Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative

Journal of Proteome Research

Volumn 16, Issue 12, 2017, Pages 4319-4329

  Alberio, Tiziana ^a   Pieroni, Luisa ^b   Ronci, Maurizio ^b,c   Banfi, Cristina ^d   Bongarzone, Italia ^e   Bottoni, Patrizia ^f   Brioschi, Maura ^d   Caterino, Marianna ^g,h   Chinello, Clizia ⁱ   Cormio, Antonella ^j   Cozzolino, Flora ^g,h   Cunsolo, Vincenzo ^k   Fontana, Simona ^l   Garavaglia, Barbara ^m   Giusti, Laura ⁿ   Greco, Viviana ^b   Lucacchini, Antonio ⁿ   Maffioli, Elisa ^o   Magni, Fulvio ⁱ   Monteleone, Francesca ^l   Monti, Maria ^g,h   Monti, Valentina ^m   Musicco, Clara ^p   Petrosillo, Giuseppe ^p   Porcelli, Vito ^j   Saletti, Rosaria ^k   Scatena, Roberto ^f   Soggiu, Alessio ^o   Tedeschi, Gabriella ^o,q   Zilocchi, Mara ^a   Roncada, Paola ^r   Urbani, Andrea ^b,f   Fasano, Mauro ^a   more..

^a UNIVERSITY OF INSUBRIA   (Italy)

^b IRCCS FONDAZIONE SANTA LUCIA   (Italy)

^c UNIVERSITY OF CHIETI   (Italy)

^d CENTRO CARDIOLOGICO MONZINO   (Italy)

^e NATIONAL CANCER INSTITUTE   (Italy)

^f CATHOLIC UNIVERSITY   (Italy)

^g UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^h CEINGE BIOTECNOLOGIE AVANZATE   (Italy)

ⁱ UNIVERSITY OF MILANO BICOCCA   (Italy)

^j UNIVERSITY OF BARI   (Italy)

^k UNIVERSITY OF CATANIA   (Italy)

^l UNIVERSITY OF PALERMO   (Italy)

^m DEPARTMENT OF NEUROSURGERY   (Italy)

ⁿ UNIVERSITY OF PISA   (Italy)

^o UNIVERSITY OF MILAN   (Italy)

^p CNR   (Italy)

^q Fondazione Filarete   (Italy)

^r Istituto Sperimentale Italiano Lazzaro Spallanzani   (Italy)

more..

Author keywords

enrichment protocol; mitochondria; Mitochondrial Human Proteome Project; standardization

Indexed keywords

MITOCHONDRIAL PROTEIN; PROTEOME;

ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY; MITOCHONDRION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEOMICS; REFERENCE DATABASE; STANDARDIZATION; STATISTICAL ANALYSIS; CELL LINE; CHEMISTRY; ITALY; LIQUID CHROMATOGRAPHY; PHYSIOLOGY; PROTEIN ANALYSIS; STANDARDS; TANDEM MASS SPECTROMETRY;

CELL LINE; CHROMATOGRAPHY, LIQUID; HUMANS; ITALY; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; PROTEIN INTERACTION MAPS; PROTEOME; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 85037328540     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.7b00350     Document Type: Article

References (40)

