An omic approach to congenital diaphragmatic hernia: a pilot study of genomic, microRNA, and metabolomic profiling.
Journal
Journal of perinatology : official journal of the California Perinatal Association
ISSN: 1476-5543
Titre abrégé: J Perinatol
Pays: United States
ID NLM: 8501884
Informations de publication
Date de publication:
06 2020
06 2020
Historique:
received:
20
09
2019
accepted:
06
02
2020
revised:
20
01
2020
pubmed:
23
2
2020
medline:
1
9
2021
entrez:
22
2
2020
Statut:
ppublish
Résumé
The omic approach can help identify a signature that can be potentially used as biomarkers in babies with congenital diaphragmatic hernia (CDH). To find a specific microRNA (miR) and metabolic fingerprint of the tracheal aspirates (TA) of CDH patients. We conducted a genetic analysis from blood samples. TA samples collected in the first 48 h of life in patients with CDH, compared with age-matched controls. Metabolomics done by a mass spectroscopy-based assay. Genomics done using chromosomal microarray analysis. CDH (n = 17) and 16 control neonates enrolled. miR-16, miR-17, miR-18, miR-19b, and miR-20a had an increased expression, while miR-19a had a twofold decreased expression in CDH patients, compared with age-matched control patients. Specific metabolites separated neonates with CDH from controls. A genetic mutation found in a small subset of patients. Specific patterns of metabolites and miR expression can be discerned in TA samples in infants with CDH.
Identifiants
pubmed: 32080334
doi: 10.1038/s41372-020-0623-3
pii: 10.1038/s41372-020-0623-3
doi:
Substances chimiques
MicroRNAs
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
952-961Références
Langham MR Jr, Kays DW, Ledbetter DJ, Frentzen B, Sanford LL, Richards DS. Congenital diaphragmatic hernia. Epidemiology and outcome. Clin Perinatol. 1996;23:671–88.
doi: 10.1016/S0095-5108(18)30201-X
Desai AA, Ostlie DJ, Juang D. Optimal timing of congenital diaphragmatic hernia repair in infants on extracorporeal membrane oxygenation. Semin Pediatr Surg. 2015;24:17–9.
doi: 10.1053/j.sempedsurg.2014.11.004
Hedrick HL. Management of prenatally diagnosed congenital diaphragmatic hernia. Semin Pediatr Surg. 2013;22:37–43.
doi: 10.1053/j.sempedsurg.2012.10.007
Jani JC, Nicolaides KH, Gratacos E, Valencia CM, Done E, Martinez JM, et al. Severe diaphragmatic hernia treated by fetal endoscopic tracheal occlusion. Ultrasound Obstet Gynecol. 2009;34:304–10.
doi: 10.1002/uog.6450
Shue EH, Miniati D, Lee H. Advances in prenatal diagnosis and treatment of congenital diaphragmatic hernia. Clin Perinatol. 2012;39:289–300.
doi: 10.1016/j.clp.2012.04.005
Chiu PP, Ijsselstijn H. Morbidity and long-term follow-up in CDH patients. Eur J Pediatr Surg. 2012;22:384–92.
doi: 10.1055/s-0032-1329412
Pennaforte T, Rakza T, Fily A, Mur S, Diouta L, Sfeir R. et al. [The long-term follow-up of patients with a congenita diaphragmatic hernia: review of the literature]. Arch Pediatr. 2013;20 (Suppl 1):S11–8.
doi: 10.1016/S0929-693X(13)71404-0
Spoel M, van den Hout L, Gischler SJ, Hop WC, Reiss I, Tibboel D, et al. Prospective longitudinal evaluation of lung function during the first year of life after repair of congenital diaphragmatic hernia. Pediatr Crit Care Med. 2012;13:e133–9.
doi: 10.1097/PCC.0b013e3182231872
Herrera-Rivero M, Zhang R, Heilmann-Heimbach S, Mueller A, Bagci S, Dresbach T, et al. Circulating microRNAs are associated with pulmonary hypertension and development of chronic lung disease in congenital diaphragmatic hernia. Sci Rep. 2018;8:10735.
doi: 10.1038/s41598-018-29153-8
Pelizzo G, Ballico M, Mimmi MC, Peiro JL, Marotta M, Federico C, et al. Metabolomic profile of amniotic fluid to evaluate lung maturity: the diaphragmatic hernia lamb model. Multidiscip Respir Med. 2014;9:54.
