A new dimension for the human genome project: towards comprehensive expression maps

Species Choice and Model Use: Reviving Research on Human Development

While model organisms have had many historians, this article places studies of humans, and particularly our development, in the politics of species choice. Human embryos, investigated directly rather than via animal surrogates, have gone through cycles of attention and neglect. In the past 60 years they moved from the sidelines to center stage. Research was resuscitated in anatomy, launched in reproductive biomedicine, molecular genetics, and stem-cell science, and made attractive in developmental biology. I explain this surge of interest in terms of rivalry with models and reliance on them. The greater involvement of medicine in human reproduction, especially through in vitro fertilization, gave access to fresh sources of material that fed critiques of extrapolation from mice and met demands for clinical relevance or "translation." Yet much of the revival depended on models. Supply infrastructures and digital standards, including biobanks and virtual atlases, emulated community resources for model organisms. Novel culture, imaging, molecular, and postgenomic methods were perfected on less precious samples. Toing and froing from the mouse affirmed the necessity of the exemplary mammal and its insufficiency justified inquiries into humans. Another kind of model-organoids and embryo-like structures derived from stem cells-enabled experiments that encouraged the organization of a new field, human developmental biology. Research on humans has competed with and counted on models.

High-throughput, high-sensitivity analysis of gene expression in Arabidopsis

High-throughput gene expression analysis of genes expressed during salt stress was performed using a novel multiplexed quantitative nuclease protection assay that involves customized DNA microarrays printed within the individual wells of 96-well plates. The levels of expression of the transcripts from 16 different genes were quantified within crude homogenates prepared from Arabidopsis (Arabidopsis thaliana) plants also grown in a 96-well plate format. Examples are provided of the high degree of reproducibility of quantitative dose-response data and of the sensitivity of detection of changes in gene expression within limiting amounts of tissue. The lack of requirement for RNA purification renders the assay particularly suited for high-throughput gene expression analysis and for the discovery of novel chemical compounds that specifically modulate the expression of endogenous target genes.

Gene-chip analysis of the effect of tripeptide tyroservatide (YSV) on gene-expression in human hepatocarcinoma BEL-7402 tumors transplanted to nude mice

Tyroservatide (YSV) is a bioactive tripeptide of tyrosyl-seryl-valine. In this study, we studied the effects of YSV on human hepatocarcinoma BEL-7402 tumors transplanted in BALB/c (nu/nu) nude mice, and gene expression in the tumor cells with gene-chip analysis. Results show that YSV significantly inhibits the growth of transplanted human hepatocarcinoma BEL-7402 in nude mice (n = 12) compared with the control group (P < 0.05); with an inhibition rate of 55% at 320 microg/kg/d. Seven hundred eighty-one genes were different between the YSV group and the control group. Fifty-two genes changed in expression level by onefold or more including 37 downregulated genes and 15 upregulated genes. Probably, YSV exhibits a significant antitumor activity by inhibiting the expression of tumor cells histone genes, then damaging tumor cell chromosome and killing tumor cells.

Mendelian disorders deserve more attention

The study of inherited monogenic diseases has contributed greatly to our mechanistic understanding of pathogenic mutations and gene regulation, and to the development of effective diagnostic tools. But interest has gradually shifted away from monogenic diseases, which collectively affect only a small fraction of the world's population, towards multifactorial, common diseases. The quest for the genetic variability associated with common traits should not be done at the expense of Mendelian disorders, because the latter could still contribute greatly to understanding the aetiology of complex traits.

Calcium at fertilization and in early development

Fertilization calcium waves are introduced, and the evidence from which we can infer general mechanisms of these waves is presented. The two main classes of hypotheses put forward to explain the generation of the fertilization calcium wave are set out, and it is concluded that initiation of the fertilization calcium wave can be most generally explained in invertebrates by a mechanism in which an activating substance enters the egg from the sperm on sperm-egg fusion, activating the egg by stimulating phospholipase C activation through a src family kinase pathway and in mammals by the diffusion of a sperm-specific phospholipase C from sperm to egg on sperm-egg fusion. The fertilization calcium wave is then set into the context of cell cycle control, and the mechanism of repetitive calcium spiking in mammalian eggs is investigated. Evidence that calcium signals control cell division in early embryos is reviewed, and it is concluded that calcium signals are essential at all three stages of cell division in early embryos. Evidence that phosphoinositide signaling pathways control the resumption of meiosis during oocyte maturation is considered. It is concluded on balance that the evidence points to a need for phosphoinositide/calcium signaling during resumption of meiosis. Changes to the calcium signaling machinery occur during meiosis to enable the production of a calcium wave in the mature oocyte when it is fertilized; evidence that the shape and structure of the endoplasmic reticulum alters dynamically during maturation and after fertilization is reviewed, and the link between ER dynamics and the cytoskeleton is discussed. There is evidence that calcium signaling plays a key part in the development of patterning in early embryos. Morphogenesis in ascidian, frog, and zebrafish embryos is briefly described to provide the developmental context in which calcium signals act. Intracellular calcium waves that may play a role in axis formation in ascidian are discussed. Evidence that the Wingless/calcium signaling pathway is a strong ventralizing signal in Xenopus, mediated by phosphoinositide signaling, is adumbrated. The central role that calcium channels play in morphogenetic movements during gastrulation and in ectodermal and mesodermal gene expression during late gastrulation is demonstrated. Experiments in zebrafish provide a strong indication that calcium signals are essential for pattern formation and organogenesis.

