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Transcription factor CgPOU3F4-like regulates expression of pheomelanin synthesis related gene CgB-aat1 in the Pacific oyster (Crassostrea gigas). Gene 2023; 861:147258. [PMID: 36754175 DOI: 10.1016/j.gene.2023.147258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/24/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023]
Abstract
Previous study has found that b (0, +) -type amino acid transporter 1 (CgB-aat1) plays an essential role on mantle pigmentation in the Pacific oyster Crassostrea gigas. However, the molecular regulation of CgB-aat1 gene expression remains unclear. Herein, three POU domain family members, CgPOU2F1, CgPOU3F4-like and CgPOU4F3-X1 were characterized and they all had POUs and HOX domains, respectively, which were important in transcriptional regulation. CgPOU3F4-like gene expression was the highest in mantle edge. Subsequently, the dual-luciferase reporter result showed that the core regulatory region of CgB-aat1 gene was from -632 to -350 bp of promoter. In transient co-transfection assays, the strongest activity was activated only by CgPOU3F4-like, suggesting CgPOU3F4-like was a valid transcriptional activator of CgB-aat1 gene promoter. And the structural integrity of CgPOU3F4-like was essential for its activation function. In addition, site directed mutagenesis assay was applied to detect three key binding sites between CgPOU3F4-like and core region of CgB-aat1 gene promoter, and this interaction was verified by ChIP test. Furthermore, CgPOU3F4-like knockdown by RNA interference led to obvious decreases in CgB-aat1 and cystathionine beta-synthase (CgCbs) expressions at both mRNA and protein levels. Collectively, these results indicate that CgPOU3F4-like positively regulate CgB-aat1 gene expression and it may be a critical upstream transcriptional regulation factor in pheomelanin synthesis in C. gigas.
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Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks. Genes (Basel) 2022; 13:genes13081391. [PMID: 36011302 PMCID: PMC9407491 DOI: 10.3390/genes13081391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 02/05/2023] Open
Abstract
Shin color diversity is a widespread phenomenon in birds. In this study, ducks were assessed to identify candidate genes for yellow, black, and spotted tibiae. For this purpose, we performed whole-genome resequencing of an F2 population consisting of 275 ducks crossed between Runzhou crested-white ducks and Cherry Valley ducks. We obtained 12.6 Mb of single nucleotide polymorphism (SNP) data, and the three shin colors were subsequently genotyped. Genome-wide association studies (GWASs) were performed to identify candidate and potential SNPs for the three shin colors. According to the results, 2947 and 3451 significant SNPs were associated with black and yellow shins, respectively, and six potential SNPs were associated with spotted shins. Based on the SNP annotations, the MITF, EDNRB2, POU family members, and the SLC superfamily were the candidate genes regulating pigmentation. In addition, the isoforms of EDNRB2, TYR, TYRP1, and MITF-M were significantly different between the black and yellow tibiae. MITF and EDNRB2 may have synergistic roles in the regulation of melanin synthesis, and their mutations may lead to phenotypic differences in the melanin deposition between individuals. This study provides new insights into the genetic factors that may influence tibia color diversity in birds.
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Affiliation(s)
- Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Analysis Identifies Candidate Genes Encoding Beak Color of Duck. Genes (Basel) 2022; 13:1271. [PMID: 35886054 PMCID: PMC9322730 DOI: 10.3390/genes13071271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/04/2022] Open
Abstract
Beak color diversity is a broadly occurring phenomenon in birds. Here, we used ducks to identify candidate genes for yellow, black, and spotted beaks. For this, an F2 population consisting of 275 ducks was genotyped using whole genome resequencing containing 12.6 M single-nucleotide polymorphisms (SNPs) and three beak colors. Genome-wide association studies (GWAS) was used to identify the candidate and potential SNPs for three beak colors in ducks (yellow, spotted, and black). The results showed that 2753 significant SNPs were associated with black beaks, 7462 with yellow, and 17 potential SNPs with spotted beaks. Based on SNP annotation, MITF, EDNRB2, members of the POU family, and the SLC superfamily were the candidate genes regulating pigmentation. Meanwhile, isoforms MITF-M and EDNRB2 were significantly different between black and yellow beaks. MITF and EDNRB2 likely play a synergistic role in the regulation of melanin synthesis, and their mutations contribute to phenotypic differences in beak melanin deposition among individuals. This study provides new insights into genetic factors that may influence the diversity of beak color.
