Transcriptome Profiling and Molecular Therapeutic Advances in Cystic Fibrosis: Recent Insights
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Madacsy, 2018, Cystic fibrosis of the pancreas: The role of CFTR channel in the regulation of intracellular Ca(2+) signaling and mitochondrial function in the exocrine pancreas, Front. Physiol., 9, 1585, 10.3389/fphys.2018.01585
Riordan, 1989, Identification of the cystic fibrosis gene: Cloning and characterization of complementary DNA, Science, 245, 1066, 10.1126/science.2475911
Veit, 2016, From CFTR biology toward combinatorial pharmacotherapy: Expanded classification of cystic fibrosis mutations, Mol. Biol. Cell, 27, 424, 10.1091/mbc.e14-04-0935
Fajac, 2017, New treatments targeting the basic defects in cystic fibrosis, Presse Med., 46, E165, 10.1016/j.lpm.2017.01.024
Carithers, 2015, The genotype-tissue expression (GTEx) project, Biopreserv. Biobank., 13, 307, 10.1089/bio.2015.29031.hmm
Burney, 2012, Gene therapy for the treatment of cystic fibrosis, Appl. Clin. Genet., 5, 29
Cooney, A.L., McCray, P.B., and Sinn, P.L. (2018). Cystic fibrosis gene therapy: Looking back, looking forward. Genes (Basel), 9.
Mekus, 2000, Categories of ΔF508 homozygous cystic fibrosis twin and sibling pairs with distinct phenotypic characteristics, Twin Res., 3, 277, 10.1375/136905200320565256
Corvol, 2015, Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis, Nat. Commun., 6, 8382, 10.1038/ncomms9382
Kormann, M.S.D., Dewerth, A., Eichner, F., Baskaran, P., Hector, A., Regamey, N., Hartl, D., Handgretinger, R., and Antony, J.S. (2017). Transcriptomic profile of cystic fibrosis patients identifies type I interferon response and ribosomal stalk proteins as potential modifiers of disease severity. PLoS ONE, 12.
Worgall, 2005, Similarity of gene expression patterns in human alveolar macrophages in response to Pseudomonas aeruginosa and Burkholderia cepacia, Infect. Immun., 73, 5262, 10.1128/IAI.73.8.5262-5268.2005
Wright, 2006, Respiratory epithelial gene expression in patients with mild and severe cystic fibrosis lung disease, Am. J. Respir. Cell Mol. Biol., 35, 327, 10.1165/rcmb.2005-0359OC
Verhaeghe, 2007, Role of IKK and ERK pathways in intrinsic inflammation of cystic fibrosis airways, Biochem. Pharmacol., 73, 1982, 10.1016/j.bcp.2007.03.019
Ribeiro, C.M., Hurd, H., Wu, Y., Martino, M.E., Jones, L., Brighton, B., Boucher, R.C., and O’Neal, W.K. (2009). Azithromycin treatment alters gene expression in inflammatory, lipid metabolism, and cell cycle pathways in well-differentiated human airway epithelia. PLoS ONE, 4.
Ogilvie, 2011, Differential global gene expression in cystic fibrosis nasal and bronchial epithelium, Genomics, 98, 327, 10.1016/j.ygeno.2011.06.008
Hampton, 2012, Does the ΔF508-CFTR mutation induce a proinflammatory response in human airway epithelial cells?, Am. J. Physiol. Lung Cell. Mol. Physiol., 303, L509, 10.1152/ajplung.00226.2011
Levy, 2012, Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes, Genes Immun., 13, 593, 10.1038/gene.2012.41
Clarke, 2013, Changes in transcriptome of native nasal epithelium expressing F508del-CFTR and intersecting data from comparable studies, Respir. Res., 14, 38, 10.1186/1465-9921-14-38
Mayer, 2013, Rescue of dysfunctional autophagy attenuates hyperinflammatory responses from cystic fibrosis cells, J. Immunol., 190, 1227, 10.4049/jimmunol.1201404
Stanke, 2014, The CF-modifying gene EHF promotes p.Phe508del-CFTR residual function by altering protein glycosylation and trafficking in epithelial cells, Eur. J. Hum. Genet., 22, 660, 10.1038/ejhg.2013.209
Chesne, J., Danger, R., Botturi, K., Reynaud-Gaubert, M., Mussot, S., Stern, M., Danner-Boucher, I., Mornex, J.F., Pison, C., and Dromer, C. (2014). Systematic analysis of blood cell transcriptome in end-stage chronic respiratory diseases. PLoS ONE, 9.
