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Kumar K, Bhowmik D, Mandloi S, Gautam A, Lahiri A, Biswas N, Paul S, Chakrabarti S. Integrating Multi-Omics Data to Construct Reliable Interconnected Models of Signaling, Gene Regulatory, and Metabolic Pathways. Methods Mol Biol 2023; 2634:139-151. [PMID: 37074577 DOI: 10.1007/978-1-0716-3008-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Alteration of the status of the metabolic enzymes could be a probable way to regulate metabolic reprogramming, which is a critical cellular adaptation mechanism especially for cancer cells. Coordination among biological pathways, such as gene-regulatory, signaling, and metabolic pathways is crucial for regulating metabolic adaptation. Also, incorporation of resident microbial metabolic potential in human body can influence the interplay between the microbiome and the systemic or tissue metabolic environments. Systemic framework for model-based integration of multi-omics data can ultimately improve our understanding of metabolic reprogramming at holistic level. However, the interconnectivity and novel meta-pathway regulatory mechanisms are relatively lesser explored and understood. Hence, we propose a computational protocol that utilizes multi-omics data to identify probable cross-pathway regulatory and protein-protein interaction (PPI) links connecting signaling proteins or transcription factors or miRNAs to metabolic enzymes and their metabolites using network analysis and mathematical modeling. These cross-pathway links were shown to play important roles in metabolic reprogramming in cancer scenarios.
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Affiliation(s)
- Krishna Kumar
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
| | - Debaleena Bhowmik
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sapan Mandloi
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
| | - Anupam Gautam
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen,, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms," Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | - Abhishake Lahiri
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Nupur Biswas
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
| | - Sandip Paul
- JIS Institute of Advanced Studies and Research, JIS University, Kolkata, India.
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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2
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Kumar K, Bose S, Chakrabarti S. Identification of Cross-Pathway Connections via Protein-Protein Interactions Linked to Altered States of Metabolic Enzymes in Cervical Cancer. Front Med (Lausanne) 2021; 8:736495. [PMID: 34790674 PMCID: PMC8591138 DOI: 10.3389/fmed.2021.736495] [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: 07/05/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Metabolic reprogramming is one of the emerging hallmarks of cancer cells. Various factors, such as signaling proteins (S), miRNA, and transcription factors (TFs), may play important roles in altering the metabolic status in cancer cells by interacting with metabolic enzymes either directly or via protein-protein interactions (PPIs). Therefore, it is important to understand the coordination among these cellular pathways, which may provide better insight into the molecular mechanism behind metabolic adaptations in cancer cells. In this study, we have designed a cervical cancer-specific supra-interaction network where signaling pathway proteins, TFs, and microRNAs (miRs) are connected to metabolic enzymes via PPIs to investigate novel molecular targets and connections/links/paths regulating the metabolic enzymes. Using publicly available omics data and PPIs, we have developed a Hidden Markov Model (HMM)-based mathematical model yielding 94, 236, and 27 probable links/paths connecting signaling pathway proteins, TFs, and miRNAs to metabolic enzymes, respectively, out of which 83 paths connect to six common metabolic enzymes (RRM2, NDUFA11, ENO2, EZH2, AKR1C2, and TYMS). Signaling proteins (e.g., PPARD, BAD, GNB5, CHECK1, PAK2, PLK1, BRCA1, MAML3, and SPP1), TFs (e.g., KAT2B, ING1, MED1, ZEB1, AR, NCOA2, EGR1, TWIST1, E2F1, ID4, RBL1, ESR1, and HSF2), and miR (e.g., mir-147a, mir-593-5p, mir-138-5p, mir-16-5p, and mir-15b-5p) were found to regulate two key metabolic enzymes, EZH2 and AKR1C2, with altered metabolites (L-lysine and tetrahydrodeoxycorticosterone, THDOC) status in cervical cancer. We believe, the biology-based approach of our system will pave the way for future studies, which could be aimed toward identifying novel signaling, transcriptional, and post-transcriptional regulators of metabolic alterations in cervical cancer.
