Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine

Quest for novel cardiovascular biomarkers by proteomic analysis

Atherosclerosis, and the resulting coronary heart disease and stroke, is the most common cause of death in developed countries. Atherosclerosis is an inflammatory process that results in the development of complex lesions or plaques that protrude into the arterial lumen. Plaque rupture and thrombosis result in the acute clinical complications of myocardial infarction (MI) and stroke. Although certain risk factors (dyslipidemias, diabetes, hypertension) and humoral markers of plaque vulnerability (C-reactive protein, interleukin-6, 10 and 18, CD40L) have been identified, a highly sensitive and specific biomarker or protein profile, which could provide information on the stability/vulnerability of atherosclerotic lesions, remains to be identified. In this review, we report several proteomic approaches which have been applied to circulating or resident cells, atherosclerotic plaques or plasma, in the search for new proteins that could be used as cardiovascular biomarkers. First, an example using a differential proteomic approach (2-DE and MS) comparing the secretome from control mammary arteries and atherosclerotic plaques is displayed. Among the different proteins identified, we showed that low levels of HSP-27 could be a potential marker of atherosclerosis. Second, we have revised several studies performed in cells involved in the pathogenesis of atherosclerosis (foam cells and smooth muscle cells). Another approach consists of performing proteomic analysis on circulating cells or plasma, which will provide a global view of the whole body response to atherosclerotic aggression. Circulating cells can bear information reflecting directly an inflammatory or pro-coagulant state related to the pathology. As an illustration, we report that circulating monocytes and plasma in patients with acute coronary syndromes has disclosed that mature Cathepsin D is increased both in the plasma and monocytes of these patients. Finally, the problems of applying proteomic approach directly to plasma will be discussed. The purpose of this review is to provide the reader with an overview of different proteomic approaches that can be used to identify new biomarkers in vascular diseases.

Production of human alpha-1-antitrypsin from transgenic rice cell culture in a membrane bioreactor

Transgenic plant cell cultures offer a number of advantages over alternative host expression systems, but so far relatively low product concentrations have been achieved. In this study, transgenic rice cells are used in a two-compartment membrane bioreactor (CELLine 350, Integra Biosciences) for the production of recombinant alpha-1-antitrypsin (rAAT). Expression of rAAT is controlled by the rice alpha-amylase (RAmy3D) promoter, which is induced in the absence of sugar. The extracellular product is retained in the bioreactor's relatively small cell compartment, thereby increasing product concentration. Due to the packed nature of the cell aggregates in the cell compartment, a clarified product solution can be withdrawn from the bioreactor. Active rAAT reached levels of 100-247 mg/L (4-10% of the total extracellular protein) in the cell compartment at 5-6 days postinduction, and multiple inductions of the RAmy3D promoter were demonstrated.

Miniaturization in functional genomics and proteomics

Proteins are the key components of the cellular machinery responsible for processing changes that are ordered by genomic information. Analysis of most human proteins and nucleic acids is important in order to decode the complex networks that are likely to underlie many common diseases. Significant improvements in current technology are also required to dissect the regulatory processes in high-throughtput and with low cost. Miniaturization of biological assays is an important prerequisite to achieve these goals in the near future.

Molecular MR imaging in oncology

The implementation and integration of systems biology approaches with the emerging nanosciences and microchip technology will revolutionize profoundly molecular imaging and fuel the drive toward a more predictive and individualized health care. In combination with informatics platforms, key gene and protein targets will be identified, and serve as more effective targets for diagnostic and therapeutic interventions. Drug development also will be expedited by the judicious selection of more appropriate molecular biomarkers that will serve as objective end points of treatment efficacy, in addition to facilitating the development of new target-specific therapeutics. Finally, with the more widespread proliferation of high-field magnets and advancements in imaging hardware; acquisition methods; and novel,"smart" MR agents, the ability to achieve higher resolution analyses of tumor biology, cell track-ing, and gene expression will be realized more fully. Although radiologists will continue to serve as diagnostic consultants and assist in management decisions, the contributions from new developments in the biologic and molecular sciences will significantly alter the scope of our profession. Radiologists will be required to participate more actively in the individualized care of the patient and cultivate a deeper understanding of the underlying molecular basis of disease and molecular pharmacology for facilitating selection of the most appropriate combination of imaging studies that address biologically relevant questions. These radical changes in our profession will necessitate the re-education and emergence of a small cadre of professionals that is educated broadly in multiple scientific disciplines, and demonstrate expertise in clinical care and the basic sciences. The optimistic view is that this already is happening.

Cytomics, the human cytome project and systems biology: top-down resolution of the molecular biocomplexity of organisms by single cell analysis

A large amount of structural and functional information is obtained by molecular cell phenotype analysis of tissues, organs and organisms at the single cell level by image or flow cytometry in combination with bioinformatic knowledge extraction (cytomics) concerning nuclei acids, proteins and metabolites (cellular genomics, proteomics and metabolomics) as well as cell function parameters like intracellular pH, transmembrane potentials or ion gradients. In addition, differential molecular cell phenotypes between diseased and healthy cells provide molecular data patterns for (i) predictive medicine by cytomics or for (ii) drug discovery purposes using reverse engineering of the data patterns by biomedical cell systems biology. Molecular pathways can be explored in this way including the detection of suitable target molecules, without detailed a priori knowledge of specific disease mechanisms. This is useful during the analysis of complex diseases such as infections, allergies, rheumatoid diseases, diabetes or malignancies. The top-down approach reaching from single cell heterogeneity in cell systems and tissues down to the molecular level seems suitable for a human cytome project to systematically explore the molecular biocomplexity of human organisms. The analysis of already existing data from scientific studies or routine diagnostic procedures will be of immediate value in clinical medicine, for example as personalized therapy by cytomics.

