1
|
Tozuka T, Noro R, Yoshida K, Takahashi S, Hirao M, Matsuda K, Kato Y, Nakamichi S, Takeuchi S, Matsumoto M, Miyanaga A, Kunugi S, Honda K, Adachi J, Seike M. Phosphoproteomic Analysis Identified Mutual Phosphorylation of FAK and Src as a Mechanism of Osimertinib Resistance in EGFR-Mutant Lung Cancer. JTO Clin Res Rep 2024; 5:100668. [PMID: 38646155 PMCID: PMC11031815 DOI: 10.1016/j.jtocrr.2024.100668] [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: 09/11/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 04/23/2024] Open
Abstract
Introduction Osimertinib is a standard treatment for patients with EGFR-mutant NSCLC. Although some osimertinib resistance mechanisms have been identified, nearly 50% of the mechanisms remain to be elucidated. This study was aimed at identifying non-genetic mechanisms underlying osimertinib resistance. Methods We established two osimertinib-resistant cell lines from EGFR mutation-positive PC-9 and HCC827 NSCLC cell lines (PC-9OR and HCC827OR, respectively) using a stepwise method. We compared the phosphoproteomic profiles of the osimertinib-resistant and parental cells using mass spectrometry. Upstream kinases were identified using the application Kinase Enrichment Analysis version 3. Results Phosphoproteomic analysis revealed 80 phosphorylation sites that were mutually up-regulated in PC-9OR and HCC827OR cells. The Kinase Enrichment Analysis version 3 analysis identified focal adhesion kinase (FAK) and proto-oncogene tyrosine-protein kinase Src (Src) as upstream kinases of these up-regulated phosphoproteins. The small-interfering RNA-mediated knockdown of FAK reduced Src phosphorylation and that of Src reduced FAK phosphorylation in both cell lines. Furthermore, FAK- or Src-specific small-interfering RNA treatments restored EGFR phosphorylation in PC-9OR and HCC827OR cells. The combination of FAK and Src inhibitors inhibited PC-9OR and HCC827OR cell proliferation in vitro and suppressed tumor growth in a xenograft mouse model. Immunohistochemistry of tumors from patients with EGFR-mutant NSCLC suggested that phosphorylated FAK and Src are involved in initial and acquired resistance to osimertinib. Conclusions Phosphoproteomic analysis may help elucidate the mechanisms of resistance to molecular-targeted therapies in lung cancer. Mutual phosphorylation of FAK and Src is involved in osimertinib resistance. Thus, FAK and Src inhibition may be novel treatment strategies for osimertinib-resistant NSCLC.
Collapse
Affiliation(s)
- Takehiro Tozuka
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Rintaro Noro
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Keisuke Yoshida
- Department of Bioregulation, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Satoshi Takahashi
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Mariko Hirao
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Kuniko Matsuda
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Yasuhiro Kato
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Shinji Nakamichi
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Susumu Takeuchi
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Masaru Matsumoto
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Akihiko Miyanaga
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Shinobu Kunugi
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Kazufumi Honda
- Department of Bioregulation, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
- Institution for Advanced Medical Science, Nippon Medical School, Tokyo, Japan
| | - Jun Adachi
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Masahiro Seike
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| |
Collapse
|
2
|
Nojima Y, Aoki M, Re S, Hirano H, Abe Y, Narumi R, Muraoka S, Shoji H, Honda K, Tomonaga T, Mizuguchi K, Boku N, Adachi J. Integration of pharmacoproteomic and computational approaches reveals the cellular signal transduction pathways affected by apatinib in gastric cancer cell lines. Comput Struct Biotechnol J 2023; 21:2172-2187. [PMID: 37013003 PMCID: PMC10066531 DOI: 10.1016/j.csbj.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Apatinib is known to be a highly selective vascular endothelial growth factor receptor 2 (VEGFR2) inhibitor with anti-angiogenic and anti-tumor properties. In a phase III study, the objective response rate to apatinib was low. It remains unclear why the effectivity of apatinib varies among patients and what type of patients are candidates for the treatment. In this study, we investigated the anti-tumor efficacy of apatinib against 13 gastric cancer cell lines and found that it differed depending on the cell line. Using integrated wet and dry approaches, we showed that apatinib was a multi-kinase inhibitor of c-Kit, RAF1, VEGFR1, VEGFR2, and VEGFR3, predominantly inhibiting c-Kit. Notably, KATO-III, which was the most apatinib-sensitive among the gastric cancer cell lines investigated, was the only cell line expressing c-Kit, RAF1, VEGFR1, and VEGFR3 but not VEGFR2. Furthermore, we identified SNW1 as a molecule affected by apatinib that plays an important role in cell survival. Finally, we identified the molecular network related to SNW1 that was affected by treatment with apatinib. These results suggest that the mechanism of action of apatinib in KATO-III cells is independent of VEGFR2 and that the differential efficacy of apatinib was due to differences in expression patterns of receptor tyrosine kinases. Furthermore, our results suggest that the differential efficacy of apatinib in gastric cell lines may be attributed to SNW1 phosphorylation levels at a steady state. These findings contribute to a deeper understanding of the mechanism of action of apatinib in gastric cancer cells.
Collapse
Affiliation(s)
- Yosui Nojima
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Center for Mathematical Modeling and Data Science, Osaka University, Osaka 560–8531, Japan
| | - Masahiko Aoki
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Department of Early Clinical Development, Graduate School of Medicine, Kyoto University Hospital, Kyoto 606–8507, Japan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
| | - Hidekazu Hirano
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya 464–8681, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Satoshi Muraoka
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Hirokazu Shoji
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
| | - Kazufumi Honda
- Department of Biomarkers for Early Detection of Cancer, National Cancer Center Research Institute, Tokyo 104–0045, Japan
- Department of Bioregulation, Graduate School of Medicine, Nippon Medical School, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Proteobiologics Co., Ltd., Osaka 567–0085, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Institute for Protein Research, Osaka University, Osaka 565–0871, Japan
| | - Narikazu Boku
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, Tokyo 108–8639, Japan
- Correspondence to: Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, 4–6-1 Minato-ku, Shiroganedai, Tokyo 108–8639, Japan.
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Correspondence to: Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, 7–6-8 Saito-asagi, Ibaraki, Osaka 567–0085, Japan.
| |
Collapse
|
3
|
Ayati M, Yılmaz S, Chance MR, Koyuturk M. Functional Characterization of Co-Phosphorylation Networks. Bioinformatics 2022; 38:3785-3793. [PMID: 35731218 PMCID: PMC9344848 DOI: 10.1093/bioinformatics/btac406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/16/2022] [Accepted: 06/18/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Protein phosphorylation is a ubiquitous regulatory mechanism that plays a central role in cellular signaling. According to recent estimates, up to 70% of human proteins can be phosphorylated. Therefore, characterization of phosphorylation dynamics is critical for understanding a broad range of biological and biochemical processes. Technologies based on mass spectrometry are rapidly advancing to meet the needs for high-throughput screening of phosphorylation. These technologies enable untargeted quantification of thousands of phosphorylation sites in a given sample. Many labs are already utilizing these technologies to comprehensively characterize signaling landscapes by examining perturbations with drugs and knockdown approaches, or by assessing diverse phenotypes in cancers, neuro-degerenational diseases, infectious diseases, and normal development. RESULTS We comprehensively investigate the concept of "co-phosphorylation", defined as the correlated phosphorylation of a pair of phosphosites across various biological states. We integrate nine publicly available phosphoproteomics datasets for various diseases (including breast cancer, ovarian cancer and Alzheimer's disease) and utilize functional data related to sequence, evolutionary histories, kinase annotations, and pathway annotations to investigate the functional relevance of co-phosphorylation. Our results across a broad range of studies consistently show that functionally associated sites tend to exhibit significant positive or negative co-phosphorylation. Specifically, we show that co-phosphorylation can be used to predict with high precision the sites that are on the same pathway or that are targeted by the same kinase. Overall, these results establish co-phosphorylation as a useful resource for analyzing phosphoproteins in a network context, which can help extend our knowledge on cellular signaling and its dysregulation.
