e/hsa-miR-99b cluster is potentially implicated in Cystic Fibrosis pathogenesis. J. Cyst. Fibros. 2015, 14, 571–579.
  14. Drumm, M.L.; Konstan, M.W.; Schluchter, M.D.; Handler, A.; Pace, R.; Zou, F.; Zariwala, M.; Fargo, D.; Xu, A.; Dunn, J.M.; et al. Genetic modifiers of lung disease in cystic fibrosis. N. Engl. J. Med. 2005, 353, 1443–1453.
  15. Collaco, J.M.; Vanscoy, L.; Bremer, L.; McDougal, K.; Blackman, S.M.; Bowers, A.; Naughton, K.; Jennings, J.; Ellen, J.; Cutting, G.R. Interactions between secondhand smoke and genes that affect cystic fibrosis lung disease. Jama 2008, 299, 417–424.
  16. Brazova, J.; Sismova, K.; Vavrova, V.; Bartosova, J.; Macek, M., Jr.; Lauschman, H.; Sediva, A. Polymorphisms of TGF-beta1 in cystic fibrosis patients. Clin. Immunol. 2006, 121, 350–357.
  17. Davies, J.C. Pseudomonas aeruginosa in cystic fibrosis: Pathogenesis and persistence. Paediatr. Respir. Rev. 2002, 3, 128–134.
  18. Harris, W.T.; Muhlebach, M.S.; Oster, R.A.; Knowles, M.R.; Clancy, J.P.; Noah, T.L. Plasma TGF-β1 in pediatric cystic fibrosis: Potential biomarker of lung disease and response to therapy. Pediatr. Pulmonol. 2011, 46, 688–695.
  19. Ryder, M.I.; Saghizadeh, M.; Ding, Y.; Nguyen, N.; Soskolne, A. Effects of tobacco smoke on the secretion of interleukin-1beta, tumor necrosis factor-alpha, and transforming growth factor-beta from peripheral blood mononuclear cells. Oral Microbiol. Immunol. 2002, 17, 331–336.
  20. Arkwright, P.D.; Laurie, S.; Super, M.; Pravica, V.; Schwarz, M.J.; Webb, A.K.; Hutchinson, I.V. TGF-beta(1) genotype and accelerated decline in lung function of patients with cystic fibrosis. Thorax 2000, 55, 459–462.
  21. Dorfman, R.; Sandford, A.; Taylor, C.; Huang, B.; Frangolias, D.; Wang, Y.; Sang, R.; Pereira, L.; Sun, L.; Berthiaume, Y.; et al. Complex two-gene modulation of lung disease severity in children with cystic fibrosis. J. Clin. Investig. 2008, 118, 1040–1049.
  22. Collaco, J.M.; Cutting, G.R. Update on gene modifiers in cystic fibrosis. Curr. Opin. Pulm. Med. 2008, 14, 559–566.
  23. Clunes, L.A.; Davies, C.M.; Coakley, R.D.; Aleksandrov, A.A.; Henderson, A.G.; Zeman, K.L.; Worthington, E.N.; Gentzsch, M.; Kreda, S.M.; Cholon, D.; et al. Cigarette smoke exposure induces CFTR internalization and insolubility, leading to airway surface liquid dehydration. FASEB J. 2012, 26, 533–545.
  24. Liu, Y.; Di, Y.P. Effects of second hand smoke on airway secretion and mucociliary clearance. Front. Physiol. 2012, 3, 342.
  25. Rab, A.; Rowe, S.M.; Raju, S.V.; Bebok, Z.; Matalon, S.; Collawn, J.F. Cigarette smoke and CFTR: Implications in the pathogenesis of COPD. Am. J. Physiol. Lung Cell. Mol. Physiol. 2013, 305, L530–L541.
  26. Snodgrass, S.M.; Cihil, K.M.; Cornuet, P.K.; Myerburg, M.M.; Swiatecka-Urban, A. Tgf-beta1 inhibits Cftr biogenesis and prevents functional rescue of DeltaF508-Cftr in primary differentiated human bronchial epithelial cells. PLoS ONE 2013, 8, e63167.
  27. Sun, H.; Harris, W.T.; Kortyka, S.; Kotha, K.; Ostmann, A.J.; Rezayat, A.; Sridharan, A.; Sanders, Y.; Naren, A.P.; Clancy, J.P. Tgf-beta downregulation of distinct chloride channels in cystic fibrosis-affected epithelia. PLoS ONE 2014, 9, e106842.
  28. Roux, J.; Carles, M.; Koh, H.; Goolaerts, A.; Ganter, M.T.; Chesebro, B.B.; Howard, M.; Houseman, B.T.; Finkbeiner, W.; Shokat, K.M.; et al. Transforming growth factor beta1 inhibits cystic fibrosis transmembrane conductance regulator-dependent cAMP-stimulated alveolar epithelial fluid transport via a phosphatidylinositol 3-kinase-dependent mechanism. J. Biol. Chem. 2010, 285, 4278–4290.
