메뉴 건너뛰기




Volumn 43, Issue , 2017, Pages 156-172

Exo-MFA – A 13C metabolic flux analysis framework to dissect tumor microenvironment-secreted exosome contributions towards cancer cell metabolism

Author keywords

13C metabolic flux analysis; Cancer metabolism; Exo MFA; Exosomes; Intercellular metabolic flux analysis; Tumor microenvironment

Indexed keywords

AMINO ACIDS; BIOMOLECULES; CARBON; CELL CULTURE; CELLS; CYTOLOGY; DISEASES; ENZYME ACTIVITY; METABOLITES; NUCLEIC ACIDS; PATHOLOGY; PHYSIOLOGY; TUMORS;

EID: 85010858485     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2017.01.001     Document Type: Article
Times cited : (64)

References (50)
  • 1
    • 84962733931 scopus 로고    scopus 로고
    • Introduction to extracellular vesicles: biogenesis RNA Cargo Selection, Content, Release, and Uptake
    • Abels, E.R., Breakefield, X.O., Introduction to extracellular vesicles: biogenesis RNA Cargo Selection, Content, Release, and Uptake. Cell. Mol. Neurobiol. 36 (2016), 301–312, 10.1007/s10571-016-0366-z.
    • (2016) Cell. Mol. Neurobiol. , vol.36 , pp. 301-312
    • Abels, E.R.1    Breakefield, X.O.2
  • 2
    • 33845679072 scopus 로고    scopus 로고
    • Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions
    • Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab. Eng. 9 (2007), 68–86, 10.1016/j.ymben.2006.09.001.
    • (2007) Metab. Eng. , vol.9 , pp. 68-86
    • Antoniewicz, M.R.1    Kelleher, J.K.2    Stephanopoulos, G.3
  • 3
    • 84855684934 scopus 로고    scopus 로고
    • Optimality and thermodynamics determine the evolution of transcriptional regulatory networks
    • Avila-Elchiver, M., Nagrath, D., Yarmush, M.L., Optimality and thermodynamics determine the evolution of transcriptional regulatory networks. Mol. Biosyst. 8 (2012), 511–530, 10.1039/c1mb05177f.
    • (2012) Mol. Biosyst. , vol.8 , pp. 511-530
    • Avila-Elchiver, M.1    Nagrath, D.2    Yarmush, M.L.3
  • 4
    • 84865683757 scopus 로고    scopus 로고
    • Oncosecretomics coupled to bioenergetics identifies α-amino adipic acid, isoleucine and GABA as potential biomarkers of cancer: Differential expression of c-Myc, Oct1 and KLF4 coordinates metabolic changes
    • Bellance, N., Pabst, L., Allen, G., Rossignol, R., Nagrath, D., Oncosecretomics coupled to bioenergetics identifies α-amino adipic acid, isoleucine and GABA as potential biomarkers of cancer: Differential expression of c-Myc, Oct1 and KLF4 coordinates metabolic changes. Biochim. Biophys. Acta 1817 (2012), 2060–2071, 10.1016/j.bbabio.2012.07.004.
    • (2012) Biochim. Biophys. Acta , vol.1817 , pp. 2060-2071
    • Bellance, N.1    Pabst, L.2    Allen, G.3    Rossignol, R.4    Nagrath, D.5
  • 5
    • 50349092811 scopus 로고    scopus 로고
    • Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach
    • Bennett, B.D., Yuan, J., Kimball, E.H., Rabinowitz, J.D., Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat. Protoc. 3 (2008), 1299–1311, 10.1038/nprot.2008.107.
    • (2008) Nat. Protoc. , vol.3 , pp. 1299-1311
    • Bennett, B.D.1    Yuan, J.2    Kimball, E.H.3    Rabinowitz, J.D.4
  • 6
    • 84892788440 scopus 로고    scopus 로고
    • Constraint-based models predict metabolic and associated cellular functions
    • Bordbar, A., Monk, J.M., King, Z.A., Palsson, B.O., Constraint-based models predict metabolic and associated cellular functions. Nat. Rev. Genet. 15 (2014), 107–120, 10.1038/nrg3643.
