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Hu Y, Hu X, Luo J, Huang J, Sun Y, Li H, Qiao Y, Wu H, Li J, Zhou L, Zheng S. Liver organoid culture methods. Cell Biosci 2023; 13:197. [PMID: 37915043 PMCID: PMC10619312 DOI: 10.1186/s13578-023-01136-x] [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: 06/05/2023] [Accepted: 09/20/2023] [Indexed: 11/03/2023] Open
Abstract
Organoids, three-dimensional structures cultured in vitro, can recapitulate the microenvironment, complex architecture, and cellular functions of in vivo organs or tissues. In recent decades, liver organoids have been developed rapidly, and their applications in biomedicine, such as drug screening, disease modeling, and regenerative medicine, have been widely recognized. However, the lack of repeatability and consistency, including the lack of standardized culture conditions, has been a major obstacle to the development and clinical application of liver organoids. It is time-consuming for researchers to identify an appropriate medium component scheme, and the usage of some ingredients remains controversial. In this review, we summarized and compared different methods for liver organoid cultivation that have been published in recent years, focusing on controversial medium components and discussing their advantages and drawbacks. We aimed to provide an effective reference for the development and standardization of liver organoid cultivation.
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Affiliation(s)
- Yiqing Hu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
| | - Xiaoyi Hu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
| | - Jia Luo
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
| | - Jiacheng Huang
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
| | - Yaohan Sun
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
| | - Haoyu Li
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
| | - Yinbiao Qiao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
| | - Hao Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
| | - Jianhui Li
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China
- Department of Hepatobiliary and Pancreatic Surgery, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, 310015, China
- The Organ Repair and Regeneration Medicine Institute of Hangzhou, Hangzhou, 310003, China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China.
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, 310003, China.
- Department of Hepatobiliary and Pancreatic Surgery, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, 310015, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China.
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Keller A, Conradi J, Weber C, Failing K, Wergin M. Efficacy of Nx4 to Reduce Plasma Cortisol and Gastrin Levels in Norwegian Sled Dogs During an Exercise Induced Stress Response: A Prospective, Randomized, Double Blinded, Placebo-Controlled Cohort Study. Front Vet Sci 2021; 8:741459. [PMID: 34765666 PMCID: PMC8576320 DOI: 10.3389/fvets.2021.741459] [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: 07/14/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Introduction: An exercise induced stress response is commonly seen in high performance sled dogs, resulting in increased plasma cortisol. A stress induced rise of cortisol might result in increased prevalence of gastritis and gastric ulcers mediated by an increase of gastrin. Neurexan® (Nx4) is a medicinal product used for stress relief by reduction of cortisol. The aim of the study was to show that Nx4 reduces plasma cortisol and plasma gastrin in high performance sled dogs and to show tolerability of Nx4 in dogs. Material and Methods: First, a pilot study was done to validate the increase of cortisol by performance. The data from the pilot study was used for sample size estimation via an adapted power analysis as well as the identification of important variables. These were then used in the randomization procedure of the main study. Second, a prospective randomized, double blinded, placebo-controlled cohort study was conducted. The main study included 45 sled dogs, assigning 23 dogs to the Nx4 group, and 22 dogs to the placebo group, to analyze plasma cortisol and plasma gastrin at four time points: before, directly after and 30 and 120 min after performance. Results: For the main target variable, area under the curve (AUC) of plasma cortisol, a significantly lower adjusted mean value in the Nx4 group compared to the placebo group (p = 0.031) was found. Plasma gastrin was also significantly reduced in the Nx4 group 30 min after performance (p = 0.023), resulting in a significantly reduced plasma gastrin AUC in the Nx4 group compared to the placebo group (p = 0.049). Discussion: Within the limitation of the study, the results carry implications for the usefulness of Nx4 to reduce exercise induced plasma cortisol and gastrin levels. The reduction of the exercise induced stress response could help to improve the welfare of high-performance sled dogs. Since activation of the hypothalamic-pituitary-adrenal axis resulting in increased cortisol is similar for exercise induced stress and psychologic stress, the same might be true independent of the stressor, making Nx4 potentially useful in any stressful situation for dogs.
