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 OJI  Vol.6 No.1 , March 2016
Proteomics and Its Applications in Diagnosis of Auto Immune Diseases
Abstract: Although the proteomics and its applications in detecting autoimmune diseases are a prominently discussed issue, this review will focus particularly some prominent aspects regarding clinical utility of these techniques in prognosis, diagnosis, and treatment of these diseases. The impact of immunofluorescent techniques, enzyme immunoassays and use of proteomics biomarkers in the characterization of the auto immune diseases is briefly discussed. The necessity of adopting existing technologies of protein chemistry, predisposition testing, targeted monitoring and prevention of diseases through nutrition coupled with life changes will be focused as modern diagnostic tools in realizing the changeover from isolated medicine to personalized medicine. Use of biological fluids, in order to identify low abundance proteins as biomarkers in detecting autoimmune diseases is attempted in the study of serum/plasma proteomics.
Cite this paper: Gebretsadik, G. and Menon, M. (2016) Proteomics and Its Applications in Diagnosis of Auto Immune Diseases. Open Journal of Immunology, 6, 14-33. doi: 10.4236/oji.2016.61003.
References

[1]   Anderson, N.L. and Anderson, N.G. (1998) Proteome and Proteomics: New Technologies, New Concepts, and New Words. Electrophoresis, 19, 1853-1861.
http://dx.doi.org/10.1002/elps.1150191103

[2]   Blackstock, W.P. and Weir, M.P. (1999) Proteomics: Quantitative and Physical Mapping of Cellular Proteins. Trends in Biotechnology, 17, 121-127.
http://dx.doi.org/10.1016/S0167-7799(98)01245-1

[3]   James, P. (1997) Protein Identification in the Post-Genome Era: The Rapid Rise of Proteomics. Quarterly Reviews of Biophysics, 30, 279-331.
http://dx.doi.org/10.1017/S0033583597003399

[4]   Abhilash, M. (2009) Applications of Proteomics. The Internet Journal of Genomics and Proteomics, 4, 1540-2630.

[5]   Xiang, Y. and Kato, T. (2006) Use of Proteomics in Analysis of Autoimmune Diseases. Lupus, 15, 431-435.
www.lupus-journal.com
http://dx.doi.org/10.1191/0961203306lu2329oa


[6]   Weston, A.D. and Hood, L. (2004) Systems Biology, Proteomics, and the Future of Health Care: Toward Predictive, Preventative, and Personalized Medicine. Journal of Proteome Research, 3, 179-196.
http://dx.doi.org/10.1021/pr0499693

[7]   Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., et al. (2001) The Sequence of the Human Genome. Science, 291, 1304-1351.
http://dx.doi.org/10.1126/science.1058040

[8]   Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., et al. (2001) Initial Sequencing and Analysis of the Human Genome. Nature, 409, 860-921.
http://dx.doi.org/10.1038/35057062

[9]   Reboul, J., Vaglio, P., Tzellas, N., Thierry-Mieg, N., Moore, T., Jackson, C., et al. (2001) Open-Reading-Frame Sequence Tags (OSTs) Support the Existence of at Least 17 300 Genes in C. elegans. Nature Genetics, 27, 332-336.
http://dx.doi.org/10.1038/85913

[10]   Liebler, D.C. (2002) Introduction to Proteomics. Humana Press, New York.

[11]   Robinson, W.H., Steinman, L. and Utz, P.J. (2002) Protein and Peptide Array Analysis of Autoimmune Disease. BioTechniques, 33, 566-569.

[12]   US Department of Health and Human Services (2005) Progresses in Auto Immune Research.

[13]   Oldstone, M.B.A. (1998) Molecular Mimicry and Immune-Mediated Diseases. The FASEB Journal, 12, 1255-1265.

[14]   Croxford, J.L., Anger, H.A. and Miller, S.D. (2005) Viral Delivery of an Epitope from Haemophilus influenzae Induces Central Nervous System Autoimmune Disease by Molecular Mimicry. The Journal of Immunology, 174, 907-917.
http://dx.doi.org/10.4049/jimmunol.174.2.907

[15]   Nissim, A., Winyard, P.G., Corrigall, V., Fatah, R., Perrett, D., Panayi, G. and Chernajovsky, Y. (2005) Generation of Neoantigenic Epitopes after Posttranslational Modification of Type II Collagen by Factors Present within the Inflamed Joint. Arthritis & Rheumatism, 52, 3829-3838.
http://dx.doi.org/10.1002/art.21479

