Protein arrays as tools for serum autoantibody marker discovery in cancer.

Protein array technology has begun to play a significant role in the study of protein-protein interactions and in the identification of antigenic targets of serum autoantibodies in a variety of autoimmune disorders. More recently, this technology has been applied to the identification of autoantibody signatures in cancer. The identification of tumour-associated antigens (TAAs) recognised by the patient's immune response represents an exciting approach to identify novel diagnostic cancer biomarkers and may contribute towards a better understanding of the molecular mechanisms involved. Circulating autoantibodies have not only been used to identify TAAs as diagnostic/prognostic markers and potential therapeutic targets, they also represent excellent biomarkers for the early detection of tumours and potential markers for monitoring the efficacy of treatment. Protein array technology offers the ability to screen the humoral immune response in cancer against thousands of proteins in a high throughput technique, thus readily identifying new panels of TAAs. Such an approach should not only aid in improved diagnostics, but has already contributed to the identification of complex autoantibody signatures that may represent disease subgroups, early diagnostics and facilitated the analysis of vaccine trials.

[1]  Jianjun Yu,et al.  Autoantibody Signatures in Prostate Cancer , 2006 .

[2]  R. DiPaola,et al.  Extracellular catalytic subunit activity of the cAMP-dependent protein kinase in prostate cancer. , 2000, Clinical cancer research : an official journal of the American Association for Cancer Research.

[3]  P. Peluso,et al.  Optimizing antibody immobilization strategies for the construction of protein microarrays. , 2003, Analytical biochemistry.

[4]  Lucas J van Vliet,et al.  Nanoarrays: a method for performing enzymatic assays. , 2004, Analytical chemistry.

[5]  J. Crowley,et al.  Prevalence of prostate cancer among men with a prostate-specific antigen level < or =4.0 ng per milliliter. , 2004, The New England journal of medicine.

[6]  S M Hanash,et al.  Protein based microarrays: A tool for probing the proteome of cancer cells and tissues , 2001, Proteomics.

[7]  H. Lehrach,et al.  Mouse protein arrays from a TH1 cell cDNA library for antibody screening and serum profiling. , 2005, Genomics.

[8]  A. Houghton,et al.  Autoimmunity and tumor immunity induced by immune responses to mutations in self , 2006, Nature Medicine.

[9]  E. Tan.  Autoantibodies as reporters identifying aberrant cellular mechanisms in tumorigenesis. , 2001, The Journal of clinical investigation.

[10]  M. Mahadaven,et al.  CA 72-4 Compared with Cea and CA 19-9 as a Marker of Some Gastrointestinal Malignancies , 1999, The International journal of biological markers.

[11]  M. Vidal,et al.  Protein interaction mapping in C. elegans using proteins involved in vulval development. , 2000, Science.

[12]  Pierre Baldi,et al.  Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[13]  You-Ming Li,et al.  Identification of hepatocellular-carcinoma-associated antigens and autoantibodies by serological proteome analysis combined with protein microarray. , 2008, Journal of proteome research.

[14]  M. Pfreundschuh,et al.  Serological analysis of human tumor antigens: molecular definition and implications. , 1997, Molecular medicine today.

[15]  Yao-Tseng Chen,et al.  A testicular antigen aberrantly expressed in human cancers detected by autologous antibody screening. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[16]  M. Gerstein,et al.  Global analysis of protein phosphorylation in yeast , 2005, Nature.

[17]  M. W. Mueller,et al.  Allergen microarray: comparison of microarray using recombinant allergens with conventional diagnostic methods to detect allergen‐specific serum immunoglobulin E , 2003, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[18]  Yanhui Hu,et al.  Next generation high density self assembling functional protein arrays , 2008, Nature Methods.

[19]  Xiaoju Wang,et al.  Autoantibodies to Annexin XIA and Other Autoantigens in the Diagnosis of Breast Cancer , 2004 .

[20]  H. Lehrach,et al.  A Nonredundant Human Protein Chip for Antibody Screening and Serum Profiling* , 2003, Molecular & Cellular Proteomics.

[21]  S M Hanash,et al.  An immune response manifested by the common occurrence of annexins I and II autoantibodies and high circulating levels of IL-6 in lung cancer , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[22]  S. Bates,et al.  Autoantibody cancer biomarker: extracellular protein kinase A. , 2006, Cancer research.

[23]  F. Naour.  Contribution of proteomics to tumor immunology , 2001 .

[24]  U. Fischer,et al.  Autoantibodies against GLEA2 and PHF3 in glioblastoma: Tumor‐associated autoantibodies correlated with prolonged survival , 2005, International journal of cancer.

[25]  N. Moran,et al.  RN181, a novel ubiquitin E3 ligase that interacts with the KVGFFKR motif of platelet integrin alpha(IIb)beta3. , 2008, Biochemical and biophysical research communications.

[26]  Dina Aronzon,et al.  Application of protein microarrays for multiplexed detection of antibodies to tumor antigens in breast cancer. , 2008, Journal of proteome research.

[27]  E. Tan,et al.  Tumor-associated Antigen Arrays for the Serological Diagnosis of Cancer* , 2006, Molecular & Cellular Proteomics.

