Differential gene expression-based connectivity mapping identified novel drug candidate and improved Temozolomide efficacy for Glioblastoma

Centromere protein U mediates the ubiquitination and degradation of RPS3 to facilitate temozolomide resistance in glioblastoma

AIMS

Temozolomide (TMZ) is the first-line chemotherapeutic agent for glioblastoma (GBM) therapy; however, resistance to TMZ remains a major obstacle in GBM treatment. The aim of this study is to elucidate the mechanisms underlying TMZ resistance and explore how to enhance the sensitivity of GBM to TMZ.

METHODS

GBM organoids were generated from patient samples, and organoid-based TMZ sensitivity testing was performed. Transcriptome sequencing was conducted on GBM organoids, which identified Centromere protein U (CENPU) as a novel key gene mediating TMZ resistance. Histopathological assessments were carried out using immunohistochemistry (IHC) and Hematoxylin and Eosin (HE) staining. Single-cell sequencing data were utilized to determine the functional states of CENPU in GBM cells. Intracranial and subcutaneous glioma mouse models were constructed to evaluate the effect of CENPU on TMZ sensitivity. The underlying mechanisms were further investigated using immunofluorescence, lentivirus transduction, co-immunoprecipitation, mass spectrometry, alkaline comet assay et al. RESULTS: CENPU was found to be highly expressed in TMZ-resistant GBM organoids and enhanced the TMZ resistance of GBM cells by promoting DNA damage repair. Its abnormal expression correlates with poor clinical outcomes in glioma patients. In vivo studies demonstrated that downregulation of CENPU enhances the sensitivity of GBM to TMZ. Correspondingly, rescue of CENPU expression reversed this effect on TMZ sensitivity in GBM cells. Mechanistically, CENPU cooperates with TRIM5α to promote the ubiquitination and degradation of RPS3 by inducing its polyubiquitination at the K214 residue. This process subsequently activates the ERK1/2 pathway and promotes the expression of E2F1 and RAD51. Consequently, the degradation of RPS3 and upregulation of RAD51 in GBM cells enhance DNA damage repair, thereby contributing to TMZ resistance.

CONCLUSION

Our study identified CENPU as a novel key gene mediating TMZ resistance and elucidated its molecular mechanisms, providing a new target to overcome TMZ resistance in GBM.

Repurposing Linezolid in Conjunction with Histone Deacetylase Inhibitor Access in the Realm of Glioblastoma Therapies

Since decades after temozolomide was approved, no effective drugs have been developed. Undoubtedly, blood-brain barrier (BBB) penetration is a severe issue that should be overcome in glioblastoma multiforme (GBM) drug development. In this research, we were inspired by linezolid through structural modification with several bioactive moieties to achieve the desired brain delivery. The results indicated that the histone deacetylase modification, referred to as compound 1, demonstrated promising cytotoxic effects in various brain tumor cell lines. Further comprehensive mechanism studies indicated that compound 1 induced acetylation, leading to DNA double-strand breaks, and induced the ubiquitination of RAD51, disrupting the DNA repair process. Furthermore, compound 1 also exhibited dramatic improvement in the orthotopic GBM mouse model, demonstrating its efficacy and satisfying BBB penetration. Therefore, the reported compound 1, provided with an independent therapeutic pathway, satisfying elongation in survival and tumor size reduction, and the ability to penetrate the BBB, was potent to achieve further development.

Differentiation therapy targeting the stalled epigenetic developmental programs in pediatric high-grade gliomas

Pediatric high-grade gliomas (pHGGs) are the most common brain malignancies in children and are characterized by blocked differentiation. The epigenetic landscape of pHGGs, particularly the H3K27-altered and H3G34-mutant subtypes, suggests these tumors may be particularly susceptible to strategies that target blocked differentiation. Differentiation therapy aims to overcome this differentiation blockade by promoting glioma cell differentiation into more mature and less malignant cells. Epigenetic modulators, including inhibitors of histone deacetylase (HDAC), enhancer of zeste homolog 2 (EZH2), BRG1/BRM-associated factor (BAF) complex, have shown promise in preclinical studies of pHGGs by altering the differentiation program of glioma cells. Although challenges remain in overcoming tumor cell heterogeneity, induced differentiation therapy holds promise for treating these currently incurable pediatric brain cancers.