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Affiliation(s)
- Qixin Guo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yong Jiang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Zhixiu Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yulin Bi
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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Min Y, Li Q, Yu H. Heme-Peroxidase 2 Modulated by POU2F1 and SOX5 is Involved in Pigmentation in Pacific Oyster (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:263-275. [PMID: 35275290 DOI: 10.1007/s10126-022-10098-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Color polymorphism is frequently observed in molluscan shellfish, while the molecular regulation of shell pigmentation is not well understood. Peroxidase is a key enzyme involved in melanogenesis. Here, we identified a heme-peroxidase 2 gene (CgHPX2), and characterized the expression patterns and transcriptional regulation of CgHPX2 in the Pacific oyster Crassostrea gigas. Tissues expression analysis showed that CgHPX2 was a mantle-specific gene and primarily expressed in the edge mantle in black shell color oyster compared with white shell oyster. In situ hybridization showed that strong signals for CgHPX2 were detected in the both inner and outer surface of the outer fold of mantle in the black shell color oyster, whereas positive signals in white shell oyster were mainly localized in the outer surface of the outer fold of mantle. In the embryos and larvae, a high expression level of CgHPX2 was detected in the trochophore stage in both black and white shell color oysters. The temporal localization of CgHPX2 was mainly detected in the shell gland and edge mantle of trochophore and calcified shell larvae, respectively. In addition, a 2227 bp of 5' flanking region sequence of CgHPX2 was cloned, which contained a presumed core promoter region and many potential transcription factor binding sites. Further luciferase assay experiment confirmed that POU domain, class 2, transcription factor 1 (POU2F1), and SRY-box transcription factor 5 (SOX5) were involved in transcriptional regulation of CgHPX2 gene through binding to its specific promoter region. After CgPOU2F1 and CgSOX5 RNA interference, the CgHPX2 gene expression was significantly decreased. These results suggested that CgPOU2F1 and CgSOX5 might be two important transcription factors that positively regulated the expression of CgHPX2 gene, improving our understanding of the transcriptional regulation of molluscan shell pigmentation.
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Affiliation(s)
- Yue Min
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education College of Fisheries, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education College of Fisheries, Ocean University of China, Qingdao, 266003, China
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Liu H, Wang J, Hu J, Wang L, Guo Z, Fan W, Xu Y, Liu D, Zhang Y, Xie M, Tang J, Huang W, Zhang Q, Zhou Z, Hou S. Genome-wide association analysis reveal the genetic reasons affect melanin spot accumulation in beak skin of ducks. BMC Genomics 2022; 23:236. [PMID: 35346029 PMCID: PMC8962612 DOI: 10.1186/s12864-022-08444-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/25/2022] [Indexed: 12/18/2022] Open
Abstract
Abstract
Background
Skin pigmentation is a broadly appearing phenomenon of most animals and humans in nature. Here we used a bird model to investigate why melanin spot deposits on the skin.
Results
Our result showed that growth age and the sunlight might induce melanin deposition in bird beak skin which was determined by genetic factors. GWAS helped us to identify two major loci affecting melanin deposition, located on chromosomes 13 and 25, respectively. The fine mapping works narrowed the candidate regions to 0.98 Mb and 1.0 Mb on chromosomes 13 and 25. The MITF and POU2F3 may be the causative genes and synergistically affect melanin deposition during duck beak skin. Furthermore, our data strongly demonstrated that the pathway of melanin metabolism contributes to melanin deposition on the skin.
Conclusions
We demonstrated that age and sunlight induce melanin deposition in bird beak skin, while heredity is fundamental. The MITF and POU2F3 likely played a synergistic effect on the regulation of melanin synthesis, and their mutations contribute to phenotypic differences in beak melanin deposition among individuals. It is pointed out that melanin deposition in the skin is related to the pathway of melanin metabolism, which provided insights into the molecular regulatory mechanisms and the genetic improvement of the melanin deposition in duck beak.