GeneNote: whole genome expression profiles in normal human tissues

A novel data set, GeneNote (Gene Normal Tissue Expression), was produced to portray complete gene expression profiles in healthy human tissues using the Affymetrix GeneChip HG-U95 set, which includes 62 839 probe-sets. The hybridization intensities of two replicates were processed and analyzed to yield the complete transcriptome for twelve human tissues. Abundant novel information on tissue specificity provides a baseline for past and future expression studies related to diseases. The data is posted in GeneNote (http://genecards.weizmann.ac.il/genenote/), a widely used compendium of human genes (http://bioinfo.weizmann.ac.il/genecards).

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina

BACKGROUND

As a biomarker of cellular activities, the transcriptome of a specific tissue or cell type during development and disease is of great biomedical interest. We have generated and analyzed 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries: embryonic day 15.5 (M15E) eye, postnatal day 2 (M2PN) eye and adult retina (MRA).

RESULTS

Annotation of 8,633 non-mitochondrial and non-ribosomal high-quality ESTs revealed that 57% of the sequences represent known genes and 43% are unknown or novel ESTs, with M15E having the highest percentage of novel ESTs. Of these, 2,361 ESTs correspond to 747 unique genes and the remaining 6,272 are represented only once. Phototransduction genes are preferentially identified in MRA, whereas transcripts for cell structure and regulatory proteins are highly expressed in the developing eye. Map locations of human orthologs of known genes uncovered a high density of ocular genes on chromosome 17, and identified 277 genes in the critical regions of 37 retinal disease loci. In silico expression profiling identified 210 genes and/or ESTs over-expressed in the eye; of these, more than 26 are known to have vital retinal function. Comparisons between libraries provided a list of temporally regulated genes and/or ESTs. A few of these were validated by qRT-PCR analysis.

CONCLUSIONS

Our studies present a large number of potentially interesting genes for biological investigation, and the annotated EST set provides a useful resource for microarray and functional genomic studies.

Human chromosome 21 gene expression atlas in the mouse

Genome-wide expression analyses have a crucial role in functional genomics. High resolution methods, such as RNA in situ hybridization provide an accurate description of the spatiotemporal distribution of transcripts as well as a three-dimensional 'in vivo' gene expression overview. We set out to analyse systematically the expression patterns of genes from an entire chromosome. We chose human chromosome 21 because of the medical relevance of trisomy 21 (Down's syndrome). Here we show the expression analysis of all identifiable murine orthologues of human chromosome 21 genes (161 out of 178 confirmed human genes) by RNA in situ hybridization on whole mounts and tissue sections, and by polymerase chain reaction with reverse transcription on adult tissues. We observed patterned expression in several tissues including those affected in trisomy 21 phenotypes (that is, central nervous system, heart, gastrointestinal tract, and limbs). Furthermore, statistical analysis suggests the presence of some regions of the chromosome with genes showing either lack of expression or, to a lesser extent, co-expression in specific tissues. This high resolution expression 'atlas' of an entire human chromosome is an important step towards the understanding of gene function and of the pathogenetic mechanisms in Down's syndrome.

Protein array technology. Potential use in medical diagnostics

The human genome is sequenced, but only a minority of genes have been assigned a function. Whole-genome expression profiling is an important tool for functional genomic studies. Automated technology allows high-throughput gene activity monitoring by analysis of complex expression patterns, resulting in fingerprints of diseased versus normal or developmentally distinct tissues. Differential gene expression can be most efficiently monitored by DNA hybridization on arrays of oligonucleotides or cDNA clones. Starting from high-density filter membranes, cDNA microarrays have recently been devised in chip format. We have shown that the same cDNA libraries can be used for high-throughput protein expression and antibody screening on high-density filters and microarrays. These libraries connect recombinant proteins to clones identified by DNA hybridization or sequencing, hence creating a direct link between gene catalogs and functional catalogs. Microarrays can now be used to go from an individual clone to a specific gene and its protein product. Clone libraries become amenable to database integration including all steps from DNA sequencing to functional assays of gene products.

Diversity in voice characteristics--interaction between genes and environment, use of microarray analysis

Genetic information is used by the cells to make proteins. These proteins are then used to perform cellular and tissue functions. This process is briefly reviewed. Research to identify genes and their expression patterns is a fruitful field in the area of voice disorders. Gene expression studies of vocal lesions illustrates why this type of research is important. The role of microarray analysis (MA) to find genes of interest is discussed. Gene expression may be influenced by various environmental factors. This interaction between environment and genes is constantly manifested in many vocal characteristics and disorders. Since the end result of the gene-environment interaction is the production of cellular and tissue proteins, the field of proteomics is relevant to voice disorders. Some voice disorders have been treated successfully through using proteomic approaches.

LEARNING OUTCOMES

(a) Understand the factors that influence genetic expression; (b) display a knowledge of why the study of proteins is important to understand voice characteristics; (c) become familiar with MA, a powerful tool for the study of gene expression; and (d) describe the interaction between genes and environment.

