Kinome inhibition reveals a role for polo-like kinase 1 in targeting post-transcriptional control in cancer

Dysfunctions in post-transcriptional control are observed in cancer and chronic inflammatory diseases. Here, we employed a kinome inhibitor library (n = 378) in a reporter system selective for 3'-untranslated region-AU-rich elements (ARE). Fifteen inhibitors reduced the ARE-reporter activity; among the targets is the polo-like kinase 1 (PLK1). RNA-seq experiments demonstrated that the PLK1 inhibitor, volasertib, reduces the expression of cytokine and cell growth ARE mRNAs. PLK1 inhibition caused accelerated mRNA decay in cancer cells and was associated with reduced phosphorylation and stability of the mRNA decay-promoting protein, tristetraprolin (ZFP36/TTP). Ectopic expression of PLK1 increased abundance and stability of high molecular weight of ZFP36/TTP likely of the phosphorylated form. PLK1 effect was associated with the MAPK-MK2 pathway, a major regulator of ARE-mRNA stability, as evident from MK2 inhibition, in vitro phosphorylation, and knockout experiments. Mutational analysis demonstrates that TTP serine 186 is a target for PLK1 effect. Treatment of mice with the PLK1 inhibitor reduced both ZFP36/TTP phosphorylation in xenograft tumor tissues, and the tumor size. In cancer patients' tissues, PLK1/ARE-regulated gene cluster was overexpressed in solid tumors and associated with poor survival. The data showed that PLK1-mediated post-transcriptional aberration could be a therapeutic target.

Challenge of forecasting demand of medical resources and supplies during a pandemic: A comparative evaluation of three surge calculators for COVID-19

Ever since the World Health Organization (WHO) declared the new coronavirus disease 2019 (COVID-19) as a pandemic, there has been a public health debate concerning medical resources and supplies including hospital beds, intensive care units (ICU), ventilators and protective personal equipment (PPE). Forecasting COVID-19 dissemination has played a key role in informing healthcare professionals and governments on how to manage overburdened healthcare systems. However, forecasting during the pandemic remained challenging and sometimes highly controversial. Here, we highlight this challenge by performing a comparative evaluation for the estimations obtained from three COVID-19 surge calculators under different social distancing approaches, taking Lebanon as a case study. Despite discrepancies in estimations, the three surge calculators used herein agree that there will be a relative shortage in the capacity of medical resources and a significant surge in PPE demand if the social distancing policy is removed. Our results underscore the importance of implementing containment interventions including social distancing in alleviating the demand for medical care during the COVID-19 pandemic in the absence of any medication or vaccine. The paper also highlights the value of employing several models in surge planning.

ARED-Plus: an updated and expanded database of AU-rich element-containing mRNAs and pre-mRNAs

Here we present an updated version of the AU-Rich Element Database (ARED-Plus) that is freely available at http://brp.kfshrc.edu.sa/ared. AREs are conserved sequence elements that were first discovered in the 3′UTR of mammalian transcripts. Over the past years, we compiled a series of ARE databases that revealed the extent and wide distribution of ARE-containing genes. For this update, we adopted an optimized search algorithm with improved specificity and sensitivity in ARE selection. The designation of the different ARE clusters was simplified by directly correlating the number of the ARE cluster to the number of overlapping AUUUA pentamers. Additionally, the new database was expanded to include genes with intronic AREs (pre-mRNAs) and their characteristics since recent observations reported their abundance and biological significance. Several enhancements were incorporated such as customized column view, additional search options and live search functionalities. The new version includes links to AREsite and AREScore, two related ARE assessment algorithms for further evaluation of the ARE characteristics. ARED-Plus now contains an updated repertoire of AREs in the human transcriptome that may be useful in several research fields.

