Promoter Region Research Articles

IGF2BP1 accelerates the aerobic glycolysis to boost its immune escape in hepatocellular carcinoma microenvironment.

Energy metabolism abnormity emerges as a crucial factor that facilitates tumorigenesis by accelerating aerobic glycolysis. However, the function of N6-methyladenosine (m6A) on hepatocellular carcinoma (HCC) aerobic glycolysis and immune escape is still unclear. Here, this investigation was intended to elucidate the regulation of m6A 'reader' IGF2BP1 involved in HCC aerobic glycolysis and immune escape. The aerobic glycolysis was tested by glucose uptake, lactate, ATP generation and ECAR. The CD8+ T cell-mediated killing effect was tested by cytotoxicity, IFN-γ and granzyme B. The molecular interaction was confirmed by luciferase reporter assay, immunoprecipitation assay and chromatin immunoprecipitation (ChIP)-PCR. Elevated IGF2BP1 expression was associated with poor prognosis in HCC patients. Functionally, IGF2BP1 emerged as an oncogenic factor that accelerated HCC aerobic glycolysis (glucose uptake, lactate, ATP generation and ECAR) and oxaliplatin resistance. Meanwhile, IGF2BP1 repressed the activated CD8+ T cell-mediated killing effect (cytotoxicity, IFN-γ and granzyme B) and apoptosis of HCC cells, indicating a suppressed cytotoxic T-cell response. By recognizing and binding to the m6A-modified sites on c-Myc mRNA, IGF2BP1 enhanced the stability of c-Myc mRNA, consequently upregulating c-Myc expression. In addition, transcription factor c-Myc targeted the programmed death ligand 1 (PD-L1) promoter region to strengthen its transcription. Taken together, this study illustrates IGF2BP1 as a potential therapeutic target in HCC, aiming to disrupt the interplay between aberrant metabolism and immune escape.

Methylation of the ESR1 promoters in visceral adipose tissue and its relationship with obesity.

Obesity is associated with decreased ESR1 expression level in visceral adipose tissue. However, it is unclear exactly what mechanisms are responsible for this decline. The aim of this study was to investigate the impact of aberrant methylation of the ESR1 alternative promoters on decreased ESR1 expression and its connection to obesity. Visceral adipose tissues and peripheral blood cells were obtained from 21 patients (non-obese and obese) undergoing inguinal hernia or gallbladder removal. Alternative promoter regions, C, E2 and F of the ESR1 gene, were analyzed by Methylation-Specific PCR (MSP) and mRNA levels were measured by quantitative real-time PCR (qPCR) in both visceral adipose tissue and peripheral blood cells. All statistical analyses were performed by SPSS (23.0). The methylation percentage in the three promoter regions of ESR1 was not different in obese individuals compared to non-obese individuals. We observed that promoter C had the highest methylation frequency in obese patients, although it was not statistically significant. Additionally, we observed that the hypermethylation of ESR1's promoter C was significantly associated with lower mRNA expression level in obesity (p = 0.020). This study suggests that methylation of ESR1 promoter C may be a factor in the development of obesity or a consequence of obesity. Further studies with advanced methods and larger study groups are needed to clarify this issue.

Structural and Functional Insight Into YefM-YoeB Complex of Toxin-Antitoxin System From Streptococcus pneumoniae.

Streptococcus pneumonia is a Gram-positive and facultative anaerobic bacterium that causes a number of diseases, including otitis media, community-acquired pneumonia, sepsis, and meningitis. With the emergence of antibiotic-resistant strains, there is an urgent need to develop antibiotics with a novel mechanism. The toxin-antitoxin (TA) system, which is primarily found in prokaryotes, consists of a toxin and its equivalent antitoxin genes. The YefM-YoeB module is a Type II TA system, where the YoeB toxin functions as a putative mRNA interferase upon activation, while the YefM antitoxin acts as a transcription repressor by binding to its promoter region along with YoeB. In this study, we determined the crystal structure of the YefM-YoeB complex from S. pneumoniae TIGR4 to comprehend the binding mechanism of the TA system. Furthermore, an in vitro ribonuclease activity assay was conducted to identify the ribonuclease activity of the YoeB toxin. Additionally, furthermore, the oligomeric state of the YefM-YoeB complex in solution was investigated, and a DNA-binding mode was proposed. These structural and functional insights into the YefM-YoeB complex could provide valuable information for the development of novel antibiotics targeting S. pneumonia-associated diseases.

