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Prediction of therapeutic microRNA based on the human metabolic network

Ming Wu, Christina Chan
2014 Computer applications in the biosciences : CABIOS  
to reduce cancer cell growth.  ...  We address this challenge by integrating miRNA-target prediction, metabolic modeling and context-specific gene expression data to predict therapeutic miRNAs that could reduce the growth of cancer.  ...  Our approach takes advantage of current knowledge of the human metabolic network to reconstruct a context-specific metabolic system for human liver cancer (HCC).  ... 
doi:10.1093/bioinformatics/btt751 pmid:24403541 pmcid:PMC3982155 fatcat:dvrour74fvdojgoeqc7bdncg3a

Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells

Jorge Ferreira, Sara Correia, Miguel Rocha
2017 Interdisciplinary Sciences Computational Life Sciences  
These methods will be applied to the reconstruction of metabolic models for hepatocyte cells and HepG2 cancer cell line.  ...  In this study, we will analyze four different algorithms (MBA, mCADRE, tINIT and FASTCORE) for tissue-specific model reconstruction, based on a template model and two types of data sources: transcriptomics  ...  Acknowledgements This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145  ... 
doi:10.1007/s12539-017-0214-y pmid:28255832 fatcat:qoj7vkgopzeudbrpntm4edw3xq

Large-scale computational models of liver metabolism: How far from the clinics?

Tanja Cvitanović, Matthias C. Reichert, Miha Moškon, Miha Mraz, Frank Lammert, Damjana Rozman
2017 Hepatology  
Understanding the dynamics of human liver metabolism is fundamental for effective diagnosis and treatment of liver diseases.  ...  Herein, we review the state-of-the-art computational models that describe liver dynamics from metabolic, gene regulatory, and signal transduction perspectives.  ...  oriented modeling; PBRK, physiologically based pharmacokinetic model; PRIME, personalized reconstruction of metabolic models; PSPH, phosphoserine phosphatase; RAVEN, Reconstruction, Analysis, and Visualization  ... 
doi:10.1002/hep.29268 pmid:28520105 fatcat:4s57ktybfzag5dk3l4jk72j2oq

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

Yuliang Wang, James A Eddy, Nathan D Price
2012 BMC Systems Biology  
Using our method, we reconstructed draft genome-scale metabolic models for 126 human tissue and cell types.  ...  The global knowledgebase of metabolic functions categorized for the human genome (Human Recon 1) coupled with abundant high-throughput data now makes possible the reconstruction of tissue-specific metabolic  ...  The Model Building Algorithm (MBA), a current stateof-the-art computational method to build tissue-specific metabolic models, has been used to build liver, generic cancer, and two cancer cell line metabolic  ... 
doi:10.1186/1752-0509-6-153 pmid:23234303 pmcid:PMC3576361 fatcat:rw3ci6v2fjgvdox2fo5hodtivu

New paradigms for metabolic modeling of human cells

Adil Mardinoglu, Jens Nielsen
2015 Current Opinion in Biotechnology  
Here we review recent work on reconstruction of GEMs for human 30  ...  Highlights 16 We presented the timeline of generation and evaluation of global reconstructions of human 17 metabolism. 18 We reviewed the generation of the context specific GEMs through the use of human  ...  Algorithms for the reconstruction of cell/tissue-type specific models were 28 also reviewed. 29 9.  ... 
doi:10.1016/j.copbio.2014.12.013 pmid:25559199 fatcat:fagnmb2zsrdihfv6dlc43rccxa

Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer

Rachel H. Ng, Jihoon W. Lee, Priyanka Baloni, Christian Diener, James R. Heath, Yapeng Su
2022 Frontiers in Oncology  
These tools are evolving rapidly and should offer a readily accessible, versatile way to model the intricacies of cancer metabolism for identifying cancer-specific metabolic features that constitute potential  ...  This review summarizes the availability of Python software for several components of COBRA methods and their applications in cancer metabolism.  ...  ACKNOWLEDGMENTS We thank Herbert Sauro for comments on initial draft for Computation Systems Biology class at University of Washington.  ... 
doi:10.3389/fonc.2022.914594 pmid:35875150 pmcid:PMC9303011 fatcat:a6ccble3ovgengwbafhdyuhtdi

Cancer Metabolism: A Modeling Perspective

Pouyan Ghaffari, Adil Mardinoglu, Jens Nielsen
2015 Frontiers in Physiology  
Here, we review cancer-associated reprogramming of metabolism and highlight the capability of genome-scale metabolic modeling approaches in perceiving a system-level perspective of cancer metabolism and  ...  cell metabolism.  ...  JN acknowledges funding from the Novo Nordisk Foundation for research in his group.  ... 
doi:10.3389/fphys.2015.00382 pmid:26733270 pmcid:PMC4679931 fatcat:oodu4ha5dbfxfgug5fxdidhl74

Addressing the heterogeneity in liver diseases using biological networks

2020 Briefings in Bioinformatics  
Here, we review recent work on the reconstruction of cell/tissue-type and cancer-specific GEMs and their use in identifying metabolic changes occurring in response to liver disease development, stratification  ...  We also discuss how GEMs can be integrated with other biological networks for generating more comprehensive cell/tissue models.  ...  The reconstruction of cancer GEMs differs from non-cancer GEMs of the same cell/tissue type by having the formation of biomass as an additional metabolic task to ensure cell growth.  ... 
doi:10.1093/bib/bbaa002 pmid:32201876 pmcid:PMC7986590 fatcat:wis2yufpenb3nbjiludbgh6kdu

[11C]acetate PET Imaging is not Always Associated with Increased Lipogenesis in Hepatocellular Carcinoma in Mice

