Multiomic Investigations into Lung Health and Disease.
disease models
lung
machine learning
multiomics
pulmonary
Journal
Microorganisms
ISSN: 2076-2607
Titre abrégé: Microorganisms
Pays: Switzerland
ID NLM: 101625893
Informations de publication
Date de publication:
19 Aug 2023
19 Aug 2023
Historique:
received:
12
07
2023
revised:
08
08
2023
accepted:
13
08
2023
medline:
26
8
2023
pubmed:
26
8
2023
entrez:
26
8
2023
Statut:
epublish
Résumé
Diseases of the lung account for more than 5 million deaths worldwide and are a healthcare burden. Improving clinical outcomes, including mortality and quality of life, involves a holistic understanding of the disease, which can be provided by the integration of lung multi-omics data. An enhanced understanding of comprehensive multiomic datasets provides opportunities to leverage those datasets to inform the treatment and prevention of lung diseases by classifying severity, prognostication, and discovery of biomarkers. The main objective of this review is to summarize the use of multiomics investigations in lung disease, including multiomics integration and the use of machine learning computational methods. This review also discusses lung disease models, including animal models, organoids, and single-cell lines, to study multiomics in lung health and disease. We provide examples of lung diseases where multi-omics investigations have provided deeper insight into etiopathogenesis and have resulted in improved preventative and therapeutic interventions.
Identifiants
pubmed: 37630676
pii: microorganisms11082116
doi: 10.3390/microorganisms11082116
pmc: PMC10459661
pii:
doi:
Types de publication
Journal Article
Review
Langues
eng
Subventions
Organisme : NIEHS NIH HHS
ID : P30 ES030285
Pays : United States
Références
Cell Discov. 2022 Jun 17;8(1):57
pubmed: 35710786
ISME J. 2020 Nov;14(11):2748-2765
pubmed: 32719402
Nat Microbiol. 2018 Jul;3(7):814-823
pubmed: 29946163
Mol Cell. 2018 Sep 6;71(5):858-871.e8
pubmed: 30078726
Am J Physiol Lung Cell Mol Physiol. 2017 Nov 1;313(5):L733-L740
pubmed: 28798251
BMC Med Genomics. 2021 Aug 25;14(Suppl 1):112
pubmed: 34433487
Front Cell Infect Microbiol. 2022 Mar 10;12:805170
pubmed: 35360097
Front Med (Lausanne). 2022 Jan 11;8:821756
pubmed: 35087854
Cell. 2014 Aug 14;158(4):929-944
pubmed: 25109877
Brief Bioinform. 2016 Sep;17(5):891-901
pubmed: 26467821
Lancet Respir Med. 2020 Jun;8(6):585-596
pubmed: 32526187
Elife. 2020 Nov 09;9:
pubmed: 33164753
Stem Cells Transl Med. 2017 Feb;6(2):622-633
pubmed: 28191779
Cells. 2019 Dec 15;8(12):
pubmed: 31847480
Ann Otol Rhinol Laryngol. 2000 Mar;109(3):271-7
pubmed: 10737310
Eur Respir J. 2023 Apr 1;61(4):
pubmed: 36858443
ISME J. 2016 Jun;10(6):1483-98
pubmed: 26623545
Am J Physiol Lung Cell Mol Physiol. 2012 Mar 15;302(6):L485-97
pubmed: 22198907
Pediatr Res. 2022 Dec;92(6):1580-1589
pubmed: 35338351
Nat Commun. 2022 Jan 21;13(1):440
pubmed: 35064122
Cancer Inform. 2018 Nov 09;17:1176935118810215
pubmed: 30455569
PLoS One. 2016 Oct 25;11(10):e0165225
pubmed: 27780255
Curr Protoc Pharmacol. 2008 Mar;Chapter 5:Unit 5.46
pubmed: 22294226
Genome Biol. 2021 May 13;22(1):154
pubmed: 33985562
Proc Natl Acad Sci U S A. 2005 May 24;102(21):7653-8
pubmed: 15894607
Microbiome. 2019 Feb 13;7(1):23
pubmed: 30760325
Ann Am Thorac Soc. 2015 Feb;12(2):221-9
pubmed: 25474078
Dev Biol. 2023 Feb;494:26-34
pubmed: 36470449
Nat Immunol. 2015 Jan;16(1):17
pubmed: 25521680
