In Silico Modeling of Liver Metabolism in a Human Disease Reveals a Key Enzyme for Histidine and Histamine Homeostasis

Cell Reports

Volumn 15, Issue 10, 2016, Pages 2292-2300

  Pagliarini, Roberto ^a   Castello, Raffaele ^a   Napolitano, Francesco ^a   Borzone, Roberta ^a   Annunziata, Patrizia ^a   Mandrile, Giorgia ^b,c   De Marchi, Mario ^b,c   Brunetti Pierri, Nicola ^a,d   di Bernardo, Diego ^a,d  

^a TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^b SAN LUIGI GONZAGA UNIVERSITY HOSPITAL   (Italy)

^c UNIVERSITY OF TURIN   (Italy)

^d UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE AMINOTRANSFERASE; ALANINE GLYOXYLATE AMINOTRANSFERASE; GLYOXYLIC ACID; HISTAMINE; OXALIC ACID; ALANINE; AMINOTRANSFERASE; GLYOXYLATE AMINOTRANSFERASE; HISTIDINE; OXALIC ACID DERIVATIVE;

AGXT GENE; AMINO ACID BLOOD LEVEL; AMINO ACID METABOLISM; ANIMAL TISSUE; ARTICLE; BLOOD VESSEL PERMEABILITY; CATABOLISM; COMPUTER MODEL; CONTROLLED STUDY; DISEASE SEVERITY; GAIN OF FUNCTION MUTATION; GENE; GENE LOSS; GENOTYPE; HISTAMINE HOMEOSTASIS; HISTIDINE HOMEOSTASIS; HOMEOSTASIS; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; LIVER CELL; LIVER METABOLISM; LOSS OF FUNCTION MUTATION; MALE; METABOLOMICS; MOLECULAR DYNAMICS; MOUSE; NONHUMAN; OXALOSIS 1; PHENOTYPE; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; VALIDATION PROCESS; ANIMAL; BIOLOGICAL MODEL; CELL LINE; COMPUTER SIMULATION; ENZYMOLOGY; GENE SILENCING; LIVER; METABOLISM; METABOLOME; PATHOLOGY; URINE;

ALANINE; ALANINE TRANSAMINASE; ANIMALS; CELL LINE; COMPUTER SIMULATION; GENE KNOCKDOWN TECHNIQUES; HEPATOCYTES; HISTAMINE; HISTIDINE; HOMEOSTASIS; HUMANS; HYPEROXALURIA, PRIMARY; LIVER; MALE; METABOLOME; MICE; MODELS, BIOLOGICAL; OXALATES; TRANSAMINASES;

EID: 84969939698     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2016.05.014     Document Type: Article

References (38)

