Nuclear phosphatase PPM1G in cellular survival and neural development

PPM1G dephosphorylates eIF4E in control of mRNA translation and cell proliferation

The mRNA 5'cap-binding eukaryotic translation initiation factor 4E (eIF4E) plays a critical role in the control of mRNA translation in health and disease. One mechanism of regulation of eIF4E activity is via phosphorylation of eIF4E by MNK kinases, which promotes the translation of a subset of mRNAs encoding pro-tumorigenic proteins. Work on eIF4E phosphatases has been paltry. Here, we show that PPM1G is the phosphatase that dephosphorylates eIF4E. We describe the eIF4E-binding motif in PPM1G that is similar to 4E-binding proteins (4E-BPs). We demonstrate that PPM1G inhibits cell proliferation by targeting phospho-eIF4E-dependent mRNA translation.

Clinical Value of PPM1G Gene in Survival Prognosis and Immune Infiltration of Hepatocellular Carcinoma

OBJECTIVE

Liver cancer is one of the most common malignancies, but its prognosis is still poor. Exploring potential biomarkers is an important direction of tumor research. We intend to use bioinformatics methods to explore potential biomarkers related to survival and prognosis of HCC.

METHODS

The mRNA and protein expressions of PPM1G in liver cancer were analyzed by HPA, TIMER, and UALCAN databases, and the effects of PPM1G on the prognosis of liver cancer patients were explored by the GEPIA database. We also explored the correlation between PPM1G expression and liver cancer immune infiltration through the TIMER database and further explored the potential protein interaction network of PPM1G through the STRING database.

RESULTS

The mRNA and protein expression of PPM1G gene in hepatocellular carcinoma tissues was lower than that in normal adjacent tissues. Liver cancer patients with high expression of PPM1G have a better prognosis than those with low expression of PPM1G. The expression of PPM1G is positively or negatively correlated with different immune cells of liver cancer, such as CD4+ T lymphocytes, CD8+ T lymphocytes, B cells, macrophages, and neutrophils.

CONCLUSION

The liver cancer patients with high expression of PPM1G have a good prognosis, and PPM1G gene may be a potential immunotherapy target and prognostic marker of liver cancer.

High expression of PPM1G is associated with the progression and poor prognosis of hepatocellular carcinoma

BACKGROUND

PPM1G, a member of the serine/threonine protease family, dephosphorylates various proteins and may be involved in cancer development. The role and mechanism of PPM1G in HCC still needs to be verified.

OBJECTIVE

This study aims to explore the role of PPM1G in the occurrence, development and prognosis of HCC.

METHODS

Using bioinformatics (UALCAN, cBioPortal, Linkedomics, STRING and GSEA) to analyze the expression of PPM1G mRNA in HCC, its clinical relevance and possible involved signaling pathways. The expression of PPM1G protein was determined by immunohistochemistry in 311 cases of HCC to evaluate the association between PPM1G and clinical features and prognosis.

RESULTS

The expression of PPM1G was significantly upregulated in HCC (P< 0.001), correlated with the metastasis (P= 0.020), pathological grade of HCC (P= 0.032), microvascular invasion (P= 0.040), and HBV infection (P= 0.041). Cox multivariate regression showed high expression of PPM1G was an independent prognostic factor for HCC. Its role in HCC may relate to methylation and frequency mutation. Furthermore, the database showed PPM1G is involved in the signal pathway such as cell cycle, WNT pathway, and mTOR pathway in HCC.

CONCLUSION

PPM1G showed an essential function involving in tumor-related pathways in HCC, providing a biological basis for targeted treatment of HCC clinically.

