Chapter 12
PROTOCOL
Nucleus Extraction from Formalin Fixed/paraffin
Embedded Tissue
THOMAS LIEHR
Introduction
Interphase cytogenetics using formalin fIxed/paraffIn embedded tissue is
now a well-established technique, which renders it possible to obtain "cytogenetic information" from interphase nuclei, especially from solid tumors (Hackel and VarellaGarcia, 1997, Wolfe and Herrington, 1997). It
is nearly the only tool to investigate specifIc numerical chromosomal aberrations, amplification of oncogenes (see Figure 1), deletion of tumor suppressor genes or chromosomal translocations in formalin-fIxed/paraffinembedded tumor tissue samples on a single cell level.
Interphase FISH-studies on formalin-fIxed/paraffm-embedded tissue
can be done, on the one hand, directly on sectioned and mounted material
(e.g. Neubauer et al. 1994) and on the other hand, on extracted interphase
nuclei, a technique first described by Hedley et al. (1983). As concluded by
Qian et al. (1996), both methods are comparable and reliable for the detection of chromosomal changes in archival tissue, however, each of them
has advantages and disadvantages. The first approach is recommended,
when the tissue architecture must be studied intact, e.g. in·the case of small
and/or invasive tumors, while the second technique can be applied successfully when more or less homogenous (tumor)-tissue samples are under study (Kopf et al. 1996). During evaluation of tissue sections, the problem often arises that overlapping nuclei, due to the presence of several
cell layers, one on top of the other; and that cut nuclei, leading to an artificial signal loss in interphase cytogenetic studies (Dinghra et al. 1992,
Liehr et al. 1994) cannot be evaluated reliably. These problems are not
present in nuclear extraction techniques (Kopf et al. 1996, Liehr et al.
1995a, Qian et al. 1996). In the following, the nucleus extraction from un~ Thomas Liehr, Institut fur Humangenetik, Kollegiengasse 10, Jena, 07743, Germany
(phone +49-3641-935533; fax +49-3641-935502; e-mail i8lith@mti-n.mti.uni-jena.de)
PROTOCOL
Nucleus Extraction from Formalin Fixed/paraffin
Embedded Tissue
THOMAS LIEHR
Introduction
Interphase cytogenetics using formalin fIxed/paraffIn embedded tissue is
now a well-established technique, which renders it possible to obtain "cytogenetic information" from interphase nuclei, especially from solid tumors (Hackel and VarellaGarcia, 1997, Wolfe and Herrington, 1997). It
is nearly the only tool to investigate specifIc numerical chromosomal aberrations, amplification of oncogenes (see Figure 1), deletion of tumor suppressor genes or chromosomal translocations in formalin-fIxed/paraffinembedded tumor tissue samples on a single cell level.
Interphase FISH-studies on formalin-fIxed/paraffm-embedded tissue
can be done, on the one hand, directly on sectioned and mounted material
(e.g. Neubauer et al. 1994) and on the other hand, on extracted interphase
nuclei, a technique first described by Hedley et al. (1983). As concluded by
Qian et al. (1996), both methods are comparable and reliable for the detection of chromosomal changes in archival tissue, however, each of them
has advantages and disadvantages. The first approach is recommended,
when the tissue architecture must be studied intact, e.g. in·the case of small
and/or invasive tumors, while the second technique can be applied successfully when more or less homogenous (tumor)-tissue samples are under study (Kopf et al. 1996). During evaluation of tissue sections, the problem often arises that overlapping nuclei, due to the presence of several
cell layers, one on top of the other; and that cut nuclei, leading to an artificial signal loss in interphase cytogenetic studies (Dinghra et al. 1992,
Liehr et al. 1994) cannot be evaluated reliably. These problems are not
present in nuclear extraction techniques (Kopf et al. 1996, Liehr et al.
1995a, Qian et al. 1996). In the following, the nucleus extraction from un~ Thomas Liehr, Institut fur Humangenetik, Kollegiengasse 10, Jena, 07743, Germany
(phone +49-3641-935533; fax +49-3641-935502; e-mail i8lith@mti-n.mti.uni-jena.de)