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Pediatric practice and education in the genomic/postgenomic era

2002; Elsevier BV; Volume: 141; Issue: 4 Linguagem: Inglês

10.1067/mpd.2002.128030

1097-6833

Russell W. Chesney, Aaron Friedman, William P. Kanto, Bonita Stanton, Terrence L. Stull,

RNA modifications and cancer

The 2002 annual meeting of the Association of Medical School Pediatric Department Chairs was devoted to the genetic revolution and its implications for pediatric education and clinical practice throughout the next decades. The result of the revolution is the development of the field of genomics, which is dedicated to understanding the structure, organization, and expression of chromosomal DNA. Recent developments have produced an explosion of information with the promise of revealing important general aspects of gene expression and regulation, as well as variations of persons. Mining the new biologic information may allow the development of a large array of products, including new vaccines, antibiotics, drug targets, diagnostics, biofuels, protection from biologic and chemical warfare, and efficient toxic-waste cleanup. Indeed, the importance of the new genomic information has been compared to Andreas Vesalius's publication of de corporis humani Fabrica in 1543, which laid the foundation for subsequent studies of blood circulation and anatomy.1McKusick V The anatomy of the human genome.JAMA. 2001; 286: 2289-2295Crossref PubMed Scopus (54) Google Scholar The quantity of available genomic data has increased at a remarkable pace. The first DNA sequence of the entire bacterial genome of Haemophilus influenzae was published in 1995.2Fleischmann R Adams M White O Clayton RA Kirkness EF Kerlavage AR et al.Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.Science. 1995; 269: 496-512Crossref PubMed Scopus (4573) Google Scholar The publicly available repertoire of genomic information now includes more than 80 bacterial genomes, and the chromosomal sequences of a large variety of plants and higher animals are available or being developed. The genome of H influenzae consists of 1.8 million base pairs; thus, the characterization of even a small genome was a major undertaking in cloning, sequence determination, and analysis. The Human Genome Project was begun on October 1, 1990, and initial drafts of the DNA sequence of the human genome were published in 2001.3Venter JC Adams MD Myers EW Li PW Mural RJ Sutton GG The sequence of the human genome.Science. 2001; 291: 1304-1351Crossref PubMed Scopus (10190) Google Scholar, 4International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome.Nature. 2001; 409: 860-921Crossref PubMed Scopus (16932) Google Scholar The genome of Homo sapiens consists of approximately 3 billion base pairs, representing the “moon shot of biology.” Several fundamental steps are required for large-scale DNA sequencing, and recent rapid improvements in technology have allowed sequencing of the larger genomes. The first step is construction of a “library” of cloned, small genome fragments. The genome is subjected to physical fragmentation for random DNA breakage, and the small fragments are cloned using well established vectors and hosts. Step two is determining the DNA sequencing of a large number of fragments. Although the chemical reactions for detecting specific nucleotides are well established, recent advances in automated sequencing and detection are continuing to shorten this step. To assure coverage of the entire genome, sequencing 8- to 10-fold the number of nucleotides in the genome is necessary. The third step requires assembling the genome sequence by computer analysis by using the overlapping regions of the fragment sequences to determine the order; this step has also been remarkably shortened by the use of more powerful computers and software. The fourth step is targeted cloning of gap regions and editing. The final step is annotation to characterize the probable gene regions, called open reading frames. The recent publication of the genome sequence of Streptococcus pyogenes provides an example of the effort and insights of genomics.5Ferretti JJ McShan WM Ajdic D Savic DJ Savic G Lyon K et al.Complete genome sequence of an M1 strain of Streptococcus pyogenes.Proc Natl Acad Sci U S A. 2001; 98: 4658-4663Crossref PubMed Scopus (765) Google Scholar Determining the genome sequence of the 1.8 million bases of S pyogenes required more than 4 years; the genome sequence of a typical bacterial genome can now be accomplished in 3 to 4 months. For S pyogenes, approximately 42,000 sequencing reactions were analyzed, and almost 16 million bases were read, covering more than 9 times the number of bases in the genome. Genomic analysis revealed 1708 open reading frames and provided insights concerning the organization of gene transcription, the number of regulatory genes, the presence of metabolic pathways, the production of extracellular products, the insertion of mobile genetic elements, and other gene