Genome, proteome, and metabolome: where are we going?

Rapid advances have been made in recent years in understanding the genetic makeup of mankind. The human genome project has identified approximately 32,000 genes that occur in humans. It is now possible to perform genetic profiling with many of the genes to understand embryogenesis, growth and development, the normal state, senescence, diseases, and tumorogenesis. Techniques in molecular diagnostics are becoming available that will expand the ability to provide more precise diagnoses, predict response to treatment, evaluate treatment, and predict prognosis and outcome. Genetic profiling will, in the future, direct therapy by providing specific targets for development of medications, antibodies, and gene therapy. More recently, the attention of the scientific community has turned toward the gene products within the cell and tissue matrix, namely proteins. The field of proteomics is an evolving area, which may shed light on the proteins associated with diseases and tumors. This will again provide a mechanism for creating personalized, designer therapies for individual patients or groups of patients with similar diseases based on expression profiling. The final avenue of exploration in understanding cell function is the metabolites that occur as the end products of cellular function (metabolome). These metabolites, or improper degradation of cellular proteins, may lead to disease and neoplasia. The role of the pathologist in expression profiling for diseases and tumorigenesis is of considerable importance in providing diagnostic information and predicting outcome based on pathobiologic features of diseases and tumors.

Imagining imaging's future

Imaging specific molecules and their interactions in space and time will be essential to understand how genomes create cells, how cells constitute organisms and how errant cells cause disease. Molecular imaging must be extended and applied from nanometre to metre scales and from milliseconds to days. This quest will require input from physics, chemistry, and the genetics and biochemistry of diverse organisms with useful talents.

Henry Kunkel, Stephanie Smith, clinical immunology, and split genes

The York Avenue (New York) 'ecosystem' from the 1940s through the 1980s enabled Henry Kunkel to apply new scientific methodology to understanding human disease. Stephanie Smith, a young woman with lupus, was treated at the Rockefeller University Hospital in the 1960s. Studies of her antinuclear antibodies by Kunkel and Eng Tan led to the discovery of a precipitin line specific for lupus, and the responsible antigen was designated Sm (for 'Smith'). This review outlines the history of Sm antigen from an interesting precipitin line to the identification of small nuclear RNA molecules and small nuclear ribonucleoproteins, and subsequently the discovery of RNA splicing. The story illustrates Henry Kunkel's approach to science, emphasizing how 'accidental' clinical observations, in the hands of skilled investigators, can have unexpected and potentially momentous implications.

The new genetics and its consequences for family, kinship, medicine and medical genetics

In the past several decades there has been an explosion in our understanding of genetics. The new genetics is an integral part of contemporary biomedicine and promises great advances in alleviating disease, prolonging human life and leading us unto the medicine of the future. The aim of this paper is to explore the ways in which people make sense of the uncertainties that are associated with the new genetics, which by definition involve family and kinship relations. We explore the degree to which medical genetics places the patient in a double bind between the qualitative certainty and quantitative uncertainty of genetic inheritance that reinforce notions both of fear, and control of a person's future health. Second, we propose that the new genetics has medicalized family and kinship creating profound ethical and practical dilemmas for both the individual and for medicine as a whole.

Nutrition and genetics: an expanding frontier

The age of molecular biology began in 1953 with the discovery of the structure of DNA. By 1961 the genetic code for the translation of the sequence of bases in DNA to amino acids in proteins was underway, and a model for the genetic regulation of protein synthesis was proposed. My interest in the genetic regulation of nutrient metabolism began in that year during my sabbatical leave in the laboratory of Sir Hans Krebs at Oxford University. In the present article, I describe 2 episodes in my career during which I used genetic concepts to explain a nutritional phenomenon; the first episode occurred before doing the experimental work, and the second occurred after the experimental work was completed. My first brainstorm, which occurred in 1961, was to investigate the hypothesis that all of the fat-soluble vitamins act by the regulation of a cluster of genes. Unfortunately, I selected vitamin K as my model and discovered that it is the only fat-soluble vitamin that does not work in full or in part by the regulation of a set of genes. In 1967 I undertook a second problem, which was to determine the mode of action of polyunsaturated fatty acids in lowering plasma lipid concentrations in humans. We discovered that linoleic acid reduced the storage and enhanced the oxidation of fatty acids. The genetic interpretation of this study has come only recently: polyunsaturated fats have been shown to down-regulate enzymes that accomplish storage of fatty acids and to up-regulate genes that enhance fatty acid oxidation.

Impact of molecular medicine on pathophysiology, medical practice, and medical education

This article brings an overview of the influence of molecular medicine on pathophysiology, medical practice, and medical education. Various aspects of the growing impact of molecular medicine on clinical practice are discussed: diagnostic and predictive testing, gene and targeted therapy, and pharmacogenomics. Insufficient data from appropriate clinical studies and evidence-based medicine presently limit the applications of molecular medicine in clinical practice. Incorporation of conceptual and clinical aspects of molecular medicine in undergraduate and postgraduate curricula and a continuing education of medical professionals is an urgent imperative for the demands of medical care quality to be met in near future. The emphasis should be put on bedside-orientated molecular medicine. The prerequisite is translational research aimed to translate basic information into the improvement of healthcare of individual patients and the population as a whole.

