NEXUS (winter 2012 issue “Global Health Nexus”)
Genomics in Dentistry
Harold C. Slavkin, Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California USA
Professor Harold Slavkin
Center for Craniofacial Molecular Biology
Herman Ostrow School of Dentistry
2250 Alcazar Street CSA-103
Los Angeles, California 90033
Telephone (323) 442-
FAX (323) 442-
INTRODUCTION
The Biological Revolution has arrived! It’s been and remains thrilling for me! As I was completing my studies to become a dentist, during my seven years of private practice, or even during my years of postdoctoral education and training, I never would have imagined that I would have attended the Asilomar Conference held in Monterey, California, in 1975 when recombinant DNA guidelines were crafted. Imagine, establishing the rules and procedures for the human gene for insulin to be inserted into the genome of a bacteria, yeast, plant, or other animal, and that organism producing recombinant human insulin protein for the treatment of diabetes. Important human therapeutics (growth factors, hormones, antibodies, anti-microbial therapeutics, and a large array of other pharmaceuticals) could be produced from bacteria, yeast, plants and animals using the guidelines for recombinant DNA technology.
And my scientific journey continued. After successful production of antibodies to detect the major protein found in enamel, (amelogenin), and after success in identification of the messenger RNAs (mRNAs) for amelogenin, my laboratory, including Mal Snead, Maggie Zeichner-David, and Alan Fincham, and in collaborations with Savio Wu then at Baylor, would be the first to clone the mouse gene for amelogenin, the major protein found in the bioceramics identified as enamel. Along the way we discovered that the amelogenin gene produces multiple and different mRNA transcripts by a process termed ‘alternative splicing,’ and thereby produces multiple translation products or proteins of varying molecular weights.
And the unexpected dominated my career. By the late 1980s, we successfully identified and mapped the human amelogenin gene to both the X as well as Y chromosomes. This was an unexpected discovery---a variant of a functional gene encoded in two different chromosomes. We could explore the molecular explanation of X-linked amelogenesis imperfecta. Thereafter, we produced a recombinant amelogenin protein for studies of protein-protein interactions associated with the initiation and control of biomineralization. We asked “How does amelogenin function with respect to the crystal formation and growth associated with enamel?”
Independently, Mary MacDougall (at that time a graduate student working with Maggie Zeichner-David and myself) isolated and characterized the major non-collagenous protein found in dentin. She then cloned the gene and eventually mapped the gene to the chromosomal location responsible for dentinogenesis imperfecta. In the mid-1990s, I was invited by Don Chambers to celebrate the discovery of DNA by James Watson and Francis Crick in Chicago (and Rosalind Franklin, a dentist named Norman Simmons who prepared the DNA used by Franklin for her x-ray diffraction studies, and Maurice Wilkins), and I spoke of emerging opportunities in oral medicine to utilize the biological revolution’s fruits for the applications to diagnostics, treatments, therapeutics, and biomaterials (Donald A. Chambers, editor, DNA The Double Helix: Perspective and Prospective at Forty Years. Annals of the New York Academy of Sciences, Volume 758, 1995). At that time, I predicted the delivery of genetic therapeutics for oral fungal infections such as candidiasis, the production of oral mucosal lubricants for xerostomia, the oral delivery of systemic gene-based therapeutics, genetic approaches to the design and fabrication of dental tissues, the production of recombinant proteins such as bone morphogenetic proteins for tissue regeneration, the production of vaccines to manage human papilloma viral infections, and the utilization of gene-based diagnostics to identify craniofacial syndromes.
The Human Genome is Completed by October 2004
And there I was, after 5 wonderful years working within Harold Varmus’ leadership team at the NIH (1995-2000), my specific role being Director of the NIDCR, standing in the East Room of the White House as President Bill Clinton spoke and celebrated the first survey map of the Human Genome. It was June 26th 2000 and I was enormously proud of Francis Collins who led the Human Genome Project and our NIH coordinated efforts, and other federal agencies (Department of Energy, National Science Foundation), and scientists from a number of nations, for the exploration of the genes that regulate our human condition. That day the limelight was shared with Craig Venter who led the private sector Celera team that provided enormous competition in the race to complete the Human Genome. The following February 2001, around Valentine’s Day, both teams published their work---roughly 95% completion of the human genome; Francis’ team published in Nature and Venter’s team in Science. Then, as of October 2004, the entire Human Genome was completed. Imagine, 100% completion by 2004 - - -the 3.2 billion nucleotides or bases, annotated within 21,000 genes encoded within and mapped to specific locations in the 23 pair of human chromosomes, were identified. We now entered into “the Post-Genomic Era.” Essentially, a “parts list of life” was now available on the world wide web or in hardcopy. It was thrilling!