[28]  Michael J Taussig,et al.  In situ synthesis of protein arrays. , 2008, Current opinion in biotechnology.

[29]  H. Lehrach,et al.  A human cDNA library for high-throughput protein expression screening. , 2000, Genomics.

[30]  Niamh Moran,et al.  ICln, a Novel Integrin αIIbβ3-Associated Protein, Functionally Regulates Platelet Activation* , 2004, Journal of Biological Chemistry.

[31]  M. Bedford,et al.  PABP1 identified as an arginine methyltransferase substrate using high‐density protein arrays , 2002, EMBO reports.

[32]  Stephen R Master,et al.  Validation and quality control of protein microarray-based analytical methods. , 2005, Methods in molecular medicine.

[33]  A. Arits,et al.  Preoperative serum CA125 levels do not predict suboptimal cytoreductive surgery in epithelial ovarian cancer , 2007, International Journal of Gynecologic Cancer.

[34]  F. Gillardon,et al.  Identification of novel substrates for Cdk5 and new targets for Cdk5 inhibitors using high‐density protein microarrays , 2008, Proteomics.

[35]  Cecelia E Schmalbach,et al.  Molecular profiling of the immune response in colon cancer using protein microarrays: Occurrence of autoantibodies to ubiquitin C‐terminal hydrolase L3 , 2003, Proteomics.

[36]  J. Belisle,et al.  Disease State Differentiation and Identification of Tuberculosis Biomarkers via Native Antigen Array Profiling*S , 2006, Molecular & Cellular Proteomics.

[37]  M. Reth,et al.  Genetic changes occurring in established tumors rapidly stimulate new antibody responses , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Hans Lehrach,et al.  Profiling humoral autoimmune repertoire of dilated cardiomyopathy (DCM) patients and development of a disease‐associated protein chip , 2006, Proteomics.

[39]  T. Soussi,et al.  p53 Antibodies in the sera of patients with various types of cancer: a review. , 2000, Cancer research.

[40]  G. Cesareni.  Peptide display on filamentous phage capsids An new powerful tool to study protein—ligand interaction , 1992, FEBS letters.

[41]  Wei Chen,et al.  Immunity to Oncogenic Proteins , 1995, Immunological reviews.

[42]  J. Hudson,et al.  C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression , 2003, Nature Genetics.

[43]  C. Niemeyer,et al.  Dendrimer‐Activated Solid Supports for Nucleic Acid and Protein Microarrays , 2001, Chembiochem : a European journal of chemical biology.

[44]  Gil Mor,et al.  Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays , 2007, Proceedings of the National Academy of Sciences.

[45]  Jian-ying Zhang.  Tumor-associated antigen arrays to enhance antibody detection for cancer diagnosis. , 2004, Cancer detection and prevention.

[46]  H. Lehrach,et al.  Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications. , 2003, Journal of chromatography. A.

[47]  Michael J Taussig,et al.  Printing protein arrays from DNA arrays , 2008, Nature Methods.

[48]  J. Morote Robles.  [What...about tumor markers]. , 1988, Actas urologicas espanolas.

[49]  E. Krebs,et al.  Phosphorylation-dephosphorylation of enzymes. , 1979, Annual review of biochemistry.

[50]  E. Paoletti,et al.  p53 as a target for cancer vaccines: recombinant canarypox virus vectors expressing p53 protect mice against lethal tumor cell challenge. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[51]  B. Karlan,et al.  DNA sequence analysis of exons 2 through 11 and immunohistochemical staining are required to detect all known p53 alterations in human malignancies. , 1996, Oncogene.

[52]  David E. Misek,et al.  Integral Protein Microarrays for the Identification of Lung Cancer Antigens in Sera That Induce a Humoral Immune Response*S , 2008, Molecular & Cellular Proteomics.

[53]  U. Stelzl,et al.  using membrane-based human proteome arrays , 2005 .

[54]  Olive Lloyd-Baker.  IDENTIFICATION OF NOVEL , 1964 .

[55]  D. Pim,et al.  Detection of antibodies against the cellular protein p53 in sera from patients with breast cancer , 1982, International journal of cancer.

[56]  Jan Fagerberg,et al.  Autoantibodies against the tumour-associated antigen GA733-2 in patients with colorectal carcinoma , 1999, Cancer Immunology, Immunotherapy.

[57]  Wayne Thomas,et al.  Microarrayed allergen molecules: diagnostic gatekeepers for allergy treatment , 2002, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[58]  Bhupinder Bhullar,et al.  Self-Assembling Protein Microarrays , 2004, Science.

[59]  A. Chinnaiyan,et al.  Serum antibodies to huntingtin interacting protein-1: a new blood test for prostate cancer. , 2005, Cancer research.

[60]  Jianjun Yu,et al.  Humoral Response Profiling Reveals Pathways to Prostate Cancer Progression*S , 2008, Molecular & Cellular Proteomics.

[61]  Heng Zhu,et al.  Protein chip fabrication by capture of nascent polypeptides , 2006, Nature Biotechnology.

