Skip to main content
SpringerLink
Log in

Oligonucleotide Microarray Expression Profiling of Contrasting Invasive Phenotypes in Colorectal Cancer

  • Protocol
  • First Online:
Book cover Laser Capture Microdissection

Part of the book series: Methods in Molecular Biology ((MIMB,volume 755))

  • 2623 Accesses

Abstract

This chapter refers to the application of laser-capture microdissection with oligonucleotide microarray analysis. The protocol described has been successfully used to identify differential transcript expression between contrasting colorectal cancer invasive phenotypes. Tissue processing, RNA extraction, quality control, amplification, fluorescent labelling, purification, hybridisation, and elements of data analysis are covered.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
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. Wernert N (1997) The multiple roles of tumour stroma. Virchows Arch; 430: 433–43.

    Article  CAS  Google Scholar 

  2. Liotta LA, Kohn EC (2001) The microenvironment of the tumour-host interface. Nature; 411: 375–9.

    Article  CAS  Google Scholar 

  3. Bhowmick NA, Moses HL (2005) Tumor-stroma interactions. Curr Opin Genet Dev; 15: 97–101.

    Article  CAS  Google Scholar 

  4. Le NH, Franken P, Fodde R (2008) Tumour-stroma interactions in colorectal cancer: converging on beta-catenin activation and cancer stemness. Br J Cancer; 98: 1886–93.

    Article  CAS  Google Scholar 

  5. Nakamura T, Mitomi H, Kanazawa H et al (2008) Tumor budding as an index to identify high-risk patients with stage II colon cancer. Dis Colon Rectum; 51: 568–72.

    Article  Google Scholar 

  6. Nakahara H, Howard L, Thompson EW et al (1997) Transmembrane/cytoplasmic domain-mediated membrane type 1-matrix metalloprotease docking to invadopodia is required for cell invasion. Proc Natl Acad Sci U S A; 94: 7959–64.

    Article  CAS  Google Scholar 

  7. Brabletz T, Jung A, Reu S et al (2001) Variable beta-catenin expression in colorectal cancers indicates tumor progression driven by the tumor environment. Proc Natl Acad Sci U S A; 98: 10356–61.

    Article  CAS  Google Scholar 

  8. Komatsu K, Kobune-Fujiwara Y, Andoh A et al (2000) Increased expression of S100A6 at the invading fronts of the primary lesion and liver metastasis in patients with colorectal adenocarcinoma. Br J Cancer; 83: 769–74.

    Article  CAS  Google Scholar 

  9. Nabeshima K, Shimao Y, Inoue T et al (2002) Immunohistochemical analysis of IQGAP1 expression in human colorectal carcinomas: its overexpression in carcinomas and association with invasion fronts. Cancer Lett; 176: 101–9.

    Article  CAS  Google Scholar 

  10. Harrell JC, Dye WW, Harvell DM et al (2008) Contaminating cells alter gene signatures in whole organ versus laser capture microdissected tumors: a comparison of experimental breast cancers and their lymph node metastases. Clin Exp Metastasis; 25: 81–8.

    Article  Google Scholar 

  11. Goldsworthy SM, Stockton PS, Trempus CS et al (1999) Effects of fixation on RNA extraction and amplification from laser capture microdissected tissue. Mol Carcinog; 25: 86–91.

    Article  CAS  Google Scholar 

  12. Huang J, Qi R, Quackenbush J et al (2001) Effects of ischemia on gene expression. J Surg Res; 99: 222–7.

    Article  CAS  Google Scholar 

  13. Nygaard V, Hovig E (2006) Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling. Nucleic Acids Res; 34: 996–1014.

    Article  CAS  Google Scholar 

  14. Ohashi Y, Creek KE, Pirisi L et al (2004) RNA degradation in human breast tissue after surgical removal: a time-course study. Exp Mol Pathol; 77: 98–103.

    Article  CAS  Google Scholar 

  15. Schoor O, Weinschenk T, Hennenlotter J et al (2003) Moderate degradation does not preclude microarray analysis of small amounts of RNA. Biotechniques; 35: 1192–6, 8–201.

    Google Scholar 

  16. Zhao H, Hastie T, Whitfield ML et al (2002) Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. BMC Genomics; 3: 31.

    Article  CAS  Google Scholar 

  17. Petalidis L, Bhattacharyya S, Morris GA et al (2003) Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res; 31: e142.

