- Research article
- Open Access
- Open Peer Review
This article has Open Peer Review reports available.
Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas
© Fedorowicz et al; licensee BioMed Central Ltd. 2009
Received: 28 October 2008
Accepted: 08 May 2009
Published: 08 May 2009
Gene expression profiling of formalin-fixed, paraffin-embedded (FFPE) samples represents a valuable approach for advancing oncology diagnostics and enhancing retrospective clinical studies; however, at present, this methodology still requires optimization and thus has not been extensively used. Here, we utilized thorough quality control methods to assess RNA extracted from FFPE samples and then compared it to RNA extracted from matched fresh-frozen (FF) counterparts. We preformed genome-wide expression profiling of FF and FFPE ovarian serous adenocarcinoma sample pairs and compared their gene signatures to normal ovary samples.
RNA from FFPE samples was extracted using two different methods, Ambion and Agencourt, and its quality was determined by profiling starting total RNA on Bioanalyzer and by amplifying increasing size fragments of beta actin (ACTB) and claudin 3 (CLDN3) by reverse-transcriptase polymerase chain reaction. Five matched FF and FFPE ovarian serous adenocarcinoma samples, as well as a set of normal ovary samples, were profiled using whole genome Agilent microarrays. Reproducibility of the FF and FFPE replicates was measured using Pearson correlation, whereas comparison between the FF and FFPE samples was done using a Z-score analysis.
Data analysis showed high reproducibility of expression within each FF and FFPE method, whereas matched FF and FFPE pairs demonstrated lower similarity, emphasizing an inherent difference between the two sample types. Z-score analysis of matched FF and FFPE samples revealed good concordance of top 100 differentially expressed genes with the highest correlation of 0.84. Genes characteristic of ovarian serous adenocarcinoma, including a well known marker CLDN3, as well as potentially some novel markers, were identified by comparing gene expression profiles of ovarian adenocarcinoma to those of normal ovary.
Conclusively, we showed that systematic assessment of FFPE samples at the RNA level is essential for obtaining good quality gene expression microarray data. We also demonstrated that profiling of not only FF but also of FFPE samples can be successfully used to identify differentially expressed genes characteristic of ovarian carcinoma.
According to the American Cancer Society, ovarian cancer is the fifth leading cause of cancer deaths in women in the United States. The most common, epithelial, type of ovarian cancer can be divided into several subtypes including: serous, endometrioid, mucinous, clear cell and undifferentiated. Serous adenocarcinoma comprises majority of cases and exhibits a poor 5-year survival rate. Up to 90% of ovarian cancers might be cured if identified in an early stage. When diagnosed in later stages, the rate drops significantly to a range of 30–50%. Detection of ovarian cancer is often delayed or missed because of a lack of clear symptoms and absence of reliable diagnostic methods. Cancer marker 125 (CA125), the product of mucin 16, is currently used for testing patients with elevated risk of ovarian cancer. However, this marker alone does not provide the required sensitivity or specificity to detect all cases . Another gene, claudin 3 (CLDN3), has been found to be highly expressed at gene and protein levels and thus has been suggested as a reliable marker of ovarian cancer [2–5].
Large repositories of formalin-fixed, paraffin-embedded (FFPE) samples are available and could be used to identify markers for diagnosis of many diseases. While tissue integrity in FFPE specimens is often better preserved than in matched fresh-frozen (FF) counterparts, the quality of nucleic acids in FFPE samples is far from optimal due to chemical crosslinking and nucleic acid fragmentation [6–8]. Despite the detrimental effect of the fixative, numerous studies using archived FFPE samples have generated satisfactory reverse-transcriptase polymerase chain reaction (RT-PCR) data [9–13]. Recently, a number of genome-wide microarray studies has been conducted to investigate gene expression in FFPE samples or to compare the performance of FFPE samples with their matched FF counterparts [14–23]. While the results of some studies are discouraging [16, 19], many archived FFPE samples have been successfully used to identify prognostic and diagnostic gene signatures for numerous diseases, including various carcinomas [21–24].
Matched FF and FFPE samples were obtained from five ovarian serous adenocarcinoma patients. Samples 3136, 3138, 3194 and 3207 were collected on 11/2004, 11/2004, 05/2005, and 06/2005, respectively. A portion of each sample was either frozen at -80°C until extraction or fixed within 30 minutes of surgery by incubation in 10% neutral-buffered formalin (NBF) for 4–18 hours at 4°C. Patient sample 390 was collected on 01/2005 and was either frozen or fixed for 24 hours at room temperature in 10% NBF within 30 minutes of surgery. Only tumor samples containing minimal necrosis (<10%) and consisting of 70% or more tumor cells were used in this study. A set of normal ovary samples was obtained from different patients by dissecting normal tissue adjacent to tumors. All tumor and normal ovary samples were acquired commercially by the Human Tissue Lab at Genentech.