Prioritizing the proteome: identifying pharmaceutically relevant targets

Considerable attention is now being placed on prioritizing the proteome as the point of delivery for genomic information. Some of the challenges faced in prioritizing efforts from a pharmaceutical perspective, when presented with an incomplete proteome picture, are described. Examples of pharmaceutically relevant proteins are used to illustrate an informatics-based analysis of the proteome using knowledge of known drug targets. We show how results can be maximized by linking informatics approaches to experimental techniques and describe methods that can be used for prioritization within unprecedented protein families using, for example, single nucleotide polymorphism data and knowledge of disease pathways.

Transcriptome analysis of the retina

The retina offers unique opportunities to define the molecular and cellular pathways mediating neuronal function and disease because of its morphological complexity, well-defined role in visual transduction and the availability of mutants. These investigations are being greatly facilitated by the ongoing identification of genes expressed in the retina using high-throughput methods.

Location analysis of DNA-bound proteins at the whole-genome level: untangling transcriptional regulatory networks

In this post-sequencing era, geneticists can focus on functional genomics on a much larger scale than ever before. One goal is the discovery and elucidation of the intricate genetic networks that co-ordinate transcriptional activation in different regulatory circuitries. High-throughput gene expression measurement using DNA arrays has thus become routine strategy. This approach, however, does not directly identify gene loci that belong to the same regulatory group; e.g., those that are bound by a common (set of) transcription factor(s). Working in yeast, two groups have recently published an elegant method that could circumvent this problem, by combining chromatin immunoprecipitation and DNA microarrays.(1,2) The method is likely to provide a powerful tool for the dissection of global regulatory networks in eukaryotic cells.

An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression

The cDNA microarray is one technological approach that has the potential to accurately measure changes in global mRNA expression levels. We report an assessment of an optimized cDNA microarray platform to generate accurate, precise and reliable data consistent with the objective of using microarrays as an acquisition platform to populate gene expression databases. The study design consisted of two independent evaluations with 70 arrays from two different manufactured lots and used three human tissue sources as samples: placenta, brain and heart. Overall signal response was linear over three orders of magnitude and the sensitivity for any element was estimated to be 2 pg mRNA. The calculated coefficient of variation for differential expression for all non-differentiated elements was 12-14% across the entire signal range and did not vary with array batch or tissue source. The minimum detectable fold change for differential expression was 1.4. Accuracy, in terms of bias (observed minus expected differential expression ratio), was less than 1 part in 10 000 for all non-differentiated elements. The results presented in this report demonstrate the reproducible performance of the cDNA microarray technology platform and the methods provide a useful framework for evaluating other technologies that monitor changes in global mRNA expression.

Differentially expressed genes in zona reticularis cells of the human adrenal cortex

The zona reticularis (ZR) cell in the human adrenal cortex is responsible for the secretion of dehydroepiandrosterone, but its biology, origin, and putative decrease in number during aging are poorly understood. In the present experiments, we investigated to what extent ZR and zona fasciculata (ZF) cells differ in patterns of gene expression. Both cell types were purified by microdissection from adult adrenal cortex specimens. After a brief period in culture, RNA was harvested from the cells and used to prepare radioactively labeled probes following amplification by PCR. Probes were used in hybridizations of arrays of cDNAs on nylon membranes (PCR products or plasmids obtained from an adrenal cDNA library). Analysis of hybridization intensities showed that 17 of the 750 genes studied differed in expression by more than 2-fold. Several genes expressed at higher levels in ZR cells encode components of the major histocompatibility complex or enzymes involved in peroxide metabolism. Members of the tubulin gene family were expressed at higher levels in ZF cells. Differential expression of four of the genes was confirmed by Northern blotting. These differences show that although ZR and ZF cells are similar in gene expression, ZR cells have a gene expression pattern related to the unique biology of this cell type.

Calpain3 expression during human cardiogenesis

Transcripts of calpain3, the gene involved in limb girdle muscular dystrophy type 2A, appear in organs other than the skeletal muscle during human development, the first of which being the early embryonic heart. We examined more precisely the spatio-temporal transcription pattern of calpain3 during human cardiogenesis and the appearance of its protein in fetal tissues, and correlated it to titin expression. Different events of the heart's maturation can be recognized: (i) the presence of titin RNA or protein constitute very precocious developmental cardiac markers appearing before the fusion of the two lateral endocardial tubes; (ii) the disappearance of calpain3 RNA from the ventricular compartment later in the embryonic heart. Finally, although calpain3 transcripts are present in the heart, the corresponding protein is not detected elsewhere than in skeletal muscle.

High throughput analysis of gene expression in the human brain

The human brain is thought to have the greatest complexity of gene expression of any region of the body, reflecting the diverse functions of neurons and glia. Studies of gene expression in the human brain may yield fundamental information about the phenotype of brain cells in different stages of development, in different brain regions, and in different physiological and pathological states. As the human genome project nears completion, several technological advances allow the analysis of thousands of expressed genes in a small brain sample. This review describes available sources of human brain material, and several high throughput techniques used to measure the expression of thousands of genes. These techniques include expressed sequence tag (EST) sequencing of cDNA libraries; differential display; subtractive hybridization; serial analysis of gene expression (SAGE); and the emerging technology of high density DNA microarrays. Measurement of gene expression with microarrays and other technologies has potential applications in the study of human brain diseases, including cognitive disorders for which animal models are typically not available. Gene expression measurements may be used to identify genes that are abnormally regulated as a secondary consequence of a disease state, or to identify the response of brain cells to pharmacological treatments.