motifs. Several new virulence factors were also identified. This knowledge provides the foundation for possible new vaccine candidates, identification of new species-specific virulence genes, new targets for antibiotics, and the investigation of gene expression through microarray analysis and proteomics. Building on the knowledge of genomics will allow investigations of gene expression by two methods, microarrays and proteomics. Recent advances in chip technology are designed to anchor a large number of DNA fragments representing the genome. For investigation of gene expression, DNA is derived from purified messenger RNA by reverse transcription. Identification of the derived DNA fragments that hybridize to the anchored genome fragments reveals which genes have been transcribed for expression. Thus, the genes expressed by certain persons or in certain diseases can be identified for therapeutic targeting. Most chip analysis is directed at differential expression of genes between affected and unaffected tissues or persons. Although microarrays reveal gene expression by identifying transcribed genes, the final expression of genes is complicated by regulation at the level of translation. Therefore, the study of proteomics is a more direct approach to studying the final products of gene expression. Although the technology of proteomics is different from DNA analysis, the technology of protein analysis has also changed profoundly. Rapid 2-dimensional gel electrophoresis and automated amino acid analyzers are providing expanding information about expressed proteins. By using the known genome sequence, only a portion of each protein's amino acid sequence is needed to identify the expressed proteins. The methods of microarray analysis and proteomics will focus the large amount of genomic information onto specific genes and proteins expressed by a specific person during a specific state of health. These approaches may allow the characterization of gene expression in health and disease, identification of new therapeutic targets, and the detection of risk factors for specific persons. Whereas it is important to appreciate these coming changes, the actual percentage of cases in which genetic information is being used is low and growing slowly. Substantial problems still exist in relating individual genomic changes to phenotypes. The understanding of genetic risks, especially in common diseases such as diabetes or asthma, require much more work before application to primary care settings. Much more research is required to tease out the array of single nucleotide polymorphisms (SNPs), variants, and haplotypes before they are fully appreciated. Finally, there exists a real dichotomy between the time available in a busy primary care setting and the time required for thorough, expert genetic examination. These and other problems will be time-consuming for years to come. The successful sequencing of the human genome is a major milestone in human history. Just as Neil Armstrong stepping upon the moon was a sentinel event that altered our view of the world and our place in it, the results of the Human Genome Project will alter our approach to clinical medicine in ways that will only be limited by our imagination. The human genome is enormous when one considers the component parts; the total genome is composed of 3 billion base pairs of DNA, with 100 to 300 million base pairs per chromosome and 100 base pairs to 2 million base pairs per gene. Key technologies that catalyzed the success of this project and enabled the project to be completed ahead of schedule are informatics and robotics. Informatics contributions include database-sequence storage, identification of functional genes and elements, sequence comparisons, and structure prediction. Included under robotics are techniques such as microchip technology, which allows the DNA of a subject to be placed on a chip and identified through computer analysis. These tools, which were invaluable in the Human Genomics Project, will be used in clinical practice but will be further refined and new techniques added. From a historic view, we can characterize the basic major events in our understanding of human biology into 3 major categories: (1) human evolution; (2) population migrations, and (3) developmental biology. Today in this third era, new techniques have allowed the rapid sequencing of human DNA that will unravel the genetic make-up of our patients, sequence the DNA of tumors to better understand the process by which they emerge as well as how to treat them, and sequence the DNA of human pathogens. These capacities will become major factors in how disease is approached as well as alter our view of what disorders have a genetic component as part of their pathophysiology. The concept of genetic disease must be broadened to include traditional polygenetic and multifactorial disease, which has always been accepted as having a genetic basis, but can be expanded to include more traditional illnesses. Even the most common