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Proc Natl Acad Sci U S A. 2008 Sep 2; 105(35): 12885–12890.
Published online 2008 Aug 26. doi:  10.1073/pnas.0806202105
PMCID: PMC2529070
Cell Biology

MicroRNAs regulate critical genes associated with multiple myeloma pathogenesis

Abstract

Progress in understanding the biology of multiple myeloma (MM), a plasma cell malignancy, has been slow. The discovery of microRNAs (miRNAs), a class of small noncoding RNAs targeting multiple mRNAs, has revealed a new level of gene expression regulation. To determine whether miRNAs play a role in the malignant transformation of plasma cells (PCs), we have used both miRNA microarrays and quantitative real time PCR to profile miRNA expression in MM-derived cell lines (n = 49) and CD138+ bone marrow PCs from subjects with MM (n = 16), monoclonal gammopathy of undetermined significance (MGUS) (n = 6), and normal donors (n = 6). We identified overexpression of miR-21, miR-106b~25 cluster, miR-181a and b in MM and MGUS samples with respect to healthy PCs. Selective up-regulation of miR-32 and miR-17~92 cluster was identified in MM subjects and cell lines but not in MGUS subjects or healthy PCs. Furthermore, two miRNAs, miR-19a and 19b, that are part of the miR-17~92 cluster, were shown to down regulate expression of SOCS-1, a gene frequently silenced in MM that plays a critical role as inhibitor of IL-6 growth signaling. We also identified p300-CBP-associated factor, a gene involved in p53 regulation, as a bona fide target of the miR106b~25 cluster, miR-181a and b, and miR-32. Xenograft studies using human MM cell lines treated with miR-19a and b, and miR-181a and b antagonists resulted in significant suppression of tumor growth in nude mice. In summary, we have described a MM miRNA signature, which includes miRNAs that modulate the expression of proteins critical to myeloma pathogenesis.

Keywords: PCAF, SOCS-1, tumor suppressor gene, MGUS, plasma cells

Multiple myeloma (MM) is a B-cell neoplasm characterized by the accumulation of clonal malignant plasma cells in the bone marrow (1). This cancer can occur de novo or develop from a benign condition called monoclonal gammopathy of undetermined significance (MGUS) at a rate of ≈1% per year (23). MM cells are endowed with a multiplicity of antiapoptotic signaling mechanisms, which account for resistance to current chemotherapy regimens (4). Therapeutic modalities that are effective in MM modulate levels of the proapoptotic and antiapoptotic Bcl-2 family of proteins and of inhibitors of apoptosis, which are primarily regulated by p53 (mutated at low frequency in MM) (4). It is well known that the bone marrow microenviroment plays a prominent role in the biology of MM; adhesion of MM cells to the bone marrow stroma triggers cytokine production, enhances cell proliferation and resistance to chemotherapy by activation of NFκB, phosphatidyl-inositol 3-kinase PIK/AKT and signal transducer and activator of transcription 3 (STAT-3) pathways through the best characterized MM growth factor, IL-6 (3, 4).

Detailed genomic analysis has revealed that MM has complex cytogenetic abnormalities (46). For example, aneuploidy, assessed by interphase fluorescence in situ hybridization and DNA flow cytometry (6), is observed in >90% of cases (56). In addition to chromosome number aberrations, specific cytogenetic abnormalities in MM are typically complex, including reciprocal chromosomal translocations involving the Ig H locus [eg, t (4, 14), t (6, 14), t (14, 16)], chromosome 13 monosomy, loss of the short arm of chromosome 17, and gains or amplifications of the long arm of the chromosome 1 (3). The presence of RAS family member mutations at codons 12, 13, and 61 of NRAS and KRAS, has been described in ≈30 to 35% of MM patients and 45% of MM cell lines (7), and more importantly it seems that is the major genetic difference between MM and MGUS (37).

