Bromodomain PHD‑finger transcription factor promotes glioma progression and indicates poor prognosis

Chromatin remodeling protein BPTF mediates chromatin accessibility at gene promoters in planarian stem cells

BACKGROUND

The regulation of chromatin accessibility is essential in eukaryotic cells as one of several mechanisms that ensure gene activation occurs at appropriate times and in appropriate cell types. Accordingly, mutations in chromatin remodeling proteins are linked to many different developmental disorders and cancers. One example of a chromatin protein that has been linked to both developmental abnormalities and cancer is BPTF/NURF301, the largest subunit of the Nucleosome Remodeling Factor (NuRF) complex. The BPTF subunit is not only important for the formation of NuRF but also helps direct its activity to particular regions of chromatin by preferentially binding histone H3 lysine four trimethylation (H3K4me3). Notably, defects caused by knockdown of bptf in Xenopus embryos mimic those caused by knockdown of wdr5, a core subunit of all H3K4me3 methyltransferase complexes. However, the mechanistic details of how and where BPTF/NuRF is recruited to regulate gene expression vary between studies and have been largely tested in vitro and/or in cultured cells. Improving our understanding of how this chromatin remodeling complex targets specific gene loci and regulates their expression in an organismal context will provide important insight into how pathogenic mutations disrupt its normal, in vivo, cellular functions.

RESULTS

Here, we report our findings on the role of BPTF in maintaining chromatin accessibility and essential function in planarian (Schmidtea mediterranea) stem cells. We find that depletion of planarian BPTF primarily affects accessibility at gene promoters near transcription start sites (TSSs). BPTF-dependent loss of accessibility did not correlate with decreased gene expression when we considered all affected loci. However, we found that genes marked by Set1-dependent H3K4me3, but not MLL1/2-dependent H3K4me3, showed increased sensitivity to the loss of BPTF-dependent accessibility. In addition, knockdown of bptf (Smed-bptf) produces loss-of-function phenotypes similar to those caused by knockdown of Smed-set1.

CONCLUSIONS

The S.mediterranea homolog of NuRF protein BPTF (SMED-BPTF) is essential for normal homeostasis in planarian tissues, potentially through its role in maintaining chromatin accessibility at a specific subset of gene promoters in planarian stem cells. By identifying loci that lose both chromatin accessibility and gene expression after depletion of BPTF, we have identified a cohort of genes that may have important functions in stem cell biology.

BPTF promotes glioma development through USP34-mediated de-ubiquitination of FOXC1

Glioma is the most prevalent malignant tumor of the brain, and the study of the molecular mechanisms associated with its development has important clinical significance. Our previous study found that BPTF promotes the malignant phenotype of glioma and is significantly associated with poor prognosis; the downstream regulatory mechanisms are explored in this study. Western blot and immunohistochemical staining were used to detect protein expression in cells or tissues. BPTF knockdown as well as FOXC1-overexpressing lentiviruses were used in combination for the construction of the U251 cell model, leading to functional rescue experiments. CCK8 assay, flow cytometry, scratch assay, and Transwell assay were used to detect cell proliferation, apoptosis, and migration, respectively. Finally, immunoprecipitation assays, combined with western blot (WB), were used to detect the interaction between proteins as well as the level of ubiquitination modification. The obtained results suggested that BPTF knockdown may inhibit the malignant behavior of glioma cells by downregulating FOXC1 expression. Moreover, FOXC1 expression was significantly higher in glioma tissues than in normal brain tissues and was significantly associated with higher tumor stage and worse patient prognosis. Finally, the mechanism of FOXC1 regulation by BPTF was found to result from the affected protein stability of FOXC1 through USP34-mediated de-ubiquitylation. In conclusion, the BPTF/FOXC1 axis was identified as a key promotor in glioma development and may be a potential target in the inhibition of glioma development.

Network Biology Approaches to Uncover Therapeutic Targets Associated with Molecular Signaling Pathways from circRNA in Postoperative Cognitive Dysfunction Pathogenesis

Postoperative cognitive dysfunction (POCD) is a cognitive deterioration and dementia that arise after a surgical procedure, affecting up to 40% of surgery patients over the age of 60. The precise etiology and molecular mechanisms underlying POCD remain uncovered. These reasons led us to employ integrative bioinformatics and machine learning methodologies to identify several biological signaling pathways involved and molecular signatures to better understand the pathophysiology of POCD. A total of 223 differentially expressed genes (DEGs) comprising 156 upregulated and 67 downregulated genes were identified from the circRNA microarray dataset by comparing POCD and non-POCD samples. Gene ontology (GO) analyses of DEGs were significantly involved in neurogenesis, autophagy regulation, translation in the postsynapse, modulating synaptic transmission, regulation of the cellular catabolic process, macromolecule modification, and chromatin remodeling. Pathway enrichment analysis indicated some key molecular pathways, including mTOR signaling pathway, AKT phosphorylation of cytosolic targets, MAPK and NF-κB signaling pathway, PI3K/AKT signaling pathway, nitric oxide signaling pathway, chaperones that modulate interferon signaling pathway, apoptosis signaling pathway, VEGF signaling pathway, cellular senescence, RANKL/RARK signaling pathway, and AGE/RAGE pathway. Furthermore, seven hub genes were identified from the PPI network and also determined transcription factors and protein kinases. Finally, we identified a new predictive drug for the treatment of SCZ using the LINCS L1000, GCP, and P100 databases. Together, our results bring a new era of the pathogenesis of a deeper understanding of POCD, identified novel therapeutic targets, and predicted drug inhibitors in POCD.