Voisin, 2014, Oxidative stress modulates the expression of genes involved in cell survival in ΔF508 cystic fibrosis airway epithelial cells, Physiol. Genomics, 46, 634, 10.1152/physiolgenomics.00003.2014
Gallins, 2015, Gene expression in transformed lymphocytes reveals variation in endomembrane and HLA pathways modifying cystic fibrosis pulmonary phenotypes, Am. J. Hum. Genet., 96, 318, 10.1016/j.ajhg.2014.12.022
Zeitlin, 2017, Digitoxin for airway inflammation in cystic fibrosis: Preliminary assessment of safety, pharmacokinetics, and dose finding, Ann. Am. Thorac. Soc., 14, 220, 10.1513/AnnalsATS.201608-649OC
Polineni, 2017, Airway mucosal host defense is key to genomic regulation of cystic fibrosis lung disease severity, Am. J. Respir. Crit. Care Med., 197, 79, 10.1164/rccm.201701-0134OC
Jiang, K., Poppenberg, K.E., Wong, L., Chen, Y., Borowitz, D., Goetz, D., Sheehan, D., Frederick, C., Tutino, V.M., and Meng, H. (2018). RNA sequencing data from neutrophils of patients with cystic fibrosis reveals potential for developing biomarkers for pulmonary exacerbations. J. Cyst. Fibros.
Levy, 2019, Identification of molecular signatures of cystic fibrosis disease status using plasma-based functional genomics, Physiol. Genom., 51, 27, 10.1152/physiolgenomics.00109.2018
Casamassimi, A., Federico, A., Rienzo, M., Esposito, S., and Ciccodicola, A. (2017). Transcriptome profiling in human diseases: New advances and perspectives. Int. J. Mol. Sci., 18.
Kasoju, 2017, Transcriptomics of human multipotent mesenchymal stromal cells: Retrospective analysis and future prospects, Biotechnol. Adv., 35, 407, 10.1016/j.biotechadv.2017.04.005
Shi, 2017, Gene expression profiling and functional analysis reveals that p53 pathway-related gene expression is highly activated in cancer cells treated by cold atmospheric plasma-activated medium, PeerJ, 5, e3751, 10.7717/peerj.3751
Westermann, A.J., Barquist, L., and Vogel, J. (2017). Resolving host–pathogen interactions by dual RNA-seq. PLoS Pathogens, 13.
Thomas, 2003, Comparative analyses of multi-species sequences from targeted genomic regions, Nature, 424, 788, 10.1038/nature01858
Collawn, 2014, CFTR and lung homeostasis, Am. J. Physiol. Lung Cell. Mol. Physiol., 307, L917, 10.1152/ajplung.00326.2014
Byrne, 2016, Pulmonary macrophages: A new therapeutic pathway in fibrosing lung disease?, Trends Mol. Med., 22, 303, 10.1016/j.molmed.2016.02.004
Ratner, 2012, Immune responses in cystic fibrosis: Are they intrinsically defective?, Am. J. Respir. Cell Mol. Biol., 46, 715, 10.1165/rcmb.2011-0399RT
Del Porto, P., Cifani, N., Guarnieri, S., Di Domenico, E.G., Mariggio, M.A., Spadaro, F., Guglietta, S., Anile, M., Venuta, F., and Quattrucci, S. (2011). Dysfunctional CFTR alters the bactericidal activity of human macrophages against Pseudomonas aeruginosa. PLoS ONE, 6.
Ideozu, J.E., Zhang, X., Pan, A., Ashrafi, Z., Woods, K.J., Hessner, M.J., Simpson, P., and Levy, H. (2017). Increased expression of plasma-induced ABCC1 mRNA in cystic fibrosis. Int. J. Mol. Sci., 18.