E2F3a activates Gadd45b gene expression through PPARα-mediated transcriptional regulation in hepatic cells

Growth arrest and DNA damage-inducible beta (GADD45b) plays a critical role in intracellular events such as cell growth and apoptosis. Although the functional study of GADD45b has been conducted, the mechanism for the transcriptional regulation of GADD45b is largely unknown. Due to the drastic induction of hepatic GADD45b mRNA by peroxisome proliferator-activated receptor alpha (PPARα) activation in wild-type mice, we investigated a key factor that affects the upregulation of GADD45b mRNA. Interestingly, we found that GADD45b-promoter luciferase activity was dramatically increased as the 5’-flanking regions were closer to the transcription start site (TSS) in Hepa1c1c7 cells. Additionally, we found two E2F (E2F-myc activator/cell cycle regulator) binding motifs in the region (-150/-1) of the GADD45b promoter. Notably, E2F3 mRNA was significantly increased only in wild-type mice treated with WY-14643, a PPARα agonist, followed by the induction of GADD45b mRNA. Furthermore, gene functional studies and Chromatin Immunoprecipitation (ChIP) assays revealed that E2F3 could regulate the GADD45b gene via the E2F binding motif. Thus, we suggest that E2F3 may play a key role in regulating the GADD45b gene as a positive transcription factor.

Abstract 4119262: Anti-atherosclerotic Potential of M2 Macrophage-Derived Exosomes by Promoting Cholesterol Efflux of Foam Cell-Like Vascular Smooth Muscle Cells via the PPARγ-LXRα-ABCA1/ ABCG1 Pathway

Background: Impediment in the excretion of lipid deposits within SMC-derived foam cells (SMC-FCs) is one of the reasons for the continuous expansion of the plaque necrotic core. This study aims to explore the effect and underlying mechanimsm of exosomes secreted by M2 macrophage (M2-exos) on SMC-FCs lipid metabolism and plaque stability. Methods: First, immunofluorescence was used to detect the expression levels of CD45 (a recognized differentially expressed molecule of myeloid and SMC-FCs) and the key proteins of cholesterol efflux pathway, ABCA1 and ABCG1, in human early and late plaques. Exosomes derived from M0 and M2 macrophages were purified by sucrose density gradient centrifugation, and characterized based on specific morphology and surface markers. Western blot, Oil red O staining and cell total cholesterol assay were used to assess the effects of M2-exos on the lipid mechanism of SMC-FCs. RNA-seq was used to detect the miRNA profiles of M2-exos. Quantitative real-time PCR was used to identify candidate miRNAs. The dual-luciferase reporting system was utilized to assess the regulatory effect of candidate miRNA on target gene. Then, the effect of M2-exos on the progression and stability of plaques in ApoE -/- mice was evaluated using Oil red O, H&E, Masson, Movat and immunohistochemistry. Results: Immunofluorescence revealed that compared with early plaques, VSMC-FCs (CD45 - ) were significantly increased in late plaques, and the expression levels of ABCG1 and ABCA1 were marked lower than those in macrophage-derived foam cells (CD45 + ). Purified M2-exos treatment significantly promoted the cholesterol efflux of SMC-FCs in vitro. In high-fat-fed ApoE -/- mice, M2-exos significantly reduced the VSMC-FCs, delayed the progression of plaques, decreased necrotic core area and enhanced plaque stability. MiRNA profiling and comprehensive analysis of signaling pathways showed that M2-exos were rich in miR-7683-3p, which played a key role in regulating SMC-FCs lipid metabolism through PPARγ-LXRα-ABCA1/ABCG1 pathway. Dual-luciferase reporting assay showed that miR-7683-3p can specifically bind to the promoter region of homeobox genes A1(HoxA1), an inhibitor of PPARγ-LXRα-ABCA1/ABCG1 pathway. Conclusion: M2-exos exerted an obvious atherosclerotic protective effect, and the underlying mechanism was closely related to MiR-7683-3p, which targeted the 3’UTR of HoxA1 mRNA and activated the PPARγ-LXRα-ABCA1/ABCG1 mediated cholesterol efflux in SMC-FCs.

