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Constructing Tissue Microarrays for Research Use

Martina Storz Schweizer1,  Lela Schumacher1,  Mark A. Rubin1

1Harvard 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

  • Unit Introduction
  • Basic Protocol: 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: Preparing and Cutting Tissue Microarray Slides

 Materials
  • Blocks (2-mm or thicker) with paraffin-embedded tissue of interest (e.g., cpmb unit 14.1)
  • Corresponding hematoxylin and eosin (H&E)–stained slides (see, e.g., unit 13.4, Support Protocol 2) 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 Support Protocol 1) or with an automated arrayer (see Support Protocol 2)

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 Basic Protocol, steps and )
  • Blank recipient blocks (see Basic Protocol, step )
  • Punching map (see Basic Protocol, step )
  • Manual arrayer (e.g., Beecher Instruments; http://www.beecherinstruments.com/prod_manarr.html) consisting of:
  • 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 Basic Protocol, steps and )
  • Blank recipient blocks (see Basic Protocol, step )
  • Picture map (see Basic Protocol, step )
  • Para/Gard paraffin repellent (Fisher)
  • Automated arrayer, e.g., Beecher Instruments ATA-27 (http://www.beecherinstruments.com/prod_autoarr.html), with instruction manual
Looking for materials?  Suppliers Guide
     
 
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Figures

  • Figure 10.7.1
    An H&E-stained slide is used as a guide to determine where to take tissue cores. A recently cut H&E slide is marked with different colors in order to distinguish different areas of interest. In this example, a prostate sample is marked red for cancer, blue for the precursor lesion (PIN), and green for benign prostate tissue. These markings are then compared to the face of the paraffin block to determine where a tissue core should be punched (not shown).

    View Image
  • Figure 10.7.2
    The process of constructing a tissue microarray. After determining the area of interest, which needs to be transferred (A), a 0.6 mm tissue core is biopsied or punched (B) and then transferred to a virgin paraffin block referred to as a recipient block (C). Using a tape system to transfer a tissue section (D), a tissue microarray slide can now be used for further analysis (E).

    View Image
  • Figure 10.7.3
    TMA picture map used for orientation when evaluating stained slide and when using automated arrayer. A physical map of the tissue microarray is planned out using an Excel spreadsheet. Colors are used to designate difference classes of tissue. This map provides an overview as to the number of tissue cores, the types of tissue, and their x-y coordinates.

    View Image
  • Figure 10.7.4
    The punching map needed for punching with the manual arrayer. A punching map shows the x and y coordinates of each TMA core (columns E and F, respectively) as well as the coordinates for the micrometer screws (column G). This map is critical for making sure that the samples are placed into the tissue microarray in the correct order.

    View Image
  • Figure 10.7.5
    A completed TMA. This array has a standard configuration with three sectors. There is good tissue alignment and on this H&E stained slide all of the TMA cores are present.

    View Image
  • Figure 10.7.6
    The automated arrayer allows the operator to designate the location of each block as the array is planned. The magnification of the block face makes it easy to precisely target the area of interest.

    View Image

Literature Cited

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

The following Web sites contain practical information regarding TMAs.

    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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