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Affiliation(s)
- Krishna Kumar
- Structural Biology and Bioinformatics Division, Council of Scientific & Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Sarpita Bose
- Structural Biology and Bioinformatics Division, Council of Scientific & Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, Council of Scientific & Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
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3
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Fatma H, Siddique HR, Maurya SK. The multiple faces of NANOG in cancer: a therapeutic target to chemosensitize therapy-resistant cancers. Epigenomics 2021; 13:1885-1900. [PMID: 34693722 DOI: 10.2217/epi-2021-0228] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The transcription factor NANOG regulates self-renewal and pluripotency in embryonic cells, and its downregulation leads to cell differentiation. Recent studies have linked upregulation of NANOG in various cancers and the regulation of expression of different molecules, and vice versa, to induce proliferation, metastasis, invasion and chemoresistance. Thus NANOG is an oncogene that functions by inducing stem cells' circuitries and heterogeneity in cancers. Understanding NANOG's role in various cancers may lead to it becoming a therapeutic target to halt cancer progression. The NANOG network can also be targeted to resensitize resistant cancer cells to conventional therapies. The current review focuses on NANOG regulation in the various signaling networks leading to cancer progression and chemoresistance, and highlights the therapeutic aspect of targeting NANOG in various cancers.
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Affiliation(s)
- Homa Fatma
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Hifzur R Siddique
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Santosh K Maurya
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
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4
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Mohan A, Raj Rajan R, Mohan G, Kollenchery Puthenveettil P, Maliekal TT. Markers and Reporters to Reveal the Hierarchy in Heterogeneous Cancer Stem Cells. Front Cell Dev Biol 2021; 9:668851. [PMID: 34150761 PMCID: PMC8209516 DOI: 10.3389/fcell.2021.668851] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
A subpopulation within cancer, known as cancer stem cells (CSCs), regulates tumor initiation, chemoresistance, and metastasis. At a closer look, CSCs show functional heterogeneity and hierarchical organization. The present review is an attempt to assign marker profiles to define the functional heterogeneity and hierarchical organization of CSCs, based on a series of single-cell analyses. The evidences show that analogous to stem cell hierarchy, self-renewing Quiescent CSCs give rise to the Progenitor CSCs with limited proliferative capacity, and later to a Progenitor-like CSCs, which differentiates to Proliferating non-CSCs. Functionally, the CSCs can be tumor-initiating cells (TICs), drug-resistant CSCs, or metastasis initiating cells (MICs). Although there are certain marker profiles used to identify CSCs of different cancers, molecules like CD44, CD133, ALDH1A1, ABCG2, and pluripotency markers [Octamer binding transcriptional factor 4 (OCT4), SOX2, and NANOG] are used to mark CSCs of a wide range of cancers, ranging from hematological malignancies to solid tumors. Our analysis of the recent reports showed that a combination of these markers can demarcate the heterogeneous CSCs in solid tumors. Reporter constructs are widely used for easy identification and quantification of marker molecules. In this review, we discuss the suitability of reporters for the widely used CSC markers that can define the heterogeneous CSCs. Since the CSC-specific functions of CD44 and CD133 are regulated at the post-translational level, we do not recommend the reporters for these molecules for the detection of CSCs. A promoter-based reporter for ABCG2 may also be not relevant in CSCs, as the expression of the molecule in cancer is mainly regulated by promoter demethylation. In this context, a dual reporter consisting of one of the pluripotency markers and ALDH1A1 will be useful in marking the heterogeneous CSCs. This system can be easily adapted to high-throughput platforms to screen drugs for eliminating CSCs.
