Skip to main content
SpringerLink
Log in

Genomic Approaches to Zebrafish Cancer

  • Chapter
  • First Online:
Cancer and Zebrafish

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 916))

Abstract

The zebrafish has emerged as an important model for studying cancer biology. Identification of DNA, RNA and chromatin abnormalities can give profound insight into the mechanisms of tumorigenesis and the there are many techniques for analyzing the genomes of these tumors. Here, I present an overview of the available technologies for analyzing tumor genomes in the zebrafish, including array based methods as well as next-generation sequencing technologies. I also discuss the ways in which zebrafish tumor genomes can be compared to human genomes using cross-species oncogenomics, which act to filter genomic noise and ultimately uncover central drivers of malignancy. Finally, I discuss downstream analytic tools, including network analysis, that can help to organize the alterations into coherent biological frameworks that can then be investigated further.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. White R, Rose K, Zon L (2013) Zebrafish cancer: the state of the art and the path forward. Nat Rev Cancer 13:624–636

    Article  CAS  PubMed  Google Scholar 

  2. Ablain J, Durand EM, Yang S, Zhou Y, Zon LI (2015) A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish. Dev Cell 32:756–764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. White RM, Sessa A, Burke C, Bowman T, LeBlanc J, Ceol C et al (2008) Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell Stem Cell 2:183–189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Patton EE, Widlund HR, Kutok JL, Kopani KR, Amatruda JF, Murphey RD et al (2005) BRAF mutations are sufficient to promote nevi formation and cooperate with p53 in the genesis of melanoma. Curr Biol 15:249–254

    Article  CAS  PubMed  Google Scholar 

  5. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW (2013) Cancer genome landscapes. Science 339:1546–1558

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P et al (2008) Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321:1801–1806

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Cancer Genome Atlas Network (2015) Genomic Classification of Cutaneous Melanoma. Cell 161:1681–1696

    Article  Google Scholar 

  8. Shen R, Olshen AB, Ladanyi M (2009) Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 25:2906–2912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C et al (2013) Mutational landscape and significance across 12 major cancer types. Nature 502:333–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Marusyk A, Tabassum DP, Altrock PM, Almendro V, Michor F, Polyak K (2014) Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity. Nature 514:54–58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Heitzer E, Tomlinson I (2014) Replicative DNA polymerase mutations in cancer. Curr Opin Genet Dev 24:107–113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, Battisti V et al (2011) The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Nature 471:513–517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Lee HJ, Lowdon RF, Maricque B, Zhang B, Stevens M, Li D et al (2015) Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. Nat Commun 6:6315

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Freeman JL, Ceol C, Feng H, Langenau DM, Belair C, Stern HM et al (2009) Construction and application of a zebrafish array comparative genomic hybridization platform. Genes Chromosomes Cancer 48:155–170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Lees JA, Hopkins N (2010) Highly aneuploid zebrafish malignant peripheral nerve sheath tumors have genetic alterations similar to human cancers. Proc Natl Acad Sci U S A 107:16940–16945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Beert E, Catchen JM et al (2013) Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery. PLoS Genet 9, e1003734

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Chen EY, Dobrinski KP, Brown KH, Clagg R, Edelman E, Ignatius MS et al (2013) Cross-species array comparative genomic hybridization identifies novel oncogenic events in zebrafish and human embryonal rhabdomyosarcoma. PLoS Genet 9, e1003727

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Rudner LA, Brown KH, Dobrinski KP, Bradley DF, Garcia MI, Smith AC et al (2011) Shared acquired genomic changes in zebrafish and human T-ALL. Oncogene 30:4289–4296

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lam SH, Wu YL, Vega VB, Miller LD, Spitsbergen J, Tong Y et al (2006) Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression. Nat Biotechnol 24:73–75

    Article  CAS  PubMed  Google Scholar 

  20. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102:15545–15550

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Langenau DM, Keefe MD, Storer NY, Guyon JR, Kutok JL, Le X et al (2007) Effects of RAS on the genesis of embryonal rhabdomyosarcoma. Genes Dev 21:1382–1395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Nguyen AT, Emelyanov A, Koh CH, Spitsbergen JM, Lam SH, Mathavan S et al (2011) A high level of liver-specific expression of oncogenic Kras(V12) drives robust liver tumorigenesis in transgenic zebrafish. Dis Model Mech 4:801–813

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Li Z, Luo H, Li C, Huo X, Yan C, Huang X et al (2014) Transcriptomic analysis of a transgenic zebrafish hepatocellular carcinoma model reveals a prominent role of immune responses in tumour progression and regression. Int J Cancer 135:1564–1573