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Heppt MV, Wessely A, Hornig E, Kammerbauer C, Graf SA, Besch R, French LE, Matthies A, Kuphal S, Kappelmann-Fenzl M, Bosserhoff AK, Berking C. HDAC2 Is Involved in the Regulation of BRN3A in Melanocytes and Melanoma. Int J Mol Sci 2022; 23:ijms23020849. [PMID: 35055045 PMCID: PMC8778714 DOI: 10.3390/ijms23020849] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
The neural crest transcription factor BRN3A is essential for the proliferation and survival of melanoma cells. It is frequently expressed in melanoma but not in normal melanocytes or benign nevi. The mechanisms underlying the aberrant expression of BRN3A are unknown. Here, we investigated the epigenetic regulation of BRN3A in melanocytes and melanoma cell lines treated with DNA methyltransferase (DNMT), histone acetyltransferase (HAT), and histone deacetylase (HDAC) inhibitors. DNMT and HAT inhibition did not significantly alter BRN3A expression levels, whereas panHDAC inhibition by trichostatin A led to increased expression. Treatment with the isoform-specific HDAC inhibitor mocetinostat, but not with PCI-34051, also increased BRN3A expression levels, suggesting that class I HDACs HDAC1, HDAC2, and HDAC3, and class IV HDAC11, were involved in the regulation of BRN3A expression. Transient silencing of HDACs 1, 2, 3, and 11 by siRNAs revealed that, specifically, HDAC2 inhibition was able to increase BRN3A expression. ChIP-Seq analysis uncovered that HDAC2 inhibition specifically increased H3K27ac levels at a distal enhancer region of the BRN3A gene. Altogether, our data suggest that HDAC2 is a key epigenetic regulator of BRN3A in melanocytes and melanoma cells. These results highlight the importance of epigenetic mechanisms in regulating melanoma oncogenes.
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Affiliation(s)
- Markus V. Heppt
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (A.W.); (C.B.)
- Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Correspondence: ; Tel.: +49-9131-85-35747
| | - Anja Wessely
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (A.W.); (C.B.)
- Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Eva Hornig
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80337 Munich, Germany; (E.H.); (C.K.); (S.A.G.); (R.B.); (L.E.F.)
| | - Claudia Kammerbauer
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80337 Munich, Germany; (E.H.); (C.K.); (S.A.G.); (R.B.); (L.E.F.)
| | - Saskia A. Graf
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80337 Munich, Germany; (E.H.); (C.K.); (S.A.G.); (R.B.); (L.E.F.)
| | - Robert Besch
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80337 Munich, Germany; (E.H.); (C.K.); (S.A.G.); (R.B.); (L.E.F.)
| | - Lars E. French
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80337 Munich, Germany; (E.H.); (C.K.); (S.A.G.); (R.B.); (L.E.F.)
| | - Alexander Matthies
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (A.M.); (S.K.); (A.K.B.)
| | - Silke Kuphal
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (A.M.); (S.K.); (A.K.B.)
| | | | - Anja K. Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (A.M.); (S.K.); (A.K.B.)
| | - Carola Berking
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (A.W.); (C.B.)
- Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
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Jung J. Characterizing therapeutic signatures of transcription factors in cancer by incorporating profiles in compound treated cells. Bioinformatics 2021; 37:1008-1014. [PMID: 32886093 DOI: 10.1093/bioinformatics/btaa765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Cancers are promoted by abnormal alterations in biological processes, such as cell cycle and apoptosis. An immediate reason for those aberrant processes is the deregulation of their involved transcription factors (TFs). Thus, the deregulated TFs in cancer have been experimented as successful therapeutic targets, such as RARA and RUNX1. This therapeutic strategy can be accelerated by characterizing new potential TF targets. RESULTS Two kinds of therapeutic signatures of TFs in A375 (skin) and HT29 (colon) cancer cells were characterized by analyzing TF activities under effective and ineffective compounds to cancer. First, the therapeutic TFs (TTs) were identified as the TFs that are significantly activated or repressed under effective compared to ineffective compounds. Second, the therapeutically correlated TF pairs (TCPs) were determined as the TF pairs whose activity correlations show substantial discrepancy between the effective and ineffective compounds. It was facilitated by incorporating (i)compound-induced gene expressions (LINCS), (ii) compound-induced cell viabilities (GDSC) and (iii) TF-target interactions (TRUST2). As a result, among 627 TFs, the 35 TTs (such as MYCN and TP53) and the 214 TCPs (such as FOXO3 and POU2F2 pair) were identified. The TTs and the proteins on the paths between TCPs were compared with the known therapeutic targets, tumor suppressors, oncogenes and CRISPR-Cas9 knockout screening, which yielded significant consequences. We expect that the results provide good candidates for therapeutic TF targets in cancer. AVAILABILITY AND IMPLEMENTATION The data and Python implementations are available at https://github.com/jmjung83/TT_and_TCP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jinmyung Jung
- Division of Data Science, College of Information and Communication Technology, The University of Suwon, Hwaseong 18323, Republic of Korea
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Liu L, Yue Q, Ma J, Liu Y, Zhao T, Guo W, Zhu G, Guo S, Wang S, Gao T, Li C, Shi Q. POU4F1 promotes the resistance of melanoma to BRAF inhibitors through MEK/ERK pathway activation and MITF up-regulation. Cell Death Dis 2020; 11:451. [PMID: 32532957 PMCID: PMC7293281 DOI: 10.1038/s41419-020-2662-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/23/2022]
Abstract
BRAF inhibitors (BRAFi) have shown remarkable clinical efficacy in the treatment of melanoma with BRAF mutation. Nevertheless, most patients end up with the development of BRAFi resistance, which strongly limits the clinical application of these agents. POU4F1 is a stem cell-associated transcriptional factor that is highly expressed in melanoma cells and contributes to BRAF-activated malignant transformation. However, whether POU4F1 contributes to the resistance of melanoma to BRAFi remains poorly understood. Here, we report that over-expressed POU4F1 contributed to the acquired resistance of melanoma cells to Vemurafenib. Furthermore, POU4F1 promoted the activation of ERK signaling pathway via transcriptional regulation on MEK expression. In addition, POU4F1 could increase the expression of MITF to retain the resistance of melanoma cells to BRAFi. Collectively, our findings reveal that POU4F1 re-activates the MAPK pathway by transcriptional regulation on MEK expression and promotes MITF expression, which ultimately results in the resistance to BRAFi in melanoma. Our study supports that POU4F1 is a potential combined therapeutic target with BRAFi therapy for melanoma.
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Affiliation(s)
- Lin Liu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Qiao Yue
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Jingjing Ma
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Yu Liu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Tao Zhao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Weinan Guo
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Guannan Zhu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Sen Guo
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Shiyu Wang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Tianwen Gao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Chunying Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China.
| | - Qiong Shi
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China.
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Larribère L, Utikal J. Stem Cell-Derived Models of Neural Crest Are Essential to Understand Melanoma Progression and Therapy Resistance. Front Mol Neurosci 2019; 12:111. [PMID: 31118886 PMCID: PMC6506783 DOI: 10.3389/fnmol.2019.00111] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/15/2019] [Indexed: 11/13/2022] Open
Abstract
During development, neural crest (NC) cells are early precursors of several lineages including melanocytes. Along their differentiation from multipotent cells to mature melanocytes, NC cells will go through successive steps which require either proliferative or motile capacities. For example, they will undergo Epithelial to Mesenchymal Transition (EMT) in order the separate from the neural tube and migrate to their final location in the epidermis (Larribere and Utikal, 2013; Skrypek et al., 2017). The differentiated melanocytes are the cells of origin of melanoma tumors which progress through several stages such as radial growth phase, vertical growth phase, metastasis formation, and often resistance to current therapies. Interestingly, depending on the stage of the disease, melanoma tumor cells share phenotypes with NC cells (proliferative, motile, EMT). These phenotypes are tightly controlled by specific signaling pathways and transcription factors (TFs) which tend to be reactivated during the onset of melanoma. In this review, we summarize first the main TFs which control these common phenotypes. Then, we focus on the existing strategies used to generate human NCs. Finally we discuss how identification and regulation of NC-associated genes provide an additional approach to improving current melanoma targeted therapies.
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Affiliation(s)
- Lionel Larribère
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
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10
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Herbert K, Binet R, Lambert JP, Louphrasitthiphol P, Kalkavan H, Sesma-Sanz L, Robles-Espinoza CD, Sarkar S, Suer E, Andrews S, Chauhan J, Roberts ND, Middleton MR, Gingras AC, Masson JY, Larue L, Falletta P, Goding CR. BRN2 suppresses apoptosis, reprograms DNA damage repair, and is associated with a high somatic mutation burden in melanoma. Genes Dev 2019; 33:310-332. [PMID: 30804224 PMCID: PMC6411009 DOI: 10.1101/gad.314633.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 01/04/2019] [Indexed: 01/04/2023]
Abstract
Herbert et al. show that BRN2 is associated with DNA damage response proteins and suppresses an apoptosis-associated gene expression program to protect against UVB-, chemotherapy-, and vemurafenib-induced apoptosis. Whether cell types exposed to a high level of environmental insults possess cell type-specific prosurvival mechanisms or enhanced DNA damage repair capacity is not well understood. BRN2 is a tissue-restricted POU domain transcription factor implicated in neural development and several cancers. In melanoma, BRN2 plays a key role in promoting invasion and regulating proliferation. Here we found, surprisingly, that rather than interacting with transcription cofactors, BRN2 is instead associated with DNA damage response proteins and directly binds PARP1 and Ku70/Ku80. Rapid PARP1-dependent BRN2 association with sites of DNA damage facilitates recruitment of Ku80 and reprograms DNA damage repair by promoting Ku-dependent nonhomologous end-joining (NHEJ) at the expense of homologous recombination. BRN2 also suppresses an apoptosis-associated gene expression program to protect against UVB-, chemotherapy- and vemurafenib-induced apoptosis. Remarkably, BRN2 expression also correlates with a high single-nucleotide variation prevalence in human melanomas. By promoting error-prone DNA damage repair via NHEJ and suppressing apoptosis of damaged cells, our results suggest that BRN2 contributes to the generation of melanomas with a high mutation burden. Our findings highlight a novel role for a key transcription factor in reprogramming DNA damage repair and suggest that BRN2 may impact the response to DNA-damaging agents in BRN2-expressing cancers.
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Affiliation(s)
- Katharine Herbert
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Romuald Binet
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Medicine, Cancer Research Centre, Université Laval, Quebec G1V 0A6, Canada; CHU de Québec Research Center, CHUL, Quebec G1V 4G2, Canada
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Halime Kalkavan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Laura Sesma-Sanz
- Genome Stability Laboratory, CHU de Oncology Division, Québec Research Center, Québec City, Quebec G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, Quebec G1V 0A6, Canada
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro 76230, Mexico.,Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Sovan Sarkar
- Department of Oncology, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Eda Suer
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Sarah Andrews
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jagat Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Nicola D Roberts
- The Cancer Genome Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Oncology Division, Québec Research Center, Québec City, Quebec G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, Quebec G1V 0A6, Canada
| | - Lionel Larue
- Institut Curie, PSL Research University, Normal and Pathological Development of Melanocytes, U1021, Institut National de la Santé et de la Recherche Médicale (INSERM), 91405 Orsay, France.,University Paris-Sud, University Paris-Saclay, UMR 3347, Centre National de la Recherche Scientifique (CNRS), 91505 Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, 91405 Orsay, France
| | - Paola Falletta
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom.,Università Vita-Salute San Raffaele, Milano, 20132 Milano MI, Italy
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
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11
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Zeng H, Jorapur A, Shain AH, Lang UE, Torres R, Zhang Y, McNeal AS, Botton T, Lin J, Donne M, Bastian IN, Yu R, North JP, Pincus L, Ruben BS, Joseph NM, Yeh I, Bastian BC, Judson RL. Bi-allelic Loss of CDKN2A Initiates Melanoma Invasion via BRN2 Activation. Cancer Cell 2018; 34:56-68.e9. [PMID: 29990501 PMCID: PMC6084788 DOI: 10.1016/j.ccell.2018.05.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 02/12/2018] [Accepted: 05/30/2018] [Indexed: 02/03/2023]
Abstract
Loss of the CDKN2A tumor suppressor is associated with melanoma metastasis, but the mechanisms connecting the phenomena are unknown. Using CRISPR-Cas9 to engineer a cellular model of melanoma initiation from primary human melanocytes, we discovered that a lineage-restricted transcription factor, BRN2, is downstream of CDKN2A and directly regulated by E2F1. In a cohort of melanocytic tumors that capture distinct progression stages, we observed that CDKN2A loss coincides with both the onset of invasive behavior and increased BRN2 expression. Loss of the CDKN2A protein product p16INK4A permitted metastatic dissemination of human melanoma lines in mice, a phenotype rescued by inhibition of BRN2. These results demonstrate a mechanism by which CDKN2A suppresses the initiation of melanoma invasion through inhibition of BRN2.
