Abstract
In the recent past, next-generation sequencing (NGS) approaches have heralded the omics era. With NGS data burgeoning, there arose a need to disseminate the omic data better. Proteogenomics has been vividly used for characterising the functions of candidate genes and is applied in ascertaining various diseased phenotypes, including cancers. However, not much is known about the role and application of proteogenomics, especially Prostate Cancer (PCa). In this review, we outline the need for proteogenomic approaches, their applications and their role in PCa.
Keywords: Prostate Cancer, Next-Generation sequencing, Genomics, Proteomics, Proteogenomics, Transcriptomics, Phosphoproteomics.
Graphical Abstract
[http://dx.doi.org/10.1074/mcp.MR117.000024] [PMID: 28456751]
[http://dx.doi.org/10.1038/nature01510] [PMID: 12634792]
[http://dx.doi.org/10.1080/14789450.2017.1352474] [PMID: 28693350]
[http://dx.doi.org/10.1002/mas.21483] [PMID: 26670565]
[http://dx.doi.org/10.1146/annurev-anchem-071015-041722] [PMID: 27049631]
[http://dx.doi.org/10.1038/nature13302] [PMID: 24870542]
[http://dx.doi.org/10.1038/s41571-018-0135-7] [PMID: 30487530]
[http://dx.doi.org/10.1186/1559-0275-11-22] [PMID: 24994965]
[http://dx.doi.org/10.3389/fimmu.2019.00987] [PMID: 31134072]
[http://dx.doi.org/10.1111/j.1399-3046.2008.01018.x] [PMID: 18764911]
[http://dx.doi.org/10.1371/journal.pcbi.1000176] [PMID: 19043537]
[http://dx.doi.org/10.1146/annurev-biochem-070611-102400] [PMID: 24606146]
[http://dx.doi.org/10.1101/gr.109280.110] [PMID: 21367939]
[http://dx.doi.org/10.1038/nchembio.1120] [PMID: 23160002]
[http://dx.doi.org/10.1074/mcp.M110.006536] [PMID: 21389108]
[http://dx.doi.org/10.1038/nature13438] [PMID: 25043054]
[http://dx.doi.org/10.1038/msb4100142] [PMID: 17437027]
[http://dx.doi.org/10.3389/fgene.2019.00496] [PMID: 31178900]
[http://dx.doi.org/10.1158/2159-8290.CD-11-0209] [PMID: 22096659]
[http://dx.doi.org/10.3389/fgene.2015.00255] [PMID: 26284111]
[http://dx.doi.org/10.1007/s11356-014-3898-0] [PMID: 25475614]
[http://dx.doi.org/10.1073/pnas.0905240106]
[http://dx.doi.org/10.1080/14789450.2019.1609944] [PMID: 31002542]
[http://dx.doi.org/10.1093/bib/bbz061] [PMID: 31197323]
[http://dx.doi.org/10.3390/ijms17101744] [PMID: 27775567]
[http://dx.doi.org/10.1007/s00439-011-1028-3] [PMID: 21706342]
[PMID: 17934568]
[http://dx.doi.org/10.2147/CMAR.S186258] [PMID: 30588097]
[http://dx.doi.org/10.3802/jgo.2017.28.e7] [PMID: 27670261]
[http://dx.doi.org/10.1016/j.cca.2019.06.006] [PMID: 31176645]
[http://dx.doi.org/10.5114/wo.2014.47136] [PMID: 25691825]
[http://dx.doi.org/10.1021/acs.jproteome.5b00861] [PMID: 26743026]
[http://dx.doi.org/10.1038/nature14001] [PMID: 25428506]
[http://dx.doi.org/10.1021/pr200766z] [PMID: 22103967]
[http://dx.doi.org/10.1021/pr500812t] [PMID: 25301683]
[http://dx.doi.org/10.1007/978-3-319-42316-6_1]
[http://dx.doi.org/10.1074/mcp.M113.031260] [PMID: 24142994]
[http://dx.doi.org/10.1021/pr400208w] [PMID: 23614390]
[http://dx.doi.org/10.1002/pmic.201400265] [PMID: 25297486]
[http://dx.doi.org/10.1021/acs.jproteome.5b00490] [PMID: 26147802]
