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WORKSHOP REPORT |
1 Visiting Professor, University of Medicine and Dentistry of New Jersey, 9 Bennington Road, Morristown, NJ, USA 07960; and 2 Acting Director, Division of Clinical Research and Health Promotion, National Institute of Dental and Craniofacial Research, National Institutes of Health, Building 45, Room 4AS43G, 45 Center Drive, Bethesda, MD, USA 20892;
* corresponding author, MLBGums{at}aol.com
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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Recent advances in such areas as genomics and proteomics, coupled with the development of new technologies, have expanded our knowledge of the etiology and pathogenesis of disease and, from this, have provided new insights into the design and conduct of clinical trials. The workshop, "Methods for Enhancing the Efficiency of Dental/Oral Health Clinical Trials: Current Status, Future Possibilities", held on May 6–7, 2004, considered a variety of ways in which these insights are being, or have the potential to be, applied to clinical trials so as to enhance their efficiency and, hence, their cost-effectiveness, without diminishing the quality of information produced. The focus of this workshop was to assess the state of the science and identify research needs for the use of biomarkers, surrogate endpoints, and new technologies in oral disease clinical trials. Examples of ways in which clinical trials of other diseases have benefited from the use of new methods and technologies and FDA considerations were also discussed.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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To facilitate discussion, Dr. Pihlstrom noted the following definitions from a 1999 joint NIH-FDA workshop (Biomarkers & Surrogate Endpoints, 2000): A clinical endpoint is a characteristic or variable that reflects how a patient feels, functions, or survives; a surrogate endpoint is a biomarker intended to substitute for a clinical endpoint and would be expected to predict clinical benefit (or harm, or lack of benefit or harm) based on epidemiologic, therapeutic, pathophysiologic, or other scientific evidence; and a biomarker is a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or (pharmacologic) responses to a therapeutic intervention. Biomarkers can be validated as surrogate endpoints by: documenting accuracy of the biomarker (i.e., showing a statistical correlation with the clinical endpoint); documenting sensitivity, specificity, and reproducibility of the measure; having substantial evidence of a causal or mechanistic linkage to the intervention; and showing that they are generalizable to include other interventions that affect the surrogate endpoint. The identification of highly precise biomarkers would allow for the testing of more candidate drugs, reduce the number of patients required for clinical trials, reduce the duration of clinical trials, expand clinicians’ capacity to predict adverse events, and potentially improve regulatory decision-making.
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CURRENT USE OF BIOMARKERS, SURROGATE ENDPOINTS, AND OTHER APPROACHES TO ENHANCE CLINICAL TRIAL EFFICIENCY: EXAMPLES FROM OTHER DISEASES/CONDITIONS (Moderator, Dr. John Stamm, School of Dentistry, University of North Carolina) |
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TOPABSTRACTINTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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Biomarkers in Head and Neck Cancer (Dr. David Sidransky, Johns Hopkins University School of Medicine)
Since cancers develop clonally as a result of specific genetic alterations, cancer cells, from the earliest stages, have associated biomarkers which may be either DNA, RNA, or altered proteins. It is important to use a panel of different markers, since not all tumors may have each of the markers. For head and neck squamous cell carcinoma, investigators have identified genetic markers that correspond to phenotypic progression from pre-malignancy to invasive carcinoma and have been shown to be predictive of the progression (or non-progression) of lesions to carcinoma. Markers in saliva associated with squamous cell carcinoma include microsatellite markers indicative of clonal genetic changes and hypermethylated DNA markers indicative of alterations in fundamental pathways, such as inactivation of tumor suppression genes. Mitochondrial DNA mutations, which occur in about half of all tumors, can be detected in tissues and saliva and can be indicative of localized and disseminated disease. The detection of the p53 mutation in histopathologically negative tumor margins has been shown to be a surrogate for residual disease. Serum protein markers useful for the detection and monitoring of tumors have been identified for head and neck carcinoma, and prostate, lung, gastrointestinal, and ovarian tumors. Individual markers and patterns of markers can be identified by mass spectroscopy. The example of the use of epithelial growth factor receptor molecular markers for individualizing treatment was discussed. New high-throughput technologies, such as automated 96-well capillary array electrophoresis, facilitate the identification of molecular markers and can be cost-effective for use in clinical trials.