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Affiliation(s)
- Amrutha Mohan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Reshma Raj Rajan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Gayathri Mohan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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Kripnerová M, Parmar HS, Šána J, Kopková A, Radová L, Sopper S, Biernacki K, Jedlička J, Kohoutová M, Kuncová J, Peychl J, Rudolf E, Červinka M, Houdek Z, Dvořák P, Houfková K, Pešta M, Tůma Z, Dolejšová M, Tichánek F, Babuška V, Leba M, Slabý O, Hatina J. Complex Interplay of Genes Underlies Invasiveness in Fibrosarcoma Progression Model. J Clin Med 2021; 10:jcm10112297. [PMID: 34070472 PMCID: PMC8197499 DOI: 10.3390/jcm10112297] [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: 04/23/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/03/2022] Open
Abstract
Sarcomas are a heterogeneous group of mesenchymal tumours, with a great variability in their clinical behaviour. While our knowledge of sarcoma initiation has advanced rapidly in recent years, relatively little is known about mechanisms of sarcoma progression. JUN-murine fibrosarcoma progression series consists of four sarcoma cell lines, JUN-1, JUN-2, JUN-2fos-3, and JUN-3. JUN-1 and -2 were established from a single tumour initiated in a H2K/v-jun transgenic mouse, JUN-3 originates from a different tumour in the same animal, and JUN-2fos-3 results from a targeted in vitro transformation of the JUN-2 cell line. The JUN-1, -2, and -3 cell lines represent a linear progression from the least transformed JUN-2 to the most transformed JUN-3, with regard to all the transformation characteristics studied, while the JUN-2fos-3 cell line exhibits a unique transformation mode, with little deregulation of cell growth and proliferation, but pronounced motility and invasiveness. The invasive sarcoma sublines JUN-2fos-3 and JUN-3 show complex metabolic profiles, with activation of both mitochondrial oxidative phosphorylation and glycolysis and a significant increase in spared respiratory capacity. The specific transcriptomic profile of invasive sublines features very complex biological relationships across the identified genes and proteins, with accentuated autocrine control of motility and angiogenesis. Pharmacologic inhibition of one of the autocrine motility factors identified, Ccl8, significantly diminished both motility and invasiveness of the highly transformed fibrosarcoma cell. This progression series could be greatly valuable for deciphering crucial aspects of sarcoma progression and defining new prognostic markers and potential therapeutic targets.
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Affiliation(s)
- Michaela Kripnerová
- Institute of Biology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Hamendra Singh Parmar
- Institute of Biology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Jiří Šána
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, 602 00 Brno, Czech Republic
| | - Alena Kopková
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
- Department of Pathology, University Hospital Brno, 625 00 Brno, Czech Republic
| | - Lenka Radová
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
| | - Sieghart Sopper
- Internal Medicine V, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Tyrolean Cancer Research Institute, 6020 Innsbruck, Austria
| | - Krzysztof Biernacki
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, 41-808 Zabrze, Poland
| | - Jan Jedlička
- Institute of Physiology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Michaela Kohoutová
- Institute of Physiology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Jitka Kuncová
- Institute of Physiology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Jan Peychl
- Department of Medical Biology and Genetics, Faculty of Medicine in Hradec Kralove, Charles University, 500 03 Hradec Kralove, Czech Republic
| | - Emil Rudolf
- Department of Medical Biology and Genetics, Faculty of Medicine in Hradec Kralove, Charles University, 500 03 Hradec Kralove, Czech Republic
| | - Miroslav Červinka
- Department of Medical Biology and Genetics, Faculty of Medicine in Hradec Kralove, Charles University, 500 03 Hradec Kralove, Czech Republic
| | - Zbyněk Houdek
- Institute of Biology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Pavel Dvořák
- Institute of Biology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Kateřina Houfková
- Institute of Biology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Martin Pešta
- Institute of Biology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Zdeněk Tůma
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Martina Dolejšová
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Filip Tichánek
- Institute of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
| | - Václav Babuška
- Institute of Medical Chemistry and Biochemistry, Faculty of Medicine in Pilsen, Charles University, 301 66 Plzen, Czech Republic
| | - Martin Leba
- Department of Cybernetics, Faculty of Applied Sciences, University of West Bohemia in Pilsen, 301 00 Plzen, Czech Republic
| | - Ondřej Slabý
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Jiří Hatina
- Institute of Biology, Faculty of Medicine in Pilsen, Charles University, 323 00 Plzen, Czech Republic
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6
