BIOMEDICAL APPLICATIONS OF PROTEOMICS
INTRODUCTION PART I ASPECTS IN BIOMEDICAL RESEARCH PROTEOMICS IN BIOMEDICINE – A TOOL, A SCIENCE, OR AN ART? DIAGNOSIS AND PROGNOSIS: AN OXYMORON THE DIMENSIONS OF PROGNOSIS PROTEIN TECHNOLOGIES, DIAGNOSIS, AND PROGNOSIS INDIVIDUAL PROTEIN PATTERNS IN CLINICAL PRACTICE NEW RESEARCH TOOLS, OLD PROBLEMS WHAT IS HUMAN MATERIAL? USING HUMAN TISSUE IN BIOMEDICAL RESEARCH – POTENTIAL PITFALLS INFORMED CONSENT SPECIFICITY OF PROTEOMICS STUDIES CONCLUSION AND SUMMARY FURTHER READING PART II BLOOD VESSELS ANTIBODY-BASED VASCULAR TARGETING: PROTEOMIC TECHNIQUES FOR THE IDENTIFICATION AND QUANTIFICATION OF MEMBRANE PROTEINS ON ENDOTHELIAL CELLS VASCULAR TARGETING ANGIOGENESIS ANGIOGENESIS-RELATED DISORDERS MARKERS OF ANGIOGENESIS LIGAND-BASED VASCULAR TARGETING TECHNOLOGIES FOR THE QUANTITATION OF MEMBRANE PROTEINS IN DIFFERENT CELL TYPES GEL-BASED QUANTITATIVE PROFILING OF MEMBRANE PROTEINS GEL-INDEPENDENT QUANTITATIVE PROFILING OF MEMBRANE PROTEINS MODEL SYSTEMS FOR THE IDENTIFICATION OF VASCULAR TARGETS IN VITRO MODEL SYSTEMS FOR THE STUDY OF GENE EXPRESSION IN RESPONSE TO ENVIRONMENTAL CHANGES IN VIVO MODEL SYSTEMS FOR THE IDENTIFICATION OF VASCULAR TARGETS CONCLUSIONS ACKNOWLEDGEMENTS REFERENCES VASCULATURE, VASCULAR DISEASE, AND ATHEROSCLEROSIS PROTEIN COMPOSITION OF HUMAN AORTA IN ATHEROSCLEROSIS – EX VIVO STUDIES CELLULAR PROTEINS INFILTRATING PROTEINS PROTEIN COMPOSITION OF HUMAN AORTA IN ATHEROSCLEROSIS – IN VITRO STUDIES LIPOPROTEINS AND APOLIPOPROTEINS AS DISEASE FACTORS TYPING OF APOLIPOPROTEIN E PHENOTYPE IN HUMANS STUDIES IN TRANSGENIC OR KNOCKOUT MICE PATHOGENETIC MECHANISMS END PATHOLOGIES: MYOCARDIAL AND CEREBRAL INFARCTION SURGICAL TREATMENTS PHARMACOLOGICAL AND DIETARY TREATMENTS ANIMAL MODELS OF ATHEROSCLEROSIS AND ITS COMPLICATIONS DISCOVERY OF NEW DIAGNOSTIC MARKERS OF STROKE STROKE FEATURES BRAIN ANATOMY CEREBROVASCULAR BLOOD CIRCULATION AETIOLOGY AND PATHOLOGY OF STROKE PATHOPHYSIOLOGY – DIFFERENT TYPES OF STROKE EPIDEMIOLOGY TREATMENT CURRENT DIAGNOSIS OF STROKE PHYSICIAN’S EVALUATION IMAGING LUMBAR PUNCTURE BIOCHEMICAL MARKERS OF STROKE PROTEOMIC-BASED APPROACH FOR THE DISCOVERY OF EARLY DIAGNOSTIC STROKE MARKERS ONE-DIMENSIONAL GEL ELECTROPHORESIS TWO-DIMENSIONAL GEL ELECTROPHORESIS SELDI-TOF PART III CANCER UNRAVELLING BIOLOGICAL PATHWAYS AND THE IDENTIFICATION OF CLINICAL MARKERS AND TARGETS IN RENAL