Genetics, genomics and beyond

Abstract

The most significant event in biology since the 1953 publication of the Watson and Crick paper describing the structure of DNA 1Watson J.D. Crick F.H.C. Molecular structure of nucleic acids.Nature. 1953; 171: 737-738Crossref PubMed Scopus (8152) Google Scholar was the publication in Science and Nature earlier this year of the sequence of the human genome 2Venter J.C. et al.The sequence of the human genome.Science. 2001; 291: 1304-1351Crossref PubMed Scopus (10440) Google Scholar, 3Lander E.S. et al.Initial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium.Nature. 2001; 409: 860-921Crossref PubMed Scopus (17439) Google Scholar. Even though they both describe only a working draft of the complete sequence, these seminal papers will change forever the face of biological and medical research. The sequencing of the human genome was a logical extension of the sequencing of various bacterial genomes and those of less complex organisms and in fact used, in the case of the Science paper, much the same approach 4Wren B.W. Microbial sequencing: insights into virulence, host adaptation and evolution.Nat. Rev. Genet. 2000; 1: 30-38Crossref PubMed Scopus (89) Google Scholar. Many genome sequences are now available and, like the human sequence, are having an enormous impact on the way biological research is done. Most relevant are the sequences of the yeast genome and the genomes of Drosophila, Caenorhabditis elegans and the mouse (which is nearly complete). Access to other, preferably complete, genome sequences (e.g. the parasite genomes) will also be important in the future, because comparative analysis of whole genome sequences help functional characterization of the proteome. Genome sequencing is not going away any time soon and it will be a part of biological research for many more years to come. It will be very interesting for example, to discover what the relationship is between the genome of the chimpanzee and the human. Are the differences that are so clear phenotypically a result of changes in the control of gene expression or changes in gene sequence? I suspect it to be the former. There is a continuing debate about the number of human genes in the genome with the current estimate being about 35000. Many of these genes code for more than one protein and these proteins can have more than one function. So, the debate is now beginning to focus on how many different proteins there are (and what their functions are). Genome sequences are like dictionaries of words (genes) but with the meaning (protein functions) of only a minority of them fully defined. The task ahead is to provide definitions for each word and to understand how they all contribute to the language of life.There are a variety of methods being used to do this, as illustrated by the proliferation of words ending in ‘-omics’ (genomics, proteomics, transcriptomics, etc.) 5Vidal M. A biological atlas of functional maps.Cell. 2001; 104: 333-339Abstract Full Text Full Text PDF PubMed Scopus (161) Google Scholar. The broad term proteomics covers a multitude of sins but obviously concentrates more on proteins than nucleic acids. Approaches involve protein chips, antibodies and protein separation techniques (e.g. 2D gels). Mass spectrometry is the method of choice for identifying the molecules analyzed. One of the more important functional genomics technologies from the perspective of application to clinical medicine is gene expression analysis. This has been particularly beneficial in tumour profiling 6Scherf U. et al.A gene expression database for the molecular pharmacology of cancer.Nat. Genet. 2000; 24: 236-244Crossref PubMed Scopus (1262) Google Scholar, 7Hughes T.R. et al.Functional discovery via a compendium of expression profiles.Cell. 2000; 102: 109-126Abstract Full Text Full Text PDF PubMed Scopus (2085) Google Scholar. In this issue, Helena Furberg and Christine Ambrosone look at the complementary approach of analyzing polymorphisms in genes known to be involved in cancer such as Ras and p53 (see page 517).The ability to do experiments to define gene function in less complex organisms such as the fly or the worm and interpret the function of the homologous genes in mammals has been further enabled by access to genome sequences 8Rubin G. et al.Comparative genomics of the eukaryotes.Science. 2000; 287: 2204-2215Crossref PubMed Scopus (1354) Google Scholar. Marie-Laure Yaspo elaborates on the power of comparing genome sequences in her article on functional genomics (seepage495), particularly from the point of view of defining pathways of interacting proteins. Nowhere has this been done better than in the study of apoptosis in C.elegans 9Hunot S. Flavell R. Death of a monopoly?.Science. 