Collapse
Affiliation(s)
- Marzieh Ayati
- Department of Computer Science, University of Texas Rio Grande Valley, Edinburg, TX, 78531, USA
| | - Serhan Yılmaz
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mark R Chance
- Department of Nutrition, Case Western Reserve University, Cleveland, OH.,Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Mehmet Koyuturk
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.,Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| |
Collapse
|
4
|
Koenig C, Martinez-Val A, Franciosa G, Olsen JV. Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing. Proteomics 2022; 22:e2100245. [PMID: 35713889 DOI: 10.1002/pmic.202100245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/28/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022]
Abstract
In large-scale quantitative mass spectrometry (MS)-based phosphoproteomics, isobaric labeling with tandem mass tags (TMTs) coupled with offline high-pH reversed-phase peptide chromatographic fractionation maximizes depth of coverage. To investigate to what extent limited sample amounts affect sensitivity and dynamic range of the analysis due to sample losses, we benchmarked TMT-based fractionation strategies against single-shot label-free quantification with spectral library-free data independent acquisition (LFQ-DIA), for different peptide input per sample. To systematically examine how peptide input amounts influence TMT-fractionation approaches in a phosphoproteomics workflow, we compared two different high-pH reversed-phase fractionation strategies, microflow (MF) and stage-tip fractionation (STF), while scaling the peptide input amount down from 12.5 to 1 μg per sample. Our results indicate that, for input amounts higher than 5 μg per sample, TMT labeling, followed by microflow fractionation (MF) and phospho-enrichment, achieves the deepest phosphoproteome coverage, even compared to single shot direct-DIA analysis. Conversely, STF of enriched phosphopeptides (STF) is optimal for lower amounts, below 5 μg/peptide per sample. As a result, we provide a decision tree to help phosphoproteomics users to choose the best workflow as a function of sample amount.
Collapse
Affiliation(s)
- Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
Zhu G, Jin L, Sun W, Wang S, Liu N. Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers. Biochim Biophys Acta Rev Cancer 2022; 1877:188735. [PMID: 35577141 DOI: 10.1016/j.bbcan.2022.188735] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the costliest health problems and ranks second in cancer-related mortality in developed countries. With the aid of proteomics, many protein biomarkers for the diagnosis, prognosis, and precise management of CRC have been identified. Furthermore, some protein biomarkers exhibit structural diversity after modifications. Post-translational modifications (PTMs), most of which are catalyzed by a variety of enzymes, extensively increase protein diversity and are involved in many complex and dynamic cellular processes through the regulation of protein function. Accumulating evidence suggests that abnormal PTM events are associated with a variety of human diseases, such as CRC, thus highlighting the need for studying PTMs to discover both the molecular mechanisms and therapeutic targets of CRC. In this review, we begin with a brief overview of the importance of protein PTMs, discuss the general strategies for proteomic profiling of several key PTMs (including phosphorylation, acetylation, glycosylation, ubiquitination, methylation, and citrullination), shift the emphasis to describing the specific methods used for delineating the global landscapes of each of these PTMs, and summarize the recent applications of these methods to explore the potential roles of the PTMs in CRC. Finally, we discuss the current status of PTM research on CRC and provide future perspectives on how PTM regulation can play an essential role in translational medicine for early diagnosis, prognosis stratification, and therapeutic intervention in CRC.
Collapse
Affiliation(s)
- Gengjun Zhu
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Lifang Jin
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Shuang Wang
- Dermatological department, The Second Hospital of Jilin University, Changchun, China.
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China; Central Laboratory, The Second Hospital of Jilin University, Changchun, China.
| |
Collapse
|
6
|
Adachi J, Kakudo A, Takada Y, Isoyama J, Ikemoto N, Abe Y, Narumi R, Muraoka S, Gunji D, Hara Y, Katayama R, Tomonaga T. Systematic identification of ALK substrates by integrated phosphoproteome and interactome analysis. Life Sci Alliance 2022; 5:5/8/e202101202. [PMID: 35508387 PMCID: PMC9069051 DOI: 10.26508/lsa.202101202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
Integrated analysis of the phosphoproteome and interactome of anaplastic lymphoma kinase (ALK)-overexpressing HEK 293 cells revealed 37 ALK substrate candidates, contributing to the improvement of kinase activity prediction. The sensitivity of phosphorylation site identification by mass spectrometry has improved markedly. However, the lack of kinase–substrate relationship (KSR) data hinders the improvement of the range and accuracy of kinase activity prediction. In this study, we aimed to develop a method for acquiring systematic KSR data on anaplastic lymphoma kinase (ALK) using mass spectrometry and to apply this method to the prediction of kinase activity. Thirty-seven ALK substrate candidates, including 34 phosphorylation sites not annotated in the PhosphoSitePlus database, were identified by integrated analysis of the phosphoproteome and crosslinking interactome of HEK 293 cells with doxycycline-induced ALK overexpression. Furthermore, KSRs of ALK were validated by an in vitro kinase assay. Finally, using phosphoproteomic data from ALK mutant cell lines and patient-derived cells treated with ALK inhibitors, we found that the prediction of ALK activity was improved when the KSRs identified in this study were used instead of the public KSR dataset. Our approach is applicable to other kinases, and future identification of KSRs will facilitate more accurate estimations of kinase activity and elucidation of phosphorylation signals.
Collapse
Affiliation(s)
- Jun Adachi
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan .,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteomics and Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Akemi Kakudo
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yoko Takada
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Junko Isoyama
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Narumi Ikemoto
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yuichi Abe
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Ryohei Narumi
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Satoshi Muraoka
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Daigo Gunji
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yasuhiro Hara
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| |
Collapse
|
7
|
Hirano H, Abe Y, Nojima Y, Aoki M, Shoji H, Isoyama J, Honda K, Boku N, Mizuguchi K, Tomonaga T, Adachi J. Temporal dynamics from phosphoproteomics using endoscopic biopsy specimens provides new therapeutic targets in stage IV gastric cancer. Sci Rep 2022; 12:4419. [PMID: 35338158 PMCID: PMC8956597 DOI: 10.1038/s41598-022-08430-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/08/2022] [Indexed: 11/09/2022] Open
Abstract
Phosphoproteomic analysis expands our understanding of cancer biology. However, the feasibility of phosphoproteomic analysis using endoscopically collected tumor samples, especially with regards to dynamic changes upon drug treatment, remains unknown in stage IV gastric cancer. Here, we conducted a phosphoproteomic analysis using paired endoscopic biopsy specimens of pre- and post-treatment tumors (Ts) and non-tumor adjacent tissues (NATs) obtained from 4 HER2-positive gastric cancer patients who received trastuzumab-based treatment and from pre-treatment Ts and NATs of 4 HER2-negative gastric cancer patients. Our analysis identified 14,622 class 1 phosphosites with 12,749 quantified phosphosites and revealed molecular changes by HER2 positivity and treatment. An inhibitory signature of the ErbB signaling was observed in the post-treatment HER2-positive T group compared with the pre-treatment HER2-positive T group. Phosphoproteomic profiles obtained by a case-by-case review using paired pre- and post-treatment HER2-positive T could be utilized to discover predictive or resistant biomarkers. Furthermore, these data nominated therapeutic kinase targets which were exclusively activated in the patient unresponded to the treatment. The present study suggests that a phosphoproteomic analysis of endoscopic biopsy specimens provides information on dynamic molecular changes which can individually characterize biologic features upon drug treatment and identify therapeutic targets in stage IV gastric cancer.
