Resistance to temozolomide (TMZ) is a major driver of treatment failure and high mortality in patients with glioblastoma (GBM). However, the mechanisms underlying TMZ resistance, especially intrinsic resistance, remain incompletely elucidated. Through integrative multi-omics analyses, we identified a novel super-enhancer-driven circular RNA, circMLB, which is highly overexpressed in TMZ-R GBM. Both in vitro and in vivo studies robustly demonstrate that circMLB significantly enhances TMZ resistance in GBM. Mechanistically, the transcription factor PAF1 forms a protein complex with BRD4 that is enriched in the super-enhancer region, thereby upregulating circMLB expression. Furthermore, highly expressed circMLB directly binds to PKR, triggering stress granule assembly and ultimately reinforcing TMZ resistance in GBM. Importantly, we identified a novel PKR inhibitor, lurasidone, which synergizes with TMZ to exert potent anti-tumor activity against TMZ-R GBM in preclinical models. Our findings uncover a previously unrecognized SE-circMLB-PKR axis mediating intrinsic TMZ resistance and highlight the lurasidone-TMZ combination as a promising therapeutic strategy to surmount TMZ resistance in GBM.

BACKGROUND:PDGFRA genetic alterations are a well-established oncogenic driver in gliomas. However, targeted monotherapy against PDGFRA such as avapritinib has achieved limited clinical efficacy, and the mechanism underlying avapritinib resistance remains poorly understood. METHODS:Multi-omics analysis of clinical samples identified super-enhancer (SE) complex components. Comprehensive preclinical evaluation was performed using glioma cell lines, glioma stem cells, patient-derived cells, xenografts, and organoids. Mechanistic investigations integrated Cleavage Under Targets and Tagmentation, chromatin immunoprecipitation, co-immunoprecipitation, mass spectrometry, protein fragment complementation, and dual-luciferase reporter assays. RESULTS:Functional and clinical analyses identified the SE complex component MED8 as significantly upregulated in gliomas and correlated with poor prognosis. MED8 was essential for tumor proliferation and survival both in vitro and in vivo. Mechanistically, MED8 cooperated with CDK7 to bind and activate the SEs of PDGFRA, sustaining high transcriptional output of this oncogene. We repurposed FDA-approved venetoclax as a first-in-class MED8-targeting agent that potently sensitizes to avapritinib, exerting synergistic effects in multiple preclinical models. CONCLUSIONS:This study delineates a novel MED8-SE-PDGFRA epigenetic axis driving resistance. The combination of avapritinib and venetoclax, co-targeting the oncogenic signal and its transcriptional regulator, presents a translatable dual-targeting strategy to improve outcomes in PDGFRA-driven glioma.

Nanoparticle-based small interfering RNA (siRNA) therapeutics have revealed potential applications in the treatment of osteosarcoma. Nevertheless, charge-related toxicity and nuclease clearance severely limit the applicability of siRNAs in osteosarcoma therapeutic field. Herein, a GSH-responsive diblock copolymer siRNAdisulfide-poly(2-(diisopropylamino)ethyl methacrylate) (siRNA-SS-PDPA) is designed and synthesized, of which the siRNA micelles are generated via self-assembly strategy. Specifically, the derived siRNA micelles not only possess the features of effective cellular internalization, endosomal escape, prolonged blood circulation time, stable and efficient release, and no charge toxicity, but also effectively knock down the EPHA2 gene that mediates the insensitivity of tumor cells to imatinib (IMA). Resultantly, EPHA2 is capable of being knocked down by siRNA micelles, which enhances the sensitivity of MG63 cell line to imatinib, synergistically inhibiting the PI3K-AKT pathway and inducing apoptosis in combination with IMA. Simultaneously, the siRNA micelles demonstrate favorable biosafety in both cell lines and animal experiments, which significantly inhibit the in-situ growth of MG63 xenograft osteosarcoma by synergizing with IMA and markedly improve the survival rate. Conclusively, such cation-free siRNA micelles provide a novel drug-encoded delivery platform for GSH-triggered synergistic treatment of osteosarcoma with RNAi and chemotherapeutic agents.

