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Park H, Imoto S, Miyano S. Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification. J Comput Biol 2023; 30:223-243. [PMID: 36450117 DOI: 10.1089/cmb.2022.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The complex mechanisms of diseases involve the disturbance of the molecular network, rather than disorder in a single gene, implying that single gene-based analysis is insufficient to understand these mechanisms. Gene regulatory networks (GRNs) have attracted a lot of interest and various approaches have been developed for their statistical inference and gene network-based analysis. Although various computational methods have been developed, relatively little attention has been paid to incorporation of biological knowledge into the computational approaches. Furthermore, existing studies on network-based analysis perform prediction/classification of status of cell lines based on preconstructed GRNs, implying that we cannot extract prediction/classification-specific gene networks, leading to difficulty in interpretation of biological mechanisms and marker identification related to the status of cancer cell lines. We developed a novel strategy to build a GRN-based classifier, called a GRN-classifier. The proposed GRN-classifier estimates GRNs and classifies cell lines simultaneously, where the gene network is estimated to minimize error in gene network estimation and the negative log-likelihood for classifying cell lines. Thus, we can identify biological status-specific gene regulatory systems, enabling us to achieve biologically reliable interpretation of the classification. We also propose an algorithm to implement the GRN-classifier based on coordinate descent update. Monte Carlo simulations were conducted to examine performance of the GRN-classifier. Results: Our strategy provides effective results in feature selection in the classification model and edge selection in gene network estimation. The GRN-classifier also shows outstanding classification accuracy. We apply the GRN-classifier to classify cancer cell lines into anticancer drug-related status, that is, 5-fluorouracil (5-FU)-sensitive/resistant and 5-FU target/nontarget cancer cell lines. We then identified 5-FU markers based on 5-FU-related status classification-specific gene networks. The mechanisms of the identified markers were verified through literature survey. Our results suggest that the molecular interplay between MYOF and AHNAK2 may play a crucial role in drug resistance and can provide information on the chemotherapy efficiency of 5-FU. It is also suggested that suppression of the identified 5-FU markers, including MYOF/AHNAK2 and AKR1C1/AKR1C3 may improve 5-FU resistance of cancer cell lines.
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Affiliation(s)
- Heewon Park
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seiya Imoto
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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2
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Wang J, Tu S, Chavda VP, Chen ZS, Chen X. Successes and failures of immunotherapy for gastric cancer. Drug Discov Today 2022; 27:103343. [PMID: 36075377 DOI: 10.1016/j.drudis.2022.103343] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/13/2022] [Accepted: 08/31/2022] [Indexed: 11/03/2022]
Abstract
Many exploratory clinical studies have been conducted on immune checkpoint inhibitors (ICIs) as new therapeutic approaches for the first-line treatment of patients with advanced gastric cancer. Despite varying interpretations of the successes and failures of this clinical research, most analyses have focused on the results from the perspective of exploring the superiority of immunotherapy. Consequently, the role of chemotherapy as an important partner of immunotherapy in first-line combination therapy regimens for gastric cancer has attracted less attention. Here, we explore and analyze first-line immunotherapies for gastric cancer from the perspective of chemotherapy, to understand reasons for the failure of studies and to indicate directions for future clinical research.
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Affiliation(s)
- Jianzheng Wang
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China
| | - Shuiping Tu
- Department of Oncology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200127, China
| | - Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA.
| | - Xiaobing Chen
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China.
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Lae Lae Phoo N, Sukhamwang A, Dejkriengkraikul P, Yodkeeree S. Diclofenac Sensitizes Signet Ring Cell Gastric Carcinoma Cells to Cisplatin by Activating Autophagy and Inhibition of Survival Signal Pathways. Int J Mol Sci 2022; 23:ijms232012066. [PMID: 36292923 PMCID: PMC9602524 DOI: 10.3390/ijms232012066] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Gastric cancer has one of the highest incidence rates of cancer worldwide while also contributing to increased drug resistance among patients in clinical practice. Herein, we have investigated the role of diclofenac (DCF) on sensitizing cisplatin resistance in signet ring cell gastric carcinoma cells (SRCGC). Non-toxic concentrations of DCF significantly augmented cisplatin-induced cell death in cisplatin-resistant SRCGC cells (KATO/DDP) but not in cisplatin-sensitive SRCGC cells (KATOIII). Consistently, concomitant treatment of DCF and cisplatin significantly enhanced autophagic cell death due to overproduction of intracellular reactive oxygen species (ROS). At the molecular level, the induction of ROS has been associated with a reduction in antioxidant enzymes expression while inhibiting nuclear factor erythroid 2-related factor 2 (Nrf2) activity. Moreover, the combination of DCF and cisplatin also inhibited the expression of survival proteins including Bcl-2, Bcl-xL, cIAP1 and cyclin D1 in KATO/DDP cells when compared with cisplatin alone. This was due, at least in part, to reduce MAPKs, Akt, NF-κB, AP-1 and STAT-3 activation. Taken together, our results suggested that DCF potentiated the anticancer effect of cisplatin in SRCGC via the regeneration of intracellular ROS, which in turn promoted cell death as an autophagy mechanism and potentially modulated the cell survival signal transduction pathway.
