Tumor suppression involves down-regulation of interleukin 3 expression in hybrids between autocrine mastocytoma and interleukin 3-dependent parental mast cells

Differential analysis of biological networks

Background

In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling and control networks are subject to some degree of localised re-wiring. Being able to detect disrupted interaction patterns induced by the presence or progression of the disease can lead to the discovery of novel molecular diagnostic and prognostic signatures. Currently there is a lack of scalable statistical procedures for two-network comparisons aimed at detecting localised topological differences.

Results

We propose the dGHD algorithm, a methodology for detecting differential interaction patterns in two-network comparisons. The algorithm relies on a statistic, the Generalised Hamming Distance (GHD), for assessing the degree of topological difference between networks and evaluating its statistical significance. dGHD builds on a non-parametric permutation testing framework but achieves computationally efficiency through an asymptotic normal approximation.

Conclusions

We show that the GHD is able to detect more subtle topological differences compared to a standard Hamming distance between networks. This results in the dGHD algorithm achieving high performance in simulation studies as measured by sensitivity and specificity. An application to the problem of detecting differential DNA co-methylation subnetworks associated to ovarian cancer demonstrates the potential benefits of the proposed methodology for discovering network-derived biomarkers associated with a trait of interest.

mRNA stability and cancer: an emerging link?

Many oncogenes, growth factor, cytokine and cell-cycle genes are regulated post-transcriptionally. The major mechanism is by controlling the rate of mRNA turnover for transcripts bearing destabilizing cis-elements. To date, only a handful of regulatory factors have been identified that appear to control a large pool of target mRNAs, suggesting that a slight perturbation in the control mechanism may generate wide-ranging effects that could contribute to the development of a complex disorder such as cancer. In support of this view, mRNA turnover responds to signalling pathways that are often overactive in cancer, suggesting a post-transcriptional component in addition to the well-recognised transcriptional aspect of oncogenesis. Here the authors review examples of deregulated post-transcriptional control in oncogenesis, discuss post-transcriptionally regulated transcripts of oncologic significance, and consider the key role of signalling pathways in linking both processes and as an enticing therapeutic prospect.

A novel mechanism of tumor suppression by destabilizing AU-rich growth factor mRNA

The occurrence of pathologically stable mRNAs of proto-oncogenes, growth factors and cyclins has been proposed to contribute to experimental and human oncogenesis. In normal resting cells, mRNAs containing an AU-rich element (ARE) in their 3' untranslated region are subjected to rapid degradation. Tristetraprolin (TTP) is an RNA-binding zinc-finger protein that promotes decay of ARE-containing mRNAs. Here we report that TTP acts as a potent tumor suppressor in a v-H-ras-dependent mast cell tumor model, where tumors express abnormally stable interleukin-3 (IL-3) mRNA as part of an oncogenic autocrine loop. Premalignant v-H-ras cells were transfected with TTP and injected into syngeneic mice. TTP expression delayed tumor progression by 4 weeks, and late appearing tumors escaped suppression by loss of TTP. When transfected into a fully established tumor line, TTP reduced cloning efficiency in vitro and growth of the inoculated cells in vivo. Transgenic TTP interfered with the autocrine loop by enhancing the degradation of IL-3 mRNA with concomitant reduction of IL-3 secretion. Our data establish the ARE as an antioncogenic target in a model situation, underline the importance of mRNA stabilization in oncogenesis and show for the first time that tumor suppression can be achieved by interfering with mRNA turnover.

Global analysis of differential gene expression after transformation with the v-H-ras oncogene in a murine tumor model

Mouse PB-3c mast cells stably transfected with the v-H-ras oncogene induce tumor formation in vivo when implanted into mice. Such tumor cells are characterized by an autocrine IL-3 loop. DNA microarrays allow simultaneous transcript imaging of several thousand genes and the technique was applied in this tumor model to analyse gene expression following malignant transformation. Using three independent tumor lines derived from the same precursor the expression of about 400 out of 11 000 genes was modulated in each tumor. A subset of only 75 genes (0.68%) is shared and up- or downregulated in all three lines. A significant portion of this gene pool possesses functions related to tumorigenesis such as cell adhesion, signaling or transcriptional regulation. Apart from a number of expressed sequence tags (EST's) we find downregulation of four interferon-inducible genes in the tumor lines. Finally, when we extrapolate our data to the complete mouse genome, we estimate that about 500 genes are differentially expressed in tumor cells compared to the precursor cell PB-3c.