Subclinical Markers of Cardiovascular Disease (Dr. David R. Jacobs, Jr., University of Minnesota and University of Oslo)
Coronary artery atherosclerosis begins in childhood and progresses in a slow and asymptomatic manner for many years. During this asymptomatic phase, clinical evaluation may reveal elevated risk factors and indices of ‘silent ischemia’, i.e., subclinical disease. Subclinical markers of atherosclerosis have been developed with the aims of: (1) understanding the pathophysiologic course leading to heart attack, ischemic stroke, and related atherosclerotic diseases; and (2) conducting studies with smaller sample sizes to increase their feasibility. Studies using surrogate endpoints that demonstrated a regression of atherosclerosis with statin treatment influenced the decision to conduct major statin clinical trials using clinical endpoints. Current studies on subclinical markers of atherosclerosis are focusing on non-invasive methods. A primary goal of the MESA study (Multiethnic Study of Atherosclerosis) is to determine whether subclinical markers are predictive of subsequent clinical events and, if so, the extent to which these add to the predictive value of risk factors alone. The subclinical markers studied include imaging methods: computed tomography of the coronary arteries to assess calcium deposits indicative of coronary artery atherosclerosis; ultrasound measures of the carotid artery to assess vascular plaque and thickening of the vessel wall; echocardiography; and magnetic resonance imaging to assess left ventricular size, wall motion abnormalities, arterial distensibility, and cardiac output. Markers obtained by physical examination include: determination of the ankle-brachial index to compare blood pressure in the arms and legs as a measure of potentially reduced peripheral blood flow; and flow-mediated dilation in the brachial artery to assess the health of the endothelium. Microalbuminuria assesses adverse changes in kidney endothelial cells that are predictive of subsequent cardiovascular and renal disease. Clinical trials using subclinical markers such as these could be conducted with much smaller sample sizes than would be needed for trials using clinical endpoints. However, these subclinical markers are generally not yet considered definitive, and ongoing studies will help to determine the predictive value of such markers for subsequent clinical events and their usefulness for enhancing clinical trial efficiency.
Osteoarthritis (Dr. Gayle E. Lester, National Institute of Arthritis and Musculoskeletal and Skin Diseases [NIAMS], NIH)
There are few effective drugs available to treat osteoarthritis, a major cause of disability and impaired quality of life. Because imaging findings (such as joint space narrowing) correlate poorly with pain and disability, and clinical endpoint studies are long and expensive, the identification of validated biomarkers would greatly facilitate the conduct of clinical trials in drug development and our understanding of the etiology and natural history of osteoarthritis. Because the magnitude of such a project is greater than any individual institute or company could support, the NIAMS, in conjunction with other NIH Institutes, developed a working partnership with three major pharmaceutical companies to establish and fund the Osteoarthritis Initiative. The goal of this project is to identify and evaluate biomarkers as surrogate endpoints for osteoarthritis. The project will prospectively follow a cohort with early and progressive osteoarthritis for five years, during which clinical and imaging data as well as biological specimens will be collected. Four clinical centers and one data-coordinating center are participating in this project. It is anticipated that the research resources produced by this initiative will stimulate basic biomarker research and facilitate drug development through the identification of biomarkers of disease onset and progression that will facilitate clinical trials. The Osteoarthritis Initiative represents a new research model in which a partnership approach is essential to achieve the ultimate reduction in disease morbidity and mortality and, hence, an improvement in the health of the public.
