Singh VK, Schwarzenberg SJ. Pancreatic insufficiency in cystic fibrosis. J Cyst Fibros. 2017;16(Suppl 2):S70–8.
Article
Google Scholar
Hector A, Schäfer H, Pöschel S, Fischer A, Fritzsching B, Ralhan A, Carevic M, Öz H, Zundel S, Hogardt M. Regulatory T-cell impairment in cystic fibrosis patients with chronic pseudomonas infection. Am J Respir Crit Care Med. 2015;191:914–23.
Article
CAS
Google Scholar
Strug LJ, Stephenson AL, Panjwani N, Harris A. Recent advances in developing therapeutics for cystic fibrosis. Hum Mol Genet. 2018;27:R173–86.
Article
CAS
Google Scholar
Cutting GR. Cystic fibrosis genetics: from molecular understanding to clinical application. Nat Rev Genet. 2015;16:45–56.
Article
CAS
Google Scholar
Terlizzi V, Castaldo G, Salvatore D, Lucarelli M, Raia V, Angioni A, Carnovale V, Cirilli N, Casciaro R, Colombo C, et al. Genotype-phenotype correlation and functional studies in patients with cystic fibrosis bearing CFTR complex alleles. J Med Genet. 2017;54:224–35.
Article
CAS
Google Scholar
Ivanov M, Matsvay A, Glazova O, Krasovskiy S, Usacheva M, Amelina E, Chernyak A, Ivanov M, Musienko S, Prodanov T, et al. Targeted sequencing reveals complex, phenotype-correlated genotypes in cystic fibrosis. BMC Med Genet. 2018;11:13.
Google Scholar
Bergougnoux A, D'Argenio V, Sollfrank S, Verneau F, Telese A, Postiglione I, Lackner KJ, Claustres M, Castaldo G, Rossman H, et al. Multicenter validation study for the certification of a CFTR gene scanning method using next generation sequencing technology. Clin Chem Lab Med. 2018;56:1046–53.
Article
CAS
Google Scholar
Lucarelli M, Porcaro L, Biffignandi A, Costantino L, Giannone V, Albert L, Bruno SM, Corbetta C, Torresani E, Colombo C, Seia M. A new targeted CFTR mutation panel based on next-generation sequencing technology. J Mol Diagn. 2017;19:788–800.
Article
CAS
Google Scholar
Levy H, Farrell PM. New challenges in the diagnosis and management of cystic fibrosis. J Pediatr. 2015;166:1337–41.
Article
Google Scholar
Xu Y, Worgall S. Immune dysfunction in cystic fibrosis. In: Cystic fibrosis-renewed hopes through research. IntechOpen. 2012. https://doi.org/10.5772/30274.
Bodas M, Mazur S, Min T, Vij N. Inhibition of histone-deacetylase activity rescues inflammatory cystic fibrosis lung disease by modulating innate and adaptive immune responses. Respir Res. 2018;19:2.
Article
Google Scholar
Tsuchiya M, Kumar P, Bhattacharyya S, Chattoraj S, Srivastava M, Pollard HB, Biswas R. Differential regulation of inflammation by inflammatory mediators in cystic fibrosis lung epithelial cells. J Interf Cytokine Res. 2013;33:121–9.
Article
CAS
Google Scholar
Gilbertson S, Federspiel JD, Hartenian E, Cristea IM, Glaunsinger B. Changes in mRNA abundance drive differential shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. Elife. 2018;7:e37663.
Hampton TH, Ballok AE, Bomberger JM, Rutkowski MR, Barnaby R, Coutermarsh B, Conejo-Garcia JR, O'Toole GA, Stanton BA. Does the ΔF508-CFTR mutation induce a proinflammatory response in human airway epithelial cells? Am J Phys Lung Cell Mol Phys. 2012;303:L509–18.
CAS
Google Scholar
Wright JM, Merlo CA, Reynolds JB, Zeitlin PL, Garcia JG, Guggino WB, Boyle MP. Respiratory epithelial gene expression in patients with mild and severe cystic fibrosis lung disease. Am J Respir Cell Mol Biol. 2006;35:327–36.