2001; 292: 865-866Crossref PubMed Scopus (64) Google Scholar. The ability to understand signalling pathways in C. elegans (such as those contributing to apoptosis or insulin action) has direct relevance to molecular medicine: either from a diagnostic perspective (which genes and proteins to look at) or from a therapeutic perspective (what are the potential points of intervention).The majority of the articles in this special edition of Trends in Molecular Medicine focus on genetics. This is quite justifiable since, for the moment, genetics provides answers that are more definite and therefore more satisfying than most of the global ‘-omics’ approaches. These tend to generate lots of data but little information of immediate value. The value will come once more complete data sets are available (e.g. comprehensive gene expression analysis of different tumours and stages of tumours). Equally satisfying in terms of defining function (but in entirely different ways) are structural genomics and transgenic animals. Structural genomics – that is, exploiting genomics for large-scale and rapid protein structure determination – will have a fundamental effect on drug discovery. The ability to understand the relationship between structure space’ and ‘chemical diversity space’ by the systematic examination of the structure of complexes of compounds with individual members of families of proteins (e.g.kinases) will lead to the synthesis of many more selective inhibitors, a proportion of which will become new drugs. This paradigm is only limited by the ability to obtain the structures and access to tailored structure-based compound libraries.Systematic methods are also being used to generate transgenic animals with all genes coding for members of various protein families being knocked out (e.g. all G-protein-coupled receptors). The phenotype data so derived will be useful for target identification and validation to elaborate which gene in the family is the best point of intervention for a particular disease. The complementary approach of screening mice that have been subjected to mutagenesis for interesting and disease-related phenotypes, followed by cloning of the changed genes, is reviewed by Janet Rossant and Colin McKerlie on page502. Although this is a time-consuming approach, it does give very precise information about the role of different genes in controlling phenotypes, including those contributing to disease.It is not just the sequence of the human genome that is important, it is the sequence of human ‘genomes’. The variation between individuals in concert with the environment is what accounts for susceptibility to disease and drug efficacy and side effects. The initiatives to find single nucleotide polymorphisms 10Holden A.L. The SNP consortium: A case study in large pharmaceutical company research and development collaboration.J. Com. Biotech. 2000; 6: 320-324Google Scholar, 11Chakravati A. To a future of genetic medicine.Nature. 2000; 409: 822-823Crossref Scopus (154) Google Scholar (SNPs) have now been augmented by initiatives to use SNPs to obtain haplotype associations (for examples, see 12Stephens C. et al.Haplotype variation and linkage disequilibrium in 313 human genes.Science. 2001; 293: 489-493Crossref PubMed Scopus (706) Google Scholar). These will be quite beneficial for the positional cloning of disease susceptibility alleles, as well as for clinical studies to find individuals in whom a drug is likely to be efficacious. The use of SNPs for pharmacogenetics (i.e. studying polymorphisms in genes involved in drug activity) is presently restricted to drug-metabolizing enzymes (such as the cytochrome P450s) and to variations in genes that are known drug targets.It is only recently that real disease susceptibility genes have been cloned for multifactorial diseases. A good example of this is the recent identification of NOD2 as a susceptibility gene for Crohn's disease 13Hugot J.P. et al.Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease.Nature. 2001; 411: 599-603Crossref PubMed Scopus (4621) Google Scholar, 14Ogura Y. et al.A frameshift in NOD2 associated with susceptibility to Crohn's disease.Nature. 2001; 411: 603-606Crossref PubMed Scopus (4114) Google Scholar. A comprehensive SNP map will allow the cloning of other susceptibility alleles, but there are many caveats to the approach, mostly to do with the populations under study and the approach taken (linkage disequilibrium mapping or association studies) rather than the technology available 15Peltonen L. et al.Use of population isolates for mapping complex traits.Nat. Rev. Genet. 2000; 1: 182-189Crossref PubMed Scopus (309) Google Scholar, 16Cardon L.R. Bell J.I. Association study designs for complex diseases.Nat. Rev. Genet. 