Biomarkers and Clinical Trials: Case Studies from Diabetes (Dr. Myrlene Staten, National Institute of Diabetes and Digestive and Kidney Diseases [NIDDKD], NIH)
The development of new therapeutic agents is often hampered by the investigators’ inability to determine the potential effectiveness of a new agent in early-stage clinical trials (e.g., proof-of-concept and dose-ranging studies) and, consequently, the need to conduct costly, high-risk trials requiring large numbers of patients for long treatment durations. The use of biomarkers as surrogate outcomes could facilitate the conduct of clinical trials, but they are not accepted as surrogates until it is proven that the therapeutic alteration of that marker will be predictive of a clinically meaningful outcome (for example, that a lowering of LDL cholesterol will result in a reduction of deaths from cardiovascular disease). For example, in the early 1990s, there was controversy as to whether lowering blood glucose levels results in a reduction of longer-term micro- and macrovascular diabetic complications. The Diabetes Control and Complications Trial (DCCT), initiated by the NIDDK, studied over 1400 patients with type 1 diabetes over a mean period of 6.5 years and demonstrated that microvascular complications were improved with intensive glycemic control compared with conventional control, as measured by HbA1c levels. As a result, HbA1c was established and accepted by the FDA as a surrogate outcome for improvement in the microvascular complications of diabetes. This facilitated the development of new therapies by reducing the cost of demonstrating clinical efficacy and led to the availability of four new major categories of diabetes drugs.
The finding in the DCCT trial that residual beta cell function and insulin production, as measured by C-peptide, were associated with lower rates of severe hypoglycemia and improved glycemic control led to the recommendation that stimulated C-peptide be accepted as a valid outcome measure for clinical trials. It is anticipated that ongoing multicenter studies will provide data leading to the acceptance of stimulated C-peptide as a surrogate outcome measure of beta cell preservation. Finally, in a long-term observational study of the DCCT cohort, patients are being phenotyped to provide data on markers of complications and actual progression to the overt expression of diabetic neuropathy, nephropathy, retinopathy, and cardiovascular disease. These data could support the validation of biomarkers as surrogate endpoints for diabetic complications that could be studied in shorter time periods and stimulate the development of therapies for diabetic complications.
Infectious Diseases: HIV/AIDS (Dr. Thomas Denny, New Jersey Medical School, University of Medicine and Dentistry of New Jersey)
The immunologic abnormalities associated with HIV infection include: a reduction in CD4 cells accompanied by abnormalities in cell function; chronic immune activation; and cytokine dysregulation, as evidenced by the production of pro-inflammatory cytokines and decreased production of IL-2 and IFN-
. There are also HIV-specific responses of CD4 and CD8 T-cells. The laboratory assays that are typically used to monitor disease progression and/or response to therapeutic intervention include immunophenotyping of cells and pathogen-specific functional assessment of available cells such as antigen-specific proliferation, cytotoxic lymphocyte activity, and cytokine production. Various immunophenotypic and immune function markers were discussed as candidates for surrogate markers in the natural history and treatment of HIV infection.
Adherence: Putting the Wraps on Achilles’ Heel (Dr. Margaret Chesney, National Center for Complementary and Alternative Medicine [NCCAM], NIH)
Obtaining patients’ adherence to (compliance with) treatment regimens presents a major challenge across all of medicine, including clinical trials, since most recommendations for health promotion, illness prevention, and treatment require some change in patient behavior. A recent meta-analysis revealed that mean adherence rates to therapy ranged from 67.5% for diabetes to 88.3% for HIV infection. The focus in achieving adherence needs to be on enhancing patients’ motivation, which can be achieved by establishing patient-specific goals. Patients should be given clear medical information and an explanation of why the action recommended for them is important. Additionally, their ambivalence should be acknowledged. Motivation can also be enhanced by offering patients a choice of regimens (including the alternative of not taking medication) and involving them in the decision. Patients often need assistance in removing barriers to behavior change and participation in clinical trials. This can range from providing convenient parking for their appointments to dealing with effects of poverty, such as unstable living arrangements which preclude the establishment of daily routines. Patients often will need direct assistance in overcoming barriers to behavior change and should be rewarded for adherent behavior.