Glioblastoma multiforme (GBM) is the most aggressive and lethal subtype of gliomas of the central nervous system. The efficacy of sonodynamic therapy (SDT) against GBM is significantly reduced by the expression of apoptosis-inhibitory proteins in GBM cells. In this study, an intelligent nanoplatform (denoted as Aza-BD@PC NPs) based on the aza-boron-dipyrromethene dye and phenyl chlorothionocarbonate-modified DSPE-PEG molecules is developed for synergistic ferroptosis-enabled gas therapy (GT) and SDT of GBM. Once internalized by GBM cells, Aza-BD@PC NPs showed effective cysteine (Cys) consumption and Cys-triggered hydrogen sulfide (H2S) release for ferroptosis-enabled GT, thereby disrupting homeostasis in the intracellular environment, affecting GBM cell metabolism, and inhibiting GBM cell proliferation. Additionally, the released Aza-BD generated abundant singlet oxygen (1O2) under ultrasound irradiation for favorable SDT. In vivo and in vitro evaluations demonstrated that the combined functions of Cys consumption, H2S production, and 1O2 production induced significant death of GBM cells and markedly inhibited tumor growth, with an impressive inhibition rate of up to 97.5%. Collectively, this study constructed a cascade nanoreactor with satisfactory Cys depletion performance, excellent H2S release capability, and prominent reactive oxygen species production ability under ultrasound irradiation for the synergistic ferroptosis-enabled GT and SDT of gliomas.

Background The mesenchymal (MES) subtype of glioblastoma (GBM) is believed to be influenced by both cancer cell-intrinsic alterations and extrinsic cellular interactions, yet the underlying mechanisms remain unexplored.Methods Identification of microglial heterogeneity by bioinformatics analysis. Transwell migration, invasion assays, and tumor models were used to determine gene function and the role of small molecule inhibitors. RNA sequencing, chromatin immunoprecipitation, and dual-luciferase reporter assays were performed to explore the underlying regulatory mechanisms.Results We identified the inflammatory microglial subtype of tumor-associated microglia (TAM) and found that its specific gene integrin beta 2 (ITGB2) was highly expressed in TAM of MES GBM tissues. Mechanistically, the activation of ITGB2 in microglia promoted the interaction between the SH2 domain of STAT3 and the cytoplasmic domain of ITGB2, thereby stimulating the JAK1/STAT3/IL-6 signaling feedback to promote the MES transition of GBM cells. Additionally, microglia communicated with GBM cells through the interaction between the receptor ITGB2 on microglia and the ligand ICAM-1 on GBM cells, while an increased secretion of ICAM-1 was induced by the proinflammatory cytokine leukemia inhibitory factor (LIF). Further studies demonstrated that inhibition of cyclin-dependent kinase 7 substantially reduced the recruitment of SNW1 to the super-enhancer of LIF, resulting in transcriptional inhibition of LIF. We identified notoginsenoside R1 as a novel LIF inhibitor that exhibited synergistic effects in combination with temozolomide.Conclusions Our research reveals that the epigenetic-mediated interaction of GBM cells with TAM drives the MES transition of GBM and provides a novel therapeutic avenue for patients with MES GBM. Graphical Abstract

