DcpS is a transcript-specific modulator of RNA in mammalian cells

Effect of the mRNA decapping enzyme scavenger (DCPS) inhibitor RG3039 on glioblastoma

BACKGROUND

Patients with glioblastoma (GBM) have a poor prognosis and limited treatment options. The mRNA decapping enzyme scavenger (DCPS) is a cap-hydrolyzing enzyme. The DCPS inhibitor RG3039 exhibited excellent central nervous system bioavailability in vivo and was safe and well tolerated in healthy volunteers in a phase 1 clinical trial. In this study, we investigated the expression of DCPS in GBM and the anti-tumor activity of RG3039 in various preclinical models of GBM.

METHODS

DCPS expression was examined in human GBM and paired peritumoral tissues. Its prognostic role was evaluated together with clinicopathological characteristics of patients. The anti-GBM effect of RG3039 was determined using GBM cell lines, patient-derived organoids, and orthotopic mouse models. The therapeutic mechanisms of DCPS inhibition were explored.

RESULTS

DCPS is overexpressed in GBM and is associated with poor survival of patients with GBM. The DCPS inhibitor RG3039 exhibited robust anti-GBM activities in GBM cell lines, patient-derived organoids and orthotopic mouse models, with drug exposure achievable in humans. Mechanistically, RG3039 downregulated STAT5B expression, thereby suppressing proliferation, survival and colony formation of GBM cells.

CONCLUSIONS

DCPS is a promising target for GBM. Inhibition of DCPS with RG3039 at doses achievable in humans downregulates STAT5B expression and reduces proliferation, survival and colony formation of GBM cells. Given the excellent anti-cancer activity and central nervous system bioavailability in vivo and good tolerance in humans, RG3039 warrants further study as a potential GBM therapy.

The Nine RNA Methylation Regulatory Gene Signature Is Associated with the Pathogenesis of Atrial Fibrillation by Modulating the Immune Microenvironment in the Atrial Tissues

Background. Atrial fibrillation (AF) is the most common type of cardiac arrhythmias and a major cause of cardiovascular disease (CVD)-related deaths globally. RNA methylation is the most frequent posttranscriptional modification in the eukaryotic RNAs. Previous studies have demonstrated close associations between the status of RNA methylation and CVD. Methods. We comprehensively evaluated the relationship between RNA methylation and AF. Least absolute shrinkage and selection operator (LASSO) logistic regression analysis was used to establish a risk score model in AF. Biological functional analysis was used to explore the relationship between RNA methylation related signatures and immune microenvironment characteristics. Machine learning was used to recognize the outstanding RNA methylation regulators in AF. Results. There was a significant variant of the mRNA expression of RNA methylation regulators in AF. RNA methylation related risk score could predict the onset of AF and closely associated with immune microenvironment features. XG-Boost algorithm and SHAP recognized that NSUN3 and DCPS might play a key role in the development of AF. Meanwhile, NSUN3 and DCPS had potential diagnostic value in AF. Conclusion. RNA methylation regulatory genes are associated with the onset of AF by modulating the immune microenvironment. The nine AF risk-related RNA methylation regulatory gene signature is a potential diagnostic biomarker and therapeutic target for AF.

Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC

The RNA decapping scavenger protein, DcpS, has recently been identified as a dependency in acute myeloid leukemia (AML). The potent DcpS inhibitor RG3039 attenuates AML cell viability, and shRNA knockdown of DcpS is also antiproliferative. Importantly, DcpS was found to be non-essential in normal human hematopoietic cells, which opens a therapeutic window for AML treatment by DcpS modulation. Considering this strong DcpS dependence in AML cell lines, we explored PROTAC-mediated degradation as an alternative strategy to modulate DcpS activity. Herein, we report the development of JCS-1, a PROTAC exhibiting effective degradation of DcpS at nanomolar concentrations. JCS-1 non-covalently binds DcpS with a RG3039-based warhead and recruits the E3 ligase VHL, which induces potent, rapid, and sustained DcpS degradation in several AML cell lines. JCS-1 serves as a chemical biology tool to interrogate DcpS degradation and associated changes in RNA processes in different cellular contexts, which may be an attractive strategy for the treatment of AML and other DcpS-dependent genetic disorders.