doi: 10.1186/2049-6958-9-54
Iorio MV, Croce CM. Causes and consequences of microRNA dysregulation. Cancer J. 2012;18:215–22.
doi: 10.1097/PPO.0b013e318250c001
Griffiths WJ, Koal T, Wang Y, Kohl M, Enot DP, Deigner HP. Targeted metabolomics for biomarker discovery. Angew Chem Int Ed Engl. 2010;49:5426–45.
doi: 10.1002/anie.200905579
Bienertova-Vasku J, Novak J, Vasku A. MicroRNAs in pulmonary arterial hypertension: pathogenesis, diagnosis and treatment. J Am Soc Hypertens. 2015;9:221–34.
doi: 10.1016/j.jash.2014.12.011
Pullamsetti SS, Doebele C, Fischer A, Savai R, Kojonazarov B, Dahal BK, et al. Inhibition of microRNA-17 improves lung and heart function in experimental pulmonary hypertension. Am J Respir Crit Care Med. 2012;185:409–19.
doi: 10.1164/rccm.201106-1093OC
Pereira-Terra P, Deprest JA, Kholdebarin R, Khoshgoo N, DeKoninck P, Munck AA, et al. Unique tracheal fluid MicroRNA signature predicts response to FETO in patients with congenital diaphragmatic hernia. Ann Surg. 2015;262:1130–40.
doi: 10.1097/SLA.0000000000001054
de Blic J, Midulla F, Barbato A, Clement A, Dab I, Eber E, et al. Bronchoalveolar lavage in children. ERS Task Force on bronchoalveolar lavage in children. European Respiratory Society. Eur Respir J. 2000;15:217–31.
doi: 10.1183/09031936.00.15121700
Piersigilli F, Lam TT, Vernocchi P, Quagliariello A, Putignani L, Aghai ZH, et al. Identification of new biomarkers of bronchopulmonary dysplasia using metabolomics. Metabolomics. 2019;15:20.
doi: 10.1007/s11306-019-1482-9
Team RC. A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2017. https://www.R-projectorg/ .
Culhane AC, Thioulouse J, Perriere G, Higgins DG. MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics. 2005;21:2789–90.
doi: 10.1093/bioinformatics/bti394
Mogilyansky E, Rigoutsos I. The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell Death Differ. 2013;20:1603–14.
doi: 10.1038/cdd.2013.125
Negi V, Chan SY. Discerning functional hierarchies of microRNAs in pulmonary hypertension. JCI Insight. 2017;2:e91327.
doi: 10.1172/jci.insight.91327
Kaartinen V, Voncken JW, Shuler C, Warburton D, Bu D, Heisterkamp N, et al. Abnormal lung development and cleft palate in mice lacking TGF-beta 3 indicates defects of epithelial-mesenchymal interaction. Nat Genet. 1995;11:415–21.
doi: 10.1038/ng1295-415
Quinn TM, Sylvester KG, Kitano Y, Kitano Y, Liechty KW, Jarrett BP, et al. TGF-beta2 is increased after fetal tracheal occlusion. J Pediatr Surg. 1999;34:701–4. discussion 704-5.
doi: 10.1016/S0022-3468(99)90359-7
Oue T, Shima H, Taira Y, Puri P. Administration of antenatal glucocorticoids upregulates peptide growth factor gene expression in nitrofen-induced congenital diaphragmatic hernia in rats. J Pediatr Surg. 2000;35:109–12.
doi: 10.1016/S0022-3468(00)80025-1
Chen H, Zhuang F, Liu YH, Xu B, Del Moral P, Deng W, et al. TGF-beta receptor II in epithelia versus mesenchyme plays distinct roles in the developing lung. Eur Respir J. 2008;32:285–95.
doi: 10.1183/09031936.00165407
McDevitt TM, Gonzales LW, Savani RC, Ballard PL. Role of endogenous TGF-beta in glucocorticoid-induced lung type II cell differentiation. Am J Physiol Lung Cell Mol Physiol. 2007;292:L249–57.