Despite recent advances in oncogenomics and MM cell-stroma interactions, further studies are needed to identify critical players in MM pathogenesis that could be targeted by pharmacological intervention to improve outcomes for this still incurable disease. The advent of new techniques, such as microarray gene expression, including noncoding RNAs, may lead to an improved understanding of MM biology by establishing associations between gene expression changes and MM molecular and clinical features, as shown by us for chronic lymphoid and acute myelogenous leukemia (89).

MicroRNAs (miRNAs) are noncoding RNAs of 19 to 25 nucleotides in length that regulate gene expression by inducing translational inhibition and degradation of their target mRNAs through base pairing to partially or fully complementary sites (10). MiRNAs are involved in critical biological processes, including development, cell differentiation, stress response, apoptosis, and proliferation (10). Recently, specific miRNA expression patterns have been linked to hematopoiesis and cancer (1113). Little is known, however, about miRNA expression in MM. A recent study has shown that, in IL-6 dependent MM cell lines, miR-21 transcription is controlled by IL-6 through a STAT-3 mechanism. Moreover, ectopic miR-21 expression is sufficient to sustain growth of IL-6-dependent cell lines in the absence of IL-6 (14). Here, we have used both miRNA microarrays and quantitative RT-PCR to assess the miRNA expression in MM-derived cell lines and CD138+ bone marrow plasma cells (PCs) from MM subjects, MGUS, and normal donors. Our findings define an miRNA signature related to expression and regulation of proteins associated with malignant transformation of PCs.

Results

A Characteristic miRNA Signature Differentiates MGUS from Healthy PCs.

Current models assume that MM evolves through a multistep transformation process (Fig. 1A) (15). To identify specific alterations associated with early pathogenetic events of MM, we profiled five CD138+ PCs from MGUS subjects and four healthy PCs [see supporting information (SI) Table S1 for patient characteristics] by using our miRNA microarray platform. We first compared MGUS to the healthy counterpart PCs by using the univariate t test within BRB tools (class comparison) (Fig. 1B and Table S2). We found 48 miRNAs significantly deregulated (P ≤ 0.05); 41 miRNAs were up-regulated and 7 down-regulated in MGUS with respect to normal CD138+ PCs (see Table S2, a representative list is shown in Fig. 1B). The most up-regulated miRNAs in MGUS were miR-21, which was described by other groups to be up-regulated in MM as well (14), miR-181a, known to have a role in B and T cell differentiation (16), and the oncogenic cluster miR-106b~25, in particular miR-93, miR-106b, and miR-25 (see Fig. 1B and Table S2).

Fig. 1.
MM and MGUS express a distinct spectrum of miRNA in comparison to normal CD138+ PCs. (A) Schematic drawing showing the multistep molecular process of PC transformation. (B) Representative list of the miRNAs significantly deregulated in MGUS versus normal ...

MiRNA Signatures in MM Patients and Cell Lines.

To determine whether miRNAs are deregulated in MM, we analyzed the global miRNA expression in 41 MM-derived cell lines (Table S3), CD138+ untreated bone marrow PCs from 10 MM, and 4 normal CD138+ PCs using our miRNA microarray (17). The degree of CD138+PCs purity after AutoMACs automated separation system (Miltenyi-Biotec) and the clinical features of the MM cases and normal PCs are listed in Table S1. First, we compared miRNA expression in primary tumors and cell lines compared to CD138+ healthy controls using univariate t test within by BRB (Table S4). Our analysis revealed up-regulation of 60 and down-regulation of 36 miRNAs in MM subjects and cell lines compared to CD138+ healthy controls (see Fig. 1C and Table S4). All miRNAs have a fold-change >2 and a P value ≤ 0.01. Because miRNA expression in cell lines could be also deregulated because of prolonged in vitro culture, we analyzed the miRNA expression only in MM subjects versus healthy PCs (Table S5). We found 37 up- and 37 down-regulated miRNAs in MM subjects with respect to normal PCs with a fold-change >2 and a P value ≤ 0.01 (see Table S5). Approximately 90% of the up-regulated miRNAs (34 out of 37) and 30% of the down-regulated miRNAs (10 out of 37) were in common to the combined group of MM subjects and cell lines, thereby validating our approach of combining cell lines and MM subject samples, at least for the analysis of up-regulated miRNAs (see Fig. 1C and Table S6). A Venn diagram in Fig. S1 shows the common miRNAs between these two groups of comparison. Similar to the signature observed in MGUS, miR-21 and the miR-106a~92 cluster were found up-regulated in MM subjects and cell lines (see Fig. 1C and Table S3). However, we identified that miR-32 and the cluster miR-17~92 (in particular miR-19a and b) were significantly up-regulated only in MM samples but not in MGUS or healthy PCs (see Fig. 1C), indicating a possible role in the malignant transformation from MGUS to MM.