NSUN5 Facilitates Hepatocellular Carcinoma Progression by Increasing SMAD3 Expression.

Hepatocellular carcinoma (HCC) is characterized by frequent intrahepatic and distant metastases, resulting in a poor prognosis for patients. Epithelial-mesenchymal transition (EMT) plays a pivotal role in this process. However, the expression of NOP2/Sun RNA methyltransferase 5 (NSUN5) in HCC and its role in mediating EMT remain poorly understood. In this study, clinicopathological analyses are conducted across multiple independent HCC cohorts and induced tumor formation in Nsun5-knockout mice. The findings reveal an upregulation of NSUN5 expression in tumor tissues; conversely, the absence of Nsun5 hinders the malignant progression of HCC, indicating that NSUN5 may serve as a significant oncogene in HCC. Furthermore, elevated levels of NSUN5 enhance EMT processes within HCC cells. NSUN5-knockout cells exhibit reduced invasion and migration capabilities under both in vivo and in vitro conditions, while overexpression of NSUN5 yields opposing effects. Mechanistically, high levels of NSUN5 promote the enrichment of trimethylated histone H3 at lysine 4 (H3K4me3) at the promoter region of SMAD3 through recruitment of the WDR5, thereby facilitating HCC metastasis via SMAD3-mediated EMT pathways. Collectively, this study identifies NSUN5 as a novel driver of metastasis in HCC and provides a theoretical foundation for potential therapeutic strategies against this malignancy.

BIOM-13. COMBINED MGMT PROMOTER METHYLATION AND LOW GENE BODY METHYLATION IS A SUPERIOR PREDICTOR OF ALKYLATING AGENT RESPONSE THAN PROMOTER METHYLATION ALONE IN GLIOBLASTOMA

Abstract BACKGROUND The DNA methylation status of the promoter region of O-6-methylguanine-DNA methyltransferase (MGMT) is a critical predictor of temozolomide response in newly diagnosed glioblastoma. However, MGMT-STP27, the dominant method for MGMT promoter methylation determination from methylation array data, considers only methylation probes located in the promoter region. In this study, we propose a robust MGMT classifier that considers MGMT methylation probes in both the promoter and gene body regions. METHODS We leveraged glioblastoma DNA methylation and/or gene expression data published by the TCGA (N=312), GLASS (N=276), and Capper et al. (N=535). We correlated MGMT gene expression and MGMT probe methylation in datasets with paired expression and methylation data. We formulated an MGMT methylation score that measured the difference between MGMT promoter probe methylation and gene body probe methylation. We then compared the prognostic utility of this score with the MGMT-STP27 model on patients treated with upfront alkylating agents in multiple datasets in both univariate and multivariate analyses. RESULTS We found that MGMT expression was prognostic in TCGA (OS HR=1.5, p=0.027, PFS HR=1.9, p=0.001) and GLASS (OS HR=1.4, p=0.088, PFS HR=1.6, p=0.03) glioblastomas among patients treated with alkylating agents. MGMT expression was negatively correlated with MGMT promoter methylation and positively correlated with MGMT gene body methylation. We defined an MGMT score as the difference between the average MGMT DNA methylation in negatively correlated promoter probes and the average methylation in positively correlated gene body probes. This score was prognostic in the TCGA (OS HR=1.6, p=0.003, PFS HR=1.6, p=0.001) and GLASS (OS HR=3.1, p=0.01, PFS HR=3.9, p=0.004) and was also superior to the MGMT-STP27 classifiers in multivariate analyses (TCGA p=0.03). CONCLUSION Overall, we defined an MGMT methylation score that considers promoter and gene body methylation and may be a superior predictor of glioblastoma response to alkylating agents compared to MGMT-STP27.