doi: 10.1152/ajplung.00088.2006
Rhodes CJ, Ghataorhe P, Wharton J, Rue-Albrecht KC, Hadinnapola C, Watson G, et al. Plasma metabolomics implicates modified transfer RNAs and altered bioenergetics in the outcomes of pulmonary arterial hypertension. Circulation. 2017;135:460–75.
doi: 10.1161/CIRCULATIONAHA.116.024602
Zhao Y, Peng J, Lu C, Hsin M, Mura M, Wu L, et al. Metabolomic heterogeneity of pulmonary arterial hypertension. PLoS ONE. 2014;9:e88727.
doi: 10.1371/journal.pone.0088727
Lewis GD, Ngo D, Hemnes AR, Farrell L, Domos C, Pappagianopoulos PP, et al. Metabolic profiling of right ventricular-pulmonary vascular function reveals circulating biomarkers of pulmonary hypertension. J Am Coll Cardiol. 2016;67:174–89.
doi: 10.1016/j.jacc.2015.10.072
Shao Z, Wang Z, Shrestha K, Thakur A, Borowski AG, Sweet W, et al. Pulmonary hypertension associated with advanced systolic heart failure: dysregulated arginine metabolism and importance of compensatory dimethylarginine dimethylaminohydrolase-1. J Am Coll Cardiol. 2012;59:1150–8.
doi: 10.1016/j.jacc.2011.12.022
Zhao YD, Chu L, Lin K, Granton E, Yin L, Peng J, et al. A biochemical approach to understand the pathogenesis of advanced pulmonary arterial hypertension: metabolomic profiles of arginine, sphingosine-1-phosphate, and heme of human lung. PLoS ONE. 2015;10:e0134958.
doi: 10.1371/journal.pone.0134958
Cheah FC, Darlow BA, Winterbourn CC. Association of hydrogen peroxide in exhaled breath condensates from infants with respiratory distress syndrome with the development of chronic lung disease. Arch Dis Child Fetal Neonatal Ed. 2006;91:F155.
doi: 10.1136/adc.2005.083089
Rosso MI, Roark S, Taylor E, Ping X, Ward JM, Roche K, et al. Exhaled breath condensate in intubated neonates–a window into the lung's glutathione status. Respir Res. 2014;115;1.
doi: 10.1186/1465-9921-15-1
Kononikhin AS, Starodubtseva NL, Chagovets VV, Ryndin AY, Burov AA, Popov IA, et al. Exhaled breath condensate analysis from intubated newborns by nano-HPLC coupled to high resolution MS. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1047:97–105.
doi: 10.1016/j.jchromb.2016.12.036
Pober BR. Overview of epidemiology, genetics, birth defects, and chromosome abnormalities associated with CDH. Am J Med Genet C Semin Med Genet. 2007;145C:158–71.
doi: 10.1002/ajmg.c.30126
Holder AM, Klaassens M, Tibboel D, de Klein A, lee b, Scott DA. Genetic factors in congenital diaphragmatic hernia. Am J Hum Genet. 2007;80:825–45.
doi: 10.1086/513442
Beck TF, Campeau PM, Jhangiani SN, Gambin T, Li AH, Abo-zahrah R, et al. FBN1 contributing to familial congenital diaphragmatic hernia. Am J Med Genet A. 2015;167A:831–6.
doi: 10.1002/ajmg.a.36960
Beck TF, Veenma D, Shchelochkov OA, Yu Z, Kim BJ, Zaveri HP, et al. Deficiency of FRAS1-related extracellular matrix 1 (FREM1) causes congenital diaphragmatic hernia in humans and mice. Hum Mol Genet. 2013;22:1026–38.
doi: 10.1093/hmg/dds507
Yu L, Wynn J, Ma L, Guha S, Mychaliska GB, Crombleholme TM, et al. De novo copy number variants are associated with congenital diaphragmatic hernia. J Med Genet. 2012;49:650–9.
doi: 10.1136/jmedgenet-2012-101135
Longoni M, High FA, Qi H, Joy MP, Hila R, Coletti CM, et al. Genome-wide enrichment of damaging de novo variants in patients with isolated and complex congenital diaphragmatic hernia. Hum Genet. 2017;136:679–91.
doi: 10.1007/s00439-017-1774-y
Qi H, Yu L, Zhou X, Wynn J, Zhao H, Guo Y, et al. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. PLoS Genet. 2018;14:e1007822.
doi: 10.1371/journal.pgen.1007822