Metal dependent protein phosphatase PPM family in cardiac health and diseases

Protein phosphorylation and dephosphorylation is central to signal transduction in nearly every aspect of cellular function, including cardiovascular regulation and diseases. While protein kinases are often regarded as the molecular drivers in cellular signaling with high specificity and tight regulation, dephosphorylation mediated by protein phosphatases is also gaining increasing appreciation as an important part of the signal transduction network essential for the robustness, specificity and homeostasis of cell signaling. Metal dependent protein phosphatases (PPM, also known as protein phosphatases type 2C, PP2C) belong to a highly conserved family of protein phosphatases with unique biochemical and molecular features. Accumulating evidence also indicates important and specific functions of individual PPM isoform in signaling and cellular processes, including proliferation, senescence, apoptosis and metabolism. At the physiological level, abnormal PPM expression and activity have been implicated in major human diseases, including cancer, neurological and cardiovascular disorders. Finally, inhibitors for some of the PPM members have been developed as a potential therapeutic strategy for human diseases. In this review, we will focus on the background information about the biochemical and molecular features of major PPM family members, with emphasis on their demonstrated or potential roles in cardiac pathophysiology. The current challenge and potential directions for future investigations will also be highlighted.

Identification and validation of a five-gene prognostic signature for hepatocellular carcinoma

BACKGROUND

ARID1A is a commonly mutated tumor suppressor gene found in all human cancer types, but its clinical significance, oncogenic functions, and relevant mechanisms in hepatocellular carcinoma (HCC) are not well understood.

OBJECTIVE

We aimed to improving the prognosis risk classification of HCC from the perspective of ARID1A mutations.

MATERIALS AND METHODS

We examined the interaction between ARID1A mutations and the overall survival via Kaplan-Meier survival analysis. We used gene set enrichment analysis (GSEA) to elucidate the influence of ARID1A mutations on signaling pathways. A prognostic model was constructed using LASSO and multivariate Cox regression analyses. A receiver operating characteristic (ROC) curve was used to estimate the performance and accuracy of the model.

RESULTS

HCC patients with ARID1A mutations presented poor prognosis. By GSEA, we showed that genes upregulated by reactive oxygen species (ROS) and regulated by MYC were positively correlated with ARID1A mutations. A prognostic signature consisting of 5 genes (SRXN1, LDHA, TFDP1, PPM1G, and EIF2S1) was constructed in our research. The signature showed good performance in predicting overall survival (OS) for HCC patients by internal and external validation.

CONCLUSION

Our research proposed a novel and robust approach for the prognostic risk classification of HCC patients, and this approach may provide new insights to improve the treatment strategy of HCC.

PPM1G restricts innate immune signaling mediated by STING and MAVS and is hijacked by KSHV for immune evasion

The adaptor proteins, STING and MAVS, are components of critical pathogen-sensing pathways that induce innate immunity. Phosphorylation of either adaptor results in activation of the type I interferon pathway. How this phosphorylation is regulated and how it is manipulated by pathogens remain largely unknown. Here, we identified host protein phosphatase, Mg²⁺/Mn²⁺ dependent 1G (PPM1G) as a negative regulator of innate immune pathways and showed that this host system is hijacked by Kaposi's sarcoma-associated herpesvirus (KSHV). Mechanistically, KSHV tegument protein ORF33 interacts with STING/MAVS and enhances recruitment of PPM1G to dephosphorylate p-STING/p-MAVS for immunosuppression. Inhibition of PPM1G expression improves the antiviral response against both DNA and RNA viruses. Collectively, our study shows that PPM1G restricts both cytosolic DNA- and RNA-sensing pathways to naturally balance the intensity of the antiviral response. Manipulation of PPM1G by KSHV provides an important strategy for immune evasion.

Metal-dependent Ser/Thr protein phosphatase PPM family: Evolution, structures, diseases and inhibitors