Reilly, 2017, Targeting the PI3K/AKT/mTOR signalling pathway in cystic fibrosis, Sci. Rep., 7, 7642, 10.1038/s41598-017-06588-z
Strubberg, 2018, CFTR modulates Wnt/β-catenin signaling and stem cell proliferation in murine intestine, Cell. Mol. Gastroenterol. Hepatol., 5, 253, 10.1016/j.jcmgh.2017.11.013
Bodas, 2010, The NF-κβ signaling in cystic fibrosis lung disease: Pathophysiology and therapeutic potential, Discov. Med., 9, 346
Liu, 2017, Nf-κβ signaling in inflammation, Signal Transduct. Target. Ther., 2, 17023, 10.1038/sigtrans.2017.23
Verhaeghe, 2007, Early inflammation in the airways of a cystic fibrosis foetus, J. Cyst. Fibros., 6, 304, 10.1016/j.jcf.2006.12.001
Quon, 2016, New and emerging targeted therapies for cystic fibrosis, BMJ, 352, i859, 10.1136/bmj.i859
Schwank, 2013, Functional repair of CFTR by CRISPR/cas9 in intestinal stem cell organoids of cystic fibrosis patients, Cell Stem Cell, 13, 653, 10.1016/j.stem.2013.11.002
Roy, 2018, CRISPR/cascade 9-mediated genome editing-challenges and opportunities, Front. Genet., 9, 240, 10.3389/fgene.2018.00240
Hadida, 2009, Rescue of CF airway epithelial cell function in vitro by a CFTR potentiator, vx-770, Proc. Natl. Acad. Sci. USA, 106, 18825, 10.1073/pnas.0904709106
Koscielny, 2017, Open targets: A platform for therapeutic target identification and validation, Nucleic Acids Res., 45, D985, 10.1093/nar/gkw1055
Beringer, 2012, Pharmacokinetics of doxycycline in adults with cystic fibrosis, Antimicrob. Agents Chemother., 56, 70, 10.1128/AAC.05710-11
Hermes, 2017, Prospective, randomized, double-blind, parallel-group, comparative effectiveness clinical trial comparing a powder vehicle compound of vitamin d with an oil vehicle compound in adults with cystic fibrosis, J. Parenter. Enteral Nutr., 41, 952, 10.1177/0148607116629673
Dalakas, 2018, Immunotherapy in myasthenia gravis in the era of biologics, Nat. Rev. Neurol., 15, 113, 10.1038/s41582-018-0110-z
Narozna, B., Langwinski, W., and Szczepankiewicz, A. (2017). Non-coding RNAs in pediatric airway diseases. Genes, 8.
Glasgow, 2018, Non-coding RNA in cystic fibrosis, Biochem. Soc. Trans., 46, 619, 10.1042/BST20170469
Peng, 2016, The role of microRNAs in human cancer, Signal Transduct. Target. Ther., 1, 15004, 10.1038/sigtrans.2015.4
Stolzenburg, 2018, The role of microRNAs in chronic respiratory disease: Recent insights, Biol. Chem., 399, 219, 10.1515/hsz-2017-0249
Oglesby, 2017, MiRNA expression in cystic fibrosis bronchial epithelial cells, Methods Mol. Biol., 1509, 57, 10.1007/978-1-4939-6524-3_7
Bhattacharyya, 2011, Elevated miR-155 promotes inflammation in cystic fibrosis by driving hyperexpression of interleukin-8, J. Biol. Chem., 286, 11604, 10.1074/jbc.M110.198390
Oglesby, 2010, MiR-126 is downregulated in cystic fibrosis airway epithelial cells and regulates TOM1 expression, J. Immunol., 184, 1702, 10.4049/jimmunol.0902669
Palazzo, 2015, Non-coding RNA: What is functional and what is junk?, Front. Genet., 6, 2, 10.3389/fgene.2015.00002
Ponting, 2009, Evolution and functions of long noncoding RNAs, Cell, 136, 629, 10.1016/j.cell.2009.02.006
Xie, 2015, NcRNA-regulated immune response and its role in inflammatory lung diseases, Am. J. Physiol. Lung Cell. Mol. Physiol., 309, L1076, 10.1152/ajplung.00286.2015
Saayman, 2016, Long non-coding RNA BGas regulates the cystic fibrosis transmembrane conductance regulator, Mol. Ther., 24, 1351, 10.1038/mt.2016.112
McKiernan, 2014, Long noncoding RNA are aberrantly expressed in vivo in the cystic fibrosis bronchial epithelium, Int. J. Biochem. Cell Biol., 52, 184, 10.1016/j.biocel.2014.02.022
Balloy, 2017, Bronchial epithelial cells from cystic fibrosis patients express a specific long non-coding RNA signature upon Pseudomonas aeruginosa infection, Front. Cell Infect. Microbiol., 7, 218, 10.3389/fcimb.2017.00218
Kamei, 2019, Integrative expression analysis identifies a novel interplay between CFTR and linc-SUMF1-2 that involves CF-associated gene dysregulation, Biochem. Biophys. Res. Commun., 509, 521, 10.1016/j.bbrc.2018.12.152
Li, 2017, Noncoding RNAs and their potential therapeutic applications in tissue engineering, Engineering, 3, 3, 10.1016/J.ENG.2017.01.005
Fabbri, E., Tamanini, A., Jakova, T., Gasparello, J., Manicardi, A., Corradini, R., Sabbioni, G., Finotti, A., Borgatti, M., and Lampronti, I. (2017). A peptide nucleic acid against microRNA miR-145-5p enhances the expression of the cystic fibrosis transmembrane conductance regulator (CFTR) in calu-3 cells. Molecules, 23.