Article
CAS
Google Scholar
Kormann MSD, Dewerth A, Eichner F, Baskaran P, Hector A, Regamey N, Hartl D, Handgretinger R, Antony JS. Transcriptomic profile of cystic fibrosis patients identifies type I interferon response and ribosomal stalk proteins as potential modifiers of disease severity. PLoS One. 2017;12:e0183526.
Article
Google Scholar
Palatnik A, Ye S, Kendziorski C, Iden M, Zigman JS, Hessner MJ, Rader JS. Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer. PLoS One. 2017;12:e0181242.
Article
Google Scholar
Kaldunski M, Jia SA, Geoffrey R, Basken J, Prosser S, Kansra S, Mordes JP, Lernmark A, Wang XJ, Hessner MJ. Identification of a serum-induced transcriptional signature associated with type 1 diabetes in the BioBreeding rat. Diabetes. 2010;59:2375–85.
Article
CAS
Google Scholar
Levy H, Wang X, Kaldunski M, Jia S, Kramer J, Pavletich SJ, Reske M, Gessel T, Yassai M, Quasney MW, et al. Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes. Genes Immun. 2012;13:593–604.
Article
CAS
Google Scholar
Levy H, Jia S, Pan A, Zhang X, Kaldunski ML, Nugent ML, Reske M, Feliciano RA, Quintero D, Renda MM, et al. Identification of molecular signatures of cystic fibrosis disease status using plasma-based functional genomics. Physiol Genomics. 2019;51(1):27–41.
Article
Google Scholar
Ratner D, Mueller C. Immune responses in cystic fibrosis: are they intrinsically defective? Am J Respir Cell Mol Biol. 2012;46:715–22.
Article
CAS
Google Scholar
Ideozu JE, Zhang X, McColley S, Levy H. Transcriptome profiling and molecular therapeutic advances in cystic fibrosis: recent insights. Genes (Basel). 2019;10(3):180.
Donaldson LF, Beazley-Long N. Alternative RNA splicing: contribution to pain and potential therapeutic strategy. Drug Discov Today. 2016;21:1787–98.
Article
CAS
Google Scholar
Cieply B, Carstens RP. Functional roles of alternative splicing factors in human disease. Wiley Interdiscip Rev RNA. 2015;6:311–26.
Article
CAS
Google Scholar
Shakola F, Suri P, Ruggiu M. Splicing regulation of pro-inflammatory cytokines and chemokines: at the Interface of the neuroendocrine and immune systems. Biomolecules. 2015;5:2073–100.
Article
CAS
Google Scholar
Niu L, Huang W, Umbach DM, Li L. IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data. BMC Genomics. 2014;15:862.
Article
Google Scholar
Stricker TP, Brown CD, Bandlamudi C, McNerney M, Kittler R, Montoya V, Peterson A, Grossman R, White KP. Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression. PLoS Genet. 2017;13:e1006589.
Article
Google Scholar
Oglesby IK, McKiernan PJ. MiRNA expression in cystic fibrosis bronchial epithelial cells. Methods Mol Biol. 2017;1509:57–69.
Article
CAS
Google Scholar
Bhattacharyya S, Balakathiresan NS, Dalgard C, Gutti U, Armistead D, Jozwik C, Srivastava M, Pollard HB, Biswas R. Elevated miR-155 promotes inflammation in cystic fibrosis by driving hyperexpression of interleukin-8. J Biol Chem. 2011;286:11604–15.
Article
CAS
Google Scholar
Glasgow AM, De Santi C, Greene CM. Non-coding RNA in cystic fibrosis. Biochem Soc Trans. 2018;46(3):619–30.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13.
Article
Google Scholar
Kasoju N, Wang H, Zhang B, George J, Gao S, Triffitt JT, Cui Z, Ye H. Transcriptomics of human multipotent mesenchymal stromal cells: retrospective analysis and future prospects. Biotechnol Adv. 2017;35:407–18.
