PPM1B depletion in U2OS cells supresses cell growth through RB1-E2F1 pathway and stimulates bleomycin-induced cell death

RNAs m6A modification facilitates UVB-induced photoaging

RNA N6-methylation (m6A) modification is common in eukaryotic mRNA and has been linked to various physiological disorders, including UVB-induced photoaging. To identify biological differences among photoaging. Three pairs of normal and photoaged skin tissues were collected for m6A RNA sequencing assay. Transcriptome profiles showed differential m6A methylation modifications in 1365 mRNAs in photoaging skin tissues. Pathway analysis revealed the involvement of cellular stress response and regulation of cell cycle G2/M phase transition in m6A-mRNAs. Further experiments validated the differential expression of m6A methyltransferases (METTL3 and METTL14) and hypermethylation modification in mRNAs (CENPE, PPM1B and TPM1). In vitro studies demonstrated that increased METTL3 and METTL14 levels promoted m6A methylation of CENPE, PPM1B and TPM1 in UVB-induced photoaging cells, and further experiments on mice showed that downregulation of METTL3 and METTL14 reduced m6A modifications in CENPE, PPM1B and TPM1, leading to the delayed appearance of photoaging phenotypes, suggesting that these genes could serve as potential therapeutic targets for treating photoaging. Our study characterized key transcriptome changes in photoaging and identified the role of METTL3 and METTL14 in mediating m6A modification, resulting in the upregulation of CENPE, PPM1B and TPM1 expression, which may be crucial in UVB-induced photoaging.

RBM10 regulates the tumorigenic potential of human cancer cells by modulating PPM1B and YBX1 activities

RNA binding protein RBM10 participates in various RNA metabolism, and its decreased expression or loss of function by mutation has been identified in many human cancers. However, how its dysregulation contributes to human cancer pathogenesis remains to be determined. Here, we found that RBM10 expression was decreased in breast tumors, and breast cancer patients with low RBM10 expression presented poorer survival rates. RBM10 depletion in breast cancer cells significantly promotes the cellular proliferation and migration. We further demonstrated that RBM10 forms a triple complex with YBX1 and phosphatase 1B (PPM1B), in which PPM1B serves as the phosphatase of YBX1. RBM10 knock-down markedly attenuated association between YBX1 and PPM1B, leading to elevated levels of YBX1 phosphorylation and its nuclear translocation. Furthermore, cancer cells with RBM10 depletion had a significantly accelerated tumor growth in nude mice. Importantly, these enhanced tumorigenic phenotypes can be reversed by overexpression of PPM1B. Our findings provide the mechanistic bases for functional loss of RBM10 in promoting tumorigenicity, and are potentially useful in the development of combined therapeutic strategies for cancer patients with defective RBM10.

A comprehensive overview of PPM1B: From biological functions to diseases

Reversible phosphorylation of proteins is an important mechanism that regulates cellular processes, which are precisely regulated by protein kinases and phosphatases. PPM1B is a metal ion-dependent serine/threonine protein phosphatase, which regulates multiple biological functions by targeting substrate dephosphorylation, such as cell cycle, energy metabolism, inflammatory responses. In this review, we summarized the occurrent understandings of PPM1B focused on its regulation of signaling pathways, related diseases, and small-molecular inhibitors, which may provide new insights for the identification of PPM1B inhibitors and the treatment of PPM1B-related diseases.

Expression of lactate-related signatures correlates with immunosuppressive microenvironment and prognostic prediction in ewing sarcoma

Objectives: Ewing sarcoma (EWS) is an aggressive tumor of bone and soft tissue. Growing evidence indicated lactate as a pivotal mediator of crosstalk between tumor energy metabolism and microenvironmental regulation. However, the contribution of lactate-related genes (LRGs) in EWS is still unclear.

Methods: We obtained the transcriptional data of EWS patients from the GEO database and identified differentially expressed-LRGs (DE-LRGs) between EWS patient samples and normal tissues. Unsupervised cluster analysis was utilized to recognize lactate modulation patterns based on the expression profile of DE-LRGs. Functional enrichment including GSEA and GSVA analysis was conducted to identify molecular signaling enriched in different subtypes. ESTIMATE, MCP and CIBERSORT algorithm was used to explore tumor immune microenvironment (TIME) between subtypes with different lactate modulation patterns. Then, lactate prognostic risk signature was built via univariate, LASSO and multivariate Cox analysis. Finally, we performed qPCR analysis to validate candidate gene expression.