RNA extraction methods
Three 10-micron sections were homogenized individually and RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen, San Diego, CA). Replicate RNA preps were pooled to obtain sufficient amounts of starting material. For normal ovary samples, RNA was extracted using Qiagen's ALLPrep method that included on-column DNase treatment.
After evaluating four FFPE RNA extraction methods (Invitrogen PureLink, Ambion RecoverAll, Ambion Optimum and Agencourt FormaPure; data not shown), the Optimum FFPE RNA Isolation Kit (Ambion, Austin, TX) and the FormaPure Kit (Agencourt, Beverly, MA) were selected for this study based on their potential to generate the most abundant population of high molecular weight RNA fragments. The two methods were used to extract RNA from five archived FFPE ovarian serous adenocarcinoma samples. Up to eight 10-micron FFPE sections were processed per patient. Ambion's RNA extraction procedure was optimized for maximum RNA recovery (Susanna Stinson, Genentech, Inc., personal communication) by elevating the temperature of the first 10 min deparaffinization to 55°C and digesting the samples for 3 hours at 55°C. After adding a fresh aliquot of Proteinase K, the samples were digested for an additional hour at 55°C. The Agencourt protocol was followed without any modifications. DNase treatment was applied to both FF and FFPE samples and was followed by phenol:chloroform:isoamyl alcohol purification and ethanol precipitation.
Quality control methods
The quantity of RNA and labeled cRNA was measured using Nanodrop ND-1000 UV-spectrophotometer (NanoDrop Technologies, Wilmington, DE). Specific activity of cRNA, calculated as picomoles of Cy5 dye per microgram (μg) of cRNA, was also measured by Nanodrop. Sample integrity was evaluated by profiling both RNA and cRNA on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA integrity was determined by amplifying different length fragments (~200, 400, 600 and 800 basepairs (bp)) of beta actin (ACTB) and CLDN3 genes using Qiagen's OneStep RT-PCR kit protocol. The following 5'-3' primers were used to amplify ACTB [GenBank:NM_001101]: 200 F GGTGATAGCATTGCTTTCGTGTAA, 400 F CAGTCGGTTGGAGCGAGCATCC, 600 F CTCCATCGTCCACCGCAAATGC, 800 F GGCACCACCATGTACCCTGGCA and R TCAAGTCAGTGTACAGGTAAGCC. The following 5'-3' primers were used to amplify CLDN3 [GenBank:NM_001306]: 200 F CCATCCAGCGTGCAGCCTTGC, 400 F GCTGCTCTGCTGCTCGTGTCC, 600 F CCAAGATCACCATCGTGGCAGG, 800 F GCCTGTGGATGAACTGCGTGG and R AGTATTGGCGGTCACCCAGGC. Five nanograms of RNA were used as a template for reverse transcription (30 min at 50°C), followed by activation of the HotStarTaq polymerase (15 min at 95°C), 35 cycles of PCR (30 sec at 95°C, 30 sec at 60°C, and 1 min at 72°C), and final 10 min extension at 72°C. Each fragment was amplified individually; however, all of them were pooled and electrophoresed in a single lane. PCR products were visualized on 4% agarose e-gels (Invitrogen, Carlsbad, CA). SimplyLoad 100 bp DNA Ladder (Lonza, Basel, Switzerland) was used to determine product size.
Total RNA was labeled according to Agilent's Low RNA Input Fluorescent Linear Amplification Kit. The test samples (i.e. RNA from FF and FFPE samples) were labeled with the Cy5 dye and the reference sample (i.e. Universal Human Reference, Stratagene, La Jolla, CA) was labeled with the Cy3 dye. Matched FF samples (5 patients, 2 replicates) and FFPE samples extracted using either the Agencourt method (5 patients, 3 replicates for 3136, 3138 and 3194, 2 replicates for 3207 and 390) or the Ambion method (5 patients, no replicates) were hybridized to Agilent Whole Human Genome 4×44K microarrays according to the manufacturer's protocol. Microarray images were analyzed using Agilent's Feature Extraction (FE) software, version 9.5.
