Clinical plasma cells-related genes to aid therapy in colon cancer.
Clinical therapy
Colon cancer
Plasma cells
Prognosis prediction
Tumor immune microenvironment
Tumor mutation burden
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
01 Aug 2023
01 Aug 2023
Historique:
received:
16
01
2023
accepted:
23
06
2023
medline:
3
8
2023
pubmed:
2
8
2023
entrez:
1
8
2023
Statut:
epublish
Résumé
The tumor immune microenvironment (TIME) of colon cancer (CC) has been associated with extensive immune cell infiltration (IMI). Increasing evidence demonstrated that plasma cells (PC) have an extremely important role in advance of antitumor immunity. Nonetheless, there is a lack of comprehensive analyses of PC infiltration in clinical prognosis and immunotherapy in CC. This study systematically addressed the gene expression model and clinical information of CC patients. Clinical samples were obtained from the TCGA (The Cancer Genome Atlas) databases. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), GSVA, and the MAlignant Tumors using Expression data (ESTIMATE) algorithm were employed to research the potential mechanism and pathways. Immunophenoscore (IPS) was obtained to evaluate the immunotherapeutic significance of risk score. Half maximal inhibitory concentration (IC50) of chemotherapeutic medicine was predicted by employing the pRRophetic algorithm. A total of 513 CC samples (including 472 tumor samples and 41 normal samples) were collected from the TCGA-GDC database. Significant black modules and 313 candidate genes were considered PC-related genes by accessing WGCNA. Five pivotal genes were established through multiple analyses, which revealed excellent prognostic. The underlying correlation between risk score with tumor mutation burden (TMB) was further explored. In addition, the risk score was obviously correlated with various tumor immune microenvironment (TIME). Also, risk CC samples showed various signaling pathways activity and different pivotal sensitivities to administering chemotherapy. Finally, the biological roles of the CD177 gene were uncovered in CC.
Identifiants
pubmed: 37528394
doi: 10.1186/s12864-023-09481-4
pii: 10.1186/s12864-023-09481-4
pmc: PMC10391883
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
430Informations de copyright
© 2023. The Author(s).
Références
Immunol Rev. 2003 Aug;194:39-47
pubmed: 12846806
Breast Cancer Res. 2021 Oct 29;23(1):99
pubmed: 34715905
Gastroenterology. 2010 Jun;138(6):2101-2114.e5
pubmed: 20420949
Ann Transl Med. 2019 Sep;7(18):427
pubmed: 31700863
J Hematol Oncol. 2019 Jun 11;12(1):59
pubmed: 31186046
J Biol Chem. 2007 Aug 10;282(32):23603-12
pubmed: 17580308
Front Immunol. 2021 Dec 23;12:769685
pubmed: 35003085
Carcinogenesis. 2018 Feb 9;39(2):272-282
pubmed: 29228136
Nat Biotechnol. 2011 Nov 13;29(12):1120-7
pubmed: 22081019
Science. 1999 Mar 26;283(5410):2089-91
pubmed: 10092233
Dev Cell. 2004 Dec;7(6):871-83
pubmed: 15572129
Nat Rev Immunol. 2020 May;20(5):294-307
pubmed: 31988391
Am J Clin Exp Urol. 2014 Apr 15;2(1):27-44
pubmed: 25143959
Nat Rev Clin Oncol. 2018 Oct;15(10):599-616
pubmed: 30061739
Clin Cancer Res. 2018 Dec 15;24(24):6125-6135