Analysis of transcription profiles for the identification of master regulators as the key players in glioblastoma

Glioblastoma (GBM) is the most common malignant brain tumor with poor overall survival. Current treatment management for GBM has low efficacy, mainly due to high inter-patient heterogeneity. The transcription profiles in GBM define cell properties essential for tumor progression. We have developed an approach for the identification of master regulators (MRs) that are responsible for the gene expression changes in GBM. The approach is based on transcription factor enrichment analysis with subsequent "upstream" analysis in the signaling network. The main feature of the approach is that all calculations are performed for transcription profiles from individual samples, which allows taking into account GBM transcription heterogeneity. We identified 451 MRs that were up-regulated or down-regulated and, thus, were important parts of positive feedback loops. The number of MRs in the samples correlated with the degree of tumor immune infiltration, while the differences in MR profiles were generally consistent with the known GBM subtypes: mesenchymal, classical, and proneural. MRs densely interact with each other in the signaling network that may be associated with the robustness to pharmacological intervention. We identified 102 receptors among MRs, which is coherent with the importance of cell-cell interactions for GBM progression. The role of some of them in GBM is not currently investigated: lysophosphatidic acid receptors 5 and 6, sphingosine-1-phosphate receptor 4, lysophosphatidylserine receptors GPR34 and GPR174, and G protein-coupled receptors 84 and 132 for fatty acids. Information on the revealed MRs can be used to search for novel therapeutic strategies to treat GBM.

HDAC1: a promising target for cancer treatment: insights from a thorough analysis of tumor functions

Background

Many significant findings from recent studies have revealed the significance of histone deacetylase 1 (HDAC1) in the development of tumors and its strong association with tumor prognosis; these studies have mainly focused on one single cancer such as in lung cancer, breast cancer, and hepatocellular carcinoma (HCC). To date, there has been no comprehensive analysis and pan-analysis conducted from the overall perspective of cancer across all types. Hence, we analyzed public databases, conducted tube formation assay, and immunohistochemistry (IHC) staining of HDAC1 on six kinds of clinical samples to explore the prognostic and oncogenic effects of HDAC1 on 33 tumors for the first time. There currently remains a lack of efficient testing methods, therapies, and diagnostic and prognostic markers of tumor formation and development in different tumors.

Methods

Our initial objective was to investigate the possible cancer-causing functions of HDAC1 in 33 different types of tumors by utilizing The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and many different online websites, such as Tumor IMmune Estimation Resource 2 (TIMER2), Gene Expression Profiling Interactive Analysis 2 (GEPIA2), Genotype Tissue Expression (GTEx) database, Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset, and University of ALabama at Brimingham CANcer data analysis portal (UALCAN) tool, and so on. We even used small interfering RNA (siRNA) to knock down HDAC2 in HCC cell lines. IHC of HDAC1 was performed.

Results

HDAC1 exhibited high expression in numerous tumors, and strong correlations were observed between the messenger RNA (mRNA) levels of HDAC1 and the prognosis of individuals diagnosed with tumors. Human umbilical vein endothelial cells (HUVECs) tube formation and migration were significantly inhibited by conditioned media from HCC cells treated with siRNA of HDAC1. Several types of cancer have been found to exhibit elevated levels of phosphorylation at S421. Furthermore, as in bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), and kidney renal papillary cell carcinoma (KIRP), HDAC1 expression was found to be correlated with inflammatory cell infiltration.

Conclusions

The levels of HDAC1 are expected to adapt to clinical adjuvant targeted therapy in most types of solid cancer.