CANCER RENAL CANCER – THE CLINICAL PERSPECTIVE CURRENT CLINICAL APPROACHES AND CLINICAL CHALLENGES IMMUNOTHERAPY FOR RENAL CANCER EXISTING MARKERS OR THERAPEUTIC TARGETS UNDERGOING CLINICAL EVALUATION PROTEOMIC STUDIES TISSUE-BASED STUDIES PRIMARY AND ESTABLISHED CELL LINES BIOLOGICAL FLUIDS HEAT SHOCK PROTEIN 27 IN CANCER GENOMIC ASPECTS STRUCTURE FUNCTIONS HSP27 EXPRESSION IN CANCER POST-TRANSLATIONAL MODIFICATION AND PROTEOMIC TOOLS PHOSPHORYLATION S-THIOLATION, OXIDATION, AND OTHERS PERSPECTIVES PROTEOMIC APPROACHES FOR BIOMARKER DISCOVERY IN COLORECTAL CANCER INTRODUCTION AND BACKGROUND TO COLORECTAL CANCER MOLECULAR BASIS OF COLORECTAL CANCER: TUMORIGENESIS IS A MULTISTEP PROCESS THE CASE FOR EARLY DETECTION: CRC IS TREATABLE IF DETECTED EARLY APPROACHES TO BIOMARKER DISCOVERY USE OF ELISAS TO DETECT CRC ONE-DIMENSIONAL SODIUM DODECYL SULFATE-POLYACRYLAMIDE GEL ELECTROPHORESIS (SDS-PAGE) PLASMA MEMBRANE PROTEOME MULTIDIMENSIONAL PROTEIN IDENTIFICATION TECHNOLOGIES PROTEOMIC PATTERN DIAGNOSTICS PROTEIN MICROARRAYS PROTEOMIC APPROACHES FOR IDENTIFYING TUMOR-SPECIFIC AUTOANTIGENS CLINICAL PROTEOMICS: OVARIAN CANCER GENERAL BACKGROUND OVARIAN CANCER OVARIAN TUMOR MARKERS SCREENING METHODS AND DIAGNOSTIC DIFFICULTIES IN OVARIAN TUMORS TREATMENT AND PROGNOSIS OF OVARIAN TUMORS CANCER PROTEOMICS PROTEIN PROFILING AND CANCER RNA EXPRESSION ANALYSIS IN CANCER CELLS: PROMISES AND PITFALLS POTENTIALS AND LIMITATIONS OF CURRENT PROTEIN PROFILING TECHNOLOGIES UNRAVELLING TUMOR COMPLEXITY PRIOR TO PROTEOME ANALYSIS THE FUTURE OF CLINICAL PROTEOMICS: CHALLENGES AND OPPORTUNITIES SHORT OVERVIEW OF OVARIAN CANCER PROTEOMICS THE PROMISE OF PROTEOMICS IN OVARIAN CANCER DIAGNOSTICS ANALYSIS OF TISSUE SAMPLES ANALYSIS OF SERUM SAMPLES DISEASE PROGNOSIS AND PROTEIN EXPRESSION DATA CONTENTS X PROTEIN EXPRESSION PROFILING ANALYSIS IN HEMATOPOIETIC STEM CELLS: PHENOTYPIC CHARACTERIZATION OF MESENCHYMAL STEM CELLS MESENCHYMAL STEM CELLS STEM CELL DEFINITION CRITERIA NEW HORIZONS IN STEM CELL BIOLOGY CURRENT AND FUTURE APPLICATIONS OF THE STEM CELL TECHNOLOGY STEMNESS AND STEM CELL-ASSOCIATED GENETIC PROGRAMS PROTEOMICS DIFFERENTIAL DISPLAY VIA TWO-DIMENSIONAL GEL ELECTROPHORESIS PROTEIN IDENTIFICATION DIFFERENTIAL PROTEOMICS PROTEIN PROFILING PROTEOMIC ANALYSIS OF MSCS LYMPHOBLASTOID AND LYMPHOMA CELLS EXPERIMENTAL MODELS EXPERIMENTAL PROCEDURES STUDIES OF PROTEIN-PATTERN