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Affiliation(s)
| | | | | | - Klaus Failing
- Unit for Biomathematics and Data Processing of the Veterinary Faculty, University Giessen, Giessen, Germany
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Fearing BV, Speer JE, Jing L, Kalathil A, P. Kelly M, M. Buchowski J, P. Zebala L, Luhmann S, C. Gupta M, A. Setton L. Verteporfin treatment controls morphology, phenotype, and global gene expression for cells of the human nucleus pulposus. JOR Spine 2020; 3:e1111. [PMID: 33392449 PMCID: PMC7770208 DOI: 10.1002/jsp2.1111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/24/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Cells of the nucleus pulposus (NP) are essential contributors to extracellular matrix synthesis and function of the intervertebral disc. With age and degeneration, the NP becomes stiffer and more dehydrated, which is associated with a loss of phenotype and biosynthetic function for its resident NP cells. Also, with aging, the NP cell undergoes substantial morphological changes from a rounded shape with pronounced vacuoles in the neonate and juvenile, to one that is more flattened and spread with a loss of vacuoles. Here, we make use of the clinically relevant pharmacological treatment verteporfin (VP), previously identified as a disruptor of yes-associated protein-TEA domain family member-binding domain (TEAD) signaling, to promote morphological changes in adult human NP cells in order to study variations in gene expression related to differences in cell shape. Treatment of adult, degenerative human NP cells with VP caused a shift in morphology from a spread, fibroblastic-like shape to a rounded, clustered morphology with decreased transcriptional activity of TEAD and serum-response factor. These changes were accompanied by an increased expression of vacuoles, NP-specific gene markers, and biosynthetic activity. The contemporaneous observation of VP-induced changes in cell shape and prominent, time-dependent changes within the transcriptome of NP cells occurred over all timepoints in culture. Enriched gene sets with the transition to VP-induced cell rounding suggest a major role for cell adhesion, cytoskeletal remodeling, vacuolar lumen, and MAPK activity in the NP phenotypic and functional response to changes in cell shape.
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Affiliation(s)
- Bailey V. Fearing
- Department of Biomedical EngineeringWashington University in St. LouisSt. LouisMissouriUSA
- Department of Orthopaedic SurgeryAtrium Health Musculoskeletal InstituteCharlotteNorth CarolinaUSA
| | - Julie E. Speer
- Department of Biomedical EngineeringWashington University in St. LouisSt. LouisMissouriUSA
| | - Liufang Jing
- Department of Biomedical EngineeringWashington University in St. LouisSt. LouisMissouriUSA
| | - Aravind Kalathil
- Department of Biomedical EngineeringWashington University in St. LouisSt. LouisMissouriUSA
| | - Michael P. Kelly
- Department of Orthopaedic SurgeryWashington University in St. LouisSt. LouisMissouriUSA
| | - Jacob M. Buchowski
- Department of Orthopaedic SurgeryWashington University in St. LouisSt. LouisMissouriUSA
| | - Lukas P. Zebala
- Department of Orthopaedic SurgeryWashington University in St. LouisSt. LouisMissouriUSA
| | - Scott Luhmann
- Department of Orthopaedic SurgeryWashington University in St. LouisSt. LouisMissouriUSA
| | - Munish C. Gupta
- Department of Orthopaedic SurgeryWashington University in St. LouisSt. LouisMissouriUSA
| | - Lori A. Setton
- Department of Biomedical EngineeringWashington University in St. LouisSt. LouisMissouriUSA
- Department of Orthopaedic SurgeryWashington University in St. LouisSt. LouisMissouriUSA
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Rex DAB, Agarwal N, Prasad TSK, Kandasamy RK, Subbannayya Y, Pinto SM. A comprehensive pathway map of IL-18-mediated signalling. J Cell Commun Signal 2019; 14:257-266. [PMID: 31863285 DOI: 10.1007/s12079-019-00544-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
Interleukin-18 (IL-18) is a member of the IL-1 family of cytokines and was initially described as an IFN-γ-inducing factor derived from anti-CD3-stimulated T-helper (Th)1 cells. IL-18 plays a significant role in the activation of hematopoietic cell types mediating both Th1 and Th2 responses and is the primary inducer of interferon-γ in these cells. The biological activity of IL-18 is mediated through its binding to the IL-18 receptor complex and activation of nuclear factor-κB (NF-κB), culminating in the production and release of several cytokines, chemokines, and cellular adhesion molecules. In certain cell types, IL-18 also activates mitogen-activated protein kinases (MAPKs) and phosphoinositide 3-kinase/ AKT serine/threonine kinase (PI3K/AKT) signaling modules leading to the production and release of proinflammatory cytokines. IL-18-mediated signaling acts as one of the vital components of the immunomodulatory cytokine networks involved in host defense, inflammation, and tissue regeneration. Albeit its biomedical importance, a comprehensive resource of IL-18 mediated signaling pathway is currently lacking. In this study, we report on the development of an integrated pathway map of IL-18/IL-18R signaling. The pathway map was developed through literature mining from published literature based on manual curation guidelines adapted from NetPath and includes information on 16 protein-protein interaction events, 38 enzyme-catalysis events, 12 protein translocation events, 26 activations/inhibition events, transcriptional regulators, 230 gene regulation events and 84 induced protein expression events. The IL-18 signaling pathway can be freely accessed through the WikiPathways database (https://www.wikipathways.org/index.php/Pathway:WP4754).