2001; 2: 91-99Crossref PubMed Scopus (1157) Google Scholar. Stephen Chanock and colleagues (page507) go into the details of how genetic variation can be used to study human disease, and Tony Brookes reflects on some of the strategies for genetic studies that are being used (page512). Some of the best genetic studies of this kind have been done on susceptibility to infectious disease. Remarkable associations have been found: for example, between chemokine receptors (CCR5) and HIV susceptibility, and between the bacterial transporter protein Nramp and resistance to macrophage-infecting bacteria such as Mycobacterium. Very recently, there has been an elegant study tracing the emergence of different alleles at the G6PDH locus associated with malaria susceptibility 17Tishkoff S.A. et al.Haplotype diversity and linkage disequilibrium at the human G6PDH: recent origin of alleles that confer malarial resistance.Science. 2001; 293: 455-461Crossref PubMed Scopus (459) Google Scholar. Jennie Blackwell synthesizes these data for us in her article looking at the genetic basis of infectious disease susceptibility (see page521).These kinds of studies are not without their ethical concerns, including questions of ownership (of the genes) and the freedom to use collected DNA for the studies. These are complex and emotional issues, especially when dealing with populations who may have been exploited (or are perceived to have been exploited) in the past. Solutions can generally be found once the purpose of the study is adequately explained. Jane Kaye highlights some controversial issues pertaining to the UK.One can continue to develop different technologies and give them names ending in ‘-omics’, but at the end of the day the driver for all the studies is actually genomics – the study of genomes. Genomics is not just about genome sequencing either. Access to full-length cDNAs and their sequence is still a major factor, given that these are, by definition, copies of mRNAs that actually exist and presumably code for proteins that exist too. There is also a need to continue to work with biochemical precision on data derived from genetic or protein-structural studies. This is not a Luddite view: it is just more illuminating to read papers that tell a story rather than to read multiple stories in parallel, the significance of which cannot as yet be understood. The most significant event in biology since the 1953 publication of the Watson and Crick paper describing the structure of DNA 1Watson J.D. Crick F.H.C. Molecular structure of nucleic acids.Nature. 1953; 171: 737-738Crossref PubMed Scopus (8152) Google Scholar was the publication in Science and Nature earlier this year of the sequence of the human genome 2Venter J.C. et al.The sequence of the human genome.Science. 2001; 291: 1304-1351Crossref PubMed Scopus (10440) Google Scholar, 3Lander E.S. et al.Initial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium.Nature. 2001; 409: 860-921Crossref PubMed Scopus (17439) Google Scholar. Even though they both describe only a working draft of the complete sequence, these seminal papers will change forever the face of biological and medical research. The sequencing of the human genome was a logical extension of the sequencing of various bacterial genomes and those of less complex organisms and in fact used, in the case of the Science paper, much the same approach 4Wren B.W. Microbial sequencing: insights into virulence, host adaptation and evolution.Nat. Rev. Genet. 2000; 1: 30-38Crossref PubMed Scopus (89) Google Scholar. Many genome sequences are now available and, like the human sequence, are having an enormous impact on the way biological research is done. Most relevant are the sequences of the yeast genome and the genomes of Drosophila, Caenorhabditis elegans and the mouse (which is nearly complete). Access to other, preferably complete, genome sequences (e.g. the parasite genomes) will also be important in the future, because comparative analysis of whole genome sequences help functional characterization of the proteome. Genome sequencing is not going away any time soon and it will be a part of biological research for many more years to come. It will be very interesting for example, to discover what the relationship is between the genome of the chimpanzee and the human. Are the differences that are so clear phenotypically a result of changes in the control of gene expression or changes in gene sequence? I suspect it to be the former. There is a continuing debate about the number of human genes in the genome with the current estimate being about 35000. Many of these genes code for more than one protein and these proteins can have more than one function. So, the debate is now