Gene Discovery for Craniofacial Disorders

Cellular and Molecular Biology, Physiology and Biotechnology Branch
Division of Basic and Translational Sciences

OBJECTIVE

We are seeking Concept Clearance for a Request for Applications (RFA) aimed at fostering creative approaches for the discovery of genes that cause or modify susceptibility to craniofacial, dental and oral disorders.  This initiative will encourage research projects focused on identifying genes that produce craniofacial disorders, modifier genes that influence risk, and environmental conditions that alter gene expression and modify susceptibility in diverse genetic backgrounds.

Advances in genetic studies will reveal the molecular networks that regulate the formation of craniofacial and dental tissues and will shed light on pathogenic mechanisms leading to structural defects and disorders.  These advances will provide a basis for gene-based diagnostic criteria, improved genetic counseling, and they will provide insights for developing novel prevention and therapeutic strategies.

BACKGROUND

Birth defects affect 5% of all infants born in the United States, and three-quarters of these involve the head, face and oral tissues.  This means that in the United States there is a child born every 5 minutes with a craniofacial defect.  While there are several hundred disorders affecting the face, skull, jaws and teeth, by far the most common craniofacial defect is isolated, or non-syndromic cleft lip with or without cleft palate (CL/P) that affects more than one child per 1000 births.  Other hereditary syndromes such as ectodermal dysplasias are marked by the absence of all or most teeth in children and adults, and lead to lifelong health problems.  The social and economic costs of craniofacial disorders are enormous and they place a disproportionately high burden on particular population subgroups.

The current initiative is the result of recommendations from several prior NIDCR-supported conferences focused on craniofacial disorders and genetics.  These meetings highlighted the major scientific opportunities created by the wealth of genomic information from the Human and Mouse Genome Projects for the discovery of genes involved in craniofacial disorders.  These meetings include: (1) the Workshop on the Prevention of Craniofacial Anomalies, held in September 1999, in Bethesda, Maryland, and sponsored by the NIDCR, Office of Rare Diseases and Office of Dietary Supplements (NIH) and the American Cleft Palate/Craniofacial Association;  (2) the NIDCR Genetics Work Group held in November 1999 in Bethesda, Maryland; and (3) a series of three NIDCR-sponsored World Health Organization meetings “International Collaborative Research on Craniofacial Anomalies” held in 2000-2001 in Geneva, Switzerland, Salt Lake City, Utah and Baura, Brazil. 

In the past decade, there has been significant progress in identifying many single-gene defects that cause craniofacial disorders (i.e., hypohidrotic ectodermal dysplasia, dentinogenesis imperfecta II, Papillon-Lefevre syndrome, DiGeorge syndrome, Treacher Collins syndrome, Apert syndrome,  hypodontia/tooth agenesis). The mode of inheritance for these single-gene disorders conforms to Mendelian rules of segregation.  In contrast, progress has been much slower for the more common craniofacial disorders such as non-syndromic cleft lip/palate (CL/P).  Complex disorders such as CL/P are caused by multiple genes interacting with each other and with environmental factors.  The search for novel genes influencing susceptibility to complex craniofacial disorders has often yielded inconsistent results.  This may be due in part, to our current lack of understanding of the role of genetic polymorphisms in response to environmental factors.  Genetic analysis may also be hampered by the use of disease categories that combine phenotypes of different severity (i.e., CL/P), which may represent genetically heterogeneous defects.

Many of the genes that have been implicated in craniofacial disorders affect basic biological processes such as patterning, cell adhesion, signaling, and cell movement.  Craniofacial malformations are often accompanied by defects in the brain, heart, fingers and toes since these same genes control the growth and differentiation of cells destined for many other tissues.

Recent science advances have considerably expanded the genes known to be involved in clefting¹.  A NIDCR-supported team led by Richard Spritz identified PVRL1 as the gene responsible for a rare autosomal recessive clefting syndrome associated with ectodermal dysplasia (CLPED1) in an isolated island population². That finding was followed by a report demonstrating an association between heterozygote carriers of the PVRL1 allele and the common, non-syndromic form of clefting³.   PVRL1 encodes a cell adhesion molecule that also serves as a receptor for herpes virus.   A second clefting advance identified mutations in the T-box transcription factor, TBX22, as the cause of a rare X-linked syndrome, CPX, in which isolated cleft palate is associated with tongue-tie⁴.  Members of the T-box gene family have been implicated in mesodermal specification during early development.  More recently, the SKI proto-oncogene has been shown to play a role in the human 1p36 deletion syndrome which is associated with oral clefting in about 15% of patients⁵.  Mice carrying the Ski null mutation show a shift in phenotype from midline facial clefting to the neural tube defect exencephaly, depending on the genetic background of the mice.  This study provides further evidence linking facial clefting and neural tube defects^6,7and, in addition, it indicates that modifier genes influence the type of craniofacial defects resulting from mutations in the Ski gene.