Enhancing antitumor activity of herceptin in HER2-positive breast cancer cells: a novel DNMT-1 inhibitor approach

HER2 antagonists remain the cornerstone of therapy for patients with HER2-positive breast cancer. This study introduces a novel small-molecule inhibitor of DNA methyltransferase 1 (DNMT-1), referred to as DI-1, designed to synergize with HER2 antagonists in treating HER2-positive breast cancer cells. Clinical data reveal a negative correlation between DNMT-1 expression and PTEN levels, and a positive correlation with the methylation rates of PTEN's promoter. In experiments with SKBR3 and BT474 cells, DI-1 effectively reduced the methylation of PTEN's promoter region, thereby upregulating PTEN expression. This upregulation, in turn, enhanced the cells' sensitivity to HER2 antagonists, indicating that DI-1’s mechanism involves inhibiting DNMT-1’s recruitment to PTEN's promoter region. Consequently, by increasing PTEN expression, DI-1 amplifies the sensitivity of HER2-positive breast cancer cells to treatment, suggesting its potential as a promising therapeutic strategy in this context.

TMOD-32. MURINE MODELLING OF THE STING PATHWAY IN GLIOMAS

Abstract The stimulator of interferon genes (STING) pathway is a critical component of innate antitumor immunity through the recognition of pathogenic cytosolic DNA and stimulating the production of type 1 interferons and pro-inflammatory cytokines. We have previously shown that STING signaling is silenced in the neoplastic compartment of the GBM tumor microenvironment, but remains intact in vascular and immune cells. In human patient derived cell lines, such silencing appears to be mediated by hypermethylation of a region of the STING promoter and can be reversed by treatment with both the DNA methyltransferase (DNMT) inhibitor Decitabine and DNMT1-selective inhibitor GSK-3685032. These results suggest that neoplastic cell STING promoter methylation represents a therapeutic vulnerability that can be exploited by epigenetic therapies to inflame the glioma tumor microenvironment. Murine models are critical tools for exploring the translational implications of STING silencing in vivo. Distinct mouse models have been developed to optimally represent specific aspects of human glioma biology. Here we characterize the STING pathway in commonly used syngeneic murine glioma models, including CT2A, GL261, SB28, and SMA560. We show that the expression of STING pathway components varies significantly across these lines. Importantly, unlike in humans, murine STING (mSTING) expression is not suppressed by promoter methylation and does not respond to decitabine treatment. Additionally, the mSTING protein is expressed in neoplastic cells in vivo. These results demonstrate a fundamental difference in epigenetic regulation of STING between human and murine glioma cells, and suggest that murine modeling of STING epigenetics requires the use of patient derived cell lines implanted in immunodeficient mice. Meanwhile, immune competent syngeneic models are appropriate for exploring the tumor immune microenvironment but would require non-epigenetic approaches (e.g. genetic knock-outs/knock-ins) for modulating STING expression. Humanized mice represent a promising emerging approach for faithfully recapitulating both epigenetic control and immune environment of human gliomas.

A Bioconductor/R Workflow for the Detection and Visualization of Differential Chromatin Loops

Background Chromatin loops play a critical role in gene regulation by connecting regulatory loci and gene promoters. The identification of changes in chromatin looping between cell types or biological conditions is an important task for understanding gene regulation; however, the manipulation, statistical analysis, and visualization of data sets describing 3D chromatin structure is challenging due to the large and complex nature of the relevant data sets. Methods Here, we describe a workflow for identifying and visualizing differential chromatin loops from Hi-C data from two biological conditions using the ‘mariner’, ‘DESeq2’ and ‘plotgardener’ Bioconductor/R packages. The workflow assumes that Hi-C data has been processed into ‘.hic’ or ‘.cool’ files and that loops have been identified using an existing loop-calling algorithm. Results First, the ‘mariner’ package is used to merge redundant loop calls and extract interaction frequency counts. Next, ‘DESeq2’ is used to identify loops that exhibit differential contact frequencies between conditions. Finally, ‘plotgardener’ is used to visualize differential loops. Conclusion Chromatin interaction data is an important modality for understanding the mechanisms of transcriptional regulation. The workflow presented here outlines the use of ‘mariner’ as a tool to manipulate, extract, and aggregate chromatin interaction data, ‘DESeq2’ to perform differential analysis of these data across conditions, samples, and replicates, and ‘plotgardener’ to explore and visualize the results.