1. Asplin J.R. Hyperoxaluric calcium nephrolithiasis. Endocrinol. Metab. Clin. North Am. 2002, 31:927-949.
2. Brunetti-Pierri N., Ng P. Helper-dependent adenoviral vectors for liver-directed gene therapy. Hum. Mol. Genet. 2011, 20(R1):R7-R13.
3. Brunetti-Pierri N., Palmer D.J., Mane V., Finegold M., Beaudet A.L., Ng P. Increased hepatic transduction with reduced systemic dissemination and proinflammatory cytokines following hydrodynamic injection of helper-dependent adenoviral vectors. Mol. Ther. 2005, 12:99-106.
4. Brunetti-Pierri N., Ng T., Iannitti D.A., Palmer D.J., Beaudet A.L., Finegold M.J., Carey K.D., Cioffi W.G., Ng P. Improved hepatic transduction, reduced systemic vector dissemination, and long-term transgene expression by delivering helper-dependent adenoviral vectors into the surgically isolated liver of nonhuman primates. Hum. Gene Ther. 2006, 17:391-404.
5. Castello R., Borzone R., D'Aria S., Annunziata P., Piccolo P., Brunetti-Pierri N. Helper-dependent adenoviral vectors for liver-directed gene therapy of primary hyperoxaluria type 1. Gene Ther. 2016, 23:129-134.
6. Cerami E.G., Gross B.E., Demir E., Rodchenkov I., Babur O., Anwar N., Schultz N., Bader G.D., Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011, 39:D685-D690.
7. Chang C.F., Fan J.Y., Zhang F.C., Ma J., Xu C.S. Transcriptome atlas of eight liver cell types uncovers effects of histidine catabolites on rat liver regeneration. J. Genet. 2010, 89:425-436.
8. Childs B. Sir Archibald Garrod's conception of chemical individuality: a modern appreciation. N. Engl. J. Med. 1970, 282:71-77.
9. Cochat P., Hulton S.A., Acquaviva C., Danpure C.J., Daudon M., De Marchi M., Fargue S., Groothoff J., Harambat J., Hoppe B., et al. Primary hyperoxaluria Type 1: indications for screening and guidance for diagnosis and treatment. Nephrol. Dial. Transplant. 2012, 27:1729-1736. OxalEurope.
10. Cramer S.D., Ferree P.M., Lin K., Milliner D.S., Holmes R.P. The gene encoding hydroxypyruvate reductase (GRHPR) is mutated in patients with primary hyperoxaluria type II. Hum. Mol. Genet. 1999, 8:2063-2069.
11. D'Eustachio P. Reactome knowledgebase of human biological pathways and processes. Methods Mol. Biol. 2011, 694:49-61.
12. Danpure C.J. Peroxisomal alanine:glyoxylate aminotransferase and prenatal diagnosis of primary hyperoxaluria type 1. Lancet 1986, 2:1168.
13. Danpure C.J. Primary hyperoxaluria type 1: AGT mistargeting highlights the fundamental differences between the peroxisomal and mitochondrial protein import pathways. Biochim. Biophys. Acta 2006, 1763:1776-1784.
14. Donelan J., Boucher W., Papadopoulou N., Lytinas M., Papaliodis D., Dobner P., Theoharides T.C. Corticotropin-releasing hormone induces skin vascular permeability through a neurotensin-dependent process. Proc. Natl. Acad. Sci. USA 2006, 103:7759-7764.
15. Donini S., Ferrari M., Fedeli C., Faini M., Lamberto I., Marletta A.S., Mellini L., Panini M., Percudani R., Pollegioni L., et al. Recombinant production of eight human cytosolic aminotransferases and assessment of their potential involvement in glyoxylate metabolism. Biochem. J. 2009, 422:265-272.
16. Duarte N.C., Becker S.A., Jamshidi N., Thiele I., Mo M.L., Vo T.D., Srivas R., Palsson B.O. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. USA 2007, 104:1777-1782.
17. Folger O., Jerby L., Frezza C., Gottlieb E., Ruppin E., Shlomi T. Predicting selective drug targets in cancer through metabolic networks. Mol. Syst. Biol. 2011, 7:501.
18. Gille C., Bölling C., Hoppe A., Bulik S., Hoffmann S., Hübner K., Karlstädt A., Ganeshan R., König M., Rother K., et al. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol. Syst. Biol. 2010, 6:411.
19. Holzhütter H.G. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur. J. Biochem. 2004, 271:2905-2922.
20. Hoppe B., Beck B.B., Milliner D.S. The primary hyperoxalurias. Kidney Int. 2009, 75:1264-1271.
21. Jerby L., Shlomi T., Ruppin E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol. Syst. Biol. 2010, 6:401.
22. Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28:27-30.
23. Lanpher B., Brunetti-Pierri N., Lee B. Inborn errors of metabolism: the flux from Mendelian to complex diseases. Nat. Rev. Genet. 2006, 7:449-460.
24. Ma H., Sorokin A., Mazein A., Selkov A., Selkov E., Demin O., Goryanin I. The Edinburgh human metabolic network reconstruction and its functional analysis. Mol. Syst. Biol. 2007, 3:135.
25. Nguyen Q.V., Kälin A., Drouve U., Casez J.P., Jaeger P. Sensitivity to meat protein intake and hyperoxaluria in idiopathic calcium stone formers. Kidney Int. 2001, 59:2273-2281.
26. Orth J.D., Thiele I., Palsson B.O. What is flux balance analysis?. Nat. Biotechnol. 2010, 28:245-248.
27. Pagliarini R., di Bernardo D. A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient. J. Comput. Biol. 2013, 20:383-397.
28. Pastore N., Blomenkamp K., Annunziata F., Piccolo P., Mithbaokar P., Maria Sepe R., Vetrini F., Palmer D., Ng P., Polishchuk E., et al. Gene transfer of master autophagy regulator TFEB results in clearance of toxic protein and correction of hepatic disease in alpha-1-anti-trypsin deficiency. EMBO Mol. Med. 2013, 5:397-412.
29. Piccolo P., Brunetti-Pierri N. Gene therapy for inherited diseases of liver metabolism. Hum. Gene Ther. 2015, 26:186-192.
30. Rosenthaler J., Guirard B.M., Chang G.W., Snell E.E. Purification and properties of histidine decarboxylase from Lactobacillus 30a. Proc. Natl. Acad. Sci. USA 1965, 54:152-158.
31. Salido E.C., Li X.M., Lu Y., Wang X., Santana A., Roy-Chowdhury N., Torres A., Shapiro L.J., Roy-Chowdhury J. Alanine-glyoxylate aminotransferase-deficient mice, a model for primary hyperoxaluria that responds to adenoviral gene transfer. Proc. Natl. Acad. Sci. USA 2006, 103:18249-18254.
32. Shlomi T., Cabili M.N., Ruppin E. Predicting metabolic biomarkers of human inborn errors of metabolism. Mol. Syst. Biol. 2009, 5:263.
33. Thiele I., Swainston N., Fleming R.M., Hoppe A., Sahoo S., Aurich M.K., Haraldsdottir H., Mo M.L., Rolfsson O., Stobbe M.D., et al. A community-driven global reconstruction of human metabolism. Nat. Biotechnol. 2013, 31:419-425.
34. Tran V.T., Snyder S.H. Histidine decarboxylase. Purification from fetal rat liver, immunologic properties, and histochemical localization in brain and stomach. J. Biol. Chem. 1981, 256:680-686.
35. Xia J., Wishart D.S. MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res. 2010, 38:W71-W77.
36. Xu H., Zisman A.L., Coe F.L., Worcester E.M. Kidney stones: an update on current pharmacological management and future directions. Expert Opin. Pharmacother. 2013, 14:435-447.
37. Yizhak K., Le Devedec S.E., Rogkoti V.M., Baenke F., de Boer V.C., Frezza C., Schulze A., van de Water B., Ruppin E. A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration. Mol. Syst. Biol. 2014, 10:744.
38. Yoshikawa T., Nakamura T., Shibakusa T., Sugita M., Naganuma F., Iida T., Miura Y., Mohsen A., Harada R., Yanai K. Insufficient intake of L-histidine reduces brain histamine and causes anxiety-like behaviors in male mice. J. Nutr. 2014, 144:1637-1641.