Identification of Alternative Splicing in Proteomes of Human Melanoma Cell Lines without RNA Sequencing Data.
alternative splicing
cell lines
melanoma
proteogenomics
proteomics
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
27 Jan 2023
27 Jan 2023
Historique:
received:
30
11
2022
revised:
06
01
2023
accepted:
13
01
2023
entrez:
11
2
2023
pubmed:
12
2
2023
medline:
15
2
2023
Statut:
epublish
Résumé
Alternative splicing is one of the main regulation pathways in living cells beyond simple changes in the level of protein expression. Most of the approaches proposed in proteomics for the identification of specific splicing isoforms require a preliminary deep transcriptomic analysis of the sample under study, which is not always available, especially in the case of the re-analysis of previously acquired data. Herein, we developed new algorithms for the identification and validation of protein splice isoforms in proteomic data in the absence of RNA sequencing of the samples under study. The bioinformatic approaches were tested on the results of proteome analysis of human melanoma cell lines, obtained earlier by high-resolution liquid chromatography and mass spectrometry (LC-MS). A search for alternative splicing events for each of the cell lines studied was performed against the database generated from all known transcripts (RefSeq) and the one composed of peptide sequences, which included all biologically possible combinations of exons. The identifications were filtered using the prediction of both retention times and relative intensities of fragment ions in the corresponding mass spectra. The fragmentation mass spectra corresponding to the discovered alternative splicing events were additionally examined for artifacts. Selected splicing events were further validated at the mRNA level by quantitative PCR.
Identifiants
pubmed: 36768787
pii: ijms24032466
doi: 10.3390/ijms24032466
pmc: PMC9916885
pii:
doi:
Substances chimiques
Proteome
0
RNA
63231-63-0
Protein Isoforms
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Russian Foundation for Basic Research
ID : 21-34-70020
Références
Nat Methods. 2017 May;14(5):513-520
pubmed: 28394336
Bioinformatics. 2020 Mar 1;36(6):1855-1863
pubmed: 31626284
Mol Cell Proteomics. 2018 Mar;17(3):422-430
pubmed: 29222161
Biomolecules. 2022 Jul 17;12(7):
pubmed: 35883549
BMC Bioinformatics. 2012 Jun 18;13:134
pubmed: 22708584
Sci Immunol. 2018 Oct 12;3(28):
pubmed: 30315122
Cell Rep. 2019 Dec 10;29(11):3751-3765.e5
pubmed: 31825849
Genome Biol. 2008;9(11):R162
pubmed: 19017398
Nat Methods. 2007 Mar;4(3):207-14
pubmed: 17327847
Nat Genet. 2008 Dec;40(12):1413-5
pubmed: 18978789
J Immunother. 2021 Jul-Aug 01;44(6):214-223
pubmed: 34028390
Cancer Control. 2022 Jan-Dec;29:10732748211051554
pubmed: 34986671
Cancer Discov. 2013 Oct;3(10):1122-1129
pubmed: 23861464
Proc Natl Acad Sci U S A. 1994 Jul 5;91(14):6458-62
pubmed: 8022805
Nat Rev Mol Cell Biol. 2022 Oct 13;:
pubmed: 36229538
PLoS Comput Biol. 2020 Oct 5;16(10):e1008287
pubmed: 33017396
PLoS Comput Biol. 2015 Jun 10;11(6):e1004325
pubmed: 26061177
Mech Ageing Dev. 2021 Jul;197:111510
pubmed: 34019916
BMC Genomics. 2021 Nov 25;22(1):853
pubmed: 34819032
Nat Rev Clin Oncol. 2020 Aug;17(8):457-474
pubmed: 32303702
Bioinformatics. 2012 Apr 15;28(8):1166-7
pubmed: 22368248
Trends Biochem Sci. 2017 Jun;42(6):407-408
pubmed: 28483376
Nat Protoc. 2016 May;11(5):993-1006
pubmed: 27123950
Melanoma Res. 2008 Oct;18(5):303-13
pubmed: 18781128
Mol Cell. 2012 Jun 29;46(6):871-83
pubmed: 22749400
Nat Rev Genet. 2019 Jul;20(7):404-416
pubmed: 30918367
Oncogene. 2016 Sep 22;35(38):5056-5069
pubmed: 27041584
Blood. 2009 Jul 16;114(3):535-46
pubmed: 19451549
Nature. 2008 Nov 27;456(7221):470-6
pubmed: 18978772
Analyst. 2016 Aug 2;141(16):4816-4832
pubmed: 27419248
Methods Mol Biol. 2016;1402:229-241
pubmed: 26721495
Front Mol Biosci. 2018 Sep 07;5:80
pubmed: 30246013
Int J Mol Sci. 2021 Jul 02;22(13):
pubmed: 34281234
Nature. 2010 Jan 28;463(7280):457-63
pubmed: 20110989
Sci Rep. 2017 Mar 08;7:44064
pubmed: 28272432
Nat Rev Genet. 2022 Nov;23(11):697-710
pubmed: 35821097
Genome Biol. 2004;5(10):R74
pubmed: 15461793
Nat Methods. 2021 Nov;18(11):1363-1369
pubmed: 34711972
Philos Trans R Soc Lond B Biol Sci. 2017 Feb 5;372(1713):
pubmed: 27994117
J Proteome Res. 2018 May 4;17(5):1801-1811
pubmed: 29619825
Mol Cancer. 2017 Nov 29;16(1):175
pubmed: 29187213
Oncol Lett. 2019 Aug;18(2):1081-1088
pubmed: 31423168
Pflugers Arch. 2018 Jul;470(7):995-1016
pubmed: 29536164
Genes (Basel). 2022 Feb 24;13(3):
pubmed: 35327956
Sci Immunol. 2019 Aug 16;4(38):
pubmed: 31420320
Cell Rep. 2015 Oct 6;13(1):43-51
pubmed: 26387950
Nat Methods. 2015 Jul;12(7):605-8
pubmed: 26125591
Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773
pubmed: 30357393
Mol Biol Cell. 2001 Nov;12(11):3451-64
pubmed: 11694580
Sci Immunol. 2019 Aug 16;4(38):
pubmed: 31420321
Trends Biochem Sci. 2017 Feb;42(2):98-110
pubmed: 27712956
Genes (Basel). 2022 Oct 08;13(10):
pubmed: 36292705
J Cell Biol. 2016 Jan 4;212(1):13-27
pubmed: 26728853
Front Oncol. 2020 Oct 15;10:568469
pubmed: 33178596
Cell Rep. 2017 Aug 1;20(5):1229-1241
pubmed: 28768205
Bioinformatics. 2013 Dec 15;29(24):3199-203
pubmed: 24078703
Nat Rev Genet. 2016 Jan;17(1):19-32
pubmed: 26593421
Med Sci Monit. 2020 Mar 21;26:e921133
pubmed: 32199022
Vestn Ross Akad Med Nauk. 2005;(7):37-40
pubmed: 16107020
PLoS Comput Biol. 2022 May 13;18(5):e1010065
pubmed: 35560144