Translating knowledge into practice in the “post-genome” era

MEDICAL ESSAY

Translating knowledge into practice in the “post-genome” era*

CR Scriver

Departments of Biology, Human Genetics, and Pediatrics, McGill University, Montreal Children’s Hospital, Montreal, Quebec, Canada

Scriver CR. Translating knowledge into practice in the “post-genome” era. Acta Pædiatr 2004; 93:294–300. Stockholm. ISSN 0803-5253

The Human Genome Project is “completed”, but it is only a beginning in the understanding ofgenomic structure and function. A “human phenome project” is waiting in the wings. The com-plexity involving a phenotype can be glimpsed, for example, if one enquires into the relationshipsbetween mutant phenylalanine hydroxylase (PAH) genotypes and the clinical disorders called PKU/Hyperphenylalaninemia—so called lessons from PKU genotypes and phenotypes. Since genomesspeak biochemistry, not phenotype (said RHA Plasterk), for genomics to penetrate medicine,biochemistry and biology must be allies.

The ideal translators and ambassadors of the knowledge that must cross the gap betweenlaboratory and bedside are the clinician scientists; restoration of that attenuated community ofcolleagues is a necessary step in the implementation of genomic medicine.

Key words: Genomics, proteomics, genotype, phenotype, phenylketonuria, clinical relevance,clinician scientist

Charles R. Scriver, Departments of Biology, Human Genetics, and Pediatrics, McGill University,McGill University Health Center, A-721, Montreal Children’s Hospital, 2300 Tupper Street,Montreal, Quebec, Canada H3H 1P3 (Tel. �1 514 412-4417, fax. �1 514 412-4329, [email protected])

Genetics has penetrated into the public mind and itgenerates concerns there. It is also poised to penetratemedicine in an era of “genomic medicine” by waysseemingly not feasible before completion of the HumanGenome Project. The outlook for the latter case isenthusiastic (3); yet a large gap exists betweenexpectations and performance both now and probablyinto the foreseeable future. The explanation lies in theincompleteness of the knowledge about the humangenome and how it accounts for the complexity andfunction of the organism. Meanwhile, persons withgenetic unhealth will be seeking health care. Suchpatients will not be offered any cures for their geneticdisease; at least, not yet; at best, the offer will be forlimited control of their disease, in which case, it is evermore important that the clinician also participate in theprocesses of care and healing. Why? Because thepatient’s biological and personal identity has beenundermined by the disadaptive genetic event. Accord-ingly, it is necessary to know the patient with thegenetic disease; something different from and asimportant as knowing the disease the patient has.

I use a classic monogenic disease (phenylketonuria)(4) here to illustrate the difference between the person(with the variant genome) and the disease (which is avariant phenotype). The reader will discover that theparticular Mendelian phenotype called PKU is far morecomplex than we imagined at first encounter (5). At thesame time, PKU is a transformative case because itbroke the barrier of medical indifference toward geneticdisease. In the pre-PKU era, it was common wisdom tobelieve that “genetic disease” could not be treated andtherefore of little relevance in medical practice. Theperception changed when PKU became the first humangenetic condition† for which there was a treatment toprevent the associated disease (mental retardation).

That simple categorical outlook has since beenrefined; half a century later the treatment of “PKU” isbeing adjusted to fit the individual patient, because eachhas his or her own form of the phenotype. The simplemessage: treat the patient, not just the disease.

A Neo-Vesalian anatomy?Herakleitos, the father of metaphysics, said something

*The written version of the Annual Karolinska Institute’s ClinicalScience lectureship is a modified version of the one delivered inStockholm on 10 November 2003. The article has drawn selectivelyon two other sources (1, 2).

†Insulin therapy of diabetes mellitus could be another, and earlier,illustration.