Am J Respir Cell Mol Biol. 2021 Oct;65(4):430-441
pubmed: 34038697
Thorax. 2012 Mar;67(3):222-8
pubmed: 22106016
Nat Genet. 2023 Jul;55(7):1198-1209
pubmed: 37386249
Genome Biol. 2020 Nov 4;21(1):271
pubmed: 33148332
Cancer Med. 2023 Jan;12(1):584-596
pubmed: 35676822
Cell Rep. 2019 Apr 23;27(4):1190-1204.e3
pubmed: 31018133
J Cyst Fibros. 2004 Aug;3 Suppl 2:191-6
pubmed: 15463957
Science. 1966 Jul 1;153(3731):34-7
pubmed: 17730601
Front Med (Lausanne). 2017 Jul 28;4:118
pubmed: 28804709
Front Big Data. 2022 Jun 22;5:894632
pubmed: 35811829
Cell Regen. 2021 Apr 26;10(1):21
pubmed: 33900491
Nature. 2014 Jul 31;511(7511):543-50
pubmed: 25079552
PLoS One. 2013 Dec 17;8(12):e82432
pubmed: 24358183
Sci Rep. 2016 Aug 04;6:31023
pubmed: 27488092
Cancer Cell Int. 2021 Aug 26;21(1):454
pubmed: 34446006
Cell. 2011 Oct 28;147(3):525-38
pubmed: 22036562
EMBO J. 2019 Feb 15;38(4):
pubmed: 30643021
Sci Rep. 2021 Aug 23;11(1):17028
pubmed: 34426605
Am J Physiol Lung Cell Mol Physiol. 2019 Jan 1;316(1):L144-L156
pubmed: 30382766
BMC Med Inform Decis Mak. 2020 Feb 7;20(1):22
pubmed: 32033604
Soc Sci Med. 2020 Sep;260:113172
pubmed: 32702587
J Cyst Fibros. 2011 Jun;10 Suppl 2:S152-71
pubmed: 21658634
Brief Bioinform. 2022 Jan 17;23(1):
pubmed: 34864875
J Intern Med. 2021 May;289(5):604-613
pubmed: 32350962
RNA. 2008 Nov;14(11):2290-6
pubmed: 18812437
Nat Methods. 2014 Mar;11(3):333-7
pubmed: 24464287
J Am Heart Assoc. 2023 Apr 18;12(8):e029024
pubmed: 37026538
Stem Cells. 2023 Jan 30;41(1):1-10
pubmed: 36190736
Front Genet. 2020 Oct 15;11:570255
pubmed: 33193667
mSystems. 2020 Jun 23;5(3):
pubmed: 32576651
Biomarkers. 2009 Feb;14(1):55-60
pubmed: 19283525
Signal Transduct Target Ther. 2022 Sep 7;7(1):312
pubmed: 36071039
Cell Rep. 2018 Apr 3;23(1):194-212.e6
pubmed: 29617660
Pharmacol Ther. 2018 Nov;191:178-189
pubmed: 29953899
J Pediatr. 2019 Jan;204:126-133.e2
pubmed: 30297287
Curr Opin Pediatr. 2015 Jun;27(3):348-55
pubmed: 25888147
Genet Epidemiol. 2021 Feb;45(1):99-114
pubmed: 32924180
Eur Respir J. 2016 Dec;48(6):1612-1621
pubmed: 27836957
J Virol. 2021 Sep 27;95(20):e0101021
pubmed: 34319784
Am J Physiol Lung Cell Mol Physiol. 2017 Dec 1;313(6):L991-L1005
pubmed: 28818871
Cell Stem Cell. 2017 Jun 1;20(6):844-857.e6
pubmed: 28366587
Genes (Basel). 2019 Jan 28;10(2):
pubmed: 30696086
Circ Res. 2022 Apr 29;130(9):1423-1444
pubmed: 35482840
Rapid Commun Mass Spectrom. 2013 Oct 30;27(20):2263-71
pubmed: 24019192
Lancet Diabetes Endocrinol. 2018 May;6(5):416-426
pubmed: 29433995
Science. 2021 Feb 5;371(6529):552
pubmed: 33542117
Genes (Basel). 2017 Jan 14;8(1):
pubmed: 28098823
Kidney Dis (Basel). 2019 Feb;5(1):11-17
pubmed: 30815459
Healthcare (Basel). 2020 Jul 31;8(3):
pubmed: 32751894
J Exp Med. 2021 Aug 2;218(8):
pubmed: 34128959
Nature. 2015 Feb 19;518(7539):317-30
pubmed: 25693563
iScience. 2022 Jan 22;25(2):103798
pubmed: 35169688
Am J Respir Crit Care Med. 2019 Sep 15;200(6):751-759
pubmed: 30995069
Microbiol Res. 2022 Dec;265:127205
pubmed: 36202007
Eur Respir J. 2022 Jul 1;:
pubmed: 35777774
Comput Struct Biotechnol J. 2021 Jun 22;19:3735-3746
pubmed: 34285775
Front Pediatr. 2021 Jun 08;9:694034
pubmed: 34169050
Bioengineered. 2021 Dec;12(1):3978-3992
pubmed: 34288818
Mol Immunol. 2021 Jul;135:147-164
pubmed: 33895579
J Clin Microbiol. 2015 Jul;53(7):2006-7
pubmed: 25972422
Cell. 2022 Dec 8;185(25):4841-4860.e25
pubmed: 36493756
Front Microbiomes. 2023;2:
pubmed: 37293566
Lancet Respir Med. 2018 Nov;6(11):846-854
