The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics

Molecular and Cellular Proteomics

Volumn 13, Issue 2, 2014, Pages 621-631

  Sigdel, Tara K ^a   Salomonis, Nathan ^a   Nicora, Carrie D ^b   Ryu, Soyoung ^c   He, Jintang ^b   Dinh, Van ^a   Orton, Daniel J ^b   Moore, Ronald J ^b   Hsieh, Szu Chuan ^a   Dai, Hong ^a   Thien Vu, Minh ^a   Xiao, Wenzhong ^c   Smith, Richard D ^b   Qian, Wei Jun ^b   Camp, David G ^b   Sarwal, Minnie M ^a  

^a CALIFORNIA PACIFIC MEDICAL CENTER   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; FIBRINOGEN; SUMO 2 PROTEIN;

ACUTE GRAFT REJECTION; ADULT; ARTICLE; BK VIRUS; BK VIRUS INFECTION; ENZYME LINKED IMMUNOSORBENT ASSAY; FEMALE; HUMAN; IMMUNE INJURY; IMMUNOSUPPRESSIVE TREATMENT; KIDNEY ALLOGRAFT REJECTION; KIDNEY INJURY; MAJOR CLINICAL STUDY; MALE; NEPHRITIS; NEPHROTIC SYNDROME; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN URINE LEVEL; TRAINING; URINALYSIS;

ACUTE KIDNEY INJURY; ADOLESCENT; ADULT; BIOLOGICAL MARKERS; CHILD; FEMALE; GRAFT REJECTION; GRAFT VS HOST REACTION; HUMANS; KIDNEY TRANSPLANTATION; MALE; PROTEIN INTERACTION MAPS; PROTEOMICS; SIGNAL TRANSDUCTION; TRANSPLANTATION, HOMOLOGOUS; URINALYSIS; VALIDATION STUDIES AS TOPIC; YOUNG ADULT;

EID: 84893286386     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.030577     Document Type: Article

References (49)