disorders have genetic components, which influence the interactions of the host with the environment. With the exception of trauma, and even it may be influenced by genetics, all diseases have some genetic component in their expression. This can range from cystic fibrosis (CF), which is primarily genetic with little environmental influence, to acquired immune deficiency syndrome, which is remarkably influenced by the environment. Nevertheless, there is a strong genetic component for both disease progression and infection. A major impact on the clinical practice of medicine as a result of the Human Genomics Project will be in the area of genetic testing. The information and techniques have facilitated our entry into an era that will become increasingly complex. Issues that will have to be addressed and understood include, but are not limited to (1) implication to others—examples would be the impact on other family members of concepts such as insurability and career opportunities when a member of the family is found to be positive for a genetic disease; another issue is the discovery of a child's paternity that was not previously known or accepted; (2) future predictions—do we, in fact, want to know the future if a devastating illness for which there is no treatment looms; (3) unknown natural history, the fact that we are identifying potential candidates for a disease before we know if the disease will in fact become clinically important in this person or persons; (4) relative risks—this educational process needs to make patients and providers aware that although the relative risk for a disease may be high, the percentage of patients who will be affected still may be small; and (5) modifying genes and the role of the environment—here the issue is the impact on the patient and their genotype by environmental factors, which influence the expression of the disease. Other issues include regulation and quality control. Partially addressed in the field of diagnostic testing by the appointment of an oversight committee by the Secretary of Health and Human Services, this committee is known as the Secretary's Advisory Committee on Genetic Testing and has encouraged increased federal oversight with the FDA as the major lead agency. Another major issue will be our ability to obtain truly informed consent for both testing and treatment that will require comprehensive educational programs and counseling services. A murky area is the issue of testing of children for adult-onset disease. Whereas the current posture is that it is inappropriate to screen children for adult-onset disease if no effective intervention exists, this principle will be debated and expanded in scope. A more pragmatic concern is that the numbers of qualified personnel (approximately 1200 American Board of Human Genetics-approved clinical geneticists and 1200 certified counselors ) required for the evaluation of cases are not sufficient to accomplish the necessary tasks. We must enhance the understanding of human genetics by healthcare providers as well as use internet technology to rapidly disseminate information. These information items will need to be tailored to the time constraints of daily practice. Issues of appropriate timing and the need for privacy are other major factors. Timing refers to the most appropriate time to screen for genetic disease. Privacy may become the most difficult-to-manage issue. Who has the right to know and use the information discovered through genetic testing? Despite the issues raised by the development of genetic testing, there are clear benefits to the application of this technology:Develop an appreciation and understanding of disease pathogenesis, eg, the genesis of cancer and its coursePrevent certain diseases or modify their impact on the patientBetter define the epidemiology of diseaseBe able to identify specific targets for drug therapyUse gene therapy to enable a cure or ameliorate for certain diseasesStudy the genetics of pathogens and gain insight into pathophysiology and new therapiesUse pharmacogenetics to target the most appropriate drug for a person This discipline defined as individualized, rational drug selection based on the genotype of a particular patient will allow more specific treatment of our patients by accounting for their variability. Sir William Osler noted this variability in 1892: “If it were not for the great variability among individuals, medicine might as well be a science and not an art.” Although the art of medicine will always be practiced, the science will be enhanced once the potential of genomics is unlocked. Our current approach is based on probability. The patient has a particular disease and based on probability, we select a drug regimen for treatment. A percentage of patients will respond favorably to the treatment, a smaller percentage will not respond as anticipated and become more ill. A smaller percentage may recover but will have significant adverse reactions. We will be able to select a therapy targeted to