Lead DEAD/H box helicase biomarkers with the therapeutic potential identified by integrated bioinformatic approaches in lung cancer.
Bioinformatics
Biomarker
Clinical significance
DEAD/H box
Helicase
Lung cancer
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2021
2021
Historique:
received:
02
09
2020
revised:
02
12
2020
accepted:
08
12
2020
entrez:
11
1
2021
pubmed:
12
1
2021
medline:
12
1
2021
Statut:
epublish
Résumé
DEAD/H box helicases are implicated in lung cancer but have not been systematically investigated for their clinical significance and function. In this study, we aimed to evaluate the potential of DEAD/H box helicases as prognostic biomarkers and therapeutic targets in lung cancer by integrated bioinformatic analysis of multivariate large-scale databases. Survival and differential expression analysis of these helicases enabled us to identify four biomarkers with the most significant alterations. These were found to be the negative prognostic factors DDX11, DDX55 and DDX56, and positive prognostic factor DDX5. Pathway enrichment analysis indicates that MYC signalling is negatively associated with expression levels of the DDX5 gene while positively associated with that of DDX11, DDX55 and DDX56. High expression levels of the DDX5 gene is associated with low mutation levels of TP53 and MUC16, the two most frequently mutated genes in lung cancer. In contrast, high expression levels of DDX11, DDX55 and DDX56 genes are associated with high levels of TP53 and MUC16 mutation. The tumour-infiltrated CD8 + T and B cells positively correlate with levels of DDX5 gene expression, while negatively correlate with that of the other three DEAD box helicases, respectively. Moreover, the DDX5-associated miRNA profile is distinguished from the miRNA profiles of DDX11, DDX55 and DDX56, although each DDX has a different miRNA signature. The identification of these four DDX helicases as biomarkers will be valuable for prognostic prediction and targeted therapeutic development in lung cancer.
Identifiants
pubmed: 33425256
doi: 10.1016/j.csbj.2020.12.007
pii: S2001-0370(20)30532-8
pmc: PMC7779375
doi:
Types de publication
Journal Article
Langues
eng
Pagination
261-278Informations de copyright
© 2020 The Author(s).
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
Transl Lung Cancer Res. 2016 Feb;5(1):2-15
pubmed: 26958489
Clin Epigenetics. 2018 Nov 20;10(1):144
pubmed: 30454026
Nucleic Acids Res. 2006;34(15):4168-80
pubmed: 16936318
Mol Ther Nucleic Acids. 2017 Dec 15;9:145-154
pubmed: 29246293
Nature. 2008 Jul 3;454(7200):56-61
pubmed: 18548003
Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22
pubmed: 18981052
Curr Genomics. 2008 Sep;9(6):394-408
pubmed: 19506729
Cell Death Differ. 2012 Jun;19(6):1038-48
pubmed: 22193543
Oncotarget. 2018 Oct 30;9(85):35528-35540
pubmed: 30473748
Curr Opin Struct Biol. 2010 Jun;20(3):313-24
pubmed: 20456941
Cancer Res. 2015 Mar 1;75(5):783-91
pubmed: 25660948
Nucleic Acids Res. 2015 Jul 1;43(W1):W460-6
pubmed: 25977294
Mol Cell Proteomics. 2012 Feb;11(2):M111.011932
pubmed: 22086602
Biochim Biophys Acta Rev Cancer. 2017 Dec;1868(2):510-520
pubmed: 28965870
Am J Hum Genet. 2019 Aug 1;105(2):302-316
pubmed: 31256877
Genes Dev. 2017 Jul 1;31(13):1370-1381
pubmed: 28790157
Stem Cells Int. 2017;2017:8596135
pubmed: 29333169
Nat Commun. 2018 Mar 30;9:16196
pubmed: 29600803
Nature. 2012 Mar 28;483(7391):603-7
pubmed: 22460905
BMC Cancer. 2019 Aug 20;19(1):824
pubmed: 31429720
Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20453-20461
pubmed: 31548374
Biochem Soc Trans. 2018 Apr 17;46(2):329-341
pubmed: 29523774
Nucleic Acids Res. 2015 Jan;43(Database issue):D805-11
pubmed: 25355519
Cancer Sci. 2019 Oct;110(10):3132-3144
pubmed: 31390121
Cancer Res. 2017 Nov 1;77(21):e108-e110
pubmed: 29092952
Future Oncol. 2011 Feb;7(2):239-51
pubmed: 21345143
Mol Cell. 2007 Oct 26;28(2):253-63
pubmed: 17964264
Nature. 2009 Jul 23;460(7254):529-33
pubmed: 19626115
