Overexpression of Limb-Bud and Heart (LBH) promotes angiogenesis in human glioma via VEGFA-mediated ERK signalling under hypoxia

Angiogenesis causes and vasculogenic mimicry formation in the context of cancer stem cells

Tumor occurrence, development, invasion, and metastasis are regulated by multiple mechanisms. Among these, angiogenesis promotes tumor progression mainly by supplying tumor tissue and providing channels for tumor metastasis. Cancer stem cells (CSCs) are another important factor affecting tumor progression by involving in tumor initiation and development, while remaining insensitive to conventional antitumor treatments. Among treatment strategies for them, owing to the existence of alternative angiogenic pathways or the risk of damaging normal stem cells, the clinical effect is not ideal. Angiogenesis and CSCs may influence each other in this process. Tumor angiogenesis can support CSC self-renewal by providing a suitable microenvironment, whereas CSCs can regulate tumor neovascularization and mediate drug resistance to anti-angiogenic therapy. This review summarized the role of vascular niche formed by angiogenesis in CSC self-renewal and stemness maintenance, and the function of CSCs in endothelial progenitor cell differentiation and pro-angiogenic factor upregulation. We also elucidated the malignant loop between CSCs and angiogenesis promoting tumor progression. Additionally, we summarized and proposed therapeutic targets, including blocking tumor-derived endothelial differentiation, inhibiting pro-angiogenic factor upregulation, and directly targeting endothelial-like cells comprising CSCs. And we analyzed the feasibility of these strategies to identify more effective methods to improve tumor treatment.

The m6A RNA demethylase FTO promotes radioresistance and stemness maintenance of glioma stem cells

Glioblastoma (GBM) was the most common and deadliest malignant brain tumor in adults, with a poor prognosis. Effective targeted drugs are still lacking, and the presence of glioblastoma stem cells (GSC) is a major factor contributing to radiotherapy resistance. Screening for targeted drugs that can sensitize GBM to radiotherapy is crucial. FTO is considered an attractive potential target for tumor therapy, as it mediates m6A demethylation to regulate the stability of target genes. In this study, we evaluated the role of FTO inhibition in promoting the sensitivity of GSC cells to radiotherapy through tumor sphere formation assays, cell apoptosis assays, and in situ GSC tumor models. We preliminarily explored the molecular mechanisms by transcriptome sequencing and m6A methylation sequencing to investigate how inhibiting FTO increases radiotherapy sensitivity. The results showed that downregulation of FTO expression or FTO inhibitor FB23-2 combined with radiotherapy significantly inhibited GSC cell proliferation and self-renewal and increased apoptosis. FB23-2 combined with radiotherapy effectively inhibited intracranial tumor growth in mice and prolonged the survival of tumor-bearing mice. Furthermore, FTO inhibition sustained the increase of γH2AX expression induced by radiotherapy while decreasing Rad51 expression. Importantly, we found that inhibiting FTO could increase m6A methylation modification of VEGFA, thereby downregulating both mRNA and protein expression of VEGFA. Our findings provide a new therapeutic strategy for enhancing GBM radiotherapy sensitivity and lay the theoretical and experimental groundwork for clinical trials targeting FTO.

HSPA5-mediated glioma hypoxia tolerance promotes M2 macrophage polarization under hypoxic microenvironment

BACKGROUND

The tumor microenvironment (TME), with hallmark features of hypoxia and immunosuppression, plays a crucial role in the progression of various solid tumors. However, the intricate interplay between tumor hypoxia and the formation of tumor immune microenvironment in glioma remains incompletely understood.

METHODS

In the present study, we initially identified genes associated with tumor hypoxia and the immune microenvironment through GSEA and IMMPORT database analysis. We subsequently identified hypoxia- and immune-related genes associated with glioma prognosis through further cross-analysis and multidatabase integrated analysis. HSPA5 was ultimately identified as a potential target gene related to the formation of the hypoxic microenvironment and immune microenvironment in glioma. Furthermore, we conducted MTT, colony formation, EdU, migration and invasion assays and intracranial orthotopic tumor model analysis to further evaluate the impact of interfering with HSPA5 expression on the hypoxic and immune microenvironments of glioma.

RESULTS

We found that HSPA5 is highly expressed in glioma cells and tissues and is associated with a poor prognosis. Further investigation revealed that hypoxia promotes the malignant biological characteristics of glioma and reshaping the Immunosuppressive phenotype of tumor-associated macrophages (TAMs) through upregulation of the HIF-1α/HSPA5 axis. Silencing HSPA5 alleviated glioma hypoxia tolerance and induced the polarization of TAMs toward the M1 phenotype. The induced macrophages could exhibit a tumor-suppressive effect.

CONCLUSION

These observations suggest that HSPA5 upregulation promotes glioma progression by inducing hypoxia tolerance and reshaping the Immunosuppressive phenotype of TAMs. Therefore, targeting HSPA5 may be a novel therapeutic strategy for glioma.

UQCRB and LBH are correlated with Gleason score progression in prostate cancer: Spatial transcriptomics and experimental validation

Prostate cancer (PCa) is a multifocal disease characterized by genomic and phenotypic heterogeneity within a single gland. In this study, Visium spatial transcriptomics (ST) analysis was applied to PCa tissues with different histological structures to infer the molecular events involved in Gleason score (GS) progression. The spots in tissue sections were classified into various groups using Principal Component Analysis (PCA) and Louvain clustering analysis based on transcriptome data. Anotation of the spots according to GS revealed notable similarities between transcriptomic profiles and histologically identifiable structures. The accuracy of macroscopic GS determination was bioinformatically verified through malignancy-related feature analysis, specifically inferred copy number variation (inferCNV), as well as developmental trajectory analyses, such as diffusion pseudotime (DPT) and partition-based graph abstraction (PAGA). Genes related to GS progression were identified from the differentially expressed genes (DEGs) through pairwise comparisons of groups along a GS gradient. The proteins encoded by the representative oncogenes UQCRB and LBH were found to be highly expressed in advanced-stage PCa tissues. Knockdown of their mRNAs significantly suppressed PCa cell proliferation and invasion. These findings were validated using The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) dataset, as well as through histological and cytological experiments. The results presented here establish a foundation for ST-based evaluation of GS progression and provide valuable insights into the GS progression-related genes UQCRB and LBH.

FUS/circZEB1/miR-128-3p/LBH feedback loop contributes to the malignant phenotype of GSCs via TNF-α-mediated NF-κB signaling pathway

Glioblastoma (GBM) is the most lethal and common primary tumor of central nervous system with a poor prognosis. Glioma stem cells (GSCs) are particularly significant in GBM proliferation, invasion, self-renewal and recurrence. Circular RNAs (circRNAs) play important roles in various physiological and pathological processes, including regulating the biological behavior of GBM. Therefore, discovering novel circRNAs related to GSCs may contribute to a promising approach for treatment of GBM. Herein, we find out a novel circRNA termed circZEB1 with a high expression in glioma. Limb-bud and heart (LBH) is a transcription cofactor and promotes glioma stem cell tumorigenicity in our study. Mechanistically, circZEB1 can upregulate the expression of transcription cofactor LBH via sponging miR-128-3p in GSCs. LBH can facilitate the expression of tumor necrosis factor-α (TNF-α), thus activating the NF-κB signaling pathway to promote the glioma progression. Meanwhile, LBH can also upregulate the RNA binding protein Fused in Sarcoma (FUS) expression, which can bind to and maintain the stability of circZEB1. A positive feedback loop is formed among FUS, circZEB1, miR-128-3p and LBH in GSCs. Our study uncovers a critical role of circZEB1 and provides a novel biomarker for treating GBM.

Machine learning algorithms for predicting glioma patient prognosis based on CD163+FPR3+ macrophage signature

Tumor-associated macrophages (TAMs) play a vital role in glioma progression and are associated with poor outcomes in glioma patients. However, the specific roles of different subpopulations of TAMs remain poorly understood. Two distinct cell types, glioma and myeloid cells, were identified through single-cell sequencing analysis in gliomas. Within the TAMs-associated weighted gene co-expression network analysis (WGCNA) module, FPR3 emerged as a hub gene and was found to be expressed on CD163+ macrophages, while also being associated with clinical outcomes. Subsequently, a comprehensive assessment was undertaken to investigate the correlation between FPR3 expression and immune characteristics, revealing that FPR3 potentially plays a role in reshaping the glioma microenvironment. We identified a macrophage subset with the nonzero expression of CD163 and FPR3 (CD163+FPR3+). Using the expression profiles of CD163+FPR3+ macrophage-related signature, we employed ten machine learning algorithms to construct a prognostic model across six glioma cohorts. Subsequently, we employed an optimal algorithm to generate an artificial intelligence-driven prognostic signature specifically for CD163+FPR3+ macrophages. The development of this model was based on the average C-index observed in the aforementioned six cohorts. The risk score of this model consistently and effectively predicted overall survival, surpassing the accuracy of conventional clinical factors and 100 previously published signatures. Consequently, the CD163+FPR3+ macrophage-related score shows potential as a prognostic biomarker for glioma patients.