accomplish a specific treatment, taking into account the specific DNA of the patient and the SNPs that may alter key enzymes and the metabolism of a drug or its effectiveness. One will select treatments specific for the disease pathogen or tumor and thus enjoy a greater success. One may select a specific treatment for a disease process and avoid adverse drug reactions such as ototoxicity in patients with A1555G mitochondria mutations or other SNPs. An example is illustrated by progress in the diagnosis and treatment of chronic myelogenous leukemia. Since the 1960s the association of the Philadelphia chromosome with this disorder has permitted diagnosis and therapeutic monitoring. More recently, the gene associated with the chromosomal aberration was identified. This resulted in the design of a drug tailored for this disease, which has shown great promise in clinical trials and is an example of what may be the future for cancer chemotherapy.6Kantarjian H Sawyers C Hochhaus A Guilhot F Schiffer C Gambacorti-Passerini C et al.Hematologic and cytogenetic responses to imatinib mesylate in chronic myelogenous leukemia.N Engl J Med. 2002; 346: 645-652Crossref PubMed Scopus (1801) Google Scholar The era of a single investigator working in a small independent laboratory may seem quaint after this scientific explosion. Today, there must exist a large infrastructure to support research. Consequently, laboratory structures have increased as well as the expense of supporting them. Science listed the top 10 funded principal research investigators in the country.7Zweiger G Transducing the genome. Information, anarchy, and revolution in the biomedical sciences. : McGraw-Hill, New York2001Google Scholar The smallest laboratory had 13 staff and the largest had 67, the National Institutes of Health (NIH) support ranged from $4.9 million to $12.5 million. The top-funded principal investigators in the country in the clinical and social sciences had NIH grants from $9.4 million to $65.3 million. The successful small lab will need to focus on specific diseases. Private industry had similar increases. The market capitalization of firms involved in genomic medicine has increased from 90 million in 1996 to more than one billion dollars in 2000. Similarly, the increase in investment in genomics by the pharmaceutical firms had reached one billion dollars in 1996.8Cohen J Biotechnology: betting on the genome: the genomic gamble.Science. 1997; 275: 767-772Crossref PubMed Scopus (45) Google Scholar The new era will result in improved health care for our patients because we can anticipate treating our patients more specifically. For example, in the treatment of childhood lymphoma one can determine the DNA arrangement of the tumor, specifically define the chemotherapy for that specific tumor, move quickly to define agents that cause infection in such patients and also predict the likely occurrence of secondary tumors. Lastly, the likelihood is that we will perfect gene therapy that will further increase our tools. The spillover of these tools into the agricultural industry will also have a major impact on health because foods will be produced with enhanced nutritional value, noxious components will be eliminated, pharmaceutical production and use of drugs will be enhanced, and we may provide oral vaccines within our foodstuffs. How we use these new technologies and to whom we make them available will be a source of continuing debate for a number of years. Just as the debate currently rages as to ethical concerns regarding how we apply these new technologies, one can anticipate that new issues will arise with each advancement. Similarly, the enormous cost associated with these advances, as well as the fact that there will still be shortages of resources, have the potential of increasing the disparity in access to care. An even greater barrier to the provision of health care may be that with genetic testing, insurance companies and other third-party providers may refuse to provide medical coverage for certain groups based on their risk as determined by genetic techniques. Information that becomes available through genetic testing done for other reasons than for the care of health of the patients will also be problematic. These last issues may be the push toward a single-payorr health care system so that risk can be spread evenly and the costs distributed over a larger population. It is now clear that the Human Genome Project is going to have an enormous impact on the practice of medicine as we know it and will likely alter our interactions with patients like no previous event. Great promise exists for good, but clear challenges must be identified and addressed. Equally important will be the requirement that professionals and the public be educated to ensure that this genetic information is properly used. Our challenge is to ensure adequate numbers of professionals who are prepared to meet the new needs. The genomic/post-genomic era offers enormous promise and challenge not only for