Biologically based treatment planning

The classical way of quantifying dose-response relations for tumors and normal tissues and their dependence on the genetic make up of the patient is briefly reviewed. Response quantifiers such as quality of life and the probability of achieving a complication-free cure are helpful in solving many of the problems of radiation therapy planning. It is shown, through the use of these quantifiers, that by introducing radiobiologically optimized, intensity-modulated dose delivery, the treatment outcome can be improved by as much as 20%, and more in cases with a complex spread of the disease. The real strength of the radiobiological models is to serve as a scientific tool for the development of treatment optimization so that the models are modified when the clinical response systematically deviates from the predictions of the models. In this way, the biological models serve as a continuously updated historical database that later on may replace the control arm in clinical trials and allow all patients to benefit from the latest developments in radiobiologically optimized treatment techniques.

Serial analysis of gene expression in a microglial cell line

We used the serial analysis of gene expression (SAGE) method to systematically analyze transcripts present in a microglial cell line. Over 10,000 SAGE tags were sequenced, and shown to represent 6,013 unique transcripts. Among the diverse transcripts that had not been previously detected in microglia were those for cytokines such as endothelial monocyte-activating polypeptide I (EMAP I), and for cell surface antigens, including adhesion molecules such as CD9, CD53, CD107a, CD147, CD162 and mast cell high affinity IgE receptor. In addition, we detected transcripts that were characteristic of hematopoietic cells or mesodermal structures, such as E3 protein, A1, EN-7, B94, and ufo. Furthermore, the profile contained a transcript, Hn1, that is important in hematopoietic cells and neurological development (Tang et al. Mamm Genome 8:695-696, 1997), suggesting the probable neural differentiation of microglia from the hematopoietic system in development. Messenger RNA expression of these genes was confirmed by RT-PCR in primary cultures of microglia. Significantly, this is the first systematic profiling of the genes expressed in a microglial cell line. The identification and further characterization of the genes described here should provide potential new targets for the study of microglial biology.

Analysis of NotI linking clones isolated from human chromosome 3 specific libraries

We have partially sequenced more than 1000 NotI linking clones isolated from human chromosome 3-specific libraries. Of these clones, 152 were unique chromosome 3-specific clones. The clones were precisely mapped using a combination of fluorescence in situ hybridization (FISH) and hybridization to somatic cell or radiation hybrids. Two- and three-color FISH was used to order the clones that mapped to the same chromosomal region, and in some cases, chromosome jumping was used to resolve ambiguous mapping. When this NotI restriction map was compared with the yeast artificial chromosome (YAC) based chromosome 3 map, significant differences in several chromosome 3 regions were observed. A search of the EMBL nucleotide database with these sequences revealed homologies (90-100%) to more than 100 different genes or expressed sequence tags (ESTs). Many of these homologies were used to map new genes to chromosome 3. These results suggest that sequencing NotI linking clones, and sequencing CpG islands in general, may complement the EST project and aid in the discovery of all human genes by sequencing random cDNAs. This method may also yield information that cannot be obtained by the EST project alone; namely, the identification of the 5' ends of genes, including potential promoter/enhancer regions and other regulatory sequences

A comprehensive view of human chromosome 1

Comprehensive representations of human chromosomes combining diverse genomic data sets, localizing expressed sequences, and reflecting physical distance are essential for disease gene identification and sequencing efforts. We have developed a method (CompView) for integrating genomic information derived from available cytogenetic, genetic linkage, radiation hybrid, physical, and transcript-based mapping approaches. CompView generates chromosome representations with substantially higher resolution, coverage, and integration than current maps of the human genome. The CompView process was used to build a representation of human chromosome 1, yielding a map with >13,000 unique elements, an effective resolution of 910 kb, and a marker density of 50 kb. CompView creates comprehensive and fully integrated depictions of a chromosome's clinical, biological, and structural information.

Gene expression profiling of fibroblasts resistant toward oncogene-mediated transformation reveals preferential transcription of negative growth regulators

The signal-transducing Ras proteins are important driving forces of diverse cellular processes such as proliferation, neoplastic transformation, differentiation and growth inhibition. As a step toward understanding the complex mechanisms underlying cellular responses, gene expression patterns were examined in two phenotypically normal fibroblast lines which differ in their sensitivity toward oncogene-mediated transformation. Suppression subtractive hybridization (SSH) was used to establish a subtracted cDNA library specific for the REF52 cell line which, like normal diploid fibroblasts, is refractory toward neoplastic transformation induced by mutated HRAS oncogenes. In contrast, rat 208F control cells can be efficiently transformed by HRAS. The nucleotide sequence of 549 subtracted cDNA clones ('REF52 minus 208F') was determined. We identified 93 preferentially expressed gene fragments in resistant REF52 cells as compared to 208F cells. Seventeen of the 52 known genes (32.6%) are capable of inhibiting cell proliferation or of adversely affecting oncogenic signal transduction pathways. These results suggest that the anti-oncogenic properties of resistant REF52 cells are determined by multiple negative growth regulators. The preneoplastic state expressed in 208F cells is characterized by impairment of unexpectedly redundant control mechanisms. Our results also demonstrate that SSH is a powerful method for identifying specific transcriptional patterns in closely related cell types.