Article
CAS
Google Scholar
Shi L, Yu L, Zou F, Hu H, Liu K, Lin Z. 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. 2017;5:e3751.
Article
Google Scholar
Westermann AJ, Barquist L, Vogel J. Resolving host–pathogen interactions by dual RNA-seq. PLoS Pathog. 2017;13:e1006033.
Article
Google Scholar
Heap S: Guidelines for the performance of the sweat test for the investigation of cystic fibrosis in the UK 2nd version. An evidence based guideline. R College Paediatr Child Health 2014, 2:1–121.
Farrell PM, White TB, Ren CL, Hempstead SE, Accurso F, Derichs N, Howenstine M, McColley SA, Rock M, Rosenfeld M, et al. Diagnosis of cystic fibrosis: consensus guidelines from the Cystic Fibrosis Foundation. J Pediatr. 2017;181S:S4–S15 e11.
Article
Google Scholar
Caudri D, Zitter D, Bronsveld I, Tiddens H. Is sweat chloride predictive of severity of cystic fibrosis lung disease assessed by chest computed tomography? Pediatr Pulmonol. 2017;52:1135–41.
Article
Google Scholar
Ahmed N, Corey M, Forstner G, Zielenski J, Tsui LC, Ellis L, Tullis E, Durie P. Molecular consequences of cystic fibrosis transmembrane regulator (CFTR) gene mutations in the exocrine pancreas. Gut. 2003;52:1159–64.
Article
CAS
Google Scholar
Ooi CY, Dorfman R, Cipolli M, Gonska T, Castellani C, Keenan K, Freedman SD, Zielenski J, Berthiaume Y, Corey M, et al. Type of CFTR mutation determines risk of pancreatitis in patients with cystic fibrosis. Gastroenterology. 2011;140:153–61.
Article
CAS
Google Scholar
Ideozu JE, Zhang X, Pan A, Ashrafi Z, Woods KJ, Hessner MJ, Simpson P, Levy H. Increased expression of plasma-induced ABCC1 mRNA in cystic fibrosis. Int J Mol Sci. 2017;18.
Walkowiak J, Herzig KH, Witt M, Pogorzelski A, Piotrowski R, Barra E, Sobczynska-Tomaszewska A, Trawinska-Bartnicka M, Strzykala K, Cichy W. Analysis of exocrine pancreatic function in cystic fibrosis: one mild CFTR mutation does not exclude pancreatic insufficiency. Eur J Clin Investig. 2001;31:796–801.
Article
CAS
Google Scholar
Law CW, Alhamdoosh M, Su S, Smyth GK, Ritchie ME. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Res. 2016;5.
Soneson C, Love MI, Robinson MD. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research. 2015;4.
Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2013;42:D68–73.
Article
Google Scholar
Tam S, Tsao MS, McPherson JD. Optimization of miRNA-seq data preprocessing. Brief Bioinform. 2015;16:950–63.
Article
CAS
Google Scholar
Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD. PANTHER version 11: expanded annotation data from gene ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res. 2016;45:D183–9.
Article
Google Scholar
Sahoo A, Im SH. Interleukin and interleukin receptor diversity: role of alternative splicing. Int Rev Immunol. 2010;29:77–109.
Article
CAS
Google Scholar
Courtney JM, Ennis M, Elborn JS. Cytokines and inflammatory mediators in cystic fibrosis. J Cyst Fibros. 2004;3:223–31.
Article
CAS
Google Scholar
Ji Y, Chen Y, Chen M, Wei J. Analysis of cancer-specific isoforms across the cancer genome atlas tumor types: potential disease linkages; 2016.
Google Scholar
Levy H, Murphy A, Zou F, Gerard C, Klanderman B, Schuemann B, Lazarus R, Garcia KC, Celedon JC, Drumm M, et al. IL1B polymorphisms modulate cystic fibrosis lung disease. Pediatr Pulmonol. 2009;44:580–93.
