Next generation sequencing results in prostate cancer cell line model.

<p>Next generation sequencing results in prostate cancer cell line model.</p

Single nucleotide variations in prostate cancer cell line model.

<p>*Not present in M12 cell line</p><p>Single nucleotide variations in prostate cancer cell line model.</p

Validation of miR-125b and miR-22 binding to the 3'-UTR of ErbB2 and PTEN respectively.

<p><b>(A)</b> Identification of two miR-125b binding sites within the 3’-UTR of ErbB2. Site 1 (position -19 to -44) downstream of the stop codon is proven by Scott et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142373#pone.0142373.ref030" target="_blank">30</a>]. Site 2 (position -70 to -96) is proposed here by an analysis with RNAhybrid [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142373#pone.0142373.ref056" target="_blank">56</a>]. Both sites display notable binding between ErbB2’s 3’-UTR (red) and miR-125b (green) with favorable MFEs. <b>(B)</b> The M12 cell line was transfected with a dual luciferase reporter construct containing various portions of ErbB2’s 3’-UTR as noted. Firefly luciferase expression is normalized to renilla luciferase activity. Results are the mean of 3 independent experiments each performed in triplicate. ANOVA test indicates a significant difference with a P-value < 0.05. <b>(C)</b> The effect of miR-22 binding on the wild type and mutant PTEN 3’-UTR target binding site was assessed on firefly versus renilla luciferase activity as described in panel B via transfection into the M12 cell line. Mutation of a single base (C to A) within the target to miR-22’s seed region [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142373#pone.0142373.ref031" target="_blank">31</a>] resulted in increased firefly luciferase activity. Results are the average of 3 experiments repeated in triplicate. <b>(D)</b> A representative western blot of whole cell extracts (30 μg) from M12, M12+miR-22i and p69 cells. Proteins were separated on a 4–12% Tris-Bis gel and incubated with a PTEN antibody. β-actin was used as a loading control. The position of migration of relevant protein size markers are noted. <b>(E)</b> Quantitation of western blot shown in panel D with PTEN levels normalized to β-actin.</p

Dysregulation of miR-125b and miR-22 expression in RNA extracted from prostate tissue samples by LCM.

<p><b>(A)</b> Frozen prostate samples were dissected via LCM into benign glandular epithelial versus tumor. Total RNA was extracted using the PicoPure RNA extraction method, as described in Materials and Methods. qRT-PCR was performed with specific primers against miR-125b and miR-22 using the TaqMan^® Universal Master Mix II. C_T values were normalized to RNU48 and reported as fold differences compared to benign tissue using the ΔΔCT method of Livak et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142373#pone.0142373.ref023" target="_blank">23</a>]. Results are the average from frozen tissue samples (n = 4) repeated in 3 technical replicates. <b>(B)</b> From 10 successive slides of a single FFPE prostate sample, miR-125b was quantitated by qRT-PCR as described in panel A for RNA extracted from stroma, benign glandular tissue, BPH, PIN and tumor of stage G4.</p

LCM is required to minimize variation due to tissue heterogeneity of human prostate tissue.

<p>This image of a frozen human prostate sample exemplifies the heterogeneity typical of human tissues: areas of adenocarcinoma, outlined in blue, are intermixed with stroma and benign prostate glands, labeled by arrows. LCM allows for targeted dissection of the malignant glands (scored as G3 and G4 for this particular sample) while avoiding the stroma and other benign structures.</p

Model for dual regulation by miR-125b and miR-22.

<p>RPPA data shows increases in ErbB3, ErbB2, MET, PI3K, pBAD and pERK protein expression in M12 cells relative to the parental p69 cell lines (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142373#pone.0142373.t003" target="_blank">Table 3</a>: green targets). Western blot (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142373#pone.0142373.g004" target="_blank">Fig 4D</a>) confirms a decrease in PTEN expression (red). These proteins figure prominently in signal transduction pathways that are targeted by miR-125b and miR-22. Intermediates in yellow (AKT, RAS and pMEK) were not included in the proteome analysis. miR-125b directly targets ErbB2, ErbB3 and MET and miR-22 targets PTEN [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142373#pone.0142373.ref030" target="_blank">30</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142373#pone.0142373.ref031" target="_blank">31</a>]. We propose that the loss of tumor suppressor miR-125b in the M12 cell line would result in enhanced signaling via the PI3K/AKT pathway and the RAS/pMEK pathway as regulated by MET. Conversely, miR-22 targets PTEN, the loss of which by increased expression of miR-22 further exacerbates PI3K signaling. In this scenario the dysregulation of these two miRs could contribute to the highly tumorigenic/metastatic phenotype displayed by the M12 cells compared to the parental p69 cell line and subsequently contribute to prostate tumorigenesis.</p

Restoration of miR-125b or inhibition of miR-22 impairs <i>in vitro</i> migratory and invasive potential of M12 cells but initially has little effect on cell proliferation.