Osteosarcoma, one of the most common primary malignancies in children and adolescents, has the primary characteristics of a poor prognosis and high rate of metastasis. This study used super-enhancer-related genes derived from two different cell lines to construct five novel super-enhancer-related gene prognostic models for patients with osteosarcoma. The training and testing datasets were used to confirm the prognostic models of the five super-enhancer-related genes, which resulted in an impartial predictive element for osteosarcoma. The immunotherapy and prediction of the response to anticancer drugs have shown that the risk signature of the five super-enhancer-related genes positively correlate with chemosensitivity. Furthermore, functional analysis of the risk signature genes revealed a significant relationship between gene groups and the malignant characteristics of tumours. TNF Receptor Superfamily Member 11b (TNFRSF11B) was selected for functional verification. Silencing of TNFRSF11B suppressed the proliferation, migration, and invasion of osteosarcoma cells in vitro and suppressed osteosarcoma growth in vivo. Moreover, transcriptome sequencing was performed on MG-63 cells to study the regulatory mechanism of TNFRSF11B in osteosarcoma cells, and it was discovered that TNFRSF11B is involved in the development of osteosarcoma via the phosphoinositide 3-kinase signalling pathway. Following the identification of TNFRSF11B as a key gene, we selected an inhibitor that specifically targeted this gene and performed molecular docking simulations. In addition, risedronic acid inhibited osteosarcoma growth at both cellular and molecular levels. In conclusion, the super-enhancer-related gene signature is a viable therapeutic tool for osteosarcoma prognosis and treatment.

Gliomas are the most common type of primary brain tumor. Despite advances in treatment, it remains one of the most aggressive and deadly tumor of the central nervous system (CNS). Gliomas are characterized by high malignancy, heterogeneity, invasiveness, and high resistance to radiotherapy and chemotherapy. It is urgent to find potential new molecular targets for glioma. The TRPM channels consist of TRPM1-TPRM8 and play a role in many cellular functions, including proliferation, migration, invasion, angiogenesis, etc. More and more studies have shown that TRPM channels can be used as new therapeutic targets for glioma. In this review, we first introduce the structure, activation patterns, and physiological functions of TRPM channels. Additionally, the pathological mechanism of glioma mediated by TRPM2, 3, 7, and 8 and the related signaling pathways are described. Finally, we discuss the therapeutic potential of targeting TRPM for glioma.

Osteosarcoma (OS) is a highly prevalent bone tumor derived from primitive mesenchymal cells that occurs mostly in adolescents and children. OS has a notable propensity for aggressive behavior and resistance to treatment. Additionally, accurately evaluating and predicting the prognosis of OS remains challenging. For this investigation, we utilized scRNA-seq data to identify seven subtypes of OS cells. Survival analysis of each OS cell subtype revealed that highly invasive OS (HIS-OS) had a poorer prognosis. Through differential expression analysis, an entire set of seven genes linked to HIS-OS was identified. Subsequently, these seven genes were employed to construct a predictive model using the LASSO approach. Based on the median risk score, the OS samples in the training set were categorized into high-risk and low-risk groups, and the high-risk group exhibited a significantly shorter survival time. The analysis of immunotherapy and anticancer treatment responsiveness indicated a negative correlation between HIS-OS-related gene signatures and immune checkpoints as well as chemotherapy sensitivity. In addition, functional analysis demonstrated high enrichment of these gene sets throughout the process of tumor invasion. Finally, SERPINE2 was identified as a therapeutically critical gene. Therefore, we subsequently selected an inhibitor, IITZ-01, that targets SERPINE2, and we performed molecular docking simulations. Furthermore, we validated the inhibitory effect of IITZ-01 on OS at the cellular level. The results suggest that HIS-OS-related genes are important for prognostic stratification and therapeutic strategies for OS.

Super-enhancers (SEs) consist of multiple typical enhancers enriched at high density with transcription factors, histone-modifying enzymes and cofactors. Oncogenic SEs promote tumorigenesis and malignancy by altering protein-coding gene expression and noncoding regulatory element function. Therefore, they play central roles in the treatment of cancer. Here, we review the structural characteristics, organization, identification, and functions of SEs and the underlying molecular mechanism by which SEs drive oncogenic transcription in tumor cells. We then summarize abnormal SE complexes, SE-driven coding genes, and noncoding RNAs involved in tumor development. In summary, we believe that SEs show great potential as biomarkers and therapeutic targets.