Cambridge Healthtech Institute's 5th Annual 'Molecular Display: The Chemistry Set for Proteins and Small Molecules' Conference

This meeting covered recent advances in the molecular display of peptides, proteins and nucleotides, including selection and mutational technologies. The scientific organisers assembled an impressive array of 'molecular display' heavyweights. It promised to be a stimulating meeting and the events of the following 2 days did not disappoint. The majority of the presentations were concerned with the development of novel display technologies and processes. Antibodies currently represent > 30% of the biopharmaceutical market, but are likely to be superseded by more efficient display frameworks which avoid their inherent drawbacks. In order to generate such novel therapeutics and diagnostics, high affinity reagents must be selected and/or generated from hitherto unexplored nucleic acid sequences and displayed on suitable frameworks. This meeting was concerned with the identification, generation and validation of novel sequences and framework molecules. The keynote addresses were followed by four themed sessions entitled New technologies and target selection, The discovery of small molecules using phage display, Applications in proteomics, and Novel therapeutics and diagnostics. There was a panel discussion after each session.

The completed human genome: implications for chemical biology

The recently completed human genome sequence represents an enormous opportunity to understand biology and accelerate the development of new therapeutics. However, it also presents equally large logistical, scientific and paradigmatic challenges to efficiently translate the enormous cache of sequence data into functional information that will be the precursor of new drug development. Small-molecule chemical biology applied on a genomic scale promises to speed this translation to novel therapeutics.

Application of proteomic technologies to cytologic specimens. A review

With the increasing use of molecular biology techniques in routine pathology practice, it seems reasonable that their application to cytologic specimens will become popular in the near future. Proteomics is a novel area of research that involves the global analysis of tissue proteins using diverse technologies, such as 2-D gel electrophoresis, mass spectrometry and bioinformatics. This review discusses recent applications of proteomic analysis to cytologic specimens as well as its potential in the diagnosis of neoplastic and nonneoplastic disease.

Nanotechnologies and microchips in genetic diseases

Microarrays or microchips represent a new area of high technology, which will completely change the methodological approach to basic research and clinical diagnostics. This technology can be used for genotyping, expression profiling and proteome analysis. Genetics and molecular medicine have an expanding need for rapid genotyping, mutational analysis and DNA re-sequencing technologies, i.e. microarrays that have a clear potential for miniaturization, parallelization, and automation and enable high-throughput screening. Expression profiling technology is a new tool for investigating expression patterns, identifying new disease genes either for monogenic disorders or for complex traits, identifying new functional and cellular relationships and identifying new pathways and possible related drugs. This technology has been successfully applied to the study of complex traits, i.e. cardiovascular diseases, cancer and type II diabetes, providing new insights into possible pathogenetic mechanisms and new therapeutical approaches. Finally, microarray can further improve proteome analysis. This review discusses these points.

Extremophiles as a source for novel enzymes

Microbial life does not seem to be limited to specific environments. During the past few decades it has become clear that microbial communities can be found in the most diverse conditions, including extremes of temperature, pressure, salinity and pH. These microorganisms, called extremophiles, produce biocatalysts that are functional under extreme conditions. Consequently, the unique properties of these biocatalysts have resulted in several novel applications of enzymes in industrial processes. At present, only a minor fraction of the microorganisms on Earth have been exploited. Novel developments in the cultivation and production of extremophiles, but also developments related to the cloning and expression of their genes in heterologous hosts, will increase the number of enzyme-driven transformations in chemical, food, pharmaceutical and other industrial applications.

Inventories to insights

"In the long course of cell life on this earth it remained, for our age, for our generation, to receive the full ownership of our inheritance. We have entered the cell, the Mansion of our birth and started the inventory of our acquired wealth." (Albert Claude, Nobel lecture, 1974).

The molecular genetics of the corneal dystrophies--current status

The pertinent literature on inherited corneal diseases is reviewed in terms of the chromosomal localization and identification of the responsible genes. Disorders affecting the cornea have been mapped to human chromosome 1 (central crystalline corneal dystrophy, familial subepithelial corneal amyloidosis, early onset Fuchs dystrophy, posterior polymorphous corneal dystrophy), chromosome 4 (Bietti marginal crystalline dystrophy), chromosome 5 (lattice dystrophy types 1 and IIIA, granular corneal dystrophy types 1, 2 and 3, Thiel-Behnke corneal dystrophy), chromosome 9 (lattice dystrophy type II), chromosome 10 (Thiel-Behnke corneal dystrophy), chromosome 12 (Meesmann dystrophy), chromosome 16 (macular corneal dystrophy, fish eye disease, LCAT disease, tyrosinemia type II), chromosome 17 (Meesmann dystrophy, Stocker-Holt dystrophy), chromosome 20 (congenital hereditary endothelial corneal dystrophy types I and II, posterior polymorphous corneal dystrophy), chromosome 21 (autosomal dominant keratoconus) and the X chromosome (cornea verticillata, cornea farinata, deep filiform corneal dystrophy, keratosis follicularis spinulosa decalvans, Lisch corneal dystrophy). Mutations in nine genes (ARSC1, CHST6, COL8A2, GLA, GSN, KRT3, KRT12, M1S1and TGFBI [BIGH3]) account for some of the corneal diseases and three of them are associated with amyloid deposition in the cornea (GSN, M1S1, TGFBI) including most of the lattice corneal dystrophies (LCDs) [LCD types I, IA, II, IIIA, IIIB, IV, V, VI and VII] recognized by their lattice pattern of linear opacities. Genetic studies on inherited diseases affecting the cornea have provided insight into some of these disorders at a basic molecular level and it has become recognized that distinct clinicopathologic phenotypes can result from specific mutations in a particular gene, as well as some different mutations in the same gene. A molecular genetic understanding of inherited corneal diseases is leading to a better appreciation of the pathogenesis of these conditions and this knowledge has made it imperative to revise the classification of inherited corneal diseases.