Evolutionary learning-derived lncRNA signature with biomarker discovery for predicting stage of colon adenocarcinoma

In recent years, long non-coding RNAs (lncRNAs) have emerged as potential regulators of biological processes and genes, with the potential to serve as valuable biomarkers for cancer diagnosis and prognosis prediction. This work proposes an evolutionary learning-based method, EL-COAD, to identify a robust lncRNA signature with biomarker discovery for predicting stages of colon adenocarcinoma (COAD). The COAD patient cohorts were obtained from both the Cancer Genome Atlas and Gene Expression Omnibus (gse17536) databases. EL-COAD incorporates a bi-objective combinatorial genetic algorithm with a support vector machine for selecting a minimal number of lncRNAs while maximizing prediction accuracy. EL-COAD identified a 15-lncRNA signature and achieved a five-fold cross-validation and area under receiver operating characteristic curve of 79.4% and 0.792, respectively. Utilising the 10 lncRNAs from the signature for an independent dataset gse17536, the Sequential Minimal Optimization model achieved a test accuracy of 64.15%. Furthermore, the lncRNAs of the signature were prioritized, with the top five being TMEM105, DUXAP8, APCDD1L-DT, PCAT6, and a novel transcript, ENSG00000226308. Furthermore, both Kyoto Encyclopedia of Genes and Genomes pathway and Disease Ontology analyses provided strong support for the viability of this model-independent signature, emphasising ENSG00000226308 as a promising biomarker.

Iron deficiency affects oxygen transport and activates HIF1 signaling pathway to regulate phenotypic transformation of VSMC in aortic dissection

BACKGROUND

Aortic dissection (AD) is a macrovascular disease which is pathologically characterized by aortic media degeneration.This experiment aims to explore how iron deficiency (ID) affects the function of vascular smooth muscle cell (VSMC) and participates in the occurrence and development of AD by regulating gene expression.

METHODS

The relationship between iron and AD was proved by Western-blot (WB) and immunostaining experiments in human and animals. Transcriptomic sequencing explored the transcription factors that were altered downstream. WB, flow cytometry and immunofluorescence were used to demonstrate whether ID affected HIF1 expression through oxygen transport. HIF1 signaling pathway and phenotypic transformation indexes were detected in cell experiments. The use of the specific HIF1 inhibitor PX478 further demonstrated that ID worked by regulating HIF1.

RESULTS

The survival period of ID mice was significantly shortened and the pathological staining results were the worst. Transcriptomic sequencing indicated that HIF1 was closely related to ID and the experimental results indicated that ID might regulate HIF1 expression by affecting oxygen balance. HIF1 activation regulates the phenotypic transformation of VSMC and participates in the occurrence and development of AD in vivo and in vitro.PX478, the inhibition of HIF1, can improve ID-induced AD exacerbation.

Single-cell transcriptome analysis of cavernous tissues reveals the key roles of pericytes in diabetic erectile dysfunction

Erectile dysfunction (ED) affects a significant proportion of men aged 40-70 and is caused by cavernous tissue dysfunction. Presently, the most common treatment for ED is phosphodiesterase 5 inhibitors; however, this is less effective in patients with severe vascular disease such as diabetic ED. Therefore, there is a need for development of new treatment, which requires a better understanding of the cavernous microenvironment and cell-cell communications under diabetic condition. Pericytes are vital in penile erection; however, their dysfunction due to diabetes remains unclear. In this study, we performed single-cell RNA sequencing to understand the cellular landscape of cavernous tissues and cell type-specific transcriptional changes in diabetic ED. We found a decreased expression of genes associated with collagen or extracellular matrix organization and angiogenesis in diabetic fibroblasts, chondrocytes, myofibroblasts, valve-related lymphatic endothelial cells, and pericytes. Moreover, the newly identified pericyte-specific marker, Limb Bud-Heart (Lbh), in mouse and human cavernous tissues, clearly distinguishing pericytes from smooth muscle cells. Cell-cell interaction analysis revealed that pericytes are involved in angiogenesis, adhesion, and migration by communicating with other cell types in the corpus cavernosum; however, these interactions were highly reduced under diabetic conditions. Lbh expression is low in diabetic pericytes, and overexpression of LBH prevents erectile function by regulating neurovascular regeneration. Furthermore, the LBH-interacting proteins (Crystallin Alpha B and Vimentin) were identified in mouse cavernous pericytes through LC-MS/MS analysis, indicating that their interactions were critical for maintaining pericyte function. Thus, our study reveals novel targets and insights into the pathogenesis of ED in patients with diabetes.

Blocking LBH expression causes replication stress and sensitizes triple-negative breast cancer cells to ATR inhibitor treatment

Triple-negative (ER-PR-HER2-) breast cancers (TNBC) are highly aggressive and difficult to treat. TNBC exhibit high genomic instability, which enables them to adapt and become resistant to chemo/radiation therapy, leading to rapid disease relapse and mortality. The pro-survival factors that safeguard genome integrity in TNBC cells are poorly understood. LBH is an essential mammary stem cell-specific transcription regulator in the WNT pathway that is aberrantly overexpressed in TNBC, correlating with poor prognosis. Herein, we demonstrate a novel role for LBH in promoting TNBC cell survival. Depletion of LBH in multiple TNBC cell models triggered apoptotic cell death both in vitro and in vivo and led to S-G2M cell cycle delays. Mechanistically, LBH loss causes replication stress due to DNA replication fork stalling, leading to ssDNA breaks, ɣH2AX and 53BP1 nuclear foci formation, and activation of the ATR/CHK1 DNA damage response. Notably, ATR inhibition in combination with LBH downmodulation had a synergistic effect, boosting TNBC cell killing and blocking in vivo tumor growth. Our findings demonstrate, for the first time, that LBH protects the genome integrity of cancer cells by preventing replicative stress. Importantly, they uncover new synthetic lethal vulnerabilities in TNBC that could be exploited for future multi-modal precision medicine.

ANGPTL4 regulates ovarian cancer progression by activating the ERK1/2 pathway

BACKGROUND

Ovarian cancer (OC) has the highest mortality rate among all gynecological malignancies. A hypoxic microenvironment is a common feature of solid tumors, including ovarian cancer, and an important driving factor of tumor cell survival and chemo- and radiotherapy resistance. Previous research identified the hypoxia-associated gene angiopoietin-like 4 (ANGPTL4) as both a pro-angiogenic and pro-metastatic factor in tumors. Hence, this work aimed to further elucidate the contribution of ANGPTL4 to OC progression.

METHODS

The expression of hypoxia-associated ANGPTL4 in human ovarian cancer was examined by bioinformatics analysis of TCGA and GEO datasets. The CIBERSORT tool was used to analyze the distribution of tumor-infiltrating immune cells in ovarian cancer cases in TCGA. The effect of ANGPTL4 silencing and overexpression on the proliferation and migration of OVCAR3 and A2780 OC cells was studied in vitro, using CCK-8, colony formation, and Transwell assays, and in vivo, through subcutaneous tumorigenesis assays in nude mice. GO enrichment analysis and WGCNA were performed to explore biological processes and genetic networks associated with ANGPTL4. The results obtained were corroborated in OC cells in vitro by western blotting.

RESULTS

Screening of hypoxia-associated genes in OC-related TCGA and GEO datasets revealed a significant negative association between ANGPTL4 expression and patient survival. Based on CIBERSORT analysis, differential representation of 14 distinct tumor-infiltrating immune cell types was detected between low- and high-risk patient groups. Silencing of ANGPTL4 inhibited OVCAR3 and A2780 cell proliferation and migration in vitro and reduced the growth rate of xenografted OVCAR3 cells in vivo. Based on results from WGCNA and previous studies, western blot assays in cultured OC cells demonstrated that ANGPTL4 activates the Extracellular signal-related kinases 1 and 2 (ERK1/2) pathway and this results in upregulation of c-Myc, Cyclin D1, and MMP2 expression. Suggesting that the above mechanism mediates the pro-oncogenic actions of ANGPTL4T in OC, the pro-survival effects of ANGPTL4 were largely abolished upon inhibition of ERK1/2 signaling with PD98059.

CONCLUSIONS

Our work suggests that the hypoxia-associated gene ANGPTL4 stimulates OC progression through activation of the ERK1/2 pathway. These findings may offer a new prospect for targeted therapies for the treatment of OC.

Effect of gold-conjugated resveratrol nanoparticles on glioma cells and its underlying mechanism

BACKGROUND

 Glioblastoma is the most aggressive brain tumor with poor prognosis. Although Resveratrol (Rsv) is known to have therapeutic effects on glioma, the effects of gold-conjugated resveratrol nanoparticles (Rsv-AuNPs) on glioma cells are rarely reported.

OBJECTIVE

We aimed to investigate the effects of Rsv-AuNPs on glioma cells and its underlying mechanism.

