From Causal Networks to Adverse Outcome Pathways: A Developmental Neurotoxicity Case Study.
adverse outcome pathway
causal network
neurotoxicity
systems toxicology
toxicological network
Journal
Frontiers in toxicology
ISSN: 2673-3080
Titre abrégé: Front Toxicol
Pays: Switzerland
ID NLM: 101777990
Informations de publication
Date de publication:
2022
2022
Historique:
received:
15
11
2021
accepted:
31
01
2022
entrez:
17
3
2022
pubmed:
18
3
2022
medline:
18
3
2022
Statut:
epublish
Résumé
The last decade has seen the adverse outcome pathways (AOP) framework become one of the most powerful tools in chemical risk assessment, but the development of new AOPs remains a slow and manually intensive process. Here, we present a faster approach for AOP generation, based on manually curated causal toxicological networks. As a case study, we took a recently published zebrafish developmental neurotoxicity network, which contains causally connected molecular events leading to neuropathologies, and developed two new adverse outcome pathways: Inhibition of Fyna (Src family tyrosine kinase A) leading to increased mortality via decreased eye size (AOP 399 on AOP-Wiki) and GSK3beta (Glycogen synthase kinase 3 beta) inactivation leading to increased mortality via defects in developing inner ear (AOP 410). The approach consists of an automatic separation of the toxicological network into candidate AOPs, filtering the AOPs according to available evidence and length as well as manual development of new AOPs and weight-of-evidence evaluation. The semiautomatic approach described here provides a new opportunity for fast and straightforward AOP development based on large network resources.
Identifiants
pubmed: 35295214
doi: 10.3389/ftox.2022.815754
pii: 815754
pmc: PMC8915909
doi:
Types de publication
Journal Article
Langues
eng
Pagination
815754Informations de copyright
Copyright © 2022 Ramšak, Modic, Li, vom Berg and Zupanic.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Trends Neurosci. 2001 Jan;24(1):32-9
pubmed: 11163885
Development. 2003 Jan;130(1):185-95
pubmed: 12441302
Vis Neurosci. 2012 Sep;29(4-5):219-28
pubmed: 23013828
PLoS One. 2014 Jul 01;9(7):e100947
pubmed: 24984063
PLoS One. 2008 Jan 16;3(1):e1434
pubmed: 18197245
J Comp Neurol. 1996 Jan 29;365(1):113-28
pubmed: 8821445
Mol Oncol. 2009 Jun;3(3):248-61
pubmed: 19393585
Risk Anal. 2020 Mar;40(3):512-523
pubmed: 31721239
Development. 2003 Sep;130(17):3989-4000
pubmed: 12874121
Toxicol Sci. 2007 Jan;95(1):5-12
pubmed: 16963515
Nucleic Acids Res. 2015 Jan;43(Database issue):D921-7
pubmed: 25313160
Cell. 1993 Oct 22;75(2):217-27
pubmed: 8402908
Wiley Interdiscip Rev Dev Biol. 2014 Sep-Oct;3(5):349-63
pubmed: 25124756
Dev Biol. 2017 Oct 1;430(1):237-248
pubmed: 28756106
Front Biol (Beijing). 2012 Jun;7(3):212-220
pubmed: 25688261
Sci Total Environ. 2017 Apr 15;584-585:751-775
