메뉴 건너뛰기




Volumn 75, Issue 11, 2015, Pages 2243-2253

Combined label-free quantitative proteomics and microRNA expression analysis of breast cancer unravel molecular differences with clinical implications

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN RECEPTOR; MICRORNA; RNA; ESTROGEN RECEPTOR ALPHA; TUMOR MARKER;

EID: 84939418932     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-14-1937     Document Type: Article
Times cited : (44)

References (56)
  • 3
    • 57449099068 scopus 로고    scopus 로고
    • Precision proteomics: The case for high resolution and high mass accuracy
    • Mann M, Kelleher NL. Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci U S A 2008;105:18132-8.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 18132-18138
    • Mann, M.1    Kelleher, N.L.2
  • 5
    • 84859892863 scopus 로고    scopus 로고
    • MicroRNA profiling: Approaches and considerations
    • Pritchard CC, Cheng HH, Tewari M. MicroRNA profiling: approaches and considerations. Nat Rev Genet 2012;13:358-69.
    • (2012) Nat Rev Genet , vol.13 , pp. 358-369
    • Pritchard, C.C.1    Cheng, H.H.2    Tewari, M.3
  • 6
    • 79960350722 scopus 로고    scopus 로고
    • Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches
    • Gamez-Pozo A, Sanchez-Navarro I, Calvo E, Diaz E, Miguel-Martin M, Lopez R, et al. Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches. Mol Biosyst 2011;7:2368-74.
    • (2011) Mol Biosyst , vol.7 , pp. 2368-2374
    • Gamez-Pozo, A.1    Sanchez-Navarro, I.2    Calvo, E.3    Diaz, E.4    Miguel-Martin, M.5    Lopez, R.6
  • 7
    • 71049141298 scopus 로고    scopus 로고
    • Equivalence of protein inventories obtained from formalin-fixed paraffinembedded and frozen tissue in multidimensional liquid chromatographytandem mass spectrometry shotgun proteomic analysis
    • SprungRWJr, Brock JW, Tanksley JP, LiM, Washington MK, Slebos RJ, et al. Equivalence of protein inventories obtained from formalin-fixed paraffinembedded and frozen tissue in multidimensional liquid chromatographytandem mass spectrometry shotgun proteomic analysis. Mol Cell Proteomics 2009;8:1988-98.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 1988-1998
    • Sprung, R.W.1    Brock, J.W.2    Tanksley, J.P.3    Li, M.4    Washington, M.K.5    Slebos, R.J.6
  • 8
    • 84864884853 scopus 로고    scopus 로고
    • Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near totalmRNA degradation
    • Hall JS, Taylor J, Valentine HR, Irlam JJ, Eustace A, Hoskin PJ, et al. Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near totalmRNA degradation. Br J Cancer 2012;107:684-94.
    • (2012) Br J Cancer , vol.107 , pp. 684-694
    • Hall, J.S.1    Taylor, J.2    Valentine, H.R.3    Irlam, J.J.4    Eustace, A.5    Hoskin, P.J.6
  • 9
    • 84874081594 scopus 로고    scopus 로고
    • A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17
    • Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, et al. A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J Proteome Res 2013;12: 45-57.
    • (2013) J Proteome Res , vol.12 , pp. 45-57
    • Liu, S.1    Im, H.2    Bairoch, A.3    Cristofanilli, M.4    Chen, R.5    Deutsch, E.W.6
  • 11
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007;8: 118-27.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 12
    • 77954079119 scopus 로고    scopus 로고
    • Comparison of gene expression profiling by reverse transcription quantitative PCR between fresh frozen and formalinfixed, paraffin-embedded breast cancer tissues
    • Sanchez-Navarro I, Gamez-Pozo A, Gonzalez-Baron M, Pinto-Marin A, Hardisson D, Lopez R, et al. Comparison of gene expression profiling by reverse transcription quantitative PCR between fresh frozen and formalinfixed, paraffin-embedded breast cancer tissues. Biotechniques 2010;48: 389-97.