Collapse
Affiliation(s)
- Hidekazu Hirano
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.,Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, 104-0045, Japan.,Department of Medicine, Keio University Graduate School of Medicine, Tokyo, 160-8582, Japan
| | - Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
| | - Yosui Nojima
- Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.,Center for Mathematical Modeling and Data Science, Osaka University, Osaka, 560-8531, Japan
| | - Masahiko Aoki
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, 104-0045, Japan.,Kyoto Innovation Center for Next Generation Clinical Trials and iPS Cell Therapy (Ki-CONNECT), Kyoto University Hospital, Kyoto, 606-8507, Japan
| | - Hirokazu Shoji
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Junko Isoyama
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan
| | - Kazufumi Honda
- Department of Biomarkers for Early Detection of Cancer, National Cancer Center Research Institute, Tokyo, 104-0045, Japan.,Department of Bioregulation, Nippon Medical School, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Narikazu Boku
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, 104-0045, Japan.,Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Kenji Mizuguchi
- Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.,Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan. .,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan. .,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan. .,Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan.
| |
Collapse
|
8
|
Shimizu Y, Okada K, Adachi J, Abe Y, Narumi R, Uchibori K, Yanagitani N, Koike S, Takagi S, Nishio M, Fujita N, Katayama R. GSK3 inhibition circumvents and overcomes acquired lorlatinib resistance in ALK-rearranged non-small-cell lung cancer. NPJ Precis Oncol 2022; 6:16. [PMID: 35301419 PMCID: PMC8931094 DOI: 10.1038/s41698-022-00260-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/11/2022] [Indexed: 12/14/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) fusion is found in ~3%–5% of patients with non-small-cell lung cancers (NSCLCs). Although the third-generation ALK tyrosine kinase inhibitor (TKI) lorlatinib shows high clinical efficacy in ALK-positive NSCLC, most of the patients eventually relapse with acquired resistance. Recently, drug-tolerant persister (DTP) cells have been considered an important seed of acquired resistance cells. In this study, we established lorlatinib intermediate resistant cells from a patient-derived cell model. Glycogen synthase kinase 3 (GSK3) inhibitions significantly suppressed lorlatinib intermediate resistant cell growth. GSK3 inhibition also sensitized acquired resistance cells derived from alectinib-treated patients with or without secondary mutations to lorlatinib. Therefore, GSK3 plays a crucial role in developing acquired resistance against lorlatinib in ALK-positive NSCLC mediated by lorlatinib intermediate resistant cells and could be a potential molecular target to prevent acquired lorlatinib resistance and overcome ALK-TKI resistance.
Collapse
Affiliation(s)
- Yuki Shimizu
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Koutaroh Okada
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Jun Adachi
- Laboratory of Proteomics for Drug Discovery, Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yuichi Abe
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Ken Uchibori
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Noriko Yanagitani
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sumie Koike
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Naoya Fujita
- Director, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
9
|
Georgiou A, Stewart A, Vlachogiannis G, Pickard L, Valeri N, Cunningham D, Whittaker SR, Banerji U. A phospho-proteomic study of cetuximab resistance in KRAS/NRAS/BRAF V600 wild-type colorectal cancer. Cell Oncol (Dordr) 2021; 44:1197-1206. [PMID: 34462871 PMCID: PMC8516765 DOI: 10.1007/s13402-021-00628-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
PURPOSE We hypothesised that plasticity in signal transduction may be a mechanism of drug resistance and tested this hypothesis in the setting of cetuximab resistance in patients with KRAS/NRAS/BRAFV600 wild-type colorectal cancer (CRC). METHODS A multiplex antibody-based platform was used to study simultaneous changes in signal transduction of 55 phospho-proteins in 12 KRAS/NRAS/BRAFV600 wild-type CRC cell lines (6 cetuximab sensitive versus 6 cetuximab resistant) following 1 and 4 h in vitro cetuximab exposure. We validated our results in CRC patient samples (n = 4) using ex vivo exposure to cetuximab in KRAS/NRAS/BRAFV600 cells that were immunomagnetically separated from the serous effusions of patients with known cetuximab resistance. RESULTS Differences in levels of phospho-proteins in cetuximab sensitive and resistant cell lines included reductions in phospho-RPS6 and phospho-PRAS40 in cetuximab sensitive, but not cetuximab resistant cell lines at 1 and 4 h, respectively. In addition, phospho-AKT levels were found to be elevated in 3/4 patient samples following ex vivo incubation with cetuximab for 1 h. We further explored these findings by studying the effects of combinations of cetuximab and two PI3K pathway inhibitors in 3 cetuximab resistant cell lines. The addition of PI3K pathway inhibitors to cetuximab led to a significantly higher reduction in colony formation capacity compared to cetuximab alone. CONCLUSION Our findings suggest activation of the PI3K pathway as a mechanism of cetuximab resistance in KRAS/NRAS/BRAFV600 wild-type CRC.
Collapse
Affiliation(s)
- Alexandros Georgiou
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sycamore House, Downs Road, London, SM2 5PT, UK.
- Department of Medicine, The Royal Marsden NHS Foundation Trust, Sycamore House, Downs Road, London, SM2 5PT, UK.
| | - Adam Stewart
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sycamore House, Downs Road, London, SM2 5PT, UK
| | - Georgios Vlachogiannis
- Division of Molecular Pathology, The Institute of Cancer Research, Sycamore House, Downs Road, London, SM2 5PT, UK
| | - Lisa Pickard
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sycamore House, Downs Road, London, SM2 5PT, UK
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, Sycamore House, Downs Road, London, SM2 5PT, UK
- Department of Medicine, The Royal Marsden NHS Foundation Trust, Sycamore House, Downs Road, London, SM2 5PT, UK
| | - David Cunningham
- Department of Medicine, The Royal Marsden NHS Foundation Trust, Sycamore House, Downs Road, London, SM2 5PT, UK
| | - Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sycamore House, Downs Road, London, SM2 5PT, UK
| | - Udai Banerji
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sycamore House, Downs Road, London, SM2 5PT, UK.