1. Urbani, A.; De Canio, M.; Palmieri, F.; Sechi, S.; Bini, L.; Castagnola, M.; Fasano, M.; Modesti, A.; Roncada, P.; Timperio, A. M.; Bonizzi, L.; Brunori, M.; Cutruzzolà, F.; De Pinto, V.; Di Ilio, C.; Federici, G.; Folli, F.; Foti, S.; Gelfi, C.; Lauro, D.; Lucacchini, A.; Magni, F.; Messana, I.; Pandolfi, P. P.; Papa, S.; Pucci, P.; Sacchetta, P.; Italian Mt-Hpp Study Group-Italian Proteomics Association The mitochondrial Italian Human Proteome Project initiative (mt-HPP) Mol. Biosyst. 2013, 9, 1984-1992 10.1039/c3mb70065h
2. Kasahara, A.; Scorrano, L. Mitochondria: from cell death executioners to regulators of cell differentiation Trends Cell Biol. 2014, 24, 761-770 10.1016/j.tcb.2014.08.005
3. Modica-Napolitano, J. S.; Singh, K. K. Mitochondrial dysfunction in cancer Mitochondrion 2004, 4, 755-762 10.1016/j.mito.2004.07.027
4. Lowell, B. B.; Shulman, G. I. Mitochondrial dysfunction and type 2 diabetes Science 2005, 307, 384-387 10.1126/science.1104343
5. Lin, M. T.; Beal, M. F. Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases Nature 2006, 443, 787-795 10.1038/nature05292
6. Rafelski, S. M. Mitochondrial network morphology: building an integrative, geometrical view BMC Biol. 2013, 11, 71 10.1186/1741-7007-11-71
7. Hoppins, S. The regulation of mitochondrial dynamics Curr. Opin. Cell Biol. 2014, 29, 46-52 10.1016/j.ceb.2014.03.005
8. Yin, F.; Cadenas, E. Mitochondria: the cellular hub of the dynamic coordinated network Antioxid. Redox Signaling 2015, 22, 961-964 10.1089/ars.2015.6313
9. Thul, P. J.; Åkesson, L.; Wiking, M.; Mahdessian, D.; Geladaki, A.; Ait Blal, H.; Alm, T.; Asplund, A.; Björk, L.; Breckels, L. M.; Bäckström, A.; Danielsson, F.; Fagerberg, L.; Fall, J.; Gatto, L.; Gnann, C.; Hober, S.; Hjelmare, M.; Johansson, F.; Lee, S.; Lindskog, C.; Mulder, J.; Mulvey, C. M.; Nilsson, P.; Oksvold, P.; Rockberg, J.; Schutten, R.; Schwenk, J. M.; Sivertsson, Å.; Sjöstedt, E.; Skogs, M.; Stadler, C.; Sullivan, D. P.; Tegel, H.; Winsnes, C.; Zhang, C.; Zwahlen, M.; Mardinoglu, A.; Pontén, F.; von Feilitzen, K.; Lilley, K. S.; Uhlén, M.; Lundberg, E. A subcellular map of the human proteome Science 2017, 356, eaal3321 10.1126/science.aal3321
10. Fasano, M.; Alberio, T.; Babu, M.; Lundberg, E.; Urbani, A. Towards a functional definition of the mitochondrial human proteome EuPa Open Proteomics 2016, 10, 24-27 10.1016/j.euprot.2016.01.004
11. R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2014. http://www.R-project.org/.
12. Carlson, M. UniProt.ws: R Interface to UniProt Web Services. R Package Version 2.14.0; R Foundation for Statistical Computing, 2016.
13. Huber, W.; Carey, V. J.; Gentleman, R.; Anders, S.; Carlson, M.; Carvalho, B. S.; Bravo, H. C.; Davis, S.; Gatto, L.; Girke, T.; Gottardo, R.; Hahne, F.; Hansen, K. D.; Irizarry, R. A.; Lawrence, M.; Love, M. I.; MacDonald, J.; Obenchain, V.; Oleś, A. K.; Pagès, H.; Reyes, A.; Shannon, P.; Smyth, G. K.; Tenenbaum, D.; Waldron, L.; Morgan, M. Orchestrating high-throughput genomic analysis with Bioconductor Nat. Methods 2015, 12, 115-121 10.1038/nmeth.3252