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Affiliation(s)
- D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Nupur Agarwal
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Richard K Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India. .,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India. .,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
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Bhat SA, Gurtoo S, Deolankar SC, Fazili KM, Advani J, Shetty R, Prasad TSK, Andrabi S, Subbannayya Y. A network map of netrin receptor UNC5B-mediated signaling. J Cell Commun Signal 2018; 13:121-127. [PMID: 30084000 DOI: 10.1007/s12079-018-0485-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
UNC-5 Homolog B (UNC5B) is a member of the dependence receptor family. This family of receptors can induce two opposite intracellular signaling cascades depending on the presence or absence of the ligand and is thus capable of driving two opposing processes. UNC5B signaling has been implicated in several cancers, where it induces cell death in the absence of its ligand Netrin-1 and promotes cell survival in its presence. In addition, inhibition of Netrin-1 ligand has been reported to decrease invasiveness and angiogenesis in tumors. UNC5B signaling pathway has also been reported to be involved in several processes such as neural development, developmental angiogenesis and inflammatory processes. However, literature pertaining to UNC5B signaling is scarce and scattered. Considering the importance of UNC5B signaling, we developed a resource of signaling events mediated by UNC5B. Using data mined from published literature, we compiled an integrated pathway map consisting of 88 UNC5B-mediated signaling events and 55 proteins. These signaling events include 27 protein-protein interaction events, 33 catalytic events involving various post-translational modifications, 9 events of UNC5B-mediated protein activation/inhibition, 27 gene regulation events and 2 events of translocation. This pathway resource has been made available to the research community through NetPath ( http://www.netpath.org /), a manually curated resource of signaling pathways (Database URL: http://www.netpath.org/pathways?path_id=NetPath_172 ). The current resource provides a foundation for the understanding of UNC5B-mediated cellular responses. The development of resource will serve researchers to explore the mechanisms of UNC-5B signaling in cancers.
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Affiliation(s)
- Sameer Ahmed Bhat
- Department of Biotechnology, University of Kashmir, Srinagar, 190006, India
| | - Sumrati Gurtoo
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, 575 018, India
| | | | | | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal Academy of Higher Education, Manipal, 576104, India
| | - Rohan Shetty
- Department of Surgical Oncology. Yenepoya Medical College, Yenepoya (Deemed to be University), Mangalore, 575 018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, 575 018, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Shaida Andrabi
- Department of Biochemistry, University of Kashmir, Srinagar, 190006, India.
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, 575 018, India.