Validation of the miRNA Signatures by q-RT-PCR.

To validate the microarray results we performed quantitative real time PCR (q-RT-PCR) for miR-32, miR-17–5, miR-19a, miR-19b, miR-20a, miR-92, miR-106a (miR-17~92 cluster), miR-106b, miR-93 and miR-25 (miR-106b~25 cluster), miR-328, and miR-181a and b using an independent set of randomly chosen CD138+PCs from healthy subjects (n = 3), MM patient samples (n = 6), and MGUS (n = 3) (see Table S1), all from different donors, plus a set of MM cell lines (n = 15) (see Table S1). We confirmed the over-expression of the miR-106b~25 cluster in MGUS and MM samples with respect to the CD138+ healthy PCs (Fig. S2A). Although the miR-106b~25 cluster shares a high degree of homology with the miR-17~92 cluster (Fig. 1D), and an oncogenic role was reported for both (1820), we are confident of the specificity of stem-loop q-RT-PCR for the analysis of highly similar miRNAs; a previous report from our laboratory showed exquisite specificity of miR-106b, miR-93, and miR-25 primers (20). Mature miR-181a was over-expressed in 2 out of 3 MGUS, 6 out of 6 MMs, and 9 out of 15 cell lines with an average on the differential expression shown in Fig. S2B. In addition, miR-181b was also over-expressed in MM and MGUS, albeit at a lower degree than miR-181a (see Fig. S2B). We further validated the over-expression of the miR-32 and miR-17~92 cluster (Fig. S2 C–F) in MM patients and cell lines. Consistent with the array data, the two miR-17~92 cluster members, miR-19a and b and miR-32, were highly over-expressed in 6 out of 6 MM PC samples and 15 out of 15 cell lines (see Fig. S2 C and F). Principally, we found that miR-19a and b have a fold-change >100 times (see Fig. S2F), although they show very low expression in 1 out of 3 MGUS and almost no expression in 2 out of 3 MGUS and 3 out of 3 healthy PC samples, validating our initial array results and suggesting that these miRNAs are MM-specific.

Several miRNAs Up-Regulated in MM Target p300-CBP-Associated Factor, a Positive Regulator of p53.

