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Nguyen PN. Biomarker discovery with quantum neural networks: a case-study in CTLA4-activation pathways. BMC Bioinformatics 2024; 25:149. [PMID: 38609844 PMCID: PMC11265126 DOI: 10.1186/s12859-024-05755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Biomarker discovery is a challenging task due to the massive search space. Quantum computing and quantum Artificial Intelligence (quantum AI) can be used to address the computational problem of biomarker discovery from genetic data. METHOD We propose a Quantum Neural Networks architecture to discover genetic biomarkers for input activation pathways. The Maximum Relevance-Minimum Redundancy criteria score biomarker candidate sets. Our proposed model is economical since the neural solution can be delivered on constrained hardware. RESULTS We demonstrate the proof of concept on four activation pathways associated with CTLA4, including (1) CTLA4-activation stand-alone, (2) CTLA4-CD8A-CD8B co-activation, (3) CTLA4-CD2 co-activation, and (4) CTLA4-CD2-CD48-CD53-CD58-CD84 co-activation. CONCLUSION The model indicates new genetic biomarkers associated with the mutational activation of CLTA4-associated pathways, including 20 genes: CLIC4, CPE, ETS2, FAM107A, GPR116, HYOU1, LCN2, MACF1, MT1G, NAPA, NDUFS5, PAK1, PFN1, PGAP3, PPM1G, PSMD8, RNF213, SLC25A3, UBA1, and WLS. We open source the implementation at: https://github.com/namnguyen0510/Biomarker-Discovery-with-Quantum-Neural-Networks .
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Affiliation(s)
- Phuong-Nam Nguyen
- Faculty of Computer Science, PHENIKAA University, Yen Nghia, Ha Dong, Hanoi, 12116, Vietnam.
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Song J, Yu Y, Yan Z, Xiao S, Zhao X, Wang F, Fang Q, Ye G. Chloride intracellular channel gene knockdown induces insect cell lines death and level increases of intracellular calcium ions. Front Physiol 2023; 14:1217954. [PMID: 37485065 PMCID: PMC10356983 DOI: 10.3389/fphys.2023.1217954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023] Open
Abstract
Chloride intracellular channel (CLIC) is a member of the chloride channel protein family for which growing evidence supports a pivotal role in fundamental cellular events. However, the physiological function of CLIC in insects is still rarely uncovered. The ovary-derived High Five (Hi-5) cell line isolated from the cabbage looper (Trichoplusia ni) is widely used in laboratories. Here, we studied both characteristics and functions of CLIC in Hi-5 cells (TnCLIC). We identified the TnCLIC gene in Hi-5 cells and annotated highly conserved CLIC proteins in most insect species. After RNA interference of TnCLIC, the phenomenon of significantly increased cell death suggests that the TnCLIC protein is essential for the survival of Hi-5 cells. The same lethal effect was also observed in Spodoptera frugiperda 9 and Drosophila melanogaster Schneider 2 cells after CLIC knockdown. Furthermore, we found that this kind of cell death was accompanied by increases in intracellular calcium ions after TnCLIC knockdown with the transcriptomic analyses and the detection of calcium levels. Our results provide insights into insect CLIC as a key factor for cell survival and lay the foundation for the cell death mechanism.