Bioinformatic Characterization of Whole Blood Neutrophils in Pelvic Inflammatory Disease: A Potential Prognostic Indicator for Transumbilical Single-Port Laparoscopic Pelvic Abscess Surgery

The purpose of this research is to determine the prognosis of patients treated with transumbilical single-port laparoscopic surgery for acute pelvic inflammatory illness. Postoperative data on 129 patients treated with laparoscopic surgery for acute pelvic inflammatory illness were obtained retrospectively. It was observed that the shorter the time required for postoperative leukocyte recovery to normal, the shorter the time required for postoperative pain and diet recovery, as well as hospital stay, in such individuals. CIBERSORT was used to examine patient data from GEO. The most significant difference between the normal and pelvic inflammatory groups was in neutrophil content. Association study found a substantial positive correlation between the quantity of neutrophils infiltrating the immune system and the abundance of monocyte M0 infiltrating the immune system. Neutrophil immune infiltration was strongly inversely linked with plasma cells, activated CD8+ Tm cells, and active CD4+ Tm cells. Four mRNAs linked with pelvic inflammatory illness were revealed to be strongly associated with neutrophil immune infiltration, notably CALML4, COQ10B, DCPS, and PPP2R1A. The ROC revealed that CALML4 (area under the curve (AUC): 0.769, 95% confidence interval (CI): 0.638-0.881), COQ10B (AUC: 0.742, 95% CI: 0.587-0.881), PPP2R1A (AUC: 0.733 95% CI: 0.593-0.857), and DCPS (AUC: 0.745, 95% CI: 0.571-0.900) were potential markers for predicting pelvic inflammatory disease. CALML4, COQ10B, PPP2R1A, and DCPS may be critical determinants determining the amount of preoperative neutrophil infiltration and the time required for leukocyte recovery after single-port laparoscopy in acute pelvic inflammatory illness.

mRNA-Decapping Associated DcpS Enzyme Controls Critical Steps of Neuronal Development

Homozygous mutations in the gene encoding the scavenger mRNA-decapping enzyme, DcpS, have been shown to underlie developmental delay and intellectual disability. Intellectual disability is associated with both abnormal neocortical development and mRNA metabolism. However, the role of DcpS and its scavenger decapping activity in neuronal development is unknown. Here, we show that human neurons derived from patients with a DcpS mutation have compromised differentiation and neurite outgrowth. Moreover, in the developing mouse neocortex, DcpS is required for the radial migration, polarity, neurite outgrowth, and identity of developing glutamatergic neurons. Collectively, these findings demonstrate that the scavenger mRNA decapping activity contributes to multiple pivotal roles in neural development and further corroborate that mRNA metabolism and neocortical pathologies are associated with intellectual disability.

Suppressors of mRNA Decapping Defects Restore Growth Without Major Effects on mRNA Decay Rates or Abundance

Faithful degradation of mRNAs is a critical step in gene expression, and eukaryotes share a major conserved mRNA decay pathway. In this major pathway, the two rate-determining steps in mRNA degradation are the initial gradual removal of the poly(A) tail, followed by removal of the cap structure. Removal of the cap structure is carried out by the decapping enzyme, containing the Dcp2 catalytic subunit. Although the mechanism and regulation of mRNA decay is well understood, the consequences of defects in mRNA degradation are less clear. Dcp2 has been reported as either essential or nonessential. Here, we clarify that Dcp2 is not absolutely required for spore germination and extremely slow growth, but in practical terms it is impossible to continuously culture dcp2∆ under laboratory conditions without suppressors arising. We show that null mutations in at least three different genes are each sufficient to restore growth to a dcp2∆, of which kap123∆ and tl(gag)g∆ appear the most specific. We show that kap123∆ and tl(gag)g∆ suppress dcp2 by mechanisms that are different from each other and from previously isolated dcp2 suppressors. The suppression mechanism for tL(GAG)G is determined by the unique GAG anticodon of this tRNA, and thus likely by translation of some CUC or CUU codons. Unlike previously reported suppressors of decapping defects, these suppressors do not detectably restore decapping or mRNA decay to normal rates, but instead allow survival while only modestly affecting RNA homeostasis. These results provide important new insight into the importance of decapping, resolve previously conflicting publications about the essentiality of DCP2, provide the first phenotype for a tl(gag)g mutant, and show that multiple distinct mechanisms can bypass Dcp2 requirement.