One of the most up-regulated miRNAs in MGUS and MM patients and cell lines were miR-181a and b, and miR-106b~25, while miR-32 was preferentially up-regulated in MM. Using “in silico” target prediction software [Target Scan (21), Pictar (22)], we found that those miRNAs are predicted to target the 3′-UTR of the p300-CBP-associated factor (PCAF) (Fig. 2A). PCAF is a histone acetyltransferase involved in the reversible acetylation of various transcriptional regulators, including the tumor suppressor protein p53 (23). Recently, Linares and colleagues have shown that PCAF possesses an intrinsic ubiquitination activity that is critical for controlling Hdm2 expression levels, and thus p53 (24) that is rarely mutated (5–10% of cases) or deleted at diagnosis in MM (2526). To examine whether these miRNAs could regulate PCAF, first we analyzed PCAF expression by q-RT-PCR (Fig. S3A) and Western blotting (Fig. S3B) in 15 MM cell lines. As control, we used two CD138+PCs isolated from healthy donors. We found that PCAF expression is almost absent (10-fold less than in control) in 10 out of 15 cell lines, whereas the remaining 5 cell lines displayed very low expression. To investigate whether this gene was deleted at the genomic level we performed whole genome comparative genomic hybridization analysis of all 15 MM cell lines using the Affymetrix SNP 6.0 arrays. However, we did not observe deletion of the PCAF gene (data not shown). Second, we cloned the PCAF 3′ UTR into a luciferase reporter vector and cotransfected with the candidate miRNAs mimics or scrambled oligonucleotides and performed luciferase assays as described in Methods. We found that miR-181a and b (Fig. 2B), 106b~25 cluster and 32 (Fig. 2 D and B), interact with the PCAF 3′UTR in vitro. However, this interaction was less significant with miR-92 (Fig. 2C) and no interaction was observed with miR-19a and b (data not shown). Mutation of the predicted miRNA binding sites in the reporter vector abrogated this effect, indicating that these miRNAs directly interact with the PCAF 3′UTR. To confirm the biological role of these miRNAs in PCAF regulation in MM cells, we validated the in vitro studies by antagonizing endogenous miR-181a, 181b, 25, 93, 106b and 92 using antisense oligos (ASOs) in U266 and JJN3 MM cell lines. In both cell lines the antagomiRs induced accumulation of PCAF protein expression at 72 h after transfection (Fig. 2 E and F). By contrast over-expression of the same miRNAs by oligonucleotide transfection reduced PCAF expression in the K562 cell line (Fig. 2 G and H). MiR-19a and b did not influence PCAF expression (Fig. 2H) and miR-92 had little effect on its expression (see Fig. 2F), confirming the luciferase expression data (see Fig. 2C). To determine whether the miRNA regulators of PCAF are able to indirectly affect p53 expression, we transfected MM1 cells with anti-miR-181a and b or with all antagomiRs simultaneously (anti-miRs-181s, 93, 106b, 25, 32) exposed the cells to UV (UV) radiation (Fig. 2I) and measured the expression of p53 and PCAF by q-RT-PCR (see Fig. 2I). Fig. S4A shows the re-expression of PCAF protein after 48 h of antagomiRs treatment. The antagonizing activity of transfectant oligos is shown in Fig. S4B. After UV treatment, p53 mRNA expression was almost doubled in cells transfected with antisense miR-181a and b, while it increased sixfold after nucleoporation with all antagomiRs simultaneously (see Fig. 2I). Furthermore, after transfection of antisense miR-181a and b oligos in MM1s, we treated the cells with a small-molecule MDM2 antagonist nutlin-3a (10 μM) and measured p53 by Western blotting. We found that the cells transfected with miR-181 ASOs displayed a higher level of p53 protein compared to scrambled and miR-92 ASOs at 9 and 12 h (Fig. 2L). Together, these data show that the miR-106b-25 cluster, miR-32, miR-181a and b target PCAF and through this gene, indirectly control p53 activity in myeloma.

Fig. 2.
miR-181s, 106b-25 cluster, 32 target PCAF. (A) miRNAs predicted to interact with PCAF gene in several consensus binding sites at its 3′-UTR, according to “in silico” target Target Scan prediction software. (B–D) Luciferase ...

miR-19a and miR-19b Target SOCS-1, a Negative Regulator of IL-6R/STAT-3 Pathway.