PATH-30. CLINICAL OUTCOMES AND PREDICTIVE BIOMARKERS FOR IDH-WILDTYPE GLIOBLASTOMAS DEVELOPING HYPERMUTATION FOLLOWING TEMOZOLOMIDE TREATMENT

Abstract Current standard of care for IDH-wildtype glioblastoma (GBM) includes maximal safe resection, adjuvant radiation, and chemotherapy with the alkylating agent temozolomide. A subset of gliomas treated with temozolomide develop somatic hypermutation with a predominance of C>T transitions due to the alkylation effects on DNA. However, the frequency of occurrence, clinical ramifications, and predictive biomarkers for developing temozolomide-induced hypermutation (TMZ-HM) in GBM are unknown. Here we performed comprehensive histopathologic, genomic, and epigenomic evaluation of paired initial and recurrent GBM from 106 patients. Seven patients (7%) developed hypermutation at time of first recurrence, while an additional five patients (5%) developed hypermutation at a subsequent recurrence. Patients who developed TMZ-HM had a significantly longer interval between initial surgery and first recurrence (27.8 vs. 9.9 months, p<0.001). In contrast to IDH-mutant gliomas where TMZ-HM is associated with poor prognosis, those patients with IDH-wildtype GBM who developed TMZ-HM had significantly longer overall survival from both initial surgery (67.9 vs. 20.3 months, p<0.001) and from time of recurrence after development of hypermutation (30.9 vs. 9.5 months, p=0.001). There was no difference in oncogenic alteration frequency in initial GBM that subsequently developed TMZ-HM. However, 4 specific CpG sites out of 12 total interrogated sites in the promoter region of MGMT (a DNA repair enzyme) and 5 specific CpG sites in the promoter region of KCNQ1DN (a negative regulator of c-Myc) were significantly more hypermethylated in those GBM that developed TMZ-HM. We then generated a weighted risk score across these CpG sites that can be used to prospectively identify GBM likely to develop TMZ-HM associated with favorable survival. In summary, patients with GBM that develop TMZ-HM follow a more favorable clinical course, and specific MGMT and KCNQ1DN promoter hypermethylation patterns could serve as a biomarker to identify these patients who may potentially benefit from extended alkylating chemotherapy treatment.

H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606.

Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606T standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606T and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.

CTNI-27. SYSTEMIC DELIVERY OF LOW ENERGY RADIOFREQUENCY ELECTROMAGNETIC FIELDS FOR THE TREATMENT OF PATIENTS WITH PRIMARY BRAIN TUMORS