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6
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Pinto SM, Subbannayya Y, Rex DAB, Raju R, Chatterjee O, Advani J, Radhakrishnan A, Keshava Prasad TS, Wani MR, Pandey A. A network map of IL-33 signaling pathway. J Cell Commun Signal 2018; 12:615-624. [PMID: 29705949 DOI: 10.1007/s12079-018-0464-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/02/2018] [Indexed: 12/19/2022] Open
Abstract
Interleukin-33 (IL-33) is a member of the IL-1 family of cytokines that play a central role in the regulation of immune responses. Its release from epithelial and endothelial cells is mediated by pro-inflammatory cytokines, cell damage and by recognition of pathogen-associated molecular patterns (PAMPs). The activity of IL-33 is mediated by binding to the IL-33 receptor complex (IL-33R) and activation of NF-κB signaling via the classical MyD88/IRAK/TRAF6 module. IL-33 also induces the phosphorylation and activation of ERK1/2, JNK, p38 and PI3K/AKT signaling modules resulting in the production and release of pro-inflammatory cytokines. Aberrant signaling by IL-33 has been implicated in the pathogenesis of several acute and chronic inflammatory diseases, including asthma, atopic dermatitis, rheumatoid arthritis and ulcerative colitis among others. Considering the biomedical importance of IL-33, we developed a pathway resource of signaling events mediated by IL-33/IL-33R in this study. Using data mined from the published literature, we describe an integrated pathway reaction map of IL-33/IL-33R consisting of 681 proteins and 765 reactions. These include information pertaining to 19 physical interaction events, 740 enzyme catalysis events, 6 protein translocation events, 4 activation/inhibition events, 9 transcriptional regulators and 2492 gene regulation events. The pathway map is publicly available through NetPath ( http://www.netpath.org /), a resource of human signaling pathways developed previously by our group. This resource will provide a platform to the scientific community in facilitating identification of novel therapeutic targets for diseases associated with dysregulated IL-33 signaling. Database URL: http://www.netpath.org/pathways?path_id=NetPath_120 .
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Affiliation(s)
- Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, India. .,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India.
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Rajesh Raju
- Computational Biology Group, Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Oishi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohan R Wani
- National Centre for Cell Science, S.P. Pune University Campus, Pune, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, India. .,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Oncology, Johns Hopkins University School of Medicine, 733, N Broadway, MRB 527, Baltimore, MD, USA.
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Mukherjee S, Bandyopadhyay A. Proteomics in India: the clinical aspect. Clin Proteomics 2016; 13:21. [PMID: 27822170 PMCID: PMC5097398 DOI: 10.1186/s12014-016-9122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 08/12/2016] [Indexed: 02/07/2023] Open
Abstract
Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human cancers and hematological disorders. Recently, some seminal works on clinical proteomics have been reported from several laboratories across India. This review aims to shed light on the increasing use of proteomics in India in a variety of biological conditions. It also highlights that India has the expertise and infrastructure needed for pursuing proteomics research in the country and to participate in global initiatives. Research in clinical proteomics is gradually picking up pace in India and its future seems very bright.
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Affiliation(s)
- Somaditya Mukherjee
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
| | - Arun Bandyopadhyay
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
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Verma R, Balakrishnan L, Sharma K, Khan AA, Advani J, Gowda H, Tripathy SP, Suar M, Pandey A, Gandotra S, Prasad TSK, Shankar S. A network map of Interleukin-10 signaling pathway. J Cell Commun Signal 2015; 10:61-7. [PMID: 26253919 DOI: 10.1007/s12079-015-0302-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/24/2015] [Indexed: 11/30/2022] Open
Abstract
Interleukin-10 (IL-10) is an anti-inflammatory cytokine with important immunoregulatory functions. It is primarily secreted by antigen-presenting cells such as activated T-cells, monocytes, B-cells and macrophages. In biologically functional form, it exists as a homodimer that binds to tetrameric heterodimer IL-10 receptor and induces downstream signaling. IL-10 is associated with survival, proliferation and anti-apoptotic activities of various cancers such as Burkitt lymphoma, non-Hodgkins lymphoma and non-small scell lung cancer. In addition, it plays a central role in survival and persistence of intracellular pathogens such as Leishmania donovani, Mycobacterium tuberculosis and Trypanosoma cruzi inside the host. The signaling mechanisms of IL-10 cytokine are not well explored and a well annotated pathway map has been lacking. To this end, we developed a pathway resource by manually annotating the IL-10 induced signaling molecules derived from literature. The reactions were categorized under molecular associations, activation/inhibition, catalysis, transport and gene regulation. In all, 37 molecules and 76 reactions were annotated. The IL-10 signaling pathway can be freely accessed through NetPath, a resource of signal transduction pathways previously developed by our group.
