Application of Proteomics in Cancer Study By: Z.Hatefi . MSc Student In Biotechnology Isfahan University Of Medical Sciences Supervisor: Dr.M.sharifi

Index Introduction Biomarker Biomarker discovery in cancer diagnosis The Proteomics Importance of proteomics Biomarker Biomarker discovery in cancer diagnosis Personalized Therapy v Cancer Classification Toxico proteomics Patient Monitoring

The cancer The numbers of deaths from cancer worldwide are gradually rising, with an estimated 12 million deaths in 2030 . More tools that are sensitive are required for early detection of cancer. Proteomics is using to biomarker discovery.

The Proteomics The proteome represents the array of proteins that are expressed in a biological compartment (cell, tissue, or organ) at a particular time, under a particular set of conditions. Large-scale, comparative analysis of proteins is the objective of proteome science (proteomics).

The key components of current proteomics technology. Protein purification Identification Two-dimensional gel electrophoresis, mass spectrometry bioinformatics

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Cy2normalization Samples 1 and 2 Cy3 for Sample 1 Cy5 for Sample 2 Cy2normalization Samples 1 and 2 2012;5:477 Circ Cardiovasc Genet.

Overview of proteomic analysis by MS/MS.  Mol Cell Proteomics. 1, 376-86.

Importance of proteomics Proteomes are also dynamic due to proteins’ varying localization, half-lives, and response to stimuli such as disease and treatment. Protein functions are regulated by a complex system of intracellular and intercellular communication with other cells and microenvironment.

Importance of proteomics Although the human genome contains 20,000–25,000 protein-coding genes it is estimated that the human proteome comprises >500,000 proteins. Alternative splicing and post-translational modifications of proteins (e.g., phosphorylation, glycosylation, and proteolytic cleavage. further increase the diversity of a human proteome

Biomarker Biomarker: molecules that can reveals : Physiological change Progress of disease Therapeutic effect .

Biomarker discovery in cancer diagnosis The best strategies to reduce the mortality and morbidity of cancer patients are early diagnosis, provide effective therapy, and subsequently monitor treatment response. Present screening tools for cancer detection, such as (CEA) , (PSA) for prostate cancer CA-125 for ovarian cancer CA 19-9 for colorectal pancreatic cancer which lack sufficient sensitivity and/or specificity for early detection.

Panel of Biomarkers The cause and pathogenesis of cancer are heterogeneous, multiple dysregulated proteins and pathways are involved in the initiation and progression of cancer. Improve the detection and clinical management of cancer patients. Higher sensitivities and specificities.

Biological sample to study cancer Cancer Cell Lines Clinical Samples Bio fluids

Cancer Cell Lines Advantage cell-culture conditions Homogenous cell types experimental manipulation. low cost secretome Advantage cell-culture conditions In vitro artifacts lack of metabolism limited (or even single) type of cells Disadvantage

Clinical Samples Resected tissues or biopsies, reflect the sheer number, complexity, and dynamics of biological events, and thus make them extremely valuable as sources for proteomics studies. One important advantage of clinical samples is that ‘‘normal’’ tissue from the surrounding area of the tumor can be used for paired analysis.

Clinical Samples Small sample size of clinical samples Disadvantage Small sample size of clinical samples Heterogeneity of human tissues(Laser Capture Micro dissection(LCM) is a technique that reduces heterogeneity in tissues). Most patients are admitted only at the moderate to late stage cancers so solid tumors offer prognostic information and less of predictive or therapeutic potential.

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Bio fluids Serum/Plasma An ideal clinical cancer biomarker or biomarker panel should be tumor-type specific, produced at the earlier stages of cancer or in response to therapy, and measurable in easily accessible body fluids.

Bio fluids Advantage Non- or less-invasive, larger quantities, human blood system perfuses. Disadvantage It has been suggested that serum/ plasma contains over 10,000 protein species, and that such tumor tissue leakage factors are present in very low concentrations in the blood

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Sample preparation Contamination. Heat.

Personalized Therapy via Molecular Targeting Strategies Effective ways of treating cancer has been a great focus of biomedical investigation for decades . Cancer affects every patient and family in a different way. The most therapeutic challenges is to design a specific drug for each individual .

Personalized Therapy Drug targeting is a new developed way of treatment achieved by new molecular detection strategies such as proteomics. These methods aid to the identification of protein biomarkers, their modification, and altered metabolic pathways by comparison of the proteomes of normal cell and cell from a patient that leads to drug designing.

Personalized Therapy One of the good examples of these molecules is PTK (Protein tyrosine Kinases) and other kinases that represent the feature of many cancers. These molecules placed in key positions in the signaling network; which are attractive targets for drug development such as inhibitors .

Cancer Classification Proteomics is one of the choices for classification of tumor origin and states, based on their molecular source. For cancer classification, the protein samples from cancer patients relative to normal or from different cancer stages analyze through MS appliance and the MS patterns uses to build a diagnostic classifier .

Cancer Classification Good cancer classification models could eliminate the unclassifiable cancers as used in current classifications. Future cancer treatments may be advanced by using an integrated model of cancer classification such as proteomics methods .

Toxico proteomics A number of chemicals contaminations present in air, water, food and workplace are capable of inducing cancer. Many studies have discovered the link of various types of environmental pollution with the development of cancer.

Toxico proteomics Although many of them have been classified as carcinogens but their mechanism is still insufficient, and remained to identify . Toxicoproteomics allow the monitoring of the body’s response to a specific toxicant . This advances supplies a means to identify and characterize mechanisms of action of toxicants in carcinogenesis.

Example The liver carcinogen N-nitrosomorpholine (NNM) investigated in rats to identify potential early protein biomarker signatures indicative of the carcinogenic processes. Analysis was performed 18 weeks following treatment revealed significant up regulation of stress proteins, including : Caspase-8 precursor Vimentin Rho GDP dissociation inhibitor Deregulates annexin A5 and fructose-1, 6-bisphosphatase.

Result Determining toxic effects of anticancer drugs at an early stage is useful for developing safer cancer therapies This finding may indicate their potential use as predictive biomarkers for early liver carcinogenicity .

Patient Monitoring It is essential to know whether patients with malignant tumors are benefiting from the administered therapy or not. Proteomic technologies, such as serum protein pattern profiling, combined with protein microarray technologies, constitute a new paradigm for detecting disease and monitoring disease response to therapy . Protein biomarkers such as CEA, CA 153, AFP,PTKs and PSA are useful for therapy monitoring.

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