METHOD

Human glioma cell line U87 was treated with different concentrations of Rsv-AuNPs. CCK-8, transwell, and wound healing assay were performed to measure the effects of Rsv-AuNPs on cell proliferation, invasion, and migration ability, respectively. Flow cytometry assay was used to detect the effects of Rsv-AuNPs on apoptosis. Changes of protein expressions related to proliferation, invasion, migration, and apoptosis were measured by Western blot assay. In addition, the inhibitory role of Rsv-AuNPs in the PI3K/AKT/mTOR signaling pathway was verified by using PI3K inhibitor LY294002.

RESULTS

Rsv-AuNPs treatment significantly suppressed proliferation, migration, and invasion of U87 cells (all P < 0.05) and increased the apoptosis rate (P < 0.05). The changes of proteins related to proliferation, migration, invasion and apoptosis were consistent (all P < 0.05). Moreover, Rsv-AuNPs treatment significantly inhibited the phosphorylation of PI3K, AKT and mTOR proteins in U87 cells (P < 0.05).

CONCLUSION

The present study found that Rsv-AuNPs inhibited the proliferation, migration, and invasion of U87 cells and induced apoptosis by inhibiting the activation of PI3K/AKT/mTOR signaling pathway. In the future, Rsv-AuNPs might be applied to the clinical treatment of glioma through more in-depth animal and clinical research.

Faecalibacterium prausnitzii promotes intestinal epithelial IL-18 production through activation of the HIF1α pathway

Introduction

Intestinal epithelial cells produce interleukin-18 (IL-18), a key factor in promoting epithelial barrier integrity. Here, we analyzed the potential role of gut bacteria and the hypoxia-inducible factor 1α (HIF1α) pathway in regulating mucosal IL18 expression in inflammatory bowel disease (IBD).

Methods

Mucosal samples from patients with IBD (n = 760) were analyzed for bacterial composition, IL18 levels and HIF1α pathway activation. Wild-type Caco-2 and CRISPR/Cas9-engineered Caco-2-HIF1A-null cells were cocultured with Faecalibacterium prausnitzii in a "Human oxygen-Bacteria anaerobic" in vitro system and analyzed by RNA sequencing.

Results

Mucosal IL18 mRNA levels correlated positively with the abundance of mucosal-associated butyrate-producing bacteria, in particular F. prausnitzii, and with HIF1α pathway activation in patients with IBD. HIF1α-mediated expression of IL18, either by a pharmacological agonist (dimethyloxallyl glycine) or F. prausnitzii, was abrogated in Caco-2-HIF1A-null cells.

Conclusion

Butyrate-producing gut bacteria like F. prausnitzii regulate mucosal IL18 expression in a HIF1α-dependent manner that may aid in mucosal healing in IBD.

Mechanistic insights into super-enhancer-driven genes as prognostic signatures in patients with glioblastoma

BACKGROUND

Glioblastoma (GBM) is one of the most common malignant brain tumors in adults and is characterized by high aggressiveness and rapid progression, poor treatment, high recurrence rate, and poor prognosis. Although super-enhancer (SE)-driven genes haven been recognized as prognostic markers for several cancers, whether it can be served as effective prognostic markers for patients with GBM has not been evaluated.

METHODS

We first combined histone modification data with transcriptome data to identify SE-driven genes associated with prognosis in patients with GBM. Second, we developed a SE-driven differentially expressed genes (SEDEGs) risk score prognostic model by univariate Cox analysis, KM survival analysis, multivariate Cox analysis and least absolute shrinkage and selection operator (LASSO) regression. Its reliability in predicting was verified by two external data sets. Third, through mutation analysis, immune infiltration, we explored the molecular mechanisms of prognostic genes. Next, Genomics of Drug Sensitivity in Cancer (GDSC) and the Connectivity Map (cMap) database were employed to assess different sensitivities to chemotherapeutic agents and small-molecule drug candidates between high- and low-risk patients. Finally, SEanalysis database was chosen to identify SE-driven transcription factors (TFs) regulating prognostic markers which will reveal a potential SE-driven transcriptional regulatory network.

RESULTS

First, we developed a 11-gene risk score prognostic model (NCF2, MTHFS, DUSP6, G6PC3, HOXB2, EN2, DLEU1, LBH, ZEB1-AS1, LINC01265, and AGAP2-AS1) selected from 1,154 SEDEGs, which is not only an independent prognostic factor for patients, but also can effectively predict the survival rate of patients. The model can effectively predict 1-, 2- and 3-year survival of patients and was validated in external Chinese Glioma Genome Atlas (CGGA) and Gene Expression Omnibus (GEO) datasets. Second, the risk score was positively correlated with the infiltration of regulatory T cell, CD4 memory activated T cell, activated NK cell, neutrophil, resting mast cell, M0 macrophage, and memory B cell. Third, we found that high-risk patients showed higher sensitivity than low-risk patients to both 27 chemotherapeutic agents and 4 small-molecule drug candidates which might benefit further precision therapy for GBM patients. Finally, 13 potential SE-driven TFs imply how SE regulates GBM patient's prognosis.

CONCLUSION

The SEDEG risk model not only helps to elucidate the impact of SEs on the course of GBM, but also provides a bright future for prognosis determination and choice of treatment for GBM patients.

Multi-cancer analysis reveals universal association of oncogenic LBH expression with DNA hypomethylation and WNT-Integrin signaling pathways

Limb-Bud and Heart (LBH) is a developmental transcription co-factor deregulated in cancer, with reported oncogenic and tumor suppressive effects. However, LBH expression in most cancer types remains unknown, impeding understanding of its mechanistic function Here, we performed systematic bioinformatic and TMA analysis for LBH in >20 different cancer types. LBH was overexpressed in most cancers compared to normal tissues (>1.5-fold; p < 0.05), including colon-rectal, pancreatic, esophageal, liver, stomach, bladder, kidney, prostate, testicular, brain, head & neck cancers, and sarcoma, correlating with poor prognosis. The cancer types showing LBH downregulation were lung, melanoma, ovarian, cervical, and uterine cancer, while both LBH over- and under-expression were observed in hematopoietic malignancies. In cancers with LBH overexpression, the LBH locus was frequently hypomethylated, identifying DNA hypomethylation as a potential mechanism for LBH dysregulation. Pathway analysis identified a universal, prognostically significant correlation between LBH overexpression and the WNT-Integrin signaling pathways. Validation of the clinical association of LBH with WNT activation in gastrointestinal cancer cell lines, and in colorectal patient samples by IHC uncovered that LBH is specifically expressed in tumor cells with nuclear beta-catenin at the invasive front. Collectively, these data reveal a high degree of LBH dysregulation in cancer and establish LBH as pan-cancer biomarker for detecting WNT hyperactivation in clinical specimens.

A Risk-Assessing Signature Based on Hypoxia- and Immune-Related Genes for Prognosis of Lung Adenocarcinoma Patients

Lung Adenocarcinoma (LUAD) drastically influences human health. Tumor hypoxia and immunity impact hugely on the immunotherapeutic effect of LUAD patients. This study is aimed at exploring the prognostic markers associated with hypoxia and immunity in LUAD patients and evaluates their reliability. The relationship between hypoxia and immune-related genes and prognoses of LUAD patients was investigated by the univariate regression analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) methods were used to reveal the enriched pathways and biological processes of prognosis-related genes. Univariate, LASSO, and multivariate Cox regression analyses were used to construct a prognostic signature and verify its independence. The reliability of the signature was evaluated by the Principal Component Analysis (PCA), the Kaplan-Meier (K-M) curve, and the receiver operating characteristic (ROC) curve. Gene set enrichment analysis (GSEA), tumor mutational burden (TMB), and single-sample GSEA (ssGSEA) further verified the performance of the signature. Finally, a prognostic signature for LUAD was constructed based on 7 hypoxia- and immune-related genes. According to riskScores acquired from the signature, the test set was divided into groups, where the prognosis of high-risk patients was poor. The feature genes had good reliability, and the riskScore could be used as an independent prognostic factor for LUAD patients. Meanwhile, high TMB scores and low immune scores were found in high-risk patients, and feature genes were enriched in signaling pathways such as cell cycle and p53 signaling pathway. In sum, a prognostic signature based on 7 hypoxia- and immune-related genes was constructed.

Limb-Bud and Heart (LBH) Upregulation in Cardiomyocytes under Hypoxia Promotes the Activation of Cardiac Fibroblasts via Exosome Secretion

The activation of cardiac fibroblasts (CFs) after myocardial infarction (MI) is essential for post-MI infarct healing, during which the regulation of transforming growth factor beta1 (TGF-β1) signaling is predominant. We have demonstrated that TGF-β1-mediated upregulation of LBH contributes to post-MI CF activation via modulating αB-crystallin (CRYAB), after being upregulated by TGF-β1. In this study, the effect of LBH-CRYAB signaling on the cardiac microenvironment via exosome communication and the corresponding mechanisms were investigated. The upregulation of LBH and CRYAB was verified in both cardiomyocytes (CMs) and CFs in hypoxic, post-MI peri-infarct tissues. CM-derived exosomes were isolated and identified, and LBH distribution was elevated in exosomes derived from LBH-upregulated CMs under hypoxia. Treatment with LBH+ exosomes promoted cellular proliferation, differentiation, and epithelial-mesenchymal transition-like processes in CFs. Additionally, in primary LBH^KO CFs, western blotting showed that LBH knockout partially inhibited TGF-β1-induced CF activation, while LBH-CRYAB signaling affected TGF-β1 expression and secretion through a positive feedback loop. The administration of a Smad3 phosphorylation inhibitor to LBH^KO CFs under TGF-β1 stimulation indicated that Smad3 phosphorylation partially accounted for TGF-β1-induced LBH upregulation. In conclusion, LBH upregulation in CMs in post-MI peri-infarct areas correlated with a hypoxic cardiac microenvironment and led to elevated exosomal LBH levels, promoting the activation of recipient CFs, which brings new insights into the studies and therapeutic strategies of post-MI cardiac repair.