Ethical issues in the use of genetic markers in occupational epidemiologic research

This review was conducted to characterize the nature of contemporary occupational epidemiologic research involving genetic markers, consider how genetic information is unique with regard to its social applications, and examine some of the ethical dilemmas that may arise over the course of studies. We have reviewed the literature and the lessons from our experience in conducting occupational epidemiologic research involving genetic markers. This review describes how occupational epidemiologic studies differ from other epidemiologic studies on issues of participation, confidentiality, and the history of including genetic markers. Of primary concern in occupational studies are genes that have multiple alleles and are sometimes referred to as "metabolic polymorphisms." They generally do not confer risk on their own but rather only in combination with a specific exposure. There is a need for a clear policy and guidelines for the conduct of occupational epidemiologic studies using genetic material. This policy should address all of the steps in study design, implementation, interpretation, and communication of results.

Monogenic traits are not simple: lessons from phenylketonuria

The classification of genetic disease into chromosomal, monogenic and multifactorial categories is an oversimplification. Phenylketonuria (PKU) is a classic 'monogenic' autosomal recessive disease in which mutation at the human PAH locus was deemed sufficient to explain the impaired function of the enzyme phenylalanine hydroxylase (enzymic phenotype), the attendant hyperphenylalaninemia (metabolic phenotype) and the resultant mental retardation (cognitive phenotype). In the era of molecular genetics, expectations for a consistently close correlation between the mutant genotype and variant phenotype have been somewhat disappointed, and PKU is used here to illustrate how and why this might be the case. So-called monogenic traits do, indeed, conform to long-accepted ideas about the expression of 'major' loci and their importance in determining parameters of phenotype, but the associated features are as complex, in their own ways, as those in so-called complex traits.

Genomics, mutations and the Internet: the naming and use of parts

Mutations are the source of genetic variation and diversity; by their effect, some are neutral, others are pathogenic. In contemporary genetics, mutations appear at the interface between genomics (structural and functional) and genetics (heredity), where they serve gene discovery and mapping (genomics) and generate challenges to modify their phenotypic effects (medical genetics). Assuming the human genome harbours 80,000 transcribed genes each possessing at least 100 different (germline) alleles in a typical population, how then to record and recover data on at least 8 million human alleles? Bioinformatics is the essential resource to create the corresponding accessible digital libraries (genomic and locus-specific mutation databases) for this purpose, a goal to which The HUGO Mutation Database Initiative (Science 279: 10-11, 1998) aspires. Guidelines now exist for naming alleles (Hum Mutat 11: 1-3, 1998). The principles behind the practice are illustrated by PAHdb (http:/(/)www.mcgill.ca/ pahdb), a prototype locus-specific mutation database (NAR 26: 220-225, 1998), and by prototype genomic mutation databases (HGMD (NAR 26: 285-287, 1998), http:/(/)www.uwcm.ac.uk/uwcm/mg/hgmd0.h tml; the EBI mutation database, http:/(/)www2.ebi.ac.uk/mutations/; and OMIM, http:/(/)www.ncbi.nlm. nih.gov/Omim.html).

Protein microarrays for gene expression and antibody screening

Proteins translate genomic sequence information into function, enabling biological processes. As a complementary approach to gene expression profiling on cDNA microarrays, we have developed a technique for high-throughput gene expression and antibody screening on chip-size protein microarrays. Using a picking/spotting robot equipped with a new transfer stamp, protein solutions were gridded onto polyvinylidene difluoride filters at high density. Specific purified protein was detected on the filters with high sensitivity (250 amol or 10 pg of a test protein). On a microarray made from bacterial lysates of 92 human cDNA clones expressed in a microtiter plate, putative protein expressors could be reliably identified. The rate of false-positive clones, expressing proteins in incorrect reading frames, was low. Product specificity of selected clones was confirmed on identical microarrays using monoclonal antibodies. Cross-reactivities of some antibodies with unrelated proteins imply the use of protein microarrays for antibody specificity screening against whole libraries of proteins. Because this application would not be restricted to antigen-antibody systems, protein microarrays should provide a general resource for high-throughput screens of gene expression and receptor-ligand interactions.

Experimental pathology and breast cancer genetics: new technologies

The goal is to understand the critical events in tumour development and to apply this understanding to new approaches to diagnosis, prevention and treatment. It is clear that breast cancer is a heterogeneous disease at the molecular level, raising the possibility of a future functional classification based on mechanisms rather than morphology. These molecular phenotypes will also confer predictive value on the potential of the tumour to invade, metastasise and respond to or resist new therapeutic strategies. Studies of the genome in individuals are predicted also to enable the identification of polymorphisms that are associated with increased susceptibility to environmental factors, in addition to possibly explaining de novo variations in responses to drugs and radiation. The difficulty is how to identify which, of the approximately 30,000 genes expressed by a typical cancer cell alone or in combination, are the ones involved in these processes. The majority of breast cancers have such a multitude of molecular changes that it is difficult to distinguish between those that are critical to tumour progression and those that are epiphenomena of genetic instability and abnormalities in DNA repair. The identification of the earliest events in carcinogenesis must be the best hope, as it will then be possible to target the events that predispose to other secondary changes before they occur. Genomics and proteomics is the current hope to take us forward. This involves the application of a number of new technologies to facilitate the profiling of individual tumours, including laser-guided microdissection of microscopic lesions, comparative genomic hybridisation and loss of heterozygosity analysis of DNA using microarray technology to study DNA and expressed RNAs and protein profiling using 2D gel mass spectroscopy. With over 100,000 mRNAs and proteins to examine in complex tissues and in various combinations, there is obviously going to be a requirement for a large investment in computing power (bioinformatics) to facilitate the analysis of these data in relation to the clinical characteristics of the individual tumour and the patient.

