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Shirley CA, Chhabra G, Amiri D, Chang H, Ahmad N. Immune escape and metastasis mechanisms in melanoma: breaking down the dichotomy. Front Immunol 2024; 15:1336023. [PMID: 38426087 PMCID: PMC10902921 DOI: 10.3389/fimmu.2024.1336023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Melanoma is one of the most lethal neoplasms of the skin. Despite the revolutionary introduction of immune checkpoint inhibitors, metastatic spread, and recurrence remain critical problems in resistant cases. Melanoma employs a multitude of mechanisms to subvert the immune system and successfully metastasize to distant organs. Concerningly, recent research also shows that tumor cells can disseminate early during melanoma progression and enter dormant states, eventually leading to metastases at a future time. Immune escape and metastasis have previously been viewed as separate phenomena; however, accumulating evidence is breaking down this dichotomy. Recent research into the progressive mechanisms of melanoma provides evidence that dedifferentiation similar to classical epithelial to mesenchymal transition (EMT), genes involved in neural crest stem cell maintenance, and hypoxia/acidosis, are important factors simultaneously involved in immune escape and metastasis. The likeness between EMT and early dissemination, and differences, also become apparent in these contexts. Detailed knowledge of the mechanisms behind "dual drivers" simultaneously promoting metastatically inclined and immunosuppressive environments can yield novel strategies effective in disabling multiple facets of melanoma progression. Furthermore, understanding progression through these drivers may provide insight towards novel treatments capable of preventing recurrence arising from dormant dissemination or improving immunotherapy outcomes.
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Affiliation(s)
- Carl A Shirley
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Gagan Chhabra
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Deeba Amiri
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Hao Chang
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States
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2
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Zhang ZY, Ding Y, Ezhilarasan R, Lhakhang T, Wang Q, Yang J, Modrek AS, Zhang H, Tsirigos A, Futreal A, Draetta GF, Verhaak RGW, Sulman EP. Lineage-coupled clonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAF V600E inhibition resistance in melanoma. Cell Discov 2022; 8:102. [PMID: 36202798 PMCID: PMC9537441 DOI: 10.1038/s41421-022-00462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Targeted cancer therapies have revolutionized treatment but their efficacies are limited by the development of resistance driven by clonal evolution within tumors. We developed "CAPTURE", a single-cell barcoding approach to comprehensively trace clonal dynamics and capture live lineage-coupled resistant cells for in-depth multi-omics analysis and functional exploration. We demonstrate that heterogeneous clones, either preexisting or emerging from drug-tolerant persister cells, dominated resistance to vemurafenib in BRAFV600E melanoma. Further integrative studies uncovered diverse resistance mechanisms. This includes a previously unrecognized and clinically relevant mechanism, chromosome 18q21 gain, which leads to vulnerability of the cells to BCL2 inhibitor. We also identified targetable common dependencies of captured resistant clones, such as oxidative phosphorylation and E2F pathways. Our study provides new therapeutic insights into overcoming therapy resistance in BRAFV600E melanoma and presents a platform for exploring clonal evolution dynamics and vulnerabilities that can be applied to study treatment resistance in other cancers.
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Affiliation(s)
- Ze-Yan Zhang
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA.
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Yingwen Ding
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ravesanker Ezhilarasan
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Tenzin Lhakhang
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA
| | - Qianghu Wang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing, Jiangsu, China
| | - Jie Yang
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aram S Modrek
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Hua Zhang
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roel G W Verhaak
- Department of Computational Biology, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Erik P Sulman
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA.
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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3
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Yue Z, Cao M, Hong A, Zhang Q, Zhang G, Jin Z, Zhao L, Wang Q, Fang F, Wang Y, Sun J. m 6A Methyltransferase METTL3 Promotes the Progression of Primary Acral Melanoma via Mediating TXNDC5 Methylation. Front Oncol 2022; 11:770325. [PMID: 35117988 PMCID: PMC8804213 DOI: 10.3389/fonc.2021.770325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
m6A modification is one of the most important post-transcriptional modifications in RNA and plays an important role in promoting translation or decay of RNAs. The role of m6A modifications has been highlighted by increasing evidence in various cancers, which, however, is rarely explored in acral melanoma. Here, we demonstrated that m6A level was highly elevated in acral melanoma tissues, along with the expression of METTL3, one of the most important m6A methyltransferase. Besides, higher expression of METTL3 messenger RNA (mRNA) correlated with a higher stage in primary acral melanoma patients. Knockdown of METTL3 decreased global m6A level in melanoma cells. Furthermore, METTL3 knockdown suppressed the proliferation, migration, and invasion of melanoma cells. In METTL3 knockdown xenograft mouse models, we observed decreased volumes and weights of melanoma tissues. Mechanistically, we found that METTL3 regulates certain m6A-methylated transcripts, thioredoxin domain containing protein 5 (TXNDC5), with the confirmation of RNA-seq, MeRIP-seq, and Western blot. These data suggest that METTL3 may play a key role in the progression of acral melanoma, and targeting the m6A dependent-METTL3 signaling pathway may serve as a promising therapeutic strategy for management of patients of acral melanomas.