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APPLICATIONS OF BIOMARKERS, SURROGATE ENDPOINTS, AND NEW TECHNOLOGIES TO CLINICAL TRIALS OF ORAL DISEASES/CONDITIONS (Moderator, Dr. Marjorie Jeffcoat, School of Dental Medicine, University of Pennsylvania) |
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TOPABSTRACTINTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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New Models for Clinical Caries Trials (Dr. George Stookey, Indiana University School of Dentistry and Emerging Technologies Center)
Although there has been remarkable progress in preventing and controlling dental caries, it still affects 78% of the population by age 17 and 85% of adults above the age of 18. There is a disproportionate distribution of the disease, with 70–75% of lesions occurring in 20–25% of the population. Since current guidelines for clinical caries trials of new therapeutic agents accepted by regulatory or review agencies (e.g., FDA and ADA) use cavitation as the definitive diagnostic parameter, clinical caries trials usually require three-year test periods and large numbers of subjects per test group. The duration and high cost of these trials have been an impediment to the development of novel preventive and therapeutic strategies. The recent International Consensus Workshop on Caries Clinical Trials (Pitts and Stamm, 2004) concluded that clinical trials involving only cavitated lesions as an outcome measure are becoming outmoded, the assessment of non-cavitated lesions is essential for future clinical caries trials, and some new diagnostic techniques may exceed the accuracy, sensitivity, and resolution of existing validation reference standards. Clinical models to enhance efficiency have used modified visual detection criteria which include non-cavitated lesions, caries-active populations, and supervision to ensure adherence to the study regimen. These models allow for studies of shorter duration with fewer subjects than would otherwise be needed. Independent studies have demonstrated treatment differences after only 9–12 months that were confirmed by continuation of the studies for up to 24 months. The development of new technologies for the early detection of dental caries, and especially those which have the capability of quantitating changes in lesion extent between examination periods, may also allow for studies of shorter duration. Clinical trials utilizing one of these technologies, quantitative light fluorescence, demonstrated that treatment effects detected within 4–6 months were confirmed through one year. Therefore, study design modifications and new technologies could permit the evaluation of new and innovative caries-preventive measures in smaller groups of subjects in shorter time periods, thereby substantially reducing study cost. However, adoption of these enhancements depends upon their acceptance by the FDA, other regulatory and professional organizations, and the scientific community.
Periodontal Diseases (Dr. Daniel Fine, New Jersey Dental School, University of Medicine and Dentistry of New Jersey)
In a typical study design for investigating a periodontitis therapy, a study population is selected based on age and clinical signs of periodontitis (i.e., probing pocket depth and attachment loss), subjects are randomly assigned to either a control or active treatment group, the deepest site or sites in each quadrant are selected for monitoring, and pocket depth and attachment levels are re-assessed at defined intervals. The critical issues associated with this design include: imprecision in diagnosis, since periodontal diseases with the same clinical presentation may have different microbial etiologies; unknown subject disease susceptibility; unknown site disease activity, e.g., selected sites may reflect past disease activity and be currently inactive; and limitations of periodontal probing as a measurement method, e.g., variability as a result of differences in angulation, force, and position on the tooth. Moreover, because of the potential variation in microbial etiology and disease activity, only a subset of subjects may respond to specific antimicrobial agents, and group means may not reflect the true efficacy of the test agent. In such a case, the study would require a larger subject population to show statistically significant treatment effects.
To increase study efficiency, subject entry criteria should include a microbial component, so that only subjects with the infectious etiology appropriate for the antimicrobial being tested are included. In addition, only subjects with active disease should be included. This might be achieved by: (1) the development of a quantitative DNA/DNA hybridization method compatible with chairside use, which can be customized to include organisms proven to have an etiologic role in disease; and (2) the identification and validation of specific biomarkers for disease activity in gingival crevicular fluid. For clinical trials of host-response modifiers, individual susceptibility to periodontal disease, rather than specific microbial etiology, is a key consideration, and clinical trial efficiency could be enhanced by the incorporation of a measure of disease susceptibility in subject inclusion criteria, to provide a more homogeneous study population with similar rates of disease progression. Since studies with subjects having a more rapid rate of progression could be shorter and need fewer subjects, this modification could be especially useful in proof-of-principle (Phase II) clinical trials. This might be achieved by identifying genetic markers or, more likely, patterns of genetic markers that correlate with increased (or decreased) susceptibility. Diagnostic methods other than periodontal probing might allow for the detection of changes in disease status more precisely and in shorter time periods. More precise and sensitive measures would: lead to reduced subject variability, thereby reducing the number of subjects required; allow for detection of changes at earlier time periods, thereby reducing the study duration; and, by detecting disease at earlier stages, facilitate the study of preventive interventions. For this to be achieved, biomarkers to serve as surrogate endpoints need to be identified and validated, and new, more sensitive or specific imaging techniques should be investigated for applicability to periodontal clinical trials.