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 107-120
    • Bordbar, A.1    Monk, J.M.2    King, Z.A.3    Palsson, B.O.4
  • 7
    • 84867589382 scopus 로고    scopus 로고
    • Pyruvate uptake is increased in highly invasive ovarian cancer cells under anoikis conditions for anaplerosis, mitochondrial function, and migration
    • Caneba, C.A., Bellance, N., Yang, L., Pabst, L., Nagrath, D., Pyruvate uptake is increased in highly invasive ovarian cancer cells under anoikis conditions for anaplerosis, mitochondrial function, and migration. Am. J. Physiol. - Endocrinol. Metab. 303 (2012), E1036–E1052, 10.1152/ajpendo.00151.2012.
    • (2012) Am. J. Physiol. - Endocrinol. Metab. , vol.303 , pp. E1036-E1052
    • Caneba, C.A.1    Bellance, N.2    Yang, L.3    Pabst, L.4    Nagrath, D.5
  • 8
    • 84928749945 scopus 로고    scopus 로고
    • New horizons in tumor microenvironment biology: challenges and opportunities
    • Chen, F., Zhuang, X., Lin, L., Yu, P., Wang, Y., Shi, Y., Hu, G., Sun, Y., New horizons in tumor microenvironment biology: challenges and opportunities. BMC Med., 13, 2015, 45, 10.1186/s12916-015-0278-7.
    • (2015) BMC Med. , vol.13 , pp. 45
    • Chen, F.1    Zhuang, X.2    Lin, L.3    Yu, P.4    Wang, Y.5    Shi, Y.6    Hu, G.7    Sun, Y.8
  • 9
    • 84886387008 scopus 로고    scopus 로고
    • Cancer cell exosomes depend on cell-surface heparan sulfate proteoglycans for their internalization and functional activity
    • Christianson, H.C., Svensson, K.J., Kuppevelt, T.H. van, Li, J.-P., Belting, M., Cancer cell exosomes depend on cell-surface heparan sulfate proteoglycans for their internalization and functional activity. Proc. Natl. Acad. Sci. 110 (2013), 17380–17385, 10.1073/pnas.1304266110.
    • (2013) Proc. Natl. Acad. Sci. , vol.110 , pp. 17380-17385
    • Christianson, H.C.1    Svensson, K.J.2    Kuppevelt, T.H.V.3    Li, J.-P.4    Belting, M.5
  • 11
    • 84904704297 scopus 로고    scopus 로고
    • Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles
    • Colombo, M., Raposo, G., Théry, C., Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles. Annu. Rev. Cell Dev. Biol. 30 (2014), 255–289, 10.1146/annurev-cellbio-101512-122326.
    • (2014) Annu. Rev. Cell Dev. Biol. , vol.30 , pp. 255-289
    • Colombo, M.1    Raposo, G.2    Théry, C.3
  • 13
    • 84990224053 scopus 로고    scopus 로고
    • Fundamentals of cancer metabolism
    • DeBerardinis, R.J., Chandel, N.S., Fundamentals of cancer metabolism. Sci. Adv., 2016, 2, 10.1126/sciadv.1600200.
    • (2016) Sci. Adv. , pp. 2
    • DeBerardinis, R.J.1    Chandel, N.S.2
  • 14
    • 84883514161 scopus 로고    scopus 로고
    • Targeting lactate metabolism for cancer therapeutics
    • Doherty, J.R., Cleveland, J.L., Targeting lactate metabolism for cancer therapeutics. J. Clin. Invest. 123 (2013), 3685–3692, 10.1172/JCI69741.
    • (2013) J. Clin. Invest. , vol.123 , pp. 3685-3692
    • Doherty, J.R.1    Cleveland, J.L.2
  • 15
    • 84862618600 scopus 로고    scopus 로고
    • Tumor-derived microvesicles: shedding light on novel microenvironment modulators and prospective cancer biomarkers
    • D'Souza-Schorey, C., Clancy, J.W., Tumor-derived microvesicles: shedding light on novel microenvironment modulators and prospective cancer biomarkers. Genes Dev. 26 (2012), 1287–1299, 10.1101/gad.192351.112.
