Originally published as JHC exPRESS on March 3, 2006. doi:10.1369/jhc.5A6859.2006
Volume 54 (7): 773-780, 2006 Copyright ©The Histochemical Society, Inc. Improved RT-PCR Amplification for Molecular Analyses with Long-term Preserved Formalin-fixed, Paraffin-embedded Tissue Specimens
Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan (KH,HE,KT,KK,MM,RI,MT,KN), and Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan (WY) Correspondence to: Kiyohiro Hamatani, Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima-shi, Hiroshima 732-0815, Japan. E-mail: hamatani{at}rerf.or.jp
Recently, in addition to DNA, RNA extracted from archival tissue specimens has become an invaluable source of material for molecular biological analysis. Successful amplification with PCR/RT-PCR is problematic when using amplicons of short size due to degradation of DNA or RNA. We established an improved method for efficient RT-PCR amplification of RNA extracted from archival formalin-fixed, paraffin-embedded tissue by the elimination of RNA modification and the restoration of RNA template activity. Namely, the preheating in citrate buffer (pH 4.0) of RNA extracted from long-term preserved tissue specimens resulted in significantly increased efficiency of RT-PCR. (J Histochem Cytochem 54:773780, 2006)
Key Words: preheating of RNA archival formalin-fixed and paraffin-embedded tissue citrate buffer modification of RNA by formalin RT-PCR amplification
RETROSPECTIVE ANALYSIS of archival tissue specimens is indispensable especially for studies of rare cancers or cancers associated with exposure to uncommon past events such as Thorotrast treatment, nuclear power station accidents, or atomic bombings. In recent years, application of new molecular techniques including polymerase chain reaction (PCR) to analysis of archival tissue samples is anticipated to bring about better understanding of the molecular mechanisms of these cancers (Mies 1994
Extraction of DNA from formalin-fixed, paraffin-embedded tissue for PCR analysis has been well documented (Jackson et al. 1990
Nevertheless, persistent demands have been made for further improvement in RNA extraction from long-term preserved tissue samples whose RNA significantly degraded being chemically modified. The problems facing this goal include degradation of RNA in tissue due to delay before fixation, prolonged fixation, or long-term preservation after fixation (Bresters et al. 1994 While performing molecular analyses on cancer tissue specimens taken from atomic bomb survivors and that were stored for several decades (up to 50 years), we frequently encountered archival unbuffered formalin-fixed, paraffin-embedded specimens that were difficult to use for RT-PCR analysis. We found that significant degradation and chemical modification of RNA greatly affected RT-PCR amplification. Removal of chemical modification from bases of RNA as well as significant reduction of amplicon size may be crucial for the enhanced availability of limited archival unbuffered formalin-fixed, paraffin-embedded tissue samples. Therefore, we examined whether the preheating of RNA extracted from archival unbuffered formalin-fixed, paraffin-embedded tissues enhances the efficiency of RT-PCR, along with determining optimal conditions for the RNA preheating. Application of this preheating technique to retrospective research is expected to enhance the availability of archival unbuffered formalin-fixed, paraffin-embedded tissue specimens for molecular analysis that have been stored for several decades and have functioned as a source for histological evaluation, to allow better understanding of molecular characteristics of various diseases.
Tissue Five archival unbuffered formalin-fixed, paraffin-embedded thyroid cancer tissue samples for in-house control were used in this study. All samples were preserved at room temperature for 19 to 21 years. After deparaffinization of 5-µm sections by Hemo-De (Fujisawa Yakuhin Kogyo; Osaka, Japan) and staining with methylgreen (Sigma-Aldrich; St. Louis, MO), cancerous regions ( 23 x 3 mm) were isolated using a laser microdissection system (Leica AS LMD; Wetzlar, Germany). All cancerous regions microdissected from six to eight successive tissue sections were combined for RNA extraction.
RNA Extraction and Measurement
Heat Treatment of RNA
cDNA Synthesis
Detection of Expression of Breakpoint Cluster Region (BCR) and N-ras Genes by RT-PCR
RNA Extracted from Unbuffered Formalin-fixed, Paraffin-embedded Tissue We extracted RNA from five different archival unbuffered formalin-fixed, paraffin-embedded thyroid cancer tissue specimens, as described in Materials and Methods. An image of electrophoresis of these RNA is shown in Figure 1 . They appeared as smears on agarose gel with no ribosomal bands observed in any of the samples. The range of smeared RNA differed slightly among five archival tissue specimens. A majority of the smeared RNA sample used for determination of the conditions for preheating of RNA ranged from 70 to 100 bases (Figure 1, Lane 2). Other RNA samples showing better efficiency of RT-PCR amplification than the previous one ranged from 70 to 200300 bases (Figure 1, Lanes 3 and 4). The size of RNA from the remaining two tissue samples was the intermediate among the other three samples.