Reproducibility of the FF and FFPE sample types was measured using Pearson correlations (r). Only "passing" probes were included in this analysis, where "passing" consisted of probes that were not recognized as outliers by the FE software, were significantly above background, and had a P value of the Cy5/Cy3 ratio below 0.05. We compared results between sample types (frozen versus fixed) by applying a Z-score analysis  to the four samples whose quality was adequate for microarray profiling (3136, 3138, 3194, and 3207). For small data sets, the Z-score technique provides a method for determining genes that have significantly different expression in a single sample relative to other samples. These scores indicate the degree of deviation from the mean, in terms of the number of standard deviations, and they are likely to reveal well-behaving probes because they impose two requirements: a large deviation in one sample compared to the remaining samples, indicating a likely true biological difference in expression, and a small standard error, indicating that the probe set gives consistent measurements in the remaining n-1 samples. Before the Z-score analyses were applied, we computed geometric means of relevant replicate measurements for the two groups: FF tumor (4 patients, excluding sample 390) and FFPE-Agencourt tumor (4 patients, excluding sample 390). FFPE-Ambion tumor samples were not included in the Z-score analysis. We then computed Z-scores for each FFPE sample relative to the remaining three FFPE samples with a constant factor of 1 added to the denominator to avoid situations where the standard error was spuriously close to zero. For comparison, we also computed Z-scores using the same methodology for each of the FF samples relative to the other three FF samples. We then evaluated three criteria for filtering data from the FFPE samples. First, we considered all probes assayed on the array. Second, we considered only those probes where the Cy5 channel had a value of 1000 or greater ("1000 Cy5"). Finally, we considered top 100 differentially expressed probes that were both "1000 Cy5" and had the largest Z-scores, namely, the top 50 positive and top 50 negative Z-scores ("100 DE"). For each matched pair, we compared the selected FFPE Z-scores with corresponding FF Z-scores. Furthermore, for each of these three criteria, we evaluated correlation both quantitatively and qualitatively. The quantitative comparison measured the Pearson correlations of the Z-scores between the FFPE and FF samples. For the qualitative comparison, we tallied the "100 DE" probes whose signs of the FFPE Z-scores were the same as or opposite of the corresponding FF scores. The reported misclassification rates reflect the number of opposite-sign probes as a fraction of the total 100 probes.
Identification of genes that were differentially expressed in serous adenocarcinoma compared to normal ovary was achieved by a stepwise analysis. First, probes "passing" in all replicates of the four groups including FF, FFPE-Agencourt, and FFPE-Ambion tumors (see replicate details above) and FF normal samples (5 patients, 2 replicates per patient) were selected. Replicate Cy5/Cy3 ratios for each passing probe were averaged within a method before performing the Cyber t-test . This t-test compared Cy5/Cy3 log10 ratios of FF tumor (n = 5) vs normal (n = 5) and FFPE tumor (n = 4) vs normal (n = 5); only probes with P values of equal to or less than 0.05 were considered further. All patient samples within a method were then averaged by calculating geometric means of the Cy5/Cy3 ratios for the genes that passed the two previous criteria ("passing" and t-test P value cutoff of 0.05). The resulting tumor-to-normal ratios are reported, where the ratio is at least 2-fold higher in all tumors than in all normals.
Quality assessment of FF and FFPE samples
cRNA yields from FF samples averaged at 12.5 μg, while those from FFPE samples ranged from 2.2 to 6.1 μg. This illustrates greater dependence of cRNA yield on RNA quality than on quantity since equal amounts of total RNA were used to generate cRNAs. High specific activities ranging from 10.9 to 13.6 pmol Cy5/μg were observed for cRNAs from FF samples. The corresponding FFPE samples resulted in noticeably lower specific activities ranging from 1.6 to 7.6 pmol Cy5/μg cRNA. FFPE sample 390 had the lowest dye incorporation compared to all other samples: 1.6 and 2.4 pmol Cy5/μg cRNA for Agencourt and Ambion, respectively. Based on this result, as well as on poor RNA quality described above, FFPE sample 390 was expected to perform poorly in subsequent expression profiling.
Similar to the quality assessment of total RNA, labeled cRNA was also examined on the 2100 Bioanalyzer (Figure 1B). The size distribution of cRNA was very different when comparing electropherograms obtained from FF and FFPE samples. In FF samples, cRNAs showed a wide profile encompassing molecular weight size above 4000 nt, with the highest frequency of fragments in ~200 nt range. In contrast, cRNAs generated from FFPE samples had narrow profiles of up to ~1000 nt, with the highest frequency of fragments in ~100 nt range. Similar to the initial total RNA profile, cRNA for sample 390 showed a very narrow distribution range and lacked fragments above ~500 nt.
Gene expression profiling
List of genes whose ratios are at least two-fold higher in ovarian serous adenocarcinoma compared to normal ovary.