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Affiliation(s)
- Hanlin Zeng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Aparna Jorapur
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - A Hunter Shain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Ursula E Lang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Rodrigo Torres
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Yuntian Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Andrew S McNeal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Thomas Botton
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew Donne
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ingmar N Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Richard Yu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA; Faculty of Medicine, University of British Columbia, Vancouver, BC V6T1Z3, Canada
| | - Jeffrey P North
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Laura Pincus
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Beth S Ruben
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA; Palo Alto Medical Foundation, Palo Alto, CA 94301, USA
| | - Nancy M Joseph
- Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA; Department of Pathology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Robert L Judson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA.
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12
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Ahi EP, Sefc KM. A gene expression study of dorso-ventrally restricted pigment pattern in adult fins of Neolamprologus meeli, an African cichlid species. PeerJ 2017; 5:e2843. [PMID: 28097057 PMCID: PMC5228514 DOI: 10.7717/peerj.2843] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/29/2016] [Indexed: 01/04/2023] Open
Abstract
Fish color patterns are among the most diverse phenotypic traits found in the animal kingdom. Understanding the molecular and cellular mechanisms that control in chromatophore distribution and pigmentation underlying this diversity is a major goal in developmental and evolutionary biology, which has predominantly been pursued in the zebrafish model system. Here, we apply results from zebrafish work to study a naturally occurring color pattern phenotype in the fins of an African cichlid species from Lake Tanganyika. The cichlid fish Neolamprologus meeli displays a distinct dorsal color pattern, with black and white stripes along the edges of the dorsal fin and of the dorsal half of the caudal fin, corresponding with differences in melanophore density. To elucidate the molecular mechanisms controlling the differences in dorsal and ventral color patterning in the fins, we quantitatively assessed the expression of 15 candidate target genes involved in adult zebrafish pigmentation and stripe formation. For reference gene validation, we screened the expression stability of seven widely expressed genes across the investigated tissue samples and identified tbp as appropriate reference. Relative expression levels of the candidate target genes were compared between the dorsal, striped fin regions and the corresponding uniform, grey-colored regions in the anal and ventral caudal fin. Dorso-ventral expression differences, with elevated levels in both white and black stripes, were observed in two genes, the melanosome protein coding gene pmel and in igsf11, which affects melanophore adhesion, migration and survival. Next, we predicted potential shared upstream regulators of pmel and igsf11. Testing the expression patterns of six predicted transcriptions factors revealed dorso-ventral expression difference of irf1 and significant, negative expression correlation of irf1 with both pmel and igsf11. Based on these results, we propose pmel, igsf11 and irf1 as likely components of the genetic mechanism controlling distinct dorso-ventral color patterns in N. meeli fins.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Zoology, Universitätsplatz 2, Universität Graz , Graz , Austria
| | - Kristina M Sefc
- Institute of Zoology, Universitätsplatz 2, Universität Graz , Graz , Austria
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13
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In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites. Adv Bioinformatics 2016; 2016:1286510. [PMID: 27698666 PMCID: PMC5028829 DOI: 10.1155/2016/1286510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 03/17/2016] [Accepted: 06/02/2016] [Indexed: 12/22/2022] Open
Abstract
Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.
