1. Proteomic Analysis for Biomarkers in Early Detection of Cancer Sherry Funston Emily Faerber Brandon Lesniak

3. Protein Biomarkers Proteins used as an indicator of a specific state (such as a disease) Proteins used as an indicator of a specific state (such as a disease) Changes in protein expression or state can be “biomarkers” for risk or progression of a disease Changes in protein expression or state can be “biomarkers” for risk or progression of a disease

4. Why use plasma? Easily obtained Easily obtained Widely used clinically Widely used clinically Contains many proteins (a good representation of the body’s proteome) Contains many proteins (a good representation of the body’s proteome) Plasma has already been used in the diagnosis of many other diseases Plasma has already been used in the diagnosis of many other diseases

5. Plasma vs Serum Plasma: Plasma: Add anti-coagulant (EDTA) Add anti-coagulant (EDTA) Centrifuge Centrifuge Remove plasma, leave cells behind Remove plasma, leave cells behind Serum: Serum: Allow blood to clot Allow blood to clot Remove supernatant = serum Remove supernatant = serum Variable results Variable results

6. Biomarkers potentially useful in cancer diagnosis BiomarkerCancer typeReferences Apolipoprotein A1Ovarian, pancreaticZhang et al., 2004; Kozak et al., 200520042005 Heptaglobin α-subunitOvarian, pancreatic, lungYe et al., 20032003 Transthyretin fragmentOvarianKozak et al., 20052005 Inter-alpha-trypsin inhibitor fragmentOvarian, pancreaticZhang et al., 20042004 Vitamin D-binding proteinProstate, breastCorder et al., 1993; Pawlik et al., 200619932006 Serum amyloid A Nasopharyngeal, pancreatic, ovarian Orchekowski et al., 2005; Moshkovskii et al., 20052005 α1-antitrypsin and α1- antichymotrypsin PancreaticOrchekowski et al., 2005; Yu et al., 20052005 OsteopontinOvarian, prostateKhodavirdi et al., 20062006

7. Why use proteomic analysis? Proteomics Proteomics The “protein complement of a given genome” (Dr. Marc Wilkins) The “protein complement of a given genome” (Dr. Marc Wilkins) Basically, all proteins that are being expressed by a cell, tissue, or genome Basically, all proteins that are being expressed by a cell, tissue, or genome Proteomic analysis reveals which proteins are being expressed with accuracy, speed, and resolution Proteomic analysis reveals which proteins are being expressed with accuracy, speed, and resolution Has the potential to diagnose diseases, disease states, and effect of treatment of those diseases Has the potential to diagnose diseases, disease states, and effect of treatment of those diseases

9. Approaches to Biomarker Discovery Target Specific Target Specific Antibodies Antibodies Requires previous knowledge of proteins Requires previous knowledge of proteins Low-throughput Low-throughput Global/Nondirected Global/Nondirected Profiling of unidentified proteins Profiling of unidentified proteins Generate profiles of identified proteins Generate profiles of identified proteins High-throughput High-throughput

10. MALDI-TOF-MS/MS

11. SELDI-TOF-MS

12. Sample depletion/enrichment

15. Sample fractionation/separation

16. Research Research has focused on ovarian, prostate, and breast cancer Research has focused on ovarian, prostate, and breast cancer SELDI-TOF-MS has identified biomarker profiles with 100% sensitivity and 95% specificity SELDI-TOF-MS has identified biomarker profiles with 100% sensitivity and 95% specificity Studies have successfully: Studies have successfully: Identified patients with tumors Identified patients with tumors Identified type of tumor Identified type of tumor Distinguished between benign and malignant Distinguished between benign and malignant Identified possible treatments Identified possible treatments Distinguished response/no response to treatment Distinguished response/no response to treatment

17. Problems to Overcome Finding biomarkers that are: Finding biomarkers that are: Tumor specific Tumor specific Tissue specific Tissue specific Sample complexity Sample complexity Correlation to population Correlation to population in vivo vs. in vitro behavior in vivo vs. in vitro behavior

18. Clinical Applications Provides improved patient treatment Provides improved patient treatment Targeted treatment Targeted treatment Reduced cost Reduced cost Reliable results Reliable results Early diagnosis Early diagnosis Identification of proper treatment Identification of proper treatment

19. References Davis, Michael A., Hanash, Samir. High-throughput genomic technology in reaserach and clinical management in early detection and t herapy. Breast Cancer Research 2006, 8:217. 18 December 2006. Reddy, Guru and Dalmasso, Enrique A. SELDI® Array Technology: Protein-Based Predictive Medicine and Drug Discovery Applications. Journal of Biomedicine and Biotechnology v. 2003(4): 237-241. Alaoui-Jamali, Moulay A., Xu, Ying-jie. Proteomic technology for biomarker profiling in cancer: an update. Joural of Zhejian University SCIENCE v. 7 (6): 411-420. Verrills, Nicole M. Clinical Proteomics: Present and Future Prospects. Clinical Biochemist Reviews v. 27 (2): 99-116.