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Affiliation(s)
- Renu Verma
- International Technology Park, Whitefield,, Institute of Bioinformatics, Bangalore, 560 066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751 024, India
| | - Lavanya Balakrishnan
- International Technology Park, Whitefield,, Institute of Bioinformatics, Bangalore, 560 066, India
| | - Kusum Sharma
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160 012, India
| | - Aafaque Ahmad Khan
- International Technology Park, Whitefield,, Institute of Bioinformatics, Bangalore, 560 066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751 024, India
| | - Jayshree Advani
- International Technology Park, Whitefield,, Institute of Bioinformatics, Bangalore, 560 066, India.,Manipal University, Madhav Nagar, Manipal, 576 104, India
| | - Harsha Gowda
- International Technology Park, Whitefield,, Institute of Bioinformatics, Bangalore, 560 066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India
| | - Srikanth Prasad Tripathy
- Department of Microbiology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (Indian Council of Medical Research), Agra, 282 004, India
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751 024, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Baltimore, MD, USA.,Departments of Biological Chemistry, Johns Hopkins University School of Medicine, 733N. Broadway, Baltimore, MD, 21205, USA.,Departments of Oncology, Johns Hopkins University School of Medicine, 733N. Broadway, Baltimore, MD, 21205, USA.,Departments of Pathology, Johns Hopkins University School of Medicine, 733N. Broadway, Baltimore, MD, 21205, USA
| | - Sheetal Gandotra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110 020, India
| | - T S Keshava Prasad
- International Technology Park, Whitefield,, Institute of Bioinformatics, Bangalore, 560 066, India. .,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India.
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9
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Tripathi S, Flobak Å, Chawla K, Baudot A, Bruland T, Thommesen L, Kuiper M, Lægreid A. The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. BMC SYSTEMS BIOLOGY 2015. [PMID: 26205660 PMCID: PMC4513977 DOI: 10.1186/s12918-015-0181-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background The gastrointestinal peptide hormones cholecystokinin and gastrin exert their biological functions via cholecystokinin receptors CCK1R and CCK2R respectively. Gastrin, a central regulator of gastric acid secretion, is involved in growth and differentiation of gastric and colonic mucosa, and there is evidence that it is pro-carcinogenic. Cholecystokinin is implicated in digestion, appetite control and body weight regulation, and may play a role in several digestive disorders. Results We performed a detailed analysis of the literature reporting experimental evidence on signaling pathways triggered by CCK1R and CCK2R, in order to create a comprehensive map of gastrin and cholecystokinin-mediated intracellular signaling cascades. The resulting signaling map captures 413 reactions involving 530 molecular species, and incorporates the currently available knowledge into one integrated signaling network. The decomposition of the signaling map into sub-networks revealed 18 modules that represent higher-level structures of the signaling map. These modules allow a more compact mapping of intracellular signaling reactions to known cell behavioral outcomes such as proliferation, migration and apoptosis. The integration of large-scale protein-protein interaction data to this literature-based signaling map in combination with topological analyses allowed us to identify 70 proteins able to increase the compactness of the map. These proteins represent experimentally testable hypotheses for gaining new knowledge on gastrin- and cholecystokinin receptor signaling. The CCKR map is freely available both in a downloadable, machine-readable SBML-compatible format and as a web resource through PAYAO (http://sblab.celldesigner.org:18080/Payao11/bin/). Conclusion We have demonstrated how a literature-based CCKR signaling map together with its protein interaction extensions can be analyzed to generate new hypotheses on molecular mechanisms involved in gastrin- and cholecystokinin-mediated regulation of cellular processes. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0181-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sushil Tripathi
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7489, Trondheim, Norway.
| | - Åsmund Flobak
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7489, Trondheim, Norway.
| | - Konika Chawla
- Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway.
| | - Anaïs Baudot
- I2M, Marseilles Institute of Mathematics CNRS - AMU, Case 907, 13288, Marseille, Cedex 9, France.
| | - Torunn Bruland
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7489, Trondheim, Norway.
| | - Liv Thommesen
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7489, Trondheim, Norway. .,Department of Technology, Sør-Trøndelag University College, N-7004, Trondheim, Norway.
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway.
| | - Astrid Lægreid
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7489, Trondheim, Norway. .,Institute of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7489, Trondheim, Norway.
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