Biomarker Application and Validation in Oral Cancer Trials: Present and Future Prospects (Dr. Adel El-Naggar, The University of Texas, M.D. Anderson Cancer Center)
Head and neck squamous cell carcinomas comprise 5% of all cancers in the US, with an estimated 40,000 new cases to be diagnosed in 2004. The incidence is rising in women and young men, and the five-year survival rate has remained at around 45–54%. Approaches for early diagnosis and treatment are needed because of the persistent morbidity and mortality of the disease. The evolution of normal tissue to carcinoma is a multi-step process in which progressive genetic and phenotypic changes occur. Elucidation of these changes is a requirement for the identification of candidate biomarkers for diagnostic and therapeutic monitoring purposes. Identification of suitable biomarkers is made more difficult by characteristics of the disease, including lack of definitive familial or hereditary association, sparse and inconsistent cytogenetic data, the occurrence of field cancerization, and phenotypic and clinical heterogeneity of lesions. Potential surrogate biomarkers should be: (1) linked to disease pathogenesis; (2) objective and reproducible (i.e., different laboratories should produce the same results); (3) independent of existing clinical parameters; (4) validated by clinical testing; (5) easily applied and affordable; and (6) subject to quality control and assurance. Biomarkers may be identified on the basis of their familiarity (e.g., the tumor suppressor gene p53), their role in cellular pathways (e.g., as a central marker of a process such as apoptosis, cell proliferation, cell differentiation, etc.), or their combination with other markers to form characteristic profiles. Potential molecular markers for screening for head and neck squamous cell carcinoma include a variety of serum- and tissue-derived proteins, tumor suppressor genes, oncogenes, growth factors, proteolytic enzymes, tumor antigens, and DNA ploidy and proliferation. Salivary markers would facilitate the early detection and screening of high-risk individuals, and might also be used as indicators of field cancerization, but none of these has, as yet, been universally validated. It was recommended that guidelines be established for the standardization of reagents and methodologies, that criteria be established for uniform scoring, and that multi-institutional prospective studies be conducted for biomarker validation.
Candida albicans: A Model for New Paradigms in Pathogenesis (Dr. Nina Agabian, School of Dentistry, University of California-San Francisco)
Candida albicans can exist as either a commensal or virulent organism and is capable of switching forms and even of forming a biofilm. As a commensal organism, it is avirulent in 30–90% of healthy individuals and is located on the oral and vaginal mucosae and skin. As a virulent organism, it can cause mucosal and systemic disease, with immunosuppressed HIV patients, neonates, and the elderly at greatest risk. Several ‘Candida-specific’ genes have been identified, the majority of which are involved with lipid and fatty acid metabolism, oxidative metabolism, and respiratory functions. Studies have suggested that although Candida albicans is typically grown fermentatively, it is also able to grow oxidatively, utilizing long-chain fatty acids and lipids as a sole carbon source. Under these growth conditions, Candida produces biologically active metabolites, one of which, 3R18 dihydroxytetraenoidic acid, has been shown to inhibit neutrophil migration. This suggests that there may be a lipid-mediated ‘dialogue’ between the pathogen and host which has a potential role in commensal and virulent colonization. Compounds produced by Candida in the course of this dialogue may provide potential therapeutics and diagnostics. In addition, by reflecting the specific environment in which it is growing, Candida might serve as a sentinel/reporter organism to provide an early indication of change.
Sjögren’s Syndrome (Dr. Stanley Pillemer, Medimmune, Inc.)