Revisiting epigenetic regulation in cancer: Evolving trends and translational implications

Cancer is a leading cause of mortality worldwide. The evolving role of epigenetics and tumor microenvironments of cancer pose significant challenges to the management of cancer. Besides genetics, epigenetic changes play a crucial role in the alteration of cellular machinery, progression, metastasis, epithelial-mesenchymal transition, and chemoresistance. Epigenetic changes such as DNA and RNA methylation, histone modifications, and chromatin modeling directly or indirectly influence the different stages of cancer from initiation to chemoresistant phenotype. In addition, alterations in the epigenetic machinery, such as hypo- or hyperactivation of proteins involved in epigenetic modifications, can lead to different health complications, including cancer. Recently, epi-drugs or epigenetic drugs offer emerging hope for the treatment and management of this deadly disease. Various epigenetic drugs targeting factors responsible for epigenetic modifications in cancer are currently under clinical trials. This chapter provides an overview of epigenetic modifications, their clinical implications, and the potential of epigenetic drugs for cancer treatment.

Epigenetics: Mechanisms, potential roles, and therapeutic strategies in cancer progression

Mutations or abnormal expression of oncogenes and tumor suppressor genes are known to cause cancer. Recent studies have shown that epigenetic modifications are key drivers of cancer development and progression. Nevertheless, the mechanistic role of epigenetic dysregulation in the tumor microenvironment is not fully understood. Here, we reviewed the role of epigenetic modifications of cancer cells and non-cancer cells in the tumor microenvironment and recent research advances in cancer epigenetic drugs. In addition, we discussed the great potential of epigenetic combination therapies in the clinical treatment of cancer. However, there are still some challenges in the field of cancer epigenetics, such as epigenetic tumor heterogeneity, epigenetic drug heterogeneity, and crosstalk between epigenetics, proteomics, metabolomics, and other omics, which may be the focus and difficulty of cancer treatment in the future. In conclusion, epigenetic modifications in the tumor microenvironment are essential for future epigenetic drug development and the comprehensive treatment of cancer. Epigenetic combination therapy may be a novel strategy for the future clinical treatment of cancer.

HAS2 facilitates glioma cell malignancy and suppresses ferroptosis in an FZD7-dependent manner

Glioma is the most common malignant tumor in the central nervous system, and it is crucial to uncover the factors that influence prognosis. In this study, we utilized Mfuzz to identify a gene set that showed a negative correlation with overall survival in patients with glioma. Gene Ontology (GO) enrichment analyses were then undertaken to gain insights into the functional characteristics and pathways associated with these genes. The expression distribution of Hyaluronan Synthase 2 (HAS2) was explored across multiple datasets, revealing its expression patterns. In vitro and in vivo experiments were carried out through gene knockdown and overexpression to validate the functionality of HAS2. Potential upstream transcription factors of HAS2 were predicted using transcriptional regulatory databases, and these predictions were experimentally validated using ChIP-PCR and dual-luciferase reporter gene assays. The results showed that elevated expression of HAS2 in glioma indicates poor prognosis. HAS2 was found to play a role in activating an antiferroptosis pathway in glioma cells. Inhibiting HAS2 significantly increased cellular sensitivity to ferroptosis-inducing agents. Finally, we determined that the oncogenic effect of HAS2 is mediated by the key receptor of the WNT pathway, FZD7.

Oncogenic Gene CNOT7 Promotes Progression and Induces Poor Prognosis of Glioma

Glioma is the most common malignant brain tumor in the central nervous system with the poor prognosis of patients. The CNOT7 (CCR4-NOT Transcription Complex Subunit 7) is an important functional subunit of CCR4-NOT protein complex that has not been reported in glioma. In this study, we aimed to explore the function of CNOT7 in glioma. The TCGA (The Cancer Genome Atlas) and CGGA (Chinese Glioma Genome Atlas) databases were used for investigating the expression and survival condition of CNOT7 in glioma. The cellular function experiments of qRT-PCR, CCK-8 assays, wound healing assays, and Transwell assays were conducted to verify the function of knockdown CNOT7 in the glioma cell lines DBTRG and U251. Enrichment analysis was used to explore the molecular mechanism of CONT7 in glioma. What is more, the upstream regulation transcription factors of CNOT7 were analyzed based on the ChIP-Atlas and cBioportal (provisional) databases, and verified by the qRT-PCR and luciferase reporter assay. The CNOT7 was highly expressed in glioma and presented the poorer prognosis. The knockdown of CNOT7 inhibited the proliferation, migration, and invasion of glioma cell line, compared to control group. The enrichment analysis revealed that the CNOT7 participated in the development of glioma via G2M checkpoint, E2F targets, IL6-JAK-STAT3, and TNF-α signaling pathways via NF-κB. Besides, it was found that the HDAC2 (Human histone deacetylase-2) contributes to increased CNOT7 expression in glioma. The high-expressed CNOT7 is an oncogene with poor prognosis and participate the progression of glioma.