New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition

The nucleosome remodeling factor (NURF) alters chromatin accessibility through interactions with its largest subunit,the bromodomain PHD finger transcription factor BPTF. BPTF is overexpressed in several cancers and is an emerging anticancer target. Targeting the BPTF bromodomain presents a potential strategy for its inhibition and the evaluation of its functional significance; however, inhibitor development for BPTF has lagged behind those of other bromodomains. Here we describe the development of pyridazinone-based BPTF inhibitors. The lead compound, BZ1, possesses a high potency (K_d = 6.3 nM) and >350-fold selectivity over BET bromodomains. We identify an acidic triad in the binding pocket to guide future designs. We show that our inhibitors sensitize 4T1 breast cancer cells to doxorubicin but not BPTF knockdown cells, suggesting a specificity to BPTF. Given the high potency and good physicochemical properties of these inhibitors, we anticipate that they will be useful starting points for chemical tool development to explore the biological roles of BPTF.

Identification of prognostic chromatin-remodeling genes in clear cell renal cell carcinoma

The aim of this study was to investigate the effects of chromatin-remodeling genes on the prognosis of patients with clear cell renal cell carcinoma (ccRCC). In TCGA-KIRC patients, two subgroups based on 86 chromatin-remodeling genes were established. The random forest algorithm was used for feature selection to identify BPTF, SIN3A and CNOT1 as characterized chromatin remodelers in ccRCC with good prognostic value. YY1 was indicated to be a transcription factor of genes highly related to BPTF, SIN3A and CNOT1. Functional annotations indicated that BPTF, SIN3A, CNOT1 and YY1 are all involved in the ubiquitin-mediated proteolysis process and that high expression of any of the five associated E3 ubiquitin ligases found in the pathway suggests a good prognosis. Protein network analysis indicated that BPTF has a targeted regulatory effect on YY1. Another independent dataset from International Cancer Genome Consortium (ICGC) showed a strong consistency with results in TCGA. In conclusion, we demonstrate that BPTF, SIN3A and CNOT1 are novel prognostic factors that predict good survival in ccRCC. We predicted that the good prognostic value of chromatin-remodeling genes BPTF and SIN3A is related to the regulation of YY1 and that YY1 regulates E3 ubiquitin ligases for further degradation of oncoproteins in ccRCC.

Upregulation of bromodomain PHD finger transcription factor in ovarian cancer and its critical role for cancer cell proliferation and survival

Bromodomain PHD finger transcription factor (BPTF) is a core subunit of the nucleosome-remodeling factor (NURF) complex, which plays an important role in the development of several cancers. However, it is unknown whether BPTF regulates the progression of ovarian cancer (OC). To investigate this, we measured the relative expression levels of BPTF in OC cell lines and tissues using Western blot and immunohistochemistry, respectively, and the results were analyzed using the χ² test. We also examined the effects from BPTF knockdown on the proliferation, migration, invasiveness, and apoptosis of OC cell lines. Mechanistic studies revealed that these effects were achieved through simultaneous modulation of multiple signaling pathways. We found that BPTF was highly expressed in OC cell lines and tissues compared with a normal human ovarian epithelial cell line and non-cancerous tissues (P < 0.05). These results are also supported by the public RNA-seq data. BPTF overexpression was correlated with a poor prognosis for OC patient survival (P < 0.05). In vitro experiments revealed that the downregulation of BPTF inhibited OC cell proliferation, colony formation, migration, and invasiveness, and induced apoptosis. BPTF knockdown also affected the epithelial-mesenchymal transition (EMT) signaling pathways and induced the cleavage of apoptosis-related proteins. Consequently, BPTF plays a critical role in OC cell survival, and functions as a potential therapeutic target for OC.

MiR-483 Targeted SOX3 to Suppress Glioma Cell Migration, Invasion and Promote Cell Apoptosis

Objective

Glioma is the most common malignant brain tumor that has high aggressiveness. The aim of this study was to investigate the potential therapeutic targets for gliomas.

Materials and Methods

Real-time quantitative polymerase chain reaction (RT-qPCR) was employed to calculate the expression of miRNA and genes. The connection between the expression of miR-483 and patients' overall survival rate was evaluated using Kaplan-Meier analysis. In addition, the underlying mechanism was detected using luciferase assay.