14. Ishihama, Y.; Oda, Y.; Tabata, T.; Sato, T.; Nagasu, T.; Rappsilber, J.; Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein Mol. Cell. Proteomics 2005, 4, 1265-1272 10.1074/mcp.M500061-MCP200
15. Calvo, S. E.; Clauser, K. R.; Mootha, V. K. MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins Nucleic Acids Res. 2016, 44, D1251-1257 10.1093/nar/gkv1003
16. Smith, A. C.; Robinson, A. J. MitoMiner v3.1, an update on the mitochondrial proteomics database Nucleic Acids Res. 2016, 44, D1258-1261 10.1093/nar/gkv1001
17. Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N. S.; Wang, J. T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 2003, 13, 2498-2504 10.1101/gr.1239303
18. Picard, M.; Wallace, D. C.; Burelle, Y. The rise of mitochondria in medicine Mitochondrion 2016, 30, 105-116 10.1016/j.mito.2016.07.003
19. Yu, J.; Vodyanik, M. A.; Smuga-Otto, K.; Antosiewicz-Bourget, J.; Frane, J. L.; Tian, S.; Nie, J.; Jonsdottir, G. A.; Ruotti, V.; Stewart, R.; Slukvin, I. I.; Thomson, J. A. Induced pluripotent stem cell lines derived from human somatic cells Science 2007, 318, 1917-1920 10.1126/science.1151526
20. Auburger, G.; Klinkenberg, M.; Drost, J.; Marcus, K.; Morales-Gordo, B.; Kunz, W. S.; Brandt, U.; Broccoli, V.; Reichmann, H.; Gispert, S.; Jendrach, M. Primary skin fibroblasts as a model of Parkinson's disease Mol. Neurobiol. 2012, 46, 20-27 10.1007/s12035-012-8245-1
21. Qiang, L.; Inoue, K.; Abeliovich, A. Instant neurons: directed somatic cell reprogramming models of central nervous system disorders Biol. Psychiatry 2014, 75, 945-951 10.1016/j.biopsych.2013.10.027
22. Tigges, J.; Krutmann, J.; Fritsche, E.; Haendeler, J.; Schaal, H.; Fischer, J. W.; Kalfalah, F.; Reinke, H.; Reifenberger, G.; Stühler, K.; Ventura, N.; Gundermann, S.; Boukamp, P.; Boege, F. The hallmarks of fibroblast ageing Mech. Ageing Dev. 2014, 138, 26-44 10.1016/j.mad.2014.03.004
23. Kovalevich, J.; Langford, D. Considerations for the use of SH-SY5Y neuroblastoma cells in neurobiology Methods Mol. Biol. 2013, 1078, 9-21 10.1007/978-1-62703-640-5-2
24. Alberio, T.; Lopiano, L.; Fasano, M. Cellular models to investigate biochemical pathways in Parkinson's disease FEBS J. 2012, 279, 1146-1155 10.1111/j.1742-4658.2012.08516.x
25. Alberio, T.; Bondi, H.; Colombo, F.; Alloggio, I.; Pieroni, L.; Urbani, A.; Fasano, M. Mitochondrial proteomics investigation of a cellular model of impaired dopamine homeostasis, an early step in Parkinson's disease pathogenesis Mol. BioSyst. 2014, 10, 1332-1344 10.1039/c3mb70611g
26. Krishna, A.; Biryukov, M.; Trefois, C.; Antony, P. M.; Hussong, R.; Lin, J.; Heinäniemi, M.; Glusman, G.; Köglsberger, S.; Boyd, O.; van den Berg, B. H.; Linke, D.; Huang, D.; Wang, K.; Hood, L.; Tholey, A.; Schneider, R.; Galas, D. J.; Balling, R.; May, P. Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease BMC Genomics 2014, 15, 1154 10.1186/1471-2164-15-1154
27. Xicoy, H.; Wieringa, B.; Martens, G. J. M. The SH-SY5Y cell line in Parkinsonís disease research: a systematic review Mol. Neurodegener. 2017, 12, 10 10.1186/s13024-017-0149-0
