The murine plasma cell tumor cell line TEPC 1165  was used both as a source of frozen sections for LCM as well as a source of reference RNA, i.e., RNA extracted without LCM processing. Cells were grown in RPMI 1640 media supplemented with 10% fetal bovine serum, 10 ng/ml IL-6, 4 mM L-glutamine and 100 units/ml penicillin and 100 units/ml streptomycin. Duplicate cell pellets were collected by low-speed centrifugation in 50-ml conical centrifuge tubes and immediately snap frozen for RNA extraction and LCM preparation.
Preparation of LCM samples
The cell pellets were frozen in a dry ice-ethanol bath, embedded with OCT frozen tissue embedding medium, and stored at -80°C. Six-micrometer serial frozen sections were cut on a cryostat at -20°C and mounted on chilled, pre-cleaned, uncoated microscope glass slides that had been heated at 200°C overnight to eliminate RNAase. Slides were kept on dry ice or at -80°C until LCM was completed. Sections were stained individually with four different methods before LCM. RNAase-free (treated with diethylpyrocarbonate) water was used for all solutions. All procedures were carried out at room temperature, unless otherwise stated, and usually on the same day as the frozen sectioning.
Methyl Green Pyronin staining
After fixation in 70% ethanol (10 sec), each slide was rinsed in DEPC-treated water (5 sec). Then, 50 μl of MGP staining solution (Sigma/Aldrich) to which RNAase inhibitor (SUPERase*In, Ambion) had been added to a final concentration of 500 U/ml, was applied to the section and incubated 2 min, followed by a quick dip in diethylpyrocarbonate-treated water, dehydration in 100% ethanol in 2 steps (quick dip, then for 10–15 sec), and xylenes in 2 steps (2 min then 3 min). It is important to note that MGP, like all histological stains, yields significantly less detail on frozen sections than on paraffin-embedded tissue, in part, owing to lack of a cover slip. MGP did enable identification of plasma cells in oil granulomas under these conditions. To be used in this way, however, one must include RNAase inhibitor if RNA extraction is desired after LCM.
Hematoxylin and eosin staining
A modification was incorporated into the manufacturer's (Sigma/Aldrich) protocol; namely, RNAase inhibitor (SUPERase*In, Ambion) was added to the aqueous hematoxylin solution to a final concentration of 500 U/ml. Briefly, slides were stained as follows: 70% EtOH for 10 sec, DEPC-treated water for 5 sec, hematoxylin with RNAase inhibitor for 20 sec, 70% EtOH for 30 sec, eosin Y in 100% EtOH for 20 sec, followed by dehydration with a series of alcohol for 30 sec each, and xylenes for 2 min.
The frozen sections were fixed with 70% ethanol (30 sec), rinsed in DEPC-treated water (30 sec), immersed in NS staining solution (Arcturus Corp.) for 30 sec, dehydrated with graded alcohols (30 sec each) and xylenes (2 min and 3 min).
Sections were fixed in ice-cold acetone for 2 min, rinsed in DEPC-treated PBS for 10 sec, incubated with a 1:250 dilution of goat anti-mouse Igκ conjugated with TXRD (Southern Biotechnology Associates, Inc.) to which RNAase inhibitor (SUPERase*In, Ambion) had been added to a final concentration of 500 U/ml, for 2 min in the dark, dehydrated with 100% ethanol and xylenes (11).
Laser capture microscopy
Cells were lifted from the slide onto CapSure LCM plastic caps (Arcturus Corp.) using a 30-μm spot size of laser at the power of 50 μv using PixCell II LCM system (Arcturus Corp.).
RNA extraction and purification
Total RNA from the unprocessed cell pellet was extracted using TriZol reagent (Sigma), treated with RNAase-free DNAase I (Qiagen, Inc.), followed by RNA purification with Qiagen RNeasy kit according to the manufacturer's protocol. RNA concentration was measured spectrophotometrically.
RNA extraction of 16 LCM-derived samples (4 from each staining group) was performed with the PicoPure RNA extraction kit (Arcturus Corp.), simultaneously treated with RNAase-free DNAase I (Qiagen, Inc) according to the manufacturer's protocol. Briefly, 50 μl of extraction buffer was pipetted onto the tissue fragments that had been collected in the cap of a sterile plastic 1.5-micro-centrifuge tube (CapSure LCM caps, Arcturus Corp.), and they were incubated together in a hot-air oven at 42°C for 30 min. Cells and buffer were collected by centrifugation at 800 × g for 2 min. RNA was DNAase-treated and purified on a preconditioned RNA-purification spin column according to the manufacturer's recommendations. LCM-derived total RNA was quantitated with Ribogreen (Molecular Probes, Inc.) using Victor 2 1420 multilabel counter (Perkin-Elmer/Wallac). To assess the RNA quality and confirm the absence of genomic DNA contamination, the Agilent 2100 Bioanalyzer (Pico RNA chip) was used to perform electrophoresis on picogram amounts of total RNA. Only samples with intact 18S and 28S rRNA peaks were used for gene expression analysis.