2004 Taylor & Francis. ISSN 0803-5253

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DOI 10.1080/08035250310024682

like this: Although the Word is common to all, mostmen live as if each had a private wisdom of his own. Ifwe substitute or add appropriate words, the sentencecould read: “Although DNA is common to all, mostmen and women live as if each had a private genome(and phenome)”. Whereas one of the rationales forpursuing the (Human) genome project was to obtain the“genetic blueprint” of a significant living organism, itwas already surmised that its individualized featureswould not be understood simply by knowing the DNAsequence of the genome and the position of its genes.Although the genome sequence could be looked upon asa “Neo-Vesalian anatomy” (6), it would not explain, byitself, how the organism developed, lived and died, anybetter than did knowing the Vesalian anatomicaldimensions of the human organism. How the structurewill function is another dimension of the knowledge.Yet Vesalius and his anatomical data did changemedicine (and sculpture and other aspects of humanculture), and so will the Neo-Vesalian knowledge—eventually.

The physician is still an esteemed professional; acertain mystery and awe are attached to the practitionerand the practice. Nonetheless the knowledge at handabout human disease and its causes is still surprisinglylimited. And if new technologies replace clinical skillsand health-care structures intrude on personal relation-ships, “medical professionalism” (7) may disappear andmedicine may become a commodity. The physicianmay still have the knowledge to cure certain types ofdisease, and to control the manifestations of other types,yet may not have time to participate in the care andhealing of the person with the disease. Care and healingare of ever greater relevance when the patient’s sense ofSelf has been undermined by a variant genotype.

Meanwhile, one cannot help but notice anotherimportant context for the Human Genome Project. Asthe environmental conditions of life improve, therelative importance of the biological contributors todisease (in the population) increases; theheritability ofdisease thus increases (8). This will account, in part, forthe relevance of the Human Genome Project inmedicine. It also offers a challenge, and opportunity,quite different from that prevailing 100 years ago when,for example, Garrod tried to show the relevance ofgenetic (Mendelian) thinking in medicine with his fewand rare examples of the “inborn errors of metabolism”(9).

Genome and genotype are only part of thestoryDiscovery of a double helical structure in the DNAmolecule was justly celebrated at its 50th anniversary in2003. Moreover, the famous throw-away sentence in thepaper by Watson and Crick (10) was not forgotten: “Ithas not escaped our notice that the specific pairing we

have postulated immediately suggests a possible copy-ing mechanism for genetic material.” Fifty years ofexperience with DNA allows it to be recognized now as“the eternal molecule” (11), passing in the germlinefrom generation to generation; passing from dividingcell to daughter cells in the soma of the organism.Biology thus acquired two interpretive paradigms: inone, DNA transcription is a process ofinformationtransmittal; faithful transcription retains essential in-formation while mutation changes it and permitsevolution of biological diversity. In the other paradigm,of information utilization, DNA is translated. Thecomplexities of both processes are far greater than werealized. Thus, even in the short time since thecompletion of the Human Genome Project, one hasbecome aware that to know the genome is only part ofthe story. A “phenome project” is perhaps the next biginitiative (12).

Lessons from PKU genotypes and phenotypesIt was anticipated that the Human Genome Projectwould allow one to know about genotype and thatgenotype would predict phenotype. The hypothesis,thought to be applicable to PKU for example (13), is anoversimplification. PKU nicely illustrates why this maybe so and why thinking at the phenomic level isnecessary to understand variant phenotypes.

The phenylalanine molecule is the ultimate villain inthe pathogenesis of mental retardation in PKU. PKU is aclassic multifactorial disease in which mutation in agene impairs the function of an enzyme; at the sametime, there must also be exposure to an essentialnutrient—the amino acid phenylalanine, which happensto be the enzyme’s substrate. Both events must acttogether to begin the pathogenic process.

Clinical inquiry in the early days of PKU historyrevealed Mendelian inheritance of this mutant auto-somal recessive phenotype. Biochemical inquiries lateridentified deviant metabolism, the associated enzymes,and eventually, through isolation of a cDNA, the geneand its locus on chromosome 12q. Thereafter mutationanalysis in the human phenylalanine hydroxylase(PAH) gene revealed over 450 mutations (seewww.pahdb.mcgill.ca), many of which have beenmapped onto the crystal structure of thePAH subunitand enzyme. Expression analysisin vitro has revealedhow some of these mutations affect enzyme function.