Systematic Analysis of AU-Rich Element Expression in Cancer Reveals Common Functional Clusters Regulated by Key RNA-Binding Proteins

Defects in AU-rich elements (ARE)-mediated posttranscriptional control can lead to several abnormal processes that underlie carcinogenesis. Here, we performed a systematic analysis of ARE-mRNA expression across multiple cancer types. First, the ARE database (ARED) was intersected with The Cancer Genome Atlas databases and others. A large set of ARE-mRNAs was over-represented in cancer and, unlike non-ARE-mRNAs, correlated with the reversed balance in the expression of the RNA-binding proteins tristetraprolin (TTP, ZFP36) and HuR (ELAVL1). Serial statistical and functional enrichment clustering identified a cluster of 11 overexpressed ARE-mRNAs (CDC6, KIF11, PRC1, NEK2, NCAPG, CENPA, NUF2, KIF18A, CENPE, PBK, TOP2A) that negatively correlated with TTP/HuR mRNA ratios and was involved in the mitotic cell cycle. This cluster was upregulated in a number of solid cancers. Experimentally, we demonstrated that the ARE-mRNA cluster is upregulated in a number of tumor breast cell lines when compared with noninvasive and normal-like breast cancer cells. RNA-IP demonstrated the association of the ARE-mRNAs with TTP and HuR. Experimental modulation of TTP or HuR expression led to changes in the mitosis ARE-mRNAs. Posttranscriptional reporter assays confirmed the functionality of AREs. Moreover, TTP augmented mitotic cell-cycle arrest as demonstrated by flow cytometry and histone H3 phosphorylation. We found that poor breast cancer patient survival was significantly associated with low TTP/HuR mRNA ratios and correlated with high levels of the mitotic ARE-mRNA signature. These results significantly broaden the role of AREs and their binding proteins in cancer, and demonstrate that TTP induces an antimitotic pathway that is diminished in cancer. Cancer Res; 76(14); 4068-80. ©2016 AACR.

Abstract B2-13: AU-rich expression in invasive ductal breast cancer: A systems biology approach in post-transcriptional regulation

AU-Rich element (ARE)-dependent post-transcriptional regulation mechanisms are increasingly emerging as key regulators that are influencing our perception of aberrant gene expression in cancer. AREs are instability determinant sequences located in the 3' UTR of mRNAs and are fundamental to the maintenance of transient expression of gene products that regulate various cellular functions such as cell proliferation, apoptosis, inflammation and immunity. Here we used a systems biology approach to examine the patterns of ARE-containing gene expression that is perturbed in invasive ductal breast cancer (IDBC). Based on IDBC mRNA expression profiles obtained from The Cancer Genome Atlas (TCGA) database, we intersected 2396 over-expressed genes with the AU-rich element database (ARED) and found that 414 comprise IDBC upregulated ARE-containing genes. Functional classification using the gene ontology tool, DAVID, showed the highest enrichment of ARE-genes in IDBC in chromosome segregation (5-fold, p<0.001). AREs are recognized by RNA binding proteins such as tristetraprolin (TTP, ZFP36), that targets mRNAs for decay, and HuR (ELAVL1), an mRNA stabilizing protein. Abnormal expression patterns of both these proteins, i.e. TTP deficiency coupled with HuR overexpression, are found in many cancers leading to prolonged expression of factors contributing to the maintenance and progression of tumors. We examined the relationship between the IDBC ARE-genes, TTP and HuR expression and the TTP/HuR ratio by looking at their correlations (R-values) with each other. Results indicated that the upregulated ARE-genes have a greater tendency to correlate with low TTP and elevated HuR expression than non-ARE genes. Using clustering assessment, we derived an 11-gene cluster from the 414 that function in chromosome positioning and segregation and mitotic kinase activity. The genes are CDC6, CENPA, CENPA, KIF11, KIF18A, NCAPG, NEK2, NUF2, PBK, PRC1, and TOP2A and their mRNA expression correlates negatively with the TTP/HuR ratio, i.e. their mRNA expression increases as TTP is deficient and HuR is simultaneously elevated (r = -0.53 to -0.66). Examination of the mRNA expression patterns of the 11 genes in the invasive breast cancer cell line MDA-MB-231 compared to MCF-7 cells and normal-like mammary cell lines, MCF10A and MCF12A showed that all of these genes were increased in MDA-MB-231 cell line compared to MCF10A by at least 2-fold (p<0.001). Immunoprecipitation of TTP protein in MDA-MB-231 cells followed by examination of associated mRNAs showed that 7 of the 11 gene-products were significantly associated with TTP (greater than 2-fold, p<0.01) compared to the control suggesting post-transcriptional regulation by TTP. Moreover, reporter experiments confirmed the functionally of the AREs. Upon examining the METBRIC breast cancer database, a larger database, we found that not only do the 11 chromosomal segregation genes overexpress, they also tend to be upregulated simultaneously in the same patients indicating that they participate in common regulatory mechanisms. Furthermore, the 11-gene cluster also correlates negatively with the TTP/HuR ratio further alluding to TTP regulation. Kaplan Meier survival analysis demonstrated a higher likelihood (1.6 times) of death due to co-overexpression of the 11 genes compared with a lower-expressing cohort. The data presented here suggest novel regulatory mechanisms related to mitosis and cellular proliferation that might be targeted by the mRNA decay-promoting protein TTP. Moreover, TTP deficiency in IDBC may, at least in part, be responsible for the aberrantly prolonged expression of factors that actively participate in chromosomal segregation and in turn, lead to enhanced maintenance and progression of tumors.