FF tumor/FF normal ratio
FFPE tumor/FF normal ratio
tumor-associated calcium signal transducer 1 (TACSTD1), mRNA [NM_002354]
ATPase family, AAA domain containing 4 (ATAD4), mRNA [NM_024320]
claudin 3 (CLDN3), mRNA [NM_001306]
Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), [THC2546981]
B-cell CLL/lymphoma 11A (zinc finger protein) (BCL11A), transcript variant 1, mRNA [NM_022893]
mRNA; cDNA DKFZp666L166 (from clone DKFZp666L166). [AL833749]
chromosome 1 open reading frame 172 (C1orf172), mRNA [NM_152365]
MARVEL domain containing 3 (MARVELD3), transcript variant 1, mRNA [NM_001017967]
SNAP25-interacting protein (SNIP), mRNA [NM_025248]
ring finger protein 183 (RNF183), mRNA [NM_145051]
thymidylate synthetase (TYMS), mRNA [NM_001071]
Incyte sequence 47 from Patent WO0220754. [AX721087]
BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) (BUB1B), mRNA [NM_001211]
AGENCOURT_10326456 NIH_MGC_141 cDNA clone IMAGE:6571686 5', mRNA [BU540282]
eyes absent homolog 2 (Drosophila) (EYA2), transcript variant 2, mRNA [NM_172113]
v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) (ERBB4), mRNA [NM_005235]
cell division cycle associated 2 (CDCA2), mRNA [NM_152562]
glucosidase, beta (bile acid) 2 (GBA2), mRNA [NM_020944]
mRNA full length insert cDNA clone EUROIMAGE 1090207. [AJ420543]
B-cell CLL/lymphoma 11A (zinc finger protein) (BCL11A), transcript variant 1, mRNA [NM_022893]
paired box gene 8 (PAX8), transcript variant PAX8A, mRNA [NM_003466]
mRNA for FLJ00399 protein. [AK090477]
clone IMAGE:5241654, mRNA. [BC038245]
pituitary tumor-transforming 2 (PTTG2), mRNA [NM_006607]
calcyphosine (CAPS), transcript variant 1, mRNA [NM_004058]
cytochrome P450, family 4, subfamily X, polypeptide 1 (CYP4X1), mRNA [NM_178033]
cDNA FLJ12206 fis, clone MAMMA1000941. [AK022268]
denticleless homolog (Drosophila) (DTL), mRNA [NM_016448]
chondrolectin (CHODL), mRNA [NM_024944]
cDNA FLJ14712 fis, clone NT2RP3000825. [AK027618]
glucosaminyl (N-acetyl) transferase 3, mucin type. Acc:NP_004742] [ENST00000267857]
colon cancer-associated antigen AgSK1-2HT-ECS mRNA, complete cds. [AF316855]
v-myb myeloblastosis viral oncogene homolog (avian) (MYB), mRNA [NM_005375]
DNA (cytosine-5-)-methyltransferase 3 beta (DNMT3B), transcript variant 6, mRNA [NM_175850]
mRNA; cDNA DKFZp686J17110 (from clone DKFZp686J17110) [CR749547]
colon cancer-associated antigen AgSK1-2HT-ECS mRNA, complete cds. [AF316855]
preferentially expressed antigen in melanoma (PRAME), transcript variant 5, mRNA [NM_206956]
agmatine ureohydrolase (agmatinase) (AGMAT), mRNA [NM_024758]
v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA [NM_004333]
cDNA clone IMAGE:4290767. [BC008476]
cell division cycle 6 homolog (S. cerevisiae) (CDC6), mRNA [NM_001254]
Q2M1U4_HUMAN (Q2M1U4) Catalase, partial (31%) [THC2640472]
dystrobrevin binding protein 1 (DTNBP1), transcript variant 2, mRNA [NM_183040]
insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3), mRNA [NM_006547]
coagulation factor V (proaccelerin, labile factor) (F5), mRNA [NM_000130]
chromatin licensing and DNA replication factor 1 (CDT1), mRNA [NM_030928]
cDNA FLJ12257 fis, clone MAMMA1001501, highly similar to CALPAIN 1. [AK022319]
zinc finger, MYND-type containing 15 (ZMYND15), mRNA [NM_032265]
POU 5 domain protein (POU5FLC1) mRNA, complete cds. [AF268613]
dihydrofolate reductase (DHFR), mRNA [NM_000791]
hypothetical protein DKFZp762E1312 (DKFZp762E1312), mRNA [NM_018410]
forkhead box F2 (FOXF2), mRNA [NM_001452]
Ras association (RalGDS/AF-6) domain family 4 (RASSF4), mRNA [NM_032023]
mRNA; cDNA DKFZp586J101 (from clone DKFZp586J101). [AL050376]
succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 3 (SDHAP3) [NR_003263]
sal-like 4 (Drosophila) (SALL4), mRNA [NM_020436]
POU domain, class 5, transcription factor 1 (POU5F1), transcript variant 1, mRNA [NM_002701]
CD44 molecule (Indian blood group) (CD44), transcript variant 1, mRNA [NM_000610]
FFPE samples are a desirable source of archival material for gene expression profiling studies due to their availability and the possibility of retrospective studies. At present, great variability is still being observed between gene expression profiles of matched FF and FFPE samples. Sample source and its classification, as well as the conditions used to fix and store samples, are some of many possible variables influencing gene expression. For example, a study relying on controlled fixation conditions to process bone marrow cells reported that FFPE samples appeared very similar to those of unfixed frozen equivalents . However, controlled fixation procedure and use of cells may not represent an optimal approach to demonstrate the performance of archived FFPE tissue samples. Unsurprisingly, we have previously observed that FFPE cell pellets dissociated faster during Proteinase K digestion and often resulted in better RNA quality compared to FFPE tissues.