- Division of Clinical Studies, The Institute of Cancer Research, Sycamore House, Downs Road, London, SM2 5PT, UK.
| |
Collapse
|
10
|
Jain AP, Radhakrishnan A, Pinto S, Patel K, Kumar M, Nanjappa V, Raja R, Keshava Prasad TS, Mathur PP, Sidransky D, Chatterjee A, Gowda H. How to Achieve Therapeutic Response in Erlotinib-Resistant Head and Neck Squamous Cell Carcinoma? New Insights from Stable Isotope Labeling with Amino Acids in Cell Culture-Based Quantitative Tyrosine Phosphoproteomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:605-616. [PMID: 34432535 DOI: 10.1089/omi.2021.0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Resistance to cancer chemotherapy is a major global health burden. Epidermal growth factor receptor (EGFR) is a proven therapeutic target for multiple cancers of epithelial origin. Despite its overexpression in >90% of head and neck squamous cell carcinoma (HNSCC) patients, tyrosine kinase inhibitors such as erlotinib have shown a modest response in clinical trials. Cellular heterogeneity is thought to play an important role in HNSCC therapeutic resistance. Genomic alterations alone cannot explain all resistance mechanisms at play in a heterogeneous system. It is thus important to understand the biochemical mechanisms associated with drug resistance to determine potential strategies to achieve clinical response. We investigated tyrosine kinase signaling networks in erlotinib-resistant cells using quantitative tyrosine phosphoproteomics approach. We observed altered phosphorylation of proteins involved in cell adhesion and motility in erlotinib-resistant cells. Bioinformatics analysis revealed enrichment of pathways related to regulation of the actin cytoskeleton, extracellular matrix (ECM)-receptor interaction, and endothelial migration. Of importance, enrichment of the focal adhesion kinase (PTK2) signaling pathway downstream of EGFR was also observed in erlotinib-resistant cells. To the best of our knowledge, we present the first report of tyrosine phosphoproteome profiling in erlotinib-resistant HNSCC, with an eye to inform new ways to achieve clinical response. Our findings suggest that common signaling networks are at play in driving resistance to EGFR-targeted therapies in HNSCC and other cancers. Most notably, our data suggest that the PTK2 pathway genes may potentially play a significant role in determining clinical response to erlotinib in HNSCC tumors.
Collapse
Affiliation(s)
- Ankit P Jain
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | | | - Sneha Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Krishna Patel
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Manish Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | | | - Remya Raja
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Premendu P Mathur
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India.,Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery; Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| |
Collapse
|
11
|
Possible Therapeutic Strategy Involving the Purine Synthesis Pathway Regulated by ITK in Tongue Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13133333. [PMID: 34283052 PMCID: PMC8269312 DOI: 10.3390/cancers13133333] [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: 06/18/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023] Open
Abstract
The epidermal growth factor receptor is the only available tyrosine kinase molecular target for treating oral cancer. To improve the prognosis of tongue squamous cell carcinoma (TSCC) patients, a novel molecular target for tyrosine kinases is thus needed. We examined the expression of interleukin-2-inducible T-cell kinase (ITK) using immunohistochemistry, and the biological function of ITK was investigated using biochemical, phosphoproteomic, and metabolomic analyses. We found that ITK is overexpressed in TSCC patients with poor outcomes. The proliferation of oral cancer cell lines expressing ITK via transfection exhibited significant increases in three-dimensional culture assays and murine inoculation models with athymic male nude mice as compared with mock control cells. Suppressing the kinase activity using chemical inhibitors significantly reduced the increase in cell growth induced by ITK expression. Phosphoproteomic analyses revealed that ITK expression triggered phosphorylation of a novel tyrosine residue in trifunctional purine biosynthetic protein adenosine-3, an enzyme in the purine biosynthesis pathway. A significant increase in de novo biosynthesis of purines was observed in cells expressing ITK, which was abolished by the ITK inhibitor. ITK thus represents a potentially useful target for treating TSCC through modulation of purine biosynthesis.
Collapse
|
12
|
Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
Collapse
Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| |
Collapse
|
13
|
Monoe Y, Jingushi K, Kawase A, Hirono T, Hirose R, Nakatsuji Y, Kitae K, Ueda Y, Hase H, Abe Y, Adachi J, Tomonaga T, Tsujikawa K. Pharmacological Inhibition of miR-130 Family Suppresses Bladder Tumor Growth by Targeting Various Oncogenic Pathways via PTPN1. Int J Mol Sci 2021; 22:ijms22094751. [PMID: 33947152 PMCID: PMC8124864 DOI: 10.3390/ijms22094751] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 12/25/2022] Open
Abstract
Previously, we have revealed that the miR-130 family (miR-130b, miR-301a, and miR-301b) functions as an oncomiR in bladder cancer. The pharmacological inhibition of the miR-130 family molecules by the seed-targeting strategy with an 8-mer tiny locked nucleic acid (LNA) inhibits the growth, migration, and invasion of bladder cancer cells by repressing stress fiber formation. Here, we searched for a functionally advanced target sequence with LNA for the miR-130 family with low cytotoxicity and found LNA #9 (A(L)^i^i^A(L)^T(L)^T(L)^G(L)^5(L)^A(L)^5(L)^T(L)^G) as a candidate LNA. LNA #9 inhibited cell growth in vitro and in an in vivo orthotopic bladder cancer model. Proteome-wide tyrosine phosphorylation analysis suggested that the miR-130 family upregulates a wide range of receptor tyrosine kinases (RTKs) signaling via the expression of phosphorylated Src (pSrcTyr416). SILAC-based proteome analysis and a luciferase assay identified protein tyrosine phosphatase non-receptor type 1 (PTPN1), which is implicated as a negative regulator of multiple signaling pathways downstream of RTKs as a target gene of the miR-130 family. The miR-130-targeted LNA increased and decreased PTPN1 and pSrcTyr416 expressions, respectively. PTPN1 knockdown led to increased tumor properties (cell growth, invasion, and migration) and increased pSrcTyr416 expression in bladder cancer cells, suggesting that the miR-130 family upregulates multiple RTK signaling by targeting PTPN1 and subsequent Src activation in bladder cancer. Thus, our newly designed miR-130 family targeting LNA could be a promising nucleic acid therapeutic agent for bladder cancer.
Collapse
MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Carcinoma, Transitional Cell/drug therapy
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/metabolism
- Cell Line, Tumor
- Drug Screening Assays, Antitumor
- Female
- Gene Expression Regulation, Neoplastic
- Genes, Reporter
- Humans
- Mice
- MicroRNAs/antagonists & inhibitors
- MicroRNAs/genetics
- Neoplasm Proteins/physiology
- Oligonucleotides/therapeutic use
- Protein Tyrosine Phosphatase, Non-Receptor Type 1/physiology
- RNA, Neoplasm/antagonists & inhibitors
- RNA, Neoplasm/genetics
- Receptor Protein-Tyrosine Kinases/biosynthesis
- Receptor Protein-Tyrosine Kinases/genetics
- Recombinant Proteins/metabolism
- Up-Regulation
- Urinary Bladder Neoplasms/drug therapy
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/metabolism
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Yuya Monoe
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
- Correspondence: ; Tel.: +81-6-6879-8192
| | - Akitaka Kawase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| | - Takayuki Hirono
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| | - Ryo Hirose
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| | - Yoshino Nakatsuji
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| | - Yuko Ueda
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| | - Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan; (Y.A.); (J.A.); (T.T.)