This monogenic disease has a complexphenotypeMutation in the PAH gene is sufficient to explainimpaired function of the enzymic gene product (phenyl-alanine hydroxylase E.C. 1.14.16.1) but not sufficient toexplain all aspects of phenotype. The metabolic con-sequence of mutation is hyperphenylalaninemia whose

ACTA PÆDIATR 93 (2004) Translating knowledge into practice in the “post-genome” era 295

distal consequence is impaired cognitive function.However, a variantPAH genotype is not necessarily arobust predictor of phenotype. Metanalyses of geno-type-metabolic/clinical phenotypic correlations (14, 15)reveal instances where a defined mutantPAH genotypeis not associated with the predicted metabolic orcognitive phenotype, providing evidence that PKU isa “complex trait” at multiple phenotypic levels (16).The evidence is found in various layers of thephenome:

(1) The enzymic phenotype will be altered by threeclasses of mutations: those conferring a nullphenotype; those associated with a missensemutation; those involving a primary kineticeffect. The latter are rare; the missense allelesconstitute over 60% ofPAH mutations. Theycause misfolding of the protein to modulateresidual catalytic activity (17). Alleles causingmisfolding affect a designated biological form(18). They are best understood at the proteomiclevel of genetic disease, and any cellular eventthat modulates the process of abnormal proteinfolding will modify the predicted genotype–phenotype correlation. Chaperones may be mod-ulators for example.

(2) The metabolic phenotype will be affected by therate of catabolic outflow of phenylalanine. In thepresence of impaired hydroxylase activity, otheroutflow paths come to influence phenylalanineconcentrations and thus the demand on dietarycontrol of phenylalanine intake. Inter-individualvariation in the transaminase-dependent outflow(forming phenylpyruvate and derivatives) willmodulate phenylalanine pool size in the presenceof blocked phenylalanine hydroxylation to formtyrosine. Inter-individuality in transaminase-dependent flux rates has been observed in siblingsharbouring identical mutantPAH genotypes (19).The difference in their transamination flux ratesexplained their different tolerances of dietaryphenylalanine. Transaminases are classical ex-amples of polymorphic proteins and, in the caseof PKU, the specific transaminase has long beensurmised to be a modifier of the metabolicphenotype (20).

(3) Cognitive development is not directly related to aPKU-causing genotype at thePAH locus (21).However, cognitive development in PKU iscorrelated with brain phenylalanine concentra-tion, which, in the usual case, reflects bloodphenylalanine concentration (22, 23). However,the quantitative relationship between the two poolsizes will be modified when the phenylalanineflux rate at the blood–brain barrier is altered.Some individuals with a classical PKU metabolicphenotype have normal cognitive developmentbecause of (beneficially) impaired inward phenyl-

alanine flux rates, at the blood brain barrier, in thepresence of high PKU-causing substrate concen-trations in blood.

Locus heterogeneity is a further explanation forcomplexity underlying the hyperphenylalaninemicphenotype. Mutations at one of the several loci involvedin synthesis and recycling of tetrahydrobiopterin co-factor will affect PAH enzymic function and causehyperphenylalaninemia (24). In these forms of hyper-phenylalaninemia, tetrahydrobiopterin is used in phar-macologic doses as a therapeutic agent. The co-factoralso restores phenylalanine homeostasis in the presenceof certain missensePAH mutations (see PAHdb); theeffect seems not to involve its primary role as co-factorfor PAH enzymic function (25); perhaps it acts as achemical chaperone.

These findings introduce novel perspectives andenquiries, such as: Can I know the energy landscapeon the surface of the protein to explain its particularfolding type, its functional domains and the way itinteracts with other macro and micromolecular objects?(26). It is an enquiry about order in a macromoleculeand about the path leading to its final form. A secondenquiry follows: If I know the energy surface of theprotein, can I use combinatorial chemistry to design apharmacologic chaperone to attach to the surface andattenuate misfolding of the mutant macromolecule, andthus alter the associated disease phenotype? The latter isa new speculation about therapy for a genetic pheno-type. In which case, one can ask (again): Is tetrahydro-biopterin acting as a pharmacologic chaperone formutantPAH enzymic forms? (25, 27).