CircKPNB1 mediates a positive feedback loop and promotes the malignant phenotypes of GSCs via TNF-α/NF-κB signaling

Glioma stem cells (GSCs) are a special kind of cells in GBM showing tumor initiation, self-renewal, and multi-lineage differentiation abilities. Finding novel circRNAs related to GSCs is of great significance for the study of glioma. qPCR, western blotting, and immunohistochemistry were used to detect the expression levels of circKPNB1, SPI1, DGCR8, and TNF-α. The expression of these molecules in GSCs was regulated by lentiviral-based infection. RNA immunoprecipitation assay, RNA pull-down, dual-luciferase reporter, and chromatin immunoprecipitation assays were used to study the direct regulation mechanisms among these molecules. All the MTS, EDU, transwell, neurosphere formation assays, ELDA assays, and xenograft experiments were used to detect the malignant phenotype of GSCs. We found a novel circRNA circKPNB1 was overexpressed in GBM and associated with GBM patients' poor prognosis. CircKPNB1 overexpression can promote the cell viabilities, proliferation, invasion, neurospheres formation abilities, and stemness of GSCs. Mechanistically, circKPNB1 regulates the protein stability and nuclear translocation of SPI1. SPI1 promotes the malignant phenotype of GSCs via TNF-α mediated NF-κB signaling. SPI1 can also transcriptionally upregulate DGCR8 expression, and the latter can maintain the stability of circKPNB1 and forms a positive feedback loop among DGCR8, circKPNB1 and SPI1. Our study found circKPNB1 was a novel oncogene in GBM and of great significance in the diagnosis and prognosis prediction of GBM and maybe a novel target for molecular targeted therapy.

Overexpression of NNMT in Glioma Aggravates Tumor Cell Progression: An Emerging Therapeutic Target

Simple Summary

Glioma is one of the most common intracranial malignancies and is incurable due to strong aggressiveness and resistance to radiotherapy and chemotherapy. The lack of effective therapeutic targets is a major problem in current treatment. In the present study, we found that nicotinamide N-methyltransferase (NNMT) is a key factor influencing the occurrence and development of glioma. High NNMT expression in glioma is a predictor of short overall survival and poor patient outcome. NNMT knockdown reduced the volume of mice xenograft glioma and the viability of glioma cells. Additionally, overexpression of NNMT epigenetically silenced GAP43 through DNA methylation, histone methylation, and deacetylation modification processes. GAP43 can inhibit the formation of microtubules in tumor and intertumor cell network connections and induce apoptosis through the SIRT1 signaling pathway. Therefore, NNMT could be a potential candidate for the clinical diagnosis and treatment of glioma.

Abstract

Purpose: Increasing evidence has revealed that nicotinamide N-methyltransferase (NNMT) is a key factor influencing the prognosis of tumors. The present study aimed to investigate the role of NNMT in glioma and to elucidate the associated functional mechanisms. Methods: Clinical samples were analyzed by immunohistochemical staining and Western blotting to evaluate NNMT expression in glioma and normal brain tissues. The correlation between NNMT expression and glioma was analyzed using the Cancer Genome Atlas (TCGA) database. Additionally, NNMT was knocked down in two types of glioma cells, U87 and U251, to evaluate the invasive ability of these cells. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate NNMT knockdown in the cells. Furthermore, ELISA was used to determine the balance between nicotinamide adenine dinucleotide and nicotinamide adenine dinucleotide hydrogen (NAD/NADH ratio), which verified the altered methylation patterns in the cells. The glioma xenograft mouse models were used to verify the regulatory role of NNMT, GAP43, and SIRT1. Results: Analysis based on our clinical glioma samples and TCGA database revealed that overexpression of NNMT was associated with poor prognosis of patients. Knockdown of NNMT reduced the invasive ability of glioma cells, and downregulation of its downstream protein GAP43 occurred due to altered cellular methylation caused by NNMT overexpression. Gene Set Enrichment Analysis confirmed that NNMT modulated the NAD-related signaling pathway and showed a negative association between NNMT and SIRT1. Moreover, the regulatory roles of NNMT, GAP43, and SIRT1 were confirmed in glioma xenograft mouse models. Conclusion: Overexpression of NNMT causes abnormal DNA methylation through regulation of the NAD/NADH ratio, which in turn leads to the downregulation of GAP43 and SIRT1, eventually altering the biological behavior of tumor cells.

A Novel Thrombosis-Related Signature for Predicting Survival and Drug Compounds in Glioblastoma

Glioblastoma is the most common primary tumor in the central nervous system, and thrombosis-associated genes are related to its occurrence and progression. Univariate Cox and LASSO regression analysis were utilized to develop a new prognostic signature based on thrombosis-associated genes. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and HALLMARK were used for functional annotation of risk signature. ESTIMATE, MCP-counter, xCell, and TIMER algorithms were used to quantify immune infiltration in the tumor microenvironment. Genomics of Drug Sensitivity in Cancer (GDSC) was used for selecting potential drug compounds. Risk signature based on thrombosis-associated genes shows moderate performance in prognosis prediction. The functional annotation of the risk signature indicates that the signaling pathways related to the cell cycle, apoptosis, tumorigenesis, and immune suppression are rich in the high-risk group. Somatic mutation analysis shows that tumor-suppressive gene TP53 and oncogene PTEN have higher expression in low-risk and high-risk groups, respectively. Potential drug compounds are explored in risk score groups and show higher AUC values in the low-risk score group. A nomogram with valuable prognostic factors exhibits high sensitivity in predicting the survival outcome of GBM patients. Our research screens out multiple thromboses-associated genes with remarkable clinical significance in GBM and further develops a meaningful prognostic risk signature predicting drug sensitivity and survival outcome.

MCPIP1 promotes cell proliferation, migration and angiogenesis of glioma via VEGFA-mediated ERK pathway

Glioma is the most common primary malignant intracranial tumor in the population, and is often associated with abundant angiogenesis. However, how angiogenesis is regulated during glioma progression is still poorly understood. Data mining of cancer patient database shows that MCPIP1 is positively correlated with VEGFA expression and negatively with survival. In this study, we report that overexpressed MCPIP1 in glioma cells is a boost of angiogenesis. Mechanistically, MCPIP1 upregulates the expression of VEGFA in glioma, and promote the secretion of VEGFA to the surroundings, which could stimulate angiogenesis through ERK pathway. Blocking VEGFA expression and secretion inhibited MCPIP1-mediated angiogenesis and glioma progression in vitro and xenograft models. Collectively, these results identify a critical role for MCPIP1 in angiogenesis and glioma progression by regulating the VEGFA-mediated ERK pathway, suggesting that targeting MCPIP1 may be a potential glioma-selective therapeutic strategy.

Long Noncoding RNA RP11-732M18.3 Promotes Glioma Angiogenesis by Upregulating VEGFA

Gliomas are the most aggressive and common type of malignant brain tumor, with limited treatment options and a dismal prognosis. Angiogenesis, a hallmarks of cancer, is one of two critical events in the progression of gliomas. Accumulating evidence has demonstrated that in glioma dysregulated molecules like long noncoding RNAs (lncRNAs), are closely linked to tumorigenesis and prognosis. However, the effects of and mechanisms of action of lncRNAs during tumor angiogenesis are poorly understood. The effect of lncRNA RP11-732M18.3 on angiogenesis was elucidated through an intracranial orthotopic glioma model, immunohistochemistry, and an in vitro angiogenesis assay. Co-culture experiments and cell migration assays were performed to investigate the function of lncRNA RP11-732M18.3 in vitro. lncRNA RP11-732M18.3 increased CD31⁺ microvessel density, and overexpression of lncRNA RP11-732M18.3 resulted in poor mouse survival. lncRNA RP11-732M18.3 promoted endothelial cell migration and tube formation. Nomogram and Kaplan-Meier survival analyses indicated that higher VEGFA is correlated with a poor prognosis. Mechanistically, lncRNA RP11-732M18.3 promotes angiogenesis by increasing the nuclear level of EP300 and facilitating the transcription and secretion of VEGFA. Our study contributes to the latest understanding of glioma angiogenesis and prognosis. lncRNA RP11-732M18.3 may be a potential treatment target in glioma.

Multiparameter Magnetic Resonance Quantitative Evaluation of Pancreatic Cancer with Vascular Invasion

Objective

To analyze the value of multiparameter magnetic resonance (mpMRI) in the diagnosis of pancreatic cancer with vascular invasion from two aspects: morphology and function, so as to provide a reliable diagnostic basis for preparing the clinical treatment plans.