CHANGES FOLLOWING TREATMENT WITH AZC SOLUBLE PROTEIN-PATTERN CHANGES INDUCED BY AZC TREATMENT MEMBRANE-ASSOCIATED PROTEIN PATTERN CHANGES INDUCED BY AZC TREATMENT PROTEOMIC STUDY OF GAL1-MEDIATED B CELL APOPTOSIS IDENTIFICATION OF THE MAJOR GAL1-BINDING MEMBRANE GLYCOPROTEIN KINETICS OF MODIFICATION OF PHOSPHORYLATION OF THE PROTEIN TYROSINE KINASE LYN LYMPHOBLASTOID AND LYMPHOMA CELLS 2-DE DATABASE PART IV PHARMACO-TOXICOLOGY CHEMORESISTANCE IN CANCER CELLS TWO-DIMENSIONAL ELECTROPHORESIS MAPS OF GASTRIC CANCER, PANCREATIC CANCER, AND MELANOMA GASTRIC CANCER PANCREATIC CANCER MELANOMA EVALUATION OF THE 2-DE PROTEIN MAPS CHEMORESISTANCE OVERVIEW MECHANISMS OF DRUG RESISTANCE DIFFERENTIALLY EXPRESSED PROTEINS IN DRUG-RESISTANT CANCER CELLS DIABETES MELLITUS: COMPLEX MOLECULAR ALTERATIONS GLUCOSE HOMEOSTASIS THE ISLETS OF LANGERHANS THE PANCREATIC BETA-CELL MOLECULAR ALTERATIONS IN THE PATHOGENESIS OF T1DM AND T2DM TYPE 1 DIABETES MELLITUS TYPE 2 DIABETES MELLITUS THE TREATMENT OF DIABETES MELLITUS PROTEOMICS: A GLOBAL APPROACH TO THE STUDY OF DIABETES MELLITUS PART V INFECTIOUS DISEASES PROTEOME APPROACH TO INFECTIOUS DISEASES: ACUTE-PHASE PROTEINS AND ANTIBODY PROFILES AS DIAGNOSTIC INDICATORS IN HUMAN PLASMA ELECTROPHORETIC MAP OF ACUTE-PHASE RESPONSE PROTEINS CLINICAL MONITORING OF APR PROTEINS BY 2-DE CHLAMYDIA TRACHOMATIS IMMUNOPROTEOME HUMAN HUMORAL IMMUNE RESPONSE TO CHLAMYDIA TRACHOMATIS INFECTIONS GENETIC SUSCEPTIBILITY TO CHLAMYDIA TRACHOMATIS DETERMINES THE OUTCOME OF THE DISEASE: DATA FROM A MOUSE MODEL PROTEOMIC STUDIES OF HUMAN LYMPHOCYTES: NEW INSIGHTS INTO HIV LYMPHOCYTE INFECTION? THE LYMPHOCYTES HUMAN IMMUNODEFICIENCY VIRUS AND THE LYMPHOCYTES PROTEOMICS OF LYMPHOCYTES ISOLATION OF LYMPHOCYTES TWO-DIMENSIONAL ELECTROPHORESIS AND MASS SPECTROMETRY RESULTS AND DISCUSSION A (PRELIMINARY) REFERENCE LYMPHOCYTE MAP (IPG: 3–10 NL) DIFFERENTIAL EXPRESSION OF PROTEINS IN CD4, CD8, AND CD LYMPHOCYTES APPLICATIONS IN HIV PHYSIOPATHOLOGY SUMMARY MODIFICATIONS OF HOST CELL PROTEOMES INDUCED BY HERPES SIMPLEX VIRUS TYPE MODIFICATIONS OF HOST CELL GENE EXPRESSION: A PROTEOMIC APPROACH CELLULAR PROTEINS ESCAPE THE VIRALLY INDUCED SHUT-OFF OF PROTEIN SYNTHESIS RIBOSOME BIOGENESIS PERSISTS IN HSV-1-INFECTED CELLS NUCLEUS AND LYTIC HSV-1 INFECTION FUNCTIONAL ORGANIZATION OF THE CELL NUCLEUS HSV-1-INDUCED MODIFICATIONS OF THE HOST CELL NUCLEUS DISTRIBUTION