Small molecule targeting of RNA structures in neurological disorders

Aberrant RNA structure and function operate in neurological disease progression and severity. As RNA contributes to disease pathology in a complex fashion, that is, via various mechanisms, it has become an attractive therapeutic target for small molecules and oligonucleotides. In this review, we discuss the identification of RNA structures that cause or contribute to neurological diseases as well as recent progress toward the development of small molecules that target them, including small molecule modulators of pre-mRNA splicing and RNA repeat expansions that cause microsatellite disorders such as Huntington's disease and amyotrophic lateral sclerosis. The use of oligonucleotide-based modalities is also discussed. There are key differences between small molecule and oligonucleotide targeting of RNA. The former targets RNA structure, while the latter prefers unstructured regions. Thus, some targets will be preferentially targeted by oligonucleotides and others by small molecules.

The natural antisense transcript NATTD regulates the transcription of decapping scavenger (DcpS) enzyme

Natural antisense transcripts (NATs) are transcribed from the opposite strand of other genes. Most of them are noncoding RNAs. They have been reported to play important roles in a variety of biological processes. In this study, we identified a novel NAT, NATTD, which is partially complementary to both the TIRAP/Mal and DcpS genes. Interestingly, NATTD only positively regulates the expression of DcpS, a decapping scavenger enzyme which is a promising therapeutic target for spinal muscular atrophy. But it has no obvious effects on the expression of TIRAP/Mal gene. The NATTD transcript primarily resides in the nucleus and does not alter the mRNA stability of DcpS. Instead, it is required for the recruitment of RNA polymerase II at the mouse DcpS promoter. Chromatin immunoprecipitation assays revealed that knocking-down NATTD transcript with shRNA enhanced the H3K27-Me3 modification at the DcpS promoter. In summary, our studies identified NATTD as a regulator of DcpS transcription through epigenetic mechanisms.

The Interplay between the RNA Decay and Translation Machinery in Eukaryotes

RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology.

A fluorescent HTS assay for phosphohydrolases based on nucleoside 5'-fluorophosphates: its application in screening for inhibitors of mRNA decapping scavenger and PDE-I

Several nucleotide-specific phosphohydrolases can cleave P-F bonds in substrate analogues containing a fluorophosphate moiety to release fluoride ions. In this work, by employing a fluoride-sensitive molecular sensor, we harnessed this cleavage reaction to develop a fluorescence assay to screen for phosphohydrolase inhibitors. The assay is rapid, sensitive, and based on simple and synthetically available reagents. The assay was adapted to the high-throughput screening (HTS) format and its utility was demonstrated by screening an 'in-house' library of small nucleotides against two enzymes: DcpS, a metal-independent mRNA decapping pyrophosphatase of the histidine triad (HIT) family; and PDE-I, a divalent cation-dependent nuclease. Our screening results agreed with the known specificities of DcpS and PDE-I, and led to the selection of several inhibitors featuring low-micromolar IC50 values. For DcpS, we also verified the results by using an alternative method with the natural substrate. Notably, the assay presented here is the first fluorescence-based HTS-adaptable assay for DcpS, an established therapeutic target for spinal muscular atrophy. The assay should be useful for phosphohydrolase specificity profiling and inhibitor discovery, particularly in the context of DcpS and other HIT-family enzymes, which play key roles in maintaining cellular functions and have been linked to disease development.

In vitro and in vivo effects of 2,4 diaminoquinazoline inhibitors of the decapping scavenger enzyme DcpS: Context-specific modulation of SMN transcript levels