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Danoy M, Tauran Y, Poulain S, Jellali R, Bruce J, Leduc M, Le Gall M, Gilard F, Kido T, Arakawa H, Araya K, Mori D, Kato Y, Kusuhara H, Plessy C, Miyajima A, Sakai Y, Leclerc E. Multi-omics analysis of hiPSCs-derived HLCs matured on-chip revealed patterns typical of liver regeneration. Biotechnol Bioeng 2021; 118:3716-3732. [PMID: 33404112 DOI: 10.1002/bit.27667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/13/2020] [Accepted: 12/20/2020] [Indexed: 12/17/2022]
Abstract
Maturation of human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes-like cells (HLCs) toward a complete hepatocyte phenotype remains a challenge as primitiveness patterns are still commonly observed. In this study, we propose a modified differentiation protocol for those cells which includes a prematuration in Petri dishes and a maturation in microfluidic biochip. For the first time, a large range of biomolecular families has been extracted from the same sample to combine transcriptomic, proteomic, and metabolomic analysis. After integration, these datasets revealed specific molecular patterns and highlighted the hepatic regeneration profile in biochips. Overall, biochips exhibited processes of cell proliferation and inflammation (via TGFB1) coupled with anti-fibrotic signaling (via angiotensin 1-7, ATR-2, and MASR). Moreover, cultures in this condition displayed physiological lipid-carbohydrate homeostasis (notably via PPAR, cholesterol metabolism, and bile synthesis) coupled with cell respiration through advanced oxidative phosphorylation (through the overexpression of proteins from the third and fourth complex). The results presented provide an original overview of the complex mechanisms involved in liver regeneration using an advanced in vitro organ-on-chip technology.
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Affiliation(s)
- Mathieu Danoy
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, Tokyo, Japan.,Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yannick Tauran
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, Tokyo, Japan.,Laboratoire des Multimatériaux et Interfaces, UMR CNRS 5615, Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Stéphane Poulain
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,Biomedical Microsystems Lab, Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Rachid Jellali
- Université de Technologie de Compiègne, CNRS, Biomechanics and Bioengineering, Centre de Recherche Royallieu-CS 60319-60203 Compiègne Cedex, Compiègne, France
| | - Johanna Bruce
- Plateforme 3P5 Proteomi'ic, Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 22 rue Méchain, Paris, France
| | - Marjorie Leduc
- Plateforme 3P5 Proteomi'ic, Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 22 rue Méchain, Paris, France
| | - Morgane Le Gall
- Plateforme 3P5 Proteomi'ic, Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 22 rue Méchain, Paris, France
| | - Francoise Gilard
- Plateforme Métabolisme Métabolome, Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Diderot, Univ. Paris Saclay, Gif-sur-Yvette Cedex, France
| | - Taketomo Kido
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Arakawa
- Laboratory of Molecular Pharmacokinetics, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City, Ishikawa, Japan
| | - Karin Araya
- Laboratory of Molecular Pharmacokinetics, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City, Ishikawa, Japan
| | - Daiki Mori
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukio Kato
- Laboratory of Molecular Pharmacokinetics, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City, Ishikawa, Japan
| | - Hiroyuki Kusuhara
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan
| | - Atsushi Miyajima
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Eric Leclerc
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, Tokyo, Japan.,Université de Technologie de Compiègne, CNRS, Biomechanics and Bioengineering, Centre de Recherche Royallieu-CS 60319-60203 Compiègne Cedex, Compiègne, France
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7
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He Y, Luo Y, Zhang D, Wang X, Zhang P, Li H, Ejaz S, Liang S. PGK1-mediated cancer progression and drug resistance. Am J Cancer Res 2019; 9:2280-2302. [PMID: 31815035 PMCID: PMC6895440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023] Open
Abstract
Phosphoglycerate kinase 1 (PGK1) is an essential enzyme in the aerobic glycolysis pathway. PGK1 catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate to ADP and produces 3-phosphoglycerate and ATP. In addition to cell metabolism regulation, PGK1 is involved in multiple biological activities, including angiogenesis, autophagy and DNA repair. Because of its multi-faceted functions, PGK1's involvement in cancer development is complicated. High intracellular expression of PGK1 leads to tumor cell proliferation. However, high extracellular expression of PGK1 suppresses cancer malignancy through a suppression of angiogenesis. PGK1 is also associated with chemoradiotherapy resistance and poor prognosis of cancer patients. In this manuscript, we summarize the influence of PGK1 and its post-translational modifications on cancer initiation and progression. PGK1-mediated drug resistance and potential small molecule inhibitors targeting PGK1 are discussed for their future clinical applications.