Methods

Totally 31 case data of pancreatic cancer patients diagnosed in our hospital from January 2020 to March 2021 were enrolled in this study. All patients underwent multiparameter magnetic resonance imaging (T1WI, T2WI, DKI, and DCE-MRI) before surgery, and then all patients underwent pancreatic cancer surgery. Two experienced radiologists analyzed these obtained images according to the image reports and combined them with the pathological results. Taking pathological results as gold standard, the sensitivity, specificity, and accuracy of quantitative parameters derived from T2WI, DKI, DCE, T2WI + DKI, T2WI + DCE, and T2WI + DKI + DCE for the diagnostic capabilities of pancreatic cancer vascular invasion were calculated using diagnostic laboratory methods. Kappa consistency test was used to estimate the consistency of two radiologists' diagnosis and analysis. The images obtained by DKI sequence were input into the postprocessing software MITK-Diffusion v2014.10.02, The images obtained from DCE sequence were processed by the Tissue 4D software on the Siemens syngo via workstation to calculate and analyze each tumor ROI's MD, MK values from DKI, and K trans, K ep, V e values from DCE. Independent samples t-test was used to compare the parameters of pancreatic cancer with vascular invasion group (16 cases) and nonvascular invasion group (15 cases). ROC curve was used to analyze the efficacy of each parameter in diagnosing pancreatic cancer vascular invasion.

Results

The sensitivity, specificity, and accuracy of T2WI were 62.5%, 53.5%, and 58.1%; those of DKI were 56.3%, 60.0%, and 58.1%; those of DCE were 68.8%, 60.0%, and 64.5%; those of T2WI + DKI were 68.8%, 66.7%, and 67.7%; those of T2WI + DCE were 75.0%, 66.7%, and 71.1%; those of T2WI + DKI + DCE were 81.2%, 73.3%, and 77.4%, respectively. These two diagnostic radiologists analyzed image data with good consistency, Kappa = 0.834. MD, MK, K trans, K ep, and V e were significantly different between the vascular invasion group and the nonvascular invasion group (p < 0.05). Each parameter's AUC of ROC curve was 0.773, 0.829, 0.794, 0.802, and 0.846 (p < 0.05). Take MD = 2.285 × 10-3 mm/s2, MK = 0.72, K trans = 0.103, K ep = 0.337, and V e = 0.353 as thresholds; the sensitivity of these parameters to diagnose vascular invasion of pancreatic cancer was 73.33%, 75%, 87.5%, 68.8%, and 68.8%. The specificity of them was 75%, 80%, 60%, 86.7%, and 86.7%, respectively.

Conclusion

The combined analysis of T2WI + DKI + DCE can improve the specificity and accuracy of diagnostic efficiency of vascular invasion of pancreatic cancer and provide an important diagnostic basis for pancreatic cancer's preoperative treatment.

Hypoxia-induced ebv-circLMP2A promotes angiogenesis in EBV-associated gastric carcinoma through the KHSRP/VHL/HIF1α/VEGFA pathway

EBV-encoded circular RNA LMP2A (ebv-circLMP2A) was found to be expressed in EBV-associated gastric carcinoma (EBVaGC) and associated with distant metastasis and poor prognosis. Angiogenesis is a key step in tumor invasion and metastasis and plays a crucial role in tumor progression. However, it is unclear whether and how ebv-circLMP2A is involved in angiogenesis. In this study, we showed that MVD, HIF1α, and VEGFA expression was increased in EBVaGC mouse xenografts with high expression of ebv-circLMP2A. The expression of ebv-circLMP2A was positively correlated with MVD, HIF1α, and VEGFA expression in clinical samples of EBVaGC. Knockdown of ebv-circLMP2A repressed tube formation and migration of HUVECs and decreased VEGFA and HIF1α expression in cancer cells under hypoxia, while ectopic expression of ebv-circLMP2A reversed these effects. Additionally, knockdown of HIF1α blocked the upregulation of ebv-circLMP2A by hypoxia, and ebv-circLMP2A interacted with KHSRP to enhance KHSRP-mediated decay of VHL mRNA, leading to the accumulation of HIF1α under hypoxia. There was a positive feedback loop between HIF1α and ebv-circLMP2A that promotes angiogenesis under hypoxia. ebv-circLMP2A was essential in regulating tumor angiogenesis in EBVaGC and might provide a valuable therapeutic target for EBVaGC.

Extracellular vesicles derived from glioblastoma promote proliferation and migration of neural progenitor cells via PI3K-Akt pathway

BACKGROUND

Glioblastomas are lethal brain tumors under the current combinatorial therapeutic strategy that includes surgery, chemo- and radio-therapies. Extensive changes in the tumor microenvironment is a key reason for resistance to chemo- or radio-therapy and frequent tumor recurrences. Understanding the tumor-nontumor cell interaction in TME is critical for developing new therapy. Glioblastomas are known to recruit normal cells in their environs to sustain growth and encroachment into other regions. Neural progenitor cells (NPCs) have been noted to migrate towards the site of glioblastomas, however, the detailed mechanisms underlying glioblastoma-mediated NPCs' alteration remain unkown.

METHODS

We collected EVs in the culture medium of three classic glioblastoma cell lines, U87 and A172 (male cell lines), and LN229 (female cell line). U87, A172, and LN229 were co-cultured with their corresponding EVs, respectively. Mouse NPCs (mNPCs) were co-cultured with glioblastoma-derived EVs. The proliferation and migration of tumor cells and mNPCs after EVs treatment were examined. Proteomic analysis and western blotting were utilized to identify the underlying mechanisms of glioblastoma-derived EVs-induced alterations in mNPCs.

RESULTS

We first show that glioblastoma cell lines U87-, A172-, and LN229-derived EVs were essential for glioblastoma cell prolifeartion and migration. We then demonstrated that glioblastoma-derived EVs dramatically promoted NPC proliferation and migration. Mechanistic studies identify that glioblastoma-derived EVs achieve their functions via activating PI3K-Akt-mTOR pathway in mNPCs. Inhibiting PI3K-Akt pathway reversed the elevated prolfieration and migration of glioblastoma-derived EVs-treated mNPCs.

CONCLUSION

Our findings demonstrate that EVs play a key role in intercellular communication in tumor microenvironment. Inhibition of the tumorgenic EVs-mediated PI3K-Akt-mTOR pathway activation might be a novel strategy to shed light on glioblastoma therapy. Video Abstract.

Exosomal LBH inhibits epithelial-mesenchymal transition and angiogenesis in nasopharyngeal carcinoma via downregulating VEGFA signaling

The limb-bud and heart (LBH) gene was reported to suppress nasopharyngeal carcinoma (NPC) progression in our previous study. Distant metastasis predominantly accounts for the unsatisfactory prognosis of NPC treatment, in which epithelial-mesenchymal transition (EMT) and tumor angiogenesis are of great significance. The roles of exosomes in mediating NPC progression have been highlighted in recent researches, and attempts have been made to explore the clinical application of NPC exosomes. Here we investigated the function of the LBH gene in NPC exosomes, and its potential mechanism. NPC xenografts were constructed, showing that vascular endothelial growth factor A (VEGFA) expression and neovascularity were attenuated by LBH overexpression, together with diminished EMT progression. NPC-derived exosomes were isolated, identified and applied for in vitro/in vivo experiments, and the exosomal distribution of LBH was elevated in exosomes derived from LBH-upregulated cells. Ectopic LBH, αB-crystallin (CRYAB) and VEGFA expression was induced by lentiviral infection or plasmid transfection to explore their functions in modulating EMT and angiogenesis in NPC. The addition of LBH+ NPC exosomes during a Matrigel plug assay in mice suppressed in vivo angiogenesis, and the treatment of human umbilical vein endothelial cells (HUVECs) with LBH+ NPC exosomes inhibited cellular proliferation, migration and tube formation. The interactions among LBH, CRYAB and VEGFA were confirmed by colocalization and fluorescence resonance energy transfer (FRET) assays, and extracellular VEGFA secretion from both HUVECs and NPC cells under the treatment with LBH+ NPC exosomes was diminished according to ELISA results. We concluded that exosomal LBH inhibits EMT progression and angiogenesis in the NPC microenvironment, and that its effects are partially implemented by modulation of VEGFA expression, secretion and related signaling. Thus, LBH could serve as a promising therapeutic target in VEGFA-focused NPC treatment.

Limb-bud and heart development (LBH) contributes to glioma progression in vitro and in vivo

Glioma is the predominant brain malignancy and is correlated with high mortality and severe morbidity. The transcription factor limb‐bud and heart (LBH) has been reported to be involved in the development of several cancers, although its role in glioma development remains elusive. Here, we examined the effect of LBH on glioma progression. The expression of LBH was increased in glioma samples from The Cancer Genome Atlas database, and upregulation of LBH was observed to be correlated with the poor survival of glioma patients. We also report that expression of LBH was elevated in clinical glioma tissues compared to adjacent normal tissues, and was also enhanced in glioma cell lines. LBH promotes proliferation and inhibits cell cycle arrest and apoptosis in glioma cells. In addition, LBH increased the migration and invasion of glioma cells in vitro. Moreover, tumorigenicity analysis revealed that LBH could promote the tumor growth of glioma cells in vivo. In conclusion, our findings suggest that LBH contributes to glioma progression in vitro and in vivo. Our findings provide new insights into the mechanism by which LBH promotes the development of glioma, improving our understanding of the correlation between LBH with cancer. LBH may have potential as a target for glioma therapy.