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan; (Y.A.); (J.A.); (T.T.)
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan; (Y.A.); (J.A.); (T.T.)
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.M.); (A.K.); (T.H.); (R.H.); (Y.N.); (K.K.); (Y.U.); (H.H.); (K.T.)
| |
Collapse
|
14
|
Abyadeh M, Meyfour A, Gupta V, Zabet Moghaddam M, Fitzhenry MJ, Shahbazian S, Hosseini Salekdeh G, Mirzaei M. Recent Advances of Functional Proteomics in Gastrointestinal Cancers- a Path towards the Identification of Candidate Diagnostic, Prognostic, and Therapeutic Molecular Biomarkers. Int J Mol Sci 2020; 21:ijms21228532. [PMID: 33198323 PMCID: PMC7697099 DOI: 10.3390/ijms21228532] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/02/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) cancer remains one of the common causes of morbidity and mortality. A high number of cases are diagnosed at an advanced stage, leading to a poor survival rate. This is primarily attributed to the lack of reliable diagnostic biomarkers and limited treatment options. Therefore, more sensitive, specific biomarkers and curative treatments are desirable. Functional proteomics as a research area in the proteomic field aims to elucidate the biological function of unknown proteins and unravel the cellular mechanisms at the molecular level. Phosphoproteomic and glycoproteomic studies have emerged as two efficient functional proteomics approaches used to identify diagnostic biomarkers, therapeutic targets, the molecular basis of disease and mechanisms underlying drug resistance in GI cancers. In this review, we present an overview on how functional proteomics may contribute to the understanding of GI cancers, namely colorectal, gastric, hepatocellular carcinoma and pancreatic cancers. Moreover, we have summarized recent methodological developments in phosphoproteomics and glycoproteomics for GI cancer studies.
Collapse
Affiliation(s)
- Morteza Abyadeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran; (M.A.); (G.H.S.)
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 1985717413, Iran
- Cell Science Research Center, Department of Stem Cells and Developmental Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
- Correspondence: (A.M.); (M.M.)
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW 2113, Australia;
| | | | - Matthew J. Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2113, Australia;
| | - Shila Shahbazian
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2113, Australia;
| | - Ghasem Hosseini Salekdeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran; (M.A.); (G.H.S.)
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2113, Australia;
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW 2113, Australia;
- Correspondence: (A.M.); (M.M.)
| |
Collapse
|
15
|
Osumi H, Muroi A, Sakahara M, Kawachi H, Okamoto T, Natsume Y, Yamanaka H, Takano H, Kusama D, Shinozaki E, Ooki A, Yamaguchi K, Ueno M, Takeuchi K, Noda T, Nagayama S, Koshikawa N, Yao R. Evaluation of the RAS signaling network in response to MEK inhibition using organoids derived from a familial adenomatous polyposis patient. Sci Rep 2020; 10:17455. [PMID: 33060766 PMCID: PMC7567075 DOI: 10.1038/s41598-020-74530-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/30/2020] [Indexed: 01/07/2023] Open
Abstract
RAS signaling is a promising target for colorectal cancer (CRC) therapy, and a variety of selective inhibitors have been developed. However, their use has often failed to demonstrate a significant benefit in CRC patients. Here, we used patient-derived organoids (PDOs) derived from a familial adenomatous polyposis (FAP) patient to analyze the response to chemotherapeutic agents targeting EGFR, BRAF and MEK. We found that PDOs carrying KRAS mutations were resistant to MEK inhibition, while those harboring the BRAF class 3 mutation were hypersensitive. We used a systematic approach to examine the phosphorylation of RAS effectors using reverse-phase protein array (RPPA) and found increased phosphorylation of MEK induced by binimetinib. A high basal level of ERK phosphorylation and its rebound activation after MEK inhibition were detected in KRAS-mutant PDOs. Notably, the phosphorylation of EGFR and AKT was more closely correlated with that of MEK than that of ERK. Transcriptome analysis identified MYC-mediated transcription and IFN signaling as significantly correlated gene sets in MEK inhibition. Our experiments demonstrated that RPPA analysis of PDOs, in combination with the genome and transcriptome, is a useful preclinical research platform to understand RAS signaling and provides clues for the development of chemotherapeutic strategies.
Collapse
Affiliation(s)
- Hiroki Osumi
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.,Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.,Director's Office, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Atsushi Muroi
- Division of Cancer Cell Research, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Yokohama, Kanagawa, 241-8515, Japan
| | - Mizuho Sakahara
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Hiroshi Kawachi
- Division of Pathology, Cancer Institute Hospital, Department of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Hiroshi Takano
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Daisuke Kusama
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Eiji Shinozaki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Akira Ooki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Masashi Ueno
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Kengo Takeuchi
- Division of Pathology, Cancer Institute Hospital, Department of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Tetsuo Noda
- Director's Office, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Naohiko Koshikawa
- Division of Cancer Cell Research, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Yokohama, Kanagawa, 241-8515, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.
| |
Collapse
|
16
|
Investigation of cancer drug resistance mechanisms by phosphoproteomics. Pharmacol Res 2020; 160:105091. [PMID: 32712320 DOI: 10.1016/j.phrs.2020.105091] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022]
Abstract
Cancer cell mutations can be identified by genomic and transcriptomic techniques. However, they are not sufficient to understand the full complexity of cancer heterogeneity. Analyses of proteins expressed in cancers and their modification profiles show how these mutations could be translated at the functional level. Protein phosphorylation is a major post-translational modification critical for regulating several cellular functions. The covalent addition of phosphate groups to serine, threonine, and tyrosine is catalyzed by protein kinases. Over the past years, kinases were strongly associated with cancer, thus inhibition of protein kinases emanated as novel cancer treatment. However, cancers frequently develop drug resistance. Therefore, a better understanding of drug effects on tumors is urgently needed. In this perspective, phosphoproteomics arose as advanced tool to monitor cancer therapies and to discover novel drugs. This review highlights the role of phosphoproteomics in predicting sensitivity or resistance of cancers towards tyrosine kinase inhibitors and cytotoxic drugs. It also shows the importance of phosphoproteomics in identifying biomarkers that could be applied in clinical diagnostics to predict responses to drugs.