Long non-coding RNAs (lncRNAs) are tissue-specific expression patterns and dysregulated in cancer. How they are regulated still needs to be determined. We aimed to investigate the functions of glioma-specific lncRNA LIMD1-AS1 activated by super-enhancer (SE) and identify the potential mechanisms. In this paper, we identified a SE-driven lncRNA, LIMD1-AS1, which is expressed at significantly higher levels in glioma than in normal brain tissue. High LIMD1-AS1 levels were significantly associated with a shorter survival time of glioma patients. LIMD1-AS1 overexpression significantly enhanced glioma cells proliferation, colony formation, migration, and invasion, whereas LIMD1-AS1 knockdown inhibited their proliferation, colony formation, migration, and invasion, and the xenograft tumor growth of glioma cells in vivo. Mechanically, inhibition of CDK7 significantly attenuates MED1 recruitment to the super-enhancer of LIMD1-AS1 and then decreases the expression of LIMD1-AS1. Most importantly, LIMD1-AS1 could directly bind to HSPA5, leading to the activation of interferon signaling. Our findings support the idea that CDK7 mediated-epigenetically activation of LIMD1-AS1 plays a crucial role in glioma progression and provides a promising therapeutic approach for patients with glioma.

P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a novel class of small regulatory RNAs (approximately 24-31 nucleotides in length) that often bind to members of the PIWI protein family. piRNAs regulate transposons in animal germ cells; piRNAs are also specifically expressed in many human tissues and regulate pivotal signaling pathways. Additionally, the abnormal expression of piRNAs and PIWI proteins has been associated with various malignant tumours, and multiple mechanisms of piRNA-mediated target gene dysregulation are involved in tumourigenesis and progression, suggesting that they have the potential to serve as new biomarkers and therapeutic targets for tumours. However, the functions and potential mechanisms of action of piRNAs in cancer have not yet been elucidated. This review summarises the current findings on the biogenesis, function, and mechanisms of piRNAs and PIWI proteins in cancer. We also discuss the clinical significance of piRNAs as diagnostic or prognostic biomarkers and therapeutic tools for cancer. Finally, we present some critical questions regarding piRNA research that need to be addressed to provide insight into the future development of the field.

Abstract Background: Gliomas are the most common malignant tumor of the central nervous system(CNS). Dysregulated pseudogene expression was significantly associated with the prognosis of glioma patients. However, the role of abnormal methylation of pseudogenes in glioma prognosis has not yet been studied. This study aimed to develop a novel six-methylated pseudogenes signature to predict the prognosis of glioma patients. Methods: Based on lasso regression analysis, a risk signature for six methylated pseudogenes was constructed. Next, a prognostic nomogram including grade, age, gender, and radiation was constructed. Besides, the immune cell infiltration analyses of patients based on the six-methylated pseudogenes were performed. Meanwhile, consensus cluster analysis of six methylated pseudogenes identified two glioma patient subgroups. Furthermore, GO, KEGG and GSEA were used to analyze related genes. Finally, the ability of glioma to proliferate, migrate and invade was used to verify subsequent functions. Results: In this study, six gene models consisting of methylated pseudogenes were identified and validated, and showed strong prognostic power in the training dataset, validation dataset, and entire dataset. The calibration diagram showed good predictive performance. In addition, the proportion of B cells and CD4+T cells was significantly higher in the high-risk group, while the proportion of mono cells was lower. By silencing the expression of SBF1P1 and SUMO1P1, the ability of glioma to proliferate, migrate, and invade can be inhibited. Conclusions: The six-methylated pseudogene signature may be a novel predictor for prognostic assessment of glioma patients, which could accurately predict patient prognosis.