the practice of clinical medicine but also for the teaching of medicine. Continuously in medical education, both educators and learners are confronted with an assault of new information; however, only rarely do we encounter a revolution in our way of conceptualizing disease and health. An understanding of the implications of genomics and postgenomics—and arguably our ability to realize the benefits of this new knowledge9Scheuerle A Limits of the genetic revolution.Arch Pediatr Adolesc Med. 2001; 155: 1204-1209Crossref PubMed Scopus (2) Google Scholar—requires such a radical change in our thinking. In current medical practice and education, to address an illness in a patient: [t]he medical questions are a) “What disease does this patient have and how do I treat it?” and b) “How can I prevent this disease?” In each question the emphasis in on the disease, its pathogenesis and its treatment or prevention, not on the patient. The patient who constitutes the arena wherein the struggle against disease is to be waged could be anyone.10Childs B Medicine through a genetic lens.in: Implications of genetics for health professional education. : Josiah Macy, Jr Foundation, New York1999: 27-51Google Scholar Our approach to the practice of, and education regarding, medical treatment has been one of probabilities, with an understanding that some treatments will work in some patients and that some, but not all, patients will have adverse side effects. Hence, we teach our students to inform our patients of possible risks and side effects and to caution them to return if the symptoms do not abate. We instruct our students to advise their patients to follow instructions carefully, but with little understanding ourselves—and therefore limited expectations—how to affect behavior or compliance. How should this educational interaction differ in the teaching of medicine informed by the genetic revolution? The questions asked when medicine is viewed through a genetic lens are a) “Why do we have disease at all and how do we define it”; b) “Why does this person have this disease at this moment in his/her lifetime”; c) “What can we do to restore this person to his/her unique steady state?”; and d) “How can we employ knowledge of an individual's special qualities to prevent disease and maintain health?” The answers comprise a conceptual basis for medical education, a set of explanatory principles within which to confront individual patients with their particular version of the disease they suffer.10Childs B Medicine through a genetic lens.in: Implications of genetics for health professional education. : Josiah Macy, Jr Foundation, New York1999: 27-51Google Scholar To adequately address the four questions posed by Barton Childs, the learner (and therefore the teacher) must understand modern genetics, a field that over time “has become more rather than less complex”.9Scheuerle A Limits of the genetic revolution.Arch Pediatr Adolesc Med. 2001; 155: 1204-1209Crossref PubMed Scopus (2) Google Scholar Looking in more detail at each question, the role of “modern genetics”—which certainly extends far beyond its biochemical basis—in approaching the ill patient becomes more apparent. To address this question, we must understand the principles of evolution and in turn the genetic basis of heterogeneity. If disease is viewed as a disharmony between environment and the person, the importance of the genes' protein products which modulate the interaction between gene and environment and determine the harmony between the person and his or her surroundings becomes apparent. Through answering this question, it becomes apparent why the mapping of the genome is only the first step down a long and complex path. It is neither the person nor the environment, but rather the interplay between the two, that creates and defines disease. As such, an understanding of culture and environment is as essential to an understanding of disease pathology as is an understanding of the biochemical basis of genetics. Likewise, asking the question in this way forces us to consider “remote” causes such as mutation and recombination, as well as “mating systems, ethnicity, founder effect, and selection.”10Childs B Medicine through a genetic lens.in: Implications of genetics for health professional education. : Josiah Macy, Jr Foundation, New York1999: 27-51Google Scholar The interplay of genetics, culture, environment, and behavior, as well as that of proximate and distal causes, is needed to address the complex issue not only of the relationship of (for example) smoking to cancer or alcohol to cirrhosis, but of why some persons smoke or drink and others do not. Again, the complex interaction between genetics and environmental exposures must be understood to address this question. Genetic disorders contribute disproportionately to intrauterine deaths and to early pediatric deaths. But within each “period” of the life cycle, environmental disorders also contribute, especially late in the phase.11Vogel F Motulksy AG