[16]   Hahn, M., Nicholson, M.J., Pyrdol, J. and Wucherpfennig, K.W. (2005) Unconventional Topology of Self Peptide-Major Histocompatibility Complex Binding by a Human Autoimmune T Cell Receptor. Nature Immunology, 6, 490-496.
http://dx.doi.org/10.1038/ni1187

[17]   Carl, P.L., Temple, B.R. and Cohen, P.L. (2005) Most Nuclear Systemic Autoantigens Are Extremely Disordered Proteins: Implications for the Etiology of Systemic Autoimmunity. Arthritis Research & Therapy, 7, R1360.
http://dx.doi.org/10.1186/ar1832

[18]   James, J. and Harley, J. (1992) Linear Epitope Mapping of an Sm B/B’ Polypeptide. The Journal of Immunology, 148, 2074-2079.

[19]   Hueber, W. and Robinson, W.H. (2006) Proteomic Biomarkers for Autoimmune Disease. Proteomics, 6, 4100-4105.
http://dx.doi.org/10.1002/pmic.200600017

[20]   Prieto, S. and Grau, J.M. (2010) The Geoepidemiology of Autoimmune Muscle Disease. Autoimmunity Reviews, 9, A330-A334.
http://dx.doi.org/10.1016/j.autrev.2009.11.006

[21]   Davidson, A. and Diamond, B. (2001) Autoimmune Disease. The New England Journal of Medicine, 345, 340-350.
http://dx.doi.org/10.1056/NEJM200108023450506

[22]   Sherer, Y., Gorstein, A., Fritzler, M.J. and Shoenfeld, Y. (2004) Autoantibody Explosion in Systemic Lupus Erythematosus: More than 100 Different Antibodies Found in SLE Patients. Seminars in Arthritis and Rheumatism, 34, 501-537.
http://dx.doi.org/10.1016/j.semarthrit.2004.07.002

[23]   Robinson, W.H., Steinman, L. and Utz, P.J. (2002) Proteomics Technologies for the Study of Autoimmune Disease. Arthritis & Rheumatism, 46, 885-893.
http://dx.doi.org/10.1002/art.10129

[24]   Hueber, W., Utz, P.J., Steinman, L. and Robinson, W.H. (2002) Autoantibody Profiling for the Study of Treatment of Auto-Immune Disease. Arthritis Research & Therapy, 4, 290-295.
http://dx.doi.org/10.1186/ar426

[25]   Thadikkaran, L., Siegenthaler, M.A., Crettaz, D., Queloz, P.-A., Schneider, P. and Tissot, J.-D. (2005) Recent Advances in Blood-Related Proteomics. Proteomics, 5, 3019-3034.
http://dx.doi.org/10.1002/pmic.200402053

[26]   Vostry, M. (2009) Multiplex Immunoassays Chips and Beads. Electronic Journal of the IFCC, 20, No. 4.

[27]   Rados, C. (2005) Genomics and Medical Devices: A New Paradigm for Health Care. FDA Consumer, 39, 34-39.
http://findarticles.com/p/articles/mi_m1370/is_6_39/ai_n27869192/

[28]   Hueber, W. and Robinson, W.H. (2009) Genomics and Proteomics: Applications in Autoimmune Diseases. Pharmacogenomics and Personalized Medicine, 2, 39-48.
http://dx.doi.org/10.2147/PGPM.S4708

[29]   Ocak, S., Chaurand, P. and Massion, P.P. (2009) Mass Spectrometry-Based Proteomic Profiling of Lung Cancer. Proceedings of the American Thoracic Society, 6, 159-170.
http://dx.doi.org/10.1513/pats.200809-108LC

[30]   Stoevesandt, O., Taussig, M.J. and He, M. (2009) Protein Microarrays: High-Throughput Tools for Proteomics. Expert Review of Proteomics, 6, 145-157.
http://dx.doi.org/10.1586/epr.09.2

[31]   Lakhan, S.E. (2006) Schizophrenia Proteomics: Biomarkers on the Path to Laboratory Medicine? Diagnostic Pathology, 1, 11.
http://dx.doi.org/10.1186/1746-1596-1-11

[32]   Walther, T.C. and Mann, M. (2010) Mass Spectrometry-Based Proteomics in Cell Biology. The Journal of Cell Biology, 190, 491-500.
http://dx.doi.org/10.1083/jcb.201004052

[33]   Issaq, H.J., Xiao, Z. and Veenstra, T.D. (2007) Serum and Plasma Proteomics. Chemical Reviews, 107, 3601-3620.
http://dx.doi.org/10.1021/cr068287r