Protein phosphatases and kinases control multiple cellular events including proliferation, differentiation, and stress responses through regulating reversible protein phosphorylation, the most important post-translational modification. Members of metal-dependent protein phosphatase (PPM) family, also known as PP2C phosphatases, are Ser/Thr phosphatases that bind manganese/magnesium ions (Mn²⁺/Mg²⁺) in their active center and function as single subunit enzymes. In mammals, there are 20 isoforms of PPM phosphatases: PPM1A, PPM1B, PPM1D, PPM1E, PPM1F, PPM1G, PPM1H, PPM1J, PPM1K, PPM1L, PPM1M, PPM1N, ILKAP, PDP1, PDP2, PHLPP1, PHLPP2, PP2D1, PPTC7, and TAB1, whereas there are only 8 in yeast. Phylogenetic analysis of the DNA sequences of vertebrate PPM isoforms revealed that they can be divided into 12 different classes: PPM1A/PPM1B/PPM1N, PPM1D, PPM1E/PPM1F, PPM1G, PPM1H/PPM1J/PPM1M, PPM1K, PPM1L, ILKAP, PDP1/PDP2, PP2D1/PHLPP1/PHLPP2, TAB1, and PPTC7. PPM-family members have a conserved catalytic core region, which contains the metal-chelating residues. The different isoforms also have isoform specific regions within their catalytic core domain and terminal domains, and these regions may be involved in substrate recognition and/or functional regulation of the phosphatases. The twenty mammalian PPM phosphatases are involved in regulating diverse cellular functions, such as cell cycle control, cell differentiation, immune responses, and cell metabolism. Mutation, overexpression, or deletion of the PPM phosphatase gene results in abnormal cellular responses, which lead to various human diseases. This review focuses on the structures and biological functions of the PPM-phosphatase family and their associated diseases. The development of specific inhibitors against the PPM phosphatase family as a therapeutic strategy will also be discussed.

Protein expression profiles that underpin the preventive and therapeutic potential of Moringa oleifera Lam against azoxymethane and dextran sodium sulfate-induced mouse colon carcinogenesis

Previous studies in a mouse model have indicated the anticancer potential of boiled Moringa oleifera pod (bMO)-supplemented diets; however, its molecular mechanisms are still unclear. Therefore, the present study aimed to explore the protein expression profiles responsible for the suppressive effect of bMO supplementation on azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced mouse colon carcinogenesis. Analysis by gel electrophoresis and liquid chromatography-tandem mass spectrophotometry demonstrated that there were 125 proteins that were differentially expressed in mouse colon tissues between 14 experimental groups of mice. The differentially expressed proteins are involved in various biological processes, such as signal transduction, metabolism, transcription and translation. Venn diagram analysis of the differentially expressed proteins was performed in six selected mouse groups, including negative control, positive control mice induced by AOM/DSS, the AOM/DSS groups receiving preventive or therapeutic bMO diets and their bMO-supplemented control groups. This analysis identified 7 proteins; 60S acidic ribosomal protein P1 (Rplp1), fragile X mental retardation, cystatin 9, round spermatids protein, zinc finger protein 638, protein phosphatase 2C (Ppm1g) and unnamed protein product as being potentially associated with the preventive and therapeutic effects of bMO in AOM/DSS-induced mouse colon cancer. Analysis based on the search tool for interactions of chemicals (STITCH) database predicted that Rplp1 interacted with the apoptotic and inflammatory pathways, whereas Ppm1g was associated only with inflammatory networks. This proteomic analysis revealed candidate proteins that are responsible for the effects of bMO supplementation, potentially by regulating apoptotic and inflammatory signaling networks in colorectal cancer prevention and therapy.

Association of PPM1G methylation with risk-taking in alcohol use disorder

Alcohol use disorder (AUD) is a chronic and relapsing disease with a substantial genetic influence. Given the recent discovery of the association of PPM1G methylation with alcohol use disorder (AUD) from a genome-wide methylation study, we sought to verify and extend the previous work of AUD-related impulsivity in a Korean population with AUD. A total of 244 men with AUD were assessed for psychological characteristics and behavioral impulsivity using stop signal task (response inhibition) and Balloon Analog Risk Task (risk-taking). Leukocyte DNA methylation at PPM1G was quantified using pyrosequencing. The effects of PPM1G methylation on severity of problematic drinking measured by Alcohol Use Disorder Identification Test (AUDIT) and multidimensional impulsivity were tested using linear regression analyses. Hypermethylation of PPM1G was significantly associated with risk-taking propensity among men with AUD. No significant association of PPM1G methylation was found to be associated with AUDIT scores and response inhibition. Our findings indicate that altered methylation of PPM1G may influence the impulsive choice of risk-taking in AUD. Further research is required in order to determine the role of PPM1G in the pathophysiology of AUD and multidimensional impulsivity.