pubmed: 28126277
Neuron. 1998 Feb;20(2):271-83
pubmed: 9491988
J Signal Transduct. 2011;2011:865819
pubmed: 21776389
Toxicol Sci. 2019 Apr 1;168(2):349-364
pubmed: 30715536
Methods Mol Biol. 2014;1130:233-243
pubmed: 24482177
Biochim Biophys Acta. 2007 Jul-Aug;1769(7-8):514-24
pubmed: 17628721
J Neurobiol. 2000 Aug;44(2):219-29
pubmed: 10934324
Biochem Biophys Res Commun. 2006 Aug 4;346(3):840-4
pubmed: 16782058
Chemosphere. 2015 Feb;120:764-77
pubmed: 25439131
Environ Pollut. 2021 Nov 15;289:117855
pubmed: 34340181
Environ Toxicol Chem. 2019 Sep;38(9):1850-1865
pubmed: 31127958
Environ Toxicol Chem. 2018 Jun;37(6):1723-1733
pubmed: 29488651
Nucleic Acids Res. 2021 Jan 8;49(D1):D1138-D1143
pubmed: 33068428
Rev Neurosci. 2011;22(1):63-73
pubmed: 21572576
Trends Genet. 2000 Jun;16(6):237-40
pubmed: 10827447
J Neurosci. 2006 Oct 11;26(41):10438-51
pubmed: 17035528
Curr Opin Genet Dev. 2000 Oct;10(5):508-14
pubmed: 10980428
Development. 2013 May;140(9):1936-45
pubmed: 23571216
ALTEX. 2021 May 17;38(4):580-594
pubmed: 34008034
Integr Environ Assess Manag. 2020 Jun;16(4):452-460
pubmed: 32125082
Dev Dyn. 2017 Jul;246(7):539-549
pubmed: 28440030
Environ Toxicol Chem. 2010 Mar;29(3):730-41
pubmed: 20821501
Nat Commun. 2020 Jul 17;11(1):3614
pubmed: 32681015
Toxicol Sci. 2015 Nov;148(1):14-25
pubmed: 26500288
Nat Genet. 1996 Apr;12(4):376-84
pubmed: 8630490
Environ Health. 2020 Feb 24;19(1):23
pubmed: 32093744
Environ Toxicol Chem. 2017 Jun;36(6):1429-1449
pubmed: 28198554
BMC Res Notes. 2014 Apr 29;7:273
pubmed: 24779365
Environ Sci Technol. 2020 Jul 21;54(14):8491-8499
pubmed: 32584560
J Neurobiol. 2002 Nov 5;53(2):157-71
pubmed: 12382273
R Soc Open Sci. 2018 Oct 31;5(10):181065
pubmed: 30473849
Database (Oxford). 2015 Apr 17;2015:bav030
pubmed: 25887162
Aquat Toxicol. 2019 Apr;209:1-12
pubmed: 30684730
Dev Biol. 2004 Jun 15;270(2):336-49
pubmed: 15183718
Environ Sci Technol. 2018 Jul 3;52(13):7524-7533
pubmed: 29863850
J Cell Physiol. 2018 Dec;233(12):9503-9515
pubmed: 29968912
Development. 1996 Dec;123:241-54
pubmed: 9007244
J Med Chem. 2007 Mar 22;50(6):1090-100
pubmed: 17315853
Ecotoxicol Environ Saf. 2004 Sep;59(1):1-9
pubmed: 15261716
Dev Dyn. 2004 Aug;230(4):781-6
pubmed: 15254912
Clin Genet. 2014 Nov;86(5):453-60
pubmed: 25174583
J Neurosci Methods. 2002 Aug 30;118(2):177-87
pubmed: 12204308
Crit Rev Toxicol. 2015 Jan;45(1):83-91
pubmed: 25605028
Toxicol Sci. 2014 Dec;142(2):312-20
pubmed: 25466378
Nat Med. 2004 Jan;10(1):55-63
pubmed: 14702635
Environ Health Perspect. 2019 Apr;127(4):47005
pubmed: 30994381
Nat Rev Cancer. 2008 Aug;8(8):632-45
pubmed: 18580951
Biotechniques. 2005 Jul;39(1):75-85
pubmed: 16060372
Aquat Toxicol. 2016 Mar;172:44-55
pubmed: 26765085
Dev Neurobiol. 2015 Sep;75(9):908-26
pubmed: 25528982
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503
pubmed: 31691815