Our findings indicate that miR-19a and b are up-regulated >100-fold in patient samples, >2,000 times in the cell lines (Fig. S2F), and are both almost absent in normal PCs and MGUS. These data suggest that both miRNAs contribute to the development of MM. Therefore, we searched for miR-19a and b mRNA targets, which are involved in myeloma pathogenesis, using available target-prediction software [Target Scan (21), Pictar (22)]. Among >100 predicted targets, SOCS-1 has been implicated in the negative regulation of several cytokine pathways including IL-6, particularly the Jak/STAT pathways (27), and is frequently silenced by methylation in MM (28). We therefore hypothesized that the high levels of miR-19s levels in MM samples may play an important role in the constitutive activation of Jak/STAT-3 signaling through down-regulation of its negative regulator SOCS-1. To examine our hypothesis, we first assessed its expression in 15 MM cell lines and two healthy CD138+ PCs and found almost no protein expression in 13 out of 15 cell lines compared to control (Fig. 3A). To examine whether SOCS-1 reduced expression levels could be a consequences of up-regulated miR-19a and b in MM cells, we performed Western blot analysis using SOCS-1 antibody after transfection of candidate antagomiRNAs or scrambled oligonucleotides in U266 (which has an active IL-6 autocrine loop) (29) and JJN3 MM cell lines that display reduced SOCS-1 expression (Fig. 3D). Moreover, miR-19a and miR-19b mimics inhibited the expression of a reporter vector containing SOCS-1 3′UTR, while mutation of the predicted miRNA-binding site abrogated this effect (Fig. 3 B and C). As shown in Fig. 3 C and D, there was significant up-regulation of SOCS-1 protein in U266 and JJN3 cells transfected with antisense oligonucleotide for miR-19a and b but not with scrambled oligonucleotides. Furthermore, constitutive STAT-3 phosphorylation in U266 cells was markedly decreased at 72 h after transfection by anti-miR-19s but not by scrambled (Fig. 3E). The ASOs activity at 72 h was detected by q-RT-PCR (Fig. 3F). These studies suggest a role of miR-19s in the IL-6 antiapoptotic signal in the pathogenesis and malignant growth of MM.

Fig. 3.
miR-19s target SOCS-1 in MM cell lines. (A) Immunoblot analysis with antisera against SOCS-1 and GADPH in 15 MM cell lines and two CD138+PCs from healthy donors (control). (B) Predicted highly conserved consensus binding site in human, mouse, rat, and ...

miR-17~92 Cluster Target BIM in MM Cells.

Because the miR-17~92 cluster has been shown to target the proapoptotic gene, BIM (1920), we examined whether BIM expression is modulated by miR-17~92 in MM cells. U266 cells were transfected with miR-19s ASOs and BIM expression was evaluated using immunoblot. We found a significant increase of BIM protein levels at 48 h after treatment with anti-miR-19s compared to scrambled oligonucleotides (Fig. S5). Together, these results have supported previous published data (1920) that show BIM as a direct target of miR-17~92 and suggest a possible mechanism through which over-expression of miR-17~92 contributes to the antiapoptotic signals in MM.

Ectopic Repression of miR-19s and miR-181a and b in MM Cell Lines Leads to Significant Suppression of Tumor Growth in Nude Mice.

To explore the in vivo relevance of our observations, we examined the tumorigenicity of U266 and JJN3 cells in athymic nu/nu mice after silencing of the endogenous miR-19s and miR-181a and b. Two independent experiments, each using 16 mice for each cell line, were conducted. U266 or JJN3 cells were transfected with ASOs or scrambled oligonucleotides in vitro. We confirmed transfection efficiency (80% for U266 and JJN3) using BLOCK-IT Fluorescent Oligo (Invitrogen). Twenty-four hours later 3 × 107 viable cells for each group, re-suspended in 100 μl of BD matrigel matrix, were injected s.c. into the right flank of nude mice. The relative expression levels of the endogenous miR-19s and miR-181a and b after ASO transfection was assessed by q-RT-PCR to confirm the down-regulation of these miRNAs in both MM cell lines (data not shown). We found that after 2 weeks of cell inoculation, 70% of mice injected with MM cells transfected with scrambled oligonucleotide developed measurable tumors. By contrast, mice transplanted with cells expressing antagomiRs showed significant inhibition of tumor growth compared with controls (P < 0.01) (Fig. 4 A and B). Both cell lines treated with anti-miR-19s showed tumor volumes >10-fold reduced and tumors treated with antago miR-181s were three times smaller in JJN3 cells and 10 times smaller in U266 cells, P = 0.02 and P = 0.01, respectively. Importantly, complete tumor suppression was observed in two mice injected with U266 cells treated with anti-miR-19s. The average tumor volume after 4 weeks for U266 cells was 308.5 mm3 and for JJN3 cells was 225 mm3. Only 50% of mice injected with MM cells transfected with the antago miR-19s and miR-181s developed measurable tumors at 4 weeks. The average tumor volume for U266/anti-miR-19s was 19.5 mm3 and for U266/anti-miR-181s was 14 mm3. Similar results were observed with JJN3 MM cells, with average tumor volumes of 25 mm3 and 80 mm3 for anti-miR-19s and anti-miR-181s, respectively (see Fig. 4 A and B). Taken together, these results strongly suggested an oncogenic role of these miRNAs in MM and we speculate that the stronger effect of anti-miR-19s is related to the IL-6 dependence of U266.