Genotype–phenotype relationship may also be per-turbed if there is heterozygosity at multiple lociaffecting protein–protein interactions and function, so-called oligogenic phenotypes (28, 29). This possibilityhas been little investigated so far.

PKU illustrates why a (rare) monogenic diseasemight have complex explanations for its phenotypicmanifestations; and may not show a robust predictablerelationship between mutant genotype and phenotype.Themes mentioned here are surely relevant to theprevalent and complex traits known as diabetes, asthma,hypertension and depression.

“Genomes speak biochemistry, not phenotype”(30)To know the effect of a mutant allele on phenotype andhow it may be buffered to maintain metrical trait valueswithin the normal distribution is a topic of renewedinterest (31–35). It helps one to appreciate whygenotype–phenotype correlations may not be so pre-dictable.

At the core of our understanding about order in abiological organism are nested mechanisms of home-

296 CR Scriver ACTA PÆDIATR 93 (2004)

ostasis comprising efficient robust modules functioningin networks (36). They determine the central tendenciesand the range of outlier values compatible with healthand adaptation. They are homeostatic systems forbuffering dispersions around the central, metrical traitvalues, and they are usually embedded in cellularnetworks. Networks in biology have become a signi-ficant theme in the post-genome era (37).

Homeostasis is a central principle of living systems;it is the relatively stable state of equilibrium, or thetendency toward such a state, between different butinterdependent elements and subsystems of an organ-ism. Because of biological individuality, any oneindividual’s trait values will have a particular locationwithin the population distribution of trait values. The“private” homeostatic value may be displaced; eitherbecause the system has been undermined by mutation inthe individual’s genome, or subverted either by ex-cessive or inadequate experience. A displaced value islikely to be disadaptive because evolution of biologicaldiversity by natural selection is the process by whichoptimal ranges of homeostatic values have beenacquired. The modules of the homeostatic system havebeen selected and combined by “tinkering” in the longstory of evolution (38). The result is robust, efficientmodules integrated into functional networks.

That most mutant alleles would be recessive (in thehuman genome), in their effect on phenotype andfunction, was surmised long ago (39). Wright ap-proached the problem of mutation and its effect onphenotype by reasoning that any network of eventslinking genotype to a metabolic phenotype (for exam-ple), would involve fluxes of molecules in the fluid stateof cellular systems. If unsaturated catalysts with nearequivalent activities mediated the flux, there would be ahyperbolic relationship between enzyme activity andthe rate of flux. Thus, half-normal activity of a singlecomponent would be unlikely to have a significanteffect on flux through the total network.

The problem was revisited many years later in classicpapers (40, 41), where Kacser and Burns analysed againthe predicted effect of mutation in complex systems.They found that the effect of a single mutant allele(heterozygosity) on metabolic homeostasis would berecessive, with only minor effect on the measuredphenotype, and only in a state of mutant homozygositywould the mutant phenotype appear. (The possibility ofoligogenic double heterozygosity is noted below. Thespecial case of dominant inheritance is explained byloss of hemizygosity; “one-step” pathways, a dominantnegative effect, or gain-of-function alleles.)

Buffering mechanisms that offset potential pheno-type-modifying mutations in organisms within cellularand organismal compartmentation are an “intrinsic”process; buffering mechanisms that involve indepen-dent circuits are “extrinsic” (31). The principal mech-anisms of buffering involve: redundancy at pairedhomologous loci or duplicated genes with overlapping

function; reduction of specificity and interdependency,or molecular specificity committed to a particularhomeostatic parameter; and negative feedback regula-tion. The extent of buffering, and of tolerance todisruption, has been examined in diploid genomes,expressing protein and gene arrays within a global set ofnetworks. In budding yeast, for example, 80% of thearray network is dedicated to buffering (42). Becausebuffering acts within systems of self-assembly and self-organization, by which emergent properties and systemsof order are obtained (43–45), robust scale-free net-works have evolved that reduce the risk of disadaptationin the presence of mutation.