    • (2012) Genes Dev. , vol.26 , pp. 1287-1299
    • D'Souza-Schorey, C.1    Clancy, J.W.2
  • 17
    • 77953154769 scopus 로고    scopus 로고
    • Cellular internalization of exosomes occurs through phagocytosis
    • Feng, D., Zhao, W.-L., Ye, Y.-Y., Bai, X.-C., Liu, R.-Q., Chang, L.-F., Zhou, Q., Sui, S.-F., Cellular internalization of exosomes occurs through phagocytosis. Traffic 11 (2010), 675–687, 10.1111/j.1600-0854.2010.01041.x.
    • (2010) Traffic , vol.11 , pp. 675-687
    • Feng, D.1    Zhao, W.-L.2    Ye, Y.-Y.3    Bai, X.-C.4    Liu, R.-Q.5    Chang, L.-F.6    Zhou, Q.7    Sui, S.-F.8
  • 18
    • 84904173553 scopus 로고    scopus 로고
    • Metabolism of stromal and immune cells in health and disease
    • Ghesquière, B., Wong, B.W., Kuchnio, A., Carmeliet, P., Metabolism of stromal and immune cells in health and disease. Nature 511 (2014), 167–176, 10.1038/nature13312.
    • (2014) Nature , vol.511 , pp. 167-176
    • Ghesquière, B.1    Wong, B.W.2    Kuchnio, A.3    Carmeliet, P.4
  • 20
    • 84957564275 scopus 로고    scopus 로고
    • Targeting the tumour microenvironment in ovarian cancer
    • Hansen, J.M., Coleman, R.L., Sood, A.K., Targeting the tumour microenvironment in ovarian cancer. Eur. J. Cancer 56 (2016), 131–143, 10.1016/j.ejca.2015.12.016.
    • (2016) Eur. J. Cancer , vol.56 , pp. 131-143
    • Hansen, J.M.1    Coleman, R.L.2    Sood, A.K.3
  • 21
    • 81155126061 scopus 로고    scopus 로고
    • Lactate: a metabolic key player in cancer
    • Hirschhaeuser, F., Sattler, U.G.A., Mueller-Klieser, W., Lactate: a metabolic key player in cancer. Cancer Res. 71 (2011), 6921–6925, 10.1158/0008-5472.CAN-11-1457.
    • (2011) Cancer Res. , vol.71 , pp. 6921-6925
    • Hirschhaeuser, F.1    Sattler, U.G.A.2    Mueller-Klieser, W.3
  • 23
    • 84912088491 scopus 로고    scopus 로고
    • Estimating relative changes of metabolic fluxes
    • Huang, L., Kim, D., Liu, X., Myers, C.R., Locasale, J.W., Estimating relative changes of metabolic fluxes. PLOS Comput Biol., 10, 2014, e1003958, 10.1371/journal.pcbi.1003958.
    • (2014) PLOS Comput Biol. , vol.10 , pp. e1003958
    • Huang, L.1    Kim, D.2    Liu, X.3    Myers, C.R.4    Locasale, J.W.5
  • 27
    • 34249708861 scopus 로고    scopus 로고
    • Integrated energy and flux balance based multiobjective framework for large-scale metabolic networks
    • Nagrath, D., Avila-Elchiver, M., Berthiaume, F., Tilles, A.W., Messac, A., Yarmush, M.L., Integrated energy and flux balance based multiobjective framework for large-scale metabolic networks. Ann. Biomed. Eng. 35 (2007), 863–885, 10.1007/s10439-007-9283-0.
    • (2007) Ann. Biomed. Eng. , vol.35 , pp. 863-885
    • Nagrath, D.1    Avila-Elchiver, M.2    Berthiaume, F.3    Tilles, A.W.4    Messac, A.5    Yarmush, M.L.6
  • 29
    • 84944279491 scopus 로고    scopus 로고
    • Extracellular vesicles as carriers of microRNA, proteins and lipids in tumor microenvironment
    • Penfornis, P., Vallabhaneni, K.C., Whitt, J., Pochampally, R., Extracellular vesicles as carriers of microRNA, proteins and lipids in tumor microenvironment. Int. J. Cancer 138 (2016), 14–21, 10.1002/ijc.29417.