Donaldson, 2016, Alternative RNA splicing: Contribution to pain and potential therapeutic strategy, Drug Discov. Today, 21, 1787, 10.1016/j.drudis.2016.06.017
Cieply, 2015, Functional roles of alternative splicing factors in human disease, Wiley Interdiscip. Rev. RNA, 6, 311, 10.1002/wrna.1276
Kim, 2018, Alternative splicing isoforms in health and disease, Pflugers Arch., 470, 995, 10.1007/s00424-018-2136-x
Niu, L., Huang, W., Umbach, D.M., and Li, L. (2014). Iuta: A tool for effectively detecting differential isoform usage from RNA-seq data. BMC Genom., 15.
Stricker, T.P., Brown, C.D., Bandlamudi, C., McNerney, M., Kittler, R., Montoya, V., Peterson, A., Grossman, R., and White, K.P. (2017). Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression. PLoS Genet., 13.
Khatoon, 2014, Introduction to RNA-seq and its applications to drug discovery and development, Drug Dev. Res., 75, 324, 10.1002/ddr.21215
Snouwaert, 1992, An animal-model for cystic-fibrosis made by gene targeting, Science, 257, 1083, 10.1126/science.257.5073.1083
Mou, 2015, Personalized medicine for cystic fibrosis: Establishing human model systems, Pediatr. Pulmonol., 50, S14, 10.1002/ppul.23233
Harris, 1997, Towards an ovine model of cystic fibrosis, Hum. Mol. Genet., 6, 2191, 10.1093/hmg/6.13.2191
Rogers, 2008, Production of CFTR-null and CFTR-ΔF508 heterozygous pigs by adeno-associated virus-mediated gene targeting and somatic cell nuclear transfer, J. Clin. Invest., 118, 1571, 10.1172/JCI34773
Rosen, 2018, Animal and model systems for studying cystic fibrosis, J. Cyst. Fibros., 17, S28, 10.1016/j.jcf.2017.09.001
Palatnik, A., Ye, S., Kendziorski, C., Iden, M., Zigman, J.S., Hessner, M.J., and Rader, J.S. (2017). Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer. PLoS ONE, 12.
Kaldunski, 2010, Identification of a serum-induced transcriptional signature associated with type 1 diabetes in the biobreeding rat, Diabetes, 59, 2375, 10.2337/db10-0372
Kanter, 2015, Single cell transcriptomics: Methods and applications, Front. Oncol., 5, 53, 10.3389/fonc.2015.00053
Chen, 2018, Profiling tumor infiltrating immune cells with cibersort, Methods Mol. Biol., 1711, 243, 10.1007/978-1-4939-7493-1_12
Bolen, C.R., Uduman, M., and Kleinstein, S.H. (2011). Cell subset prediction for blood genomic studies. BMC Bioinform., 12.
Aran, 2017, Xcell: Digitally portraying the tissue cellular heterogeneity landscape, Genome Biol., 18, 220, 10.1186/s13059-017-1349-1