    Article  CAS  Google Scholar 

  18. Kitahara O, Furukawa Y, Tanaka T et al (2001) Alterations of gene expression during colorectal carcinogenesis revealed by cDNA microarrays after laser-capture microdissection of tumor tissues and normal epithelia. Cancer Res; 61: 3544–9.

    CAS  Google Scholar 

  19. Alevizos I, Mahadevappa M, Zhang X et al (2001) Oral cancer in vivo gene expression profiling assisted by laser capture microdissection and microarray analysis. Oncogene; 20: 6196–204.

    Article  CAS  Google Scholar 

  20. Luo L, Salunga RC, Guo H et al (1999) Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med; 5: 117–22.

    Article  CAS  Google Scholar 

  21. Luzzi V, Holtschlag V, Watson MA (2001) Expression profiling of ductal carcinoma in situ by laser capture microdissection and high-density oligonucleotide arrays. Am J Pathol; 158: 2005–10.

    Article  CAS  Google Scholar 

  22. Miura K, Bowman ED, Simon R et al (2002) Laser capture microdissection and microarray expression analysis of lung adenocarcinoma reveals tobacco smoking- and prognosis-related molecular profiles. Cancer Res; 62: 3244–50.

    CAS  Google Scholar 

  23. Zhu G, Reynolds L, Crnogorac-Jurcevic T et al (2003) Combination of microdissection and microarray analysis to identify gene expression changes between differentially located tumour cells in breast cancer. Oncogene; 22: 3742–8.

    Article  CAS  Google Scholar 

  24. Thorn CC, Freeman TC, Scott N et al (2009) Laser microdissection expression profiling of marginal edges of colorectal tumours reveals evidence of increased lactate metabolism in the aggressive phenotype. Gut; 58: 404–12.

    Article  CAS  Google Scholar 

  25. Hewitt SM, Lewis FA, Cao Y et al (2008) Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue. Archives of pathology & laboratory medicine; 132: 1929–35.

    Google Scholar 

  26. Schroeder A, Mueller O, Stocker S et al (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC molecular biology; 7: 3.

    Article  Google Scholar 

  27. Knapen D, Vergauwen L, Laukens K et al (2009) Best practices for hybridization design in two-colour microarray analysis. Trends in biotechnology; 27: 406–14.

    Article  CAS  Google Scholar 

  28. Simone NL, Bonner RF, Gillespie JW et al (1998) Laser-capture microdissection: opening the microscopic frontier to molecular analysis. Trends Genet; 14: 272–6.

    Article  CAS  Google Scholar 

  29. Wang H, Owens JD, Shih JH et al (2006) Histological staining methods preparatory to laser capture microdissection significantly affect the integrity of the cellular RNA. BMC Genomics; 7: 97.

    Article  Google Scholar 

  30. Bahn S, Augood SJ, Ryan M et al (2001) Gene expression profiling in the post-mortem human brain–no cause for dismay. Journal of chemical neuroanatomy; 22: 79–94.

    Article  CAS  Google Scholar 

  31. Betsuyaku T, Griffin GL, Watson MA et al (2001) Laser capture microdissection and real-time reverse transcriptase/ polymerase chain reaction of bronchiolar epithelium after bleomycin. Am J Respir Cell Mol Biol; 25: 278–84.

    CAS  Google Scholar 

  32. Pan J, Kunkel EJ, Gosslar U et al (2000) A novel chemokine ligand for CCR10 and CCR3 expressed by epithelial cells in mucosal tissues. J Immunol; 165: 2943–9.

    CAS  Google Scholar 

  33. Causton HC, Quackenbush J, Brazma A (2003) Microarray Gene Expression Data Analysis: A Beginner’s Guide. Blackwell, Oxford.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Academic Surgery, St. James’s University Hospital, Leeds, UK

    Christopher C. Thorn

  2. MRC Harwell, Oxford, UK

    Deborah Williams

  3. Roslin Institute, University of Edinburgh, Edinburgh, UK

    Thomas C. Freeman

Authors
  1. Christopher C. Thorn
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Deborah Williams
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Thomas C. Freeman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christopher C. Thorn .

Editor information

Editors and Affiliations

  1. , Department of Pathology, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom

    Graeme I. Murray

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Thorn, C.C., Williams, D., Freeman, T.C. (2011). Oligonucleotide Microarray Expression Profiling of Contrasting Invasive Phenotypes in Colorectal Cancer. In: Murray, G. (eds) Laser Capture Microdissection. Methods in Molecular Biology, vol 755. Humana Press. https://doi.org/10.1007/978-1-61779-163-5_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-163-5_17

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-162-8

  • Online ISBN: 978-1-61779-163-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation