One of the remaining unanswered mysteries in human biology is the identity of the genes are responsible for the lighter skin of East Asians. The goal of this revision application of AR052535, entitled Genetic analysis of genomic instability and cancer in zebrafish is to work towards finding one or more of those genes. Solving this mystery will be a major contribution towards understanding basic mechanisms of human pigmentation, a phenotype of profound influence to human welfare. This work will also be important to our understanding of human skin cancer, since the light skin mechanisms of Europeans confer greater susceptibility to cancer than the mechanisms in East Asians and Amerindians. This collaborative and interdisciplinary project combines the power of a developmental model, the zebrafish, with the power of systems biology. This will be accomplished through the coordinated work of a team that includes the lab of a second NIH-funded investigator, Dr. Ross Hardison, whose expertise is the development of bioinformatics tools for discovery of functional, noncoding sequences. This work will be accomplished in three related specific aims that are extensions of ongoing work in both labs.
Specific Aim 1 is to take a systems approach to identifying coding and noncoding sequences of potential functional importance in East Asians.
This aim will be accomplished using tools 1) developed in the course of discovery of a functionally important coding single nucleotide polymorphism (SNP) in SLC24A5, which appears to have played an important role in the evolution of light skin in European populations, 2) developed and being developed in the Hardison lab for studying noncoding sequences. The results of these analyses will correlate SNPs of high frequency distinction between East Asian (CHB and JPT) and African (YRI) HapMap populations that are associated with large regions of reduced heterozygosity.
Specific Aim 2 is to map East Asian pigment genes using whole-genome SNP and copy number analysis. The first part of this aim will be to obtain human skin reflectance measurements and DNA from the saliva of individuals in families and unrelated individuals from populations of East Asian (or Amerindian)/African admixture. Initial whole genome SNP/copy number analysis will be done using the highly reliable Illumina platform, to map candidate regions defined by regions of diminished heterozygosity in individuals of the most extreme skin color variation, focusing on SNPs whose ancestral allele is in the African HapMap population. The relevant populations have been found by the PI and specific communities were found by collaborators in the University of West Indies and Oxford University.
Specific Aim 3 will be to test the most promising candidates for pigmentary function by tissue localization (whole mount in situ) and antisense morpholino knock-down analysis in zebrafish. Within the year, we will have completed collaborative bioinformatics analysis, find candidate East Asian genes by genetic mapping, and test candidate genes using functional studies in zebrafish. Even early discussion has led the investigators to realize that the work will greatly enhance both of the NIH-funded projects in the course of fine tuning and validating a new systems genetics approach for the study of quantitative traits in humans. This work can also be expected to contribute towards the missions of multiple Institutes at the National Institutes of Health. ? ? ?
The goal of this revision application is to find one or more of the genes responsible for the lighter skin of East Asians. Solving this mystery will be a major contribution towards understanding basic mechanisms of human pigmentation, a phenotype of profound influence to human welfare. This work will also be important to our understanding of human skin cancer, since the light skin mechanisms of Europeans confer greater susceptibility to skin cancer than those of East Asians and Amerindians.
| Canfield, Victor A; Berg, Arthur; Peckins, Steven et al. (2013) Molecular phylogeography of a human autosomal skin color locus under natural selection. G3 (Bethesda) 3:2059-67 |
| Ang, Khai C; Ngu, Mee S; Reid, Katherine P et al. (2012) Skin color variation in Orang Asli tribes of Peninsular Malaysia. PLoS One 7:e42752 |
| Cheng, Keith C; Hinton, David E; Mattingly, Carolyn J et al. (2012) Aquatic models, genomics and chemical risk management. Comp Biochem Physiol C Toxicol Pharmacol 155:169-73 |
| Tsetskhladze, Zurab R; Canfield, Victor A; Ang, Khai C et al. (2012) Functional assessment of human coding mutations affecting skin pigmentation using zebrafish. PLoS One 7:e47398 |
| Cheng, Keith C; Xin, Xuying; Clark, Darin P et al. (2011) Whole-animal imaging, gene function, and the Zebrafish Phenome Project. Curr Opin Genet Dev 21:620-9 |
| Cheng, Keith C (2008) Skin color in fish and humans: impacts on science and society. Zebrafish 5:237-42 |