    • (2010) Biotechniques , vol.48 , pp. 389-397
    • Sanchez-Navarro, I.1    Gamez-Pozo, A.2    Gonzalez-Baron, M.3    Pinto-Marin, A.4    Hardisson, D.5    Lopez, R.6
  • 13
    • 79959805164 scopus 로고    scopus 로고
    • MiRWalk-database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes
    • Dweep H, Sticht C, Pandey P, Gretz N. miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 2011;44:839-47.
    • (2011) J Biomed Inform , vol.44 , pp. 839-847
    • Dweep, H.1    Sticht, C.2    Pandey Gretz, P.N.3
  • 14
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • Schwarz G. Estimating the dimension of a model. Ann Stat 1978;6:461-4.
    • (1978) Ann Stat , vol.6 , pp. 461-464
    • Schwarz, G.1
  • 15
    • 0004047518 scopus 로고    scopus 로고
    • Oxford United Kingdom: Oxford University Press
    • Lauritzen S. Graphical models. Oxford, United Kingdom: Oxford University Press; 1996.
    • (1996) Graphical Models
    • Lauritzen, S.1
  • 16
    • 84933530882 scopus 로고
    • Approximating discrete probability distributions with dependence trees
    • Chow CK, Liu CN. Approximating discrete probability distributions with dependence trees. IEEE Trans Inform Theory 1968;14:462-7.
    • (1968) IEEE Trans Inform Theory , vol.14 , pp. 462-467
    • Chow, C.K.1    Liu, C.N.2
  • 17
    • 70350674995 scopus 로고
    • On the shortest spanning subtree of a graph and the traveling salesman problem
    • Kruskal JB. On the shortest spanning subtree of a graph and the traveling salesman problem. Proc Am Math Soc 1956;7:48-50.
    • (1956) Proc Am Math Soc , vol.7 , pp. 48-50
    • Kruskal, J.B.1
  • 19
  • 20
    • 78650561674 scopus 로고    scopus 로고
    • High-dimensional graphical model search with the gRapHD R package
    • Abreu GCG, Edwards D, Labouriau R. High-dimensional graphical model search with the gRapHD R package. J StatSoftw 2010;37:1-18.
    • (2010) J StatSoftw , vol.37 , pp. 1-18
    • Abreu, G.C.G.1    Edwards, D.2    Labouriau, R.3
  • 23
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Cancer Genome Atlas Network
    • Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 2012;490:61-70.
    • (2012) Nature , vol.490 , pp. 61-70
  • 25
    • 80051923932 scopus 로고    scopus 로고
    • Functional genomics reveal that the serine synthesis pathway is essential in breast cancer
    • Possemato R, Marks KM, Shaul YD, Pacold ME, Kim D, Birsoy K, et al. Functional genomics reveal that the serine synthesis pathway is essential in breast cancer. Nature 2011;476:346-50.
    • (2011) Nature , vol.476 , pp. 346-350
    • Possemato, R.1    Marks, K.M.2    Shaul, Y.D.3    Pacold, M.E.4    Kim, D.5    Birsoy, K.6
  • 26
  • 28
    • 84863570015 scopus 로고    scopus 로고
    • Glucose-regulated protein 78 controls cross-talk between apoptosis and autophagy to determine antiestrogen responsiveness
    • Cook KL, Shajahan AN, Warri A, Jin L, Hilakivi-Clarke LA, Clarke R. Glucose-regulated protein 78 controls cross-talk between apoptosis and autophagy to determine antiestrogen responsiveness. Cancer Res 2012;72: 3337-49.
    • (2012) Cancer Res , vol.72 , pp. 3337-3349
    • Cook, K.L.1    Shajahan, A.N.2    Warri, A.3    Jin, L.4    Hilakivi-Clarke, L.A.5    Clarke, R.6
  • 29
    • 0037463227 scopus 로고    scopus 로고
    • HAG-2 and hAG-3, human homologues of genes involved in differentiation, are associated with oestrogen receptor-positive breast tumours and interact with metastasis gene C4.4a and dystroglycan
    • Fletcher GC, Patel S, Tyson K, Adam PJ, Schenker M, Loader JA, et al. hAG-2 and hAG-3, human homologues of genes involved in differentiation, are associated with oestrogen receptor-positive breast tumours and interact with metastasis gene C4.4a and dystroglycan. Br J Cancer 2003;88:579-85.