Fig. 4.
Antagonizing miR-19s and miR-181s expression in MM cell lines resulted in significant tumor suppression in nude mice. U266 and JJN3 cells (30 × 106 cells) were injected subcutaneously into the flanks of nude mice with 100 μl of matrigel ...

Discussion

Over the past few years several studies have illustrated the biological relevance of miRNAs for the differentiation of normal hematopoietic cells and the contribution of deregulated miRNA expression in malignant counterparts (11, 30, 31). Our study has provided a unique comprehensive global miRNA expression profiling of MM, MGUS and contrasted these expression patterns with that of normal PCs. The similar miRNA expression pattern observed in MM cell lines and in primary newly diagnosed MMs supports the research design of this study. In addition, previous MM microarray studies have combined MM cell lines with primary patient samples, validating our strategy (32). We sought to identify a miRNA signature that could be associated with a MM multistep transformation process from normal PCs via MGUS to clinically overt myeloma, conscious of limitations because of the low number of MGUS and primary tumor samples. In MGUS patients, we identified up-regulated miRNAs with oncogenic function, such as the miR-21 and the miR-106b~25 cluster. MiR-21 is up-regulated in many solid and hematological tumors (11, 25). The ectopic expression of miR-21 in glioblastoma cells blocks apoptosis (33), while silencing its expression in several cancer cells inhibits cell growth and leads to increased apoptotic cell death by unblocking the expression of its targets: tumor suppressor genes like phosphatase and tensin homolog (PTEN) and protein programmed cell death 4 (PDCD4) (34). Petrocca and colleagues (20), have shown that the miR-106b~25 cluster plays a role in gastric cancer tumorigenesis by targeting the proapoptotic BIM and p21. Thus, these two miRNAs may contribute to earlier steps in plasma cell transformation by blocking apoptosis, promoting PC survival, and predisposing to secondary genetic abnormalities that will ultimately result in a full blown malignancy.

In MM (including MM cell lines and primary tumors versus normal PCs) we identified a signature comprised of multiple up-regulated miRNAs, including among others miR-32, miR-21, miR-17~92, miR-106~25, and miR-181a and b. While miR-106~25, miR-181a and b, and miR-21 were up-regulated also in MGUS patients with respect to normal PCs, miR-32 and the miR-17~92 cluster were highly expressed only in MM patients, suggesting that these miRNAs are MM-specific. Besides RAS mutations, no other genetic abnormality has been found to differentiate MGUS from MM (3). Therefore, miR-32 and the miR-17~92 cluster may represent MM-specific genetic changes. However, this will require further independent validation because we used a small number of patient samples and normal plasma cells.

Similar to the miR-106~25 cluster, the oncogenic role of the miR-17~92 cluster in B cell lymphoma is well known and several known proapoptotic genes, including PTEN, E2F1, and Bcl2l11/BIM are confirmed as targets of miR-17~92 (3536). Recently, Ventura and colleagues (19) have shown that the miR-17~92 cluster is also essential for B cell development and that the absence of miR-17~92 leads to increased levels of the proapoptotic protein BIM and inhibits B cell development at the pro-B to pre-B transition. However, given the nearly identical sequences, it is very likely that miR-106b~25 and miR-17~92 clusters cooperate in exerting similar, if not identical, functions as in targeting BIM (1920).