Is a phenome project the next big one?The phenome is the sum of all of its parts—and more(Fig. 1). It has been proposed that “a phenome project”should follow the genome project (12). The phenomecan be analysed component by component; to investi-gate the transcriptome or the proteome, for example, inever greater detail is one way to understand thephenome in health and disease (2).

The proteome contains proteins encoded by morethan 1000 mutant loci in the human genome, each ofwhich harbours at least one disease-causing mutantallele (46). The proteins affected by these mutationshave been identified in 923 Mendelian disorders (47), asenzymes, modulators, receptors, transcription factors,intracellular matrix proteins, extracellular matrix pro-teins, transmembrane transporters, ion channels, cell-signalling proteins, hormones, extracellular transpor-ters, immunoglobulins, other classes of proteins, andunknown. Almost 95% of the 923 mutant proteins fallinto one of the known classes (47).

The most prevalent mutant proteins involved in thesubset of Mendelian diseases, at all ages, are enzymes(31.2% of total). But when the protein classes arestratified by age at onset of disease, those appearinginutero are predominantly mutant transcription factors(26% of total); and among the 225 Mendelian pheno-

Fig. 1. A vocabulary of words with the suffix “-ome” is a by-productof the Genome Projects. The words are useful if they confer an ideaof the complexity of a living organism. The figure is only onesimplified version of an “ome” network.


types presenting between puberty and 50 y age, themodulator proteins predominate. Research focused onthese age-related protein classes will reveal mechan-isms of disease not yet known.

New technologies (48) reveal protein interactionnetworks in diploid organisms (49, 50); one can thenstudy the corresponding protein and gene interactionnetworks (42). Proteins interact to form scale-freenetworks; some proteins are hubs through whichinteractions with other proteins form ordered networksof function; other proteins have limited interactionswith one or a few other proteins. Might there beindependent “silent” mutations in the genes for twodifferent interacting proteins? On their own, suchmutations would probably behave as recessives, but ifthey were co-expressed, affecting an essential inter-action of one protein with another, might there be aharmful phenotype? This “oligogenic hypothesis” forpathogenesis of quasi-Mendelian or complex-trait dis-ease phenotypes is not improbable and the list of humandiseases with digenic/oligogenic origins grows steadily(29). A new way to study the origins of human geneticdisease emerges as the evidence grows for combinator-ial genetic complexity within specific quantitative traits(51).

The metabolome is operative when proteins (en-zymes) convert chemical substrates into catalyticproducts. Metabolic homeostasis is said to be a processboth noisy and complex (52). Modelling of galactoseutilization (in the diploid organismSaccharomycescerevisiae, for example) finds 997 mRNAs involvedin homeostatic responses to 20 different experimentalperturbations of the pathway; 289 proteins are involved,of which 15 are regulated by post-transcription mod-ifications (53). Metabolism has complexity hithertounknown and its components will be new targets fortherapeutic agents.

A modern diagram of the metabolome, formulated interms of networks and systems biology, sees chemicalmetabolites as nodes and the enzyme-based conversionsas links (in pathways). The metabolome emerges as aninhomogeneous system functioning as a scale-freenetwork where the links between nodes are notrandomly distributed (34). The targets (proteins) formutation are numerous and thus the chance of a major“crash” in the metabolome is unlikely; only rare inbornerrors of metabolism are the result. As suggested earlierin this essay, natural selection has refined biologicalorder within such networks. The corresponding compo-nents in genome, transcriptome and proteome areintegrated in the layers of a larger network that operatesthe metabolome through regulatory motifs; the catalyticpathways are its components; the latter, as nestedfunctional modules, generate a scale-free hierarchicalarchitecture at the level of the organism (35). At theselevels, one is looking at the malleable adaptive archi-tecture of the phenome.

A human phenome project (12) can begin even now

with a “phenogenetic approach” to the analysis ofhuman genetic disease (54). However, any real progressin this direction will be dependent on secure taxonomiesof phenotypes, and on accurate clinical descriptions(55). Therefore, the clinician will be a necessaryparticipant in genomic (phenomic) medicine.