Result: A total of 35 DE-LRGs were identified and functional enrichment analysis indicated that these LRGs were involved in mitochondrial function. Unsupervised cluster analysis divided EWS patients into two lactate modulation patterns and we revealed that patients with Cluster 1 pattern were linked to poor prognosis and high lactate secretion status. Moreover, TIME analysis indicated that the abundance of multiple immune infiltrating cells were dramatically elevated in Cluster 1 to Cluster 2, including CAFs, endothelial cells, Macrophages M2, etc., which might contribute to immunosuppressive microenvironment. We also noticed that expression of several immune checkpoint proteins were clearly increased in Cluster 1 to Cluster 2. Subsequently, seven genes were screened to construct LRGs prognostic signature and the performance of the resulting signature was validated in the validation cohort. Furthermore, a nomogram integrating LRGs signature and clinical characteristics was developed to predict effectively the 4, 6, and 8-year prognosis of EWS patients.

Conclusion: Our study revealed the role of LRGs in immunosuppressive microenvironment and predicting prognosis in EWS and provided a robust tool to predict the prognosis of EWS patients.

Protein Phosphatase PPM1B Inhibits Gastric Cancer Progression and Serves as a Favorable Prognostic Biomarker

BACKGROUND

Protein phosphatase PPM1B, also named as PP2Cβ, is a member of serine/threonine phosphatase family. Dysregulated expression of PPM1B has been reported in several malignancies; nevertheless, its role in gastric cancer remains unknown. Here, we aimed to initially investigate the expression and function of PPM1B in gastric adenocarcinoma.

METHODS

We firstly evaluated the protein expression of PPM1B in our enrolled retrospective cohort (n=161) via immunohistochemistry staining. Univariate and multivariate analyses were conducted to assess its prognostic value. Cellular experiments and xenografts in mice model were also performed to validate the role of PPM1B in gastric adenocarcinoma progression.

RESULTS

The advanced tumor stage was characterized with a lower PPM1B level. Lower PPM1B was associated with poor prognosis in both The Cancer Genome Atlas (TCGA) dataset and our cohort (P<0.05). Furthermore, Cox regression analysis demonstrated that PPM1B was a novel independent prognostic factor for gastric adenocarcinoma patients (hazard ratio=0.35, P=0.001). Finally, cellular and xenografts data confirmed that overexpressing PPM1B can remarkably attenuated gastric adenocarcinoma growth.

CONCLUSION

Low expression of PPM1B may be a potential molecular marker for poor prognosis in gastric adenocarcinoma.

Exosomal miR-181a-5p reduce Mycoplasma gallisepticum (HS strain) infection in chicken by targeting PPM1B and activating the TLR2-mediated MyD88/NF-κB signaling pathway

Mycoplasma gallisepticum (MG) is one of the most important pathogens that causes chronic respiratory disease (CRD) in chickens. Exosomes secreted from cells have been well demonstrated to deliver miRNAs to recipient cells to modulate cellular functions. The purpose of this study is to explore the underlying functions and mechanisms of exosomal miR-181a-5p in MG-HS infection. In this study, we found that miR-181a-5p expression in vivo and in vitro was significantly up-regulated after MG-HS infection. It was also upregulated in exosomes, which were derived from MG-HS-infected type-II pneumocytes cells (CP-II). In addition, exosomes secreted by MG-HS-infected CP-II were able to transfer miR-181a-5p to recipient chicken embryo fibroblast cells (DF-1), resulting in a significant upregulation of miR-181a-5p expression in recipient DF-1 cells. We further identified that Mg²⁺/Mn²⁺-dependent protein phosphatase 1B (PPM1B) was the target gene of miR-181a-5p. Overexpression of miR-181a-5p or knockdown of PPM1B activated the nuclear factor-κB (NF-κB) signaling pathway, whereas inhibition of miR-181a-5p and overexpression of PPM1B led to the opposite results. Besides, up-regulation of miR-181a-5p significantly increased the expression of toll-like receptor 2 (TLR2), myeloid differentiation factor 88 (MyD88), tumor necrosis factors alpha (TNF-α) and interleukin-1β (IL-1β), whereas inhibition of miR-181a-5p showed a contrary result. Up-regulation of miR-181a-5p promoted cell proliferation, cell cycle progression and inhibited apoptosis to resist MG-HS infection. Moreover, overexpression of miR-181a-5p significantly negative regulated the expression of Mycoplasma gallisepticum adhesin protein (pMGA1.2) by directly inhibiting PPM1B. Thus, we concluded that exosomal miR-181a-5p from CP-II cells activated the TLR2-mediated MyD88/NF-κB signaling pathways by directly targeting PPM1B to promote the expression of pro-inflammatory cytokines for defending against MG-HS infection in recipient DF-1 cells.