Plast Reconstr Surg. 2010 Aug;126(2):619-625
pubmed: 20679844
RNA Biol. 2013 Jan;10(1):121-32
pubmed: 23353573
Nat Struct Mol Biol. 2006 Nov;13(11):981-6
pubmed: 17072313
Cancer Sci. 2015 Oct;106(10):1303-12
pubmed: 26212035
Redox Biol. 2015 Dec;6:334-343
pubmed: 26335399
Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7
pubmed: 21071399
BMC Mol Biol. 2004 Aug 06;5:11
pubmed: 15298701
OMICS. 2012 May;16(5):284-7
pubmed: 22455463
Cell Death Dis. 2016 May 05;7:e2211
pubmed: 27148684
Wiley Interdiscip Rev RNA. 2011 Jan-Feb;2(1):135-52
pubmed: 21297876
Proc Natl Acad Sci U S A. 2018 Aug 14;115(33):8412-8417
pubmed: 30061412
Cancer Sci. 2005 Feb;96(2):111-5
pubmed: 15723655
Cancer Immunol Immunother. 2018 Jul;67(7):1031-1040
pubmed: 29541787
RNA. 1998 Oct;4(10):1216-29
pubmed: 9769096
Biochem Soc Trans. 2017 Dec 15;45(6):1313-1321
pubmed: 29150525
Stem Cell Res Ther. 2020 Jul 23;11(1):314
pubmed: 32703285
Cell. 2006 Apr 21;125(2):287-300
pubmed: 16630817
Clin Cancer Res. 2017 Jul 15;23(14):3906-3917
pubmed: 28196872
Annu Rev Genet. 2016 Nov 23;50:235-266
pubmed: 27648642
PLoS One. 2013 Dec 18;8(12):e82241
pubmed: 24367507
Nat Struct Mol Biol. 2008 Mar;15(3):268-79
pubmed: 18311151
Am J Cancer Res. 2016 Jan 15;6(2):387-402
pubmed: 27186411
Mol Cell Biol. 2011 May;31(9):1812-21
pubmed: 21343338
Curr Opin Genet Dev. 2016 Feb;36:83-91
pubmed: 27153352
Prog Nucleic Acid Res Mol Biol. 2002;72:307-31
pubmed: 12206455
Oncogene. 2013 Jul 18;32(29):3461-9
pubmed: 22986526
Cancer Res. 2006 Jul 1;66(13):6579-88
pubmed: 16818630
Mol Cell Biol. 1999 May;19(5):3540-50
pubmed: 10207077
Int J Mol Sci. 2018 Jul 09;19(7):
pubmed: 29987267
Nat Rev Cancer. 2014 Aug;14(8):535-46
pubmed: 25056707
Br J Cancer. 2016 Aug 9;115(4):497-504
pubmed: 27415011
Oncoimmunology. 2018 Aug 6;7(10):e1487914
pubmed: 30288353
Front Bioeng Biotechnol. 2020 Jun 26;8:588
pubmed: 32671031
Oncogene. 2019 Jul;38(28):5725-5738
pubmed: 31015574
J Gastroenterol. 2014 Nov;49(11):1441-52
pubmed: 24127074
Biochim Biophys Acta. 2016 May;1859(5):719-30
pubmed: 27012366
Nat Struct Mol Biol. 2008 Mar;15(3):259-67
pubmed: 18311153
Nucleic Acids Res. 2019 May 7;47(8):4349-4362
pubmed: 30828714
J Mol Biol. 2017 Oct 27;429(21):3121-3131
pubmed: 27940037
Mol Cancer. 2015 Apr 01;14:73
pubmed: 25889562
Int J Med Sci. 2019 Jun 10;16(7):981-989
pubmed: 31341411
Nucleic Acids Res. 2018 Sep 28;46(17):8689-8699
pubmed: 30102385
Nat Rev Cancer. 2006 Oct;6(10):813-23
pubmed: 16990858
Nucleic Acids Res. 2011 Sep 1;39(16):7161-78
pubmed: 21586581
Oncogene. 2013 Apr 25;32(17):2189-99
pubmed: 22710716
Virology. 2017 Jan;500:169-177
pubmed: 27821284
J Thorac Dis. 2011 Sep;3(3):183-8
pubmed: 22263086
Sci Data. 2018 Apr 17;5:180061
pubmed: 29664468
Nat Rev Mol Cell Biol. 2011 Jul 22;12(8):505-16
pubmed: 21779027
Cell Physiol Biochem. 2017;44(5):2017-2028
pubmed: 29237164
Ther Adv Respir Dis. 2016 Apr;10(2):113-29
pubmed: 26620497
Cell. 2000 Jan 7;100(1):57-70
pubmed: 10647931
Mol Cancer. 2012 Nov 01;11:82
pubmed: 23116066
J Gastrointest Surg. 2020 Mar 3;:
pubmed: 32128678
Nature. 2012 Sep 27;489(7417):519-25
pubmed: 22960745
Sci Rep. 2015 Mar 18;5:9247
pubmed: 25782664
Oncol Res. 2017 Jul 5;25(6):887-895
pubmed: 28244855
Cancer Sci. 2013 May;104(5):543-51
pubmed: 23398123
J Cancer. 2019 Jul 10;10(18):4208-4216
pubmed: 31413739
Nature. 1989 Jan 12;337(6203):121-2
pubmed: 2563148
Mol Oncol. 2010 Oct;4(5):397-403
pubmed: 20594926
CA Cancer J Clin. 2018 Nov;68(6):394-424
pubmed: 30207593
J Hematol Oncol. 2018 Sep 5;11(1):113
pubmed: 30185232
Nucleic Acids Res. 2000 Feb 15;28(4):917-24
pubmed: 10648783
RNA Biol. 2013 Jan;10(1):19-32
pubmed: 22995829
Nucleic Acids Res. 2006;34(15):4206-15
pubmed: 16935882
Clin Med (Lond). 2018 Apr 1;18(Suppl 2):s41-s46
pubmed: 29700092
Nat Rev Cancer. 2011 Aug 05;11(9):644-56
pubmed: 21822212
Sci Rep. 2016 Sep 22;6:33763
pubmed: 27653209
PLoS One. 2013;8(1):e54150
pubmed: 23349811
Transl Lung Cancer Res. 2016 Jun;5(3):288-300
pubmed: 27413711