    Article  CAS  PubMed  Google Scholar 

  24. He S, Krens SG, Zhan H, Gong Z, Hogendoorn PC, Spaink HP et al (2011) A DeltaRaf1-ER-inducible oncogenic zebrafish liver cell model identifies hepatocellular carcinoma signatures. J Pathol 225:19–28

    Article  CAS  PubMed  Google Scholar 

  25. White RM, Cech J, Ratanasirintrawoot S, Lin CY, Rahl PB, Burke CJ et al (2011) DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature 471:518–522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Dovey M, White RM, Zon LI (2009) Oncogenic NRAS cooperates with p53 loss to generate melanoma in zebrafish. Zebrafish 6:397–404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Lister JA, Robertson CP, Lepage T, Johnson SL, Raible DW (1999) nacre encodes a zebrafish microphthalmia-related protein that regulates neural-crest-derived pigment cell fate. Development 126:3757–3767

    CAS  PubMed  Google Scholar 

  28. Berghmans S, Murphey RD, Wienholds E, Neuberg D, Kutok JL, Fletcher CD et al (2005) tp53 mutant zebrafish develop malignant peripheral nerve sheath tumors. Proc Natl Acad Sci U S A 102:407–412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S et al (2005) Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436:117–122

    Article  CAS  PubMed  Google Scholar 

  30. Garraway LA, Weir BA, Zhao X, Widlund H, Beroukhim R, Berger A et al (2005) “Lineage addiction” in human cancer: lessons from integrated genomics. Cold Spring Harb Symp Quant Biol 70:25–34

    Article  CAS  PubMed  Google Scholar 

  31. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG et al (2001) The sequence of the human genome. Science 291:1304–1351

    Article  CAS  PubMed  Google Scholar 

  32. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    Article  CAS  PubMed  Google Scholar 

  33. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD et al (2006) The consensus coding sequences of human breast and colorectal cancers. Science 314:268–274

    Article  PubMed  Google Scholar 

  34. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ et al (2007) The genomic landscapes of human breast and colorectal cancers. Science 318:1108–1113

    Article  CAS  PubMed  Google Scholar 

  35. Liu L, Li Y, Li S, Hu N, He Y, Pong R et al (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364

    PubMed  PubMed Central  Google Scholar 

  36. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD et al (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463:191–196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Yen J, White RM, Wedge DC, Van Loo P, de Ridder J, Capper A et al (2013) The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models. Genome Biol 14:R113

    Article  PubMed  PubMed Central  Google Scholar 

  38. Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K et al (2012) Mutational processes molding the genomes of 21 breast cancers. Cell 149:979–993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E et al (2012) Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366:883–892

    Article  CAS  PubMed  Google Scholar 

  40. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J et al (2011) Tumour evolution inferred by single-cell sequencing. Nature 472:90–94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Yachida S, Jones S, Bozic I, Antal T, Leary R, Fu B et al (2010) Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 467:1114–1117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C (2013) Emerging landscape of oncogenic signatures across human cancers. Nat Genet 45:1127–1133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Iyengar S, Houvras Y, Ceol CJ (2012) Screening for melanoma modifiers using a zebrafish autochthonous tumor model. J Vis Exp. e50086

    Google Scholar 

  44. Kulahoglu C, Brautigam A (2014) Quantitative transcriptome analysis using RNA-seq. Methods Mol Biol 1158:71–91

    Article  PubMed  Google Scholar 

  45. Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M et al (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498–503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Lindner R, Friedel CC (2012) A comprehensive evaluation of alignment algorithms in the context of RNA-seq. PLoS One 7, e52403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C et al (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31:213–219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by the NIH Directors New Innovator Award (DP2CA186572), K08AR055368, the Melanoma Research Alliance Young Investigator Award, an AACR/ASCO Young Investigator Award, and the Alan and Sandra Gerry Metastasis Research Initiative.

Author information

Authors and Affiliations

  1. Memorial Sloan Kettering Cancer Center, 415 East 68th Street, New York, NY, 10065, USA

    Richard M. White M.D., Ph.D.

Authors
  1. Richard M. White M.D., Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Richard M. White M.D., Ph.D. .

Editor information

Editors and Affiliations

  1. Molecular Pathology and Cancer Center, Massachusetts General Hospital, CHARLESTOWN, Massachusetts, USA

    David M. Langenau

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

White, R.M. (2016). Genomic Approaches to Zebrafish Cancer. In: Langenau, D. (eds) Cancer and Zebrafish. Advances in Experimental Medicine and Biology, vol 916. Springer, Cham. https://doi.org/10.1007/978-3-319-30654-4_6

Download citation

Publish with us

Policies and ethics

Search

Navigation