Collapse
|
17
|
Hartley AV, Wang B, Jiang G, Wei H, Sun M, Prabhu L, Martin M, Safa A, Sun S, Liu Y, Lu T. Regulation of a PRMT5/NF-κB Axis by Phosphorylation of PRMT5 at Serine 15 in Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21103684. [PMID: 32456215 PMCID: PMC7279388 DOI: 10.3390/ijms21103684] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/19/2022] Open
Abstract
The overexpression of PRMT5 is highly correlated to poor clinical outcomes for colorectal cancer (CRC) patients. Importantly, our previous work demonstrated that PRMT5 overexpression could substantially augment activation of the nuclear factor kappa B (NF-κB) via methylation of arginine 30 (R30) on its p65 subunit, while knockdown of PRMT5 showed the opposite effect. However, the precise mechanisms governing this PRMT5/NF-κB axis are still largely unknown. Here, we report a novel finding that PRMT5 is phosphorylated on serine 15 (S15) in response to interleukin-1β (IL-1β) stimulation. Interestingly, we identified for the first time that the oncogenic kinase, PKCι could catalyze this phosphorylation event. Overexpression of the serine-to-alanine mutant of PRMT5 (S15A), in either HEK293 cells or CRC cells HT29, DLD1, and HCT116 attenuated NF-κB transactivation compared to WT-PRMT5, confirming that S15 phosphorylation is critical for the activation of NF-κB by PRMT5. Furthermore, the S15A mutant when compared to WT-PRMT5, could downregulate a subset of IL-1β-inducible NF-κB-target genes which correlated with attenuated promoter occupancy of p65 at its target genes. Additionally, the S15A mutant reduced IL-1β-induced methyltransferase activity of PRMT5 and disrupted the interaction of PRMT5 with p65. Furthermore, our data indicate that blockade of PKCι-regulated PRMT5-mediated activation of NF-κB was likely through phosphorylation of PRMT5 at S15. Finally, inhibition of PKCι or overexpression of the S15A mutant attenuated the growth, migratory, and colony-forming abilities of CRC cells compared to the WT-PRMT5. Collectively, we have identified a novel PKCι/PRMT5/NF-κB signaling axis, suggesting that pharmacological disruption of this pivotal axis could serve as the basis for new anti-cancer therapeutics.
Collapse
Affiliation(s)
- Antja-Voy Hartley
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (A.-V.H.); (H.W.); (M.S.); (L.P.); (M.M.); (A.S.); (S.S.)
| | - Benlian Wang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Guanglong Jiang
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (G.J.); (Y.L.)
| | - Han Wei
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (A.-V.H.); (H.W.); (M.S.); (L.P.); (M.M.); (A.S.); (S.S.)
| | - Mengyao Sun
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (A.-V.H.); (H.W.); (M.S.); (L.P.); (M.M.); (A.S.); (S.S.)
| | - Lakshmi Prabhu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (A.-V.H.); (H.W.); (M.S.); (L.P.); (M.M.); (A.S.); (S.S.)
| | - Matthew Martin
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (A.-V.H.); (H.W.); (M.S.); (L.P.); (M.M.); (A.S.); (S.S.)
| | - Ahmad Safa
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (A.-V.H.); (H.W.); (M.S.); (L.P.); (M.M.); (A.S.); (S.S.)
| | - Steven Sun
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (A.-V.H.); (H.W.); (M.S.); (L.P.); (M.M.); (A.S.); (S.S.)
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (G.J.); (Y.L.)
| | - Tao Lu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (A.-V.H.); (H.W.); (M.S.); (L.P.); (M.M.); (A.S.); (S.S.)
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Correspondence: ; Tel.: +1-(317)-278-0520; Fax: +1-(317)-274-7714
| |
Collapse
|
18
|
Chua XY, Mensah T, Aballo T, Mackintosh SG, Edmondson RD, Salomon AR. Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome. Mol Cell Proteomics 2020; 19:730-743. [PMID: 32071147 PMCID: PMC7124467 DOI: 10.1074/mcp.tir119.001865] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers' ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, the BOOST (Broad-spectrum Optimization Of Selective Triggering) method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of pervanadate (PV) boost channels (cells treated with the broad-spectrum tyrosine phosphatase inhibitor PV) selectively increased the relative abundance of pTyr-containing peptides. After PV boost channels facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered accurate quantitation of each peptide for the experimental samples while the quantitation from PV boost channels was ignored. This method yielded up to 6.3-fold boost in pTyr quantification depth of statistically significant data derived from contrived ratios, compared with TMT without PV boost channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The BOOST strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly elevate the levels of those modifications across the proteome are available.
Collapse
Affiliation(s)
- Xien Yu Chua
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Theresa Mensah
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Timothy Aballo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
| |
Collapse
|
19
|
Abe Y, Hirano H, Shoji H, Tada A, Isoyama J, Kakudo A, Gunji D, Honda K, Boku N, Adachi J, Tomonaga T. Comprehensive characterization of the phosphoproteome of gastric cancer from endoscopic biopsy specimens. Theranostics 2020; 10:2115-2129. [PMID: 32089736 PMCID: PMC7019165 DOI: 10.7150/thno.37623] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022] Open
Abstract
Rationale: Cancer phosphoproteomics can provide insights regarding kinases that can be targeted for therapeutic applications. Monitoring the phosphoproteomics in cancer is expected to play a key role in optimizing treatments with kinase inhibitors. Clinical phosphoproteomics in surgical tissues and patient-derived models has been studied intensively. However, the reported data may not accurately reflect the phosphosignaling status in patients due to the effect of ischemia occurring during surgery or changes in the characteristics of cancer cells when establishing the models. In contrast, endoscopic biopsies have an advantage for clinical phosphoproteomics because they can be rapidly cryo-preserved. We aimed to develop a highly sensitive method for phosphoproteomics in endoscopic biopsies of gastric cancer. Methods: Three tumor biopsies and three normal gastric biopsies were obtained by endoscopy at one time, and subjected to our optimized phosphoproteomics. Phosphopeptides were enriched with an immobilized metal affinity chromatography, and labeled with Tandem Mass Tag reagent. Quantified phosphosites were compared between the pairs of tumor/normal biopsies within same patient. Cancer-specific activated pathways and kinases were identified by pathway enrichment analysis and kinase-substrate enrichment analysis. Results: Our protocol enabled the identification of more than 10,000 class 1 phosphosites from endoscopic biopsies. A comparison between samples from cancer tissue and normal mucosa demonstrated differences in the phosphosignaling, including biomarkers of response to DNA damage. Finally, cancer-specific activation of DNA damage response signaling was validated by additional phosphoproteomics of other patients and western blotting of gastric cancer/normal cells. Conclusion: In summary, our pioneering approach will facilitate more accurate clinical phosphoproteomics in endoscopic biopsies, which can be applied to monitor the activities of therapeutic kinases and, ultimately, can be a useful tool to precision medicine.
Collapse
|
20
|
Stepath M, Zülch B, Maghnouj A, Schork K, Turewicz M, Eisenacher M, Hahn S, Sitek B, Bracht T. Systematic Comparison of Label-Free, SILAC, and TMT Techniques to Study Early Adaption toward Inhibition of EGFR Signaling in the Colorectal Cancer Cell Line DiFi. J Proteome Res 2019; 19:926-937. [DOI: 10.1021/acs.jproteome.9b00701] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Birgit Zülch
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum, Bochum 44892, Germany
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Russo R, Matrone N, Belli V, Ciardiello D, Valletta M, Esposito S, Pedone PV, Ciardiello F, Troiani T, Chambery A. Macrophage Migration Inhibitory Factor Is a Molecular Determinant of the Anti-EGFR Monoclonal Antibody Cetuximab Resistance in Human Colorectal Cancer Cells. Cancers (Basel) 2019; 11:cancers11101430. [PMID: 31557914 PMCID: PMC6826402 DOI: 10.3390/cancers11101430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
Background: The clinical impact of the monoclonal antibody cetuximab targeting the EGFR in colorectal cancer (CRC) is widely recognized. Nevertheless, the onset of cetuximab resistance is a serious issue that limits the effectiveness of this drug in targeted therapies. Unraveling the molecular players involved in cancer resistance is the first step towards the identification of alternative signaling pathways that can be targeted to circumvent resistance mechanisms restoring the efficacy of therapeutic treatments in a tailored manner. Methods: By applying a nanoLC-MS/MS TMT isobaric labeling-based approach, we have delineated a molecular hallmark of cetuximab-resistance in CRC. Results: We identified macrophage migration inhibitory factor (MIF) as a molecular determinant capable of triggering cancer resistance in sensitive human CRC cells. Blocking the MIF axis in resistant cells by a selective MIF inhibitor restores cell sensitivity to cetuximab. The combined treatment with cetuximab and the MIF inhibitor further enhanced cell growth inhibition in CRC resistant cell lines with a synergistic effect depending on inhibition of key downstream effectors of the MAPK and AKT signaling pathways. Conclusions: Collectively, our results suggest the association of MIF signaling and its dysregulation to cetuximab drug resistance, paving the way to the development of personalized combination therapies targeting the MIF axis.
