Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma.
Swagatika Sahoo,Ranjith Kumar,Brandon Nicolay,Omkar Satyavan Mohite,Omkar Satyavan Mohite,Karthikeyan Sivaraman,Vikas Khetan,Pukhraj Rishi,Suganeswari Ganesan,Krishnakumar Subramanyan,Karthik Raman,Wayne O. Miles,Wayne O. Miles,Sailaja Elchuri +13 more
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This is the first study that uses constraint‐based reconstruction and analysis approaches to identify and explain RB‐specific survival strategies, which are RB tumor specific, and suggests that novel biomarkers involved in lipid metabolism may be important.About:
This article is published in FEBS Letters.The article was published on 2019-01-01 and is currently open access. It has received 10 citations till now. The article focuses on the topics: Retinoblastoma.read more
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Leveraging genome-scale metabolic models for human health applications.
TL;DR: This review focuses on recent application of GEMs to studying cancer and the human microbiome by describing the enabling methodologies and outcomes of these studies and proposing some areas of research that are likely to arise as a result of recent methodological advances.
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Integrated Analysis of Cancer Tissue and Vitreous Humor from Retinoblastoma Eyes Reveals Unique Tumor-Specific Metabolic and Cellular Pathways in Advanced and Non-Advanced Tumors
Vishnu Suresh Babu,Ashwin Mallipatna,Deepak Sa,Gagan Dudeja,Ramaraj Kannan,Rohit Shetty,Archana Padmanabhan Nair,Seetharamanjaneyulu Gundimeda,Shyam S Chaurasia,Navin Kumar Verma,Rajamani Lakshminarayanan,Stephane Heymans,Veluchamy A. Barathi,Nilanjan Guha,Arkasubhra Ghosh +14 more
TL;DR: An integrated omics analysis of the transcriptomics and metabolomics of Rb uncovered a significantly altered tumor-specific metabolic circuit that reduces its dependence on glycolytic pathways and is governed by Rb1 and HK1.
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The regulatory landscape of retinoblastoma: a pathway analysis perspective
Laura Gómez-Romero,Diana Alvarez-Suarez,Enrique Hernández-Lemus,M V Ponce-Castañeda,Hugo Tovar +4 more
TL;DR: This work reanalyse a dataset that contains normal retina samples to identify the individual genes whose expression is different in Rb in contrast with normal tissue, and determined the pathways whose global expression pattern is more distant from the global expression observed in normal tissue.
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Lack of Retinoblastoma Protein Shifts Tumor Metabolism from Glycolysis to OXPHOS and Allows the Use of Alternate Fuels
Vishnu Suresh Babu,Gagan Dudeja,Deepak Sa,Anadi Bisht,Rohit Shetty,Stephane Heymans,Nilanjan Guha,Arkasubhra Ghosh +7 more
TL;DR: RB1 or HK1 are demonstrated as critical regulators of the cellular bioenergetic profile and identify the altered tumor metabolism as a potential therapeutic target for cancers lacking functional Rb protein.
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Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer
TL;DR: This review summarizes the availability of Python software for several components of COBRA methods and their applications in cancer metabolism and concludes that these tools are evolving rapidly and should offer a readily accessible, versatile way to model the intricacies of cancer metabolism.
References
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The ins and outs of cholesterol in the vertebrate retina
TL;DR: What is known about these processes and the dynamics of cholesterol in the vertebrate retina are reviewed and some future avenues of research in this area are indicated.
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Incidence of retinoblastoma from 1958 to 1998 in Northern Europe: advantages of birth cohort analysis.
TL;DR: In this paper, the authors compared commonly used methods for calculating retinoblastoma incidence against birth cohort analysis, and found that the incidence of retinal cancer is stable in Northern Europe.
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GABA's control of stem and cancer cell proliferation in adult neural and peripheral niches.
TL;DR: GABA's presence as a near-universal signal that may be altered in tumor cells resulting in modified mitotic activity is discussed.
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Using the reconstructed genome-scale human metabolic network to study physiology and pathology.
TL;DR: Using the reconstructed genome‐scale human metabolic network to study physiology and pathology (Key Symposium) and J Intern Med 2012; 271: 131–141.
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Immunocytochemical localization of l-glutamate decar☐ylase, gamma-aminobutyric acid transaminase, cysteine sulfinic acid decar☐ylase, aspartate aminotransferase and somatostatin in rat retina
TL;DR: Findings suggest that in rat retina, GABA-containing cells occur in some types of amacrine cells only, while taurine and somatostatin appear in bothAmacrine and horizontal cells.