FFPE samples are routinely prepared by fixing tissues in 10% neutral-buffered formalin for 12 to 24 hours at ambient temperature. The FFPE samples used in this study, except for sample 390, were fixed in formalin for 4 to 18 hours at 4°C. These samples appear to perform better than sample 390 which was fixed using routine conditions. Thus, it appears that shorter time and lower temperature of fixation can significantly affect FFPE sample quality. Other variables such as size of collected tissue, time elapsed to fixation and storage time could have further affected this outcome [33, 34]. Regarding storage time, we have noticed that ribosomal RNA peaks could be detected in FFPE samples that were stored properly for up to one year and not for longer periods of time (data not shown).
Two commercially available FFPE RNA isolation kits, Ambion Optimum and Agencourt FormaPure, were tested here for extracting RNA from five FFPE ovarian serous adenocarcinoma samples. Sufficient amounts of total RNA for gene expression profiling were achieved by processing two to eight FFPE sections per patient. Despite pooling multiple sections, the RNA yields from FFPE samples were always significantly lower compared to those obtained from FF samples (data not shown). In addition, the obtained RNA amount was not proportional to the surface area of tissues used for RNA extraction. Although significant necrosis was not detected in any of the sections, we noticed differences in tissue density and composition. For example, presence of vasculature and adipose was detected in some sections and undoubtedly affected the amounts of recovered nucleic acids. With respect to tissue content, all FFPE samples used in this study were required to contain 70–85% tumor cells, ensuring that they truly represented ovarian serous adenocarcinomas.
Two quality control assays, the Agilent 2100 Bioanalyzer and RT-PCR, were employed to assess the integrity of RNA obtained from FF and FFPE samples. Although RNA profiles from FFPE samples lacked well defined 18S and 28S ribosomal peaks, the method was successful in identifying inadequate samples, such as sample 390, containing predominantly small molecular weight fragments (<200 nt). Our RT-PCR assay tested the RNA for the presence of different size fragments of two genes, ACTB and CLDN3. Not surprisingly, we were not able to amplify any fragments in FFPE sample 390. Thus, the data synergy observed between the Bioanalyzer and the RT-PCR assay proved to be very useful in qualifying FFPE samples suitable for gene expression profiling on microarrays. These two assays also demonstrated that both the Ambion Optimum and the Agencourt FormaPure methods were successful in obtaining RNA of similar quality. Together, the combination of quality control methods used here should be effective in recognizing poor-performing FFPE samples and could be used to prevent unnecessary array hybridizations. A different method for identifying unacceptable FFPE samples has been described by NuGEN Technologies .
Gene expression profiling data of ovarian tumors demonstrated high correlations between replicate FF (≥0.988) and FFPE samples (≥0.983), illustrating good reproducibility of each method. Although reproducible, gene expression profiling of FFPE samples is affected by reduced number of "passing" probes (33–46% compared to 44–49% in FF) and thus detects fewer differentially expressed genes compared to FF samples. Lassmann et al. recently reported similar findings by detecting 36% and 50% of probes for FFPE and FF samples, respectively . Our comparison between FF and their matched FFPE samples revealed the highest concordance of 0.84 for sample 3194. Although not directly comparable, a mean concordance of 0.86 was reported previously when comparing matched FF and FFPE samples on a different microarray platform . Haque et al. reported a correlation of 0.65 between unmatched FF and FFPE pediatric glioblastomas . While the magnitude of differential expression in FFPE samples might not be accurate, our Z-score analysis indicated that the direction of the change was correct in most cases, as demonstrated by low misclassification rates.
The comparison of ovarian serous adenocarcinoma to normal ovary identified 56 genes that are overexpressed in both FF and FFPE tumor samples. Several genes among them, including CLDN3, were previously recognized for their roles in ovarian tumorigenesis, [2–5, 30–32]; additional genes with unknown roles were also identified. Profiling of archival FFPE samples has been used previously to identify gene signatures that may serve as prognostic and diagnostic markers [20–24]. Regarding ovarian cancer, a set of 86 gene signatures that seems to predict overall survival was recently identified by microarray profiling . Furthermore, 57 of these 86 genes were confirmed in an independent dataset . Together, these findings suggest that archival FFPE samples can be successfully used to identify potentially novel disease markers. At the same time, it is recognized that gene expression profiling of FFPE samples on microarrays has some limitations. In our study, as well as in Van Deerlin et al. , the magnitude of differential expression was typically higher in FFPE than in FF samples, suggesting higher level of noise in the FFPE data. Therefore, the elimination of false positives and identification of subtle changes in gene expression in FFPE samples remain challenging, especially in studies lacking FF counterparts.