Costunolide represses hepatic fibrosis through WW domain-containing protein 2-mediated Notch3 degradation

BACKGROUND AND PURPOSE

This study investigates the antifibrotic activities and potential mechanisms of costunolide (COS), a natural sesquiterpene compound.

EXPERIMENTAL APPROACH

Rats subjected to bile duct ligation and mice challenged with CCl₄ were used to study the antifibrotic effects of COS in vivo. Mouse primary hepatic stellate cells (pHSCs) and human HSC line LX-2 also served as an in vitro liver fibrosis models. The expression of fibrogenic genes and signaling proteins in the neurogenic locus notch homologue protein 3 (Notch3)-hairy/enhancer of split-1 (HES1) pathway was examined using western blot and/or real-time PCR. Notch3 degradation was analysed using immunofluorescence and coimmunoprecipitation.

KEY RESULTS

In animals, COS administration attenuated hepatic histopathological injury and collagen accumulation and reduced the expression of fibrogenic genes. COS time- and dose-dependently suppressed the levels of fibrotic markers in LX-2 cells and mouse pHSCs. Mechanistic studies showed COS destabilized Notch3 and subsequently inhibited the Notch3-HES1 pathway, thus inhibiting HSC activation. Furthermore, COS blocked the WW domain-containing protein 2 (WWP2)/protein phosphatase 1G (PPM1G) interaction and enhanced the effect of WWP2 on Notch3 degradation.

CONCLUSIONS AND IMPLICATIONS

COS exerted potent antifibrotic effects in vitro and in vivo by disrupting the WWP2/PPM1G complex, promoting Notch3 degradation and inhibiting the Notch3/HES1 pathway. This indicates that COS may be a potential therapeutic candidate for the treatment of liver fibrosis.

PPM1G forms a PPP-type phosphatase holoenzyme with B56δ that maintains adherens junction integrity

Serine/threonine phosphatases achieve substrate diversity by forming distinct holoenzyme complexes in cells. Although the PPP family of serine/threonine phosphatase family members such as PP1 and PP2A are well known to assemble and function as holoenzymes, none of the PPM family members were so far shown to act as holoenzymes. Here, we provide evidence that PPM1G, a member of PPM family of serine/threonine phosphatases, forms a distinct holoenzyme complex with the PP2A regulatory subunit B56δ. B56δ promotes the re-localization of PPM1G to the cytoplasm where the phosphatase can access a discrete set of substrates. Further, we unveil α-catenin, a component of adherens junction, as a new substrate for the PPM1G-B56 phosphatase complex in the cytoplasm. B56δ-PPM1G dephosphorylates α-catenin at serine 641, which is necessary for the appropriate assembly of adherens junctions and the prevention of aberrant cell migration. Collectively, we reveal a new holoenzyme with PPM1G-B56δ as integral components, in which the regulatory subunit provides accessibility to distinct substrates for the phosphatase by defining its cellular localization.

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation

Background

Investigating cell fate decision and subpopulation specification in the context of the neural lineage is fundamental to understanding neurogenesis and neurodegenerative diseases. The differentiation process of neural-tube-like rosettes in vitro is representative of neural tube structures, which are composed of radially organized, columnar epithelial cells and give rise to functional neural cells. However, the underlying regulatory network of cell fate commitment during early neural differentiation remains elusive.