Article
Google Scholar
Liu H, Ning H, Men H, Hou R, Fu M, Zhang H, Liu J. Regulation of CCL5 expression in smooth muscle cells following arterial injury. PLoS One. 2012;7:e30873.
Article
CAS
Google Scholar
Lee AH, Jeong-Ho H, Yeon-Soo S. Tumour necrosis factor-α and interferon-γ synergistically activate the RANTES promoter through nuclear factor κB and interferon regulatory factor 1 (IRF-1) transcription factors. Biochem J. 2000;350:131–8.
Article
CAS
Google Scholar
Huang C-Y, Fong Y-C, Lee C-Y, Chen M-Y, Tsai H-C, Hsu H-C, Tang C-H. CCL5 increases lung cancer migration via PI3K, Akt and NF-κB pathways. Biochem Pharmacol. 2009;77:794–803.
Article
CAS
Google Scholar
Celegato M, Borghese C, Umezawa K, Casagrande N, Colombatti A, Carbone A, Aldinucci D. The NF-kappaB inhibitor DHMEQ decreases survival factors, overcomes the protective activity of microenvironment and synergizes with chemotherapy agents in classical Hodgkin lymphoma. Cancer Lett. 2014;349:26–34.
Article
CAS
Google Scholar
Zhang Q, Lenardo MJ, Baltimore D. 30 years of NF-κB: a blossoming of relevance to human pathobiology. Cell. 2017;168:37–57.
Article
CAS
Google Scholar
Bodas M, Vij N. The NFκB signaling in cystic fibrosis lung disease: pathophysiology and therapeutic potential. Discov Med. 2010;9:346.
PubMed
PubMed Central
Google Scholar
Vij N, Mazur S, Zeitlin PL. CFTR is a negative regulator of NFκB mediated innate immune response. PLoS One. 2009;4:e4664.
Article
Google Scholar
Cohen TS, Prince A. Cystic fibrosis: a mucosal immunodeficiency syndrome. Nat Med. 2012;18:509–19.
Article
CAS
Google Scholar
Kochumon S, Wilson A, Chandy B, Shenouda S, Tuomilehto J, Sindhu S, Ahmad R. Palmitate activates CCL4 expression in human Monocytic cells via TLR4/MyD88 dependent activation of NF-kappaB/MAPK/ PI3K signaling systems. Cell Physiol Biochem. 2018;46:953–64.
Article
CAS
Google Scholar
Huang K-H, Wang C-H, Lee K-Y, Lin S-M, Lin C-H, Kuo H-P. NF-κB repressing factor inhibits chemokine synthesis by peripheral blood mononuclear cells and alveolar macrophages in active pulmonary tuberculosis. PLoS One. 2013;8:e77789.
Article
CAS
Google Scholar
del Fresno C, Gomez-Pina V, Lores V, Soares-Schanoski A, Fernandez-Ruiz I, Rojo B, Alvarez-Sala R, Caballero-Garrido E, Garcia F, Veliz T, et al. Monocytes from cystic fibrosis patients are locked in an LPS tolerance state: Down-regulation of TREM-1 as putative underlying mechanism. PLoS One. 2008;3:e2667.
Article
Google Scholar
Schwitalla S, Ziegler PK, Horst D, Becker V, Kerle I, Begus-Nahrmann Y, Lechel A, Rudolph KL, Langer R, Slotta-Huspenina J, et al. Loss of p53 in enterocytes generates an inflammatory microenvironment enabling invasion and lymph node metastasis of carcinogen-induced colorectal tumors. Cancer Cell. 2013;23:93–106.
Article
CAS
Google Scholar
Lowe JM, Menendez D, Bushel PR, Shatz M, Kirk EL, Troester MA, Garantziotis S, Fessler MB, Resnick MA. p53 and NF-κB coregulate proinflammatory gene responses in human macrophages. Cancer Res. 2014;74:2182–92.
Article
CAS
Google Scholar
Schneider G, Krämer OH. NFκB/p53 crosstalk—a promising new therapeutic target. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer. 2011;1815:90–103.