Citation Format: Norah A. Alsouhibani, Edward Hitti, Tala Bakheet, Khalid SA Khabar. AU-rich expression in invasive ductal breast cancer: A systems biology approach in post-transcriptional regulation. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-13.

Sequence variations affecting AU-rich element function and disease

Adenylate-uridylate rich elements (AREs) in the 3'UTRs of many transiently expressed genes regulate mRNA instability and translation. Such ARE-genes are involved in vital biological processes like cellular growth, differentiation, and immunity. Defects in their expression contribute to a variety of disease conditions like cancer, autoimmune diseases, diabetes, and cardiovascular and chronic inflammatory diseases. Over the past two decades, considerable progress has been made in understanding the mode of regulation of AREs containing mRNAs by RNA-binding proteins, miRNAs, and signaling pathways. This review focuses on the less documented sequence variation affecting ARE functions and its relation to disease. We discuss reports describing genetic polymorphisms, alternative polyadenylation, and alternative splicing that can lead to the loss or gain of function of AREs, often with significant implications to disease.

Global assessment of GU-rich regulatory content and function in the human transcriptome

Unlike AU-rich elements (AREs) that are largely present in the 3'UTRs of many unstable mammalian mRNAs, the function and abundance of GU-rich elements (GREs) are poorly understood. We performed a genome-wide analysis and found that at least 5% of human genes contain GREs in their 3'UTRs with functional over-representation in genes involved in transcription, nucleic acid metabolism, developmental processes, and neurogenesis. GREs have similar sequence clustering patterns with AREs such as overlapping GUUUG pentamers and enrichment in 3'UTRs. Functional analysis using T-cell mRNA expression microarray data confirms correlation with mRNA destabilization. Reporter assays show that compared to AREs the ability of GREs to destabilize mRNA is modest and does not increase with the increasing number of overlapping pentamers. Naturally occurring GREs within U-rich contexts were more potent in destabilizing GFP reporter mRNAs than synthetic GREs with perfectly overlapping pentamers. Overall, we find that GREs bear a resemblance to AREs in sequence patterns but they regulate a different repertoire of genes and have different dynamics of mRNA decay. A dedicated resource on all GRE-containing genes of the human, mouse and rat genomes can be found at brp.kfshrc.edu.sa/GredOrg.

MAPKAP kinases MK2 and MK3 in inflammation: complex regulation of TNF biosynthesis via expression and phosphorylation of tristetraprolin

Downstream of mitogen-activated protein kinases (MAPKs), three structurally related MAPK-activated protein kinases (MAPKAPKs or MKs) - MK2, MK3 and MK5 - signal to diverse cellular targets. Although there is no known common function for all three MKs, MK2 and MK3 are mainly involved in regulation of gene expression at the post-transcriptional level and are implicated in inflammation and cancer. MK2 and MK3 are phosphorylated and activated by p38(MAPKα,β) and, in turn phosphorylate various substrates involved in diverse cellular processes. In addition to forwarding of the p38-signal by MK2/3, protein complex formation between MK2/3 and p38 mutually stabilizes these enzymes and affects p38(MAPK) signaling in general. Among the substrates of MK2/3, there are mRNA-AU-rich-element (ARE)-binding proteins, such as tristetraprolin (TTP) and hnRNP A0, which regulate mRNA stability and translation in a phosphorylation-dependent manner. Phosphorylation by MK2 stabilizes TTP, releases ARE-containing mRNAs, such as TNF-mRNA, from default translational repression and inhibits their nucleolytic degradation. Here we demonstrate that MK2/3 also contribute to the de novo synthesis of TTP. Whether this contribution proceeds via transcription factors directly targeted by MK2/3 or via chromatin remodeling by the reported binding of MK2/3 to the polycomb repressive complex is still open. A model is proposed, which demonstrates how this new function of transcriptional activation of TTP by MK2/3 cooperates with the role of MK2/3 in post-transcriptional gene expression to limit the inflammatory response.