Results

In this study, we investigated the genome-wide transcriptome profile of single cells from six consecutive reprogramming and neural differentiation time points and identified cellular subpopulations present at each differentiation stage. Based on the inferred reconstructed trajectory and the characteristics of subpopulations contributing the most toward commitment to the central nervous system lineage at each stage during differentiation, we identified putative novel transcription factors in regulating neural differentiation. In addition, we dissected the dynamics of chromatin accessibility at the neural differentiation stages and revealed active cis-regulatory elements for transcription factors known to have a key role in neural differentiation as well as for those that we suggest are also involved. Further, communication network analysis demonstrated that cellular interactions most frequently occurred in the embryoid body stage and that each cell subpopulation possessed a distinctive spectrum of ligands and receptors associated with neural differentiation that could reflect the identity of each subpopulation.

Conclusions

Our study provides a comprehensive and integrative study of the transcriptomics and epigenetics of human early neural differentiation, which paves the way for a deeper understanding of the regulatory mechanisms driving the differentiation of the neural lineage.

The Protein Phosphatase PPM1G Destabilizes HIF-1α Expression

Hypoxia-inducible factors (HIFs) are key regulators of hypoxic responses, and their stability and transcriptional activity are controlled by several kinases. However, the regulation of HIF by protein phosphatases has not been thoroughly investigated. Here, we found that overexpression of Mg²⁺/Mn²⁺-dependent protein phosphatase 1 gamma (PPM1G), one of Ser/Thr protein phosphatases, downregulated protein expression of ectopic HIF-1α under normoxic or acute hypoxic conditions. In addition, the deficiency of PPM1G upregulated protein expression of endogenous HIF-1α under normoxic or acute oxidative stress conditions. PPM1G decreased expression of HIF-1α via the proteasomal pathway. PPM1G-mediated HIF-1α degradation was dependent on prolyl hydroxylase (PHD), but independent of von Hippel-Lindau (VHL). These data suggest that PPM1G is critical for the control of HIF-1α-dependent responses.

Genome-wide association study provides strong evidence of genes affecting the reproductive performance of Nellore beef cows

Reproductive traits are economically important for beef cattle production; however, these traits are still a bottleneck in indicine cattle since these animals typically reach puberty at older ages when compared to taurine breeds. In addition, reproductive traits are complex phenotypes, i.e., they are controlled by both the environment and many small-effect genes involved in different pathways. In this study, we conducted genome-wide association study (GWAS) and functional analyses to identify important genes and pathways associated with heifer rebreeding (HR) and with the number of calvings at 53 months of age (NC53) in Nellore cows. A total of 142,878 and 244,311 phenotypes for HR and NC53, respectively, and 2,925 animals genotyped with the Illumina Bovine HD panel (Illumina^®, San Diego, CA, USA) were used in GWAS applying the weighted single-step GBLUP (WssGBLUP) method. Several genes associated with reproductive events were detected in the 20 most important 1Mb windows for both traits. Significant pathways for HR and NC53 were associated with lipid metabolism and immune processes, respectively. MHC class II genes, detected on chromosome 23 (window 25-26Mb) for NC53, were significantly associated with pregnancy success of Nellore cows. These genes have been proved previously to be associated with reproductive traits such as mate choice in other breeds and species. Our results suggest that genes associated with the reproductive traits HR and NC53 may be involved in embryo development in mammalian species. Furthermore, some genes associated with mate choice may affect pregnancy success in Nellore cattle.

Genome-wide association study for conformation traits in three Danish pig breeds

Background

Selection for sound conformation has been widely used as a primary approach to reduce lameness and leg weakness in pigs. Identification of genomic regions that affect conformation traits would help to improve selection accuracy for these lowly to moderately heritable traits. Our objective was to identify genetic factors that underlie leg and back conformation traits in three Danish pig breeds by performing a genome-wide association study followed by meta-analyses.

Methods

Data on four conformation traits (front leg, back, hind leg and overall conformation) for three Danish pig breeds (23,898 Landrace, 24,130 Yorkshire and 16,524 Duroc pigs) were used for association analyses. Estimated effects of single nucleotide polymorphisms (SNPs) from single-trait association analyses were combined in two meta-analyses: (1) a within-breed meta-analysis for multiple traits to examine if there are pleiotropic genetic variants within a breed; and (2) an across-breed meta-analysis for a single trait to examine if the same quantitative trait loci (QTL) segregate across breeds. SNP annotation was implemented through Sus scrofa Build 10.2 on Ensembl to search for candidate genes.

