Mass Spectrometry-Based Workflow for the Identification and Quantification of Alternative and Canonical Proteins in Pancreatic Cancer Cells.

Autor: Guillon C; Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS/UT3/INPT, 31320 Auzeville-Tolosane, France., Pichereaux C; Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, France.; Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (AIB), CNRS, 31326 Toulouse, France.; Infrastructure Nationale de Protéomique, ProFI, FR 2048, 31077 Toulouse, France., Lazar I; MCD, Centre de Biologie Intégrative (CBI), CNRS, UT3, Université de Toulouse, 31400 Toulouse, France., Chaoui K; Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, France.; Infrastructure Nationale de Protéomique, ProFI, FR 2048, 31077 Toulouse, France., Mouton-Barbosa E; Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, France.; Infrastructure Nationale de Protéomique, ProFI, FR 2048, 31077 Toulouse, France., Liauzun M; Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III-Paul Sabatier, ERL5294 CNRS, 31432 Toulouse, France.; Equipe Labellisée Ligue Contre Le Cancer, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France., Gourbeyre E; MCD, Centre de Biologie Intégrative (CBI), CNRS, UT3, Université de Toulouse, 31400 Toulouse, France., Altiner P; Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, France.; Infrastructure Nationale de Protéomique, ProFI, FR 2048, 31077 Toulouse, France., Bouyssié D; Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, France.; Infrastructure Nationale de Protéomique, ProFI, FR 2048, 31077 Toulouse, France., Stella A; Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, France.; Infrastructure Nationale de Protéomique, ProFI, FR 2048, 31077 Toulouse, France., Burlet-Schiltz O; Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université de Toulouse, 31077 Toulouse, France.; Infrastructure Nationale de Protéomique, ProFI, FR 2048, 31077 Toulouse, France., Plaza S; Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS/UT3/INPT, 31320 Auzeville-Tolosane, France., Martineau Y; Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III-Paul Sabatier, ERL5294 CNRS, 31432 Toulouse, France.; Equipe Labellisée Ligue Contre Le Cancer, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France., Fabre B; Laboratoire de Recherche en Sciences Végétales (LRSV), CNRS/UT3/INPT, 31320 Auzeville-Tolosane, France.
Jazyk: angličtina
Zdroj: Cells [Cells] 2024 Nov 28; Vol. 13 (23). Date of Electronic Publication: 2024 Nov 28.
DOI: 10.3390/cells13231966
Abstrakt: The identification of small proteins and proteins produced from unannotated open reading frames (called alternative proteins or AltProts) has changed our vision of the proteome and has attracted more and more attention from the scientific community. Despite several studies investigating particular AltProts in diseases and demonstrating their importance in such context, we are still missing data on their expression and functions in many pathologies. Among these, pancreatic ductal adenocarcinoma (PDAC) is a particularly relevant case to study alternative proteins. Indeed, late detection of this disease, notably due to the lack of reliable biomarkers of early-stage PDAC, and the fact that tumors rapidly develop resistance to most of the treatments used in the clinics warrant the exploration of new repertoires of molecules. In the present article, we aim to investigate the alternative proteome of pancreatic cancer cell lines as a first attempt to decipher the expression of AltProts in PDAC. Thanks to a combined data-dependent and data-independent acquisition mass spectrometry workflow, we were able to identify tryptic peptides matching 113 AltProts in a panel of 6 cell lines. In addition, we identified AltProts differentially expressed between pancreatic cancer cell lines and other cells (HeLa and HEK293T). Finally, mining the TCGA and Gtex databases showed that the corresponding transcripts encoding several AltProts we identified are differentially expressed between PDAC tumors and normal tissues and are correlated with the patient's survival.
Databáze: MEDLINE
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