  29. Mitash, N.; Mu, F.; Donovan, J.E.; Myerburg, M.M.; Ranganathan, S.; Greene, C.M.; Swiatecka-Urban, A. Transforming Growth Factor-beta1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells. Int. J. Mol. Sci. 2019, 20, 4933.
  30. Lutful Kabir, F.; Ambalavanan, N.; Liu, G.; Li, P.; Solomon, G.M.; Lal, C.V.; Mazur, M.; Halloran, B.; Szul, T.; Gerthoffer, W.T.; et al. MicroRNA-145 Antagonism Reverses TGF-beta Inhibition of F508del CFTR Correction in Airway Epithelia. Am. J. Respir. Crit. Care Med. 2018, 197, 632–643.
  31. Dutta, R.K.; Chinnapaiyan, S.; Rasmussen, L.; Raju, S.V.; Unwalla, H.J. A Neutralizing Aptamer to TGFBR2 and miR-145 Antagonism Rescue Cigarette Smoke- and TGF-beta-Mediated CFTR Expression. Mol. Ther. J. Am. Soc. Gene Ther. 2019, 27, 442–455.
  32. De Santi, C.; Fernandez Fernandez, E.; Gaul, R.; Vencken, S.; Glasgow, A.; Oglesby, I.K.; Hurley, K.; Hawkins, F.; Mitash, N.; Mu, F.; et al. Precise Targeting of miRNA Sites Restores CFTR Activity in CF Bronchial Epithelial Cells. Mol. Ther. J. Am. Soc. Gene Ther. 2020, 28, 1190–1199.
  33. Morty, R.E.; Königshoff, M.; Eickelberg, O. Transforming growth factor-beta signaling across ages: From distorted lung development to chronic obstructive pulmonary disease. Proc. Am. Thorac. Soc. 2009, 6, 607–613.
  34. Dransfield, M.T.; Wilhelm, A.M.; Flanagan, B.; Courville, C.; Tidwell, S.L.; Raju, S.V.; Gaggar, A.; Steele, C.; Tang, L.P.; Liu, B.; et al. Acquired cystic fibrosis transmembrane conductance regulator dysfunction in the lower airways in COPD. Chest 2013, 144, 498–506.
  35. Mak, J.C.; Chan-Yeung, M.M.; Ho, S.P.; Chan, K.S.; Choo, K.; Yee, K.S.; Chau, C.H.; Cheung, A.H.; Ip, M.S. Elevated plasma TGF-beta1 levels in patients with chronic obstructive pulmonary disease. Respir. Med. 2009, 103, 1083–1089.
  36. Takizawa, H.; Tanaka, M.; Takami, K.; Ohtoshi, T.; Ito, K.; Satoh, M.; Okada, Y.; Yamasawa, F.; Nakahara, K.; Umeda, A. Increased expression of transforming growth factor-beta1 in small airway epithelium from tobacco smokers and patients with chronic obstructive pulmonary disease (COPD). Am. J. Respir. Crit. Care Med. 2001, 163, 1476–1483.
  37. Sailland, J.; Grosche, A.; Baumlin, N.; Dennis, J.S.; Schmid, A.; Krick, S.; Salathe, M. Role of Smad3 and p38 Signalling in Cigarette Smoke-induced CFTR and BK dysfunction in Primary Human Bronchial Airway Epithelial Cells. Sci. Rep. 2017, 7, 10506.
  38. Griesenbach, U.; Geddes, D.M.; Alton, E.W. The pathogenic consequences of a single mutated CFTR gene. Thorax 1999, 54 (Suppl. 2), S19–S23.
  39. Willinger, C.M.; Rong, J.; Tanriverdi, K.; Courchesne, P.L.; Huan, T.; Wasserman, G.A.; Lin, H.; Dupuis, J.; Joehanes, R.; Jones, M.R.; et al. MicroRNA Signature of Cigarette Smoking and Evidence for a Putative Causal Role of MicroRNAs in Smoking-Related Inflammation and Target Organ Damage. Circ. Cardiovasc. Genet. 2017, 10, e001678.
  40. Ramachandran, S.; Karp, P.H.; Jiang, P.; Ostedgaard, L.S.; Walz, A.E.; Fisher, J.T.; Keshavjee, S.; Lennox, K.A.; Jacobi, A.M.; Rose, S.D.; et al. A microRNA network regulates expression and biosynthesis of wild-type and DeltaF508 mutant cystic fibrosis transmembrane conductance regulator. Proc. Natl. Acad. Sci. USA 2012, 109, 13362–13367.
  41. Bartoszewska, S.; Kamysz, W.; Jakiela, B.; Sanak, M.; Króliczewski, J.; Bebok, Z.; Bartoszewski, R.; Collawn, J.F. miR-200b downregulates CFTR during hypoxia in human lung epithelial cells. Cell. Mol. Biol. Lett. 2017, 22, 23.

Related entries