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Affiliation(s)
- Jiqiang Song
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yanping Yu
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhichao Yan
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Shan Xiao
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xianxin Zhao
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fang Wang
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Natural Marine Products: Anti-Colorectal Cancer In Vitro and In Vivo. Mar Drugs 2022; 20:md20060349. [PMID: 35736152 PMCID: PMC9229715 DOI: 10.3390/md20060349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer, a malignant tumor with high mortality, has a poor prognosis due to drug resistance and toxicity in clinical surgery and chemotherapy. Thus, finding safer and more efficient drugs for clinical trials is vital and urgent. Natural marine compounds, with rich resources and original chemical structures, are applied widely in anticancer treatments. We provide a systematic overview of recently reported marine compounds such as alkaloids, peptides, terpenoids, polysaccharides, and carotenoids from in vitro, in vivo, and clinical studies. The in vitro studies summarized the marine origins and pharmacological mechanisms, including anti-proliferation, anti-angiogenesis, anti-migration, anti-invasion, the acceleration of cycle arrest, and the promotion of tumor apoptosis, of various compounds. The in vivo studies outlined the antitumor effects of marine compounds on colorectal cancer model mice and evaluated their efficacy in terms of tumor inhibition, hepatotoxicity, and nephrotoxicity. The clinical studies summarized the major chemical classifications and targets of action of the clinical drugs that have entered clinical approval and completed approval for marine anticancer. In summary, we present the current situation regarding the application of natural anti-colorectal cancer marine compounds and prospects for their clinical application.
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Pajot A, Hao Huynh G, Picot L, Marchal L, Nicolau E. Fucoxanthin from Algae to Human, an Extraordinary Bioresource: Insights and Advances in up and Downstream Processes. Mar Drugs 2022; 20:md20040222. [PMID: 35447895 PMCID: PMC9027613 DOI: 10.3390/md20040222] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 12/11/2022] Open
Abstract
Fucoxanthin is a brown-colored pigment from algae, with great potential as a bioactive molecule due to its numerous properties. This review aims to present current knowledge on this high added-value pigment. An accurate analysis of the biological function of fucoxanthin explains its wide photon absorption capacities in golden-brown algae. The specific chemical structure of this pigment also leads to many functional activities in human health. They are outlined in this work and are supported by the latest studies in the literature. The scientific and industrial interest in fucoxanthin is correlated with great improvements in the development of algae cultures and downstream processes. The best fucoxanthin producing algae and their associated culture parameters are described. The light intensity is a major influencing factor, as it has to enable both a high biomass growth and a high fucoxanthin content. This review also insists on the most eco-friendly and innovative extraction methods and their perspective within the next years. The use of bio-based solvents, aqueous two-phase systems and the centrifugal partition chromatography are the most promising processes. The analysis of the global market and multiple applications of fucoxanthin revealed that Asian companies are major actors in the market with macroalgae. In addition, fucoxanthin from microalgae are currently produced in Israel and France, and are mostly authorized in the USA.
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Affiliation(s)
- Anne Pajot
- Ifremer, GENALG Laboratory, Unité PHYTOX, F-44000 Nantes, France; (G.H.H.); (E.N.)
- Correspondence:
| | - Gia Hao Huynh
- Ifremer, GENALG Laboratory, Unité PHYTOX, F-44000 Nantes, France; (G.H.H.); (E.N.)
| | - Laurent Picot
- Unité Mixte de Recherche CNRS 7266 Littoral Environnement et Sociétés (LIENSs), Université La Rochelle, F-17042 La Rochelle, France;
| | - Luc Marchal
- Génie des Procédés Environnement (GEPEA), Université Nantes, F-44000 Saint Nazaire, France;
| | - Elodie Nicolau
- Ifremer, GENALG Laboratory, Unité PHYTOX, F-44000 Nantes, France; (G.H.H.); (E.N.)