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Affiliation(s)
- Nang Lae Lae Phoo
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Amonnat Sukhamwang
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pornngarm Dejkriengkraikul
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Center for Research and Development of Natural Products for Health, Chiang Mai University, Chiang Mai 50200, Thailand
- Anticarcinogenesis and Apoptosis Research Cluster, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supachai Yodkeeree
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Center for Research and Development of Natural Products for Health, Chiang Mai University, Chiang Mai 50200, Thailand
- Anticarcinogenesis and Apoptosis Research Cluster, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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4
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Janiczek-Polewska M, Szylberg Ł, Malicki J, Marszałek A. Role of Interleukins and New Perspectives in Mechanisms of Resistance to Chemotherapy in Gastric Cancer. Biomedicines 2022; 10:1600. [PMID: 35884907 PMCID: PMC9312950 DOI: 10.3390/biomedicines10071600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
Gastric cancer (GC) is the fourth most common cancer in the world in terms of incidence and second in terms of mortality. Chemotherapy is the main treatment for GC. The greatest challenge and major cause of GC treatment failure is resistance to chemotherapy. As such, research is ongoing into molecular evaluation, investigating mechanisms, and screening therapeutic targets. Several mechanisms related to both the tumor cells and the tumor microenvironment (TME) are involved in resistance to chemotherapy. TME promotes the secretion of various inflammatory cytokines. Recent studies have revealed that inflammatory cytokines affect not only tumor growth, but also chemoresistance. Cytokines in TME can be detected in blood circulation and TME cells. Inflammatory cytokines could serve as potential biomarkers in the assessment of chemoresistance and influence the management of therapeutics in GC. This review presents recent data concerning research on inflammatory cytokines involved in the mechanisms of chemoresistance and provides new clues in GC treatment.
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Affiliation(s)
- Marlena Janiczek-Polewska
- Department of Electroradiology, Poznan University of Medical Sciences, 61-701 Poznan, Poland;
- Department of Clinical Oncology, Greater Poland Cancer Center, 61-866 Poznan, Poland
| | - Łukasz Szylberg
- Department of Perinatology, Gynaecology and Gynaecologic Oncology, Collegium Medicum, Nicolaus Copernicus University, 85-067 Bydgoszcz, Poland;
- Department of Tumor Pathology and Pathomorphology, Oncology Centrer of Franciszek Łukaszczyk Memorial Hospital, 85-796 Bydgoszcz, Poland
| | - Julian Malicki
- Department of Electroradiology, Poznan University of Medical Sciences, 61-701 Poznan, Poland;
| | - Andrzej Marszałek
- Department of Oncologic Pathology, Prophylaxis Poznan University, Medical Sciences and Greater Poland Cancer Center, 61-866 Poznan, Poland;
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Tanprasert P, Limpakan Yamada S, Chattipakorn SC, Chattipakorn N, Shinlapawittayatorn K. Targeting mitochondria as a therapeutic anti-gastric cancer approach. Apoptosis 2022; 27:163-183. [PMID: 35089473 DOI: 10.1007/s10495-022-01709-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2022] [Indexed: 11/29/2022]
Abstract
Gastric cancer is regarded as the fifth most common cancer globally but the third most common cancer death. Although systemic chemotherapy is the primary treatment for advanced gastric cancer patients, the outcome of chemotherapy is unsatisfactory. Novel therapeutic strategies and potential alternative treatments are therefore needed to overcome the impact of this disease. At a cellular level, mitochondria play an important role in cell survival and apoptosis. A growing body of studies have shown that mitochondria play a central role in the regulation of cellular function, metabolism, and cell death during carcinogenesis. Interestingly, the impact of mitochondrial dynamics, including fission/fusion and mitophagy, on carcinogenesis and cancer progression has also been reported, suggesting the potential targeting of mitochondrial dynamics for the treatment of cancer. This review not only comprehensively summarizes the homeostasis of gastric cancer cells, but the potential therapeutic interventions for the targeting of mitochondria for gastric cancer therapy are also highlighted and discussed.
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Affiliation(s)
- Peticha Tanprasert
- Division of Gastrointestinal Surgery and Endoscopy, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sirikan Limpakan Yamada
- Division of Gastrointestinal Surgery and Endoscopy, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Siriporn C Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nipon Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand.,Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Krekwit Shinlapawittayatorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
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