[34]   Edgar, P.F., Schonberger, S.J., Dean, B., Faull, R.L., Kydd, R. and Cooper, G.J. (1999) A Comparative Proteome Analysis of Hippocampal Tissue from Schizophrenic and Alzheimer’s Disease Individuals. Molecular Psychiatry, 4, 173-178.
http://dx.doi.org/10.1038/sj.mp.4000463

[35]   Master, S.R. (2005) Diagnostic Proteomics: Back to Basics? Clinical Chemistry, 51, 1333-1334.
http://dx.doi.org/10.1373/clinchem.2005.053686

[36]   Conrads, T.P., Zhou, M., Petricoin III, E.F., Liotta, L. and Veenstra, T.D. (2003) Cancer Diagnosis Using Proteomic Patterns. Expert Review of Molecular Diagnostics, 3, 411-420.
http://dx.doi.org/10.1586/14737159.3.4.411

[37]   Johann Jr., D.J. and Blonder, J. (2007) Biomarker Discovery: Tissues versus Fluids versus Both. Expert Review of Molecular Diagnostics, 7, 473-475.
http://dx.doi.org/10.1586/14737159.7.5.473

[38]   Hortin, G.L. (2005) Can Mass Spectrometric Protein Profiling Meet Desired Standards of Clinical Laboratory Practice? Clinical Chemistry, 51, 3-5.
http://dx.doi.org/10.1373/clinchem.2004.043281

[39]   Plebani, M., Pittoni, M., Celadin, M., Bernardi, D. and Mion, M.M. (2009) Recent Advances in Diagnostic Technologies for Autoimmune Diseases. Autoimmunity Reviews, 8, 238-243.
http://dx.doi.org/10.1016/j.autrev.2008.07.032

[40]   Kononen, J., Bubendorf, L., Kallioniemi, A., Bärlund, M., Schraml, P., Leighton, S., Torhorst, J., Mihatsch, M.J., Sauter, G. and Kallioniemi, O.P. (1998) Tissue Microarrays for High-Throughput Molecular Profiling of Tumor Specimens. Nature Medicine, 4, 844-847.
http://dx.doi.org/10.1038/nm0798-844

[41]   Pejcic, M., Stojnev, S. and Stefanovic, V. (2010) Urinary Proteomics—A Tool for Biomarker Discovery. Renal Failure, 32, 259-268.
http://dx.doi.org/10.3109/08860221003599759

[42]   Proteomics, K.J. (2002) Public-Private Group Maps out Initiatives. Science, 296, 827.

[43]   Silva, J.C., Gorenstein, M.V., Li, G.Z., Vissers, J.P. and Geromanos, S.J. (2006) Absolute Quantification of Proteins by LCMSE: A Virtue of Parallel MS Acquisition. Molecular & Cellular Proteomics, 5, 144-156.
http://dx.doi.org/10.1074/mcp.M500230-MCP200

[44]   Manolio, T.A. (2010) Genomewide Association Studies and Assessment of the Risk of Disease. The New England Journal of Medicine, 363, 166-176.
http://dx.doi.org/10.1056/NEJMra0905980

[45]   Calzone, K., Wattendorf, D. and Dunn, B.K. (2010) The Application of Genetics and Genomics to Cancer Prevention. Seminars in Oncology, 37, 407-418.
http://dx.doi.org/10.1053/j.seminoncol.2010.05.005

[46]   Cowin, P.A., Anglesio, M., Etemadmoghadam, D. and Bowtell, D.D. (2010) Profiling the Cancer Genome. Annual Review of Genomics and Human Genetics, 11, 133-159.
http://dx.doi.org/10.1146/annurev-genom-082509-141536

[47]   Salamunic, I. (2010) Laboratory Diagnosis of Autoimmune Diseases—New Technologies, Old Dilemmas. Biochemia Medica, 20, 45-56.
http://dx.doi.org/10.11613/BM.2010.006

[48]   Dahle, C., Skogh, T., Åberg, A.K., Jalal, A. and Olcén, P. (2004) Methods of Choice for Diagnostics Antinuclear Antibody (ANA) Screening: Benefit of Adding Antigen-Specific Assays to Immunofluorescence Microscopy. Journal of Autoimmunity, 22, 241-248.
http://dx.doi.org/10.1016/j.jaut.2003.12.004

[49]   Binder, S.R. (2006) Autoantibody Detection Using Multiplex Technologies. Lupus, 15, 412-421.
http://dx.doi.org/10.1191/0961203306lu2326oa