Identification of HN252 as a potent inhibitor of protein phosphatase PPM1B

Protein phosphatase 1B (PPM1B), a member of metal-dependent protein serine/threonine phosphatase family, is involved in the regulation of several signalling pathways. However, our understanding of its substrate interaction and physiological functions is still largely limited. There is no reported PPM1B inhibitor to date. In this study, we identified HN252, a p-terphenyl derivative, as a potent PPM1B inhibitor (K_i  = 0.52 ± 0.06 µM). HN252 binding to PPM1B displayed remarkable and specific inhibition of PPM1B in both in vitro and ex vivo. With the aid of this small molecular inhibitor, we identified 30 proteins' serine/threonine phosphorylation as potential substrates of PPM1B, 5 of which were demonstrated by immunoprecipitation, including one known (CDK2) and 4 novel ones (AKT1, HSP90B, β-catenin and BRCA1). Furthermore, GO and KEGG analysis of dramatically phosphorylated proteins by PPM1B inhibition indicated that PPM1B plays roles in the regulation of multiple cellular processes and signalling pathways, such as gene transcription, inflammatory regulation, ageing and tumorigenesis. Our work provides novel insights into further investigation of molecular mechanisms of PPM1B.

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.

Screening and identification of biomarkers associated with clinicopathological parameters and prognosis in oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is a major type of malignant tumor of the oral cavity. Despite marked advances in the management and diagnosis of OSCC, the associated overall survival ratio has only exhibited a modest increase in recent years. The present study aimed to identify potential crucial genes associated with clinical features and prognosis for OSCC, and to provide a basis for further investigation. RNA-sequencing data and corresponding clinical information were downloaded from The Cancer Genome Atlas database and differentially expressed mRNAs (DEmRNAs) were identified using the edgeR package. Bioinformatics analysis was performed to identify differentially expressed clinical features-associated mRNAs (CFmRNAs) and enhance the current knowledge of the function of them. Functional enrichment analysis and protein-protein interplay (PPI) network analysis were then performed to better understand CFmRNAs. Survival-associated genes were analyzed with Kaplan-Meier survival curves and the log-rank test. A total of 2,013 DEmRNAs between OSCC samples and normal tissues were identified, 180 of which were associated with clinical features. A total of 17 GO terms and 4 KEGG pathways were significantly enriched in functional enrichment analysis. A total of 4 hub genes (albumin, statherin, neurotensin and mucin 7) were identified in the PPI network analysis. A total of 6 genes (DDB1 and CUL4 associated factor 4 like 2, opiorphin prepropeptide, R3H domain containing like, transmembrane phosphatase with tensin homology, actin like 8 and protocadherin α 11) were observed to have an influence on survival. The DEmRNAs identified may have a crucial role in the genesis and development of OSCC and may be further developed for diagnostic, therapeutic and prognostic applications for OSCC in the future.

A heterozygous deficiency in protein phosphatase Ppm1b results in an altered ovulation number in mice

Ppm1b, a metal‑dependent serine/threonine protein phosphatase, catalyzes the dephosphorylation of a variety of phosphorylated proteins. Ppm1b‑/‑ mouse embryos die at the fertilized oocyte stage, whereas Ppm1b+/‑ mice with a C57BL/6 background exhibit no phenotypic abnormalities. Because the C57BL/6 strain produces a limited number of pups, in an attempt to produce Ppm1b‑/‑ mice, congenic Ppm1b+/‑ mice with an ICR background were established, which are more fertile and gave birth to more pups. As a result, however, no Ppm1b‑/‑ offspring were obtained when pairs of Ppm1b+/‑ ICR mice were bred again. Ppm1b+/‑ male and female ICR mice were analyzed from the viewpoint of fecundity. The Ppm1b haploinsufficiency had no effect on testicular weight or the number of sperm in male mice. Despite the fact that the levels of Ppm1b protein in the ovaries of sexually mature Ppm1b+/‑ mice were decreased compared with those of Ppm1b+/+ mice, there appeared to be no significant difference in the histological appearance of the ovaries, litter sizes or plasma progesterone levels at the estrous stage. When superovulation was induced by stimulation using a hormone treatment, the number of ovulated oocytes were the same for Ppm1b+/‑ and Ppm1b+/+ mice at 4 weeks of age when the estrous cycle did not proceed, however, the number of ovulated oocytes was lower in sexually mature Ppm1b+/‑ mice at 11 weeks of age compared with Ppm1b+/+ mice in the first and the second superovulation cycles. These collective results suggest that follicle development is excessive in Ppm1b+/‑ mice, and that this leads to a partial depletion of matured follicles and a corresponding decrease in the number of ovulated oocytes.