[62]  M. W. Mueller,et al.  Microarrayed allergens for IgE profiling. , 2004, Methods.

[63]  P. Brown,et al.  Autoantigen microarrays for multiplex characterization of autoantibody responses , 2002, Nature Medicine.

[64]  S O'Malley,et al.  Detection of multiple allergen-specific IgEs on microarrays by immunoassay with rolling circle amplification. , 2000, Clinical chemistry.

[65]  R. Ward,et al.  Antibody immunity to the HER-2/neu oncogenic protein in patients with colorectal cancer. , 1999, Human immunology.

[66]  Konrad Büssow,et al.  Characterization of Cyclin L2, a Novel Cyclin with an Arginine/Serine-rich Domain , 2004, Journal of Biological Chemistry.

[67]  R. Levy,et al.  Clinical outcome of lymphoma patients after idiotype vaccination is correlated with humoral immune response and immunoglobulin G Fc receptor genotype. , 2004, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[68]  Xiaoju Wang,et al.  Autoantibodies to Annexin XI-A and Other Autoantigens in the Diagnosis of Breast Cancer , 2004, Cancer Research.

[69]  C. Haglund,et al.  Preoperative serum levels of CEA and CA 242 in colorectal cancer. , 1995, British Journal of Cancer.

[70]  M. Pfreundschuh,et al.  Human neoplasms elicit multiple specific immune responses in the autologous host. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[71]  J. Koziol,et al.  Enhancement of antibody detection in cancer using panel of recombinant tumor-associated antigens. , 2003, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[72]  H. Lehrach,et al.  Toward optimized antibody microarrays: a comparison of current microarray support materials. , 2002, Analytical biochemistry.

[73]  S. Schreiber,et al.  Printing proteins as microarrays for high-throughput function determination. , 2000, Science.

[74]  H Morgan,et al.  Microfluidic array platform for simultaneous lipid bilayer membrane formation. , 2009, Biosensors & bioelectronics.

[75]  H. Lehrach,et al.  A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. , 1998, Nucleic acids research.

[76]  P. Brown,et al.  Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions , 2001, Genome Biology.

[77]  Wei Chen,et al.  Existent T-cell and antibody immunity to HER-2/neu protein in patients with breast cancer. , 1994, Cancer research.

[78]  Jian-ying Zhang,et al.  Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma. , 2008, Journal of proteome research.

[79]  Yanhui Hu,et al.  Proteome-scale purification of human proteins from bacteria , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[80]  A. Poustka,et al.  Automated production of recombinant human proteins as resource for proteome research , 2008, Proteome Science.

[81]  D. Ghosh,et al.  Autoantibody profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma. , 2007, Cancer research.

[82]  D. Murphy,et al.  Rapid characterization of binding specificity and cross-reactivity of antibodies using recombinant human protein arrays. , 2009, Journal of immunological methods.

[83]  Kim-Anh Do,et al.  Fingerprinting the circulating repertoire of antibodies from cancer patients , 2003, Nature Biotechnology.

[84]  G. McKnight,et al.  Deletion of Type IIα Regulatory Subunit Delocalizes Protein Kinase A in Mouse Sperm without Affecting Motility or Fertilization* , 1999, Journal of Biological Chemistry.

[85]  H. Lehrach,et al.  A system for dual protein expression in Pichia pastoris and Escherichia coli. , 2000, Protein expression and purification.

[86]  Rolf M. Zinkernagel,et al.  What is missing in immunology to understand immunity? , 2000, Nature Immunology.

[87]  N. Petrelli,et al.  The onset and extent of genomic instability in sporadic colorectal tumor progression. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[88]  N. Krogan,et al.  Ubiquitination Screen Using Protein Microarrays for Comprehensive Identification of Rsp5 Substrates in Yeast , 2022 .

[89]  D. Cahill,et al.  ICln, a novel integrin alphaIIbbeta3-associated protein, functionally regulates platelet activation. , 2004, The Journal of biological chemistry.

[90]  S. Bates,et al.  Extracellular protein kinase A as a cancer biomarker: its expression by tumor cells and reversal by a myristate-lacking Calpha and RIIbeta subunit overexpression. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[91]  D. Lane,et al.  Clinical utility of the immunocytochemical detection of p53 protein in cytological specimens. , 1994, Cancer research.

[92]  Barry Schweitzer,et al.  Microarrays to characterize protein interactions on a whole‐proteome scale , 2003, Proteomics.

[93]  Jürgen Kreutzberger,et al.  Generation of High Density Protein Microarrays by Cell-free in Situ Expression of Unpurified PCR Products * , 2006, Molecular & Cellular Proteomics.

[94]  H. Lehrach,et al.  Generation of Arabidopsis protein chips for antibody and serum screening , 2003, Plant Molecular Biology.

[95]  A. Butte,et al.  Multiplexed protein array platforms for analysis of autoimmune diseases. , 2006, Annual review of immunology.

[96]  G Sybrecht,et al.  Role of amplified genes in the production of autoantibodies. , 1999, Blood.

[97]  M. Gerstein,et al.  Global Analysis of Protein Activities Using Proteome Chips , 2001, Science.