Results

The expression level of miR-483 was significantly decreased in glioma tissue samples and cell lines, compared to the adjacent tissues and normal cell lines. Downregulation of miR-483 or upregulation of SOX3 was associated with overall survival of glioma patients. Additionally, overexpression of miR-483 promotes cell invasion and migration and inhibits apoptosis. In addition, miR-483 directly targeted to SOX3, and the expression of miR-483 has a negative correlation with SOX3 in glioma tissues. SOX3 reversed partial functions of miR-483 on cell migration, invasion, and promoted cell apoptosis in glioma.

Conclusion

MiR-483 inhibited glioma cell migration, invasion, and promoted glioma cell apoptosis by targeting SOX3. MiR-483 maybe acted as a potential target for the treatment of glioma.

The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer

Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.

miR-454-3p promotes of human glioma cell growth by targeting EGR3

Gliomas are the most common primary brain tumors in adults and are associated with high mortality rates. In the present study, the aim was to evaluate the role of miR-454-3p in the pathogenesis of human glioma and to explore the underlying mechanism. Reverse transcription-quantitative PCR was performed to compare the expression levels of miR-454-3p in glioma and adjacent normal tissue. The effects of miR-454-3p on cell proliferation was tested by combining MTT and colony formation assays. Dual-luciferase assay was used to identify the target gene of miR-454-3p. The results showed that miR-454-3p was upregulated in glioma tissues where it exerts a positively regulatory role on cell growth. Dual-luciferase assay confirmed Early Growth Response 3 (EGR3) to be a target for miR-454-3p. Overexpression of EGR3 in glioma cells was found to impair miR-454-3p mimic-induced cell proliferation. These results suggested that upregulated miR-454-3p served an important role in glioma tumorigenesis by targeting EGR3, which provided valuable insights into the underlying mechanism of the disease that may lead to possible novel therapeutic strategies.

STC1 regulates glioblastoma migration and invasion via the TGF‑β/SMAD4 signaling pathway

Stanniocalcin-1 (STC1) is involved in cancer progression; however, the function of STC1 in glioblastoma remains unknown. In the present study, the expression levels of STC1 protein in glioblastoma were detected using immunohistochemistry. The expression levels of STC1, SMAD2/3 and SMAD4 proteins, following silencing of STC1, were assessed via western blotting. EdU and Transwell assays were performed to determine the proliferation and migration ability of the cells. The mRNA expression levels of STC1, SMAD4 and microRNA (miR)-34a were determined using quantitative PCR. The expression levels of STC1 were increased in glioblastoma tissues. STC1 revealed a significant association with poor outcome in patients with glioblastoma (P<0.05). The proliferation and invasion abilities were repressed in LN229 cells infected with LV3-shSTC1-1 and LV3-shSTC1-2 compared with LV3-NC. By contrast, the proliferation and invasion abilities were increased in T98G cells infected with LV5-STC1 compared with LV5-NC (P<0.05). The expression levels of STC1, SMAD2/3 and SMAD4 were decreased in LN229 cells infected with LV3-shSTC1-1 and LV3-shSTC1-2 compared with LV3-NC. However, the expression levels of STC1, SMAD2/3 and SMAD4 were elevated in T98G cells infected with LV5-STC1 compared with LV5-NC. The expression levels of miR-34a were decreased following silencing of STC1 (P<0.05). The expression levels of SMAD4 were decreased when transfected with miR-34a mimics (P<0.05). The luciferase activity of the wild-type 3′untranslated region of SMAD4 was decreased following transfection with miR-34a mimics (P<0.05). Silencing of STC1 inhibited the growth of LN229 in vivo. In conclusion, STC1 expression levels were increased in the present study, and it was revealed that STC1 regulated glioblastoma malignancy. This phenotype was observed in the SMAD2/3 and SMAD4 pathways.

DGKζ Plays Crucial Roles in the Proliferation and Tumorigenicity of Human glioblastoma

Glioblastoma is one of the most malignant brain cancers in adults, and it is a fatal disease because of its untimely pathogenetic location detection, infiltrative growth, and unfavorable prognosis. Unfortunately, multimodal treatment with maximal safe resection, chemotherapy and radiation has not increased the survival rate of patients with glioblastoma. Gene- and molecular-targeted therapy is considered to be a promising anticancer strategy for glioblastoma. The identification of novel potential targets in glioblastoma is of high importance. In this study, we found that both the mRNA and protein levels of diacylglycerol kinase ζ (DGKζ) were significantly higher in glioblastoma tissues than in precancerous lesions. The silencing of DGKζ by lentivirus-delivered shRNA reduced glioblastoma cell proliferation and induced G0/G1 phase arrest. Moreover, knockdown of DGKζ expression in U251 cells markedly reduced in vitro colony formation and in vivo tumorigenic capability. Further study showed that DGKζ inhibition resulted in decreases in cyclin D1, p-AKT and p-mTOR. Moreover, the rescue or overexpression of DGKζ in glioblastoma cells demonstrated the oncogenic function of DGKζ. In conclusion, these studies suggest that the suppression of DGKζ may inhibit the tumor growth of glioblastoma cells with high DGKζ expression. Thus, DGKζ might be a potential therapeutic target in malignant glioblastoma.