C5-substituted 2,4-diaminoquinazoline inhibitors of the decapping scavenger enzyme DcpS (DAQ-DcpSi) have been developed for the treatment of spinal muscular atrophy (SMA), which is caused by genetic deficiency in the Survival Motor Neuron (SMN) protein. These compounds are claimed to act as SMN2 transcriptional activators but data underlying that claim are equivocal. In addition it is unclear whether the claimed effects on SMN2 are a direct consequence of DcpS inhibitor or might be a consequence of lysosomotropism, which is known to be neuroprotective. DAQ-DcpSi effects were characterized in cells in vitro utilizing DcpS knockdown and 7-methyl analogues as probes for DcpS vs non-DcpS-mediated effects. We also performed analysis of Smn transcript levels, RNA-Seq analysis of the transcriptome and SMN protein in order to identify affected pathways underlying the therapeutic effect, and studied lysosomotropic and non-lysosomotropic DAQ-DCpSi effects in 2B/- SMA mice. Treatment of cells caused modest and transient SMN2 mRNA increases with either no change or a decrease in SMNΔ7 and no change in SMN1 transcripts or SMN protein. RNA-Seq analysis of DAQ-DcpSi-treated N2a cells revealed significant changes in expression (both up and down) of approximately 2,000 genes across a broad range of pathways. Treatment of 2B/- SMA mice with both lysomotropic and non-lysosomotropic DAQ-DcpSi compounds had similar effects on disease phenotype indicating that the therapeutic mechanism of action is not a consequence of lysosomotropism. In striking contrast to the findings in vitro, Smn transcripts were robustly changed in tissues but there was no increase in SMN protein levels in spinal cord. We conclude that DAQ-DcpSi have reproducible benefit in SMA mice and a broad spectrum of biological effects in vitro and in vivo, but these are complex, context specific, and not the result of simple SMN2 transcriptional activation.

The effects of C5-substituted 2,4-diaminoquinazolines on selected transcript expression in spinal muscular atrophy cells

C5-substituted 2,4-diaminoquinazolines (2,4-DAQs) ameliorate disease severity in SMA mice. It is uncertain, however, that these compounds increase SMN protein levels in vivo even though they were identified as activators of the SMN2 promoter. These compounds also regulate the expression of other transcripts in neuroblastoma cells. In this study, we investigate the mechanism by which the 2,4-DAQs regulate the expression of SMN2 as well as other targets. D156844, D158872, D157161 and D157495 (RG3039) increased SMN2 promoter-driven reporter gene activity by at least 3-fold in NSC-34 cells. These compounds, however, did not significantly increase SMN2 mRNA levels in type II SMA fibroblasts nor in NSC-34 cells, although there was a trend for these compounds increasing SMN protein in SMA fibroblasts. The number of SMN-containing gems was increased in SMA fibroblasts in response to 2,4-DAQ treatment in a dose-dependent manner. ATOH7 mRNA levels were significantly lower in type II SMA fibroblasts. 2,4-DAQs significantly increased ATOH7, DRNT1 and DRTN2 transcript levels in type II SMA fibroblasts and restored ATOH7 levels to those observed in healthy fibroblasts. These compounds also increase Atoh7 mRNA expression in NSC-34 cells. In conclusion, 2,4-DAQs regulate SMN2 by increasing protein levels and gem localization. They also increase ATOH7, DRNT1 and DRNT2 transcript levels. This study reveals that the protective effects of 2,4-DAQs in SMA may be independent of SMN2 gene regulation. These compounds could be used in concert with a proven SMN2 inducer to develop a multi-faceted approach to treating SMA.

Overgrazing induces alterations in the hepatic proteome of sheep (Ovis aries): an iTRAQ-based quantitative proteomic analysis

Background

The degradation of the steppe of Inner Mongolia, due to overgrazing, has resulted in ecosystem damage as well as extensive reductions in sheep production. The growth performance of sheep is greatly reduced because of overgrazing, which triggers massive economic losses every year. The liver is an essential organ that has very important roles in multiple functions, such as nutrient metabolism, immunity and others, which are closely related to animal growth. However, to our knowledge, no detailed studies have evaluated hepatic metabolism adaption in sheep due to overgrazing. The molecular mechanisms that underlie these effects remain unclear.

Methods

In the present study, our group applied isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analysis to investigate changes in the protein profiles of sheep hepatic tissues when nutrition was reduced due to overgrazing (12.0 sheep/ha), with the goal of characterizing the molecular mechanisms of hepatic metabolism adaption in sheep in an overgrazing condition.