Article
CAS
Google Scholar
Ryan KM, Ernst MK, Rice NR, Vousden KH. Role of NF-kappaB in p53-mediated programmed cell death. Nature. 2000;404:892–7.
Article
CAS
Google Scholar
Hensler M, Vančurová I, Becht E, Palata O, Strnad P, Tesařová P, Čabiňaková M, Švec D, Kubista M, Bartůňková J. Gene expression profiling of circulating tumor cells and peripheral blood mononuclear cells from breast cancer patients. Oncoimmunology. 2016;5:e1102827.
Article
Google Scholar
Rajasekaran S, Rajaguru P, Gandhi PSS. MicroRNAs as potential targets for progressive pulmonary fibrosis. Front Pharmacol. 2015;6:254.
Article
Google Scholar
Sonneville F, Ruffin M, Guillot L, Rousselet N, Le Rouzic P, Corvol H, Tabary O. New insights about miRNAs in cystic fibrosis. Am J Pathol. 2015;185:897–908.
Article
CAS
Google Scholar
Zeitlin PL, Diener-West M, Callahan KA, Lee S, Talbot CC Jr, Pollard B, Boyle MP, Lechtzin N. Digitoxin for airway inflammation in cystic fibrosis: preliminary assessment of safety, pharmacokinetics, and dose finding. Ann Am Thorac Soc. 2017;14:220–9.
Article
Google Scholar
Liang M, Jiang Z, Huang Q, Liu L, Xue Y, Zhu X, Yu Y, Wan W, Yang H, Zou H. Clinical Association of Chemokine (C-X-C motif) ligand 1 (CXCL1) with interstitial pneumonia with autoimmune features (IPAF). Sci Rep. 2016;6:38949.
Article
CAS
Google Scholar
Tsuchida A, Ohno S, Wu W, Borjigin N, Fujita K, Aoki T, Ueda S, Takanashi M, Kuroda M. miR-92 is a key oncogenic component of the miR-17–92 cluster in colon cancer. Cancer Sci. 2011;102:2264–71.
Article
CAS
Google Scholar
Shigoka M, Tsuchida A, Matsudo T, Nagakawa Y, Saito H, Suzuki Y, Aoki T, Murakami Y, Toyoda H, Kumada T. Deregulation of miR-92a expression is implicated in hepatocellular carcinoma development. Pathol Int. 2010;60:351–7.
Article
CAS
Google Scholar
Z-l C, Zhao X-h, Li B-z, Sun J, F-w T, D-p D, Xu X-h, Zhou F, X-g T, Hang J. microRNA-92a promotes lymph node metastasis of human esophageal squamous cell carcinoma via E-cadherin. J Biol Chem. 2010. https://doi.org/10.1074/jbc.M110.165654.
Li ML, Guan XF, Sun YQ, Mi J, Shu XH, Liu F, Li CG. miR-92a family and their target genes in tumorigenesis and metastasis. Exp Cell Res. 2014;323:1–6.
Article
CAS
Google Scholar
Song H, Zhang Y, Liu N, Zhao S, Kong Y, Yuan L. miR-92a-3p exerts various effects in glioma and glioma stem-like cells specifically targeting CDH1/β-catenin and Notch-1/Akt signaling pathways. Int J Mol Sci. 2016;17:1799.
Article
Google Scholar
Panganiban RP, Pinkerton MH, Maru SY, Jefferson SJ, Roff AN, Ishmael FT. Differential microRNA epression in asthma and the role of miR-1248 in regulation of IL-5. Am J Clin Exp Immunol. 2012;1:154–65.
PubMed
PubMed Central
Google Scholar
Zhao H, Chen M, Tellgren-Roth C, Pettersson U. Fluctuating expression of microRNAs in adenovirus infected cells. Virology. 2015;478:99–111.
Article
CAS
Google Scholar
Zhao Y, Xu K, Liu P. Post-transcriptional control of angiotensin II type 1 receptor regulates osteosarcoma cell death. Cell Physiol Biochem. 2018;45:1581–9.
Article
CAS
Google Scholar