Lei Li, Li Che, Chunmei Wang, Joseph E. Blecha, Xiaolei Li, Henry F. VanBrocklin, Diego F. Calvisi, Michelle Puchowicz, Xin Chen, Youngho Seo
2015 Molecular Imaging and Biology  
Purpose-Altered metabolism, including increased glycolysis and de novo lipogenesis, is one of the hallmarks of cancer.  ...  Conclusion-Altogether, our study suggests that [ 11 C]acetate PET imaging can be a useful tool for imaging of a subset of HCCs.  ...  Acknowledgments We would like to thank Mariia Yuneva for her thoughtful comments for the manuscript. We also thank Stephanie T.  ... 
doi:10.1007/s11307-015-0915-8 pmid:26567114 pmcid:PMC4866912 fatcat:hllh4w2qene4rjhifdbuunblcy

Mechanistic Modeling of Gene Regulation and Metabolism Identifies Potential Targets for Hepatocellular Carcinoma

Renliang Sun, Yizhou Xu, Hang Zhang, Qiangzhen Yang, Ke Wang, Yongyong Shi, Zhuo Wang
2020 Frontiers in Genetics  
Comprehensive personalized metabolic analysis based on models generated from data of liver HCC in The Cancer Genome Atlas revealed 18 genes essential for tumorigenesis in all three subtypes of patients  ...  Taken together, the multi-scale regulatory-metabolic model provided a new approach to assess key mechanisms of HCC cell proliferation in the context of systems and suggested potential targets.  ...  Metabolic Network Models The genome-scale metabolic model of liver tissue used for integration was retrieved from the Human metabolic Atlas (HMA) Database (the 1 ).  ... 
doi:10.3389/fgene.2020.595242 pmid:33424926 pmcid:PMC7786279 fatcat:dzj2o5erzrca3fbyflntuycjaq

Stratification of Hepatocellular Carcinoma Patients Based on Acetate Utilization

Elias Björnson, Bani Mukhopadhyay, Anna Asplund, Nusa Pristovsek, Resat Cinar, Stefano Romeo, Mathias Uhlen, George Kunos, Jens Nielsen, Adil Mardinoglu
2015 Cell Reports  
Graphical Abstract Highlights d Reconstruction of a genome-scale metabolic model for HCC tumors d Revealing metabolic alterations in HCC d Analysis of the heterogeneous expression of ACSS1 and ACSS2 between  ...  We investigated the correlation between transcriptome and proteome of HCC and reconstructed a functional genome-scale metabolic model (GEM) for HCC.  ...  Cancer development involves major metabolic alterations (Carracedo et al., 2013) , and the complexity of metabolism has been captured by the reconstruction of genome-scale metabolic models (GEMs) (Lewis  ... 
doi:10.1016/j.celrep.2015.10.045 pmid:26655911 fatcat:knq7xujs4fc3hojecjltf5zy7e

Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a

Hua-Qing Wu, Mei-Ling Cheng, Jin-Mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu-Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F. Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang (+1 others)
2017 PLoS Computational Biology  
of liver cancer cells.  ...  metabolomics of liver cancer cells.  ...  In the future, a liver-specific metabolic model has to be reconstructed to achieve a non-zero flux of cell growth rate to account for metabolite dilution.  ... 
doi:10.1371/journal.pcbi.1005618 pmid:28686599 pmcid:PMC5536358 fatcat:6adpisomrjeovkkcihzf5ekuea

Reconstruction of Tissue-Specific Metabolic Networks Using CORDA

André Schultz, Amina A. Qutub, Costas D. Maranas
2016 PLoS Computational Biology  
Using CORDA, we developed a library of 76 healthy and 20 cancer tissue-specific reconstructions. These reconstructions identified which metabolic pathways are shared across diverse human tissues.  ...  Using CORDA, we developed a library of 76 healthy and 20 cancer-specific models of metabolism, which we used to identify PLOS Computational Biology |  ...  Britton for helpful discussions on the manuscript. We would also like to thank Dr. Jay Storz, from University of Nebraska, Dr. Zac Cheviron, from University of Montana, and Dr.  ... 
doi:10.1371/journal.pcbi.1004808 pmid:26942765 pmcid:PMC4778931 fatcat:t6gakilsofaj3htnsxmyitwrny

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

R. Agren, A. Mardinoglu, A. Asplund, C. Kampf, M. Uhlen, J. Nielsen
2014 Molecular Systems Biology  
Genome-scale metabolic models (GEMs) have proven useful as scaffolds for the integration of omics data for understanding the genotype-phenotype relationship in a mechanistic manner.  ...  We used this information to reconstruct personalized GEMs for six HCC patients based on the proteomics data, HMR 2.0, and a task-driven model reconstruction algorithm (tINIT).  ...  Author contributions RA and AM developed the tINIT algorithm and method for identifying antimetabolites. AM and RA performed the analysis of clinical data.  ... 
doi:10.1002/msb.145122 pmid:24646661 pmcid:PMC4017677 fatcat:mgnwxofuhnbi3lratrp7uhnvd4

Using the reconstructed genome-scale human metabolic network to study physiology and pathology

A. Bordbar, B. O. Palsson
2012 Journal of Internal Medicine  
In this mini-review, we focus on the reconstruction of the global human metabolic network and four classes of its application.  ...  There are currently more than 20 publications that utilize Recon 1, including studies of cancer, diabetes, host-pathogen interactions, heritable metabolic disorders and off-target drug binding effects.  ...  Acknowledgements We would like to thank Roger Chang for suggestions and discussions on the manuscript. This work was supported through a Grant from the National Institutes of Health (GM068837).  ... 
doi:10.1111/j.1365-2796.2011.02494.x pmid:22142339 pmcid:PMC3243107 fatcat:tpexhn5n5jh3xg6kpku5yz5boe
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