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Vallés-Martí A, Mantini G, Manoukian P, Waasdorp C, Sarasqueta AF, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Giovannetti E, Bijlsma MF, Jiménez CR. Phosphoproteomics guides effective low-dose drug combinations against pancreatic ductal adenocarcinoma. Cell Rep 2023; 42:112581. [PMID: 37269289 DOI: 10.1016/j.celrep.2023.112581] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/04/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited set of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a readout of aberrant signaling and has the potential to identify new targets and guide treatment decisions. Using two-step sequential phosphopeptide enrichment, we generate a comprehensive phosphoproteome and proteome of nine PDAC cell lines, encompassing more than 20,000 phosphosites on 5,763 phospho-proteins, including 316 protein kinases. By using integrative inferred kinase activity (INKA) scoring, we identify multiple (parallel) activated kinases that are subsequently matched to kinase inhibitors. Compared with high-dose single-drug treatments, INKA-tailored low-dose 3-drug combinations against multiple targets demonstrate superior efficacy against PDAC cell lines, organoid cultures, and patient-derived xenografts. Overall, this approach is particularly more effective against the aggressive mesenchymal PDAC model compared with the epithelial model in both preclinical settings and may contribute to improved treatment outcomes in PDAC patients.
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Affiliation(s)
- Andrea Vallés-Martí
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands
| | - Giulia Mantini
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands; Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Pisa, Italy
| | - Paul Manoukian
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Cynthia Waasdorp
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | | | - Richard R de Goeij-de Haas
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Alex A Henneman
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Sander R Piersma
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Thang V Pham
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Jaco C Knol
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands
| | - Elisa Giovannetti
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Pharmacology Laboratory, Amsterdam, the Netherlands; Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Pisa, Italy
| | - Maarten F Bijlsma
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Connie R Jiménez
- Amsterdam University Medical Center, VU University, Department of Medical Oncology, Amsterdam, the Netherlands; Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, the Netherlands.
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Yin X, Xu R, Song J, Ruze R, Chen Y, Wang C, Xu Q. Lipid metabolism in pancreatic cancer: emerging roles and potential targets. CANCER COMMUNICATIONS (LONDON, ENGLAND) 2022; 42:1234-1256. [PMID: 36107801 PMCID: PMC9759769 DOI: 10.1002/cac2.12360] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/05/2022] [Accepted: 08/05/2022] [Indexed: 01/25/2023]
Abstract
Pancreatic cancer is one of the most serious health issues in developed and developing countries, with a 5-year overall survival rate currently <9%. Patients typically present with advanced disease due to vague symptoms or lack of screening for early cancer detection. Surgical resection represents the only chance for cure, but treatment options are limited for advanced diseases, such as distant metastatic or locally progressive tumors. Although adjuvant chemotherapy has improved long-term outcomes in advanced cancer patients, its response rate is low. So, exploring other new treatments is urgent. In recent years, increasing evidence has shown that lipid metabolism can support tumorigenesis and disease progression as well as treatment resistance through enhanced lipid synthesis, storage, and catabolism. Therefore, a better understanding of lipid metabolism networks may provide novel and promising strategies for early diagnosis, prognosis estimation, and targeted therapy for pancreatic cancer patients. In this review, we first enumerate and discuss current knowledge about the advances made in understanding the regulation of lipid metabolism in pancreatic cancer. In addition, we summarize preclinical studies and clinical trials with drugs targeting lipid metabolic systems in pancreatic cancer. Finally, we highlight the challenges and opportunities for targeting lipid metabolism pathways through precision therapies in pancreatic cancer.
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Affiliation(s)
- Xinpeng Yin
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijing100023P. R China
| | - Ruiyuan Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijing100023P. R China
| | - Jianlu Song
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijing100023P. R China
| | - Rexiati Ruze
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijing100023P. R China
| | - Yuan Chen
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijing100023P. R China
| | - Chengcheng Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijing100023P. R China
| | - Qiang Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijing100023P. R China
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Xu M, Liu X, Wang Q, Zhu Y, Jia C. Phosphoproteomic analysis reveals the effects of sleep deprivation on the hippocampus in mice. Mol Omics 2022; 18:677-685. [PMID: 35776070 DOI: 10.1039/d2mo00061j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sleep is essential for brain physiology, including nerve repair, neuronal activity, and metabolite clearance. The hippocampus is responsible for short-term memory, long-term memory, and spatial positioning. Herein, we investigated the effects of sleep deprivation on protein phosphorylation and related signaling pathways in the mouse hippocampus. The treatment group was sleep deprived for nine hours a day, and at the end of sleep deprivation, we removed the hippocampus for phosphoproteomic analysis. Through this analysis, we identified 65 sites and 27 proteins whose phosphorylation was significantly different between sleep-deprived animals and control animals. Differentially phosphorylated proteins (DPPs) were mainly distributed in the postsynaptic density, cytoplasm, and synapse. They participated in metabolic pathways, endocytosis, oxidative phosphorylation and other processes, and they were associated with Huntington's disease, Parkinson's disease, Alzheimer's disease, etc. Functional analysis of the phosphoproteome shows that sleep deprivation significantly affects the level of protein phosphorylation in the hippocampus of mice. This is the first reported study that has used phosphoproteomics to investigate the effects of sleep deprivation on hypothalamic regions. This study provides data resources that can serve as a valuable reference for sleep mechanism research, sleep disorder treatment, and drug development.