Optimized radiation therapy based on radiobiological objectives

In the broad field of radiation therapy optimization, both simple and complex problems have their origins in the interaction of the radiation beams with the biological structures of normal and malignant tissues of the human body. Therefore, it is no great surprise that many treatment optimization problems are best handled by the use of well-designed radiobiological models. The classic way of quantifying dose-response relations for tumors and normal tissues as well as their cross-correlation with each other and their dependence on the underlying genetic and molecular biology of the cell are first briefly reviewed. Radiobiological objective functions, such as the probability of achieving complication-free cure and its expectation value under influence of stochastic processes during the course of treatment, are defined and shown to solve many of the problems of radiation therapy planning. Finally, it is shown through the use of these quantifiers that, simply by introducing biologically optimal intensity modulated dose delivery, the treatment outcome can be improved by about 20% or more in cases with a complex spread of the disease. Once radiobiological optimal plans have been developed, they can be approximated by ordinary physical planning, but the biological objective functions are still needed to have a figure of merit for the quality of the treatment.

The expression of genes in human preimplantation embryos

The study of gene expression in human preimplantation embryos is establishing itself as a necessary dimension of developmental biology and medical genetics. Transcripts identified in human preimplantation embryos include housekeeping genes, transcription and growth factor genes, sex-determining genes, tissue-specific genes and novel genes, as well as genes of unknown function. Strategies are being developed which will eventually permit the most sophisticated gene expression studies on single human embryos of co-ordinated transcription and translational regulation. There is both a need for international co-operation for the systematic construction of expression maps and a need to establish databases of expression patterns during different stages of human development. Understanding how genes are regulated in humans is essential for understanding both normal development and disease. Until recently, studies of gene expression and regulation during embryogenesis were almost exclusively limited to prokaryotes and to eukaryotes other than man. The introduction of artificial reproductive technologies in conjunction with the development of recombinant molecular technologies applicable to single cells has made possible the study of human development at its earliest stages (Pergament and Bonnicksen, 1994). Although there are still enormous technical challenges, robust strategies have been, and continue to be, developed for connecting DNA sequence to such endophenotypes as timing and level of genes expression at the single cell level. Questions currently being asked in human developmental genetic studies concern the pronucleus, the zygote and the preimplantation embryo: what genes are expressed? When are they expressed? What functions do they perform and how, in sequence or in combination? And, what elements control and regulate their expression? This review provides an overview of current knowledge about the expression of different embryonic genes during early human development and discusses future prospects, which includes a need for international co-operation similar to the Human Genome Project.

Insulin-like 4 (INSL4) gene expression in human embryonic and trophoblastic tissues

Polypeptide growth factors play an important role in the regulation of human embryonic development. Insulin-like 4 gene (INSL4) is a member of the insulin family, which includes insulin, IGF-I, IGF-II, relaxin, and INSL3. Using RT-PCR, we previously found abundant INSL4 mRNA in the human placenta. In this study, we examined the chronology and spatial expression of this gene in sections of human placenta and conceptus by means of in situ hybridization. Expression of the IGF-II gene was studied as a positive control. INSL4 distribution was tissue- and cell-specific. Indeed, INSL4 mRNA was most abundant in syncytiotrophoblast cells. In fetal tissues, INSL4 mRNA was identified in the perichondrium of all four limbs, vertebrae, and ribs. Moreover, INSL4 mRNA was abundant in interbone ligaments. These findings indicate that the INSL4 gene may play an important role in trophoblast development and regulation of bone formation. IGF-II mRNA, in agreement with the literature, are mainly located in the mesodermal core in the villous trophoblast and in most embryonic tissues.

Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies

We present here a simple and fast method allowing the isolation of DNA binding sites for transcription factors from families of coregulated genes, with results illustrated in Saccharomyces cerevisiae. Although conceptually simple, the algorithm proved efficient for extracting, from most of the yeast regulatory families analyzed, the upstream regulatory sequences which had been previously found by experimental analysis. Furthermore, putative new regulatory sites are predicted within upstream regions of several regulons. The method is based on the detection of over-represented oligonucleotides. A specificity of this approach is to define the statistical significance of a site based on tables of oligonucleotide frequencies observed in all non-coding sequences from the yeast genome. In contrast with heuristic methods, this oligonucleotide analysis is rigorous and exhaustive. Its range of detection is however limited to relatively simple patterns: short motifs with a highly conserved core. These features seem to be shared by a good number of regulatory sites in yeast. This, and similar methods, should be increasingly required to identify unknown regulatory elements within the numerous new coregulated families resulting from measurements of gene expression levels at the genomic scale. All tools described here are available on the web at the site http://copan.cifn.unam.mx/Computational_Biology/ yeast-tools

The impact of two-hybrid and related methods on biotechnology

Two-hybrid technology has contributed significantly to the unraveling of molecular regulatory networks by facilitating the discovery of protein interactions. Outgrowths of these methods are developing rapidly, including interaction mating to identify false positives and map protein networks, two-bait systems, systems not based on transcription, and systems permitting the selection of peptide aptamers to manipulate gene and allele function. These advances promise to have a significant impact on industrial biotechnology and drug development.