Collapse
Affiliation(s)
- Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Nunzia Matrone
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Valentina Belli
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Davide Ciardiello
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Sabrina Esposito
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Fortunato Ciardiello
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Teresa Troiani
- Department of Precision Medicine, Università degli studi della Campania "Luigi Vanvitelli", 80131 Naples, Italy.
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Università degli studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| |
Collapse
|
22
|
Liu Z, Wang Y, Yao Y, Fang Z, Miao QR, Ye M. Quantitative proteomic and phosphoproteomic studies reveal novel 5-fluorouracil resistant targets in hepatocellular carcinoma. J Proteomics 2019; 208:103501. [PMID: 31454556 DOI: 10.1016/j.jprot.2019.103501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/12/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023]
Abstract
The development of chemoresistance remains the major obstacles to successful chemotherapy of hepatocellular carcinoma. The molecular mechanisms of drug resistance are complex. Identifying the key markers is crucial for development of therapeutic strategies to overcome resistance. In this study, we employed a cell-line model consisting of the 5-fluorouracil resistant Bel/5-Fu cell line and its parental Bel cell line. Using stable isotope dimethyl labeling combined with high-resolution mass spectrometry, in total, 8272 unique proteins and 22,095 phosphorylation sites with high localization confidence were identified. Our data indicated that the GnRH signaling pathway was involved in acquiring drug resistance, which has not been well elucidated. The western blotting results confirmed that the expression levels of PLCβ3 and PLCβ3 pS1105 in Bel/5-Fu cells were increased as compared to Bel cells. Furthermore, the protein levels of SRC and PKCδ, which could phosphorylate PLCβ3 at ser1105, were higher in Bel/5-Fu cells than in Bel cells. The knockdown of SRC, PKCδ and PLCβ3 increased the susceptibility of Bel/5-Fu cells to 5-Fu. Besides, the increased transcription levels of PLCβ3, PKCδ and SRC were significantly associated with decreased overall survival. Together, our deep proteomic and phosphoproteomic data reveal novel therapeutic targets for attenuating 5-Fu resistance in anti-cancer therapy. SIGNIFICANCE: It was reported that many hepatocellular carcinoma patients are resistance to 5-Fu. Although some studies related to drug resistance have been reported, the underlying mechanisms were not well elucidated. Unlike many single molecular studies, we focused on the global proteome and phosphoproteome analysis of Bel and Bel5-/Fu cell line using stable isotope dimethyl labeling to identify the previously unrecognized signaling pathway for causing 5-Fu resistance. Our results showed that the phosphorylation levels of PLCβ3 pS1105 and the protein levels of PLCβ3, PKCδ and SRC, which are major components of GnRH signaling pathway were higher in Bel/5-Fu cells than in Bel cells. Furthermore, knockdown of PLCβ3, PKCδ and SRC increased the susceptibility of Bel/5-Fu cells to 5-Fu. Overall, this is the first comprehensive proteomic and phosphoproteomic studies on 5-Fu resistant cell line Bel/5-Fu to identify the potential targets of attenuating chemoresistance in hepatocellular carcinoma.
Collapse
Affiliation(s)
- Zhen Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing R Miao
- Divisions of Pediatric Surgery and Pediatric Pathology, Departments of Surgery and Pathology, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, United States of America; New York University Winthrop Hospital, Mineola, NY 11501, United States of America.
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
23
|
Sacco F, Perfetto L, Cesareni G. Combining Phosphoproteomics Datasets and Literature Information to Reveal the Functional Connections in a Cell Phosphorylation Network. Proteomics 2019; 18:e1700311. [PMID: 29280302 DOI: 10.1002/pmic.201700311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/11/2017] [Indexed: 01/08/2023]
Abstract
Protein phosphorylation modulates many biological processes. However, the characterization of the complex regulatory circuits underlying cell response to external and internal stimuli is still limited by our inability to describe the phosphorylation network on a global scale. Modern MS-based phosphoproteomics allows monitoring tens of thousands of phosphorylation sites in multiple conditions, making the approach ideal to explore signaling pathways mediated by phosphorylation. Here, we review recent advances in phosphoproteomics and discuss some of the computational approaches developed to facilitate extraction of signaling information from these datasets. Finally, this review focuses on approaches that integrate prior literature information with unbiased phosphoproteomics experiments.
Collapse
Affiliation(s)
- Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
| | - Livia Perfetto
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
| |
Collapse
|
24
|
Ayati M, Wiredja D, Schlatzer D, Maxwell S, Li M, Koyutürk M, Chance MR. CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis. PLoS Comput Biol 2019; 15:e1006678. [PMID: 30811403 PMCID: PMC6411229 DOI: 10.1371/journal.pcbi.1006678] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 03/11/2019] [Accepted: 11/26/2018] [Indexed: 12/30/2022] Open
Abstract
We present CoPhosK to predict kinase-substrate associations for phosphopeptide substrates detected by mass spectrometry (MS). The tool utilizes a Naïve Bayes framework with priors of known kinase-substrate associations (KSAs) to generate its predictions. Through the mining of MS data for the collective dynamic signatures of the kinases' substrates revealed by correlation analysis of phosphopeptide intensity data, the tool infers KSAs in the data for the considerable body of substrates lacking such annotations. We benchmarked the tool against existing approaches for predicting KSAs that rely on static information (e.g. sequences, structures and interactions) using publically available MS data, including breast, colon, and ovarian cancer models. The benchmarking reveals that co-phosphorylation analysis can significantly improve prediction performance when static information is available (about 35% of sites) while providing reliable predictions for the remainder, thus tripling the KSAs available from the experimental MS data providing to a comprehensive and reliable characterization of the landscape of kinase-substrate interactions well beyond current limitations.
