Rapid discovery and identification of a tissue-specific tumor biomarker from 39 human cancer cell lines using the SELDI ProteinChip platform.

Useful biomarkers are needed for early detection of cancers. To demonstrate the potential diagnostic usefulness of a new proteomic technology, we performed Expression Difference Mapping analysis on 39 cancer cell lines from 9 different tissues using ProteinChip technology. A protein biomarker candidate of 12kDa was found in colon cancer cells. We then optimized the purification conditions for this biomarker by utilizing Retentate Chromatography mass spectrometry (RC-MS). The optimized purification conditions developed "on-chip" were directly transferred to conventional chromatography to purify the biomarker, which was identified as prothymosin-alpha by ProteinChip time-of-flight mass spectrometry (TOF MS) and ProteinChip-Tandem MS systems. The relative expression level of prothymosin-alpha between colon cancer cells and normal colon mucosal cells was evaluated on the same ProteinChip platform. Prothymosin-alpha expression in colon cancer cells was clearly higher than in normal colon cells. These results indicate that prothymosin-alpha could be a potential biomarker for colon cancer, and that the ProteinChip platform could perform the whole process of biomarker discovery from screening to evaluation of the identified marker.

[1]  E. Dalmasso,et al.  Contribution of Human α-Defensin 1, 2, and 3 to the Anti-HIV-1 Activity of CD8 Antiviral Factor , 2002, Science.

[2]  T. Yip,et al.  New desorption strategies for the mass spectrometric analysis of macromolecules , 1993 .

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

[4]  J. Balibrea,et al.  Prognostic significance of preoperative serum CA 19.9 assay in patients with colorectal carcinoma. , 1994, Anticancer research.

[5]  T. Yip,et al.  Comprehensive proteomic profiling identifies serum proteomic signatures for detection of hepatocellular carcinoma and its subtypes. , 2003, Clinical chemistry.

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

[7]  L. Liotta,et al.  Proteomic Patterns of Nipple Aspirate Fluids Obtained by SELDI-TOF: Potential for New Biomarkers to Aid in the Diagnosis of Breast Cancer , 2002, Disease markers.

[8]  P. Schellhammer,et al.  Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. , 2002, Clinical chemistry.

[9]  D. Chan,et al.  Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. , 2002, Clinical chemistry.

[10]  O John Semmes,et al.  Normal, benign, preneoplastic, and malignant prostate cells have distinct protein expression profiles resolved by surface enhanced laser desorption/ionization mass spectrometry. , 2002, Clinical cancer research : an official journal of the American Association for Cancer Research.

[11]  E. Mitchell.  Role of carcinoembryonic antigen in the management of advanced colorectal cancer. , 1998, Seminars in oncology.

[12]  J. Beyer,et al.  Prognostic factors in metastatic germ cell tumors. , 1998, Seminars in oncology.

[13]  P. Schellhammer,et al.  Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. , 2002, Cancer research.

[14]  S. Weinberger,et al.  Tagless extraction‐retentate chromatography: A new global protein digestion strategy for monitoring differential protein expression , 2002, Electrophoresis.

[15]  G. Wright,et al.  Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. , 2001, The American journal of pathology.

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

[17]  J. Y. Wang,et al.  Value of carcinoembryonic antigen in the management of colorectal cancer , 1994, Diseases of the colon and rectum.

[18]  K Chapman,et al.  The ProteinChip Biomarker System from Ciphergen Biosystems: a novel proteomics platform for rapid biomarker discovery and validation. , 2001, Biochemical Society transactions.

[19]  E. Petricoin,et al.  General keynote: proteomic patterns in sera serve as biomarkers of ovarian cancer. , 2003, Gynecologic oncology.

[20]  S. Weinberger,et al.  Surface-enhanced laser desorption-ionization retentate chromatography mass spectrometry (SELDI-RC-MS): a new method for rapid development of process chromatography conditions. , 2002, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[21]  A. Riggs,et al.  DNA affinity capture and protein profiling by SELDI-TOF mass spectrometry: effect of DNA methylation. , 2002, Nucleic acids research.

[22]  A. Rees,et al.  A strategy for mapping and neutralizing conformational immunogenic sites on protein therapeutics , 2002, Proteomics.

[23]  M. Mori,et al.  Prothymosin-α mRNA expression correlates with that of c-myc in human colon cancer , 1993 .

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

[25]  T. Yip,et al.  SELDI ProteinChip® Array in Oncoproteomic Research , 2002, Technology in cancer research & treatment.

[26]  T. Tsuruo,et al.  Potent antitumor activity of MS-247, a novel DNA minor groove binder, evaluated by an in vitro and in vivo human cancer cell line panel. , 1999, Cancer research.

[27]  T. Zhukov,et al.  Discovery of distinct protein profiles specific for lung tumors and pre-malignant lung lesions by SELDI mass spectrometry. , 2003, Lung cancer.

[28]  H. Davies,et al.  Profiling of amyloid beta peptide variants using SELDI Protein Chip arrays. , 1999, BioTechniques.

[29]  K. Lillemoe,et al.  Identification of hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology. , 2002, Cancer research.

[30]  B. Ye,et al.  New technologies for the identification of markers for early detection of ovarian cancer , 2003, Current opinion in obstetrics & gynecology.

[31]  J. Oesterling,et al.  Prostate specific antigen: a critical assessment of the most useful tumor marker for adenocarcinoma of the prostate. , 1991, The Journal of urology.

[32]  G. Goodall,et al.  Prothymosin alpha: isolation and properties of the major immunoreactive form of thymosin alpha 1 in rat thymus. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Yusuke Nakamura,et al.  An integrated database of chemosensitivity to 55 anticancer drugs and gene expression profiles of 39 human cancer cell lines. , 2002, Cancer research.

[34]  S. Weinberger,et al.  Rapid Identification of Probiotic Lactobacillus Biosurfactant Proteins by ProteinChip Tandem Mass Spectrometry Tryptic Peptide Sequencing , 2002, Applied and Environmental Microbiology.

[35]  C. Hew,et al.  Multiple Mechanisms for Pitx-1 Transactivation of a Luteinizing Hormone β Subunit Gene* , 2002, The Journal of Biological Chemistry.

[36]  F. Freiha,et al.  Serum markers in germ cell neoplasms. , 1991, Hematology/oncology clinics of North America.

[37]  D. L. Diamond,et al.  Purification and characterization of the mammaglobin/lipophilin B complex, a promising diagnostic marker for breast cancer. , 2002, Biochemistry.