Quercetin attenuates inflammation in rosacea by directly targeting p65 and ICAM-1

AIMS

Rosacea is an inflammatory skin disease with immune and vascular dysfunction. Although there are multiple treatment strategies for rosacea, the clinical outcomes are unsatisfactory.

MAIN METHODS

Combining transcriptome data and the Connectivity Map database quercetin was identified as a novel candidate for rosacea. Next, the therapeutic efficacy of quercetin was substantiated through proteomic analyses, in vivo experiments, and in vitro assays. Additionally, the utilization of DARTS, molecular docking and experimental verification revealed the therapeutic mechanisms of quercetin.

KEY FINDINGS

Treatment with quercetin resulted in the following effects: (i) it effectively ameliorated rosacea-like features by reducing immune infiltration and angiogenesis; (ii) it suppressed the expression of inflammatory mediators in HaCaT cells and HDMECs; (iii) it interacted with p65 and ICAM-1 directly, and this interaction resulted in the repression of NF-κB signal and ICAM-1 expression in rosacea.

SIGNIFICANCE

We show for the first time that quercetin interacted with p65 and ICAM-1 directly to alleviated inflammatory and vascular dysfunction, suggesting quercetin is a novel, promising therapeutic candidate for rosacea.

GARNL3 identified as a crucial target for overcoming temozolomide resistance in EGFRvIII-positive glioblastoma

OBJECT

Amplification of the epidermal growth factor receptor (EGFR) and its active mutant type III (EGFRvIII), frequently occurr in glioblastoma (GBM), contributing to chemotherapy and radiation resistance in GBM. Elucidating the underlying molecular mechanism of temozolomide (TMZ) resistance in EGFRvIII GBM could offer valuable insights for cancer treatment.

METHODS

To elucidate the molecular mechanisms underlying EGFRvIII-mediated resistance to TMZ in GBM, we conducted a comprehensive analysis using Gene Expression Omnibus and The cancer genome atlas (TCGA) databases. Initially, we identified common significantly differentially expressed genes (DEGs) and prioritized those correlating significantly with patient prognosis as potential downstream targets of EGFRvIII and candidates for drug resistance. Additionally, we analyzed transcription factor expression changes and their correlation with candidate genes to elucidate transcriptional regulatory mechanisms. Using estimate method and databases such as Tumor IMmune Estimation Resource (TIMER) and CellMarker, we assessed immune cell infiltration in TMZ-resistant GBM and its relationship with candidate gene expression. In this study, we examined the expression differences of candidate genes in GBM cell lines following EGFRvIII intervention and in TMZ-resistant GBM cell lines. This preliminary investigation aimed to verify the regulatory impact of EGFRvIII on candidate targets and its potential involvement in TMZ resistance in GBM.

RESULTS

Notably, GTPase Activating Rap/RanGAP Domain Like 3 (GARNL3) emerged as a key DEG associated with TMZ resistance and poor prognosis, with reduced expression correlating with altered immune cell profiles. Transcription factor analysis suggested Epiregulin (EREG) as a putative upstream regulator of GARNL3, linking it to EGFRvIII-mediated TMZ resistance. In vitro experiments confirmed EGFRvIII-mediated downregulation of GARNL3 and decreased TMZ sensitivity in GBM cell lines, further supported by reduced GARNL3 levels in TMZ-resistant GBM cells.

CONCLUSION

GARNL3 downregulation in EGFRvIII-positive and TMZ-resistant GBM implicates its role in TMZ resistance, suggesting modulation of EREG/GARNL3 signaling as a potential therapeutic strategy.

Association of body mass index with clinical outcome of primary WHO grade 4 glioma

Background

The prognostic value of body mass index (BMI) in primary WHO grade 4 gliomas is not widely acknowledged. This study aims to assess the survival outcomes of patients with different BMIs.