    • (2003) Br J Cancer , vol.88 , pp. 579-585
    • Fletcher, G.C.1    Patel, S.2    Tyson, K.3    Adam, P.J.4    Schenker, M.5    Loader, J.A.6
  • 30
    • 84878638627 scopus 로고    scopus 로고
    • Prolactininduced protein (PIP) regulates proliferation of luminal A type breast cancer cells in an estrogen-independent manner
    • Baniwal SK, Chimge NO, Jordan VC, Tripathy D, Frenkel B. Prolactininduced protein (PIP) regulates proliferation of luminal A type breast cancer cells in an estrogen-independent manner. PLoS ONE 2013;8: e62361.
    • (2013) PLoS ONE , vol.8 , pp. e62361
    • Baniwal, S.K.1    Chimge, N.O.2    Jordan, V.C.3    Tripathy, D.4    Frenkel, B.5
  • 31
    • 84862874981 scopus 로고    scopus 로고
    • Identification of potential prognostic biomarkers for node-negative breast tumours by proteomic analysis: A multicentric 2004 national PHRC study
    • Descotes F, Jezequel P, Spyratos F, Campion L, Grenot C, Lerebours F, et al. Identification of potential prognostic biomarkers for node-negative breast tumours by proteomic analysis: a multicentric 2004 national PHRC study. Int J Oncol 2012;41:92-104.
    • (2012) Int J Oncol , vol.41 , pp. 92-104
    • Descotes, F.1    Jezequel, P.2    Spyratos, F.3    Campion, L.4    Grenot, C.5    Lerebours, F.6
  • 32
    • 84868028972 scopus 로고    scopus 로고
    • Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells
    • Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bahler J. Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell 2012;151:671-83.
    • (2012) Cell , vol.151 , pp. 671-683
    • Marguerat, S.1    Schmidt, A.2    Codlin, S.3    Chen, W.4    Aebersold, R.5    Bahler, J.6
  • 33
    • 69949189728 scopus 로고    scopus 로고
    • MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer
    • Lowery AJ, Miller N, Devaney A, McNeill RE, Davoren PA, Lemetre C, et al. MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer. Breast Cancer Res 2009; 11:R27.
    • (2009) Breast Cancer Res , vol.11 , pp. R27
    • Lowery, A.J.1    Miller, N.2    Devaney, A.3    McNeill, R.E.4    Davoren, P.A.5    Lemetre, C.6
  • 34
    • 84873120034 scopus 로고    scopus 로고
    • MiR-342 is associated with estrogen receptor-alpha expression and response to tamoxifen in breast cancer
    • He YJ, Wu JZ, Ji MH, Ma T, Qiao EQ, Ma R, et al. miR-342 is associated with estrogen receptor-alpha expression and response to tamoxifen in breast cancer. Exp Ther Med 2013;5:813-8.
    • (2013) Exp Ther Med , vol.5 , pp. 813-818
    • He, Y.J.1    Wu, J.Z.2    Ji, M.H.3    Ma, T.4    Qiao, E.Q.5    Ma, R.6
  • 36
    • 84900397618 scopus 로고    scopus 로고
    • MicroRNA profiling implies newmarkers of chemoresistance of triple-negative breast cancer
    • Ouyang M, Li Y, Ye S, Ma J, Lu L, Lv W, et al. MicroRNA profiling implies newmarkers of chemoresistance of triple-negative breast cancer. PLoSONE 2014;9:e96228.