1. Nankivell, B. J., and Alexander, S. I. (2010) Rejection of the kidney allograft. N. Engl. J. Med. 363, 1451-1462
2. de Fijter, J. W. (2010) Rejection and function and chronic allograft dysfunction. Kidney Int 119, S38-S41
3. Sigdel, T. K., Gao, X., and Sarwal, M. M. (2012) Protein and peptide biomarkers in organ transplantation. Biomark Med. 6, 259-271
4. Turka, L. A., and Lechler, R. I. (2009) Towards the identification of biomarkers of transplantation tolerance. Nat. Rev. Immunol. 9, 521-526
5. Green, E. D., and Guyer, M. S. (2011) Charting a course for genomic medicine from base pairs to bedside. Nature 470, 204-213
6. Ozsolak, F., Platt, A. R., Jones, D. R., Reifenberger, J. G., Sass, L. E., McInerney, P., Thompson, J. F., Bowers, J., Jarosz, M., and Milos, P. M. (2009) Direct RNA sequencing. Nature 461, 814-818
7. Li, L., Khatri, P., Sigdel, T. K., Tran, T., Ying, L., Vitalone, M. J., Chen, A., Hsieh, S., Dai, H., Zhang, M., Naesens, M., Zarkhin, V., Sansanwal, P., Chen, R., Mindrinos, M., Xiao, W., Benfield, M., Ettenger, R. B., Dharnidharka, V., Mathias, R., Portale, A., McDonald, R., Harmon, W., Kershaw, D., Vehaskari, V. M., Kamil, E., Baluarte, H. J., Warady, B., Davis, R., Butte, A. J., Salvatierra, O., and Sarwal, M. M. (2012) A peripheral blood diagnostic test for acute rejection in renal transplantation. Am. J. Trans-plant. 12, 2710-2718
8. 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
9. Einecke, G., Melk, A., Ramassar, V., Zhu, L. F., Bleackley, R. C., Famulski, K. S., and Halloran, P. F. (2005) Expression of CTL associated transcripts precedes the development of tubulitis in T-cell mediated kidney graft rejection. Am. J. Transplant. 5, 1827-1836
10. Mas, V., Maluf, D., Archer, K., Yanek, K., Mas, L., King, A., Gibney, E., Massey, D., Cotterell, A., Fisher, R., and Posner, M. (2007) Establishing the molecular pathways involved in chronic allograft nephropathy for testing new noninvasive diagnostic markers. Transplantation 83, 448-457
11. Anglicheau, D., Sharma, V. K., Ding, R., Hummel, A., Snopkowski, C., Dadhania, D., Seshan, S. V., and Suthanthiran, M. (2009) MicroRNA expression profiles predictive of human renal allograft status. Proc. Natl. Acad. Sci. U.S.A. 106, 5330-5335
12. 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
13. Schaub, S., Rush, D., Wilkins, J., Gibson, I. W., Weiler, T., Sangster, K., Nicolle, L., Karpinski, M., Jeffery, J., and Nickerson, P. (2004) Proteomicbased detection of urine proteins associated with acute renal allograft rejection. J. Am. Soc. Nephrol. 15, 219-227
14. Schaub, S., Wilkins, J. A., Rush, D., and Nickerson, P. (2006) Developing a tool for noninvasive monitoring of renal allografts. Expert Rev. Proteomics 3, 497-509
15. Chen, R., Sigdel, T. K., Li, L., Kambham, N., Dudley, J. T., Hsieh, S. C., Klassen, R. B., Chen, A., Caohuu, T., Morgan, A. A., Valantine, H. A., Khush, K. K., Sarwal, M. M., and Butte, A. J. (2010) Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PLoS Comput Biol. 6, 1-12
16. Ling, X. B., Sigdel, T. K., Lau, K., Ying, L., Lau, I., Schilling, J., and Sarwal, M. M. (2010) Integrative urinary peptidomics in renal transplantation identifies biomarkers for acute rejection. J. Am. Soc. Nephrol. 21, 646-653
17. Sigdel, T. K., Kaushal, A., Gritsenko, M., Norbeck, A. D., Qian, W. J., Xiao, W., Camp, D. G., 2nd, Smith, R. D., and Sarwal, M. M. (2010) Shotgun proteomics identifies proteins specific for acute renal transplant rejection. Proteomics Clin. Appl. 4, 32-47
18. Solez, K., Colvin, R. B., Racusen, L. C., Haas, M., Sis, B., Mengel, M., Halloran, P. F., Baldwin, W., Banfi, G., Collins, A. B., Cosio, F., David, D. S., Drachenberg, C., Einecke, G., Fogo, A. B., Gibson, I. W., Glotz, D., Iskandar, S. S., Kraus, E., Lerut, E., Mannon, R. B., Mihatsch, M., Nankivell, B. J., Nickeleit, V., Papadimitriou, J. C., Randhawa, P., Regele, H., Renaudin, K., Roberts, I., Seron, D., Smith, R. N., and Valente, M. (2008) Banff 07 classification of renal allograft pathology: updates and future directions. Am. J. Transplant 8, 753-760