Our study provided important functional insights about miRNAs deregulated in MM. We have confirmed that the proapoptotic BIM is a target of the miR-17~92 cluster in MM cells. Therefore, miR-17~92, along with miR-21, blocks apoptosis and promotes cell survival. On the other hand, miR-106b~25, miR-181a, and miR-32 but not miR17~92 cluster (specifically miR-19s and miR-92), target PCAF, a p53 positive regulator. We speculate, consistent with the low frequency of p53 mutations in MM, that down-regulation of PCAF by the miR-106b~25 cluster, miR-181s, and miR-32, keeps p53 at low level or partially inactivated by controlling its stability through Hdm2 (24) and working as a histone acetyltransferase (23). We have also described the specific role of miR-19s on the STAT-3/IL-6R negative regulator SOCS-1. In fact, IL-6 pathways in MM are among the best characterized survival pathways participating in PC transformation and oncogenesis through STAT-3, impacting apoptosis regulators such as the Bcl-2 family members (1, 16). Our findings demonstrate that the up-regulation of miR-19s in MM could contribute to SOCS-1 down-regulation and IL-6 activation at later stages in MM pathogenesis.

The role of miR-19s and miR-181s in MM cells as oncomiRNAs was confirmed by in vivo studies. Our data demonstrate significant tumor regression of transplanted tumors after treatment with miR-19s and 181s antagomiRs. These data may suggest that miRNAs could have a therapeutic potential in antagonizing the growth of transformed PCs.

In conclusion, we reported distinctive miRNA signatures in MM and MGUS, characterized by over-expression of miRNAs with known oncogenic activity. Our data provided insights into the miRNA function in MM by establishing links with the regulation of critical pathways in MM by miRNAs, including apoptosis, survival, and proliferation. These results indicate an additional level of control by this class of regulatory molecules in the multistep process associated with malignant transformation of PCs.

Materials and Methods

RNA Extraction and miRNA Microarray Experiments.

RNA extraction and miRNA microchip experiments were performed as described in detail elsewhere (37). The miRNA microarray is based on a one-channel system (35). Five micrograms of total RNA was used for hybridization on the Ohio State University custom miRNA microarray chips (OSU_CCC version 3.0), which contains ≈1,100 miRNA probes, including 345 human and 249 mouse miRNA genes, spotted in duplicates.

RT-PCR.

The single tube TaqMan miRNA assays were used to detect and quantify mature miRNAs as previously described (10) using ABI Prism 7900HT sequence detection systems (Applied Biosystems). Normalization was performed with RNU6B. Comparative real-time PCR was performed in triplicate, including no-template controls. Relative expression was calculated using the comparative Ct method.

ASOs and Mimics Transfection Experiments.

Cells were transfected by using nucleoporation (Amaxa) kit V (for JJN3 and MM1s cell lines) and kit C (for U266 cell line) using 100 nM miRNA precursors (Ambion), or 100 nM LNA miRNA antisense oligonucleotides (Ambion). Protein lysates and total RNA were collected at the time indicated. miRNA processing and expression were verified by Northern blot and stem-loop q-RT-PCR. We confirmed transfection efficiency (≈80% for U266 and JJN3 and 50% for MM1s) using BLOCK-IT Fluorescent Oligo (Invitrogen) for all of the cell lines. Untreated cells transfected with negative control oligonucleotides were used as a calibrator.

Supplementary Material

Supporting Information:

Acknowledgments.

We thank Dr. Kay Huebner and Dr. Hiroshi Okumura for their support and scientific advice, Dorothee Wernicke-Jameson for research supervision, and Sharon Palko for administrative support. This work was supported by National Cancer Institute grants (to C.M.C.), Kimmel Foundation awards (to R.I.A., N.Z., and R.G.), and an Ohio Cancer Research Associates grant (to R.I.A.).

Footnotes

The authors declare no conflict of interest.

Data deposition: The microarray data have been deposited in the Array Express database, www.ebi.ac.uk/arrayexpress (accession no. E-TABM-508).

This article contains supporting information online at www.pnas.org/cgi/content/full/0806202105/DCSupplemental.

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