Aquat Toxicol. 2015 Oct;167:200-8
pubmed: 26349946
EMBO Rep. 2008 Sep;9(9):865-71
pubmed: 18660749
Drug Discov Today. 2014 Feb;19(2):193-8
pubmed: 24444544
Cell. 1999 Oct 1;99(1):71-80
pubmed: 10520995
Methods Mol Biol. 2008;468:45-65
pubmed: 19099245
Biotechniques. 2002 Nov;33(5):1126-8, 1130, 1132 passim
pubmed: 12449394
Dev Biol. 2005 Sep 15;285(2):462-76
pubmed: 16112104
Nature. 2003 Nov 20;426(6964):247-54
pubmed: 14628042
Sci Rep. 2016 Feb 26;6:21978
pubmed: 26917256
FEBS J. 2018 Jan;285(1):72-86
pubmed: 29091353
J Comp Neurol. 2001 Sep 17;438(2):173-90
pubmed: 11536187
Environ Pollut. 2021 Jan 1;268(Pt B):115733
pubmed: 33011576
Toxicol Sci. 2016 Apr;150(2):510-20
pubmed: 26895641
Dev Dyn. 2002 Apr;223(4):427-58
pubmed: 11921334
Curr Top Dev Biol. 2010;90:343-86
pubmed: 20691855
Prog Neurobiol. 2001 Nov;65(4):391-426
pubmed: 11527574
Nucleic Acids Res. 2021 Jan 8;49(D1):D605-D612
pubmed: 33237311
Dev Dyn. 2011 Apr;240(4):828-38
pubmed: 21360792
Chem Res Toxicol. 2019 Jun 17;32(6):1212-1222
pubmed: 31074622
Neuron. 2002 Aug 29;35(5):907-20
pubmed: 12372285
Cont Lens Anterior Eye. 2016 Apr;39(2):133-40
pubmed: 26482903
Nat Genet. 1999 Sep;23(1):113-7
pubmed: 10471511
Toxicol Sci. 2014 Dec;142(2):321-30
pubmed: 25466379
Development. 2014 Jun;141(12):2473-82
pubmed: 24917502
Reprod Toxicol. 2015 Aug 15;56:52-5
pubmed: 25889759
Reprod Toxicol. 2021 Aug;103:159-170
pubmed: 34147625
Development. 2003 Mar;130(5):929-40
pubmed: 12538519
Toxicol Appl Pharmacol. 2018 Mar 15;343:71-83
pubmed: 29454060
Chem Res Toxicol. 2020 Oct 19;33(10):2550-2564
pubmed: 32638588
CSH Protoc. 2008 Mar 01;2008:pdb.prot4973
pubmed: 21356789
Zoology (Jena). 2008;111(1):62-75
pubmed: 18054216
Front Genet. 2021 Jun 15;12:652632
pubmed: 34211495
Bioinformatics. 2021 Oct 30;:
pubmed: 34718414
Exp Mol Med. 2018 Apr 13;50(4):1-13
pubmed: 29650976
Curr Environ Health Rep. 2016 Mar;3(1):53-63
pubmed: 26809562
Regul Toxicol Pharmacol. 2015 Aug;72(3):514-37
pubmed: 25863193
Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2415-20
pubmed: 18272492
Cold Spring Harb Protoc. 2016 Dec 1;2016(12):
pubmed: 27934691
Nature. 2009 Apr 2;458(7238):591-6
pubmed: 19234442
Zebrafish. 2013 Sep;10(3):264-74
pubmed: 23234507
Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):7286-90
pubmed: 8041782
Toxicology. 2013 Oct 4;312:158-65
pubmed: 23978457
Chem Res Toxicol. 2014 Dec 15;27(12):2100-12
pubmed: 25354311
Assay Drug Dev Technol. 2009 Dec;7(6):560-72
pubmed: 20105026
Dis Model Mech. 2018 Jun 15;11(6):
pubmed: 29914980
Differentiation. 2018 Jan - Feb;99:28-40
pubmed: 29289755
Environ Toxicol Chem. 2018 Jun;37(6):1734-1748
pubmed: 29492998
Environ Toxicol Chem. 2020 Apr;39(4):913-922
pubmed: 31965587
Zebrafish. 2016 Apr;13(2):79-86
pubmed: 26982161
Dev Biol. 2005 Jan 1;277(1):27-41
pubmed: 15572137
Regul Toxicol Pharmacol. 2020 Jul;114:104652
pubmed: 32251711