Comprehensive Analysis of the Prognostic Significance of Hsa-miR-100-5p and Its Related Gene Signature in Stomach Adenocarcinoma

Stomach adenocarcinoma (STAD) is one of the most common cancers in the world. However, the prognosis of STAD remains poor, and the therapeutic effect of chemotherapy and immunotherapy varies from person to person. MicroRNAs (miRNAs) play vital roles in tumor development and metastasis and can be used for cancer diagnosis and prognosis. In this study, hsa-miR-100-5p was identified as the only dysregulated miRNA in STAD samples through an analysis of three miRNA expression matrices. A weighted gene co-expression network analysis (WGCNA) was performed to select hsa-miR-100-5p-related genes. A least absolute shrinkage and selection operator (LASSO) Cox regression analysis was performed to establish a miR-100-5p-related prognostic signature. Kaplan–Meier analyses, nomograms, and univariate and multivariate Cox regression analyses were used to evaluate the prognostic signature, which was subsequently identified as an independent risk factor for STAD patients. We investigated the tumor immune environment between low- and high-risk groups and found that, among component types, M2 macrophages contributed the most to the difference between these groups. A drug sensitivity analysis suggested that patients with high-risk scores may be more sensitive to docetaxel and cisplatin chemotherapy and that patients in the low-risk group may be more likely to benefit from immunotherapy. Finally, external cohorts were evaluated to validate the robustness of the prognostic signature. In summary, this study may provide new ideas for developing more individualized therapeutic strategies for STAD patients.

Gallic acid for cancer therapy: Molecular mechanisms and boosting efficacy by nanoscopical delivery

Cancer is the second leading cause of death worldwide. Majority of recent research efforts in the field aim to address why cancer resistance to therapy develops and how to overcome or prevent it. In line with this, novel anti-cancer compounds are desperately needed for chemoresistant cancer cells. Phytochemicals, in view of their pharmacological activities and capacity to target various molecular pathways, are of great interest in the development of therapeutics against cancer. Plant-derived-natural products have poor bioavailability which restricts their anti-tumor activity. Gallic acid (GA) is a phenolic acid exclusively found in natural sources such as gallnut, sumac, tea leaves, and oak bark. In this review, we report on the most recent research related to anti-tumor activities of GA in various cancers with a focus on its underlying molecular mechanisms and cellular pathwaysthat that lead to apoptosis and migration of cancer cells. GA down-regulates the expression of molecular pathways involved in cancer progression such as PI3K/Akt. The co-administration of GA with chemotherapeutic agents shows improvements in suppressing cancer malignancy. Various nano-vehicles such as organic- and inorganic nano-materials have been developed for targeted delivery of GA at the tumor site. Here, we suggest that nano-vehicles improve GA bioavailability and its ability for tumor suppression.

Association Between LIN28A Gene Polymorphisms and Glioma Susceptibility in Chinese Children

Gliomas are the most prevalent brain tumors among children and adolescents. The occurrence and development of various malignant tumors is closely related with LIN28A gene, but its relationship with glioma susceptibility has not been widely discovered. In this case-control study, we conducted four single nucleotide polymorphisms (SNPs) (rs3811464 G>A, rs3811463 T>C, rs34787247 G>A, and rs11247957 G>A) of LIN28A gene to investigate whether they increase the risk of glioma. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate their relationship. There was no significant correlation between four SNPs and glioma risk in single polymorphism and conjoint analysis. However, in stratification analysis, we found that rs3811463 TC/CC may add to the risk of glioma with clinical stage III (adjusted OR = 3.16, 95% CI = 1.15-8.70, P = .026) or stage III+IV patients (adjusted OR = 2.05, 95% CI = 1.02-4.13, P = .044). Our research suggested that four SNPs of LIN28A gene have a weak relationship with the risk of glioma in Chinese children. LIN28A rs3811463 TC/CC may increase the possibility of glioma in clinical stage III or stage III+IV patients which need larger samples and further confirmation.

FMR1/circCHAF1A/miR-211-5p/HOXC8 feedback loop regulates proliferation and tumorigenesis via MDM2-dependent p53 signaling in GSCs

Glioma is the most common and fatal primary malignant brain tumor. Glioma stem cells (GSCs) may be an important factor in glioma cell proliferation, invasion, chemoradiotherapy tolerance, and recurrence. Therefore, discovering novel GSCs related circular RNAs (circRNAs) may finds out a prospective target for the treatment of glioma. A novel circRNA-CHAF1A (circCHAF1A) was first found in our study. CircCHAF1A was overexpressed in glioma and related to the low survival rate. Functionally, it was found that no matter in vitro or in vivo, circCHAF1A can facilitate the proliferation and tumorigenesis of TP53wt GSCs. Mechanistically, circCHAF1A upregulated transcription factor HOXC8 expression in GSCs through miR-211-5p sponging. Then, HOXC8 can transcriptionally upregulate MDM2 expression and inhibited the antitumor effect of p53. Furtherly, the RNA binding protein FMR1 can bind to and promoted the expression of circCHAF1A via maintaining its stability, while HOXC8 also transcribed the FMR1 expression to form a feedback loop, which may be involved in the malignant transformation of glioma. The novel feedback loop among FMR1, circCHAF1A, miR-211-5p, and HOXC8 in GSCs can facilitate the proliferation and tumorigenesis of glioma and GSCs. It also provided a helpful biomarker for diagnosis and prognostic evaluation of glioma and may be applied to molecular targeted therapy.

Expression-based prediction of human essential genes and candidate lncRNAs in cancer cells

MOTIVATION

Essential genes are required for the reproductive success at either cellular or organismal level. The identification of essential genes is important for understanding the core biological processes and identifying effective therapeutic drug targets. However, experimental identification of essential genes is costly, time consuming and labor intensive. Although several machine learning models have been developed to predict essential genes, these models are not readily applicable to lncRNAs. Moreover, the currently available models cannot be used to predict essential genes in a specific cancer type.

RESULTS

In this study, we have developed a new machine learning approach, XGEP (eXpression-based Gene Essentiality Prediction), to predict essential genes and candidate lncRNAs in cancer cells. The novelty of XGEP lies in the utilization of relevant features derived from the TCGA transcriptome dataset through collaborative embedding. When evaluated on the pan-cancer dataset, XGEP was able to accurately predict human essential genes and achieve significantly higher performance than previous models. Notably, several candidate lncRNAs selected by XGEP are reported to promote cell proliferation and inhibit cell apoptosis. Moreover, XGEP also demonstrated superior performance on cancer-type-specific datasets to identify essential genes. The comprehensive lists of candidate essential genes in specific cancer types may be used to guide experimental characterization and facilitate the discovery of drug targets for cancer therapy.

AVAILABILITY AND IMPLEMENTATION

The source code and datasets used in this study are freely available at https://github.com/BioDataLearning/XGEP.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Comprehensive analyses of correlation and survival reveal informative lncRNA prognostic signatures in colon cancer

BACKGROUND

Colon cancer is a commonly worldwide cancer with high morbidity and mortality. Long non-coding RNAs (lncRNAs) are involved in many biological processes and are closely related to the occurrence of colon cancer. Identification of the prognostic signatures of lncRNAs in colon cancer has great significance for its treatment.

METHODS

We first identified the colon cancer-related mRNAs and lncRNAs according to the differential analysis methods using the expression data in TCGA. Then, we performed correlation analysis between the identified mRNAs and lncRNAs by integrating their expression values and secondary structure information to estimate the co-regulatory relationships between the cancer-related mRNAs and lncRNAs. Besides, the competing endogenous RNA regulation network based on co-regulatory relationships was constructed to reveal cancer-related regulatory patterns. Meanwhile, we used traditional regression analysis (univariate Cox analysis, random survival forest analysis, and lasso regression analysis) to screen the cancer-related lncRNAs. Finally, by combining the identified colon cancer-related lncRNAs according to the above analyses, we constructed a risk prognosis model for colon cancer through multivariate Cox analysis and also validated the model in the colon cancer dataset in TCGA cohorts.

RESULTS

Six lncRNAs were found highly correlated with the overall survival of colon cancer patients, and a risk prognosis model based on them was constructed to predict the overall survival of colon cancer patients. In particular, EVX1-AS, ZNF667-AS1, CTC-428G20.6, and CTC-297N7.9 were first reported to be related to colon cancer by using our model, among which EVX1-AS and ZNF667-AS1 have been predicted to be related to colon cancer in LncRNADisease database.

CONCLUSIONS

This study identified the potential regulatory relationships between lncRNAs and mRNAs by integrating their expression values and secondary structure information and presented a significant 6-lncRNA risk prognosis model to predict the overall survival of colon cancer patients.

