Constructing Tissue Microarrays for Research Use

Martina Storz Schweizer1, Lela Schumacher1, Mark A. Rubin1

1 Harvard Medical School, Boston, Massachusetts
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 10.7
DOI:  10.1002/0471142905.hg1007s39
Online Posting Date:  February, 2004
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Abstract

Tissue microarrays (TMAs) were recently developed to facilitate tissue‐based research. TMAs can be used for any type of study where standard tissue slides have previously been used. However, there are numerous advantages in using TMAs. TMAs allow for screening of a large number of tissue samples under similar experimental conditions. They are also useful in that they conserve tissue and resources and can greatly multiply the number of experiments that can be performed with a limited amount of tissue samples. The basic protocol in this unit discusses how to prepare and cut tissue microarray slides. The resulting arrays may then be constructed manually or automatically, as described in the support protocols.

     
 
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Table of Contents

  • Basic Protocol 1: Preparing and Cutting Tissue Microarray Slides
  • Support Protocol 1: Creating a Manual Array
  • Support Protocol 2: Creating an Array with an Automated Arrayer
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Preparing and Cutting Tissue Microarray Slides

  Materials
  • Blocks (2‐mm or thicker) with paraffin‐embedded tissue of interest (e.g., CPMB UNIT )
  • Corresponding hematoxylin and eosin (H&E)–stained slides (see, e.g., unit 13.4, protocol 3) of sections cut from block with the paraffin‐embedded tissue
  • Standard tissue cassettes (e.g., Tissue Path IV from Fisher) of appropriate size for array that is to be punched
  • Paraffin, m.p. 50° to 60°C (e.g., S/P Brand Ameraffin, Baxter)
  • Xylene
  • Clean glass slides
  • Paraffin Tape‐Transfer System (Instrumedics, Inc.; http://www.instrumedics.com/PSA.htm)
  • Rotary microtome to cut the array blocks
  • Additional reagents and equipment for creating a tissue microarray manually (see protocol 2) or with an automated arrayer (see protocol 3)

Support Protocol 1: Creating a Manual Array

  Materials
  • Paraffin‐embedded blocks of tissue of interest and corresponding H&E stained slides, marked and organized for arrays (see protocol 1, steps and )
  • Blank recipient blocks (see protocol 1, step )
  • Punching map (see protocol 1, step )
  • Manual arrayer (e.g., Beecher Instruments; http://www.beecherinstruments.com/prod_manarr.html) consisting of:
    • Recipient block holders
    • One donor block bridge
    • Tool set for adjusting the arrayer
    • Two pairs of punches with stylets, in size 0.6‐mm diameter (other sizes are available; http://www.beecherinstruments.com/prod_acc_punch.html)
  • Fisher Brand Colorfrost microscope slides

Support Protocol 2: Creating an Array with an Automated Arrayer

  Materials
  • Paraffin‐embedded blocks of tissue of interest and corresponding H&E stained slides, marked and organized for arrays (see protocol 1, steps and )
  • Blank recipient blocks (see protocol 1, step )
  • Picture map (see protocol 1, step )
  • Para/Gard paraffin repellent (Fisher)
  • Automated arrayer, e.g., Beecher Instruments ATA‐27 (http://www.beecherinstruments.com/prod_autoarr.html), with instruction manual
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Figures

Videos

Literature Cited

   Berman, J.J., Edgerton, M.E., and Friedman, B.A. 2003. The Tissue Microarray Data Exchange Specification: A community‐based, open source tool for sharing tissue microarray data. BMC Med. Inform. Decis. Mak. 3:5.
   Bubendorf, L., Nocito, A., Moch, H., and Sauter, G. 2001. Tissue microarray (TMA) technology: Miniaturized pathology archives for high‐throughput in situ studies. J. Pathol. 195:72‐79.
   Chen, W., Foran, D.J., and Reiss, M. Unsupervised imaging, registration and archiving of tissue microarrays. 2002. Proc. AMIA Symp. 136‐139.
   Hsu, F.D., Nielsen, T.O., Alkushi, A., et al. 2002. Tissue microarrays are an effective quality assurance tool for diagnostic immunohistochemistry. Mod Pathol. 15:1374‐1380.
   Kallioniemi, O.P., Wagner, U., Kononen, J., and Sauter, G. 2001. Tissue microarray technology for high‐throughput molecular profiling of cancer. Hum. Mol. Genet. 10:657‐662.
   Kononen, J., Bubendorf, L., Kallioniemi, A., Barlund, M., Schraml, P., Leighton, S., Torhorst, J., Mihatsch, M.J., Sauter, G., and Kallioniemi, O.P. 1998. Tissue microarrays for high‐throughput molecular profiling of tumor specimens. Nat. Med. 4:844‐847.
   Liu, C.L., Prapong, W., Natkunam, Y., Alizadeh, A., Montgomery, K., Gilks, C.B., and van de Rijn, M. 2002. Software tools for high‐throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays. Am. J. Pathol. 161:1557‐1565.
   Manley, S., Mucci, N.R., De Marzo, A.M., and Rubin, M.A. 2001. Relational database structure to manage high‐density tissue microarray data and images for pathology studies focusing on clinical outcome: The prostate specialized program of research excellence model. Am. J. Pathol. 159:837‐843.
   Rhodes, D.R., Sanda, M.G., Otte, A.P., Chinnaiyan, A.M., and Rubin, M.A. 2003. Multiplex biomarker approach for determining risk of prostate‐specific antigen‐defined recurrence of prostate cancer. J. Natl. Cancer Inst. 95:661‐668.
   Rimm, D.L., Camp, R.L., Charette, L.A., Costa, J., Olsen, D.A., and Reiss, M. 2001. Tissue microarray: A new technology for amplification of tissue resources. Cancer J. 7:24‐31.
   Rubin, M.A. 2001. Use of laser capture microdissection, cDNA microarrays, and tissue microarrays in advancing our understanding of prostate cancer. J. Pathol. 195:80‐86.
   Rubin, M.A., Dunn, R., Strawderman, M., and Pienta, KJ. 2002. Tissue microarray sampling strategy for prostate cancer biomarker analysis. Am. J. Surg. Pathol. 26:312‐319.
   Simon, R. and Sauter, G. 2002. Tissue microarrays for miniaturized high‐throughput molecular profiling of tumors. Exp. Hematol. 30:1365‐1372.
Internet Resources
  http://www.nhgri.nih.gov/DIR/CGB/TMA/
  NHGRI Tissue Microarray Project
  http://tmalab.jhmi.edu/index.html
  Johns Hopkins TMA Core
  http://www.yalepath.org/DEPT/research/YCCTMA/tisarray.htm
  Yale TMA Core
  http://rubinlab.tch.harvard.edu/
  Harvard TMA Core
  http://genome-www.stanford.edu/TMA/
  Stanford TMA Software
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