28. Tseng, L. M.; Yin, P. H.; Yang, C. W.; Tsai, Y. F.; Hsu, C. Y.; Chi, C. W.; Lee, H. C. Somatic mutations of the mitochondrial genome in human breast cancers Genes, Chromosomes Cancer 2011, 50, 800-811 10.1002/gcc.20901
29. Imanishi, H.; Hattori, K.; Wada, R.; Ishikawa, K.; Fukuda, S.; Takenaga, K.; Nakada, K.; Hayashi, J. Mitochondrial DNA mutations regulate metastasis of human breast cancer cells PLoS One 2011, 6, e23401 10.1371/journal.pone.0023401
30. Tu, Y. F.; Kaipparettu, B. A.; Ma, Y.; Wong, L. J. Mitochondria of highly metastatic breast cancer cell line MDA-MB-231 exhibits increased autophagic properties Biochim. Biophys. Acta, Bioenerg. 2011, 1807, 1125-1132 10.1016/j.bbabio.2011.04.015
31. Fazzini, A.; D'Antongiovanni, V.; Giusti, L.; Da Valle, Y.; Ciregia, F.; Piano, I.; Caputo, A.; D'Ursi, A. M.; Gargini, C.; Lucacchini, A.; Mazzoni, M. R. Altered protease-activated receptor-1 expression and signaling in a malignant pleural mesothelioma cell line, NCI-H28, with homozygous deletion of the β-catenin gene PLoS One 2014, 9, e111550 10.1371/journal.pone.0111550
32. Onat, D.; Brillon, D.; Colombo, P. C.; Schmidt, A. M. Human vascular endothelial cells: a model system for studying vascular inflammation in diabetes and atherosclerosis Curr. Diabetes Rep. 2011, 11, 193-202 10.1007/s11892-011-0182-2
33. Qin, Z. The use of THP-1 cells as a model for mimicking the function and regulation of monocytes and macrophages in the vasculature Atherosclerosis 2012, 221, 2-11 10.1016/j.atherosclerosis.2011.09.003
34. Chanput, W.; Mes, J. J.; Wichers, H. J. THP-1 cell line: an in vitro cell model for immune modulation approach Int. Immunopharmacol. 2014, 23, 37-45 10.1016/j.intimp.2014.08.002
35. Yin, P. H.; Wu, C. C.; Lin, J. C.; Chi, C. W.; Wei, Y. H.; Lee, H. C. Somatic mutations of mitochondrial genome in hepatocellular carcinoma Mitochondrion 2010, 10, 174-182 10.1016/j.mito.2009.12.147
36. Kamalian, L.; Chadwick, A. E.; Bayliss, M.; French, N. S.; Monshouwer, M.; Snoeys, J.; Park, B. K. The utility of HepG2 cells to identify direct mitochondrial dysfunction in the absence of cell death Toxicol. In Vitro 2015, 29, 732-740 10.1016/j.tiv.2015.02.011
37. Costantini, S.; Di Bernardo, G.; Cammarota, M.; Castello, G.; Colonna, G. Gene expression signature of human HepG2 cell line Gene 2013, 518, 335-345 10.1016/j.gene.2012.12.106
38. Yates, J. R., III. Change J. Proteome Res. 2016, 15, 2355 10.1021/acs.jproteome.6b00640
39. Hämäläinen, R. H.; Manninen, T.; Koivumäki, H.; Kislin, M.; Otonkoski, T.; Suomalainen, A. Tissue- and cell-type-specific manifestations of heteroplasmic mtDNA 3243A > G mutation in human induced pluripotent stem cell-derived disease model Proc. Natl. Acad. Sci. U. S. A. 2013, 110, E3622-3630 10.1073/pnas.1311660110
40. Meissner, A.; Mikkelsen, T. S.; Gu, H.; Wernig, M.; Hanna, J.; Sivachenko, A.; Zhang, X.; Bernstein, B. E.; Nusbaum, C.; Jaffe, D. B.; Gnirke, A.; Jaenisch, R.; Lander, E. S. Genome-scale DNA methylation maps of pluripotent and differentiated cells Nature 2008, 454, 766-770 10.1038/nature07107