    • (2016) Int. J. Cancer , vol.138 , pp. 14-21
    • Penfornis, P.1    Vallabhaneni, K.C.2    Whitt, J.3    Pochampally, R.4
  • 30
    • 66949164842 scopus 로고    scopus 로고
    • OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis
    • Quek, L.-E., Wittmann, C., Nielsen, L.K., Krömer, J.O., OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis. Microb. Cell Factor., 8, 2009, 25, 10.1186/1475-2859-8-25.
    • (2009) Microb. Cell Factor. , vol.8 , pp. 25
    • Quek, L.-E.1    Wittmann, C.2    Nielsen, L.K.3    Krömer, J.O.4
  • 32
    • 84920972493 scopus 로고    scopus 로고
    • Nitric oxide mediates metabolic coupling of omentum-derived adipose to ovarian and endometrial cancer cells
    • Salimian, B., Caneba, C., Nowicka, A., Nabiyar, A.W., Liu, X., Chen, K., Klopp, A., Nagrath, D., Nitric oxide mediates metabolic coupling of omentum-derived adipose to ovarian and endometrial cancer cells. Cancer Res. canres., 1337, 2014, 2014, 10.1158/0008-5472.CAN-14-1337.
    • (2014) Cancer Res. canres. , vol.1337 , pp. 2014
    • Salimian, B.1    Caneba, C.2    Nowicka, A.3    Nabiyar, A.W.4    Liu, X.5    Chen, K.6    Klopp, A.7    Nagrath, D.8
  • 33
  • 34
    • 0343471424 scopus 로고    scopus 로고
    • Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices
    • Schmidt, K., Carlsen, M., Nielsen, J., Villadsen, J., Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55 (1997), 831–840, 10.1002/(SICI)1097-0290(19970920)55:6<831::AID-BIT2>3.0.CO;2-H.
    • (1997) Biotechnol. Bioeng. , vol.55 , pp. 831-840
    • Schmidt, K.1    Carlsen, M.2    Nielsen, J.3    Villadsen, J.4
  • 35
    • 13544265458 scopus 로고    scopus 로고
    • Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of mus musculus
    • Sheikh, K., Förster, J., Nielsen, L.K., Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of mus musculus. Biotechnol. Prog. 21 (2005), 112–121, 10.1021/bp0498138.
    • (2005) Biotechnol. Prog. , vol.21 , pp. 112-121
    • Sheikh, K.1    Förster, J.2    Nielsen, L.K.3
  • 38
    • 84927943823 scopus 로고    scopus 로고
    • Extracellular vesicles: potential applications in cancer diagnosis, prognosis, and epidemiology
    • Verma, M., Lam, T.K., Hebert, E., Divi, R.L., Extracellular vesicles: potential applications in cancer diagnosis, prognosis, and epidemiology. BMC Clin. Pathol., 2015, 15, 10.1186/s12907-015-0005-5.
    • (2015) BMC Clin. Pathol. , pp. 15
    • Verma, M.1    Lam, T.K.2    Hebert, E.3    Divi, R.L.4
  • 39
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • Wang, Y., Eddy, J.A., Price, N.D., Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst. Biol., 6, 2012, 153, 10.1186/1752-0509-6-153.
    • (2012) BMC Syst. Biol. , vol.6 , pp. 153
    • Wang, Y.1    Eddy, J.A.2    Price, N.D.3
  • 40
    • 84871768724 scopus 로고    scopus 로고
    • 13CFLUX2—high-performance software suite for 13C-metabolic flux analysis
    • Weitzel, M., Nöh, K., Dalman, T., Niedenführ, S., Stute, B., Wiechert, W., 13CFLUX2—high-performance software suite for 13C-metabolic flux analysis. Bioinformatics 29 (2013), 143–145, 10.1093/bioinformatics/bts646.