19. Isoniemi, H., Taskinen, E., and Hayry, P. (1994) Histological chronic allograft damage index accurately predicts chronic renal allograft rejection. Transplantation 58, 1195-1198
20. Racusen, L. C., Halloran, P. F., and Solez, K. (2004) Banff 2003 meeting report: new diagnostic insights and standards. Am. J. Transplant 4, 1562-1566
21. Racusen, L. C., Solez, K., Colvin, R. B., Bonsib, S. M., Castro, M. C., Cavallo, T., Croker, B. P., Demetris, A. J., Drachenberg, C. B., Fogo, A. B., Furness, P., Gaber, L. W., Gibson, I. W., Glotz, D., Goldberg, J. C., Grande, J., Halloran, P. F., Hansen, H. E., Hartley, B., Hayry, P. J., Hill, C. M., Hoffman, E. O., Hunsicker, L. G., Lindblad, A. S., Yamaguchi, Y., and et al. (1999) The Banff 97 working classification of renal allograft pathology. Kidney Int. 55, 713-723
22. Solez, K., Colvin, R. B., Racusen, L. C., Sis, B., Halloran, P. F., Birk, P. E., Campbell, P. M., Cascalho, M., Collins, A. B., Demetris, A. J., Drachenberg, C. B., Gibson, I. W., Grimm, P. C., Haas, M., Lerut, E., Liapis, H., Mannon, R. B., Marcus, P. B., Mengel, M., Mihatsch, M. J., Nankivell, B. J., Nickeleit, V., Papadimitriou, J. C., Platt, J. L., Randhawa, P., Roberts, I., Salinas-Madriga, L., Salomon, D. R., Seron, D., Sheaff, M., and Weening, J. J. (2007) Banff '05 Meeting Report: differential diagnosis of chronic allograft injury and elimination of chronic allograft nephropathy ('CAN). Am. J. Transplant. 7, 518-526
23. Schwartz, G. J., and Work, D. F. (2009) Measurement and estimation of GFR in children and adolescents. Clin. J. Am. Soc. Nephrol. 4, 1832-1843
24. Li, L., Chaudhuri, A., Chen, A., Zhao, X., Bezchinsky, M., Concepcion, W., Salvatierra, O., Jr., and Sarwal, M. M. (2010) Efficacy and safety of thymoglobulin induction as an alternative approach for steroid-free maintenance immunosuppression in pediatric renal transplantation. Transplantation 90, 1516-1520
25. Sigdel, T. K., Lau, K., Schilling, J., and Sarwal, M. (2008) Optimizing protein recovery for urinary proteomics, a tool to monitor renal transplantation. Clin. Transplant. 22, 617-623
26. Wang, Y., Yang, F., Gritsenko, M. A., Clauss, T., Liu, T., Shen, Y., Monroe, M. E., Lopez-Ferrer, D., Reno, T., Moore, R. J., Klemke, R. L., Camp, D. G., 2nd, and Smith, R. D. (2011) Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 11, 2019-2026
27. Kelly, R. T., Page, J. S., Luo, Q., Moore, R. J., Orton, D. J., Tang, K., and Smith, R. D. (2006) Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. Anal. Chem. 78, 7796-7801
28. Qian, W. J., Liu, T., Monroe, M. E., Strittmatter, E. F., Jacobs, J. M., Kangas, L. J., Petritis, K., Camp, D. G., 2nd, and Smith, R. D. (2005) Probabilitybased evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J. Proteome Res. 4, 53-62
29. Polpitiya, A. D., Qian, W. J., Jaitly, N., Petyuk, V. A., Adkins, J. N., Camp, D. G., 2nd, Anderson, G. A., and Smith, R. D. (2008) DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics 24, 1556-1558
30. Kawai, M., Masuda, A., and Kuwana, M. (2008) A CD40-CD154 interaction in tissue fibrosis. Arthritis Rheum. 58, 3562-3573
31. Challa, A. A., and Stefanovic, B. (2011) A novel role of vimentin filaments: binding and stabilization of collagen mRNAs. Mol. Cell. Biol. 31, 3773-3789
32. Martin, M., Lefaix, J. L., Pinton, P., Crechet, F., and Daburon, F. (1993) Temporal modulation of TGF-beta 1 and beta-actin gene expression in pig skin and muscular fibrosis after ionizing radiation. Radiat. Res. 134, 63-70
33. Nakerakanti, S., and Trojanowska, M. (2012) The Role of TGF-beta Receptors in Fibrosis. Open Rheumatol. J. 6, 156-162
