Molecular oncology in the post-genomic era: the challenge of proteomics.

One of the greatest challenges in modern medicine is to dissect the cascade of molecular events that lead to the development and progression of tumors. The genome-wide study of proteins embodies the exciting promise of proteomics. Unlike genomics, proteomics aims ambitiously to study not only protein expression profiles but also protein functions, which should provide researchers with a more comprehensive view of the molecular machinery that governs tumor biology. Recent technological advances are making proteomics a user-friendly, high-throughput laboratory tool that is likely to have an unprecedented impact on the pace of discovery in medicine.

[1]  David E. Misek,et al.  Proteomics-based identification of RS/DJ-1 as a novel circulating tumor antigen in breast cancer. , 2001, Clinical cancer research : an official journal of the American Association for Cancer Research.

[2]  M. Dwek,et al.  Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues , 2003, British Journal of Cancer.

[3]  E. Petricoin,et al.  Clinical proteomics: translating benchside promise into bedside reality , 2002, Nature Reviews Drug Discovery.

[4]  E. Petricoin,et al.  Use of proteomic patterns in serum to identify ovarian cancer , 2002, The Lancet.

[5]  R. Simpson,et al.  Cancer proteomics: from signaling networks to tumor markers. , 2001, Trends in biotechnology.

[6]  I. Brockhausen.  Pathways of O-glycan biosynthesis in cancer cells. , 1999, Biochimica et biophysica acta.

[7]  T. Ørntoft,et al.  Proteomics and immunohistochemistry define some of the steps involved in the squamous differentiation of the bladder transitional epithelium: a novel strategy for identifying metaplastic lesions. , 1999, Cancer research.

[8]  John I. Clark,et al.  Shotgun identification of protein modifications from protein complexes and lens tissue , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Dieter Stoll,et al.  Protein microarray technology. , 2002, Frontiers in bioscience : a journal and virtual library.

[10]  Thomas P Conrads,et al.  The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. , 2002, Biochemical and biophysical research communications.

[11]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[12]  D. Hochstrasser,et al.  Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. , 1996, Biotechnology & genetic engineering reviews.

[13]  O. Kallioniemi,et al.  Tissue microarray technology for high-throughput molecular profiling of cancer. , 2001, Human molecular genetics.

[14]  Mukesh Verma,et al.  Proteomics for Cancer Biomarker Discovery , 2002 .

[15]  C. Verschraegen,et al.  Increased expression of heat shock protein 70 in adherent ovarian cancer and mesothelioma following treatment with manumycin, a farnesyl transferase inhibitor. , 2002, Anticancer research.

[16]  A. Pandey,et al.  Tackling the phosphoproteome: tools and strategies. , 2003, Current opinion in chemical biology.

[17]  Hanno Steen,et al.  Proteomics goes quantitative: measuring protein abundance. , 2002, Trends in biotechnology.

[18]  John R Yates,et al.  Large-scale protein identification using mass spectrometry. , 2003, Biochimica et biophysica acta.

[19]  F. Révillion,et al.  Proteomics of breast cancer for marker discovery and signal pathway profiling , 2001, Proteomics.

[20]  E. Petricoin,et al.  Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front , 2001, Oncogene.

[21]  S. Fields,et al.  Protein analysis on a proteomic scale , 2003, Nature.

[22]  Robert F. Bonner,et al.  Laser Capture Microdissection: Molecular Analysis of Tissue , 1997, Science.

[23]  R. Stierum,et al.  Proteome analysis reveals novel proteins associated with proliferation and differentiation of the colorectal cancer cell line Caco-2. , 2003, Biochimica et biophysica acta.

[24]  P. Nelson,et al.  From genomics to proteomics: techniques and applications in cancer research. , 2001, Trends in cell biology.

[25]  M. Mann,et al.  Proteomics to study genes and genomes , 2000, Nature.

[26]  Emanuel F Petricoin,et al.  Clinical Proteomics for Cancer Biomarker Discovery and Therapeutic Targeting , 2002, Technology in cancer research & treatment.

[27]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[28]  P. Sinha,et al.  Proteomics for studying cancer cells and the development of chemoresistance , 2001, Proteomics.

[29]  A Tiengo,et al.  Serum protein profiles of patients with pancreatic cancer and chronic pancreatitis: searching for a diagnostic protein pattern. , 2001, Rapid communications in mass spectrometry : RCM.

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

[31]  Pierre Legrain,et al.  Comprehensive Proteomic Analysis of Breast Cancer Cell Membranes Reveals Unique Proteins with Potential Roles in Clinical Cancer* 210 , 2003, The Journal of Biological Chemistry.

[32]  Richard D. Smith,et al.  Trends in mass spectrometry instrumentation for proteomics. , 2002, Trends in biotechnology.

[33]  S. Gygi,et al.  Proteomics: the move to mixtures. , 2001, Journal of mass spectrometry : JMS.

[34]  Barry Schweitzer,et al.  Measuring proteins on microarrays. , 2002, Current opinion in biotechnology.

[35]  D. Schadendorf,et al.  Study of Therapy Resistance in Cancer Cells with Functional Proteome Analysis , 2002, Clinical chemistry and laboratory medicine.