Abstract BACKGROUND Tumor Treating Fields plus maintenance temozolomide (mTMZ) showed a survival advantage in the first-line glioblastoma (GBM) treatment. The survival benefit remains limited in patients with unmethylated MGMT gene promoter. The AutEMsys device emits low-energy amplitude modulated systemic electromagnetic fields (EMF) at patient specific frequencies. It is an outpatient procedure that can be integrated with mTMZ. METHODS This study involved a prospective compassionate access program targeting adult GBM patients using an intrabuccal EMF exposure via AutEMsys in addition to chemoRT+mTMZ. The program explored the effects on survival and patients’ reported quality-of-life (QOL) by EORTC-QL-C30. Patients underwent a 90-minute session of EMF exposure therapy repeated every 2 weeks until progression, deterioration in QOL or death. All patients had pathological specimens for diagnosis, IDH mutation status through NGS techniques, and MGMT promoter region methylation status. RESULTS 31 participants were enrolled, including 29 with GBM and 2 with diffuse midline glioma. 14 patients (45%) received EMF+chemoRT followed by EMF+mTMZ and 17 patients (55%) received EMF+mTMZ (post chemoRT). Survival time was measured from the start of mTMZ to the date of the last follow-up. The median overall survival (mOS) for all 31 patients was 26.0 months (95% CI: 14.4 – 37.2 months). Specifically for 21 patients with unmethylated MGMT, the mOS was 25.0 months (95% CI: 15.9 – 34.1 months). Similarly, for the 28 patients with IDH wildtype status, the mOS remained 26.0 months (95% CI: 9.6 – 42.4 months). The addition of AutEMsys with chemoRT+mTMZ demonstrated an improved role functioning in 79% of patients with 25% of these with >10-point score. CONCLUSION The AutEMsys device has shown promising initial results when added to chemoRT+mTMZ treatment of GBM. These findings warrant further prospective investigation and validation in a multicenter clinical trial setting.

Wheat Topoisomerase VI Positively Regulates the Biosynthesis of Cuticular Wax and Cutin.

Lipophilic cuticles mainly composed of wax mixtures and cutin matrices seal the plant epidermis and control plant development and environmental adaptation. Although cuticle-associated traits have been selected in the breeding of agronomically important cereal bread wheat, the biosynthesis of wheat cuticular wax and cutin remains poorly understood. Herein, wheat topoisomerase VI was characterized as an essential activator of cuticular wax and cutin biosynthesis. Knock-down of wheat TaTOP6A, TaTOP6B, TaRHL1, or TaBIN4 gene encoding component of topoisomerase VI resulted in decreased loads of leaf cuticular wax and cutin, as well as increased leaf cuticle permeability. Moreover, TaCYP86A2 was identified as a key component of the wheat cutin biosynthetic machinery. Reduction of wheat TaCYP86A2 expression led to decreased cutin accumulation and enhanced cuticle permeability. In addition, TaTOP6A, TaTOP6B, TaRHL1, or TaBIN4 was shown to enrich at the promoter regions of the wax biosynthesis gene TaKCS1 and the cutin biosynthesis gene TaCYP86A2. Importantly, chromatin at TaKCS1 and TaCYP86A2 promoters is marked by high nucleosome occupancy and low histone acetylation in TaTOP6A-, TaTOP6B-, TaRHL1-, or TaBIN4-silenced wheat leaves. These results collectively support that wheat topoisomerase VI positively regulates the biosynthesis of cuticular wax and cutin probably via maintaining a permissive chromatin state at TaKCS1 and TaCYP86A2 genes.

Evaluation of Xihuang Pill in inducing pyroptosis in glioma cells through modulation of miR-21-5p.

This study aims to elucidate the mechanism by which Xihuang Pill induces pyroptosis in glioma cells via the regulation of miR-21-5p. Human glioma cell lines U-87 and LN-229 were used as experimental models to assess the effects of Xihuang Pill on glioma pyroptosis. Cells were incubated with Xihuang Pill extract at concentrations of 7.5, 15, and 30µg/mL for 24h, alongside transfection with miR-21-5p mimic, an overexpression vector for STAT3, or incubation with 50µg/mL of the STAT3 activator Colivelin for 4h. Cell viability was measured using the CCK-8 assay, apoptosis was detected by flow cytometry, and expression levels of p-STAT3/STAT3 and pyroptosis-related proteins were determined by Western Blot. Additionally, cleaved caspase-1 was assessed by immunofluorescence, miR-21-5p expression by qRT-PCR, and STAT3 binding to the miR-21-5p promoter region by ChIP and dual-luciferase reporter assays. Results showed that Xihuang Pill significantly reduced cell viability, increased apoptosis, and upregulated the expression of pyroptosis-related proteins such as NLRP3, IL-1β, cleaved caspase-1, and GSDMD-N, while reducing p-STAT3/STAT3 and miR-21-5p levels (P < 0.05). Xihuang Pill inhibited STAT3 activation, which modulated miR-21-5p expression by binding to its promoter region. Co-transfection with miR-21-5p mimic reversed the effect of Xihuang Pill on glioma pyroptosis (P < 0.05). In conclusion, Xihuang Pill promotes glioma cell pyroptosis through the STAT3/miR-21-5p pathway.