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14
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do Vale Coelho IE, Arruda DC, Taranto AG. In silico studies of the interaction between BRN2 protein and MORE DNA. J Mol Model 2016; 22:228. [PMID: 27568376 DOI: 10.1007/s00894-016-3078-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/03/2016] [Indexed: 01/26/2023]
Abstract
The incidence of skin cancer has increased in recent decades, and melanoma is the most aggressive form with the lowest chance of successful treatment. Currently, drug design projects are in progress, but available treatments against metastatic melanoma have not significantly increased survival, and few patients are cured. Thus, new therapeutic agents should be developed as more effective therapeutic options for melanoma. High levels of the BRN2 transcription factor have been related to melanoma development. However, neither the three-dimensional (3D) structure of BRN2 protein nor its POU domain has been determined experimentally. Construction of the BRN2 3D structure, and the study of its interaction with its DNA target, are important strategies for increasing the structural and functional knowledge of this protein. Thus, the aim of this work was to study the interaction between BRN2 and MORE DNA through in silico methods. The full-length BRN2 3D structure was built using the PHYRE2 and Swiss-Model programs, and molecular dynamics of this protein in complex with MORE DNA was simulated for 20 ns by the NAMD program. The BRN2 model obtained includes helix and loop regions, and the BRN2 POU domain shares structural similarity with other members of the transcription factor family. No significant conformational change of this protein occurred during dynamics simulation. These analyses revealed BRN2 residues important for the specific interaction with nucleotide bases and with more than one DNA nucleotide. This study may contribute to the design of inhibitors against BRN2 or MORE DNA as molecular targets of melanoma skin cancer. Graphical Abstract Model of complete Brn2 protein in complex with MORE DNA after building through comparative modeling and refinement by molecular dynamics simulation.
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Affiliation(s)
- Ivan Evangelista do Vale Coelho
- Laboratório de Química Farmacêutica, Universidade Federal de São João del-Rei, Campus Centro-Oeste Dona Lindu, Divinópolis, MG, Brazil
| | | | - Alex Gutterres Taranto
- Laboratório de Química Farmacêutica, Universidade Federal de São João del-Rei, Campus Centro-Oeste Dona Lindu, Divinópolis, MG, Brazil.
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15
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Kang H, Tan M, Bishop JA, Jones S, Sausen M, Ha PK, Agrawal N. Whole-Exome Sequencing of Salivary Gland Mucoepidermoid Carcinoma. Clin Cancer Res 2016; 23:283-288. [PMID: 27340278 DOI: 10.1158/1078-0432.ccr-16-0720] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/26/2016] [Accepted: 06/19/2016] [Indexed: 12/16/2022]
Abstract
PURPOSE Mucoepidermoid carcinoma (MEC) is the most common salivary gland malignancy. To explore the genetic origins of MEC, we performed systematic genomic analyses of these tumors. EXPERIMENTAL DESIGN Whole-exome sequencing and gene copy-number analyses were performed for 18 primary cancers with matched normal tissue. FISH was used to determine the presence or absence of the MECT1-MAML2 translocation in 17 tumors. RESULTS TP53 was the most commonly mutated gene in MEC (28%), and mutations were found only in intermediate- and high-grade tumors. Tumors with TP53 mutations had more mutations overall than tumors without TP53 mutations (P = 0.006). POU6F2 was the second most frequently mutated gene, found in three low-grade MECs with the same in-frame deletion. Somatic alterations in IRAK1, MAP3K9, ITGAL, ERBB4, OTOGL, KMT2C, and OBSCN were identified in at least two of the 18 tumors sequenced. FISH analysis confirmed the presence of the MECT1-MAML2 translocation in 15 of 17 tumors (88%). CONCLUSIONS Through these integrated genomic analyses, MECT1-MAML2 translocation and somatic TP53 and POU6F2 mutations appear to be the main drivers of MEC. Clin Cancer Res; 23(1); 283-8. ©2016 AACR.