Somatic mRNA turnover mutants implicate tristetraprolin in the interleukin-3 mRNA degradation pathway

Control of mRNA stability is critical for expression of short-lived transcripts from cytokines and proto-oncogenes. Regulation involves an AU-rich element (ARE) in the 3' untranslated region (3'UTR) and cognate trans-acting factors thought to promote either degradation or stabilization of the mRNA. In this study we present a novel approach using somatic cell genetics designed to identify regulators of interleukin-3 (IL-3) mRNA turnover. Mutant cell lines were generated from diploid HT1080 cells transfected with a reporter construct containing green fluorescent protein (GFP) linked to the IL-3 3'UTR. GFP was expressed at low levels due to rapid decay of the mRNA. Following chemical mutagenesis and selection of GFP-overexpressing cells, we could isolate three mutant clones (slowA, slowB, and slowC) with a specific, trans-acting defect in IL-3 mRNA degradation, while the stability of IL-2 and tumor necrosis factor alpha reporter transcripts was not affected. Somatic cell fusion experiments revealed that the mutants are genetically recessive and form two complementation groups. Expression of the tristetraprolin gene in both groups led to reversion of the mutant phenotype, thereby linking this gene to the IL-3 mRNA degradation pathway. The genetic approach described here should allow identification of the defective functions by gene transfer and is also applicable to the study of other mRNA turnover pathways.

Calcium-dependent and oncogenic IL-3 mRNA stabilization can be distinguished pharmacologically and by sequence requirements in the 3'UTR

In interleukin-3 (IL-3)-dependent PB-3c mast cells, the normally short-lived IL-3 mRNA is stabilized upon calcium-ionophore treatment or following v-H-ras induced oncogenesis. We compared the underlying stabilization mechanisms by analysing the response to the post-transcriptionally acting drugs cyclosporin A (CsA), FK506 and SB202190. Stable IL-3 transcripts in the PB-3c-derived tumour cell line V2D1 decayed in response to CsA and FK506, but not in response to SB202190. Transcripts stabilized by elevating intracellular calcium levels in PB-3c cells were destabilized in response to all three drugs. In PB-3c cells, six AUUUA pentamers within the AU-rich element were sufficient to confer responsiveness to calcium-ionophore and CsA treatment. In V2D1 tumour cells, sensitivity to CsA required additional nucleotides flanking these pentamers. Our data suggest that IL-3 mRNA stabilization by either calcium-dependent or oncogenic pathways involves different intracellular mechanisms.

Search for oncogenic regulators in an autocrine tumor model using differential display PCR: identification of novel candidate genes including the calcium channel mtrp6

A hemopoietic multistep tumor model, in which IL-3 dependent PB-3c mast cells, following expression of v-H-ras progress in vivo to IL-3 producing autocrine tumors has previously been established. Central for this oncogenic progression is a recessive step, which is reversible by cell fusion and leads to stabilization of IL-3 mRNA with concomitant activation of the autocrine loop. Comparing the IL-3 dependent PB-3c and the IL-3 autocrine V2D1 tumor cells with differential display PCR revealed 12 differentially expressed genes of which eight were upregulated and four downregulated in the tumor. They included four proteases (mouse mast cell protease 2, granzyme B, pepsinogen F and serine protease 1) and two metabolic enzymes (adenine phosphoribosyltransferase and fructose1,6-bisphosphatase). For validation, expression of the identified genes was tested in independent PB-3c precursor clones and their tumor derivatives. Expression of an endogenous retroviral IAP element and three unknown transcripts were consistently upregulated in all tumor lines. In somatic cell hybrids, two of these unknown cDNAs showed a dominant and one a recessive expression pattern. One transcript, expressed in the precursor but downregulated in the tumor cells, was cloned and identified as the murine calcium channel mtrp6.

