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Zhou Z, Zhang R, Zhou A, Lv J, Chen S, Zou H, Zhang G, Lin T, Wang Z, Zhang Y, Weng S, Han X, Liu Z. Proteomics appending a complementary dimension to precision oncotherapy. Comput Struct Biotechnol J 2024; 23:1725-1739. [PMID: 38689716 PMCID: PMC11058087 DOI: 10.1016/j.csbj.2024.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Recent advances in high-throughput proteomic profiling technologies have facilitated the precise quantification of numerous proteins across multiple specimens concurrently. Researchers have the opportunity to comprehensively analyze the molecular signatures in plentiful medical specimens or disease pattern cell lines. Along with advances in data analysis and integration, proteomics data could be efficiently consolidated and employed to recognize precise elementary molecular mechanisms and decode individual biomarkers, guiding the precision treatment of tumors. Herein, we review a broad array of proteomics technologies and the progress and methods for the integration of proteomics data and further discuss how to better merge proteomics in precision medicine and clinical settings.
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Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Ruiqi Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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Bellat V, Verchère A, Ashe SA, Law B. Transcriptomic insight into salinomycin mechanisms in breast cancer cell lines: synergistic effects with dasatinib and induction of estrogen receptor β. BMC Cancer 2020; 20:661. [PMID: 32678032 PMCID: PMC7364656 DOI: 10.1186/s12885-020-07134-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Tumors are heterogeneous in nature, composed of different cell populations with various mutations and/or phenotypes. Using a single drug to encounter cancer progression is generally ineffective. To improve the treatment outcome, multiple drugs of distinctive mechanisms but complementary anticancer activities (combination therapy) are often used to enhance antitumor efficacy and minimize the risk of acquiring drug resistance. We report here the synergistic effects of salinomycin (a polyether antibiotic) and dasatinib (a Src kinase inhibitor). METHODS Functionally, both drugs induce cell cycle arrest, intracellular reactive oxygen species (iROS) production, and apoptosis. We rationalized that an overlapping of the drug activities should offer an enhanced anticancer effect, either through vertical inhibition of the Src-STAT3 axis or horizontal suppression of multiple pathways. We determined the toxicity induced by the drug combination and studied the kinetics of iROS production by fluorescence imaging and flow cytometry. Using genomic and proteomic techniques, including RNA-sequencing (RNA-seq), reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and Western Blot, we subsequently identified the responsible pathways that contributed to the synergistic effects of the drug combination. RESULTS Compared to either drug alone, the drug combination showed enhanced potency against MDA-MB-468, MDA-MB-231, and MCF-7 human breast cancer (BC) cell lines and tumor spheroids. The drug combination induces both iROS generation and apoptosis in a time-dependent manner, following a 2-step kinetic profile. RNA-seq data revealed that the drug combination exhibited synergism through horizontal suppression of multiple pathways, possibly through a promotion of cell cycle arrest at the G1/S phase via the estrogen-mediated S-phase entry pathway, and partially via the BRCA1 and DNA damage response pathway. CONCLUSION Transcriptomic analyses revealed for the first time, that the estrogen-mediated S-phase entry pathway partially contributed to the synergistic effect of the drug combination. More importantly, our studies led to the discoveries of new potential therapeutic targets, such as E2F2, as well as a novel drug-induced targeting of estrogen receptor β (ESR2) approach for triple-negative breast cancer treatment, currently lacking of targeted therapies.
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Affiliation(s)
- Vanessa Bellat
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Alice Verchère
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Sally A Ashe
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Benedict Law
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, NY, USA. .,Lead contact, New York, USA.