Sjögren’s syndrome is a systemic autoimmune disease associated with lymphocytic infiltration in exocrine and other epithelial tissues. It affects from 0.05–4.8% of the population, with females affected 9 times as frequently as males. The disease has a wide clinical spectrum, ranging from mild symptoms of fatigue and oral and ocular dryness to severe multisystem involvement, including pulmonary infiltration and fibrosis, renal tubular acidosis and glomerulonephritis, peripheral neuropathy, central nervous system involvement, and vasculitis. While there are no universally accepted outcome measures for Sjögren’s syndrome clinical trials, the time needed to develop suitable outcome measures may be accelerated based on lessons learned from the development of outcome measures for another autoimmune disease, rheumatoid arthritis. Outcome measures used in Sjögren’s syndrome studies have included symptomatic assessment of ocular and oral dryness, fatigue, health-related quality of life, unstimulated and stimulated salivary flow rates, laboratory measures of IgG and acute phase reactants, serial labial salivary gland biopsies, and salivary scintigraphy. Additional data from clinical trials and long-term outcome studies will be needed to determine the optimal set of outcome measures for Sjögren’s syndrome and the subsequent identification and validation of biomarkers with which to diagnose and monitor the disease.
Biomarkers, Surrogate Endpoints, and Emerging Technologies to Support Temporomandibular Joint Disorder Clinical Trials (Dr. James Fricton, Schools of Dentistry and Medicine, University of Minnesota)
Temporomandibular joint disorders (TMJD) are quite common in the population, with an estimated 7% of affected individuals requiring treatment. The most frequently occurring symptoms are regional pain over the muscles of mastication or in the temporomandibular joint region. TMJD can also include facial pain, earaches, headaches, and tooth pain. Patients often report limited or asymmetric jaw movement, difficulty in chewing, or joint sounds. These symptoms are not the result of a single condition, but can result from any of a variety of diagnostic subtypes which include TMJ arthralgia, disk displacement, degenerative joint disease, myofascial pain, and fibromyalgia. Clinical trials to study these disorders have produced diverse outcomes because the study methods used have lacked consistency, reflecting an incomplete understanding of these disorders. Patient-reported outcomes were the most common clinical endpoints, with pain the outcome measure most often cited. Efforts to make the outcomes more objective have included clinician-reported signs and physiologic outcomes. However, correlations among symptoms, clinical signs, and imaging findings have been weak. The investigation of potential biomarkers that could correlate with clinical endpoints is still in its early stages. Biomarkers could be derived from synovial fluid, joint and muscle tissues, images, blood and serum, and saliva, with the latter of particular interest because of its ready accessibility. Biomarkers reflecting early disease processes would have great applicability in diagnosing disease and monitoring therapy.
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STATE OF THE SCIENCE OF METHODS AND TECHNOLOGIES (Moderator, Dr. Alan Guttmacher, National Human Genome Research Institute, NIH) |
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TOPABSTRACTINTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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Application of Clinical Proteomics for Cancer Diagnosis and Risk Stratification (Dr. Lance Liotta, National Cancer Institute [NCI], NIH)
The serum proteome consists of proteins or protein fragments which may arise from any point along the vascular tree and thus reflects events occurring in all the cells and tissues of the body, whether normal or pathologic. It was hypothesized that the serum proteome contains proteins that reflect changes associated with early cancer development and therefore contains biomarkers that would provide the ability to detect cancer and allow for intervention in its earliest stages. A technique developed at the NCI uses mass spectrometry to produce a ‘bar code’ or proteomic image of serum that can be used to detect relevant proteins by computer-aided analysis. The new approach to biomarker discovery assumes that diagnostic patterns, rather than single molecules, will be of greatest utility; that is, panels comprised of hundreds, or even thousands, of markers derived from disease and non-diseased cells will constitute a diagnostic pattern. There is no preconceived assumption about the identity, number, or even the existence of molecules predictive for a disease set. Therefore, large studies are needed in which samples from unaffected and diseased patients are compared so that differences in the serum proteome can be identified. Protein microarrays provide another technology using known proteins for individualizing patient therapy and monitoring the success of therapy. Serum proteomics provides a means for profiling the ongoing pathophysiology of the whole organism and has potential for the early diagnosis of disease and early warning of toxicity in drug trials.