Overexpression of NPTX2 Promotes Malignant Phenotype of Epithelial Ovarian Carcinoma via IL6-JAK2/STAT3 Signaling Pathway Under Hypoxia

Background

Epithelial ovarian cancer (EOC) is the main subtype of ovarian cancer and shows an aggressive phenotype and poor prognosis. Neuronal pentraxin II (NPTX2) is a member of the neuronal pentraxin family and plays a contradictory role in different tumors. However, there has been no report about the possible role and effect of NPTX2 in EOC.

Methods

Bioinformatics analysis, qPCR, western blotting and immunohistochemistry were used to detect the expression of NPTX2 in EOC. Lentivirus-based transfection for NPTX2 overexpression or knockdown was performed on the EOC cell lines A2780, HEY, SKOV3 and OVCAR-3. The effect of NPTX2 on the malignant phenotype of EOC was examined through methods of MTS assay, Edu assay, transwell assay, western blotting analysis, qPCR analysis, luciferase reporter assay and xenograft experiment.

Results

EOC tissues showed higher NPTX2 expression than the normal tissues with poor prognosis. NPTX2 overexpression can promote the proliferation, invasion, migration and tumorigenesis of EOC via IL6-JAK2/STAT3 signaling pathway. Moreover, hypoxia-inducible factor-1(HIF-1) can promote the transcription and expression of NPTX2 under the hypoxic environment. NPTX2 knockdown abolished the hypoxia-induced malignant phenotypes in ECO.

Conclusions

The above results suggest that NPTX2 may play a novel role in ovarian cancer's malignant phenotype and act as a promising treatment target for EOC molecular therapy.

Limb-bud and Heart (LBH) mediates proliferation, fibroblast-to-myofibroblast transition and EMT-like processes in cardiac fibroblasts

Cardiac fibrosis is an important pathological change after myocardial infarction (MI). Its progression is essential for post-MI infarct healing, during which transforming growth factor beta1 (TGF-β1) plays a critical role. Limb-bud and Heart (LBH), a newly discovered target gene of TGF-β1, was shown to promote normal cardiogenesis. αB-crystallin (CRYAB), an LBH-interacting protein, was demonstrated to be involved in TGF-β1-induced fibrosis. The roles and molecular mechanisms of LBH and CRYAB during cardiac fibrosis remain largely unexplored. In this study, we investigated the alterations of LBH and CRYAB expression in mouse cardiac tissue after MI. LBH and CRYAB were upregulated in activated cardiac fibroblasts (CFs), while in vitro TGF-β1 stimulation induced the upregulation of LBH, CRYAB, and fibrogenic genes in primary CFs of neonatal rats. The results of the ectopic expression of LBH proved that LBH accelerated CF proliferation under hypoxia, mediated the expression of CRYAB and fibrogenic genes, and promoted epithelial-mesenchymal transition (EMT)-like processes in rat CFs, while subsequent CRYAB silencing reversed the effects induced by elevated LBH expression. We also verified the protein-protein interaction (PPI) between LBH and CRYAB in fibroblasts. In summary, our work demonstrated that LBH promotes the proliferation of CFs, mediates TGF-β1-induced fibroblast-to-myofibroblast transition and EMT-like processes through CRYAB upregulation, jointly functioning in post-MI infarct healing. These findings suggest that LBH could be a promising potential target for the study of cardiac repair and cardiac fibrosis.

VHL gene methylation contributes to excessive erythrocytosis in chronic mountain sickness rat model by upregulating the HIF-2α/EPO pathway

AIMS

Hypoxia-inducible factors (HIFs) play important roles in the pathogenesis of erythrocytosis in chronic mountain sickness (CMS). von Hippel-Lindau (VHL) is a key regulator of hypoxia that can direct the poly-ubiquitylation and degradation of HIFs. Epigenetic mechanisms are believed to contribute toward adaption to chronic hypoxia. Here, we investigated the contribution and mechanism of VHL methylation in rats with erythrocytosis in CMS.

MAIN METHODS

The methylation status of VHL was measured via bisulfite sequencing PCR, while VHL, DNMT1, DNMT3α, and DNMT3β expression were assessed using real-time reverse transcription PCR and western blotting. HIF-2α and EPO expression levels in bone marrow were determined via immunohistochemical staining, and erythroid hyperplasia in bone marrow sections were observed with hematoxylin and eosin staining.

KEY FINDINGS

We found that chronic hypoxia triggered erythroid hyperplasia in the bone marrow and increased the quantity of peripheral red blood cells in CMS rats. Chronic hypoxia significantly induced methylation at the CpG site in the VHL promoter, decreased VHL expression, and increased HIF-2α and EPO expression. Chronic hypoxia increased DNMT3α and DNMT3β expression, consistent with the decrease in VHL expression. The DNA methyltransferase inhibitor 5-azacytidine reduced chronic hypoxia-induced erythroid proliferation in the bone marrow of rats with CMS by suppressing VHL methylation and DNMTs expression.

SIGNIFICANCE

Our study suggests that VHL methylation contributes toward excessive erythrocytosis in CMS by upregulating the HIF-2α/EPO pathway in the bone marrow of rats. We demonstrated that the DNMT inhibitor 5-azacytidine can attenuate erythroid hyperplasia in the bone marrow by demethylating the VHL promoter.

lncRNA DLEU2 acts as a miR-181a sponge to regulate SEPP1 and inhibit skeletal muscle differentiation and regeneration

Sarcopenia is a serious public health problem associated with the loss of muscle mass and function. The purpose of this study was to identify molecular markers and construct a ceRNA pathway as a significant predictor of sarcopenia. We designed a prediction model to select important differentially expressed mRNAs (DEMs), and constructed a sarcopenia associated ceRNA network. After correlation analysis of each element in the ceRNA network based on clinical samples and GTEX database, C2C12 mouse myoblasts were used as a model to verify the identified ceRNA pathways. A new model for predicting sarcopenia based on four molecular markers SEPP1, SV2A, GOT1, and GFOD1 was developed. The model was used to construct a ceRNA network and showed high accuracy. Correlation analysis showed that the expression levels of lncDLEU2, SEPP1, and miR-181a were closely associated with a high risk of sarcopenia. lncDLEU2 inhibits muscle differentiation and regeneration by acting as a miR-181a sponge regulating SEPP1 expression. In this study, a highly accurate prediction tool was developed to improve the prediction outcomes of sarcopenia. These findings suggest that the lncDLEU2-miR-181a-SEPP1 pathway inhibits muscle differentiation and regeneration. This pathway may be a new therapeutic target for the treatment of sarcopenia.

Analyses of metastasis-associated genes in IDH wild-type glioma

Background

Glioma is the most common malignant tumor of the brain. The existence of metastatic tumor cells is an important cause of recurrence even after radical glioma resection.

Methods

Single-cell sequencing data and high-throughput data were downloaded from GEO database and TCGA/CGGA database. By means of PCA and tSNE clustering methods, metastasis-associated genes in glioma were identified. GSEA explored possible biological functions that these metastasis-associated genes may participate in. Univariate and multivariate Cox regression were used to construct a prognostic model.

Results

Glioma metastatic cells and metastasis-associated genes were identified. The prognostic model based on metastasis-associated genes had good sensitivity and specificity for the prognosis of glioma. These genes may be involved in signal pathways such as cellular protein catabolic process, p53 signaling pathway, transcriptional misregulation in cancer and JAK-STAT signaling pathway.

Conclusion

This study explored glioma metastasis-associated genes through single-cell sequencing data mining, and aimed to identify prognostic metastasis-associated signatures for glioma and may provide potential targets for further cancer research.

The U2AF2 /circRNA ARF1/miR-342-3p/ISL2 feedback loop regulates angiogenesis in glioma stem cells

BACKGROUND

Glioma is the most common and lethal primary brain tumor in adults, and angiogenesis is one of the key factors contributing to its proliferation, aggressiveness, and malignant transformation. However, the discovery of novel oncogenes and the study of its molecular regulating mechanism based on circular RNAs (circRNAs) may provide a promising treatment target in glioma.

METHODS

Bioinformatics analysis, qPCR, western blotting, and immunohistochemistry were used to detect the expression levels of ISL2, miR-342-3p, circRNA ARF1 (cARF1), U2AF2, and VEGFA. Patient-derived glioma stem cells (GSCs) were established for the molecular experiments. Lentiviral-based infection was used to regulate the expression of these molecules in GSCs. The MTS, EDU, Transwell, and tube formation assays were used to detect the proliferation, invasion, and angiogenesis of human brain microvessel endothelial cells (hBMECs). RNA-binding protein immunoprecipitation, RNA pull-down, dual-luciferase reporter, and chromatin immunoprecipitation assays were used to detect the direct regulation mechanisms among these molecules.