A versatile ribosomal protein promoter-based reporter system for selective assessment of RNA stability and post-transcriptional control

Assessment of post-transcriptional control relies on use of transcriptional inhibitors and is masked by copious and cryptic transcriptional induction. We screened several cellular promoters that are constitutively active yet noninducible to external stimuli. The ribosomal protein RPS30 promoter was chosen; its TATA signal and sp1 site location were optimized. The modified promoter (RPS30M) is selective to post-transcriptional effects of AU-rich elements (ARE) in the 3'UTR, while it is not transcriptionally responsive to a wide variety of agents including pro-inflammatory cytokines and RNA-binding proteins. Specific cis-acting elements can be appended to RPS30M by a cloning-free approach to allow coupled transcriptional/post-transcriptional assessment, as demonstrated with NF-kappaB and beta-catenin/wnt signaling experiments. Moreover, efficient tetracycline-regulated RPS30M was created for quantitative assessment of the half-lives of mRNAs containing AREs. The described approach provides enhanced versatility and suitability for selective post-transcriptional assessment with or without transcriptional induction.

The p38 MAPK pathway inhibits tristetraprolin-directed decay of interleukin-10 and pro-inflammatory mediator mRNAs in murine macrophages

p38 mitogen-activated protein kinase (MAPK) stabilises pro-inflammatory mediator mRNAs by inhibiting AU-rich element (ARE)-mediated decay. We show that in bone-marrow derived murine macrophages tristetraprolin (TTP) is necessary for the p38 MAPK-sensitive decay of several pro-inflammatory mRNAs, including cyclooxygenase-2 and the novel targets interleukin (IL)-6, and IL-1alpha. TTP(-/-) macrophages also strongly overexpress IL-10, an anti-inflammatory cytokine that constrains the production of the IL-6 despite its disregulation at the post-transcriptional level. TTP directly controls IL-10 mRNA stability, which is increased and insensitive to inhibition of p38 MAPK in TTP(-/-) macrophages. Furthermore, TTP enhances deadenylation of an IL-10 3'-untranslated region RNA in vitro.

MAP-kinase-activated protein kinase 2 expression and activity is induced after neuronal depolarization

Mitogen-activated protein kinase-activated protein kinase (MK)2 is one of several downstream targets of p38 mitogen-activated protein kinase and has a well documented role in inflammation. Here, we describe a possible new function of MK2. We show that triggering depolarization by potassium chloride or increasing the cellular cAMP by forskolin treatment led to elevated levels of expression and activity of mouse MK2. In both treatments, the kinase inhibitor H89 completely prevented the up-regulation of MK2 at the transcript level. By the use of different cell lines we demonstrated that the induction of MK2 expression is characteristic of neuronal cells and is absent in fibroblasts, macrophages and kidney cells. In vivo, induction of a status epilepticus by systemic administration of the chemoconvulsant kainic acid resulted in markedly reduced neurodegeneration in the pyramidal layer of the hippocampus, dentate gyrus and hilus of MK2-deficient mice compared with wild-type mice. Together, our data suggest a possible role of MK2 in the cellular response after neuronal depolarization, in particular in excitotoxicity.

MAPKAP kinase 2-deficiency prevents neurons from cell death by reducing neuroinflammation--relevance in a mouse model of Parkinson's disease

The inflammatory response in the brain is closely associated with the pathogenesis of degenerative neurological disorders. A role for the p38 stress-activated protein kinase/MAPK-activated protein kinase 2 (MK2) axis in inflammation and apoptosis is well documented. Here, we provide evidence that neurodegeneration can be prevented by eliminating MK2. In primary mesencephalic neuron-glia co-cultures dopaminergic neurons from MK2-deficient (MK2-/-) mice were significantly more resistant to lipopolysaccharide-induced neurotoxicity compared with cells from wild-type mice. This neuroprotection in MK2-deficient cultures was associated with a reduced inflammatory response, especially with reduced production of the inflammatory mediators tumor necrosis factor alpha, keratinocyte-derived chemokine, interleukin-6, and nitric oxide (NO). Interestingly, in primary neuron-enriched cell cultures p38 MAPK, but not MK2, also participates in NO-mediated neuronal cell death. In the MPTP mouse model for Parkinson's disease, MK2-deficient mice show a reduced neuroinflammation and less degeneration of dopaminergic neurons in the substantia nigra after MPTP lesion compared with wild-type mice. In conclusion, our results reveal that MK2 does not directly participate in neuronal cell death, but indirectly contributes to neurodegeneration by the production of neurotoxic substances, such as NO or tumor necrosis factor alpha, from activated glia cells.