pubmed: 30001996
Bioinformatics. 2006 Jul 15;22(14):e184-90
pubmed: 16873470
Mol Oncol. 2013 Apr;7(2):165-77
pubmed: 23481268
Am J Respir Crit Care Med. 2016 Mar 1;193(5):504-15
pubmed: 26492486
Nucleic Acids Res. 2020 Jan 8;48(D1):D127-D131
pubmed: 31504780
Front Cell Infect Microbiol. 2020 Apr 28;10:174
pubmed: 32411616
J Pediatr. 2015 Jul;167(1):138-47.e1-3
pubmed: 25818499
Front Mol Biosci. 2022 Nov 14;9:967205
pubmed: 36452456
Inf Fusion. 2019 Oct;50:71-91
pubmed: 30467459
Cells. 2019 Jul 30;8(8):
pubmed: 31366153
J Proteome Res. 2015 Jun 5;14(6):2707-13
pubmed: 25873244
Eur Respir J. 2018 Jul 4;52(1):
pubmed: 29794131
Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6822-6827
pubmed: 29891677
BMC Med Inform Decis Mak. 2020 Sep 15;20(1):225
pubmed: 32933515
Comput Struct Biotechnol J. 2023 Jan 31;21:1372-1382
pubmed: 36817954
Signal Transduct Target Ther. 2022 Apr 23;7(1):135
pubmed: 35461318
PLoS One. 2021 Oct 6;16(10):e0257838
pubmed: 34613995
J Proteome Res. 2015 Feb 6;14(2):1203-19
pubmed: 25590149
Am J Respir Cell Mol Biol. 2015 Jun;52(6):683-94
pubmed: 25317669
Hum Mol Genet. 2023 Jul 20;32(15):2441-2454
pubmed: 37133451
Comput Biol Med. 2023 Mar;155:106639
pubmed: 36805214
Emerg Microbes Infect. 2018 May 9;7(1):84
pubmed: 29743570
Nucleic Acids Res. 2020 Jan 8;48(D1):D882-D889
pubmed: 31713622
J Korean Med Sci. 2019 Apr 29;34(16):e128
pubmed: 31020816
Nat Protoc. 2019 Feb;14(2):518-540
pubmed: 30664680
J Biomed Semantics. 2019 Oct 24;10(1):18
pubmed: 31651362
Front Oncol. 2022 Aug 30;12:917667
pubmed: 36110941
Lab Invest. 2004 Jun;84(6):736-52
pubmed: 15077120
Clin Cancer Res. 2019 Jun 15;25(12):3689-3701
pubmed: 30846479
Comput Struct Biotechnol J. 2020 Apr 25;18:1056-1073
pubmed: 32419906
Clin Rev Allergy Immunol. 2008 Apr;34(2):146-62
pubmed: 17960347
Biotechnol Adv. 2021 Jul-Aug;49:107739
pubmed: 33794304
Am J Respir Crit Care Med. 2014 Jul 15;190(2):175-84
pubmed: 24927234
Sci Rep. 2017 Aug 22;7(1):9109
pubmed: 28831060
Front Pharmacol. 2020 Sep 03;11:569821
pubmed: 33013411
Genome. 2021 Apr;64(4):416-425
pubmed: 33091314
Nature. 2012 Sep 27;489(7417):519-25
pubmed: 22960745
Am J Physiol Lung Cell Mol Physiol. 2018 Nov 1;315(5):L810-L815
pubmed: 30113227
Dev Cell. 2022 Jan 10;57(1):112-145.e2
pubmed: 34936882
Bioinformatics. 2019 Nov 1;35(21):4336-4343
pubmed: 30957844
Genet Med. 2021 Nov;23(11):2076-2086
pubmed: 34183789
Front Cell Dev Biol. 2021 Feb 18;9:641840
pubmed: 33681226
Am J Respir Crit Care Med. 2003 Oct 15;168(8):918-51
pubmed: 14555458
Front Bioeng Biotechnol. 2020 Apr 09;8:322
pubmed: 32328489
JCI Insight. 2018 Mar 8;3(5):
pubmed: 29515035
Nat Protoc. 2020 Apr;15(4):1484-1506
pubmed: 32103204
Chest. 2015 Aug;148(2):507-515
pubmed: 25611918
Am J Respir Crit Care Med. 2011 Sep 15;184(6):647-55
pubmed: 21680948
Nat Microbiol. 2022 Sep;7(9):1361-1375
pubmed: 35995842
Front Bioeng Biotechnol. 2022 Dec 08;10:1066869
pubmed: 36568297
Nat Commun. 2023 May 29;14(1):3086
pubmed: 37248224
Nat Biotechnol. 2014 Dec;32(12):1202-12
pubmed: 24880487
Nucleic Acids Res. 2015 Jan;43(Database issue):D153-9
pubmed: 25416803
Mol Syst Biol. 2018 Jun 20;14(6):e8124
pubmed: 29925568
Ultrasound Obstet Gynecol. 2019 Jul;54(1):110-118
pubmed: 30381856
Pediatr Res. 2023 Jan;93(2):308-315
pubmed: 35804156
Science. 2006 Sep 29;313(5795):1929-35
pubmed: 17008526
FEBS J. 2020 Sep;287(17):3633-3650
pubmed: 32446285
Curr Protoc Stem Cell Biol. 2018 May;45(1):e51
pubmed: 30040246