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Iketani M, Hatomi M, Fujita Y, Watanabe N, Ito M, Kawaguchi H, Ohsawa I. Inhalation of hydrogen gas mitigates sevoflurane-induced neuronal apoptosis in the neonatal cortex and is associated with changes in protein phosphorylation. J Neurochem 2024. [PMID: 38849977 DOI: 10.1111/jnc.16142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/03/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024]
Abstract
Inhalation of hydrogen (H2) gas is therapeutically effective for cerebrovascular diseases, neurodegenerative disorders, and neonatal brain disorders including pathologies induced by anesthetic gases. To understand the mechanisms underlying the protective effects of H2 on the brain, we investigated the molecular signals affected by H2 in sevoflurane-induced neuronal cell death. We confirmed that neural progenitor cells are susceptible to sevoflurane and undergo apoptosis in the retrosplenial cortex of neonatal mice. Co-administration of 1-8% H2 gas for 3 h to sevoflurane-exposed pups suppressed elevated caspase-3-mediated apoptotic cell death and concomitantly decreased c-Jun phosphorylation and activation of the c-Jun pathway, all of which are induced by oxidative stress. Anesthesia-induced increases in lipid peroxidation and oxidative DNA damage were alleviated by H2 inhalation. Phosphoproteome analysis revealed enriched clusters of differentially phosphorylated proteins in the sevoflurane-exposed neonatal brain that included proteins involved in neuronal development and synaptic signaling. H2 inhalation modified cellular transport pathways that depend on hyperphosphorylated proteins including microtubule-associated protein family. These modifications may be involved in the protective mechanisms of H2 against sevoflurane-induced neuronal cell death.
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Affiliation(s)
- Masumi Iketani
- Biological Process of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Mai Hatomi
- Biological Process of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
- Department of Life Sciences, Toyo University, Asaka, Japan
| | - Yasunori Fujita
- Biological Process of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Nobuhiro Watanabe
- Autonomic Neuroscience, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Masafumi Ito
- Biological Process of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | | | - Ikuroh Ohsawa
- Biological Process of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
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Vallés-Martí A, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Verheij J, Dijk F, Halfwerk H, Giovannetti E, Jiménez CR, Bijlsma MF. Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues. Mol Oncol 2024. [PMID: 38650175 DOI: 10.1002/1878-0261.13625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/12/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited number of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a direct read-out of aberrant signaling and the resultant clinically relevant phenotype. Mass spectrometry (MS)-based proteomics and phosphoproteomics were applied to 42 PDAC tumors. Data encompassed over 19 936 phosphoserine or phosphothreonine (pS/T; in 5412 phosphoproteins) and 1208 phosphotyrosine (pY; in 501 phosphoproteins) sites and a total of 3756 proteins. Proteome data identified three distinct subtypes with tumor intrinsic and stromal features. Subsequently, three phospho-subtypes were apparent: two tumor intrinsic (Phos1/2) and one stromal (Phos3), resembling known PDAC molecular subtypes. Kinase activity was analyzed by the Integrative iNferred Kinase Activity (INKA) scoring. Phospho-subtypes displayed differential phosphorylation signals and kinase activity, such as FGR and GSK3 activation in Phos1, SRC kinase family and EPHA2 in Phos2, and EGFR, INSR, MET, ABL1, HIPK1, JAK, and PRKCD in Phos3. Kinase activity analysis of an external PDAC cohort supported our findings and underscored the importance of PI3K/AKT and ERK pathways, among others. Interestingly, unfavorable patient prognosis correlated with higher RTK, PAK2, STK10, and CDK7 activity and high proliferation, whereas long survival was associated with MYLK and PTK6 activity, which was previously unknown. Subtype-associated activity profiles can guide therapeutic combination approaches in tumor and stroma-enriched tissues, and emphasize the critical role of parallel signaling pathways. In addition, kinase activity profiling identifies potential disease markers with prognostic significance.
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Affiliation(s)
- Andrea Vallés-Martí
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Richard R de Goeij-de Haas
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Alex A Henneman
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Frederike Dijk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Italy
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Maarten F Bijlsma
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, University of Amsterdam, The Netherlands
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Higgins L, Gerdes H, Cutillas PR. Principles of phosphoproteomics and applications in cancer research. Biochem J 2023; 480:403-420. [PMID: 36961757 PMCID: PMC10212522 DOI: 10.1042/bcj20220220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies.
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Affiliation(s)
- Luke Higgins
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Henry Gerdes
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
| | - Pedro R. Cutillas
- Cell Signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, U.K
- Alan Turing Institute, The British Library, London, U.K
- Digital Environment Research Institute, Queen Mary University of London, London, U.K
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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.
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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.
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Kanda M, Terashima M, Kinoshita T, Yabusaki H, Tokunaga M, Kodera Y. A multi-institutional study to evaluate the feasibility of next-generation sequencing and genomic analysis using formalin-fixed, paraffin-embedded biopsies of gastric cancer. Gastric Cancer 2023; 26:108-115. [PMID: 36369312 DOI: 10.1007/s10120-022-01351-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Formalin-fixed, paraffin-embedded (FFPE) samples acquired and preserved adequately are expected to faithfully maintain tumor characteristics. Endoscopic biopsy tissues represent an attractive resource for identifying predictive biomarkers to evaluate pretreatment responses of patients with advanced gastric cancer (GC). However, whether genomic profiles obtained through next-generation sequencing (NGS) using biopsy samples match well with those gained from surgical FFPE samples remains a concern. METHODS We collected 50 FFPE samples (26 biopsies and 24 surgical samples) from patients with GC who participated in phase III clinical trial JCOG1509. The quality and quantity of FFPE samples were determined for deep sequencing using NGS. We queried a 435-gene panel CANCERPLEX-JP to generate comprehensive genomic profiling data including the tumor mutation burden (TMB). RESULTS The median DNA yields and NGS success rates of biopsy samples compared with surgical samples were 879 ng and 80.8% vs 8523 ng and 100%, respectively. Epstein-Barr virus and microsatellite instability-high were detected in 9.5% of biopsy samples. Comparing the genomic profiles of 18 paired samples for which NGS data were available, we detected identical somatic mutations in paired biopsy and surgical samples (kappa coefficient, 0.8692). TMB positively correlated between paired biopsy and surgical samples (correlation coefficient, 0.6911). CONCLUSIONS NGS is applicable to the analysis of FFPE samples of GC acquired by the endoscopic biopsy, and the data were highly concordant with those obtained from surgical specimens of the same patients.
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Affiliation(s)
- Mitsuro Kanda
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan.
| | | | - Takahiro Kinoshita
- Department of Gastric Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiroshi Yabusaki
- Department of Gastroenterological Surgery, Niigata Cancer Center Hospital, Niigata, Japan
| | - Masanori Tokunaga
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
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