The types of research that would be encouraged by the proposed initiative include:

• Discovery of genes involved in single-gene or multigenic disorders that affect dental, oral, and craniofacial tissues throughout the lifespan.
• Genotype-phenotype analysis including correlations of specific allelic variants in primary or modifier genes and their clinical phenotype.
• Studies focused on distinguishing heterogeneous genetic subgroups that show similar clinical presentations.
• Research strategies for gene discovery for craniofacial disorders may include traditional linkage analysis, case-control association studies, linkage disequilibrium mapping, candidate gene analyses, positional cloning techniques, SNP variant analyses, gene expression profiling and proteomics using microarray and other high-throughput technologies.
• Studies in model organisms( e.g., mouse, rat, zebrafish, chick) for identifying and validating candidate and modifier genes, and for analyzing molecular mechanisms that underlie genetic malformations are encouraged as research indicates that key molecules involved in facial specification and assembly are evolutionarily conserved.
• Backcross strategies such as speed congenics for mapping susceptibility loci and evaluating modifier genes that influence penetrance and expressivity.

High-throughput human and mouse genotyping services will be available to applicants through the Center for Inherited Disease Research (CIDR).  Since NIDCR is one of the NIH Institutes participating in the support of CIDR, research projects funded under this initiative are eligible to apply for no-cost genotyping services at CIDR through a competitive peer review process. 

This initiative will encourage multidisciplinary approaches involving epidemiologists, geneticists, molecular biologists, dental and medical clinicians, bioinformaticians, and other researchers in order to enhance gene discovery research.

Moreover, applicants will be strongly encouraged to develop comprehensive operational diagnostic criteria that include state-of-the-art diagnostic methodologies such as imaging techniques. Diagnostic criteria for many rare craniofacial disorders are highly variable and thus hamper attempts to combine data across samples and to replicate findings. Analysis of genetic and environmental etiologies for complex traits such as clefting, will benefit from the application of sophisticated methodologies that permit phenotypic subgroups to be distinguished.

CURRENT PORTFOLIO OVERVIEW

The current NIDCR portfolio includes broad coverage of many areas of genetics research focused on craniofacial, tooth and bone disorders and development. There are, however, many gap areas that need to be addressed which will benefit from the current initiative. These areas include: 1) the discovery of causal genes that are, as yet, unidentified for many craniofacial disorders; 2) research correlating allelic variants and phenotype; and 3)  studies that establish the risk of craniofacial anomalies associated with gene variants, gene/gene interactions, and gene/environment interactions.

FUNDING MECHANISMS

The proposed RFA will utilize the Investigator Initiated Research Project Grant (R01) and the Exploratory/Developmental Research Grant (R21) funding mechanisms.

REFERENCES

1. Murray, J.C. Time for T.  Nature Genet. 29, 107-109 (2001).
2. Suzuki K, Hu D, Bustos T, Zlotogora J, Richieri-Costa A, Helms JA, Spritz RA. Mutations of PVRL1, encoding a cell-cell adhesion molecule/herpesvirus receptor, in cleft lip/palate-ectodermal dysplasia. Nature Genet. 25, 427-430 (2000).
3. Sozën MA, Suzuki K, Tolarova MM, Bustos T, Fernandez Iglesias JE, Spritz RA.
4. Mutation of PVRL1 is associated with sporadic, non-syndromic cleft lip/palate in northern Venezuela.Nature Genet. 29, 141-142 (2001).
5. Braybrook C, Doudney K, Marçano AB, Arnason A, Bjornsson A, Patton MA, Goodfellow PJ, Gudrun EM, & Stanier P.  The T-box transcription factor gene TBX22 is mutated in X-linked cleft palate and ankyloglossia. Nature Genet. 29,  179-183 (2001).
6. Colmenares, C, Heilstedt, HA, Shaffer, LG, Schwartz, S, Berk, M, Murray, JC, & Stavnezer, E. Loss of the SKI proto-oncogene in individuals affected with 1p36 deletion syndrome is predicted by strain-dependent defects in Ski -/- mice.  Nature Genet. 30, 106-109 (2002).
7. Harris MJ & Juriloff DM.  Mini-review: toward understanding mechanisms of genetic neural tube defects in mice. Teratology 60, 292-305 (1999)
8. Juriloff DM, Harris MJ, Gunn TM, Wu MK, Mah DG, Dewell SL. Liability loci for multifactorial cleft lip and palate map to the same chromosomal locations as liability loci for multifactorial neural tube closure defects in mice. Abstr. Am J Human Genetics 69, 533 (2001).