Mass spectrometry based proteomics and metabolomics in personalized oncology

Kowalczyk, Tomasz; Ciborowski, Michał; Kiśluk, Joanna; Krętowski, Adam; Barbas, Coral

doi:10.1016/j.bbadis.2020.165690

Cited by 56 publications

(34 citation statements)

References 151 publications

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“…A new approach in biomarker research is provided by metabolomics, an emerging omics science focused on analysis of the full set of metabolites present in a biological sample [ 137 , 138 , 139 ]. The metabolic profile of the organism under investigation describes the undergoing biochemical events and reflects the complex interactions among gene transcription, protein expression, and physio-pathological conditions, including gut microbiome activity and environmental effects [ 139 , 140 ].…”

Section: Metabolite Biomarkersmentioning

confidence: 99%

Soft Tissue Sarcoma: An Insight on Biomarkers at Molecular, Metabolic and Cellular Level

Pillozzi

Bernini

Palchetti

et al. 2021

Cancers

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Soft tissue sarcomas (STSs) are a heterogeneous group of rare tumors. Although constituting only 1% of all human malignancies, STSs represent the second most common type of solid tumors in children and adolescents and comprise an important group of secondary malignancies. Over 100 histologic subtypes have been characterized to date (occurring predominantly in the trunk, extremity, and retroperitoneum), and many more are being discovered due to molecular profiling. STS mortality remains high, despite adjuvant chemotherapy. New prognostic stratification markers are needed to help identify patients at risk of recurrence and possibly apply more intensive or novel treatments. Recent scientific advancements have enabled a more precise molecular characterization of sarcoma subtypes and revealed novel therapeutic targets and prognostic/predictive biomarkers. This review aims at providing a comprehensive overview of the most relevant cellular, molecular and metabolic biomarkers for STS, and highlight advances in STS-related biomarker research.

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Section: Metabolite Biomarkersmentioning

confidence: 99%

Soft Tissue Sarcoma: An Insight on Biomarkers at Molecular, Metabolic and Cellular Level

Pillozzi

Bernini

Palchetti

et al. 2021

Cancers

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“…New approaches for serum biomarker research are provided by metabolomics, an emerging omics field focused on the analysis of the entire set of metabolites present in biological samples [ 19 ]. The main outcome of metabolomics studies is the metabolite profile of the biological system under investigation.…”

Section: Introductionmentioning

confidence: 99%

Integration of Serum Metabolomics into Clinical Assessment to Improve Outcome Prediction of Metastatic Soft Tissue Sarcoma Patients Treated with Trabectedin

Miolo

Gregorio

Saorin

et al. 2020

Cancers

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Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers with few diagnostic or prognostic biomarkers. This metabolomics study aimed to identify new serum prognostic biomarkers to improve the prediction of overall survival in patients with metastatic STS. The study enrolled 24 patients treated with the same trabectedin regimen. The baseline serum metabolomics profile, targeted to 68 metabolites encompassing amino acids and bile acids pathways, was quantified by liquid chromatography-tandem mass spectrometry. Correlations between individual metabolomics profiles and overall survival were examined and a risk model to predict survival was built by Cox multivariate regression. The median overall survival of the studied patients was 13.0 months (95% CI, 5.6–23.5). Among all the metabolites investigated, only citrulline and histidine correlated significantly with overall survival. The best Cox risk prediction model obtained integrating metabolomics and clinical data, included citrulline, hemoglobin and patients’ performance status score. It allowed to distinguish patients into a high-risk group with a low median overall survival of 2.1 months and a low- to moderate-risk group with a median overall survival of 19.1 months (p < 0.0001). The results of this metabolomics translation study indicate that citrulline, an amino acid belonging to the arginine metabolism, represents an important metabolic signature that may contribute to explain the high inter-patients overall survival variability of STS patients. The risk prediction model based on baseline serum citrulline, hemoglobin and performance status may represent a new prognostic tool for the early classification of patients with metastatic STS, according to their overall survival expectancy.

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“…Normally, mass spectrometry (MS) and antibody-based technology are employed to explore new biomarkers that are beneficial for diagnosing and managing diseases (Cifani and Kentsis, 2017;Kowalczyk et al, 2020). MS-based proteomics, a powerful technology for the study of biomarkers, can obtain highly accurate peptide mass and fragment spectrum from protein sequence-specific digestion products (Geyer et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Advances in Aptamer-Based Biomarker Discovery

Huang

Chen

et al. 2021

Front. Cell Dev. Biol.

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The discovery and identification of biomarkers promote the rational and fast development of medical diagnosis and therapeutics. Clinically, the application of ideal biomarkers still is limited due to the suboptimal technology in biomarker discovery. Aptamers are single-stranded deoxyribonucleic acid or ribonucleic acid molecules and can selectively bind to varied targets with high affinity and specificity. Compared with antibody, aptamers have desirable advantages, such as flexible design, easy synthesis and convenient modification with different functional groups. Currently, different aptamer-based technologies have been developed to facilitate biomarker discovery, especially CELL-SELEX and SOMAScan technology. CELL-SELEX technology is mainly used to identify cell membrane surface biomarkers of various cells. SOMAScan technology is an unbiased biomarker detection method that can analyze numerous and even thousands of proteins in complex biological samples at the same time. It has now become a large-scale multi-protein biomarker discovery platform. In this review, we introduce the aptamer-based biomarker discovery technologies, and summarize and highlight the discovered emerging biomarkers recently in several diseases.

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Mass spectrometry based proteomics and metabolomics in personalized oncology

Cited by 56 publications

References 151 publications

Soft Tissue Sarcoma: An Insight on Biomarkers at Molecular, Metabolic and Cellular Level

Soft Tissue Sarcoma: An Insight on Biomarkers at Molecular, Metabolic and Cellular Level

Integration of Serum Metabolomics into Clinical Assessment to Improve Outcome Prediction of Metastatic Soft Tissue Sarcoma Patients Treated with Trabectedin

Advances in Aptamer-Based Biomarker Discovery

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