RESULTS

We first identified a novel transcription factor related to neural development. ISL2 was overexpressed in glioma and correlated with poor patient survival. ISL2 transcriptionally regulated VEGFA expression in GSCs and promoted the proliferation, invasion, and angiogenesis of hBMECs via VEGFA-mediated ERK signaling. Regarding its mechanism of action, cARF1 upregulated ISL2 expression in GSCs via miR-342-3p sponging. Furthermore, U2AF2 bound to and promoted the stability and expression of cARF1, while ISL2 induced the expression of U2AF2, which formed a feedback loop in GSCs. We also showed that both U2AF2 and cARF1 had an oncogenic effect, were overexpressed in glioma, and correlated with poor patient survival.

CONCLUSIONS

Our study identified a novel feedback loop among U2AF2, cARF1, miR-342-3p, and ISL2 in GSCs. This feedback loop promoted glioma angiogenesis, and could provide an effective biomarker for glioma diagnosis and prognostic evaluation, as well as possibly being used for targeted therapy.

Retracted: Identification and validation of hypoxic markers of glioblastoma multiforme in methylation, somatic CNV characteristics based on large-scale samples

Retraction: Wang J, Xu S, Lv W, Shan A, Shi F, Xu J, Mei S, and Yang Y. Identification and validation of hypoxic markers of glioblastoma multiforme in methylation, somatic CNV characteristics based on large-scale samples. J Biochem Mol Toxicol. 2020; e22585. https://doi.org/10.1002/jbt.22585 The above article, published online on 24 July 2020 in Wiley Online Library (wileyonlinelibrary.com) has been retracted by agreement between the authors, the journal's Editor-in-Chief, Hari K. Bhat, and Wiley Periodicals, LLC. The retraction has been agreed due to the authors raising concerns about the accuracy of their data following their article's acceptance. The authors had agreed with the Editor-in-Chief to withdraw their manuscript before publication. However, unfortunately, the Version of Record was mistakenly published online on the journal's Early View service before it could be withdrawn. The Publisher apologizes to the authors for this error.

Identification of a Hypoxia-Associated Signature for Lung Adenocarcinoma

Background

A hypoxia microenvironment plays a role in the initiation and progression of many cancer types, but its involvement in lung adenocarcinoma is still unclear. This study aimed to explore the potential correlation between hypoxia and lung adenocarcinoma and establish the hypoxia-associated gene signature in lung adenocarcinoma.

Methods

Lung adenocarcinoma cases were retrieved from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. The genes to be included in the hypoxia-associated signature were selected by performing univariate Cox regression analysis and lasso regression analysis. Then, the gene signature was verified by performing a survival analysis and constructing the multiple receiver operating characteristic (ROC) curve. The CIBERSORT tool was then used to investigate the potential correlation between the gene signature and immune cells. Moreover, a nomogram was constructed and evaluated by calculating the C-index.

Results

Four genes (XPNPEP1, ANGPTL4, SLC2A1, and PFKP) were included in the final signature. The results showed that patients in the high-risk group showed worse survival than those in the low-risk group. Moreover, we found two types of immune cells (memory activated CD4⁺ T cell and M0 macrophages) which showed a significant infiltration in the tissues of the high-risk group patients.

Conclusion

The hypoxia-associated gene signature established and validated in this study could be used as a potential prognostic factor in lung adenocarcinoma and may guide the immunotherapy choice.

Upregulation of lncRNA AGAP2-AS1 is an independent predictor of poor survival in patients with clear cell renal carcinoma

Long non-coding RNA (lncRNA) AGAP2-AS1 has been reported to be a potential biomarker for a variety of cancer types, while its function in clear cell renal carcinoma (ccRCC) has not yet been fully determined. The current study aimed to determine the value of lncRNA AGAP2-AS1 in ccRCC based on The Cancer Genome Atlas (TCGA) database. The association between AGAP2-AS1 expression and associated clinical characters were analyzed using the Wilcoxon signed-rank test and logistic regression. The diagnostic value of AGAP2-AS1 expression in ccRCC tissue was assessed using receiver operating characteristic (ROC) curve analysis. Clinicopathological characteristics associated with overall survival in patients with TCGA were analyzed using Cox regression and the Kaplan-Meier method. Gene set enrichment analysis (GSEA) was also performed to assess the biological function of AGAP2-AS1. The results demonstrated that increased expression of AGAP2-AS1 in ccRCC was significantly associated with male, T3/T4, lymph node metastasis, distant metastasis and high tumor stage (III/IV; all, P<0.05). The area under the ROC curve (normal vs. all tumors) was revealed to be 0.891. Kaplan-Meier survival analysis indicated that ccRCC with high lncRNA AGAP2-AS1 exhibited a worse prognosis compared with low AGAP2-AS1 (P<0.001). The univariate analysis revealed that high expression of AGAP2-AS1 was significantly associated with poor overall survival [hazard ratio (HR). 1.85; 95% confidence interval (CI), 1.48-2.33; P<0.001). Multivariate analysis revealed that AGAP2-AS1 remained independently associated with overall survival, with a HR of 1.57 (CI, 1.21-2.03; P<0.01). GSEA outcome demonstrated that stromal stimulation, angiogenesis, epithelial to mesenchymal transition, basal cell carcinoma, ECM receptor interaction and the Notch signaling pathway were differentially enriched in the AGAP2-AS1 high expression phenotype. Therefore, the high expression of AGAP2-AS1 may be an independent predictor of poor survival in patients with ccRCC.

MicroRNA-1298-3p inhibits proliferation and invasion of glioma cells by downregulating Nidogen-1

Glioma is the most prevalent tumor of the central nervous system. To identify differentially expressed miRNAs (DEMs) in gliomas of different grades, bioinformatics analysis was performed. The DEMs between low-grade gliomas (LGGs) and high-grade gliomas (HGGs) were identified by screening the Gene Expression Omnibus and The Cancer Genome Atlas databases using the LIMMA package. Six overlapping DEMs were identified by comparing LGGs and HGGs. Downregulation of miR-1298-3p correlated with poor overall survival rates in glioma patients. Overexpression of miR-1298-3p induced apoptosis of glioma cells and inhibited glioma cell proliferation, migration, and invasion. The basement membrane protein Nidogen-1 (NID1) was identified as a direct binding target of miR-1298-3p in glioma cells. MiR-1298-3p agonist downregulated the NID1 and vimentin levels, but upregulated the level of E-cadherin in glioma cells. Importantly, overexpression of miR-1298-3p induced apoptosis and reduced tumor growth in a mouse xenograft model of glioma. Our results show that miR-1298-3p functions as a tumor suppressor in glioma cells, and suggest that it might serve as a potential biomarker and therapeutic target in glioma patients.

A Practical Guide to the Automated Analysis of Vascular Growth, Maturation and Injury in the Brain

The distinct organization of the brain's vasculature ensures the adequate delivery of oxygen and nutrients during development and adulthood. Acute and chronic pathological changes of the vascular system have been implicated in many neurological disorders including stroke and dementia. Here, we describe a fast, automated method that allows the highly reproducible, quantitative assessment of distinct vascular parameters and their changes based on the open source software Fiji (ImageJ). In particular, we developed a practical guide to reliably measure aspects of growth, repair and maturation of the brain's vasculature during development and neurovascular disease in mice and humans. The script can be used to assess the effects of different external factors including pharmacological treatments or disease states. Moreover, the procedure is expandable to blood vessels of other organs and vascular in vitro models.

Chronic Hypoxia-Induced Microvessel Proliferation and Basal Membrane Degradation in the Bone Marrow of Rats Regulated through the IL-6/JAK2/STAT3/MMP-9 Pathway

Chronic hypoxia (CH) is characterized by long-term hypoxia that is associated with microvessel proliferation and basal membrane (BM) degradation in tissues. The IL-6/JAK2/STAT3/MMP-9 pathway has been described in a variety of human cancers and plays an essential role in microvessel proliferation and BM degradation. Therefore, this study investigated the role of the IL-6/JAK2/STAT3/MMP-9 pathway in hypoxia-mediated microvessel proliferation and BM degradation in the rat bone marrow. Eighty pathogen-free Sprague Dawley male rats were randomly divided into four groups (20 per group)—control group, CH group (exposed to hypoxia in a hypobaric chamber at a simulated altitude of 5000 m for 28 d), CH + STAT3 inhibitor group (7.5 mg/kg/d), and CH + DMSO group. Microvessel density (MVD) and BM degradation in the bone marrow were determined by immunofluorescence staining and transmission electron microscopy. Serum IL-6 levels were assessed by enzyme-linked immunosorbent assay (ELISA), and the levels of P-JAK2, P-STAT3, and MMP-9 were assessed by western blot analysis and real-time reverse transcription PCR (RT-PCR). Hypoxia increased serum IL-6 levels, which in turn increased JAK2 and STAT3 phosphorylation, which subsequently upregulated MMP-9. Overexpression of MMP-9 significantly promoted the elevation of MVD and BM degradation. Inhibition of STAT3 using an inhibitor, SH-4-54, significantly downregulated MMP-9 expression and decreased MVD and BM degradation. Surprisingly, STAT3 inhibition also decreased serum IL-6 levels and JAK2 phosphorylation. Our results suggest that the IL-6/JAK2/STAT3/MMP-9 pathway might be related to CH-induced microvessel proliferation and BM degradation in the bone marrow.