Collapse
Affiliation(s)
- Marzieh Ayati
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH
- Department of Computer Science, University of Texas Rio Grande Valley, Edinburg, TX
| | - Danica Wiredja
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
| | - Daniela Schlatzer
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
| | - Sean Maxwell
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
| | - Ming Li
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Mehmet Koyutürk
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Mark R. Chance
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
- Department of Nutrition, Case Western Reserve University, Cleveland, OH
| |
Collapse
|
25
|
Mazzio EA, Soliman KFA. Whole-transcriptomic Profile of SK-MEL-3 Melanoma Cells Treated with the Histone Deacetylase Inhibitor: Trichostatin A. Cancer Genomics Proteomics 2018; 15:349-364. [PMID: 30194076 DOI: 10.21873/cgp.20094] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/09/2018] [Accepted: 07/16/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Malignant melanoma cells can rapidly acquire phenotypic properties making them resistant to radiation and mainline chemotherapies such as decarbonize or kinase inhibitors that target RAS-proto-oncogene independent auto-activated mitogen-activated protein kinases (MAPK)/through dual specificity mitogen-activated protein kinase (MEK). Both drug resistance and inherent transition from melanocytic nevi to malignant melanoma involve the overexpression of histone deacetylases (HDACs) and a B-Raf proto-oncogene (BRAF) mutation. MATERIALS AND METHODS In this work, the effects of an HDAC class I and II inhibitor trichostatin A (TSA) on the whole transcriptome of SK-MEL-3 cells carrying a BRAF mutation was examined. RESULTS The data obtained show that TSA was an extremely potent HDAC inhibitor within SK-MEL-3 nuclear lysates, where TSA was then optimized for appropriate sub-lethal concentrations for in vitro testing. The whole-transcriptome profile shows a basic phenotype dominance in the SK-MEL-3 cell line for i) synthesis of melanin, ii) phagosome acidification, iii) ATP hydrolysis-coupled proton pumps and iv) iron transport systems. While TSA did not affect the aforementioned major systems, it evoked a dramatic change to the transcriptome: reflected by a down-regulation of 810 transcripts and up-regulation of 833, with fold-change from -15.27 to +31.1 FC (p<0.00001). Largest differentials were found for the following transcripts: Up-regulated: Tetraspanin 13 (TSPAN13), serpin family i member 1 (SERPINI1), ATPase Na+/K+ transporting subunit beta 2 (ATP1B2), nicotinamide nucleotide adenylyl transferase 2 (NMNAT2), platelet-derived growth factor receptor-like (PDGFRL), cytochrome P450 family 1 subfamily A member 1 (CYP1A1), prostate androgen-regulated mucin-like protein 1 (PARM1), secretogranin II (SCG2), SYT11 (synaptotagmin 11), rhophilin associated tail protein 1 like (ROPN1L); down-regulated: polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3), carbonic anhydrase 14 (CAXIV), BCL2-related protein A1 (BCL2A1), protein kinase C delta (PRKCD), transient receptor potential cation channel subfamily M member 1 (TRPM1), ubiquitin associated protein 1 like (UBAP1L), glutathione peroxidase 8 (GPX8), interleukin 16 (IL16), tumor protein p53 (TP53), and serpin family H member 1 (SERPINH1). There was no change to any of the HDAC transcripts (class I, II and IV), the sirtuin HDAC family (1-6) or the BRAF proto-oncogene v 599 transcripts. However, the data showed that TSA down-regulated influential transcripts that drive the BRAF-extracellular signal-regulated kinase (ERK)1/2 oncogenic pathway (namely PRKCD and MYC proto-oncogene which negatively affected the cell-cycle distribution. Mitotic inhibition was corroborated by functional pathway analysis and flow cytometry confirming halt at the G2 phase, occurring in the absence of toxicity. CONCLUSION TSA does not alter HDAC transcripts nor BRAF itself, but down-regulates critical components of the MAPK/MEK/BRAF oncogenic pathway, initiating a mitotic arrest.
Collapse
Affiliation(s)
- Elizabeth A Mazzio
- College of Pharmacy and Pharmaceutical Sciences, Florida A and M University, Tallahassee, FL, U.S.A
| | - Karam F A Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A and M University, Tallahassee, FL, U.S.A.
| |
Collapse
|
26
|
Phosphoproteomic analysis reveals PAK2 as a therapeutic target for lapatinib resistance in HER2-positive breast cancer cells. Biochem Biophys Res Commun 2018; 505:187-193. [PMID: 30243723 DOI: 10.1016/j.bbrc.2018.09.086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/02/2018] [Accepted: 09/13/2018] [Indexed: 11/24/2022]
Abstract
The human epidermal growth factor receptor 2 (HER2)-positive breast cancer with overexpression of HER2 accounts for approximately 25% of breast cancers and is more aggressive than other types of breast cancer. Lapatinib has been widely used as a HER2-targeted therapy, however, a number of patients develop lapatinib resistance and still suffer from poor prognosis. Therefore, it is essential to identify novel therapeutic targets that could overcome lapatinib resistance. In this study, we carried out phosphoproteomic analysis of lapatinib sensitive and resistant cell lines (SKBR3 and SKBR3-LR) using stable isotope labeling with amino acids in cell culture (SILAC). We identified 3808 phosphopeptides from 1807 proteins and then analyzed signaling pathways, Gene Ontology, and protein-protein interaction networks. Finally, we identified PAK2 as a therapeutic target from the network analysis and validated that PAK2 knockdown and PAK inhibitor treatment resensitize the lapatinib resistant cells to lapatinib. This results suggest that PAK2 is a potent therapeutic target to overcome acquired lapatinib resistance in HER2-positive breast cancer cells.
Collapse
|
27
|
Abe Y, Tada A, Isoyama J, Nagayama S, Yao R, Adachi J, Tomonaga T. Improved phosphoproteomic analysis for phosphosignaling and active-kinome profiling in Matrigel-embedded spheroids and patient-derived organoids. Sci Rep 2018; 8:11401. [PMID: 30061712 PMCID: PMC6065387 DOI: 10.1038/s41598-018-29837-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/04/2018] [Indexed: 11/17/2022] Open
Abstract
Many attempts have been made to reproduce the three-dimensional (3D) cancer behavior. For that purpose, Matrigel, an extracellular matrix from Engelbreth-Holm-Swarm mouse sarcoma cell, is widely used in 3D cancer models such as scaffold-based spheroids and patient-derived organoids. However, severe ion suppression caused by contaminants from Matrigel hampers large-scale phosphoproteomics. In the present study, we successfully performed global phosphoproteomics from Matrigel-embedded spheroids and organoids. Using acetone precipitations of tryptic peptides, we identified more than 20,000 class 1 phosphosites from HCT116 spheroids. Bioinformatic analysis revealed that phosphoproteomic status are significantly affected by the method used for the recovery from the Matrigel, i.e., Dispase or Cell Recovery Solution. Furthermore, we observed the activation of several phosphosignalings only in spheroids and not in adherent cells which are coincident with previous study using 3D culture. Finally, we demonstrated that our protocol enabled us to identify more than 20,000 and nearly 3,000 class 1 phosphosites from 1.4 mg and 150 μg of patient-derived organoid, respectively. Additionally, we were able to quantify phosphosites with high reproducibility (r = 0.93 to 0.95). Our phosphoproteomics protocol is useful for analyzing the phosphosignalings of 3D cancer behavior and would be applied for precision medicine with patient-derived organoids.
Collapse
Affiliation(s)
- Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Asa Tada
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Junko Isoyama
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 135-8550, Tokyo, Japan
| | - Ryoji Yao
- Division of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, 135-8550, Tokyo, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan. .,Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.
| |
Collapse
|
28
|
Thygesen C, Boll I, Finsen B, Modzel M, Larsen MR. Characterizing disease-associated changes in post-translational modifications by mass spectrometry. Expert Rev Proteomics 2018; 15:245-258. [DOI: 10.1080/14789450.2018.1433036] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Camilla Thygesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bente Finsen
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|