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Affiliation(s)
- Yu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, P. R. China
| | - Yang Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, P. R. China
| | - Dan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, P. R. China
| | - Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, P. R. China
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan UniversityChengdu 610041, P. R. China
| | - Haocheng Li
- Department of Mathematics and Statistics, University of CalgaryCalgary, AB T2N 1N4, Canada
| | - Samina Ejaz
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur, Pakistan
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for BiotherapyChengdu 610041, P. R. China
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8
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Chen M, Guan Y, Li A, Zhao YZ, Zhang L, Zhang L, Gong Y. LncRNA SOX2OT Mediates Mitochondrial Dysfunction in Septic Cardiomyopathy. DNA Cell Biol 2019; 38:1197-1206. [PMID: 31618067 DOI: 10.1089/dna.2019.4839] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Researches establish an indispensable role of mitochondrial dysfunction in septic cardiomyopathy. We aimed to investigate the effects of long noncoding RNA (LncRNA) SOX2 overlapping transcript (SOX2OT) on mitochondrial dysfunction in septic cardiomyopathy. We observed an obvious overexpression of SOX2OT in septic hearts and cardiomyocytes. Knockdown of SOX2OT in mice recovered the reduced cardiac function, and improved the mitochondrial membrane potential impaired by lipopolysaccharide (LPS). SOX2OT overexpressed mice showed the opposite situation. In parallel, knockdown of SOX2OT in cardiomyocytes restored the mitochondrial membrane potential, along with reduced mitochondrial reactive oxygen species production induced by LPS, while overexpression of SOX2OT reversed these effects. Mechanistically, SOX2OT could regulate mitochondrial dysfunction in septic cardiomyopathy via SOX2. In general, SOX2OT contributed to mitochondrial dysfunction progression via inhibiting SOX2 expression in septic cardiomyopathy, which may provide a new insight for treatment of septic cardiomyopathy.