Methods

Real-world data of patients diagnosed with primary WHO grade 4 (2021 version) glioma was assessed. All 127 patients admitted in this study were administered with standard-of-care from September 2018 to September 2021. The outcomes of overall survival and progression-free survival were analyzed.

Results

The baseline characteristics of clinical features, molecular features, and secondary treatment in BMI subsets showed no significant difference. The survival analyses showed a significantly superior overall survival (OS) in the overweight group compared to the normal weight group. A trend of better OS in the overweight group compared to the obesity group was observed. The univariate Cox regression demonstrated patients of round-BMI 25 and 26 had superior OS outcomes.

Conclusion

In this real-world setting, patients with a BMI between 24 and 28 have superior overall survival. Patients in the proper BMI range may acquire survival benefits undergoing standard-of-care of primary WHO grade 4 gliomas. The prospective studies on a larger scale on these subsets of patients are necessary to solve the paradox of BMI in glioma.

GINS2 regulates temozolomide chemosensitivity via the EGR1/ECT2 axis in gliomas

Temozolomide (TMZ), a DNA alkylating agent, has become the primary treatment for glioma, the most common malignancy of the central nervous system. Although TMZ-containing regimens produce significant clinical response rates, some patients inevitably suffer from inferior treatment outcomes or disease relapse, likely because of poor chemosensitivity of glioma cells due to a robust DNA damage response (DDR). GINS2, a subunit of DNA helicase, contributes to maintaining genomic stability and is highly expressed in various cancers, promoting their development. Here, we report that GINS2 was upregulated in TMZ-treated glioma cells and co-localized with γH2AX, indicating its participation in TMZ-induced DDR. Furthermore, GINS2 regulated the malignant phenotype and TMZ sensitivity of glioma cells, mostly by promoting DNA damage repair by affecting the mRNA stability of early growth response factor 1 (EGR1), which in turn regulates the transcription of epithelial cell-transforming sequence 2 (ECT2). We constructed a GINS2-EGR1-ECT2 prognostic model, which accurately predicted patient survival. Further, we screened Palbociclib/BIX-02189 which dampens GINS2 expression and synergistically inhibits glioma cell proliferation with TMZ. These findings delineate a novel mechanism by which GINS2 regulates the TMZ sensitivity of glioma cells and propose a promising combination therapy to treat glioma.

Connectivity mapping-based identification of pharmacological inhibitor targeting HDAC6 in aggressive pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains highly lethal due to limited therapeutic options and expensive/burdensome drug discovery processes. Utilizing genomic-data-driven Connectivity Mapping (CMAP) to identify a drug closer to real-world PC targeting may improve pancreatic cancer (PC) patient outcomes. Initially, we mapped CMAP data to gene expression from 106 PC patients, identifying nine negatively connected drugs. These drugs were further narrowed down using a similar analysis for PC cell lines, human tumoroids, and patient-derived xenografts datasets, where ISOX emerged as the most potent agent to target PC. We used human and mouse syngeneic PC cells, human and mouse tumoroids, and in vivo mice to assess the ability of ISOX alone and in combination with 5FU to inhibit tumor growth. Global transcriptomic and pathway analysis of the ISOX-LINCS signature identified HDAC 6/cMyc as the target axis for ISOX. Specifically, we discovered that genetic and pharmacological targeting of HDAC 6 affected non-histone protein cMyc acetylation, leading to cMyc instability, thereby disrupting PC growth and metastasis by affecting cancer stemness. Finally, KrasG12D harboring tumoroids and mice responded effectively against ISOX and 5FU treatment by enhancing survival and controlling metastasis incidence. Overall, our data validate ISOX as a new drug to treat advanced PC patients without toxicity to normal cells. Our study supports the clinical utility of ISOX along with 5FU in future PC clinical trials.