Big science (e.g. the Genome Project) working onsmall molecules has not altered the importance ofmaking small observations from which big hypothesesgrow. Patients present us with phenomic data. If thecorresponding observation involves a variant of meta-bolome or proteome, it is still part of the phenome weseek to know. When Garrod studied his patients, hemade observations that were considered trivial by hiscolleagues of the day. Nonetheless Garrod—a prototypeclinician scientist—began a medical journey that led tothe double helix. There is work to be done by theclinician scientist in the phenome project.

The clinician scientistThe clinician scientist is not extinct, but almost so in mynation, for example. A profoundly effective reductiveapproach to biological science set the agenda for thepast quarter century of medical and related research. Itwas an almost irresistible attractant and it recruitedmany people into the corresponding domains of basicresearch in biology and medicine; and into disease-oriented research. While this was happening, thecomplexity of contemporary medical diseases wasincreasing in association with the rising heritability ofdisease in the population. While there was great needfor patient-oriented research, the competition forresearch funding drove the latter interests undergroundand the gap between laboratory and bedside widened,even though the need for the clinician scientist wasactually increasing. The need for those who couldtranslate the new science into medical practices and theclinical problems into new scientific hypotheses becamegreater rather than less. Nonetheless these “translators”of knowledge became an endangered species in thepeer-reviewed ways of doing science (56, 57). Habitatsfor the protection of the species are needed and I see thisas a significant priority in the new era of genomicmedicine (3).

Dobzhansky opined (correctly) that nothing inbiology makes sense except in the light of evolution(58) to which I would add—and nothing in genomicmedicine will make sense except in the light of biology.In this context, the clinician scientist will be at homewith two sets of questions of which there are five in themedical set: (1) What is wrong (diagnosis)?; (2) Whatcan be done (treatment)?; (3) What will happen (prog-nosis)?; (4) How/why did it happen (cause)?; (5) Will ithappen again (heredity)? In the biological set, there arefour questions: (1) How does a biological entityfunction? (2) How did it evolve? (3) How does it


develop? (4) What regulates its behaviour? When thereare answers to these nine questions, the chasm betweenthe clinician and the scientist can be bridged. The resultwill be an informed approach (Fig. 2), by which weunderstand the biological components interacting withthe varieties of experience which become “cause” of adisease. The origins of the pathogenic process under-lying the disease phenotype are then better understood,and with such knowledge, better tests and treatmentsbecome available, withprevention of disease as apotential goal.

A respected science-trained popular author, whileobserving the Human Genome Project, wrote: “Medi-cine need no longer treat the population; it must start totreat the individual instead. We are each of us membersof one genetic minority or another; nobody is typical”(Matt Ridley,Daily Telegraph, 2/3/98). In which case,five types of knowledge will be recruited whenbiological individuality penetrates medical practice:(1) Prohibited knowledge (censorship and propaganda,both losses of knowledge); (2)I-don’t-want-to-know(fear, another loss); (3) theknown (which includes allmateria medica); (4) the unknown (the domain ofscience (or any enquiry into our ignorance)); (5) theunknowable (an ultimate source of humility).

Possessed with and accepting these forms of knowl-edge, each individual has a different way of looking atthe known and how to use it. When the different ways(those of the scientist, those of the clinician) arerecognized and accepted, there is a cooperative com-munity of creators and of users. The invitation is athand; recognize the diversity that is us—and respondaccordingly.

Acknowledgements.—I am grateful to Professor Agne Larsson for theinvitation to give this lecture. I thank my institutions (McGillUniversity, the Montreal Children’s Hospital and its ResearchInstitute) for being my “place of business” for the past 4 decadesand more. Peers reviewed and supported my work. Lynne Prevostmade the manuscript possible (once again); Christineh SarkissianPh.D. and I created the PowerPoint presentation for the lecture.

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Received Dec. 2, 2002; accepted Dec. 2, 2003


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Translating knowledge into practice in the “post-genome” era