Neural crest cells are an embryonic structure unique to vertebrates that gives rise to multiple lineages including the pigment-producing melanocytes. Pigmentation, defined as the placement of pigment in skin, hair, and eyes for coloration, is distinctive because the location, amount, and type of pigmentation provides a visual manifestation of genetic heterogeneity in pathways regulating the pigment-producing cells. The scope of this genetic heterogeneity ranges from normal to pathological pigmentation phenotypes. Clinically, normal human pigmentation encompasses a variety of skin and hair color as well as punctate pigmentation such as melanocytic nevi (moles) or ephelides (freckles), while abnormal human pigmentation exhibits markedly reduced or increased pigment levels, known as hypopigmentation and hyperpigmentation, respectively. Elucidation of the molecular genetics underlying pigmentation has revealed genes important for melanocyte development and function. Furthermore, many pigmentation disorders show additional defects in cells other than melanocytes, and identification of the genetic insults in these disorders has revealed pleiotropism, where a single gene is required for various functions in different cell types. Thus, unraveling the genetics of easily visualized pigmentation disorders has identified molecular similarities between melanocytes and less visible cell types/tissues, arising from a common developmental origin and/or shared genetic regulatory pathways. We utilize a variety of genetic and genomic approaches to discover the etiology of human pigmentation disorders, often focusing on the fact that the developmental mutations disrupting pigmentation are instructive for understanding abnormal pathways governing related disorders. 1. Melanoma, skin cancer of melanocytes. We have previously shown that the transcription factor SOX10 is essential for survival and proper differentiation of neural crest cell lineages, where it plays an important role in the generation and maintenance of melanocytes. SOX10 is also highly expressed in melanoma tumors. The complex genetic changes underlying metastatic melanoma need to be deciphered to develop new and effective therapeutics. Previously, genome-wide microarray analyses of human melanoma identified two reciprocal gene expression programs, including transcripts regulated by either transforming growth factor, beta 1 (TGFβ1) pathways, or microphthalmia-associated transcription factor (MITF)/SRY-box containing gene 10 (SOX10) pathways. We extended this knowledge by discovering that melanoma cell lines with these two expression programs exhibit distinctive microRNA (miRNA) expression patterns. We also demonstrated that hypoxia-inducible factor 1 alpha (HIF1A) is increased in TGFβ1 pathway-expressing melanoma cells and that HIF1A upregulates miR-210, miR-218, miR-224, and miR-452. Reduced expression of these four miRNAs in TGFβ1 pathway-expressing melanoma cells arrests the cell cycle, while their overexpression in mouse melanoma cells increases the expression of the hypoxic response gene Bnip3. Taken together, these data suggest that HIF1A may regulate some of the gene expression and biological behavior of TGFβ1 pathway-expressing melanoma cells, in part via alterations in these four miRNAs. 2. Genomics of melanocyte gene regulation. SOX10 is required for melanocyte development and maintenance, and has been linked to melanoma initiation and progression. However, the molecular mechanisms by which SOX10 guides the appropriate gene expression programs necessary to promote the melanocyte lineage are not fully understood. We employed genetic and epigenomic analysis approaches to uncover novel genomic targets and previously unappreciated molecular roles of SOX10 in melanocytes. Through global analysis of SOX10-binding sites and epigenetic characteristics of chromatin states, we uncover an extensive catalog of SOX10 targets genome-wide. Our findings reveal that SOX10 predominantly engages 'open' chromatin regions and binds to distal regulatory elements, including novel and previously known melanocyte enhancers. Integrated chromatin occupancy and transcriptome analysis suggest a role for SOX10 in both transcriptional activation and repression to regulate functionally distinct classes of genes. We demonstrate that distinct epigenetic signatures and cis-regulatory sequence motifs predicted to bind putative co-regulatory transcription factors define SOX10-activated and SOX10-repressed target genes. Collectively, these findings uncover a central role of SOX10 as a global regulator of gene expression in the melanocyte lineage by targeting diverse regulatory pathways.

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17
Fiscal Year
2015
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Human Genome Research
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Harris, Melissa L; Fufa, Temesgen D; Palmer, Joseph W et al. (2018) A direct link between MITF, innate immunity, and hair graying. PLoS Biol 16:e2003648
Loftus, Stacie K; Baxter, Laura L; Cronin, Julia C et al. (2017) Hypoxia-induced HIF1? targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis. Pigment Cell Melanoma Res 30:339-352
Watkins-Chow, Dawn E; Varshney, Gaurav K; Garrett, Lisa J et al. (2017) Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Injection. G3 (Bethesda) 7:719-722
Crawford, Nicholas G; Kelly, Derek E; Hansen, Matthew E B et al. (2017) Loci associated with skin pigmentation identified in African populations. Science 358:
Seberg, Hannah E; Van Otterloo, Eric; Loftus, Stacie K et al. (2017) TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF. PLoS Genet 13:e1006636
Saldana-Caboverde, Amy; Perera, Erasmo M; Watkins-Chow, Dawn E et al. (2015) The transcription factors Ets1 and Sox10 interact during murine melanocyte development. Dev Biol 407:300-12
Fufa, Temesgen D; Harris, Melissa L; Watkins-Chow, Dawn E et al. (2015) Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. Hum Mol Genet 24:5433-50
Hwang, Hun-Way; Baxter, Laura L; Loftus, Stacie K et al. (2014) Distinct microRNA expression signatures are associated with melanoma subtypes and are regulated by HIF1A. Pigment Cell Melanoma Res 27:777-87
Fufa, Temesgen D; Pavan, William J (2014) Axing the cancer loop. Pigment Cell Melanoma Res 27:691-3
Watkins-Chow, Dawn E; Cooke, Joanna; Pidsley, Ruth et al. (2013) Mutation of the diamond-blackfan anemia gene Rps7 in mouse results in morphological and neuroanatomical phenotypes. PLoS Genet 9:e1003094

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