Background Super-enhancers (SEs), driving high-level expression of genes with tumor-promoting functions, have been investigated recently. However, the roles of super-enhancer-associated lncRNAs (SE-lncRNAs) in tumors remain undetermined, especially in gliomas. We here established a SE-lncRNAs expression-based prognostic signature to choose the effective treatment of glioma and identify a novel therapeutic target. Methods Combined analysis of RNA sequencing (RNA-seq) data and ChIP sequencing (ChIP-seq) data of glioma patient-derived glioma stem cells (GSCs) screened SE-lncRNAs. Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets served to construct and validate SE-lncRNA prognostic signature. The immune profiles and potential immuno- and chemotherapies response prediction value of the signature were also explored. Moreover, we verified the epigenetic activation mechanism of LINC00945 via the ChIP assay, and its effect on glioma was determined by performing the functional assay and a mouse xenograft model. Results 6 SE-lncRNAs were obtained and identified three subgroups of glioma patients with different prognostic and clinical features. A risk signature was further constructed and demonstrated to be an independent prognostic factor. The high-risk group exhibited an immunosuppressive microenvironment and was higher enrichment of M2 macrophage, regulatory T cells (Tregs), and Cancer-associated fibroblasts (CAFs). Patients in the high-risk group were better candidates for immunotherapy and chemotherapeutics. The SE of LINC00945 was further verified via ChIP assay. Mechanistically, BRD4 may mediate epigenetic activation of LINC00945. Additionally, overexpression of LINC00945 promoted glioma cell proliferation, EMT, migration, and invasion in vitro and xenograft tumor formation in vivo. Conclusion Our study constructed the first prognostic SE-lncRNA signature with the ability to optimize the choice of patients receiving immuno- and chemotherapies and provided a potential therapeutic target for glioma.

Gliomas are a group of the most aggressive primary central nervous system tumors with limited treatment options. The abnormal expression of long non-coding RNA (lncRNA) is related to the prognosis of glioma. However, the role of endoplasmic reticulum (ER) stress-associated lncRNAs in glioma prognosis has not been reported. In this paper, we obtained ER stress-related lncRNAs by co-expression analysis, and then a risk signature composed of 6 ER stress-related lncRNAs was constructed using Cox regression analysis. Glioma samples in The Cancer Genome Atlas (TCGA) were separated into high- and low-risk groups based on the median risk score. Compared with the low-risk group, patients in the high-risk group had shorter survival times. Additionally, we verified the predictive ability of these candidate lncRNAs in the testing set. Three glioma patient subgroups (cluster 1/2/3) were identified by consensus clustering. We further analysed the abundance of immune-infiltrating cells and the expression levels of immune checkpoint molecules in both three subgroups and two risk groups, respectively. Immunotherapy and anticancer drug response prediction showed that ER stress-related lncRNA risk signature positively correlates with responding to immune checkpoints and chemosensitivity. Functional analysis showed that these gene sets are enriched in the malignant process of tumors. Finally, LINC00519 was chosen for functional experiments. The silence of LINC00519 restrained the migration and invasion of glioma cells. Hence, those results indicated that ER stress-related lncRNA risk signature could be a potential treatment target and a prognosis biomarker for glioma patients.

Abstract Background: Gliomas are the most common malignant tumor from the central nervous system(CNS). Dysregulated pseudogene expression was significantly associated with the prognosis of glioma patients. However, the role of abnormal methylation of pseudogenes in glioma prognosis has not yet been studied. This study aimed to develop a novel six-methylated pseudogenes signature to predict prognosis of glioma patients.Methods: Based on multiple screening, a risk signature for six-methylated pseudogenes was constructed, and then classified glioma patients into high-risk and low-risk groups. Next, a prognostic nomogram including grade, age, gender, and radiation was constructed. Besides, the immune cell infiltration analyses of patients based on the six-methylated pseudogenes in two risk groups were performed. Meanwhile, consensus cluster analysis of six methylated pseudogenes identified two glioma patient subgroups (cluster1/2). Furthermore, Gene Ontology (GO) , Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA) were used to analyzed related genes. Finally, the ability of glioma to proliferate, migrate and invade were used to verify subsequent functions. Results: In this study, six gene models consisting of methylated pseudogenes were identified and validated, and showed strong prognostic power in the training dataset, validation dataset, and entire dataset. The calibration diagram showed good predictive performance. In addition, the proportion of B cells and CD4+T cells was significantly higher in the high-risk group, while the proportion of Mono cells was lower. By silencing the expression of SBF1P1 and SUMO1P1, the ability of glioma proliferation, migration and invasion can be inhibited.Conclusion: The six-methylated pseudogenes signature may be a novel predictor for prognostic assessment of glioma patients, which could accurately predict patient prognosis.