Human post-implantation embryo collection: medical and surgical techniques

Knowledge of the genetic control of early human development is limited with most information being extrapolated from studies in animal models. There is compelling evidence that undertaking gene expression studies in human embryos can be expected to dramatically enhance our understanding of embryonic formation and malformation. Such studies require the systematic and coordinated collection, storage and study of human embryos. We have successfully collected intact embryos from cases undergoing termination of pregnancy (TOP). Embryonic material was collected from 62% of attempts using a technique of surgical aspiration carried out under ultrasound guidance. Collection rates were lower after medical termination of pregnancy (41%) although the proportion of undisrupted embryos was identical with the two methods (26%). Surgical aspiration provided intact embryos between Carnegie stages (CS) 16-22 while earlier developmental stages were collected from medical terminations. Our collection of over 60 intact specimens, spanning Carnegie stages 10 to 22 (about 21 to 53 days of development) covers a huge window of critical developmental events and hence represents an exciting and valuable research resource.

Identification of genes expressed in human CD34(+) hematopoietic stem/progenitor cells by expressed sequence tags and efficient full-length cDNA cloning

Hematopoietic stem/progenitor cells (HSPCs) possess the potentials of self-renewal, proliferation, and differentiation toward different lineages of blood cells. These cells not only play a primordial role in hematopoietic development but also have important clinical application. Characterization of the gene expression profile in CD34(+) HSPCs may lead to a better understanding of the regulation of normal and pathological hematopoiesis. In the present work, genes expressed in human umbilical cord blood CD34(+) cells were catalogued by partially sequencing a large amount of cDNA clones [or expressed sequence tags (ESTs)] and analyzing these sequences with the tools of bioinformatics. Among 9,866 ESTs thus obtained, 4,697 (47.6%) showed identity to known genes in the GenBank database, 2, 603 (26.4%) matched to the ESTs previously deposited in a public domain database, 1,415 (14.3%) were previously undescribed ESTs, and the remaining 1,151 (11.7%) were mitochondrial DNA, ribosomal RNA, or repetitive (Alu or L1) sequences. Integration of ESTs of known genes generated a profile including 855 genes that could be divided into different categories according to their functions. Some (8.2%) of the genes in this profile were considered related to early hematopoiesis. The possible function of ESTs corresponding to so far unknown genes were approached by means of homology and functional motif searches. Moreover, attempts were made to generate libraries enriched for full-length cDNAs, to better explore the genes in HSPCs. Nearly 60% of the cDNA clones of mRNA under 2 kb in our libraries had 5' ends upstream of the first ATG codon of the ORF. With this satisfactory result, we have developed an efficient working system that allowed fast sequencing of 32 full-length cDNAs, 16 of them being mapped to the chromosomes with radiation hybrid panels. This work may lay a basis for the further research on the molecular network of hematopoietic regulation.

A method for analyzing the qualitative and quantitative aspects of gene expression: a transcriptional profile revealed for HeLa cells

A number of strategies have been devised by which differentially expressed genes in different cell types or tissues can be identified. We here report an efficient method to analyze the qualitative and quantitative aspects of transcripts and to construct an extensive gene expression profile in any kind of cell or tissue of interest. This method enables us to analyze the composition of mRNA species, reflecting gene activities, by measuring the frequency of appearance of concatamerized 17mer cDNA mini-fragments, which are proportional to the abundance of mRNA. As compared with a related method previously described by others, we can analyze approximately 3-4 bp longer cDNA fragments derived from amounts of total RNA as small as 1 microg. Using this technique we examined 10 100 cDNA mini-fragments from HeLa cells and constructed a gene expression profile consisting of 3665 genes. This method should thus provide an overall indication of gene activities and a rational means for monitoring gene fluctuation in different cells or tissues at different stages of development, in normal and disease states.

Identification and cloning of differentially expressed genes by long-distance differential display

Differential mRNA display (DD-PCR) amplifies short cDNAs (average size 100-350 bp), representing mainly the 3' untranslated regions (3' UTR) of transcripts. Sequencing of these cDNAs is predominantly uninformative for prediction of function and selection of clones for further analysis. Differential display of longer amplicons (0.5-2.0 kb) could enable isolation of cDNAs that encompass both 3' UTR and at least part of the 3' end of the coding region. The coding sequence information could facilitate selection of candidate clones for further analysis without the necessity of screening cDNA libraries. By combining DD-PCR protocols with long-distance PCR and using hot-start PCR with rTth DNA polymerase we have successfully amplified and comparatively displayed cDNAs ranging in size from 150 bp to 2 kb. Long-distance DD-PCR (LDD-PCR) has generated highly reproducible primer-specific patterns of cDNA fragments, as well as reproducible duplicate fingerprints, obtained from different RNA and cDNA samples. Sequencing and expression analyses of LDD-PCR clones have shown that LDD-PCR (a) enables nonredundant clone sampling, (b) generates many clones that encompass part of the coding region, and (c) samples both abundant and rare transcripts, approximately 60% of which are differentially expressed as confirmed by Northern analysis. Coupled with high-throughput cDNA sequencing and multiplex hybridization of cDNA microarrays for confirmation of differential expression, LDD-PCR could prove to be useful for simultaneous scanning of transcripts from multiple cDNA samples and faster selection of differentially expressed transcripts of interest.