beginning to focus on how many different proteins there are (and what their functions are). Genome sequences are like dictionaries of words (genes) but with the meaning (protein functions) of only a minority of them fully defined. The task ahead is to provide definitions for each word and to understand how they all contribute to the language of life. There are a variety of methods being used to do this, as illustrated by the proliferation of words ending in ‘-omics’ (genomics, proteomics, transcriptomics, etc.) 5Vidal M. A biological atlas of functional maps.Cell. 2001; 104: 333-339Abstract Full Text Full Text PDF PubMed Scopus (161) Google Scholar. The broad term proteomics covers a multitude of sins but obviously concentrates more on proteins than nucleic acids. Approaches involve protein chips, antibodies and protein separation techniques (e.g. 2D gels). Mass spectrometry is the method of choice for identifying the molecules analyzed. One of the more important functional genomics technologies from the perspective of application to clinical medicine is gene expression analysis. This has been particularly beneficial in tumour profiling 6Scherf U. et al.A gene expression database for the molecular pharmacology of cancer.Nat. Genet. 2000; 24: 236-244Crossref PubMed Scopus (1262) Google Scholar, 7Hughes T.R. et al.Functional discovery via a compendium of expression profiles.Cell. 2000; 102: 109-126Abstract Full Text Full Text PDF PubMed Scopus (2085) Google Scholar. In this issue, Helena Furberg and Christine Ambrosone look at the complementary approach of analyzing polymorphisms in genes known to be involved in cancer such as Ras and p53 (see page 517). The ability to do experiments to define gene function in less complex organisms such as the fly or the worm and interpret the function of the homologous genes in mammals has been further enabled by access to genome sequences 8Rubin G. et al.Comparative genomics of the eukaryotes.Science. 2000; 287: 2204-2215Crossref PubMed Scopus (1354) Google Scholar. Marie-Laure Yaspo elaborates on the power of comparing genome sequences in her article on functional genomics (seepage495), particularly from the point of view of defining pathways of interacting proteins. Nowhere has this been done better than in the study of apoptosis in C.elegans 9Hunot S. Flavell R. Death of a monopoly?.Science. 2001; 292: 865-866Crossref PubMed Scopus (64) Google Scholar. The ability to understand signalling pathways in C. elegans (such as those contributing to apoptosis or insulin action) has direct relevance to molecular medicine: either from a diagnostic perspective (which genes and proteins to look at) or from a therapeutic perspective (what are the potential points of intervention). The majority of the articles in this special edition of Trends in Molecular Medicine focus on genetics. This is quite justifiable since, for the moment, genetics provides answers that are more definite and therefore more satisfying than most of the global ‘-omics’ approaches. These tend to generate lots of data but little information of immediate value. The value will come once more complete data sets are available (e.g. comprehensive gene expression analysis of different tumours and stages of tumours). Equally satisfying in terms of defining function (but in entirely different ways) are structural genomics and transgenic animals. Structural genomics – that is, exploiting genomics for large-scale and rapid protein structure determination – will have a fundamental effect on drug discovery. The ability to understand the relationship between structure space’ and ‘chemical diversity space’ by the systematic examination of the structure of complexes of compounds with individual members of families of proteins (e.g.kinases) will lead to the synthesis of many more selective inhibitors, a proportion of which will become new drugs. This paradigm is only limited by the ability to obtain the structures and access to tailored structure-based compound libraries. Systematic methods are also being used to generate transgenic animals with all genes coding for members of various protein families being knocked out (e.g. all G-protein-coupled receptors). The phenotype data so derived will be useful for target identification and validation to elaborate which gene in the family is the best point of intervention for a particular disease. The complementary approach of screening mice that have been subjected to mutagenesis for interesting and disease-related phenotypes, followed by cloning of the changed genes, is reviewed by Janet Rossant and Colin McKerlie on page502. Although this is a time-consuming approach, it does give very precise information about the role of different genes in controlling phenotypes, including those contributing to disease. It is not just the sequence of the human genome that is important, it is the sequence of human ‘genomes’. The variation between individuals in concert with the environment is what accounts for susceptibility to disease and drug efficacy and side effects. The initiatives to find single nucleotide polymorphisms 10Holden A.L. The SNP consortium: A case study in large pharmaceutical company research and development collaboration.J. Com. Biotech. 