Discovery of Biomarker Candidates within Disease by Protein Profiling: Principles and Concepts†

Proteins and peptides present within clinical samples represent a valuable library of information regarding the ongoing processes within cells and tissues in health and disease. We have developed and validated novel technology applications that can be used to characterize the patterns of global protein expression in tissue and biofluids in either gel-based systems or by automated multidimensional nanocapillary liquid chromatography. Mass spectrophotometry platforms using MALDI MS and MS/MS or LTQ ion trap MS were capable of delivering sensitive and accurate identifications of hundreds of proteins contained in individual samples including individual forms of processing intermediates such as phospho peptides. The Systems Biology approach of integrating protein expression data with clinical data such as histopathology, clinical functional measurements, medical imaging scores, patient demographics, and clinical outcome provides a powerful tool for linking biomarker expression with biological processes that can be segmented and linked to disease presentation.

Biophotonic and Other Physical Methods for Characterizing Oral Mucosa

This article discusses biophotonic and other physical methods for characterizing oral mucosa.

Systems biology in drug discovery

The hope of the rapid translation of 'genes to drugs' has foundered on the reality that disease biology is complex, and that drug development must be driven by insights into biological responses. Systems biology aims to describe and to understand the operation of complex biological systems and ultimately to develop predictive models of human disease. Although meaningful molecular level models of human cell and tissue function are a distant goal, systems biology efforts are already influencing drug discovery. Large-scale gene, protein and metabolite measurements ('omics') dramatically accelerate hypothesis generation and testing in disease models. Computer simulations integrating knowledge of organ and system-level responses help prioritize targets and design clinical trials. Automation of complex primary human cell-based assay systems designed to capture emergent properties can now integrate a broad range of disease-relevant human biology into the drug discovery process, informing target and compound validation, lead optimization, and clinical indication selection. These systems biology approaches promise to improve decision making in pharmaceutical development.

Genomics, proteomics and integrative "omics" in hypertension research

PURPOSE OF REVIEW

During the past few years, genomics, proteomics and other "omics" fields have been applied extensively to several areas of biomedical research. This review provides an overview and summarizes the current status of applications of these omics fields to essential and secondary hypertension. Some perspectives of these fields for future hypertension research are discussed.

RECENT FINDINGS

Genome-wide scans applying to essential hypertension have demonstrated numerous chromosomal regions with significant and/or suggestive evidence of linkage. The consistency of these results among several different studies is, however, problematic; probably because of the variability in number of families, ethnicity, family types, phenotyping strategy, study design and statistical analyses in those studies. Findings from such studies will be more valuable when more-complete sets of data and their integration are available. Proteomics is in its early phase in hypertension research, but has shown some significant data on the pathophysiology of hypoxia-induced and renovascular hypertension. Recently, integrative omics and systems biology have been emerging and seem to be the ideal approach for future hypertension research.

SUMMARY

Genomics, proteomics and integrative omics have demonstrated their potential in hypertension research to better understand the pathogenesis and pathophysiology of hypertension. In addition, they may contribute to identification of new therapeutic targets, biomarker discovery, prediction of therapeutic response, personalized treatment regimens, better therapeutic outcome and ultimately prevention of the disease.

Mass Spectrometers for the Analysis of Biomolecules

Mass spectrometry (MS) has become a vital enabling technology in the life sciences. This chapter summarizes the fundamental aspects of MS, with reference to topics such as isotopic abundance and accurate mass and resolution. A broad and comprehensive overview of the instrumentation, techniques, and methods required for the analysis of biomolecules is presented. Emphasis is placed on describing the soft ionization methods and separation techniques employed in current state-of-the-art mass spectrometers.

Integrating disease knowledge and technology to deliver protein targets and biomarkers into drug discovery projects

Biomarker discovery is dependent upon two disciplines: the field of clinical bioanalysis linked to disease aetiology and the application of high level technology platforms for identifying proteins/peptides in complex samples. However, diagnostic biomarker measurements require certain definitions of context that can only be achieved by combining protein science with clinical science. The evaluation of biomarkers requires careful attention to match (1) a specific biological question with (2) the appropriate clinical sample and (3) high resolution technology systems which link protein identities to clinical informatics.:

New directions of miniaturization within the biomarker research area

An overview of the current trends within protein expression profiling is given where multidimensional separation of both gel and liquid phase techniques linked to mass spectrometry is viewed as a major route in the global proteome mapping. A clear trend in these biochemical developments is the effort to sequence and identify low-abundant protein expressions where assay miniaturization and integrated sample processing play a central role. Two areas of miniaturization within the proteomics field are addressed: (i) sample cleanup and enrichment, and (ii) silicon microstructure developments for protein chip microarrays.