Interpreting gene-expression profiles in transplantation: A critical appraisal

Frontiers in Genetics

Volumn 2, Issue DEC, 2011, Pages

  Pallet, Nicolas ^a,b,c   Thervet, Eric ^d,e   Desjardins, Michel ^a,b  

^a Infectiologie et Immunologie   (Canada)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

^c NOTRE DAME HOSPITAL   (Canada)

^d HÔPITAL EUROPÉEN GEORGES POMPIDOU   (France)

^e INSERM   (France)

Author keywords

cDNA microarrays; Gene expression profiles; Kidney transplantation

Indexed keywords

EID: 84875913678     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2011.00098     Document Type: Note

References (41)

1. Bando, Y., Tsukamoto, Y., Katayama, T., Ozawa, K., Kitao, Y., Hori, O., Stern, D. M., Yamauchi, A., and Ogawa, S. (2004). ORP150/HSP12A protects renal tubular epithelium from ischemia-induced cell death. FASEB J. 18, 1401-1403.
2. Barthelson, R. A., Lambert, G. M., Vanier, C., Lynch, R. M., and Galbraith, D. W. (2007). Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells. BMC Genomics 8, 340. doi: 10.1186/1471-2164-8-340
3. Bonventre, J. V., and Zuk, A. (2004). Ischemic acute renal failure: an inflammatory disease? Kidney Int. 66, 480-485.
4. Boulais, J., Trost, M., Landry, C. R., Dieckmann, R., Levy, E. D., Soldati, T., Michnick, S. W., Thibault, P., and Desjardins, M. (2010). Molecular characterization of the evolution of phagosomes. Mol. Syst. Biol. 6, 423.
5. Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayir, A., Bakkaloglu, A., Ozen, S., Sanjad, S., Nelson-Williams, C., Farhi, A., Mane, S., and Lifton, R. P. (2009). Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl. Acad. Sci. U.S.A. 106, 19096-19101.
6. Cirulli, E. T., Singh, A., Shianna, K. V., Ge, D., Smith, J. P., Maia, J. M., Heinzen, E. L., Goedert, J. J., and Goldstein, D. B. (2010). Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol. 11, R57.
7. de Verteuil, D., Muratore-Schroeder, T. L., Granados, D. P., Fortier, M. H., Hardy, M. P., Bramoulle, A., Caron, E., Vincent, K., Mader, S., Lemieux, S., Thibault, P., and Perreault, C. (2010). Deletion of immunoproteasome subunits imprints on the transcriptome and has a broad impact on peptides presented by major histocompatibility complex I molecules. Mol. Cell Proteomics 9, 2034-2047.
8. Dell'Oglio, M. P., Zaza, G., Rossini, M., Divella, C., Pontrelli, P., Verrienti, R., Rutigliano, M., Ditonno, P., Stifanelli, P., Ancona, N., Schena, F. P., and Grandaliano, G. (2010). The anti-fibrotic effect of mycophenolic acid-induced neutral endopeptidase. J. Am. Soc. Nephrol. 21, 2157-2168.
9. Einecke, G., Reeve, J., Sis, B., Mengel, M., Hidalgo, L., Famulski, K. S., Matas, A., Kasiske, B., Kaplan, B., and Halloran, P. F. (2010). A molecular classifier for predicting future graft loss in late kidney transplant biopsies. J. Clin. Invest. 120, 1862-1872.
10. Eyrich, B., Sickmann, A., and Zahedi, R. P. (2011). Catch me if you can: mass spectrometry-based phosphoproteomics and quantification strategies. Proteomics 11, 554-570.
11. Findeisen, P., and Neumaier, M. (2009). Mass spectrometry-based clinical proteomics profiling: current status and future directions. Expert Rev. Proteomics 6, 457-459.