Results

The body weight daily gain of sheep was greatly decreased due to overgrazing. Overall, 41 proteins were found to be differentially abundant in the hepatic tissue between a light grazing group and an overgrazing group. Most of the differentially expressed proteins identified are involved in protein metabolism, transcriptional and translational regulation, and immune response. In particular, the altered abundance of kynureninase (KYNU) and HAL (histidine ammonia-lyase) involved in protein metabolic function, integrated with the changes of serum levels of blood urea nitrogen (BUN) and glucose (GLU), suggest that overgrazing triggers a shift in energy resources from carbohydrates to proteins, causing poorer nitrogen utilization efficiency. Altogether, these results suggest that the reductions in animal growth induced by overgrazing are associated with liver proteomic changes, especially the proteins involved in nitrogen compounds metabolism and immunity.

Conclusions

This provides new information that can be used for nutritional supplementation to improve the growth performance of sheep in an overgrazing condition.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-016-0111-z) contains supplementary material, which is available to authorized users.

Small Molecules in Development for the Treatment of Spinal Muscular Atrophy

Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disease resulting from pathologically low levels of survival motor neuron (SMN) protein. The majority of mRNA from the SMN2 allele undergoes alternative splicing and excludes critical codons, causing an SMN protein deficiency. While there is currently no FDA-approved treatment for SMA, early therapeutic efforts have focused on testing repurposed drugs such as phenylbutyrate (2), valproic acid (3), riluzole (6), hydroxyurea (7), and albuterol (9), none of which has demonstrated clinical effectiveness. More recently, clinical trials have focused on novel small-molecule compounds identified from high-throughput screening and medicinal chemistry optimization such as olesoxime (11), CK-2127107, RG7800, LMI070, and RG3039 (17). In this paper, we review both repurposed drugs and small-molecule compounds discovered following medicinal chemistry optimization for the potential treatment of SMA.

Novel mRNA-silencing bodies at the synapse: A never-ending story

Several cellular responses depend on translational regulation and in most cases, this involves the formation of cytoplasmic granules that contain repressed mRNAs. In neurons, numerous mRNAs travel along dendrites to be locally regulated upon synapse activity and we have recently shown that the exoribonuclease XRN1 forms dynamic aggregates at the post synapse that respond to specific stimuli.¹ These foci were termed SX-bodies and are distinct from stress granules (SGs), processing bodies (PBs) and other RNA granules previously described. Together with Smaug1-foci and FMRP-granules, the SX-bodies contribute to dynamically shape the transcriptome available for translation at the post-synapse.

Cellular thermal shift and clickable chemical probe assays for the determination of drug-target engagement in live cells

Proof of drug-target engagement in physiologically-relevant contexts is a key pillar of successful therapeutic target validation.

The human decapping scavenger enzyme DcpS modulates microRNA turnover

The decapping scavenger enzyme DcpS is known for its role in hydrolyzing the cap structure following mRNA degradation. Recently, we discovered a new function in miRNA degradation activation for the ortholog of DcpS in C. elegans. Here we show that human DcpS conserves its role in miRNA turnover. In human cells, DcpS is a nucleocytoplasmic shuttling protein that activates miRNA degradation independently of its scavenger decapping activity in the cytoplasmic compartment. We also demonstrate that this new function for DcpS requires the contribution of the 5′-3′ exonuclease Xrn2. Our findings support a conserved role of DcpS as a modulator of miRNA turnover in animals.

Cytoplasmic mRNA turnover and ageing

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We address the cytoplasmic mRNA decay processes that determine the mRNAs half-life.

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We briefly describe the major, evolutionary conserved, ageing pathways and mechanisms.

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We summarize critical findings that link mRNA turnover and ageing modulators.

Messenger RNA (mRNA) turnover that determines the lifetime of cytoplasmic mRNAs is a means to control gene expression under both normal and stress conditions, whereas its impact on ageing and age-related disorders has just become evident. Gene expression control is achieved at the level of the mRNA clearance as well as mRNA stability and accessibility to other molecules. All these processes are regulated by cis-acting motifs and trans-acting factors that determine the rates of translation and degradation of transcripts. Specific messenger RNA granules that harbor the mRNA decay machinery or various factors, involved in translational repression and transient storage of mRNAs, are also part of the mRNA fate regulation. Their assembly and function can be modulated to promote stress resistance to adverse conditions and over time affect the ageing process and the lifespan of the organism. Here, we provide insights into the complex relationships of ageing modulators and mRNA turnover mechanisms.