34. Quintana, L. F., Banon-Maneus, E., Sole-Gonzalez, A., and Campistol, J. M. (2009) Urine proteomics biomarkers in renal transplantation: an overview. Transplantation 88, S45-S49
35. Sigdel, T. K., Klassen, R. B., and Sarwal, M. M. (2009) Interpreting the proteome and peptidome in transplantation. Adv. Clin. Chem. 47, 139-169
36. Sigdel, T. K., Lee, S., and Sarwal, M. M. (2011) Profiling the proteome in renal transplantation. Proteomics Clin. Appl. 5, 269-280
37. Dadhania, D., Muthukumar, T., Ding, R., Li, B., Hartono, C., Serur, D., Seshan, S. V., Sharma, V. K., Kapur, S., and Suthanthiran, M. (2003) Molecular signatures of urinary cells distinguish acute rejection of renal allografts from urinary tract infection. Transplantation 75, 1752-1754
38. Ding, R., Li, B., Muthukumar, T., Dadhania, D., Medeiros, M., Hartono, C., Serur, D., Seshan, S. V., Sharma, V. K., Kapur, S., and Suthanthiran, M. (2003) CD103 mRNA levels in urinary cells predict acute rejection of renal allografts. Transplantation 75, 1307-1312
39. Keslar, K. S., Lin, M., Zmijewska, A. A., Sigdel, T. K., Tran, T. Q., Ma, L., Bhasin, M., Rao, P., Ding, R., Ikle, D. N., Mannon, R. B., Sarwal, M. M., Strom, T. B., Reed, E. F., Heeger, P. S., Suthanthiran, M., and Fairchild, R. L. Multicenter evaluation of a standardized protocol for noninvasive gene expression profiling. Am. J. Transplant. 13, 1891-1897
40. Exaire, E., Flores-Izquierdo, G., Ortiz, F., Pizzuto, J., Cruz, M., and Gutierrez, M. L. (1978) Detection of urinary fibrin-fibrinogen degradation products in kidney transplantation. Arch. Invest. Med. 9, 503-510
41. Maryniak, R. K., First, M. R., and Weiss, M. A. (1985) Transplant glomerulopathy: evolution of morphologically distinct changes. Kidney Int. 27, 799-806
42. Bray, R. A., Harris, S. B., Josephson, C. D., Hillyer, C. D., and Gebel, H. M. (2004) Unappreciated risk factors for transplant patients: HLA antibodies in blood components. Hum. Immunol. 65, 240-244
43. Jayle, C., Favreau, F., Zhang, K., Doucet, C., Goujon, J. M., Hebrard, W., Carretier, M., Eugene, M., Mauco, G., Tillement, J. P., and Hauet, T. (2007) Comparison of protective effects of trimetazidine against experimental warm ischemia of different durations: early and long-term effects in a pig kidney model. Am. J. Physiol. Renal Physiol. 292, F1082-F1093
44. Tiruppathi, C., Miyamoto, Y., Ganapathy, V., Roesel, R. A., Whitford, G. M., and Leibach, F. H. (1990) Hydrolysis and transport of proline-containing peptides in renal brush-border membrane vesicles from dipeptidyl peptidase IV-positive and dipeptidyl peptidase IV-negative rat strains. J. Biol. Chem. 265, 1476-1483
45. Girardi, A. C., Knauf, F., Demuth, H. U., and Aronson, P. S. (2004) Role of dipeptidyl peptidase IV in regulating activity of Na+/H+ exchanger isoform NHE3 in proximal tubule cells. Am. J. Physiol. Cell Physiol. 287, C1238-C1245
46. Sanchez, D., Tuckova, L., Sebo, P., Michalak, M., Whelan, A., Sterzl, I., Jelinkova, L., Havrdova, E., Imramovska, M., Benes, Z., Krupickova, S., and Tlaskalova-Hogenova, H. (2000) Occurrence of IgA and IgG autoantibodies to calreticulin in coeliac disease and various autoimmune diseases. J. Autoimmun. 15, 441-449
47. Watanabe, K., Ohira, H., Orikasa, H., Saito, K., Kanno, K., Shioya, Y., Obara, K., and Sato, Y. (2006) Anti-calreticulin antibodies in patients with inflammatory bowel disease. Fukushima J. Med. Sci. 52, 1-11
48. Seddiki, N., Nato, F., Lafaye, P., Amoura, Z., Piette, J. C., and Mazie, J. C. (2001) Calreticulin, a potential cell surface receptor involved in cell penetration of anti-DNA antibodies. J. Immunol. 166, 6423-6429
49. Zhao, J., Wei, J., Mialki, R. K., Mallampalli, D. F., Chen, B. B., Coon, T., Zou, C., Mallampalli, R. K., and Zhao, Y. (2012) F-box protein FBXL19-mediated ubiquitination and degradation of the receptor for IL-33 limits pulmonary inflammation. Nat. Immunol. 13, 651-658 Diseases Diseases Diseases