    • (2014) PLoSONE , vol.9 , pp. e96228
    • Ouyang, M.1    Li, Y.2    Ye, S.3    Ma, J.4    Lu, L.5    Lv, W.6
  • 38
    • 79951879747 scopus 로고    scopus 로고
    • Integrating multiple types of data for signaling research: Challenges and opportunities
    • Wiley HS. Integrating multiple types of data for signaling research: challenges and opportunities. Sci Signal 2011;4:pe9.
    • (2011) Sci Signal , vol.4 , pp. pe9
    • Wiley, H.S.1
  • 39
    • 77954195272 scopus 로고    scopus 로고
    • Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
    • Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010;26:i237-45.
    • (2010) Bioinformatics , vol.26 , pp. i237-i245
    • Vaske, C.J.1    Benz, S.C.2    Sanborn, J.Z.3    Earl, D.4    Szeto, C.5    Zhu, J.6
  • 40
    • 79954613661 scopus 로고    scopus 로고
    • Micro- RNA-301 mediates proliferation and invasion in human breast cancer
    • Shi W, Gerster K, Alajez NM, Tsang J, Waldron L, Pintilie M, et al. Micro- RNA-301 mediates proliferation and invasion in human breast cancer. Cancer Res 2011;71:2926-37.
    • (2011) Cancer Res , vol.71 , pp. 2926-2937
    • Shi, W.1    Gerster, K.2    Alajez, N.M.3    Tsang, J.4    Waldron, L.5    Pintilie, M.6
  • 42
    • 22044442434 scopus 로고    scopus 로고
    • Cytokines and growth factors involved in apoptosis and proliferation of vascular smooth muscle cells
    • Rakesh K, Agrawal DK. Cytokines and growth factors involved in apoptosis and proliferation of vascular smooth muscle cells. Int Immunopharmacol 2005;5:1487-506.
    • (2005) Int Immunopharmacol , vol.5 , pp. 1487-1506
    • Rakesh, K.1    Agrawal, D.K.2
  • 43
    • 84885234215 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of microdissected breast cancer tissues: Comparison of label-free and SILAC-based quantification with shotgun, directed, and targeted MS approaches
    • Liu NQ, Dekker LJ, Stingl C, Guzel C, De Marchi T, Martens JW, et al. Quantitative proteomic analysis of microdissected breast cancer tissues: comparison of label-free and SILAC-based quantification with shotgun, directed, and targeted MS approaches. J Proteome Res 2013; 12:4627-41.
    • (2013) J Proteome Res , vol.12 , pp. 4627-4641
    • Liu, N.Q.1    Dekker, L.J.2    Stingl, C.3    Guzel, C.4    De Marchi, T.5    Martens, J.W.6
  • 44
    • 84876434755 scopus 로고    scopus 로고
    • Loss of FBP1 by Snail-mediated repression provides metabolic advantages in basal-like breast cancer
    • Dong C, Yuan T, Wu Y, Wang Y, Fan TW, Miriyala S, et al. Loss of FBP1 by Snail-mediated repression provides metabolic advantages in basal-like breast cancer. Cancer Cell 2013;23:316-31.
    • (2013) Cancer Cell , vol.23 , pp. 316-331
    • Dong, C.1    Yuan, T.2    Wu, Y.3    Wang, Y.4    Fan, T.W.5    Miriyala, S.6
  • 45
    • 12444279265 scopus 로고
    • On the origin of cancer cells
    • Warburg O. On the origin of cancer cells. Science 1956;123:309-14.
    • (1956) Science , vol.123 , pp. 309-314
    • Warburg, O.1
  • 46
    • 84857992195 scopus 로고    scopus 로고
    • Targeting cancer metabolism-aiming at a tumour's sweet-spot
    • Jones NP, Schulze A. Targeting cancer metabolism-aiming at a tumour's sweet-spot. Drug Discov Today 2012;17:232-41.
    • (2012) Drug Discov Today , vol.17 , pp. 232-241
    • Jones, N.P.1    Schulze, A.2
  • 47
    • 84869208957 scopus 로고    scopus 로고
    • An integrated genomic screen identifies LDHB as an essential gene for triple-negative breast cancer
    • McClelandML, Adler AS, Shang Y, Hunsaker T, Truong T, Peterson D, et al. An integrated genomic screen identifies LDHB as an essential gene for triple-negative breast cancer. Cancer Res 2012;72:5812-23.