Results

Among the 14, 12 and 13 QTL that were detected in the single-trait association analyses for the three breeds, the most significant SNPs explained 2, 2.3 and 11.4% of genetic variance for back quality in Landrace, overall conformation in Yorkshire and back quality in Duroc, respectively. Several candidate genes for these QTL were also identified, i.e. LRPPRC, WRAP73, VRTN and PPARD likely control conformation traits through the regulation of bone and muscle development, and IGF2BP2, GH1, CCND2 and MSH2 can have an influence through growth-related processes. Meta-analyses not only confirmed many significant SNPs from single-trait analyses with higher significance levels, but also detected several additional associated SNPs and suggested QTL with possible pleiotropic effects.

Conclusions

Our results imply that conformation traits are complex and may be partly controlled by genes that are involved in bone and skeleton development, muscle and fat metabolism, and growth processes. A reliable list of QTL and candidate genes was provided that can be used in fine-mapping and marker assisted selection to improve conformation traits in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0289-2) contains supplementary material, which is available to authorized users.

Phosphatidylinositol-3 kinase-dependent translational regulation of Id1 involves the PPM1G phosphatase

Id1 is a helix-loop-helix transcriptional modulator that increases the aggressiveness of malignant glial neoplasms. Since most glioblastomas (GBMs) show increased phosphatidylinositol-3 kinase (PI-3K) signaling, we sought to determine whether this pathway regulates Id1 expression. Higher basal Id1 expression correlates with dysregulated PI-3K signaling in multiple established GBM cell lines. Further characterization of PI-3K-dependent Id1 regulation reveals that chemical or genetic inhibition of PI-3K signaling reduces Id1 protein but not mRNA expression. Overall, PI-3K signaling appears to enhance Id1 translation with no significant effect on its stability. PI-3K signaling is known to regulate protein translation through mTORC1-dependent phosphorylation of 4E-BP1, which reduces its association with and inhibition of the translation initiation factor eIF4E. Interestingly, while inhibition of PI-3K and AKT lowers 4E-BP1 phosphorylation and expression of Id1 in all cases, inhibition of TORC1 with rapamycin does not consistently have a similar effect suggesting an alternative mechanism for PI-3K-dependent regulation of Id1 translation. We now identify a potential role for the serine-threonine phosphatase PPM1G in translational regulation of Id1 protein expression. PPM1G knockdown by siRNA increase both 4E-BP1 phosphorylation and Id1 expression and PPM1G and 4E-BP1 co-associates in GBM cells. Furthermore, PPM1G is a phosphoprotein and this phosphorylation appears to be regulated by PI-3K activity. Finally, PI-3K inhibition increases PPM1G activity when assessed by an in vitro phosphatase assay. Our findings provide the first evidence that the PI-3K/AKT signaling pathway modulates PPM1G activity resulting in a shift in the balance between hyper- and hypo-phosphorylated 4E-BP1 and translational regulation of Id1 expression.

Genetic, epigenetic, and environmental contributions to neural tube closure

The formation of the embryonic brain and spinal cord begins as the neural plate bends to form the neural folds, which meet and adhere to close the neural tube. The neural ectoderm and surrounding tissues also coordinate proliferation, differentiation, and patterning. This highly orchestrated process is susceptible to disruption, leading to neural tube defects (NTDs), a common birth defect. Here, we highlight genetic and epigenetic contributions to neural tube closure. We describe an online database we created as a resource for researchers, geneticists, and clinicians. Neural tube closure is sensitive to environmental influences, and we discuss disruptive causes, preventative measures, and possible mechanisms. New technologies will move beyond candidate genes in small cohort studies toward unbiased discoveries in sporadic NTD cases. This will uncover the genetic complexity of NTDs and critical gene-gene interactions. Animal models can reveal the causative nature of genetic variants, the genetic interrelationships, and the mechanisms underlying environmental influences.