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Fucoxanthin and Colorectal Cancer Prevention. Cancers (Basel) 2021; 13:cancers13102379. [PMID: 34069132 PMCID: PMC8156579 DOI: 10.3390/cancers13102379] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Colorectal cancer (CRC) is suggested to be preventable by certain food intakes. Fucoxanthin (Fx) is an anticancer agent contained abundantly in edible brown algae. However, epidemiological studies, in vivo and in vitro experiments for CRC, using Fx and Fx-rich foods, have not been fully outlined. To date, it has been reported that Fx, its metabolite of fucoxanthinol (FxOH) and Fx-rich algal extracts exerted anticancer potentials in human CRC cell lines, their cancer stem-cells-like spheroids and CRC animal models through a number of molecular mechanisms. Moreover, many in vivo experiments and interventional human trials have demonstrated that Fx, Fx-rich algal extracts and brown alga itself may improve CRC and/or certain risks, such as obesity, diabetes, metabolic syndrome, inflammation, oxidation, tumor microenvironment and/or gut microbiota. This review is the first report that summarizes the improving effects by Fx, FxOH and its rich brown algae for CRC and the risk factors. Abstract Colorectal cancer (CRC), which ranks among the top 10 most prevalent cancers, can obtain a good outcome with appropriate surgery and/or chemotherapy. However, the global numbers of both new cancer cases and death from CRC are expected to increase up to 2030. Diet-induced lifestyle modification is suggested to be effective in reducing the risk of human CRC; therefore, interventional studies using diets or diet-derived compounds have been conducted to explore the prevention of CRC. Fucoxanthin (Fx), a dietary carotenoid, is predominantly contained in edible brown algae, such as Undaria pinnatifida (wakame) and Himanthalia elongata (Sea spaghetti), which are consumed particularly frequently in Asian countries but also in some Western countries. Fx is responsible for a majority of the anticancer effects exerted by the lipophilic bioactive compounds in those algae. Interventional human trials have shown that Fx and brown algae mitigate certain risk factors for CRC; however, the direct mechanisms underlying the anti-CRC properties of Fx remain elusive. Fx and its deacetylated type “fucoxanthinol” (FxOH) have been reported to exert potential anticancer effects in preclinical cancer models through the suppression of many cancer-related signal pathways and the tumor microenvironment or alteration of the gut microbiota. We herein review the most recent studies on Fx as a potential candidate drug for CRC prevention.
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Terasaki M, Nishizaka Y, Murase W, Kubota A, Kojima H, Kojoma M, Tanaka T, Maeda H, Miyashita K, Mutoh M, Takahashi M. Effect of Fucoxanthinol on Pancreatic Ductal Adenocarcinoma Cells from an N-Nitrosobis(2-oxopropyl)amine-initiated Syrian Golden Hamster Pancreatic Carcinogenesis Model. Cancer Genomics Proteomics 2021; 18:407-423. [PMID: 33994364 PMCID: PMC8240037 DOI: 10.21873/cgp.20268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/04/2021] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND/AIM Fucoxanthinol (FxOH) is a marine carotenoid metabolite with potent anti-cancer activity. However, little is known about the efficacy of FxOH in pancreatic cancer. In the present study, we investigated the inhibitory effect of FxOH on six types of cells cloned from N-nitrosobis(2-oxopropyl)amine (BOP)-induced hamster pancreatic cancer (HaPC) cells. MATERIALS AND METHODS FxOH action and its molecular mechanisms were investigated in HaPC cells using flow-cytometry, comprehensive gene array, and western blotting analyses. RESULTS FxOH (5.0 μM) significantly suppressed the growth of four out of six types of HaPC cells. Moreover, FxOH significantly suppressed cell cycle, chemokine, integrin, actin polymerization, microtubule organization and PI3K/AKT and TGF-β signals, and activated caspase-3 followed by apoptosis and anoikis induction in HaPC-5 cells. CONCLUSION FxOH may have a high potential as a cancer chemopreventive agent in a hamster pancreatic carcinogenesis model.
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Affiliation(s)
- Masaru Terasaki
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan;
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Yusaku Nishizaka
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Wataru Murase
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Atsuhito Kubota
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Hiroyuki Kojima
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Mareshige Kojoma
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Takuji Tanaka
- Department of Diagnostic Pathology and Research Center of Diagnostic Pathology, Gifu Municipal Hospital, Gifu, Japan
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Kazuo Miyashita
- Center for Industry-University Collaboration, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Michihiro Mutoh
- Department of Molecular-Targeting Prevention, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mami Takahashi
- Central Animal Division, National Cancer Center, Tokyo, Japan
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