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Affiliation(s)
- Zhanghui Yue
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Meng Cao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Anlan Hong
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Qian Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Guoqiang Zhang
- Department of Dermatology, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhibin Jin
- Department of Ultrasound, Nanjing Drum Tower Hospital, Nanjing, China
| | - Liang Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Qiang Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Fang Fang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yan Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Jianfang Sun
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
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4
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Loss of NECTIN1 triggers melanoma dissemination upon local IGF1 depletion. Nat Genet 2022; 54:1839-1852. [PMID: 36229674 PMCID: PMC9729115 DOI: 10.1038/s41588-022-01191-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/24/2022] [Indexed: 01/14/2023]
Abstract
Cancer genetics has uncovered many tumor-suppressor and oncogenic pathways, but few alterations have revealed mechanisms involved in tumor spreading. Here, we examined the role of the third most significant chromosomal deletion in human melanoma that inactivates the adherens junction gene NECTIN1 in 55% of cases. We found that NECTIN1 loss stimulates melanoma cell migration in vitro and spreading in vivo in both zebrafish and human tumors specifically in response to decreased IGF1 signaling. In human melanoma biopsy specimens, adherens junctions were seen exclusively in areas with low IGF1 levels, but not in NECTIN1-deficient tumors. Our study establishes NECTIN1 as a major determinant of melanoma dissemination and uncovers a genetic control of the response to microenvironmental signals.
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Kramer ET, Godoy PM, Kaufman CK. TRANSCRIPTIONAL PROFILE AND CHROMATIN ACCESSIBILITY IN ZEBRAFISH MELANOCYTES AND MELANOMA TUMORS. G3-GENES GENOMES GENETICS 2021; 12:6428538. [PMID: 34791221 PMCID: PMC8727958 DOI: 10.1093/g3journal/jkab379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/02/2021] [Indexed: 11/14/2022]
Abstract
Transcriptional and epigenetic characterization of melanocytes and melanoma cells isolated from their in vivo context promises to unveil key differences between these developmentally related normal and cancer cell populations. We therefore engineered an enhanced Danio rerio (zebrafish) melanoma model with fluorescently labeled melanocytes to allow for isolation of normal (wild type) and premalignant (BRAFV600E-mutant) populations for comparison to fully transformed BRAFV600E-mutant, p53 loss-of-function melanoma cells. Using fluorescence-activated cell sorting to isolate these populations, we performed high-quality RNA- and ATAC-seq on sorted zebrafish melanocytes vs. melanoma cells, which we provide as a resource here. Melanocytes had consistent transcriptional and accessibility profiles, as did melanoma cells. Comparing melanocytes and melanoma, we note 4128 differentially expressed genes and 56,936 differentially accessible regions with overall gene expression profiles analogous to human melanocytes and the pigmentation melanoma subtype. Combining the RNA- and ATAC-seq data surprisingly revealed that increased chromatin accessibility did not always correspond with increased gene expression, suggesting that though there is widespread dysregulation in chromatin accessibility in melanoma, there is a potentially more refined gene expression program driving cancerous melanoma. These data serve as a resource to identify candidate regulators of the normal vs. diseased states in a genetically controlled in vivo context.
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Affiliation(s)
- Eva T Kramer
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO 63110 USA
| | - Paula M Godoy
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO 63110 USA
| | - Charles K Kaufman
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO 63110 USA
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6
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Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nat Commun 2021; 12:6094. [PMID: 34667153 PMCID: PMC8526749 DOI: 10.1038/s41467-021-26234-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 09/14/2021] [Indexed: 11/09/2022] Open
Abstract
Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant. Activation of the zygotic genome is a critical transition during development, though the link to tissue-specific gene regulation remains unclear. Here the authors demonstrate distinct functions for Satb2 before and after zygotic genome activation, highlighting the temporal coordination of these roles.
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7
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Katz SR, Yakovlev MA, Vanselow DJ, Ding Y, Lin AY, Parkinson DY, Wang Y, Canfield VA, Ang KC, Cheng KC. Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT. eLife 2021; 10:68920. [PMID: 34528510 PMCID: PMC8445617 DOI: 10.7554/elife.68920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/19/2021] [Indexed: 01/10/2023] Open
Abstract
We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.
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Affiliation(s)
- Spencer R Katz
- Division of Experimental Pathology, Department of Pathology, Pennsylvania State University College of Medicine, Hershey, United States.,The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States.,Medical Scientist Training Program, Penn State College of Medicine, Hershey, United States
| | - Maksim A Yakovlev
- Division of Experimental Pathology, Department of Pathology, Pennsylvania State University College of Medicine, Hershey, United States.,The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
| | - Daniel J Vanselow
- Division of Experimental Pathology, Department of Pathology, Pennsylvania State University College of Medicine, Hershey, United States.,The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
| | - Yifu Ding
- Division of Experimental Pathology, Department of Pathology, Pennsylvania State University College of Medicine, Hershey, United States.,The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States.,Medical Scientist Training Program, Penn State College of Medicine, Hershey, United States
| | - Alex Y Lin
- Division of Experimental Pathology, Department of Pathology, Pennsylvania State University College of Medicine, Hershey, United States.,The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
| | | | - Yuxin Wang
- Mobile Imaging Innovations, Inc, Palatine, United States
| | - Victor A Canfield
- Division of Experimental Pathology, Department of Pathology, Pennsylvania State University College of Medicine, Hershey, United States.,The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
| | - Khai C Ang
- Division of Experimental Pathology, Department of Pathology, Pennsylvania State University College of Medicine, Hershey, United States.,The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States.,Zebrafish Functional Genomics Core, Penn State College of Medicine, Hershey, United States
| | - Keith C Cheng
- Division of Experimental Pathology, Department of Pathology, Pennsylvania State University College of Medicine, Hershey, United States.,The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States.,Zebrafish Functional Genomics Core, Penn State College of Medicine, Hershey, United States
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