The Short-Term Dividends From the Human Genome
Francis Collins is now Director of the entire NIH enterprise. Back in 2000, when Francis was serving as Director of the Human Genome Project, he shared his predictions with NIH leadership as to where the biological revolution was going. According to Francis and his PowerPoint presentation of 2000, there will be six major themes delivered as dividends from the completion of the Human Genome:
Predictive genetic tests will be available for a dozen conditions;
Interventions to reduce risk will be available for several of these disorders;
Many primary-care providers will begin to practice genetic medicine;
Pre-implantation genetic diagnosis will be widely available, and its limits will be fiercely debated;
A ban on genetic discrimination will be in place in the United States; and
Access to genetic medicine will remain inequitable, especially in the developing world.
Importantly, all six of Francis’ predictions from the year 2000 have come true! It is also fair to assert that the promise of a biological revolution in human health remains very real. It is further valid that many of us overestimate the short-term impacts of new technologies and underestimate their long-term effects.
The Biological Revolution Continues
I have repeatedly learned that science informs clinical practice! Sometimes the translation of a basic discovery to eventually become a clinical activity or material takes time, lots of time; sometimes one or two decades and many millions of dollars expended for clinical trials. For over a century, scientific discoveries have been translated into diagnostics, treatments and procedures, therapeutics and materials that have revolutionized the oral health professions. Discoveries from physics, chemistry, and biology have been extraordinary over the past 100 years. The discovery of chemicals to achieve anesthesia revolutionized surgery. The discovery of x-rays led to radiology and how we image hard and soft tissue structures. The discovery of antimicrobial therapeutics profoundly changed clinic outcomes associated with acute and chronic infectious diseases – viral, bacterial, and yeast infections. A number of discoveries through adhesive chemistry led to sealants , an array of composite resins, and the bonding of porcelain to enamel. The discovery of fluoride and fluoridated drinking water to reduce the prevalence of tooth decay has been extraordinary. The discoveries from the digital revolution have and will continue to enhance how we see, how we take impressions, and how we design and fabricate restorations for tooth replacement. Science remains the fuel for innovations, applications, and the advances in clinical dentistry, medicine, pharmacy, and nursing.
Genomics 101
Following fertilization, the single cell contains the entire human genome, 21,000 functional genes and 19,000 psuedogenes, in the nucleus. In addition, a few dozen genes are inherited directly from our mothers via her transmission of the mitochondrial organelles within her ova. The mitochondria contains mitDNA. Genomics is the study of all of these genes and their interactions with one another as well as with the environment. These collective genes encoded within the nuclear DNA and the mitochondrial DNA represent “the parts list of life.”
Beyond the fertilized ovum, following a series of cell divisions, we eventually become mature adults consisting of 10,000,000,000,000,000 cells (ten trillion cells), each somatic cell containing the complete human genome. The length of DNA that encodes these genes within each somatic cell is approximately 6 feet in length. The functional genes encoded within the nucleus as well as the mitochondria produce a total of 100,000 different proteins and this is called “the proteome.”
Introducing “ –omics” in the Post-Genomic Era
How will we utilize the various “ –omics” in the oral health professions? First, let’s untangle some of the emerging terminology. In the emerging lexicon of “-omics,” we identify genomics, transcriptomics, proteomics, metabolomics, diseasomics, and pharmacogenomics. In these examples, “-omics” is used to modify a term based upon large databases that enable alignment and integration of enormous amounts of information. For example, genomics describes the complete set of genes in organisms in terms of gene structure and function(s) . Comparative genomics is the study of many diverse organisms - - - viral, bacterial, yeast, plant, and animal - - -for analyses in evolution, environmental studies, and/or in health and disease. Transcriptomics describes the total numbers of messenger RNA transcripts derived from genes. In humans, the process of alternative splicing results in multiple and diverse transcripts produced from a single gene. As humans contain 21,000 different functional genes in the nucleus of every somatic cell in the body, the number of transcripts (the transcriptomes) is far greater, likely exceeding 100,000 different mRNAs. Proteomics describes the total number of proteins produced from a particular genome. In humans, our proteome is greater than 200,000 different proteins. Metabolomics describes all the genes associated with metabolism, metabolism of nutrients as well as drugs. Genes encoded within chromosomes in the nucleus of every somatic cell in our body, as well as genes encoded within the mitochondrial DNA in the mitochondria directly inherited from our mothers, cooperatively regulate metabolism.