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Affiliation(s)
- Hyunseok Kang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marietta Tan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Justin A Bishop
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Siân Jones
- Personal Genome Diagnostics, Baltimore, Maryland
| | - Mark Sausen
- Personal Genome Diagnostics, Baltimore, Maryland
| | - Patrick K Ha
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nishant Agrawal
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Department of Surgery, Section of Otolaryngology-Head and Neck Surgery, University of Chicago, Chicago, Illinois
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16
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Sha J, Gastman BR, Morris N, Mesinkovska NA, Baron ED, Cooper KD, McCormick T, Arbesman J, Harter ML. The Response of microRNAs to Solar UVR in Skin-Resident Melanocytes Differs between Melanoma Patients and Healthy Persons. PLoS One 2016; 11:e0154915. [PMID: 27149382 PMCID: PMC4858311 DOI: 10.1371/journal.pone.0154915] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/21/2016] [Indexed: 12/12/2022] Open
Abstract
The conversion of melanocytes into cutaneous melanoma is largely dictated by the effects of solar ultraviolet radiation (UVR). Yet to be described, however, is exactly how these cells are affected by intense solar UVR while residing in their natural microenvironment, and whether their response differs in persons with a history of melanoma when compared to that of healthy individuals. By using laser capture microdissection (LCM) to isolate a pure population of melanocytes from a small area of skin that had been intermittingly exposed or un-exposed to physiological doses of solar UVR, we can now report for the first time that the majority of UV-responsive microRNAs (miRNAs) in the melanocytes of a group of women with a history of melanoma are down-regulated when compared to those in the melanocytes of healthy controls. Among the miRNAs that were commonly and significantly down-regulated in each of these women were miR-193b (P<0.003), miR-342-3p (P<0.003), miR186 (P<0.007), miR-130a (P<0.007), and miR-146a (P<0.007). To identify genes potentially released from inhibition by these repressed UV-miRNAs, we analyzed databases (e.g., DIANA-TarBase) containing experimentally validated microRNA-gene interactions. In the end, this enabled us to construct UV-miRNA-gene regulatory networks consisting of individual genes with a probable gain-of-function being intersected not by one, but by several down-regulated UV-miRNAs. Most striking, however, was that these networks typified well-known regulatory modules involved in controlling the epithelial-to-mesenchymal transition and processes associated with the regulation of immune-evasion. We speculate that these pathways become activated by UVR resulting in miRNA down regulation only in melanocytes susceptible to melanoma, and that these changes could be partially responsible for empowering these cells toward tumor progression.
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Affiliation(s)
- Jingfeng Sha
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Brian R. Gastman
- Department of Immunology, Cleveland Clinic, Cleveland, OH, 44195, United States of America
| | - Nathan Morris
- Statistical Science Core in the Center for Clinical Investigation, Case Western Reserve University, Cleveland, OH, 44106, United States of America
| | - Natasha A. Mesinkovska
- Department of Dermatology, Cleveland Clinic, Cleveland, OH, 44195, United States of America
| | - Elma D. Baron
- Department of Dermatology, Case Western Reserve University/University Hospitals Case Medical Center, Cleveland, OH, 44106, United States of America
| | - Kevin D. Cooper
- Department of Dermatology, Case Western Reserve University/University Hospitals Case Medical Center, Cleveland, OH, 44106, United States of America
| | - Thomas McCormick
- Department of Dermatology, Case Western Reserve University/University Hospitals Case Medical Center, Cleveland, OH, 44106, United States of America
| | - Joshua Arbesman
- Department of Dermatology, Case Western Reserve University/University Hospitals Case Medical Center, Cleveland, OH, 44106, United States of America
| | - Marian L. Harter
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, United States of America
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, United States of America
- * E-mail:
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17
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Marzese DM, Witz IP, Kelly DF, Hoon DSB. Epigenomic landscape of melanoma progression to brain metastasis: unexplored therapeutic alternatives. Epigenomics 2015; 7:1303-11. [PMID: 26638944 DOI: 10.2217/epi.15.77] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Melanoma brain metastasis is a complication with rising incidence. Despite the high rate of somatic mutations driving the initial stages of melanocyte transformation, the brain colonization requires a phenotypic reprogramming that is, in part, influenced by epigenomic modifications. This special report summarizes recent findings in the epigenomic landscape of melanoma progression to brain metastasis, with particular emphasis on the clinical utility of DNA methylation, chromatin modifications and ncRNA expression as theragnostic markers, as well as the significance of the metastatic microenvironment on melanoma brain metastasis epigenome.
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Affiliation(s)
- Diego M Marzese
- Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, 2200 Santa Monica Boulevard, Santa Monica, CA 90404, USA
| | - Isaac P Witz
- Department of Cell Research & Immunology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Daniel F Kelly
- Brain Tumor Center, Providence Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Dave S B Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, 2200 Santa Monica Boulevard, Santa Monica, CA 90404, USA
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