Technological improvements in handling FFPE samples are constantly evolving; some of them clearly lead towards better quality of microarray expression data. One such improvement entails a change in primers used during amplification. At present, commonly used procedures rely on oligo (dT) primers which introduce 3' end bias [17, 39]; consequently, most commercial microarrays have probes designed within the last several hundred bases of each transcript. A new amplification procedure, developed recently by NuGEN, utilizes random primers in addition to oligo (dT) primers, thus alleviating the 3' end bias. Initial studies suggest that such whole transcript amplification provides a significant advantage when processing FFPE samples [14, 20]. Thus, this amplification method deserves further investigation and holds promise for improving the performance of FFPE samples in future microarray profiling studies.
Five matched FFPE and FF ovarian tumor samples were profiled on microarrays, illustrating the level of gene expression similarity between the two sample types. Ovarian tumor and normal samples were also compared, identifying a set of differentially expressed genes characteristic of ovarian adenocarcinoma. Conclusively, our study demonstrates that archived clinical samples, such as FFPE ovarian adenocarcinomas, represent a valuable source for genome-wide expression profiling and can be successfully used for the identification of potentially novel carcinoma markers. Further improvements in FFPE sample handling and new amplification approaches hold promise for even better performance of FFPE samples in future microarray studies.
We would like to thank Susanna Stinson for optimizing the FFPE RNA extraction procedure, Deepali Bhatt for extracting normal ovary RNA, Human Tissue Bank and Pathology personnel for providing matched FF and FFPE serous adenocarcinomas, and the Oligo group for synthesizing primers.
- Rosen DG, Wang L, Atkinson N, Yu Y, Lu KH, Diamandis EP, Hellstrom I, Mok SC, Liu J, Bast RC: Potential markers that complement expression of CA125 in epithelial ovarian cancer. Gynecol Oncol. 2005, 99: 267-277. 10.1016/j.ygyno.2005.06.040.View ArticlePubMedGoogle Scholar
- Choi YL, Kim J, Kwon MJ, Choi JS, Kim TJ, Bae DS, Koh SS, In YH, Park YW, Kim SH, Ahn G, Shin YK: Expression profile of tight junction protein claudin 3 and claudin 4 in ovarian serous adenocarcinoma with prognostic correlation. Histol Histopathol. 2007, 22: 1185-95.PubMedGoogle Scholar
- Bignotti E, Tassi RA, Calza S, Ravaggi A, Romani C, Rossi E, Falchetti M, Odicino FE, Pecorelli S, Santin AD: Differential gene expression profiles between tumor biopsies and short-term primary cultures of ovarian serous carcinomas: Identification of novel molecular biomarkers for early diagnosis and therapy. Gynecol Oncol. 2006, 103: 405-416. 10.1016/j.ygyno.2006.03.056.View ArticlePubMedGoogle Scholar
- Peters DG, Kudla DM, Deloia JA, Chu TJ, Fairfull L, Edwards RP, Ferrell RE: Comparative gene expression analysis of ovarian carcinoma and normal ovarian epithelium by serial analysis of gene expression. Cancer Epidemiol Biomarkers Prev. 2005, 14: 1717-1723. 10.1158/1055-9965.EPI-04-0704.View ArticlePubMedGoogle Scholar
- Hough CD, Sherman-Baust CA, Pizer ES, Montz FJ, Im DD, Rosenshein NB, Cho KR, Riggins GJ, Morin PJ: Large-scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer. Cancer Res. 2000, 60: 6281-7.PubMedGoogle Scholar
- Krafft AE, Duncan BW, Bijwaard KE, Taubenberger JK, Lichy JH: Optimization of the isolation and amplification of RNA from formalin-fixed, paraffin-embedded tissue: The Armed Forces Institute of Pathology Experience and Literature Review. Mol Diagn. 1997, 2: 217-230. 10.1016/S1084-8592(97)80032-X.View ArticlePubMedGoogle Scholar
- Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K: Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology application for such samples. Nucleic Acids Res. 1999, 27: 4436-4443. 10.1093/nar/27.22.4436.View ArticlePubMedPubMed CentralGoogle Scholar