    • (2012) Cancer Res , vol.72 , pp. 5812-5823
    • McCleland, M.L.1    Adler, A.S.2    Shang, Y.3    Hunsaker, T.4    Truong, T.5    Peterson, D.6
  • 48
    • 77956516647 scopus 로고    scopus 로고
    • Cancer metabolism: Is glutamine sweeter than glucose?
    • Lu W, Pelicano H, Huang P. Cancer metabolism: is glutamine sweeter than glucose? Cancer Cell 2010;18:199-200.
    • (2010) Cancer Cell , vol.18 , pp. 199-200
    • Lu, W.1    Pelicano, H.2    Huang, P.3
  • 51
    • 84879491733 scopus 로고    scopus 로고
    • Expression of glutamine metabolismrelated proteins according to molecular subtype of breast cancer
    • Kim S, Kim do H, Jung WH, Koo JS. Expression of glutamine metabolismrelated proteins according to molecular subtype of breast cancer. Endocr Relat Cancer 2013;20:339-48.
    • (2013) Endocr Relat Cancer , vol.20 , pp. 339-348
    • Kim, S.1    Kim Do, H.2    Jung, W.H.3    Koo, J.S.4
  • 52
    • 53849105441 scopus 로고    scopus 로고
    • Human Delta1- pyrroline-5-carboxylate synthase: Function and regulation
    • Hu CA, Khalil S, Zhaorigetu S, Liu Z, Tyler M, Wan G, et al. Human Delta1- pyrroline-5-carboxylate synthase: function and regulation. Amino Acids 2008;35:665-72.
    • (2008) Amino Acids , vol.35 , pp. 665-672
    • Hu, C.A.1    Khalil, S.2    Zhaorigetu, S.3    Liu, Z.4    Tyler, M.5    Wan, G.6
  • 53
    • 84860512005 scopus 로고    scopus 로고
    • Links between metabolism and cancer
    • Dang CV. Links between metabolism and cancer. Genes Dev 2012;26: 877-90.
    • (2012) Genes Dev , vol.26 , pp. 877-890
    • Dang, C.V.1
  • 54
    • 70350217425 scopus 로고    scopus 로고
    • Glioblastoma cells require glutamate dehydrogenase to survive impairments of glucose metabolism or Akt signaling
    • Yang C, Sudderth J, Dang T, Bachoo RM, McDonald JG, DeBerardinis RJ. Glioblastoma cells require glutamate dehydrogenase to survive impairments of glucose metabolism or Akt signaling. Cancer Res 2009;69: 7986-93.
    • (2009) Cancer Res , vol.69 , pp. 7986-7993
    • Yang, C.1    Sudderth, J.2    Dang, T.3    Bachoo, R.M.4    McDonald, J.G.5    DeBerardinis, R.J.6
  • 55
    • 75149148563 scopus 로고    scopus 로고
    • Q's next: The diverse functions of glutamine in metabolism, cell biology and cancer
    • DeBerardinis RJ, Cheng T. Q's next: the diverse functions of glutamine in metabolism, cell biology and cancer. Oncogene 2010;29:313-24.
    • (2010) Oncogene , vol.29 , pp. 313-324
    • DeBerardinis, R.J.1    Cheng, T.2
  • 56
    • 84878466503 scopus 로고    scopus 로고
    • MicroRNA-449a is downregulated in non-small cell lung cancer and inhibits migration and invasion by targeting c-Met
    • Luo W, Huang B, Li Z, Li H, Sun L, Zhang Q, et al. MicroRNA-449a is downregulated in non-small cell lung cancer and inhibits migration and invasion by targeting c-Met. PLoS ONE 2013;8:e64759.
    • (2013) PLoS ONE , vol.8 , pp. e64759
    • Luo, W.1    Huang, B.2    Li, Z.3    Li, H.4    Sun, L.5    Zhang, Q.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.