[http://dx.doi.org/10.1093/bioinformatics/btt543] [PMID: 24058055]
[http://dx.doi.org/10.1093/bioinformatics/btp324] [PMID: 19451168]
[http://dx.doi.org/10.1038/nmeth.1923] [PMID: 22388286]
[http://dx.doi.org/10.1002/0471250953.bi1107s32]
[http://dx.doi.org/10.1093/nar/gku1283] [PMID: 25510491]
[http://dx.doi.org/10.1093/bioinformatics/btv236]
[http://dx.doi.org/10.1038/nmeth.2517] [PMID: 23807191]
[http://dx.doi.org/10.1093/nar/gkt439] [PMID: 23703215]
[http://dx.doi.org/10.1093/bioinformatics/btn297]
[http://dx.doi.org/10.1038/nprot.2016.136] [PMID: 27809316]
[http://dx.doi.org/10.1038/msb.2012.68] [PMID: 23340843]
[http://dx.doi.org/10.1038/nmeth.3959] [PMID: 27575624]
[http://dx.doi.org/10.1038/nbt.3109]
[http://dx.doi.org/10.1021/acs.jproteome.5b00029] [PMID: 25760677]
[http://dx.doi.org/10.3390/proteomes5040028] [PMID: 29068423]
[http://dx.doi.org/10.1021/acs.jproteome.5b01091] [PMID: 26860878]
[http://dx.doi.org/10.1074/mcp.TIR119.001673] [PMID: 31308250]
[http://dx.doi.org/10.1016/j.cell.2019.03.030] [PMID: 31031003]
[http://dx.doi.org/10.1038/nature18003] [PMID: 27251275]
[http://dx.doi.org/10.1016/j.cell.2016.05.069] [PMID: 27372738]
[http://dx.doi.org/10.1038/s41467-019-11452-x] [PMID: 31395880]
[http://dx.doi.org/10.1158/2326-6066.CIR-19-0541] [PMID: 32047025]
[PMID: 17683188]
[http://dx.doi.org/10.1016/S1470-2045(14)70211-6] [PMID: 25281467]
[http://dx.doi.org/10.1038/onc.2013.206] [PMID: 23752182]
[http://dx.doi.org/10.1007/s11912-018-0707-9] [PMID: 29858674]
[http://dx.doi.org/10.1073/pnas.1411446111]
[http://dx.doi.org/10.1016/j.cell.2015.10.025] [PMID: 26544944]
[http://dx.doi.org/10.1016/j.eururo.2011.06.035] [PMID: 21719191]
[http://dx.doi.org/10.1038/nature09744] [PMID: 21307934]
[http://dx.doi.org/10.1038/ng.2279] [PMID: 22610119]
[http://dx.doi.org/10.12688/f1000research.14499.1] [PMID: 30135717]
[http://dx.doi.org/10.1038/nature11125] [PMID: 22722839]
[http://dx.doi.org/10.18632/oncotarget.2406] [PMID: 25277175]
[http://dx.doi.org/10.1126/science.1117679]
[http://dx.doi.org/10.1038/nature20788] [PMID: 28068672]
[http://dx.doi.org/10.1038/s41467-019-13084-7] [PMID: 31748536]
[http://dx.doi.org/10.1016/j.ebiom.2018.05.002] [PMID: 29759485]
[http://dx.doi.org/10.1158/1078-0432.CCR-18-0729] [PMID: 30274982]
[http://dx.doi.org/10.1038/s41588-018-0078-z] [PMID: 29610475]
[http://dx.doi.org/10.1016/S0092-8674(00)81683-9] [PMID: 10647931]
[http://dx.doi.org/10.1038/s41467-018-03573-6] [PMID: 29563510]
[http://dx.doi.org/10.1016/j.cell.2016.07.007] [PMID: 27499020]
[http://dx.doi.org/10.1073/pnas.1319948110]
[http://dx.doi.org/10.1016/j.ccell.2019.02.005] [PMID: 30889379]
[http://dx.doi.org/10.21873/cgp.20086] [PMID: 29976633]
[http://dx.doi.org/10.18632/oncoscience.453] [PMID: 30234142]
[http://dx.doi.org/10.5772/61789]
[http://dx.doi.org/10.1002/jcb.27156] [PMID: 29923622]
[http://dx.doi.org/10.1002/prca.200900220] [PMID: 21137047]
[http://dx.doi.org/10.1038/nrclinonc.2013.30] [PMID: 23459624]
[http://dx.doi.org/10.1186/1755-8794-7-S1-S3] [PMID: 25080090]
[http://dx.doi.org/10.1080/14737159.2019.1675515] [PMID: 31577907]