- Stanta G, Mucelli SP, Petrera F, Bonin S, Bussolati G: A novel fixative improves opportunities of nucleic acids and proteomic analysis in human archive's tissues. Diagn Mol Pathol. 2006, 15: 115-123. 10.1097/00019606-200606000-00009.View ArticlePubMedGoogle Scholar
- Specht K, Richter T, Müller U, Walch A, Werner M, Höfler H: Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol. 2001, 158: 419-429.View ArticlePubMedPubMed CentralGoogle Scholar
- Cronin M, Pho M, Dutta D, Stephans JC, Shak S, Kiefer MC, Esteban JM, Baker JB: Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am J Pathol. 2004, 164: 35-42.View ArticlePubMedPubMed CentralGoogle Scholar
- Gloghini A, Canal B, Klein U, Dal Maso L, Perin T, Dalla-Favera R, Carbone A: RT-PCR analysis of RNA extracted from Bouin-fixed and paraffin-embedded lymphoid tissues. J Mol Diagn. 2004, 6: 290-296.View ArticlePubMedPubMed CentralGoogle Scholar
- Pagedar NA, Wang W, Chen DH, Davis RR, Lopez I, Wright CG, Alagramam KN: Gene expression analysis of distinct populations of cells isolated from mouse and human inner ear FFPE tissue using laser capture microdissection – a technical report based on preliminary findings. Brain Res. 2006, 1091: 289-299. 10.1016/j.brainres.2006.01.057.View ArticlePubMedGoogle Scholar
- Hamatani K, Eguchi H, Takahashi K, Koyama K, Mukai M, Ito R, Taga M, Yasui W, Nakachi K: Improved RT-PCR amplification for molecular analyses with long-term preserved formalin-fixed, paraffin-embedded tissue specimens. J Histochem Cytochem. 2006, 54: 773-780. 10.1369/jhc.5A6859.2006.View ArticlePubMedGoogle Scholar
- Scicchitano MS, Dalmas DA, Bertiaux MA, Anderson SM, Turner LR, Thomas RA, Mirable R, Boyce RW: Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. J Histochem Cytochem. 2006, 54: 1229-1237. 10.1369/jhc.6A6999.2006.View ArticlePubMedGoogle Scholar
- Coudry RA, Meireles SI, Stoyanova R, Cooper HS, Carpino A, Wang X, Engstrom PF, Clapper ML: Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue. J Mol Diagn. 2007, 9: 70-79. 10.2353/jmoldx.2007.060004.View ArticlePubMedPubMed CentralGoogle Scholar
- Karsten SL, Van Deerlin VMD, Sabatti C, Gill LH, Geschwind DH: An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res. 2002, 30: e4-10.1093/nar/30.2.e4.View ArticlePubMedPubMed CentralGoogle Scholar
- Frank M, Döring C, Metzler D, Eckerle S, Hansmann ML: Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays. Virchows Arch. 2007, 450: 699-711. 10.1007/s00428-007-0412-9.View ArticlePubMedGoogle Scholar
- Linton KM, Hey Y, Saunders E, Jeziorska M, Denton J, Wilson CL, Swindell R, Dibben S, Miller CJ, Pepper SD, Radford JA, Freemont AJ: Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer. 2008, 98: 1403-1414. 10.1038/sj.bjc.6604316.View ArticlePubMedPubMed CentralGoogle Scholar
- Penland SK, Keku TO, Torrice C, He X, Krishnamurthy J, Hoadley KA, Woosley JT, Thomas NE, Perou CM, Sandler RS, Sharpless NE: RNA expression analysis of formalin-fixed paraffin-embedded tumors. Lab Invest. 2007, 87: 383-391.PubMedGoogle Scholar
- Lassmann S, Kreutz C, Schoepflin A, Hopt U, Timmer J, Werner M: A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. J Mol Med. 2009, 87: 211-24. 10.1007/s00109-008-0419-y.View ArticlePubMedGoogle Scholar
- Chung CH, Parker JS, Ely K, Carter J, Yi Y, Murphy BA, Ang KK, El-Naggar AK, Zanation AM, Cmelak AJ, Levy S, Slebos RJ, Yarbrough WG: Gene expression profiles identify epithelial-to-mesenchymal transition and activation of nuclear factor-(kappa)B signaling as characteristics of a high-risk head and neck squamous cell carcinoma. Cancer Res. 2006, 66: 8210-8218. 10.1158/0008-5472.CAN-06-1213.View ArticlePubMedGoogle Scholar
- Onken MD, Worley LA, Ehlers JP, Harbour JW: Gene expression profiling in unveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res. 2004, 64: 7205-7209. 10.1158/0008-5472.CAN-04-1750.View ArticlePubMedGoogle Scholar
- Haque T, Faury D, Albrecht S, Lopez-Aquilar E, Hauser P, Garami M, Hanzély Z, Bognár L, Del Maestro RF, Atkinson J, Nantel A, Jabado N: Gene expression profiling from formalin-fixed paraffin-embedded tumors of pediatric glioblastoma. Clin Cancer Res. 2007, 13: 6284-6292. 10.1158/1078-0432.CCR-07-0525.View ArticlePubMedGoogle Scholar