New Therapeutic Method for Alleviating Damage of Acute Kidney Injury Through BCL-2 Gene Promoter I-Motif.

Acute kidney injury (AKI) is a global public health problem with its pathogenesis not fully understood. Excessive apoptosis of renal tubular epithelial cells is an important feature of AKI patients, and therefore an anti-apoptotic approach could be used in the treatment for AKI. Up-regulation of B-cell lymphoma-2 (BCL-2) gene and protein has been found to be correlated with anti-apoptosis of cells. It has been found that the presence of the C-rich sequence on the upstream region of the BCL-2 gene promoter could form DNA secondary i-motif structure, and its stabilization by small molecules could up-regulate gene transcription and translation. In the present study, we constructed AKI models through folic acid (FA) induction. With these in vitro and in vivo models, we demonstrated that the acridone derivative A22 could up-regulate the expression of BCL-2 by targeting its gene promoter i-motif to reduce renal tubular epithelial cell apoptosis and improve renal function in many ways. A22 could alleviate FA-induced oxidative stress injury, inflammatory response, and endoplasmic reticulum stress in mouse kidneys. Our results provided a potentially new anti-apoptotic approach for the treatment of early stages of AKI. Our employed model focused on its short-term effect on AKI, while its long-term efficacy and safety, particularly regarding the regeneration of renal tubular epithelial cells, require further investigation before clinical application. This study further demonstrated that promoter i-motif could be targeted for up-regulating BCL-2 expression for the treatment of important diseases caused by excessive apoptosis.

Regulatory Effect of Transcriptional Regulator TetR on the Synthesis of Conjugated Linoleic Acid in Lactiplantibacillus plantarum AR195.

Conjugated linoleic acid (CLA) possesses anticancer, anti-inflammatory, and antiobesity properties, making it a significant research focus. In this study, we identified TetR, a TetR/AcrR family transcriptional regulator encoded by AR1031, as the transcriptional regulator of CLA synthesis in Lactiplantibacillus plantarum AR195. TetR binds to the promoter regions of the CLA synthesis genes, including the cla operon and cla-hy, thereby enhancing CLA biosynthesis. Knockout of tetR led to the downregulation of cla-hy by 68%, cla-dh by 86%, and cla-dc by 33%, resulting in reduced CLA yield. Further bioinformatic analysis and segmented electrophoretic mobility shift assay (EMSA) experiments revealed that TetR recognizes a conserved sequence (5'-TGTAGATTG-n4-CTTCA-3') and binds to multiple sites within the regulatory region of the cla operon and cla-hy, thus promoting CLA biosynthesis. Overexpression of tetR increased the CLA yield by 7%. These findings provide precise insights into the regulation of CLA biosynthesis and suggest strategies for enhancing CLA production.

KHDRBS1 regulates the pentose phosphate pathway and malignancy of GBM through SNORD51-mediated polyadenylation of ZBED6 pre-mRNA

Glioblastoma is one of the most common and aggressive primary brain tumors. The aberration of metabolism is the important character of GBM cells and is tightly related to the malignancy of GBM. We mainly verified the regulatory effects of KHDRBS1, SNORD51 and ZBED6 on pentose phosphate pathway and malignant biological behavior in glioblastoma cells, such as proliferation, migration and invasion. KHDRBS1 and SNORD51 were upregulated in GBM tissues and cells. But ZBED6 had opposite tendency in GBM tissues and cells. KHDRBS1 may improve the stability of SNORD51 by binding to SNORD51, thus elevating the expression of SNORD51. More importantly, SNORD51 can competitively bind to WDR33 with 3’UTR of ZBED6 pre-mRNA which can inhibit the 3’ end processing of ZBED6 pre-mRNA, thereby inhibiting the expression of ZBED6 mRNA. ZBED6 inhibited the transcription of G6PD by binding to the promoter region of G6PD. Therefore, the KHDRBS1/SNORD51/ZBED6 pathway performs an important part in regulating the pentose phosphate pathway to influence malignant biological behavior of GBM cells, providing new insights and potential targets for the treatment of GBM.