Translating the Human Genome: From Sequence to Health (Dr. Christopher Austin, National Human Genome Research Institute [NHGRI], NIH)
The completion of the human genome project has great potential for applications to research and patient care. In the short term, there will be an enhanced understanding of biology, pathophysiology, and evolution. This will result in new genetic tests for common diseases that have not been traditionally thought of as genetic in origin, such as stroke and heart disease. New therapeutics based on genomics will take much longer, perhaps up to 10–15 years, in part because of the requirements of the drug development process. Diseases can be classified as single-gene diseases and multiple-gene diseases. Single-gene diseases, in which a mutation causes the disease (e.g., Huntington’s disease, cystic fibrosis), are relatively rare in the population. The more common genomic (polygenic) diseases (e.g., hypertension, schizophrenia, Alzheimer’s disease) are associated with genetic polymorphisms. Most, if not all, common diseases have a genetic component, and the challenge is to identify genetic risk factors—that is, genes that individually affect disease risk when combined with an environmental insult such as smoking, alcohol use, etc. The approximately 30,000 human genes give rise to at least 100,000 proteins, making the development of drugs based on the genome a formidable challenge. Currently, about 120 proteins are targeted by drugs, leaving more than 90% of proteins to be investigated as drug targets.
Biologic applications of the genome will lead to a characterization of heritable variation that will allow for more accurate diagnosis and treatment. The reference sequence for the human genome was determined by sequencing the DNA from a mixture derived from several people. However, there may be millions of variants within the population, and it will ultimately be necessary to identify the precise locations of genetic variants to make connections between the variants and traits of interest, such as disease and drug response, diagnosis, etc. An international project is under way to produce a haplotype map that will identify all the genetic polymorphisms in the human population and group them into haplotypes or descriptions of patterns of polymorphisms. In the medicine of the future, diseases will be classified by molecular taxonomy. We will be able to choose among targets to develop for therapeutics, and, through an understanding of genes and pathways, we will be able to understand the mechanisms for reactions that today are considered ‘idiosyncratic’. Use of the human genome to benefit patients will require astute clinical phenotyping, since genes are only as powerful as the traits with which they are associated. Clinicians will need to finely hone their diagnostic abilities so as to be able to connect genes, proteins, and polymorphisms with clinical syndromes and precise diagnoses.
DNA Microchips: Detection of Microbes in Oral Cavity Fluids (Dr. David Stahl, University of Washington)
DNA microarrays are being developed for identifying biomarker molecular signature patterns in saliva and supra- and subgingival plaque, and for assessing gene expression of microbial virulence determinants and factors involved in cell-to-cell communication and biofilm formation. More than 600 microbial species can be found in the oral cavity, with the majority organized in complex multi-species biofilms. Since less than 50% of the oral microbiota is cultivable, there is a need for methods with which to detect and identify bacteria which might be present, especially in view of the etiologic role of plaque organisms in periodontal diseases and dental caries, and the association of these organisms with several systemic diseases. Biochip technology uses an array comprised of small acrylamide gel pads to which DNA probes are applied. The gel pads are affixed to a glass slide, enabling investigators to achieve a probe density 1000 times larger than would be obtained with a glass surface alone. RNA is isolated directly from plaque and saliva samples, chemically fragmented, and labeled with a fluorescent dye for microarray analysis. Strategies for confirming hybridization specificity and for developing standard operating and quality assurance procedures were described, and it was noted that work is under way to develop a portable microarray reader.