OF HSV-1 PROTEINS WITHIN DIFFERENT NUCLEAR DOMAINS FRANCISELLA TULARENSIS INTRACELLULAR PATHOGEN FRANCISELLA TULARENSIS SUBTYPES OF F TULARENSIS THE MAJOR OBJECTIVES OF PROTEOME STUDIES OF F TULARENSIS CONSTRUCTION OF TWO-DIMENSIONAL ELECTROPHORESIS (2-DE) REFERENCE PROTEIN MAPS OF NON-VIRULENT AND HIGHLY VIRULENT F TULARENSIS STRAINS COMPARATIVE PROTEOME ANALYSIS OF F TULARENSIS SUBSPECIES APPLICATION OF MALDI-TOF MASS SPECTROMETRY FOR TYPING OF F TULARENSIS IDENTIFICATION OF TULAREMIC ANTIGENS RECOGNIZED BY SERA COLLECTED FROM NATURALLY INFECTED INDIVIDUALS CONTENTS PART VI CENTRAL NERVOUS SYSTEM PROTEOMICS IN CLINICAL NEUROSCIENCES NERVOUS SYSTEM-RELATED SAMPLES BRAIN TISSUE CEREBROSPINAL FLUID PROTEOMICS STUDIES IN NEUROLOGICAL DISEASES BRAIN TUMOR MULTIPLE SCLEROSIS STROKE AND CEREBROVASCULAR DISEASES CREUTZFELDT-JAKOB DISEASE ALZHEIMER’S DISEASE AND RELATED DEMENTIAS PARKINSON’S DISEASE HUNTINGTON’S DISEASE MISCELLANEOUS HUMAN CEREBROSPINAL FLUID EXPERIMENTAL DESIGN SAMPLE COLLECTION AND PREPARATION TWO-DIMENSIONAL GELS OF CSF, WITH PROTEIN IDENTIFICATION BY ANTIBODIES, EDMAN DEGRADATION CHEMISTRY, MALDI/MS OR LC/MS OF INDIVIDUAL “SPOTS” PREFRACTIONATION OF CSF PRIOR TO 2-DE TWO-DIMENSIONAL LIQUID-PHASE ELECTROPHORESIS AND OTHER LC-COUPLED MS APPROACHES CSF PROTEOMIC APPLICATIONS IN CENTRAL NERVOUS SYSTEM DISEASES FUTURE CHALLENGES PROTEOMIC APPLICATIONS FOR MOLECULAR ASSESSMENT OF ALZHEIMER’S DISEASE TWO-DIMENSIONAL GEL ELECTROPHORESIS STUDIES GENERAL SCREENING STUDIES TAU PROTEIN AMYLOID PRECURSOR PROTEIN OXIDATIVE STRESS AND ANTIOXIDANT RESPONSE SELDI AMYLOID BETA PEPTIDE ANALYZED BY SELDI SCREENING OF AD WITH SELDI ON A STRONG ANIONIC EXCHANGE SURFACE SCREENING OF AD, FTD, LBD, AND VD WITH SELDI ON A WEAK CATIONIC EXCHANGE (WCX2) SURFACE PART VII MASS SPECTROMETRY AND BIOINFORMATICS MALDI-MS IMAGING IN BIOMEDICAL RESEARCH BACKGROUND METHODS TISSUE PREPARATION TECHNIQUE APPLICATIONS BETA-AMYLOID IMAGING PROTEIN VARIATIONS: RESOURCES AND TOOLS MEDICAL PROTEIN ANNOTATION DATABASES CENTRAL DATABASES SPECIALIZED DATABASES THE SWISS-PROT PROTEIN KNOWLEDGEBASE AND INFORMATION ON DISEASE AND SEQUENCE VARIATIONS TECHNIQUES OF SEARCH CHALLENGES FOR DATABASES ANALYSIS TOOLS IN THE CONTEXT OF PROTEIN VARIANTS PROTEOMIC TOOLS FOR PROTEIN IDENTIFICATION AND THE CHARACTERIZATION OF VARIANTS TOOLS FOR ANALYZING AND/OR PREDICTING THE EFFECTS OF PROTEIN VARIANTS