OTUD7B inhibited hepatic injury from NAFLD by inhibiting K48-linked ubiquitination and degradation of β-catenin

Non-alcoholic fatty liver disease (NAFLD) is the prevalent liver disease. Ovarian tumor domain-containing 7B (OTUD7B) is a deubiquitinating enzyme and its role in NAFLD remains unclear. In high-fat diet (HFD)-induced NAFLD mouse model and palmitic acid (PA)-treated HepG2 cells, OTUD7B expression was decreased. Adenoviral overexpression of OTUD7B in mice resulted in reduced body weight and liver injury, with decreased serum aminotransferase (ALT) and aspartate aminotransferase (AST) levels. OTUD7B overexpression attenuated hepatic lipid deposition (serum TG, TC, LDL-C, HDLC, and FFA levels), which might be through the suppression of lipogenesis and β-oxidation-related genes. The contents of hepatic inflammatory factors (TNF-α, IL-6, and IL-1β) were decreased following OTUD7B overexpression in NAFLD mice. A mechanism study indicated that the protective effect of OTUD7B overexpression might be associated with β-catenin signal activation. OTUD7B overexpression promoted PA-induced β-catenin activity in TopFlash assay, and increased total β-catenin and c-myc levels in cells. The increase in β-catenin levels was contributed to the stabilization via inhibiting K48-linked ubiquitination and proteasomal degradation by OTUD7B. NR4A2 role in NASH has been proved. NR4A2 ChIP-seq and RNA-seq data excluded transcriptional regulation of NR4A2 to OTUD7B, and it was experimentally evidenced that NR4A2 bound to OTUD7B promoter region and positively transcriptionally regulate OTUD7B expression. In summary, OTUD7B overexpression ameliorated hepatic inflammation and steatosis in NAFLD. The possible mechanism of OTUD7B might be through the inhibition of β-catenin degradation by removing K48-linked ubiquitination, which might be regulated by NR4A2.

PARylation of GCN5 by PARP1 mediates its recruitment to DSBs and facilitates both HR and NHEJ Repair

Efficient DNA double strand break (DSB) repair is necessary for genomic stability and determines efficacy of DNA damaging cancer therapeutics. Spatiotemporal dynamics and post-translational modifications of repair proteins at DSBs dictate repair efficacy. Here, we identified a non-canonical function of GCN5 in regulating both HR and NHEJ repair post genotoxic stress. Mechanistically, genotoxic stress induced GCN5 recruitment to DSBs. GCN5 PARylation by PARP1 was essential for its recruitment, acetyltransferase activity and DSB repair function. Liquid chromatography-mass spectrometry (LC–MS) identified DNA-PKcs as part of GCN5 interactome. In-vitro acetyltransferase assays revealed that GCN5 acetylates DNA-PKcs at K3241 residue, a prerequisite for DNA-PKcs S2056 phosphorylation and DSB recruitment. Alongside, ChIP-qPCR revealed GCN5 mediates transcription of PRKDC via H3K27Ac acetylation in its promoter region (− 710 to − 554). Genetic perturbation of GCN5 also decreased CHEK1, NBN1, TP53BP1, POL-L transcription and abrogated ATM, BRCA1 activation. Accordingly, GCN5 loss led to persistent ɣ-H2AX foci formation, compromised in-vivo HR-NHEJ and caused GBM radio-sensitization. Importantly, PARP1 inhibition phenocopied GCN5 loss. Together, this study identifies an untraversed DSB repair function of GCN5 and provides mechanistic insights into transcriptional as well as post-translational regulation of pivotal HR-NHEJ factors. Alongside, it highlights the translational importance of PARP1-GCN5 axis in mediating GBM radio-resistance.