Cyclosporin A promotes translational silencing of autocrine interleukin-3 via ribosome-associated deadenylation

Translation is regulated predominantly by an interplay between cis elements at the 3' and 5' ends of mRNAs and trans-acting proteins. Cyclosporin A (CsA), a calcineurin antagonist and blocker of interleukin-2 (IL-2) transcription in T cells, was found to inhibit translation of IL-3 mRNA in autocrine mast cell tumor lines. The mechanism involved ribosome-associated poly(A) shortening and required an intact AU-rich element in the 3' untranslated region. FK506, another calcineurin inhibitor, shared the effect. The translational inhibition by CsA was specific to oncogenically induced lymphokines IL-3 and IL-4 but not to IL-6, c-jun, and c-myc, which are expressed in the nonmalignant precursor cells. Furthermore, no translational down-regulation of the mRNA was observed in IL-3-transfected precursor cells. These data suggest that translational silencing is associated with the tumor phenotype.

c-jun N-terminal kinase is involved in AUUUA-mediated interleukin-3 mRNA turnover in mast cells

Whereas signalling pathways involved in transcriptional control have been studied extensively, the pathways regulating mRNA turnover remain poorly understood. We are interested in the role of mRNA stability in cell activation and oncogenesis using PB-3c mast cells as a model system. In these cells the short-lived interleukin-3 (IL-3) mRNA is stabilized by ionomycin treatment and following oncogenesis. To identify the signalling pathways involved in these mechanisms, we analysed the effect of different kinase inhibitors. SB202190 and wortmannin were shown to antagonize ionomycin-induced IL-3 mRNA stabilization in PB-3c cells in the presence of actinomycin D, and this effect coincided with their ability to inhibit c-jun N-terminal kinase (JNK) activation by ionomycin. Moreover, transfection of activated MEKK1 amplified ionomycin-induced IL-3 mRNA expression at the post-transcriptional level, and a dominant-negative mutant of JNK counteracted mRNA stabilization by ionomycin. Taken together, these data indicate that JNK is involved in the regulation of IL-3 mRNA turnover in mast cells. In addition, transfection experiments revealed that the cis-acting AU-rich element in the 3' untranslated region of IL-3 mRNA is necessary and sufficient to confer JNK-dependent mRNA stabilization in response to cell activation.

Rapamycin destabilizes interleukin-3 mRNA in autocrine tumor cells by a mechanism requiring an intact 3' untranslated region

We analyzed the effect of rapamycin on autocrine mast cell tumor lines with abnormally stable interleukin-3 (IL-3) transcripts due to a defect in mRNA degradation. Rapamycin inhibited IL-3 mRNA expression specifically, while transcripts of IL-4 and IL-6 were not affected. As indicated by the use of the transcriptional inhibitor actinomycin D or by reporter constructs, inhibition was posttranscriptional and resulted from destabilization of the mRNA. Transcripts from transgenes lacking the AU-rich 3' untranslated region were refractory to drug-induced degradation, suggesting that these 3' sequences contain the target of the rapamycin effect. Rapamycin did not promote IL-3 mRNA degradation in cells of a tumor variant lacking expression of FKBP12, the binding protein of rapamycin. Experiments with wortmannin indicated that rapamycin does not act via p70S6 kinase. FK-506, another ligand of FKBP12 affecting the phosphatase calcineurin, did not antagonize but shared the effect of rapamycin. Our data fit a model whereby both FKBP12 and calcineurin target an unknown regulator of IL-3 mRNA turnover.

Impaired interleukin-3 mRNA decay in autocrine mast cell tumors after transient calcium ionophore stimulation

Autocrine interleukin-3 (IL-3) expression of v-H-ras transformed mast cell tumors involves either IL-3 mRNA stabilization (class-I tumors) or enhanced IL-3 transcription (class-II tumors). Since calcium ionophores induce IL-3 expression in untransformed PB-3c cells by transcript stabilization, we asked whether class-I tumor could still respond to calcium ionophores. We found that ionomycin treatment further increased IL-3 mRNA expression of class-I tumor cells. Following ionomycin wash-out, IL-3 mRNA decay was slower in class-I tumor cells than in class-II tumor or precursor cell lines (t1/2 > 50 min versus < 20 min, respectively). Somatic cell fusion of the class-I tumor cells with the non-tumorigenic PB-3c cells resulted in reversion to rapid decay after ionomycin wash-out. The data indicate that a recessive defect of IL-3 mRNA degradation can be revealed in class-I tumor cells by transient calcium ionophore stimulation. However, IL-3 mRNA stabilization operating constitutively in class-I tumor cells appears to be distinct from the ionomycin induced process.