12. Galluzzi, L., Vitale, I., Abrams, J. M., Alnemri, E. S., Baehrecke, E. H., Blagosklonny, M. V., Dawson, T. M., Dawson, V. L., El-Deiry, W. S., Fulda, S., Gottlieb, E., Green, D. R., Hengartner, M. O., Kepp, O., Knight, R. A., Kumar, S., Lipton, S. A., Lu, X., Madeo, F., Malorni, W., Mehlen, P., Nuñez, G., Peter, M. E., Piacentini, M., Rubinsztein, D. C., Shi, Y., Simon, H. U., Vandenabeele, P., White, E., Yuan, J., Zhivotovsky, B., Melino, G., and Kroemer, G. (2012). Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death Differ. 19, 107-120.
13. Halbeisen, R. E., and Gerber, A. P. (2009). Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol. 7, e105. doi: 10.1371/journal.pbio.1000105
14. Halbeisen, R. E., Scherrer, T., and Gerber, A. P. (2009). Affinity purification of ribosomes to access the translatome. Methods 48, 306-310.
15. Hertig, A., Verine, J., Mougenot, B., Jouanneau, C., Ouali, N., Sebe, P., Glotz, D., Ancel, P. Y., Rondeau, E., and Xu-Dubois, Y. C. (2006). Risk factors for early epithelial to mesenchymal transition in renal grafts. Am. J. Transplant. 6, 2937-2946.
16. Hitomi, J., Christofferson, D. E., Ng, A., Yao, J., Degterev, A., Xavier, R. J., and Yuan, J. (2008). Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway. Cell 135, 1311-1323.
17. Hollien, J., Lin, J. H., Li, H., Stevens, N., Walter, P., and Weissman, J. S. (2009). Regulated Ire1-dependent decay of messenger RNAs in mammalian cells. J. Cell Biol. 186, 323-331.
18. Kepp, O., Galluzzi, L., Lipinski, M., Yuan, J., and Kroemer, G. (2011). Cell death assays for drug discovery. Nat. Rev. Drug Discov. 10, 221-237.
19. Klionsky, D. J., Abeliovich, H., Agostinis, P., Agrawal, D. K., Aliev, G., Askew, D. S., Baba, M., Baehrecke, E. H., Bahr, B. A., Ballabio, A., Bamber, B. A., Bassham, D. C., Bergamini, E., Bi, X., Biard-Piechaczyk, M., Blum, J. S., Bredesen, D. E., Brodsky, J. L., Brumell, J. H., Brunk, U. T, Bursch, W., Camougrand, N., Cebollero, E., Cecconi, F., Chen, Y., Chin, L. S., Choi, A., Chu, C. T., Chung, J., Clarke, P. G., Clark, R. S., Clarke, S. G., Clavé, C., Cleveland, J. L., Codogno, P., Colombo, M. I., Coto-Montes, A., Cregg, J. M., Cuervo, A. M., Debnath, J., Demarchi, F., Dennis, P. B., Dennis, P. A., Deretic, V., Devenish, R. J., Di Sano, F., Dice, J. F., Difiglia, M., Dinesh-Kumar, S., Distelhorst, C. W., Djavaheri-Mergny, M., Dorsey, F. C., Dröge, W., Dron, M., Dunn, W. A. Jr., Duszenko, M., Eissa, N. T., Elazar, Z., Esclatine, A., Eskelinen, E. L., Fésüs, L., Finley, K. D., Fuentes, J. M., Fueyo, J., Fujisaki, K., Galliot, B., Gao, F. B., Gewirtz, D. A., Gibson, S. B., Gohla, A., Goldberg, A. L., Gonzalez, R., González-Estévez, C., Gorski, S., Gottlieb, R. A., Häussinger, D., He, Y. W., Heidenreich, K., Hill, J. A., Høyer-Hansen, M., Hu, X., Huang, W. P., Iwasaki, A., Jäättelä, M., Jackson, W. T., Jiang, X., Jin, S., Johansen, T., Jung, J. U., Kadowaki, M., Kang, C., Kelekar, A., Kessel, D. H., Kiel, J. A., Kim, H. P., Kimchi, A., Kinsella, T. J., Kiselyov, K., Kitamoto, K., Knecht, E., Komatsu, M., Kominami, E., Kondo, S., Kovács, A. L., Kroemer, G., Kuan, C. Y., Kumar, R., Kundu, M., Landry, J., Laporte, M., Le, W., Lei, H. Y., Lenardo, M. J., Levine, B., Lieberman, A., Lim, K. L., Lin, F. C., Liou, W., Liu, L. F., Lopez-Berestein, G., López-Otín, C., Lu, B., Macleod, K. F., Malorni, W., Martinet, W., Matsuoka, K., Mautner, J., Meijer, A. J., Meléndez, A., Michels, P., Miotto, G., Mistiaen, W. P., Mizushima, N., Mograbi, B., Monastyrska, I., Moore, M. N., Moreira, P. I., Moriyasu, Y., Motyl, T., Münz, C., Murphy, L. O., Naqvi, N. I., Neufeld, T. P., Nishino, I., Nixon, R. A., Noda, T., Nürnberg, B., Ogawa, M., Oleinick, N. L., Olsen, L. J., Ozpolat, B., Paglin, S., Palmer, G. E., Papassideri, I., Parkes, M., Perlmutter, D. H., Perry, G., Piacentini, M., Pinkas-Kramarski, R., Prescott, M., Proikas-Cezanne, T., Raben, N., Rami, A., Reggiori, F., Rohrer, B., Rubinsztein, D. C., Ryan, K. M., Sadoshima, J., Sakagami, H., Sakai, Y., Sandri, M., Sasakawa, C., Sass, M., Schneider, C., Seglen, P. O., Seleverstov, O., Settleman, J., Shacka, J. J., Shapiro, I. M., Sibirny, A., Silva-Zacarin, E. C., Simon, H. U., Simone, C., Simonsen, A., Smith, M. A., Spanel-Borowski, K., Srinivas, V., Steeves, M., Stenmark, H., Stromhaug, P. E., Subauste, C. S., Sugimoto, S., Sulzer, D., Suzuki, T., Swanson, M. S., Tabas, I., Takeshita, F., Talbot, N. J., Tallóczy, Z., Tanaka, K., Tanaka, K., Tanida, I., Taylor, G. S., Taylor, J. P., Terman, A., Tettamanti, G., Thompson, C. B., Thumm, M., Tolkovsky, A. M., Tooze, S. A., Truant, R., Tumanovska, L. V., Uchiyama, Y., Ueno, T., Uzcátegui, N. L., van der Klei, I., Vaquero, E. C., Vellai, T., Vogel, M. W., Wang, H. G., Webster, P., Wiley, J. W., Xi, Z., Xiao, G., Yahalom, J., Yang, J. M., Yap, G., Yin, X. M., Yoshimori, T., Yu, L., Yue, Z., Yuzaki, M., Zabirnyk, O., Zheng, X., Zhu, X., and Deter, R. L. (2008). Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 4, 151-175.
20. Laplante, P., Sirois, I., Raymond, M. A., Kokta, V., Beliveau, A., Prat, A., Pshezhetsky, A. V., and Hebert, M. J. (2010). Caspase-3-mediated secretion of connective tissue growth factor by apoptotic endothelial cells promotes fibrosis. Cell Death Differ. 17, 291-303.
21. Li, L., Wadia, P., Chen, R., Kambham, N., Naesens, M., Sigdel, T. K., Miklos, D. B., Sarwal, M. M., and Butte, A. J. (2009). Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures. Proc. Natl. Acad. Sci. U.S.A. 106, 4148-4153.
22. Ma, L., Mauro, C., Cornish, G. H., Chai, J. G., Coe, D., Fu, H., Patton, D., Okkenhaug, K., Franzoso, G., Dyson, J., Nourshargh, S., and Marelli-Berg, F. M. (2010). Ig gene-like molecule CD31 plays a nonredundant role in the regulation of T-cell immunity and tolerance. Proc. Natl. Acad. Sci. U.S.A. 107, 19461-19466.
23. Metzker, M. L. (2010). Sequencing technologies - the next generation. Nat. Rev. Genet. 11, 31-46.
24. Miller, C., Schwalb, B., Maier, K., Schulz, D., Dumcke, S., Zacher, B., Mayer, A., Sydow, J., Marcinowski, L., Dolken, L., Martin, D. E., Tresch, A., and Cramer, P. (2011). Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol. Syst. Biol. 7, 458.
25. Mustroph, A., Zanetti, M. E., Jang, C. J., Holtan, H. E., Repetti, P. P., Galbraith, D. W., Girke, T., and Bailey-Serres, J. (2009). Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 106, 18843-18848.