pubmed: 30049748
J Clin Oncol. 2015 Jun 1;33(16):1787-96
pubmed: 25918287
Int J Med Sci. 2021 Jan 1;18(1):226-238
pubmed: 33390791
BMC Gastroenterol. 2013 Jul 30;13:122
pubmed: 23899160
Science. 2006 Sep 29;313(5795):1960-4
pubmed: 17008531
Genome Res. 2018 Nov;28(11):1747-1756
pubmed: 30341162
Nucleic Acids Res. 2023 Jan 6;51(D1):D587-D592
pubmed: 36300620
Ann Palliat Med. 2020 Nov;9(6):3985-3992
pubmed: 33302660
OMICS. 2012 May;16(5):284-7
pubmed: 22455463
Diagnostics (Basel). 2022 Aug 08;12(8):
pubmed: 36010268
Comput Biol Chem. 2021 Feb;90:107358
pubmed: 33243703
Evid Based Complement Alternat Med. 2022 Mar 3;2022:7825272
pubmed: 35280505
Stat Med. 2013 Dec 30;32(30):5381-97
pubmed: 24027076
Front Immunol. 2018 Mar 19;9:455
pubmed: 29616018
N Engl J Med. 2012 Jun 28;366(26):2443-54
pubmed: 22658127
Nat Methods. 2015 May;12(5):453-7
pubmed: 25822800
Nat Med. 2015 Aug;21(8):938-945
pubmed: 26193342
Methods Mol Biol. 2021;2239:269-303
pubmed: 33226625
Nat Cell Biol. 2002 Apr;4(4):323-7
pubmed: 11912492
N Engl J Med. 2004 Apr 29;350(18):1828-37
pubmed: 15115829
Oncoimmunology. 2012 Oct 1;1(7):1156-1158
pubmed: 23170262
J Cell Mol Med. 2019 May;23(5):3050-3057
pubmed: 30801950
Science. 2018 Oct 12;362(6411):
pubmed: 30309915
Thorac Surg Clin. 2020 May;30(2):215-220
pubmed: 32327180
Nat Rev Gastroenterol Hepatol. 2019 Jun;16(6):361-375
pubmed: 30886395
Biochem Biophys Res Commun. 2018 Jun 18;501(1):313-319
pubmed: 29738769
Int J Cancer. 2016 Sep 1;139(5):1129-39
pubmed: 27074317
Cell Rep. 2017 Jan 3;18(1):248-262
pubmed: 28052254
World J Urol. 2021 May;39(5):1331-1343
pubmed: 32915313
Protein Sci. 2019 Nov;28(11):1947-1951
pubmed: 31441146
Cancer Manag Res. 2021 Jul 08;13:5477-5489
pubmed: 34267555
Pathol Res Pract. 2015 Aug;211(8):557-69
pubmed: 26092594
Immunity. 2017 Feb 21;46(2):197-204
pubmed: 28228279
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
Nat Commun. 2021 Oct 1;12(1):5764
pubmed: 34599187
Evid Based Complement Alternat Med. 2022 Apr 30;2022:6316158
pubmed: 35535159
Front Immunol. 2021 Aug 27;12:709986
pubmed: 34512630
PeerJ. 2017 Feb 15;5:e3003
pubmed: 28229027
Lung Cancer. 2012 May;76(2):228-34
pubmed: 22070884
Curr Probl Surg. 2018 Sep;55(9):330-379
pubmed: 30526930
J Cancer Res Clin Oncol. 2023 Jan;149(1):173-189
pubmed: 36352147
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Anticancer Res. 2018 Jul;38(7):3929-3933
pubmed: 29970514
Immunity. 2016 Jun 21;44(6):1255-69
pubmed: 27332730
Genome Biol. 2014 Mar 03;15(3):R47
pubmed: 24580837
CA Cancer J Clin. 2018 Nov;68(6):394-424
pubmed: 30207593
Front Immunol. 2021 Aug 27;12:711433
pubmed: 34512634
Front Cell Dev Biol. 2022 Aug 23;10:971992
pubmed: 36081904
Nature. 2017 Sep 7;549(7670):101-105
pubmed: 28813417
Science. 2000 Aug 18;289(5482):1194-7
pubmed: 10947987
Oxid Med Cell Longev. 2021 Aug 14;2021:6290261
pubmed: 34497681
Int J Oncol. 2018 May;52(5):1674-1684
pubmed: 29512758
N Engl J Med. 2022 Jun 23;386(25):2363-2376
pubmed: 35660797
Mol Cancer. 2019 Mar 30;18(1):64
pubmed: 30927925
J Hematol Oncol. 2020 Aug 12;13(1):111
pubmed: 32787882
Surg Oncol Clin N Am. 2018 Apr;27(2):235-242
pubmed: 29496087