Temperature in Preheating of RNA At first we tested the effects of incubation at different temperatures on RNA stability using intact RNA prepared from human thyroid cancer cell lines, because it is hard to evaluate the preheating effect using already degraded RNA extracted from formalin-fixed, paraffin-embedded tissue specimens (Figure 2 ). Preheating of RNA at >80C for 30 min in H2O resulted in vigorous degradation. Considering our result and a report by Masuda et al. (1999)
Effects of pH in Preheating of RNA on RT-PCR Amplification Using the RNA with the worst efficiency of RT-PCR amplification among the five archival tissue samples, we examined the effects of preheating on RT-PCR efficiency by amplifying the fragments of different sizes in the BCR gene and the N-ras gene (Figure 3 ). There were 61-bp fragments in the BCR and N-ras genes detected in the RNA that were not undergoing preheating, although the intensity of the bands was weak compared with that in the RNA with preheating (Figure 3). Preheating of RNA in 10 mM citrate buffer at pH 35 at 70C for 30 min made amplification of 94- and 127-bp fragments possible in the BCR gene and 98-bp fragments in the N-ras gene. These same fragments could not be amplified by RT-PCR without undergoing preheating (Figure 3). Preheating of RNA in citrate buffer with pH 4 was the most effective method in the RT-PCR amplification of the BCR and N-ras genes. To determine optimal pH, we further investigated in detail the effects of pH on RT-PCR amplification using preheated RNA. As shown in Figure 4
, RNA treated with pH 4.0 showed the most efficient RT-PCR amplification of both the BCR and N-ras genes among citrate buffers with different pH values ranging from 3 to 5 and TE (pH 7.0). We also examined the effect of pH range (6.510) on RT-PCR amplification using 10 mM sodium borate solution and TE. Among buffers ranging from pH 7.0 to pH 8.0 (TE buffers with pH 7.0, 7.5, and 8.0 and borate buffer with 8.0), little difference was found in the effect of preheating with these buffers at a concentration of 10 mM (data not shown). The effect of preheating decreased with increased pH, and adverse effect was observed in RNA treated with pH 9.0 or 10.0 (data not shown). Little difference was found in efficiency of RT-PCR amplification enhanced by preheating of RNA between citrate buffer (pH 6.5) and sodium borate (pH 6.5) (data not shown).
Effects of Buffer Concentration in Preheating of RNA on RT-PCR Amplification We examined the effects of different buffer concentrations on RT-PCR amplification. In both BCR and N-ras target genes, when RNA was heated with 50 mM citrate buffer at 70C, even 61-bp fragments were hard to detect. There was a lower efficiency of RT-PCR amplification than amplification without preheating (Figure 5 ). On the other hand, treatment with 10 mM citrate buffer resulted in the greatest efficiency of RT-PCR amplification among concentrations investigated (Figure 5).
Effects of Preheating Time of RNA on RT-PCR Amplification
Multiple papers have reported improvement in efficiency of RNA extraction from buffered formalin-fixed, paraffin-embedded tissue. Few reports, however, have reported on elimination of modification induced by buffered formalin fixation, although RT-PCR amplification of RNA extracted from archival formalin-fixed, paraffin-embedded tissue was hindered not only by degradation of RNA but also by modification of RNA bases by formalin. Preheating of RNA in TE buffer (pH 7.0) restored the template activity of RNA extracted from buffered formalin-fixed tissue where clear bands of 18S and 28S rRNA were still detected with partial degradation (Masuda et al. 1999 Our results indicate that efficiency of RT-PCR amplification with degraded RNA extracted from long-term preserved unbuffered formalin-fixed, paraffin-embedded tissue specimens (for 19 to 21 years) is improved by the heating of RNA in citrate buffer prior to cDNA synthesis. This enhanced efficiency was possibly caused by RNA modification elimination and subsequent RNA template activity restoration.
Fragment sizes of Furthermore, when amplicon size is very small, it is often difficult to design primers in restricted regions such as fusion points. Therefore, increased efficiency of RT-PCR amplification by the preheating of RNA is most effective when only limited quantities of archival formalin-fixed, paraffin-embedded tissue samples are available for study or when the designing of primers in restricted regions cannot be avoided.
Heat treatment with alkaline solution (pH 912) for DNA extraction from archival formalin-fixed, paraffin-embedded tissue increased the efficiency of DNA extraction, resulting in enhanced PCR amplification (Shi et al. 2002 Treatment with highly concentrated citrate buffer reduced the efficiency of RT-PCR amplification of RNA compared with non-treated RNA. In our experiment, incubation time of 3060 min in citrate buffer with pH 4.0 was the most efficient method for RT-PCR amplification. A longer incubation time, such as 2 hr, resulted in slightly decreased efficiency of RT-PCR amplification, suggesting that degradation of RNA may occur to some extent during the long preheating in citrate buffer at 70C. Preheating of RNA in citrate buffer resulted in improved efficiency of RT-PCR amplification in all five archival tissue specimens examined, suggesting that this method is useful for molecular analyses of long-term preserved tissue specimens. This technique will enable the qualitative analysis such as DNA rearrangement using degraded RNA extracted from archival unbuffered formalin-fixed, paraffin-embedded tissue specimens that have been stored for more than several decades. It will shed light on the retrospective studies of rare cancers or cancers associated with exposure to uncommon past events such as Thorotrast treatment, nuclear power station accidents, or atomic bombings.
The Radiation Effects Research Foundation (RERF), Hiroshima and Nagasaki, Japan is a private, non-profit foundation funded by the Japanese Ministry of Health, Labor and Welfare (MHLW) and the U.S. Department of Energy (DOE), the latter through the National Academy of Sciences. This publication was supported by RERF Research Protocol (RP) No. 5-02 and in part by Grant-in-Aid for JapanU.S. Cooperative Science Program Joint Project from the Japan Society for the Promotion of Science, for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and for Cancer Research from the Ministry of Health, Labor and Welfare of Japan. We thank Shiho Yano and Kanya Hamasaki for excellent technical assistance.
Received for publication October 19, 2005; accepted February 14, 2006
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