The mitogen-activated protein kinase (MAPK)-activated protein kinases MK2 and MK3 cooperate in stimulation of tumor necrosis factor biosynthesis and stabilization of p38 MAPK

MK2 and MK3 represent protein kinases downstream of p38 mitogen-activated protein kinase (MAPK). Deletion of the MK2 gene in mice resulted in an impaired inflammatory response although MK3, which displays extensive structural similarities and identical functional properties in vitro, is still present. Here, we analyze tumor necrosis factor (TNF) production and expression of p38 MAPK and tristetraprolin (TTP) in MK3-deficient mice and demonstrate that there are no significant differences with wild-type animals. We show that in vivo MK2 and MK3 are expressed and activated in parallel. However, the level of activity of MK2 is always significantly higher than that of MK3. Accordingly, we hypothesized that MK3 could have significant effects only in an MK2-free background and generated MK2/MK3 double-knockout mice. Unexpectedly, these mice are viable and show no obvious defects due to loss of compensation between MK2 and MK3. However, there is a further reduction of TNF production and expression of p38 and TTP in double-knockout mice compared to MK2-deficient mice. This finding, together with the observation that ectopically expressed MK3 can rescue MK2 deficiency similarly to MK2, indicates that both kinases share the same physiological function in vivo but are expressed to different levels.

Mitogen-activated protein kinase-activated protein kinase 2 regulates tumor necrosis factor mRNA stability and translation mainly by altering tristetraprolin expression, stability, and binding to adenine/uridine-rich element

The mitogen-activated protein kinase (MAPK) p38/MAPK-activated protein kinase 2 (MK2) signaling pathway plays an important role in the posttranscriptional regulation of tumor necrosis factor (TNF), which is dependent on the adenine/uridine-rich element (ARE) in the 3' untranslated region of TNF mRNA. After lipopolysaccharide (LPS) stimulation, MK2-deficient macrophages show a 90% reduction in TNF production compared to the wild type. Tristetraprolin (TTP), a protein induced by LPS, binds ARE and destabilizes TNF mRNA. Accordingly, macrophages lacking TTP produce large amounts of TNF. Here, we generated MK2/TTP double knockout mice and show that, after LPS stimulation, bone marrow-derived macrophages produce TNF mRNA and protein levels comparable to those of TTP knockout cells, indicating that in the regulation of TNF biosynthesis TTP is genetically downstream of MK2. In addition, we show that MK2 is essential for the stabilization of TTP mRNA, and phosphorylation by MK2 leads to increased TTP protein stability but reduced ARE affinity. These data suggest that MK2 inhibits the mRNA destabilizing activity of TTP and, in parallel, codegradation of TTP together, with the target mRNA resulting in increased cellular levels of TTP.

The double-stranded RNA-binding protein X1rbpa promotes RNA strand annealing

RNA-annealing activity is a common feature of several RNA-binding proteins. The Xenopus RNA-binding protein X1rbpa is composed of three tandemly arranged double-stranded RNA-binding domains (dsRBDs) but lacks any other catalytic or functional domains, therefore making the assessment of biological functions of this protein rather difficult. Here we show that full-length X1rbpa but also isolated dsRBDs from this protein can facilitate RNA strand annealing. RNA annealing can be efficiently inhibited by heparin. However, dsRBDs with a neutral pI still promote strand annealing, suggesting that charged residues within the dsRBD are important for strand annealing. Additionally, mutant versions of the dsRBD, unable to bind dsRNA in northwestern assays, were tested. Of these, some show RNA-annealing activity while others fail to do so, indicating that RNA annealing and dsRNA binding are separable functions. Our data, together with the previously reported association of the protein with most cellular RNAs, suggests an RNA chaperone-like function of X1rbpa.