Human genetics.in: : Springer-Verlag, Berlin1997: 297-298Google Scholar So for example, although most pregnancy-related deaths may be genetic, the disorders of late pregnancy are often related to maternal factors such as toxemia and placental disorder. Advances from the genomic and postgenomic eras will allow us to move beyond symptomatic treatment. In theory, no longer will we be playing an exercise of probabilities (“two thirds of patients will benefit from this drug but 5% will experience significant side effects”), but now we should enjoy a much greater certainty of effect—if other conditions of drug treatment and environment control are met. Returning to the teachings of medicine a century ago, a physician will be able to treat his or her patient as the unique person he or she is. Of perhaps even greater importance, our range of treatment options—including potential targets of our treatment—will increase and again can be tailored to the patient.1McKusick V The anatomy of the human genome.JAMA. 2001; 286: 2289-2295Crossref PubMed Scopus (54) Google Scholar We shall be able to identify persons at “greater risk” through more frequent screening, interventions designed to influence the environmental exposures and/or ultimately interventions designed to alter protein products of the person. But again, the interplay of genetics, environment, and culture, as well as behavior, behavioral change, and patient-physician communication will be more crucial than ever before in the practice of medicine. Medical education will require a focus on complexity and individuality and a renewed emphasis on prevention, including purposeful behavioral change and patient communication. Certainly the challenge for medical educators is enormous, but significant resources exist. The “National Coalition for Health Professional Education in Genetics” (www.nchpeg.org ), consisting of 120 member organizations representing genetics, health care, consumer, government, education, and pharmacy is dedicated to the integration of genetics content into clinical practice and accordingly has developed tools and resources towards this end, including descriptions of “core competencies” for all health professionals.12McInerney J Core competencies in genetics essential for all healthcare professionals.in: : National Coalition for Health Professional Education in Genetics, Lutherville (MD)2001: 1-8Google Scholar These core competencies, reflecting the new way of thinking about disease discussed in the previous section, include knowledge, attitude, and skill competencies regarding content traditionally contained within the disciplines of medical genetics, ethics, behavioral science, environmental science, anthropology, epidemiology, and communication. A variety of other resources are available or are currently being developed to assist medical schools in adapting or radically altering their curricula. “Genetics in Primary Care (GPC): A Faculty Development Initiative” was designed “to enhance the ability of the faculty to incorporate the clinical application of genetic information into undergraduate and graduate primary care medical education” whose advisory board includes primary care organizations from pediatrics, family medicine, internal medicine, and osteopathy, as well as genetics and other relevant organizations. In addition to preparing a syllabus with specific genetics learning modules for use in medical school curricula, the GPC is maintaining a list of “Resources on the World Wide Web” currently including dozens of listings of relevant organizations (such as Genetic Alliance, www.geneticalliance.org, and the National Human Genome Project, www.nhgri.nih.gov ), sites describing disease disorders (such as Rare Genetic Disease in Children, http://mcrcr2.med.nyu.edu/murphp01/homenew.htm, and Online Mendelian Inheritance in Man, http://www3.ncbi.nlm.nih.gov/Omim ), as well as sites addressing consumer concerns, ethical, and legal issues. These resources contain materials useful not only for clinicians, but also for educators developing curricula and as reference sites for medical students, residents, and other learners. That these resources are available should be encouraging to us. But these resources will not themselves address the multiple issues pediatric educators must face in tackling this complex interdisciplinary challenge. Concepts and skills in culture, behavioral change, and patient communication that may not have been adequately addressed in most medical school curricula to date must be central and highly integrated in the next iteration of curricula that embrace “medicine through a genetic lens.” The increased interest in gene therapy and genomics within the scientific community and by the public in general has refocused attention on the number of ethical issues raised by “new science.” These issues, along with concerns that already exist regarding such issues as information technology make ethical questions concerning genomics an important topic. During the 2002 AMSPDC me