Diseasomics describes diseases and their relationship to genes, micro- and macroenvironments, and social determinants. This field of inquiry incorporates a taxonomy of networks that has the potential to unify various forms of databases. Biomedical researchers are attempting to redefine diseases by clustering or finding patterns and associations between different symptoms, signs, physiology, socioeconomic determinants, genes, protein and so much more. The various databases suggest that diseases often cluster within specific socioeconomic groups that further align with a number of risk factors associated with disease and disorder patterns. For example, analyses between children, poverty, diabetes, obesity, hypoglycemia, and hyper-insulin databases is starting to change nosology or the classification of disease.
Pharmacogenomics describes all genes that affect or are affected by pharmaceuticals such as non-steroid anti-inflammatory drugs, analgesics, and psychotropic drugs. These areas of exploration, and the plethora datasets reflecting the yield from the biological revolution of the last 60 years, clearly impact diagnostics, therapeutics, biomaterials, and clinical outcomes throughout the health professions including the oral health professions. I’m imagining the dividends from these quarters will significantly impact how we understand and manage autoimmune disorders, chronic facial pain, and xerostomia.
Personal Reflections Regarding the Biological Revolution
There is a nexus formed by the convergence of clinical medicine, clinical dentistry, and the biological revolution. The dividends from the discovery of DNA, recombinant DNA technology, and the emerging field identified by “ –omics” continue to change the human condition and how we advance as health professions.
Fundamental scientific discoveries were augmented by clinical observations that elucidated the inheritance of single-gene, or monogenic disorders, also known as Mendelian disorders since they are transmitted in a manner consonant with Mendel’s laws of inheritance. Today, the National Library of Medicine at the NIH in Bethesda, Maryland, hosts the online compendium known as Mendelian Inheritance in Man (OMIM) that has annotated more than 100 years of documented human genetic disorders. We now have many thousands of disorders and these can be readily accessed on the Internet or in hardcopy.
In tandem, a number of guidelines to ensure safety were adopted and offered to governments for the regulation of recombinant DNA technology. A few years later, the first biotechnology company was formed in Emeryville, California, based upon the discoveries of how to produce recombinant protein products such as human recombinant insulin for the treatment of diabetes. Today, the United States has more than 4,000 biotechnology companies utilizing these technologies and producing more than 64 billion dollars each year.
As we look to our futures, the future of the oral health professions, I suggest we ask ourselves a simple question. “Are we ready for the dividends from the biological revolution?” Are we allocating resources to educate and train for the future, a future that offers the promise of gene therapies, increased cell, tissue and organ regeneration, an integration between digital and biological ways of knowing, and so much more. Are we ready?
References
Slavkin, H.C. (in press) Birth of a Discipline: Craniofacial Biology. Aegis Communications, Newtown, Pennsylvania.
Slavkin H.C. (2011) Biotechnology in Dentistry: Advances in Genomics, Biomimetics and Tissue Engineering. In Dental Horizons: Essentials of Oral Health (edited by Rajiv Saini and Santosh Saini), Paras Medical Publisher, New Delhi, India, pp. 276-287.
Chai Y, Lee M, Slavkin, HC, Warburton D (2011) Regulation of Embryogenesis. In: Fetal and Neonatal Physiology. Fourth Edition (eds. R. Polin, W. Fox and S. Abman) Philadelphia, PA: WB Saunders Co.
Slavkin H.C., Navazesh M, Patel P. (2008) Basic principles of human genetics: a primer for oral medicine. In Burket's Oral Medicine. 11 ed. (eds. Greenberg M, Glick M, Ship J) Hamilton, Ontario: BC Decker Inc. pp 549-568.
Slavkin, H.C. (2002). Molecules and Faces: What is on the Horizon? In: Understanding Craniofacial Anomalies (eds. Mooney, M. and Siegel, M.). John Wiley and Sons, New York, pp.549-560
Shum L, Takahashi K, Takahashi I, Nagata M, Tanaka O, Semba I, Tan DP, Nuckolls GH, and Slavkin, HC. (2000) Embryogenesis and the Classification of Craniofacial Dysmorphogenesis. In: Oral and Maxillofacial Surgery, Vol. 6. (eds. Baker, SB and Fonseca, RJ). W.B. Saunders Co., pp149-158.
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Cohen W., Slavkin H.C. (1999) Periodontal Disease and Systemic Disease. In: Periodontal Medicine (eds. Genco R, Mealey B, Cohen W, Rose L). B.C. Decker, Inc. pp. 1-8