    • (2013) Bioinformatics , vol.29 , pp. 143-145
    • Weitzel, M.1    Nöh, K.2    Dalman, T.3    Niedenführ, S.4    Stute, B.5    Wiechert, W.6
  • 41
    • 0031554628 scopus 로고    scopus 로고
    • Bidirectional reaction steps in metabolic networks: II. Flux estimation and statistical analysis
    • Wiechert, W., Siefke, C., de Graaf, A.A., Marx, A., Bidirectional reaction steps in metabolic networks: II. Flux estimation and statistical analysis. Biotechnol. Bioeng. 55 (1997), 118–135, 10.1002/(SICI)1097-0290(19970705)55:1<118::AID-BIT13>3.0.CO;2-I.
    • (1997) Biotechnol. Bioeng. , vol.55 , pp. 118-135
    • Wiechert, W.1    Siefke, C.2    de Graaf, A.A.3    Marx, A.4
  • 42
    • 0031554635 scopus 로고    scopus 로고
    • Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments
    • Wiechert, W., de Graaf, A.A., Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnol. Bioeng. 55 (1997), 101–117, 10.1002/(SICI)1097-0290(19970705)55:1<101::AID-BIT12>3.0.CO;2-P.
    • (1997) Biotechnol. Bioeng. , vol.55 , pp. 101-117
    • Wiechert, W.1    de Graaf, A.A.2
  • 45
    • 84899511589 scopus 로고    scopus 로고
    • INCA: a computational platform for isotopically non-stationary metabolic flux analysis
    • Young, J.D., INCA: a computational platform for isotopically non-stationary metabolic flux analysis. Bioinformatics 30 (2014), 1333–1335, 10.1093/bioinformatics/btu015.
    • (2014) Bioinformatics , vol.30 , pp. 1333-1335
    • Young, J.D.1
  • 46
    • 66749182798 scopus 로고    scopus 로고
    • 13C-based metabolic flux analysis
    • Zamboni, N., Fendt, S.-M., Rühl, M., Sauer, U., 13C-based metabolic flux analysis. Nat. Protoc. 4 (2009), 878–892, 10.1038/nprot.2009.58.
    • (2009) Nat. Protoc. , vol.4 , pp. 878-892
    • Zamboni, N.1    Fendt, S.-M.2    Rühl, M.3    Sauer, U.4
  • 47
    • 84925686613 scopus 로고    scopus 로고
    • Exosome and exosomal microRNA: trafficking, sorting, and function
    • Zhang, J., Li, S., Li, L., Li, M., Guo, C., Yao, J., Mi, S., Exosome and exosomal microRNA: trafficking, sorting, and function. Genom. Proteom. Bioinforma. 13 (2015), 17–24, 10.1016/j.gpb.2015.02.001.
    • (2015) Genom. Proteom. Bioinforma. , vol.13 , pp. 17-24
    • Zhang, J.1    Li, S.2    Li, L.3    Li, M.4    Guo, C.5    Yao, J.6    Mi, S.7
  • 49
    • 84917735280 scopus 로고    scopus 로고
    • Pancreatic cancer diagnosis by free and exosomal miRNA
    • Zöller, M., Pancreatic cancer diagnosis by free and exosomal miRNA. World J. Gastrointest. Pathophysiol. 4 (2013), 74–90, 10.4291/wjgp.v4.i4.74.
    • (2013) World J. Gastrointest. Pathophysiol. , vol.4 , pp. 74-90
    • Zöller, M.1
  • 50
    • 0028036096 scopus 로고
    • Modeling of isotope distributions and intracellular fluxes in metabolic networks using atom mapping matrices
    • Zupke, C., Stephanopoulos, G., Modeling of isotope distributions and intracellular fluxes in metabolic networks using atom mapping matrices. Biotechnol. Prog. 10 (1994), 489–498, 10.1021/bp00029a006.
    • (1994) Biotechnol. Prog. , vol.10 , pp. 489-498
    • Zupke, C.1    Stephanopoulos, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.