[50]   Gonzalez, C., Garcia-Berrocal, B., Talavan, T., Cassas, M.L., Navajo, J.A. and Gonzalez-Buitargo, J.M. (2005) Clinical Evaluation of a Microsphere Bead-Based Flow Cytometry Assay for the Simultaneous Determination of Anti Thyroid Peroxidase and Anti Thyroglobulin Antibodies. Clinical Biochemistry, 38, 966-972.
http://dx.doi.org/10.1016/j.clinbiochem.2005.08.004

[51]   Apweiler, R., Aslandis, C., Defuel, T., Gerstner, A., Hansen, J., Hochstrasser, D., et al. (2009) Approaching Clinical Proteomics: Current State and Future Fields of Application in Fluid Proteomics. Clinical Chemistry and Laboratory Medicine, 47, 724-744.
http://dx.doi.org/10.1515/CCLM.2009.167

[52]   http://lup.sagepub.com/content/15/7/431

[53]   Liu, W.L., Zhang, G., Wang, J.Y., Cao, J.Y., Guo, X.Z., et al. (2008) Proteomics-Based Identification of Autoantibody against CDC25B as a Novel Serum Marker in Esophageal Squamous Cell Carcinoma. Biochemical and Biophysical Research Communications, 375, 440-445.
http://dx.doi.org/10.1016/j.bbrc.2008.08.039

[54]   Wild, N., Karl, J., Grunert, V.P., Schmitt, R.I., Garczarek, U., et al. (2008) Diagnosis of Rheumatoid Arthritis: Multivariate Analysis of Biomarkers. Biomarkers, 13, 88-105.
http://dx.doi.org/10.1080/13547500701669410

[55]   Liotta, L.A. and Petricoin, E.F. (2000) Beyond the Genome to Tissue Proteomics. Breast Cancer Research, 2, 13-14.
http://dx.doi.org/10.1186/bcr23

[56]   Zolg, J.W. and Langen, H. (2004) How Industry Is Approaching the Search for New Diagnostic Markers and Biomarkers. Molecular & Cellular Proteomics, 3, 345-354.
http://dx.doi.org/10.1074/mcp.M400007-MCP200

[57]   Hueber, W., Kidd, B., Toomoka, B., Lee, B.-J., Bruce, B., et al. (2005) Antigen Microarray Profiling of Autoantibodies in Rheumatoid Arthritis. Arthritis & Rheumatology, 52, 2645-2655.
http://dx.doi.org/10.1002/art.21269

[58]   Schellekens, G.A., de Jong, B.A., van den Hoogen, F.H., van de Putte, L.B. and van Venrooij, W.J. (1998) Citrulline Is an Essential Constituent of Antigenic Determinants Recognized by Rheumatoid Arthritis-Specific Autoantibodies. Journal of Clinical Investigation, 101, 273-281.
http://dx.doi.org/10.1172/JCI1316

[59]   de Vegvar, H.E.N., Amara, R.R., Steinman, L., Utz, P.J., Robinson, H.L. and Robinson, W.H. (2003) Microarray Profiling of Antibody Responses against Simian-Human Immunodeficiency Virus: Postchallenge Convergence of Reactivities Independent of Host Histocompatibility Type and Vaccine Regimen. Journal of Virology, 77, 11125-11138.
http://dx.doi.org/10.1128/JVI.77.20.11125-11138.2003

[60]   Liu, B., Qiu, F.H., Voss, C., Xu, Y., Zhao, M., Wu, Y., Nie, J. and Wang, Z. (2011) Evaluation of Three High Abundance Protein Depletion Kits for Umbilical Cord Serum Proteomics. Proteome Science, 9, 24.
http://dx.doi.org/10.1186/1477-5956-9-24

[61]   Vanarsa, K. and Mohan, C. (2010) Proteomics in Rheumatology: The Dawn of a New Era. F1000 Medicine Reports, 2, 87.

[62]   Robinson, W.H., Di Gennaro, C., Hueber, W., Haab, B.B., Kamachi, M., Dean, E.J., Fournel, S., Fong, D., Genovese, M.C., Neuman de Vegvar, H.E., Skriner, K., Hirschberg, D.L., Morris, R.I., Muller, S., Pruijn, G.J., van Venrooij, W.J., Smolen, J.S., Brown, P.O., Steinman, L. and Utz, P.J. (2002) Autoantigen Microarrays for Multiplex Characterization of Autoantibody Responses. Nature Medicine, 8, 295-301.
http://dx.doi.org/10.1038/nm0302-295

[63]   Pietropaolo, M. and Eisenbarth, G.S. (2001) Autoantibodies in Human Diabetes. Current Directions in Autoimmunity, 4, 252-282.
http://dx.doi.org/10.1159/000060541

 
 
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