26. Muthukumar, T., Dadhania, D., Ding, R., Snopkowski, C., Naqvi, R., Lee, J. B., Hartono, C., Li, B., Sharma, V. K., Seshan, S. V., Kapur, S., Hancock, W. W., Schwartz, J. E., and Suthanthiran, M. (2005). Messenger RNA for FOXP3 in the urine of renal-allograft recipients. N. Engl. J. Med. 353, 2342-2351.
27. Ozsolak, F., and Milos, P. M. (2011). RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet. 12, 87-98.
28. Pallet, N., Bouvier, N., Bendjallabah, A., Rabant, M., Flinois, J. P., Hertig, A., Legendre, C., Beaune, P., Thervet, E., and Anglicheau, D. (2008). Cyclosporine-induced endoplasmic reticulum stress triggers tubular phenotypic changes and death. Am. J. Transplant. 8, 2283-2296.
29. Rabani, M., Levin, J. Z., Fan, L., Adiconis, X., Raychowdhury, R., Garber, M., Gnirke, A., Nusbaum, C., Hacohen, N., Friedman, N., Amit, I., and Regev, A. (2011). Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat. Biotechnol. 29, 436-442.
30. Ruiz, C., Lenkiewicz, E., Evers, L., Holley, T., Robeson, A., Kiefer, J., Demeure, M. J., Hollingsworth, M. A., Shen, M., Prunkard, D., Rabinovitch, P. S., Zellweger, T., Mousses, S., Trent, J. M., Carpten, J. D., Bubendorf, L., Von Hoff, D., and Barrett, M. T. (2011). Advancing a clinically relevant perspective of the clonal nature of cancer. Proc. Natl. Acad. Sci. U.S.A. 108, 12054-12059.
31. Saba, J., Bonneil, E., Pomies, C., Eng, K., and Thibault, P. (2009). Enhanced sensitivity in proteomics experiments using FAIMS coupled with a hybrid linear ion trap/orbitrap mass spectrometer. J. Proteome Res. 8, 3355-3366.
32. Sarwal, M., Chua, M. S., Kambham, N., Hsieh, S. C., Satterwhite, T., Masek, M., and Salvatierra, O. Jr. (2003). Molecular heterogeneity in acute renal allograft rejection identified by DNA microarray profiling. N. Engl. J. Med. 349, 125-138.
33. Schnaper, H. W., Jandeska, S., Runyan, C. E., Hubchak, S. C., Basu, R. K., Curley, J. F., Smith, R. D., and Hayashida, T. (2009). TGF-beta signal transduction in chronic kidney disease. Front. Biosci. 14, 2448-2465.
34. Shen-Orr, S. S., Tibshirani, R., Khatri, P., Bodian, D. L., Staedtler, F., Perry, N. M., Hastie, T., Sarwal, M. M., Davis, M. M., and Butte, A. J. (2010). Cell type-specific gene expression differences in complex tissues. Nat. Methods 7, 287-289.
35. Thery, C., Ostrowski, M., and Segura, E. (2009). Membrane vesicles as conveyors of immune responses. Nat. Rev. Immunol. 9, 581-593.
36. Underwood, J. G., Uzilov, A. V., Katzman, S., Onodera, C. S., Mainzer, J. E., Mathews, D. H., Lowe, T. M., Salama, S. R., and Haussler, D. (2010). FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat. Methods 7, 995-1001.
37. Werner, T. (2010). Next generation sequencing in functional genomics. Brief. Bioinformatics 11, 499-511.
38. Yunger, S., Rosenfeld, L., Garini, Y., and Shav-Tal, Y. (2010). Single-allele analysis of transcription kinetics in living mammalian cells. Nat. Methods 7, 631-633.
39. Zanetti, M. E., Chang, I. F., Gong, F., Galbraith, D. W., and Bailey-Serres, J. (2005). Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol. 138, 624-635.
40. Zeisberg, M., and Duffield, J. S. (2010). Resolved: EMT produces fibroblasts in the kidney. J. Am. Soc. Nephrol. 21, 1247-1253.
41. Zhang, C., Barthelson, R. A., Lambert, G. M., and Galbraith, D. W. (2008). Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol. 147, 30-40.