2000; 6: 320-324Google Scholar, 11Chakravati A. To a future of genetic medicine.Nature. 2000; 409: 822-823Crossref Scopus (154) Google Scholar (SNPs) have now been augmented by initiatives to use SNPs to obtain haplotype associations (for examples, see 12Stephens C. et al.Haplotype variation and linkage disequilibrium in 313 human genes.Science. 2001; 293: 489-493Crossref PubMed Scopus (706) Google Scholar). These will be quite beneficial for the positional cloning of disease susceptibility alleles, as well as for clinical studies to find individuals in whom a drug is likely to be efficacious. The use of SNPs for pharmacogenetics (i.e. studying polymorphisms in genes involved in drug activity) is presently restricted to drug-metabolizing enzymes (such as the cytochrome P450s) and to variations in genes that are known drug targets. It is only recently that real disease susceptibility genes have been cloned for multifactorial diseases. A good example of this is the recent identification of NOD2 as a susceptibility gene for Crohn's disease 13Hugot J.P. et al.Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease.Nature. 2001; 411: 599-603Crossref PubMed Scopus (4621) Google Scholar, 14Ogura Y. et al.A frameshift in NOD2 associated with susceptibility to Crohn's disease.Nature. 2001; 411: 603-606Crossref PubMed Scopus (4114) Google Scholar. A comprehensive SNP map will allow the cloning of other susceptibility alleles, but there are many caveats to the approach, mostly to do with the populations under study and the approach taken (linkage disequilibrium mapping or association studies) rather than the technology available 15Peltonen L. et al.Use of population isolates for mapping complex traits.Nat. Rev. Genet. 2000; 1: 182-189Crossref PubMed Scopus (309) Google Scholar, 16Cardon L.R. Bell J.I. Association study designs for complex diseases.Nat. Rev. Genet. 2001; 2: 91-99Crossref PubMed Scopus (1157) Google Scholar. Stephen Chanock and colleagues (page507) go into the details of how genetic variation can be used to study human disease, and Tony Brookes reflects on some of the strategies for genetic studies that are being used (page512). Some of the best genetic studies of this kind have been done on susceptibility to infectious disease. Remarkable associations have been found: for example, between chemokine receptors (CCR5) and HIV susceptibility, and between the bacterial transporter protein Nramp and resistance to macrophage-infecting bacteria such as Mycobacterium. Very recently, there has been an elegant study tracing the emergence of different alleles at the G6PDH locus associated with malaria susceptibility 17Tishkoff S.A. et al.Haplotype diversity and linkage disequilibrium at the human G6PDH: recent origin of alleles that confer malarial resistance.Science. 2001; 293: 455-461Crossref PubMed Scopus (459) Google Scholar. Jennie Blackwell synthesizes these data for us in her article looking at the genetic basis of infectious disease susceptibility (see page521). These kinds of studies are not without their ethical concerns, including questions of ownership (of the genes) and the freedom to use collected DNA for the studies. These are complex and emotional issues, especially when dealing with populations who may have been exploited (or are perceived to have been exploited) in the past. Solutions can generally be found once the purpose of the study is adequately explained. Jane Kaye highlights some controversial issues pertaining to the UK. One can continue to develop different technologies and give them names ending in ‘-omics’, but at the end of the day the driver for all the studies is actually genomics – the study of genomes. Genomics is not just about genome sequencing either. Access to full-length cDNAs and their sequence is still a major factor, given that these are, by definition, copies of mRNAs that actually exist and presumably code for proteins that exist too. There is also a need to continue to work with biochemical precision on data derived from genetic or protein-structural studies. This is not a Luddite view: it is just more illuminating to read papers that tell a story rather than to read multiple stories in parallel, the significance of which cannot as yet be understood.