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Affiliation(s)
- Mengfei Chen
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region (The First Affiliated Hospital of Northwest Minzu University), Ningxia, China
| | - Yan Guan
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region (The First Affiliated Hospital of Northwest Minzu University), Ningxia, China
| | - Ao Li
- Medical College of Northwest Minzu University, Lanzhou, China
| | - Ying-Zhu Zhao
- People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi, China
| | - Ling Zhang
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region (The First Affiliated Hospital of Northwest Minzu University), Ningxia, China
| | - Liang Zhang
- Department of Emergency, People's Hospital of Ningxia Hui Autonomous Region (The First Affiliated Hospital of Northwest Minzu University), Ningxia, China
| | - Yanxuan Gong
- Department of Geratology, Lanzhou University, Lanzhou, China.,Department of Geratology, Gansu Second Provincial Hospital, Lanzhou, China.,Xi'An International University, Xi'An, China
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9
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Abstract
Tumors display reprogrammed metabolic activities that promote cancer progression. We currently possess a limited understanding of the processes governing tumor metabolism in vivo and of the most efficient approaches to identify metabolic vulnerabilities susceptible to therapeutic targeting. While much of the literature focuses on stereotyped, cell-autonomous pathways like glycolysis, recent work emphasizes heterogeneity and flexibility of metabolism between tumors and even within distinct regions of solid tumors. Metabolic heterogeneity is important because it influences therapeutic vulnerabilities and may predict clinical outcomes. This Review describes current concepts about metabolic regulation in tumors, focusing on processes intrinsic to cancer cells and on factors imposed upon cancer cells by the tumor microenvironment. We discuss experimental approaches to identify subtype-selective metabolic vulnerabilities in preclinical cancer models. Finally, we describe efforts to characterize metabolism in primary human tumors, which should produce new insights into metabolic heterogeneity in the context of clinically relevant microenvironments.
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Affiliation(s)
- Jiyeon Kim
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ralph J DeBerardinis
- Howard Hughes Medical Institute and Children's Medical Center Research Institute, UT Southwestern Medical Center, Dallas, TX, USA.
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10
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Chang CW, Lo JF, Wang XW. Roles of mitochondria in liver cancer stem cells. Differentiation 2019; 107:35-41. [PMID: 31176254 DOI: 10.1016/j.diff.2019.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/03/2019] [Accepted: 04/09/2019] [Indexed: 02/08/2023]
Abstract
Primary liver cancer (PLC) is heterogeneous and it is an aggressive malignancy with a poor prognostic outcome. Current evidence suggests that PLC tumorigenesis is driven by rare subpopulations of cancer stem cells (CSCs), which contribute to tumor initiation, progression, and therapy resistance through particular molecular mechanisms. Energy metabolism and mitochondrial function play an important role in the regulation of cancer stemness and stem cell specifications. Since the role of mitochondrial function as central hubs in cell growth and survival, studies on the critical physiological mechanisms of the liver underlying their therapy-resistant phenotype is important. In this review, we focus on liver CSC-related mitochondrial metabolism that contributes to the liver CSC features, in terms of enhanced drug-resistance and increased tumorigenicity, and to discuss their roles on potential therapies windows for PLC therapies.
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Affiliation(s)
- Ching-Wen Chang
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Jeng-Fan Lo
- Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan; Cancer Progression Center of Excellence, National Yang-Ming University, Taipei, Taiwan
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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Dvořánková B, Lacina L, Smetana K. Isolation of Normal Fibroblasts and Their Cancer-Associated Counterparts (CAFs) for Biomedical Research. Methods Mol Biol 2018; 1879:393-406. [PMID: 29675784 DOI: 10.1007/7651_2018_137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cancer-associated fibroblasts (CAFs) represent a crucial component of cancer microenvironment. CAFs significantly influence biological properties of various types of cancer in terms of local aggressiveness, recurrence, and metastatic behaviour. This chapter summarizes a simple protocol for isolation of normal fibroblasts and their cancer-associated counterparts from normal human skin and mucosa, respectively, as well as from samples of human tumours such as basal/squamous carcinoma, melanoma, and breast cancer, and employment of this procedure for other types of cancer is possible. Isolated fibroblasts can be expanded in vitro and employed for further analysis of, e.g., DNA, RNA, protein, etc.
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Affiliation(s)
- BarboraBarbora Dvořánková
- First Faculty of Medicine, Institute of Anatomy and BIOCEV, Charles University, Prague, Czech Republic
| | - Lukáš Lacina
- First Faculty of Medicine, Institute of Anatomy and BIOCEV, Charles University, Prague, Czech Republic.
| | - Karel Smetana
- First Faculty of Medicine, Institute of Anatomy and BIOCEV, Charles University, Prague, Czech Republic
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