- Rogerson L, Darby S, Jabbar T, Mathers ME, Leung HY, Robson CN, Sahadevan K, O'Toole K, Gnanapragasam VJ: Application of transcript profiling in formalin-fixed paraffin-embedded diagnostic prostate cancer needle biopsies. BJU Int. 2008, 102: 364-370. 10.1111/j.1464-410X.2008.07627.x.View ArticlePubMedGoogle Scholar
- Cheadle C, Vawter MP, Freed WJ, Becker KG: Analysis of microarray data using Z score transformation. J Mol Diagn. 2003, 5: 73-81.View ArticlePubMedPubMed CentralGoogle Scholar
- Baldi P, Long AD: A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics. 2001, 17: 509-519. 10.1093/bioinformatics/17.6.509.View ArticlePubMedGoogle Scholar
- Borlado LR, Mendez J: CDC6: from DNA replication to cell cycle checkpoints and oncogenesis. Carcinogenesis. 2008, 29: 237-243. 10.1093/carcin/bgm268.View ArticlePubMedGoogle Scholar
- Liontos M, Koutsami M, Sideridou M, Evangelou K, Kletsas D, Levy B, Kotsinas A, Nahum O, Zoumpourlis V, Kouloukoussa M, Lygerou Z, Taraviras S, Kittas C, Bartkova J, Papavassiliou AG, Bartek J, Halazonetis TD, Gorgoulis VG: Deregulated overexpression of hCdt1 and hCdc6 promotes malignant behaviour. Cancer Res. 2007, 67: 10899-10909. 10.1158/0008-5472.CAN-07-2837.View ArticlePubMedGoogle Scholar
- Sansam CL, Shepard JL, Lai K, Ianari A, Danielian PS, Amsterdam A, Hopkins N, Lees JA: DTL/CDT2 is essential for both CDT1 regulation and the early G2/M checkpoint. Genes Dev. 2006, 20: 3117-3129. 10.1101/gad.1482106.View ArticlePubMedPubMed CentralGoogle Scholar
- Giordano TJ, Shedden KA, Schwartz DR, Kuick R, Taylor JM, Lee N, Misek DE, Greenson JK, Kardia SL, Beer DG, Rennert G, Cho KR, Gruber SB, Fearon ER, Hanash S: Organ-specific molecular classification of primary lung, colon, and ovarian adenocarcinomas using gene expression profiles. Am J Pathol. 2001, 159: 1231-1238.View ArticlePubMedPubMed CentralGoogle Scholar
- Gilmour LM, Macleod KG, McCaig A, Gullick WJ, Smyth JF, Langdon SP: Expression of erbB-4/HER-4 growth factor receptor isoforms in ovarian cancer. Cancer Res. 2001, 61: 2169-2176.PubMedGoogle Scholar
- Nonaka D, Chiriboga L, Soslow RA: Expression of Pax8 as a useful marker in distinguishing ovarian carcinomas from mammary carcinomas. Am J Surg Pathol. 2008, 32: 1566-1571. 10.1097/PAS.0b013e31816d71ad.View ArticlePubMedGoogle Scholar
- Gruber AD, Moennig V, Hewicker-Trautwein M, Trautwein G: Effect of formalin fixation and long-term storage on the detectability of bovine viral-diarrhoea-virus (BVDV) RNA in archival brain tissue using polymerase chain reaction. Zentralbl Veterinarmed B. 1994, 41: 654-661.PubMedGoogle Scholar
- Macabeo-Ong M, Ginzinger DG, Dekker N, McMillan A, Regezi JA, Wong DT, Jordan RC: Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses. Mod Pathol. 2002, 15: 979-987. 10.1097/01.MP.0000026054.62220.FC.View ArticlePubMedGoogle Scholar
- The NuGEN website. [http://www.nugeninc.com/tasks/sites/nugen/assets/File/technical_documents/techdoc_wt_ov_ffpe_rep_01.pdf]
- Crijns AP, Fehrmann RS, de Jong S, Gerbens F, Meersma GJ, Klip HG, Hollema H, Hofstra RM, Meerman GJ, de Vries EG, Zee van der AG: Survival-related profile, pathways, and transcription factors in ovarian cancer. PLoS Med. 2009, 6: e24-10.1371/journal.pmed.1000024.View ArticlePubMedGoogle Scholar
- Dressman HK, Berchuck A, Chan G, Zhai J, Bild A, Sayer R, Cragun J, Clarke J, Whitaker RS, Li L, Gray J, Marks J, Ginsburg GS, Potti A, West M, Nevins JR, Lancaster JM: An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer. J Clin Oncol. 2007, 25: 517-525. 10.1200/JCO.2006.06.3743.View ArticlePubMedGoogle Scholar
- Van Deerlin VM, Gill LH, Nelson PT: Optimizing gene expression analysis in archival brain tissue. Neurochem Res. 2002, 27: 993-1003. 10.1023/A:1020996519419.View ArticlePubMedGoogle Scholar
- Srivastava PK, Küffer S, Brors B, Shahi P, Li L, Kenzelmann M, Gretz N, Gröne HJ: A cut-off based approach for gene expression analysis of formalin-fixed and paraffin-embedded tissue samples. Genomics. 2008, 91: 522-529. 10.1016/j.ygeno.2008.03.003.View ArticlePubMedGoogle Scholar
- The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1755-8794/2/23/prepub
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.