Interleukin-3 mRNA stabilization by a trans-acting mechanism in autocrine tumors lacking interleukin-3 gene rearrangements

Tumors obtained from v-Ha-ras-transformed PB-3c cells are characterized by autocrine interleukin-3 (IL3) expression, which occurs either without (class I tumors) or with enhanced transcription (class II tumors). To address possible post-transcriptional mechanisms of IL3 expression, IL3 mRNA stability was examined in both tumor classes. Increased stability of IL3 mRNA was detected in class I tumor lines (t1/2 > 3 h), whereas rapid decay of IL3 transcripts (t1/2 < 0.5 h) was found in class II tumor lines. In both tumor classes, the c-myc and interleukin-6 transcripts were short-lived. Transcripts of a constitutively expressed IL3 reporter gene were stable in class I tumor cells but unstable in class II tumor cells, suggesting that IL3 mRNA stabilization involved a trans-acting mechanism. Rapid decay of IL3 reporter transcripts was observed in untransformed PB-3c as well as in v-Ha-ras expressing precursor cells linking transcript stabilization to the tumor stage. Reporter transcript stabilization in class I tumor cells correlated with increased IL3 production. Deletion of the AU-rich element from the IL3 reporter gene further augmented IL3 mRNA levels as well as IL3 production, suggesting that the stabilizing mechanism in class I tumor cells is not equivalent to AU-rich element deletion.

Regulation of granulocyte-macrophage colony-stimulating factor and interleukin 3 expression

Granulocyte-macrophage colony stimulating factor (GM-CSF) and interleukin 3 (IL-3) are multilineage acting hematopoietic growth factors which have overlapping but distinct biological properties. Cellular sources of IL-3 are confined to activated T cells, natural killer (NK) cells, mast cells and possibly megakaryocytes, while these cells and activated macrophages, fibroblasts and endothelial cells are important sources of GM-CSF. In vitro studies have implicated both cytokines in the autocrine growth of human myeloid or murine mast cell leukemias. The human GM-CSF and IL-3 genes map to the long arm of chromosome 5, show similar genomic structures, and share several conserved elements in their 5' and 3' flanking regions. The promoters of these genes contain a variety of positive and negative regulatory regions, and the level of expression of these genes is controlled by both transcriptional and post-transcriptional mechanisms.

Cyclosporin A inhibits growth of autocrine tumour cell lines by destabilizing interleukin-3 mRNA

In T cells, cyclosporin A (CsA) exerts its immunosuppressive effect by preventing transcriptional induction of the expression of interleukin(IL)-2. This is achieved by a mechanism that involves binding of a CsA-cyclophilin complex to calcineurin, which in turn inhibits the phosphatase-controlled translocation of transcription factor NFAT to the nucleus. We have previously identified IL-3 as an autocrine oncogenic regulator in tumour cell lines generated by introducing the v-H-ras oncogene into IL-3-dependent mast cells. Here we report that CsA specifically blocks autocrine tumour cell growth. The mechanism involves down-regulation of IL-3 expression by destabilization of the messenger RNA and requires ongoing transcription. Transcripts from exogenous IL-3 genes lacking the (A+U)-rich element (ARE) in the 3' untranslated terminal repeat could not be destabilized, suggesting that at least part of this sequence, which is known to mediate decay of short-lived mRNA, participates in a CsA-sensitive regulatory mechanism.

Suppressible and nonsuppressible autocrine mast cell tumors are distinguished by insertion of an endogenous retroviral element (IAP) into the interleukin 3 gene

After v-H-ras expression, the interleukin 3 (IL-3)-dependent PB-3c mast cells progress in vivo to two different classes of IL-3 autocrine tumors. Class I tumors show a germline configuration of the IL-3 gene and represent more than 90% of tumors analyzed so far. Somatic cell fusion of class I tumor lines with the nontumorigenic parental PB-3c resulted in loss of oncogenic IL-3 expression by a posttranscriptional mechanism with concomitant tumor suppression. Class II tumors arise rarely and contain an insertion in one IL-3 allele. This alteration was linked to enhanced IL-3 gene transcription. For one tumor, the insertion was shown to be an endogenous retroviral element (intracisternal A-particle). Cell hybrids of class II tumors with PB-3c remained IL-3 independent, expressed IL-3, and formed tumors rapidly. These results suggest that the v-H-ras oncogene synergizes with a recessive and a dominant lesion in class I and II tumors, respectively, both of which lead to the autocrine production of IL-3.