Biomedical Imaging Research, Biomarkers, and Efficient Clinical Trials (Dr. Roderic Pettigrew, National Institute of Biomedical Imaging and Bioengineering [NIBIB], NIH)
Clinical symptoms often appear only after significant tissue degeneration has already occurred and may not be sensitive indicators of underlying pathology. The availability of new technologies for detecting molecular markers is critical for determining therapeutic effectiveness and would be particularly valuable for studies of therapies designed to slow disease progression. Novel MRI approaches under development may provide more detailed information about structural changes associated with cartilage degeneration. Infrared spectroscopy absorption can identify and quantify molecular markers in cartilage, such as collagen and proteoglycans, and may therefore be able to detect early changes in cartilage composition in vivo during degenerative processes. Infrared micro-imaging technologies utilizing synchrotron light sources are being developed that can quantitate compositional differences in bone that occur with aging and disease. Multiphoton microscopy, capable of penetrating approximately 500 microns into tissue and providing tissue contrast without staining, may allow for the assessment of collagen. Advances in bioengineering include functional tissue engineering of articular condyles, optical coherence tomography to detect cells and tissue matrices, the development of vibrating nanostructures to prevent biofouling of implanted devices, and the creation of nanoarrays of carbon-based nanofibers that function as needles capable of injecting substances into individual cells.
Characterization of Humans and their Oral Microbial Flora by Genomic Approaches (Dr. David Relman, School of Medicine, Stanford University)
The application of genomic information has led to molecular approaches to the study of the microbial flora. Molecular data provide enhanced reliability, portability, breadth of coverage, and ease of measurement. The robustness and comprehensiveness of these measurements will have a significant impact on the efficiency of human clinical trials and will be especially relevant because of the large percentage of the oral flora which is non-cultivable and therefore can be identified only by genetic methods. For example, when ribosomal RNA was used to identify subgingival bacteria in periodontal sites, TM7 group bacteria were most abundant in sites with early (mild) periodontitis. Although this association does not prove causality, it can lead to hypotheses which could significantly enhance our understanding of periodontal disease etiology. Similarly, archaea were associated with severe periodontitis in a subset of subjects and had reduced levels after treatment. It may be that the community of organisms is the pathogen and, therefore, for disease to be understood, patterns of disruption of community structure should be studied, along with host patterns of gene expression. Correlations may exist between commensal microflora status and host gene expression profiles that may yield important new insights for improving the design and assessment of clinical trials of oral diseases.
Informatics (Dr. David Lipman, National Center for Biotechnology Information [NCBI], National Library of Medicine, NIH)
Biomedical research has become more data-intensive. Biomedical scientists are generating more data in their own research and also using more data from other investigators. Two examples of new NCBI database resources are: (1) the dbMHC database (www.ncbi.nih.gov/mhc) that provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC); and (2) the GEO (http://www.ncbi.nlm.nih.gov/geo/) or Gene Expression Omnibus, a public repository for high-throughput gene expression data of various types, including microarrays (cDNA, oligo, genomic), SAGE, and MS proteomics. The GEO can be used to: (1) provide confirmation of lab results or literature reports for the behavior of genes of interest; (2) provide possible candidates for genes worthy of further study in the lab; (3) form hypotheses on novel pathways or gene interactions; and (4) find novel roles for characterized genes.
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FDA PERSPECTIVE: REGULATORY CONSIDERATIONS (Dr. David Feigel, Former Director, Center for Devices and Radiological Health, US Food and Drug Administration [FDA]) |
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TOPABSTRACTINTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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REACTOR PANEL |
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TOPABSTRACTINTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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SUMMARY |
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TOPABSTRACTINTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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ACKNOWLEDGMENTS |
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Received June 16, 2004; Last revision July 14, 2004; Accepted July 15, 2004
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TOPABSTRACTINTRODUCTIONCURRENT USE OF BIOMARKERS,...APPLICATIONS OF BIOMARKERS,...STATE OF THE SCIENCE...FDA PERSPECTIVE: REGULATORY...REACTOR PANELSUMMARYREFERENCE |
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Pitts NB, Stamm JW (2004). International consensus workshop on caries clinical trials (ICW-CCT)—final consensus statements: agreeing where the evidence leads. J Dent Res 83(Spec Iss C):C125–C128.
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| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| IADR Journals | Advances in Dental Research ® |
| Journal of Dental Research ® | Critical Reviews (1990-2004) |