[36]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[37]  Ming Zhou,et al.  Cancer diagnosis using proteomic patterns , 2003, Expert review of molecular diagnostics.

[38]  Mark S. Boguski,et al.  Biomedical informatics for proteomics , 2003, Nature.

[39]  E. Petricoin,et al.  New technologies for biomarker analysis of prostate cancer progression: Laser capture microdissection and tissue proteomics. , 2001, Urology.

[40]  Bill C. White,et al.  Proteomic patterns of tumour subsets in non-small-cell lung cancer , 2003, The Lancet.

[41]  E. Petricoin,et al.  Early detection: Proteomic applications for the early detection of cancer , 2003, Nature Reviews Cancer.

[42]  K. Heider,et al.  Identification and characterization of 9D7, a novel human protein overexpressed in renal cell carcinoma , 2002, International journal of cancer.

[43]  R. Christopherson,et al.  Immunophenotyping of leukemias using a cluster of differentiation antibody microarray. , 2001, Cancer research.

[44]  F. Marincola,et al.  Dissecting tumor responsiveness to immunotherapy: the experience of peptide-based melanoma vaccines. , 2003, Biochimica et biophysica acta.

[45]  E. Petricoin,et al.  Proteomics of human breast ductal carcinoma in situ. , 2002, Cancer research.

[46]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[47]  Chun-Ming Huang,et al.  Proteomics reveals protein profile changes in doxorubicin--treated MCF-7 human breast cancer cells. , 2002, Cancer letters.

[48]  Simona Fontana,et al.  Proteomic Patterns of Cultured Breast Cancer Cells and Epithelial Mammary Cells , 2002, Annals of the New York Academy of Sciences.

[49]  S. Hanash,et al.  Proteomics-based identification of protein gene product 9.5 as a tumor antigen that induces a humoral immune response in lung cancer. , 2001, Cancer research.

[50]  E. Petricoin,et al.  Serum proteomic patterns for detection of prostate cancer. , 2002, Journal of the National Cancer Institute.

[51]  M. Tyers,et al.  From genomics to proteomics , 2003, Nature.

[52]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[53]  E. Petricoin,et al.  Clinical proteomics: personalized molecular medicine. , 2001, JAMA.

[54]  S. Arkin,et al.  Taxol and anti-stathmin therapy: a synergistic combination that targets the mitotic spindle. , 2000, Cancer research.

[55]  S. Hanash.  Disease proteomics : Proteomics , 2003 .

[56]  M. Mann,et al.  4. Proteomic Analysis of Posttranslational Modifications , 2013 .

[57]  E. Kohn,et al.  Proteomic analysis and identification of new biomarkers and therapeutic targets for invasive ovarian cancer , 2002, Proteomics.

[58]  Patricia A Fetsch,et al.  Proteomic evaluation of archival cytologic material using SELDI affinity mass spectrometry: potential for diagnostic applications. , 2002, American journal of clinical pathology.

[59]  M. Lise,et al.  Protein profiles in sera of patients with malignant cutaneous melanoma. , 2000, Rapid communications in mass spectrometry : RCM.

[60]  H. Lippert,et al.  The Role of Proteomics in the Diagnosis and Outcome Prediction in Colorectal Cancer , 2002, Technology in cancer research & treatment.

[61]  David E. Misek,et al.  Identification of β-Tubulin Isoforms as Tumor Antigens in Neuroblastoma , 2000 .

[62]  Yingdong Zhao,et al.  Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness. , 2002, Cancer research.

[63]  P. Lønning.  Study of suboptimum treatment response: lessons from breast cancer. , 2003, The Lancet. Oncology.

[64]  C. Klade.  Proteomics approaches towards antigen discovery and vaccine development. , 2002, Current opinion in molecular therapeutics.

[65]  R. Kobayashi.  A proteomics approach to find a new breast cancer-specific antigenic marker. , 2001, Clinical cancer research : an official journal of the American Association for Cancer Research.

[66]  S. Hanash,et al.  Identification of novel targets for cancer therapy using expression proteomics , 2002, Leukemia.

[67]  S M Hanash,et al.  Proteomic Approaches within the NCI Early Detection Research Network for the Discovery and Identification of Cancer Biomarkers , 2001, Annals of the New York Academy of Sciences.

[68]  Maria Kavallaris,et al.  Drug resistance mechanisms in cancer cells: a proteomics perspective. , 2003, Current opinion in molecular therapeutics.

[69]  Gavin MacBeath,et al.  Protein microarrays and proteomics , 2002, Nature Genetics.

[70]  J. Pietenpol,et al.  Combined modality management of breast cancer: development of predictive markers through proteomics. , 2003, Seminars in oncology.

[71]  M. Mann,et al.  Proteomic analysis of post-translational modifications , 2003, Nature Biotechnology.

[72]  J. Kononen,et al.  Tissue microarrays for high-throughput molecular profiling of tumor specimens , 1998, Nature Medicine.

[73]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[74]  Nasreen S Jessani,et al.  Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[75]  J. Celis,et al.  Proteomics in translational cancer research: toward an integrated approach. , 2003, Cancer cell.