Biomarkers From Discovery to Clinical Application: In Silico Pre-Clinical Validation Approach in the Face of Lung Cancer

dc.contributor.authorKori, Medi
dc.contributor.authorGov, Esra
dc.contributor.authorArga, Kazim Yalcin
dc.contributor.authorSinha, Raghu
dc.date.accessioned2025-01-06T17:44:05Z
dc.date.available2025-01-06T17:44:05Z
dc.date.issued2024
dc.description.abstractBackground: Clinical biomarkers, allow better classification of patients according to their disease risk, prognosis, and/or response to treatment. Although affordable omics-based approaches have paved the way for quicker identification of putative biomarkers, validation of biomarkers is necessary for translation of discoveries into clinical application.Objective: Accordingly, in this study, we emphasize the potential of in silico approaches and have proposed and applied 3 novel sequential in silico pre-clinical validation steps to better identify the biomarkers that are truly desirable for clinical investment.Design: As protein biomarkers are becoming increasingly important in the clinic alongside other molecular biomarkers and lung cancer is the most common cause of cancer-related deaths, we used protein biomarkers for lung cancer as an illustrative example to apply our in silico pre-clinical validation approach.Methods: We collected the reported protein biomarkers for 3 cases (lung adenocarcinoma-LUAD, squamous cell carcinoma-LUSC, and unspecified lung cancer) and evaluated whether the protein biomarkers have cancer altering properties (i.e., act as tumor suppressors or oncoproteins and represent cancer hallmarks), are expressed in body fluids, and can be targeted by FDA-approved drugs.Results: We collected 3008 protein biomarkers for lung cancer, 1189 for LUAD, and 182 for LUSC. Of these protein biomarkers for lung cancer, LUAD, and LUSC, only 28, 25, and 6 protein biomarkers passed the 3 in silico pre-clinical validation steps examined, and of these, only 5 and 2 biomarkers were specific for lung cancer and LUAD, respectively.Conclusion: In this study, we applied our in silico pre-clinical validation approach the protein biomarkers for lung cancer cases. However, this approach can be applied and adapted to all cancer biomarkers. We believe that this approach will greatly facilitate the transition of cancer biomarkers into the clinical phase and offers great potential for future biomarker research. Biomarkers, which are routinely used in clinics, allow better classification of patients according to their disease risk, prognosis, and/or response to treatment. Although affordable omics-based approaches have paved the way for quicker identification of putative biomarkers, validation of biomarkers is necessary for translation of discoveries into clinical application. This research article highlights the challenges of translating cancer biomarkers into clinical practice and summarizes feasible step toward in silico pre-clinical validation using the example of lung cancer types. Accordingly, protein biomarkers proposed for lung cancer are being investigated using the in silico pre-clinical validation approach to determine whether they have cancer altering properties (i.e., oncoprotein, tumor suppressor, and cancer hallmark), are expressed in body fluids (i.e., plasma/serum, saliva, urine, and bronchoalveolar lavage) and can be targeted with FDA-approved drugs. We believe that the step of in silico pre-clinical validation is the future of biomarker research for all professionals involved in clinical, biological, epidemiological, biostatistical and health research, and that it will greatly facilitate the transition of biomarkers to the clinical phase.
dc.description.sponsorshipNot applicable.
dc.identifier.doi10.1177/11772719241287400
dc.identifier.issn1177-2719
dc.identifier.pmid39371614
dc.identifier.scopus2-s2.0-85206107547
dc.identifier.scopusqualityQ2
dc.identifier.urihttps://doi.org/10.1177/11772719241287400
dc.identifier.urihttps://hdl.handle.net/20.500.14669/2925
dc.identifier.volume19
dc.identifier.wosWOS:001326130000001
dc.identifier.wosqualityN/A
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherSage Publications Ltd
dc.relation.ispartofBiomarker Insights
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241211
dc.subjectProtein biomarkers
dc.subjectin silico pre-clinical validation step
dc.subjectlung cancer
dc.subjectoncoprotein
dc.subjecttumor suppressor
dc.subjectcancer hallmark
dc.subjectbody fluids
dc.subjectapproved drugs
dc.titleBiomarkers From Discovery to Clinical Application: In Silico Pre-Clinical Validation Approach in the Face of Lung Cancer
dc.typeArticle

Dosyalar