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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kisluk J, Michalska-Falkowska A, Reszec J, Sierko E, Nikliński J. Identification of protein changes in the blood plasma of lung cancer patients subjected to chemotherapy using a 2D-DIGE approach. PLoS One 2019; 14:e0223840. [PMID: 31622403 PMCID: PMC6797170 DOI: 10.1371/journal.pone.0223840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 10/01/2019] [Indexed: 12/17/2022] Open
Abstract
A comparative analysis of blood samples (depleted of albumin and IgG) obtained from lung cancer patients before chemotherapy versus after a second cycle of chemotherapy was performed using two-dimensional difference gel electrophoresis (2D-DIGE). The control group consisted of eight patients with non-cancerous lung diseases, and the experimental group consisted of four adenocarcinoma (ADC) and four squamous cell carcinoma (SCC) patients. Analyses of gels revealed significant changes in proteins and/or their proteoforms between control patients and lung cancer patients, both before and after a second cycle of chemotherapy. Most of these proteins were related to inflammation, including acute phase proteins (APPs) such as forms of haptoglobin and transferrin, complement component C3, and clusterin. The variable expression of APPs can potentially be used for profiling lung cancer. The greatest changes observed after chemotherapy were in transferrin and serotransferrin, which likely reflect disturbances in iron turnover after chemotherapy-induced anaemia. Significant changes in plasma proteins between ADC and SCC patients were also revealed, suggesting use of plasma vitronectin as a potential marker of SCC.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | | | - Joanna Reszec
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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Guerin M, Gonçalves A, Toiron Y, Baudelet E, Pophillat M, Granjeaud S, Fourquet P, Jacot W, Tarpin C, Sabatier R, Agavnian E, Finetti P, Adelaide J, Birnbaum D, Ginestier C, Charafe-Jauffret E, Viens P, Bertucci F, Borg JP, Camoin L. Development of parallel reaction monitoring (PRM)-based quantitative proteomics applied to HER2-Positive breast cancer. Oncotarget 2018; 9:33762-33777. [PMID: 30333908 PMCID: PMC6173470 DOI: 10.18632/oncotarget.26031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/04/2018] [Indexed: 02/06/2023] Open
Abstract
Introduction treatments targeting the Human Epidermal Growth Factor Receptor 2 (HER2/ERBB2) have improved the natural history of HER2-positive breast cancer. However, except HER2 protein expression and gene amplification, there is no predictive biomarker to guide the HER2-targeted therapies. We developed Parallel reaction monitoring (PRM) a powerful approach, to quantify and evaluate key proteins involved in the HER2 pathway and/or anti-HER2 treatment sensitivity. Results in BCLs, PRM measurements correlated with western blot immunocytochemistry and transcriptomic data. At baseline, higher expression of HER2, EGFR, PTEN and HER3 but lower expression of phospho-HER2 correlated with trastuzumab sensitivity. Under trastuzumab, PRM demonstrated a decrease in HER2 and an increase in phospho-HER2, which correlated with drug sensitivity. The opposite was observed under lapatinib. HER2 quantification was also correlated with immunohistochemistry in PDXs and clinical breast cancer samples. Discussion in conclusion, PRM-based assay, developed to quantify proteins of the HER2 pathway in breast cancer samples revealed a large magnitude of expression, which may have relevance in terms of treatment sensitivity. Materials and Methods we first evaluated PRM in term of sensitivity, linearity and reproducibility. PRM was then applied to breast cancer cell lines (BCLs) including BCLs exposed to anti-HER2 agents, patient-derived xenografts (PDXs) and frozen breast cancer samples.
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Affiliation(s)
- Mathilde Guerin
- Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Anthony Gonçalves
- Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology Team, Marseille, France
| | - Yves Toiron
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Emilie Baudelet
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Matthieu Pophillat
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Samuel Granjeaud
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Patrick Fourquet
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - William Jacot
- IRCM, INSERM, Institut Régional du Cancer, Department of Medical Oncology, Montpellier, France
| | - Carole Tarpin
- Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France
| | - Renaud Sabatier
- Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology Team, Marseille, France
| | - Emilie Agavnian
- Institut Paoli-Calmettes, Department of Anatomo-pathology, Marseille, France
| | - Pascal Finetti
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology Team, Marseille, France
| | - José Adelaide
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology Team, Marseille, France
| | - Daniel Birnbaum
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology Team, Marseille, France
| | - Christophe Ginestier
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Institut Paoli-Calmettes, Department of Anatomo-pathology, Marseille, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Team, Marseille, France
| | - Patrice Viens
- Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology Team, Marseille, France
| | - François Bertucci
- Institut Paoli-Calmettes, Department of Medical Oncology, Marseille, France.,Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Predictive Oncology Team, Marseille, France
| | - Jean-Paul Borg
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
| | - Luc Camoin
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Proteomics, Marseille, France
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