Genomic strategies for defining and dissecting developmental and physiological pathways

A major challenge in genetics research is defining and dissecting the diversity of developmental and physiological pathways that lie between genes and traits. New functional genomics methods are transforming these studies by providing comprehensive and systematic approaches that complement traditional methods of formal genetics, biochemistry, and cell biology. Together, these complementary approaches will test whether reductionism can account for the complex web of interactions that lead from genetic variation to morphological, physiological, and behavioral traits in health and disease.

Internet databases for clinical geneticists--an overview

In this paper, we provide an overview of databases that are of importance to clinical geneticists. Some suggestions for the fruitful use for both research and diagnosis are given. For beginning 'web-surfers' we also list some well-known search engines and give a short overview of how to use these and other services. In addition, the URLs of some of the most important databases, gateways and tutorials are listed.

Expression of genes (CAPN3, SGCA, SGCB, and TTN) involved in progressive muscular dystrophies during early human development

The developmental expression pattern of four human genes, three of which are involved in progressive muscular dystrophies, was investigated. The rationale for these experiments is that these patterns might provide useful information on the pathophysiology underlying these myopathies. Despite the presence of overlapping clinical signs, the spatiotemporal expression profiles of the corresponding genes differed widely. Transcripts of alpha-sarcoglycan (SGCA) were visible as soon as myotomes were formed, and constitute, together with titin transcripts, precocious muscular system landmarks. beta-sarcoglycan (SGCB) was initially transcribed in a ubiquitous manner, and, toward the second part of the embryonic period, became specific to striated muscle, heart, and the central nervous system. Whereas titin (TTN) transcription and translation seem to be coupled, for the sarcoglycans, translation seemed restricted to skeletal muscle. Calpain3 (CAPN3) RNA was found in only skeletal muscles during the fetal period. It was, however, present earlier in the whole heart, where it selectively disappeared. Finally, evidence for differentially spliced calpain3 variants in smooth muscles was also seen. The expression profiles of these genes is suggestive of their having a role during myogenesis, knowledge of which could be pertinent to the understanding of the pathophysiology of the associated diseases.

Integrated methods to solve the biological basis of common diseases

Biological variations influence population variations of many common traits. Identification of the biological basis of many common diseases has been particularly difficult, but new reagents and analytical tools will greatly facilitate this process. The goal of this review is to discuss how to identify the biological basis of common traits by using mouse models. No single method will work for all traits. Understanding complex problems will require broadly based holistic approaches that use a wide array of tools and resources. A multiplicity of developed methods together provide the tools needed to identify the biological basis of any common trait. These tools, whole-genome linkage maps, maps of expressed genes, and statistical methods, deal with the complexities of multiple loci or correlated traits. This review provides some criteria for making choices about the likely productive approaches at each stage in the process of finding genes that influence common traits.

Random mutagenesis screen for dominant behavioral mutations in mice

Large-scale mutagenesis and screening for altered phenotypes have been used effectively in many (lower) model organisms to identify mutations in genes that control biological processes. In the mouse, the cost of maintaining the large breeding colonies necessary to screen for recessive mutations makes it important to consider alternate approaches such as region-specific saturation mutagenesis or screening for mutations with a dominant mode of inheritance. In this article, a pilot screen for (semi)dominant visible and behavioral mutations in the mouse induced by a potent chemical mutagen, N-ethyl-N-nitrosourea (ENU), is described. An efficient protocol for ENU mutagenesis and strain-specific differences in the effect of mutagen on the sterility period and long-term survival are reported. In addition to a description of the screen for abnormal circadian wheel running activity that was used previously, the suitability of a high-throughput screen of mutagenized progeny in the Porsolt swim test, used to test the efficacy of antidepressant agents, and in the prepulse inhibition of the acoustic startle response, used to detect anomalies in sensorimotor gating, is tested. By demonstrating strain specific differences and prescreening 100 G1 progeny of mutagenized males, the feasibility of using these behavioral assays for a large-scale screen is illustrated. In this review, details of a mutagenesis screen for behavioral abnormalities are described and issues important in the initial characterization of novel ENU-induced mutations are considered.

Functional genomics: going forwards from the databases

Extrapolating systematically from gene sequence to function is undoubtedly the major challenge facing industry and academia alike as we approach the end of the millennium. Many electronic and laboratory approaches are being developed to meet this challenge but the rate of evolution of these is not keeping pace with the speed of sequence generation.

The new partnership of genomics and chemistry for accelerated drug development

Genomics and combinatorial chemistry are two methods that are revolutionizing drug discovery efforts. Analysis of gene sequences allows identification of novel proteins which are potential therapeutic targets. Recent advances relate to the rate of gene sequencing and data handling resulting from the enormous flow of new gene sequences. Cathepsin K, a cysteine protease involved in bone resorption, was recently identified from a bone cell cDNA library as a potential target for osteoporosis therapy. New sources of chemical agents will rely on advances in high throughput chemical synthesis and structure-based design.