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Affiliation(s)
- Mengting Xu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, 230032, China.,State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Xinyue Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China. .,State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Qianqian Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Yunping Zhu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, 230032, China.,State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Chenxi Jia
- State Key Laboratory of Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China.
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Babu N, Bhat MY, John AE, Chatterjee A. The role of proteomics in the multiplexed analysis of gene alterations in human cancer. Expert Rev Proteomics 2021; 18:737-756. [PMID: 34602018 DOI: 10.1080/14789450.2021.1984884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Proteomics has played a pivotal role in identifying proteins perturbed in disease conditions when compared with healthy samples. Study of dysregulated proteins aids in identifying diagnostic markers and potential therapeutic targets. Cancer is an outcome of interplay of several such disarrayed proteins and molecular pathways which perturb cellular homeostasis, resulting in transformation. In this review, we discuss various facets of proteomic approaches, including tools and technological advancements, aiding in understanding differentially expressed molecules and signaling mechanisms. AREAS COVERED In this review, we have taken the approach of documenting the different methods of proteomic studies, ranging from labeling techniques, data analysis methods, and the nature of molecule detected. We summarize each technique and provide a glimpse of cancer research carried out using them, highlighting the advantages and drawbacks in comparison with others. Literature search using online resources, such as PubMed and Google Scholar were carried out for this approach. EXPERT OPINION Technological advancements in proteomics studies have come a long way from the study of two-dimensional mapping of proteins separated on gels in the early 1970s. Higher precision in molecular identification and quantification (high throughput), and greater number of samples analyzed have been the focus of researchers.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Mohd Younis Bhat
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
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Tyrosine Phosphoproteomics of Patient-Derived Xenografts Reveals Ephrin Type-B Receptor 4 Tyrosine Kinase as a Therapeutic Target in Pancreatic Cancer. Cancers (Basel) 2021; 13:cancers13143404. [PMID: 34298619 PMCID: PMC8303779 DOI: 10.3390/cancers13143404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/04/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Pancreatic cancer is one of the deadliest solid malignancies. Pancreatic ductal adenocarcinoma accounts for 90% of pancreatic cancer cases with minimal response to traditional chemotherapies. Protein tyrosine kinases have been shown to be hyperactivated in cancers and thus can serve as therapeutic targets. Patient-derived tumor xenografts (PDXs) in animal models such as mice are an appropriate resource to identify such activated kinases. PDXs models are excellent for the identification of therapeutic targets as compared to cell line models as they better reflect an in vivo environment. We identified ephrin type-B receptor 4 (EphB4) as hyperactivated in PDXs derived from pancreatic ductal adenocarcinoma. Abstract Pancreatic ductal adenocarcinoma is a recalcitrant tumor with minimal response to conventional chemotherapeutic approaches. Oncogenic signaling by activated tyrosine kinases has been implicated in cancers resulting in activation of diverse effector signaling pathways. Thus, the discovery of aberrantly activated tyrosine kinases is of great interest in developing novel therapeutic strategies in the treatment and management of pancreatic cancer. Patient-derived tumor xenografts (PDXs) in mice serve as potentially valuable preclinical models as they maintain the histological and molecular heterogeneity of the original human tumor. Here, we employed high-resolution mass spectrometry combined with immunoaffinity purification using anti-phosphotyrosine antibodies to profile tyrosine phosphoproteome across 13 pancreatic ductal adenocarcinoma PDX models. This analysis resulted in the identification of 1199 tyrosine-phosphorylated sites mapping to 704 proteins. The mass spectrometric analysis revealed widespread and heterogeneous activation of both receptor and non-receptor tyrosine kinases. Preclinical studies confirmed ephrin type-B receptor 4 (EphB4) as a potential therapeutic target based on the efficacy of human serum albumin-conjugated soluble EphB4 in mice bearing orthotopic xenografts. Immunohistochemistry-based validation using tissue microarrays from 346 patients with PDAC showed significant expression of EphB4 in >70% of patients. In summary, we present a comprehensive landscape of tyrosine phosphoproteome with EphB4 as a promising therapeutic target in pancreatic ductal adenocarcinoma.
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