TY - JOUR
T1 - International harmonization of nomenclature and diagnostic criteria (INHAND) progress to date and future plans
AU - Keenan, Charlotte M.
AU - Baker, Julia F.
AU - Bradley, Alys E.
AU - Goodman, Dawn G.
AU - Harada, Takanori
AU - Herbert, Ronald
AU - Kaufmann, Wolfgang
AU - Kellner, Rupert
AU - Mahler, Beth
AU - Meseck, Emily
AU - Nolte, Thomas
AU - Rittinghausen, Susanne
AU - Vahle, John
AU - Yoshizawa, Katsuhiko
N1 - Publisher Copyright:
© 2015 The Japanese Society of Toxicologic Pathology.
PY - 2015
Y1 - 2015
N2 - Recently, large-scale gene expression profiling is often performed using RNA extracted from unfixed frozen or formalinfixed paraffin embedded (FFPE) samples. However, both types of samples have drawbacks in terms of the morphological preservation and RNA quality. In the present study, we investigated 30 human prostate tissues using the PFA-AMeX method (fixation using paraformaldehyde (PFA) followed by embedding in paraffin by AMeX) with a DNA microarray combined with laser-capture microdissection. Morphologically, in contrast to the case of atypical adenomatous hyperplasia, loss of basal cells in prostate adenocarcinomas was as obvious in PFA-AMeX samples as in FFPE samples. As for quality, the loss of rRNA peaks 18S and 28S on the capillary electropherograms from both FFPE and PFA-AMeX samples showed that the RNA was degraded equally during processing. However, qRT-PCR with 3’ and 5’ primer sets designed against human beta-actin revealed that, although RNA degradation occurred in both methods, it occurred more mildly in the PFA-AMeX samples. In conclusion, the PFA-AMeX method is good with respect to morphology and RNA quality, which makes it a promising tool for DNA microarrays combined with laser-capture microdissection, and if the appropriate RNA quality criteria are used, the capture of credible GeneChip data is well over 80% efficient, at least in human prostate specimens.
AB - Recently, large-scale gene expression profiling is often performed using RNA extracted from unfixed frozen or formalinfixed paraffin embedded (FFPE) samples. However, both types of samples have drawbacks in terms of the morphological preservation and RNA quality. In the present study, we investigated 30 human prostate tissues using the PFA-AMeX method (fixation using paraformaldehyde (PFA) followed by embedding in paraffin by AMeX) with a DNA microarray combined with laser-capture microdissection. Morphologically, in contrast to the case of atypical adenomatous hyperplasia, loss of basal cells in prostate adenocarcinomas was as obvious in PFA-AMeX samples as in FFPE samples. As for quality, the loss of rRNA peaks 18S and 28S on the capillary electropherograms from both FFPE and PFA-AMeX samples showed that the RNA was degraded equally during processing. However, qRT-PCR with 3’ and 5’ primer sets designed against human beta-actin revealed that, although RNA degradation occurred in both methods, it occurred more mildly in the PFA-AMeX samples. In conclusion, the PFA-AMeX method is good with respect to morphology and RNA quality, which makes it a promising tool for DNA microarrays combined with laser-capture microdissection, and if the appropriate RNA quality criteria are used, the capture of credible GeneChip data is well over 80% efficient, at least in human prostate specimens.
KW - Regulatory science
KW - Rodent
KW - Terminology
KW - Toxicologic pathology
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U2 - 10.1293/tox.2014-0049
DO - 10.1293/tox.2014-0049
M3 - Letter
AN - SCOPUS:84923365254
SN - 0914-9198
VL - 28
SP - 51
EP - 53
JO - Journal of Toxicologic Pathology
JF - Journal of Toxicologic Pathology
IS - 1
ER -