We performed antisense RNA amplification of each RNA sample with RiboAmp™ RNA Amplification kit (Arcturus, Inc.) based on T7 RNA polymerase in vitro transcription of cDNA synthesized by reverse transcription primed by oligo-dT attached to the T7 RNA polymerase promoter . To avoid bias caused by different starting amounts of total RNA in the amplification process, 5 ng of total RNA were used in all experimental and reference samples. To obtain sufficient antisense RNA for microarray experiments, two rounds of amplification were performed on all samples. The total yield of amplification products was determined using Ribogreen (Molecular Probes, Inc.), and the sizes of the amplified RNAs were determined with the Agilent Bioanalyzer (nano RNA chip).
Probe labeling and cDNA array hybridization
Probes were synthesized and labeled from 4 μg of amplified RNA (aRNA) by the method of Xiang et al . In brief, 4 μg of amplified RNA were combined with 4 μg amine-modified random primer and 5 units of RNAase inhibitor (SUPERase*In, Ambion). The mixture was incubated at 70°C for 10 min, then chilled on ice for 10 min, and left at room temperature for 10 min. Primer-RNA solution was added to the reverse transcriptase mix (including 0.5 mM dATP, dGTP, dCTP, 0.3 mM dTTP, and 0.2 mM aminoallyl-dUTP) and incubated at 42°C for 2 h. The reaction was terminated by adding 10 μl 0.5 M EDTA, and RNA was hydrolyzed with 10 μl 1 M NaOH at 65°C for 30 min. The solution was neutralized with 10 μl 1 M HCl, and then MinElute PCR purification kits (Qiagen, Inc) were used to purify the cDNAs. The cDNA was eluted three times with 10 μl of H2O. In each staining group 3 of the 4 reference RNA samples were labeled with Cy5, while 1 of the 4 was labeled with Cy3. Three of each group of 4 experimental samples were labeled with Cy3, and 1 of 4 was labeled with Cy5 to test for bias from labeling. Probes were mixed and hybridized overnight at 42°C in hybridization solution (New England Nuclear) to microarray chips with a total of 9998 cDNA elements (InCyte) printed by the NCI microarray facility.
Evaluation of gene-specific dye bias
Four arrays were hybridized for each of the 4 groups (MGP, HE, IF, NS). In each group 3 arrays had cDNA derived from the reference, unsectioned pellet of cells labeled with Cy5 and the LCM-derived test sample labeled with Cy3, and one array had the labeling reversed. We were interested in evaluating the possibility of gene-specific dye bias that was not removed by the normalization process. To evaluate this possibility, we computed the average difference in log2 ratio between normalized forward- and reverse-label experiments for each array element as an estimate of the residual dye bias for the associated gene. Of the 8534 array elements, none had an average difference of log2 ratio in absolute value greater than 1 (i.e., 2-fold difference). Thus, we concluded that after normalization there was no systematic bias favoring either dye.
Array scanning and data processing
Arrays were scanned at 10-μm resolution using a GenePix 4000 (Axon Inc.) array scanner. PMT voltages were varied to gain optimum intensity of the spots. Four duplicate hybridizations/slides were used in each experiment. LCM-derived RNAs were regarded as "experimental" samples, and 3 of the 4 cDNA probes derived from them were labeled with Cy3, whereas the "reference" samples, derived from RNA from unprocessed cell pellets were usually labeled with Cy5. To rule out color bias produced by the labeling process itself, the fluorochromes were reversed once in each group of four repeats. Quantification files were obtained by using the GenePixPro 4.0 software (Axon Inc.). The fluorescence signal intensity was determined as the volume in a fixed-size circle, and background was estimated as the median pixel value in a diamond-shaped region between each adjacent four-spot region.
Data filtering and normalization
Log-ratios of local median background-subtracted intensity levels were analyzed. For each array element, if the intensity was less than 75 in one channel but greater than 75 in the other channel, the intensity <75 was set at 75. Array elements that were flagged as poor quality during image analysis or that had intensities less than 75 in both channels were not reliable and treated as missing . Six percent of the array elements were found to be missing in this way. Those samples with missing values for a particular array element were excluded from all analyses involving that array element. In order to have enough samples in each group to compare expression profiles between the groups, array elements were further filtered out and removed from analysis if their number of non-missing values in each group was less than three. Eleven percent of the array elements were filtered out in this way, resulting in 8534 array elements for analysis. Log-ratios for each microarray were normalized by the locally robust lowess smoother (20) to adjust for any dye bias and variation in PMT voltage settings.
Average linkage hierarchical analysis of differentially expressed genes was performed by using 1-Pearson correlation as the distance metric to group genes based on their patterns of variation across the staining groups. The clusters and associated heat maps were implemented in R.
Enumeration of differentially expressed genes
Identification of array elements that were differentially expressed between each subgroup and the reference sample and among subgroups was done using one-sample t-tests and two-sample t-tests, respectively. Differentially expressed genes were identified as those genes that were significant at the 0.001 level (p < 0.001) and which were at least 2-fold different in the geometric mean of the expression measurements. A treated subgroup was considered to have weaker expression than another treated subgroup if, among the genes that were differentially expressed between these two subgroups, it had more lower-expressed genes than higher-expressed genes. A global permutation test was used as a global test to assess if one subgroup had statistically significant weaker expression than the other subgroup. Specifically, two-sample t-tests were performed by randomly permuting the group labels. In each permutation, the difference between the number of lower-expressed genes and the number of higher-expressed genes was recorded. The p-value of the permutation test was the proportion of permutations with the same or larger difference as those observed in the original data. Two subgroups would be defined as having globally significant different expression profiles if the p-value from the permutation test is less than 0.05.