<p><b>(A)</b> A representative growth curve of M12 versus M12+miR-22inhibitor cells is shown. Cells (20,000) were plated in triplicate and viable cells counted at 0, 48, and 72 hours in a Beckman Coulter Vi-CELL automated cell viability analyzer using trypan blue exclusion (cell viability >94%). The average viable cell number was plotted on an exponential curve with the standard deviation noted. Analysis of cell growth at the 48 and 72 hour time points using a student t-test yielded a p-value of 0.11 and 0.009, respectively <b>(B)</b> Cells (50,000) were plated in triplicate in serum free media in the top chamber of a ThinCert^™ tissue culture insert and processed as described in Materials and Methods. Panel A confirmed no significant difference in growth potential at 20 hours at which time the number of migrated cells was counted in 10 random fields and the total number of migratory cells estimated by summing up each of the individual fields. The average mean sum of each well is presented, along with the standard error. The invasion assay used the same experimental set up with the additional step of coating the membrane with Culturex^® growth factor reduced basement membrane (60 μl) prior to cell addition. Results are shown for parental M12 cells or M12 cells stably transformed with a scrambled RNA sequence as a negative control (M12+scrambled RNA), a miR-22 inhibitor (M12+miR-22 inhibitor) or restored miR-125b (M12+miR-125b). Data is the mean of 3 independent experiments, each performed in triplicate. ANOVA test indicates a significant difference with a P-value < 0.05.</p

RPPA analysis shows increased protein expression from the PI3K/RAS pathways in M12 versus p69 Cell Lines.

<p>*All p values for these comparisons are < 0.001</p><p>RPPA analysis shows increased protein expression from the PI3K/RAS pathways in M12 versus p69 Cell Lines.</p

Activation of NF-κB complex in TC-83 infected cells.

<p>A) UV inactivation of the virus was carried out using a Stratalinker UV crosslinker (model 1800). The inactivation was achieved by delivering an energy dose equivalent to 1200 µJoules X 100 per dose five times with a 2 minute interval between dosing. UV-TC-83 and TC-83 were serially diluted and used to infect Vero cells. UV-TC-83 inactivation was confirmed by plaque assay. Plaques were photographed and counted 48 hours post-infection. Plaque counts are represented graphically. B) U87MG cells were either mock infected, treated with LPS (1 µg/mL) or infected with TC-83 or UV-TC-83 (MOI: 1). At 30 minutes, 1 and 2 hours post-infection cells were lysed and protein extracts were resolved by SDS-PAGE and subsequently immunoblotted with antibodies against phosphorylated p65 and phosphorylated IκBα. Total p65, total IκBα and β-actin served as controls. The western blot is representative of 2 independent experiments. C) U87MGs were either mock infected, treated with LPS (1 µg/mL) or UV-TC-83 or TC-83 infected (MOI: 3). One hour post-infection cells were fixed, probed with p65 antibody followed by incubation with Alexa-Fluor 568. The cells were stained with DAPI to observe the nuclei. Images were taken using Nikon Eclipse TE2000-U at 60× magnification and are representative of 2 independent experiments. ND = not detectable.</p

IKKβ inhibitors decrease TC-83 replication in rat AP7 neuronal cells.

<p>A) Neurons were pre-treated with DMSO or with IKK inhibitors (1 µM) for 2 hours and 24 hours later cell viability was measured using the Cell-Titer-Glo Luminescent Cell Viability Assay. B) Neurons were pretreated with IKK inhibitors (1 µM), BAY-11-7082, BAY-11-7085 and IKK2-IV for 2 hours. Following the pretreatment, the conditioned media (media containing inhibitor) was removed and the cells infected at MOI: 1 for 1 hour. The viral inoculum was removed and the conditioned media replaced. Supernatants were collected 24 hours post-infection, and infectious viral titers were determined by plaque assay. C) Neurons were pretreated with IKK inhibitors (1 µM) for 2 hours and infected with TC-83 for 1 hour. Conditioned media was replaced after removal of the viral inoculum. Cell viability assay was performed 48 hours later using the Cell-Titer-Glo Luminescent Cell Viability Assay. The red line is representative of the base line for luminescence units, such that luminescence units above this are indicative of increased cell viability. The graphs are representative of 2 independent experiments. Error bars for the independent experiments were calculated and are represented thusly. *** p≤0.005, ** p≤0.01 and * p≤0.05.</p