Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line.
LC-MS/MS
LC-SRM
PANC-1 cell line, KRAS, TP53
PRISM-SRM
deleterious mutation
single amino acid variant
Journal
Journal of proteome research
ISSN: 1535-3907
Titre abrégé: J Proteome Res
Pays: United States
ID NLM: 101128775
Informations de publication
Date de publication:
03 04 2020
03 04 2020
Historique:
pubmed:
15
2
2020
medline:
22
6
2021
entrez:
15
2
2020
Statut:
ppublish
Résumé
Identifying single amino acid variants (SAAVs) in cancer is critical for precision oncology. Several advanced algorithms are now available to identify SAAVs, but attempts to combine different algorithms and optimize them on large data sets to achieve a more comprehensive coverage of SAAVs have not been implemented. Herein, we report an expanded detection of SAAVs in the PANC-1 cell line using three different strategies, which results in the identification of 540 SAAVs in the mass spectrometry data. Among the set of 540 SAAVs, 79 are evaluated as deleterious SAAVs based on analysis using the novel AssVar software in which one of the driver mutations found in each protein of KRAS, TP53, and SLC37A4 is further validated using independent selected reaction monitoring (SRM) analysis. Our study represents the most comprehensive discovery of SAAVs to date and the first large-scale detection of deleterious SAAVs in the PANC-1 cell line. This work may serve as the basis for future research in pancreatic cancer and personal immunotherapy and treatment.
Identifiants
pubmed: 32058723
doi: 10.1021/acs.jproteome.9b00840
pmc: PMC7162681
mid: NIHMS1571827
doi:
Substances chimiques
Amino Acids
0
Antiporters
0
Monosaccharide Transport Proteins
0
Proteins
0
SLC37A4 protein, human
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1635-1646Subventions
Organisme : NCI NIH HHS
ID : R01 CA160254
Pays : United States
Organisme : NIH HHS
ID : S10 OD010700
Pays : United States
Organisme : NCI NIH HHS
ID : R21 CA223887
Pays : United States
Organisme : NLM NIH HHS
ID : T15 LM007359
Pays : United States
Organisme : NCI NIH HHS
ID : R21 CA223715
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM049500
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA022453
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM125991
Pays : United States
Organisme : NIEHS NIH HHS
ID : P30 ES020957
Pays : United States
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