HDAC1 mediates epithelial-mesenchymal transition and promotes cancer cell invasion in glioblastoma

Glioblastoma multiforme (GBM) is one of the most malignant tumors of the central nervous system, and its treatment has always been a difficult clinical problem. Here, we evaluated HDAC1 expression patterns and their effect on prognosis based on GBM cases from TCGA and CGGA databases. Expression was compared between GBM samples and normal controls. High HDAC1 expression was found to be an indicator of poor prognosis in glioblastoma. We also established a protein-protein interaction network to explore HDAC1-related interacting proteins, including the epithelial-mesenchymal transition (EMT)-related protein VIM, which is closely associated with HDAC1. Consistently, functional enrichment analysis showed that several GBM tissues with high HDAC1 were enriched in the expression of cancer markers, such as those involved in glycolysis, hypoxia, inflammation, and some signaling pathways. Next, this study analyzed the effect of HDAC1 on invasive ability and the EMT signaling pathway in GBM cells in vitro. The results showed that an HDAC1 inhibitor (RGFP109) could inhibit the EMT process in glioma cells in vitro, thereby affecting the invasion and migration of cells. Similar results were obtained based on in vivo studies. Our data suggest that HDAC1 has the potential to be a powerful prognostic biomarker, which might provide a basis for developing therapeutic targets for GBM.

Introducing HDAC-Targeting Radiopharmaceuticals for Glioblastoma Imaging and Therapy

Despite recent advances in multimodality therapy for glioblastoma (GB) incorporating surgery, radiotherapy, chemotherapy and targeted therapy, the overall prognosis remains poor. One of the interesting targets for GB therapy is the histone deacetylase family (HDAC). Due to their pleiotropic effects on, e.g., DNA repair, cell proliferation, differentiation, apoptosis and cell cycle, HDAC inhibitors have gained a lot of attention in the last decade as anti-cancer agents. Despite their known underlying mechanism, their therapeutic activity is not well-defined. In this review, an extensive overview is given of the current status of HDAC inhibitors for GB therapy, followed by an overview of current HDAC-targeting radiopharmaceuticals. Imaging HDAC expression or activity could provide key insights regarding the role of HDAC enzymes in gliomagenesis, thus identifying patients likely to benefit from HDACi-targeted therapy.

Smurf1 Suppression Enhances Temozolomide Chemosensitivity in Glioblastoma by Facilitating PTEN Nuclear Translocation

The tumor suppressor PTEN mainly inhibits the PI3K/Akt pathway in the cytoplasm and maintains DNA stability in the nucleus. The status of PTEN remains therapeutic effectiveness for chemoresistance of the DNA alkylating agent temozolomide (TMZ) in glioblastoma (GB). However, the underlying mechanisms of PTEN's interconnected role in the cytoplasm and nucleus in TMZ resistance are still unclear. In this study, we report that TMZ-induced PTEN nuclear import depends on PTEN ubiquitylation modification by Smurf1. The Smurf1 suppression decreases the TMZ-induced PTEN nuclear translocation and enhances the DNA damage. In addition, Smurf1 degrades cytoplasmic PTEN K289E (the nuclear-import-deficient PTEN mutant) to activate the PI3K/Akt pathway under TMZ treatment. Altogether, Smurf1 interconnectedly promotes PTEN nuclear function (DNA repair) and cytoplasmic function (activation of PI3K/Akt pathway) to resist TMZ. These results provide a proof-of-concept demonstration for a potential strategy to overcome the TMZ resistance in PTEN wild-type GB patients by targeting Smurf1.

Scavenger receptor class F member 2 (SCARF2) as a novel therapeutic target in glioblastoma

Scavenger receptor class F member 2 (SCARF2) is expressed by endothelial cells with very large cytoplasmic domains and is the second isotype, also known as scavenger receptor expressed by endothelial cells 2 (SREC-2). SREC-1 plays an important role in the binding and endocytosis of various endogenous and exogenous ligands. Many studies have been carried out on modified low-density lipoprotein internalization activity, but there have been few studies on SCARF2. Higher expression of SCARF2 has been found in glioblastoma (GBM) than normal brain tissue. Through analysis of The Cancer Genome Atlas database, it was confirmed that SCARF2 is widely expressed in GBM, and increased SCARF2 expression correlated with a poor prognosis in patients with glioma. The results of this study showed that the expression of SCARF2 is increased in GBM cell lines and patients, suggesting that SCARF2 may be a potential diagnostic marker and therapeutic molecule for cancers including glioma.