Peptide absent sequences emerging in human cancers.

Autor: Tsiatsianis GC; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA; National Technical University of Athens, School of Electrical and Computer Engineering, Athens, Greece., Chan CSY; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Mouratidis I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Chantzi N; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA., Tsiatsiani AM; National Technical University of Athens, School of Electrical and Computer Engineering, Athens, Greece; School of Medicine, National and Kapodistrian University of Athens, Athens, Greece., Yee NS; Division of Hematology-Oncology, Department of Medicine, Penn State Health Milton S. Hershey Medical Center, Next-Generation Therapies Program, Penn State Cancer Institute, Hershey, PA, USA., Zaravinos A; Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 1516, Cyprus; Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus., Kantere V; School of Electrical Engineering and Computer Science, Faculty of Engineering, University of Ottawa, Canada., Georgakopoulos-Soares I; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA. Electronic address: izg5139@psu.edu.
Jazyk: angličtina
Zdroj: European journal of cancer (Oxford, England : 1990) [Eur J Cancer] 2024 Jan; Vol. 196, pp. 113421. Date of Electronic Publication: 2023 Nov 07.
DOI: 10.1016/j.ejca.2023.113421
Abstrakt: Early diagnosis of cancer can significantly improve survival of cancer patients; however sensitive and highly specific biomarkers for cancer detection are currently lacking for most cancer types. Nullpeptides are short peptides that are absent from the human proteome. Here, we examined the emergence of nullpeptides during cancer development. We analyzed 3,600,964 somatic mutations across 10,064 whole exome sequencing tumor samples spanning 32 cancer types. We analyze RNA-seq data from primary tumor samples to identify the subset of nullpeptides that emerge in highly expresed genes. We show that nullpeptides, and particularly the subset that is highly recurrent across cancer patients, can be identified in tumor biopsy samples. We find that cancer genes show an excess of nullpeptides and detect nullpeptide hotspots in specific loci of oncogenes and tumor suppressors. We also observe that recurrent nullpeptides are more likely to be found in neoantigens, which have been shown to be effective targets for immunotherapy, suggesting that they can be used to prioritize candidates. Our findings provide evidence for the utility of nullpeptides as cancer detection and therapeutic biomarkers.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2023 Elsevier Ltd. All rights reserved.)
Databáze: MEDLINE
Externí odkaz: