LncRNA FOXD1-AS1 acts as a potential oncogenic biomarker in glioma

Feature gene selection and functional validation of SH3KBP1 in infantile hemangioma using machine learning

BACKGROUND

Infantile hemangioma (IH) is a prevalent vascular tumor in infancy with a complex pathogenesis that remains unclear. This study aimed to investigate the underlying mechanisms of IH using comprehensive bioinformatics analyses and in vitro experiments.

METHODS

Using GSE127487, we identified differentially expressed genes (DEGs) in IH patients across three age groups (6, 12, and 24 months). GO and KEGG enrichment analyses were performed to identify biological processes and pathways. Immune cell infiltration, transcription factor target genes, miRNA expression, and metabolic pathways were analyzed. WGCNA classified IH patients into clusters, and machine learning algorithms identified key genes. The role of SH3KBP1, the most abundantly expressed gene in the skin, was investigated using shRNA knockdown and functional assays.

RESULTS

Gene expression in IH patients exhibited dynamic changes with age. Cellular processes and signaling pathways were consistent in the early proliferative phase, with gradual resolution in the late phase. Immune infiltration analysis revealed reduced immune cells in patients, while Pericytes were increased. NR5A1 was downregulated, while ZNF112, HSF4, and multiple miRNAs were upregulated with age. Metabolic pathways confirmed differences between proliferative and involution phases. WGCNA identified two clusters: Cluster 1 (angiogenesis and signal transduction) and Cluster 2 (metabolic and synthetic processes). Key genes, including SH3KBP1, were identified using machine learning algorithms. In vitro experiments demonstrated SH3KBP1's crucial role in cell migration and invasion.

CONCLUSION

This study unravels the gene expression and regulatory mechanisms of IH at different stages, providing new insights into its pathophysiology. SH3KBP1 offers a potential biomarker for future diagnostic and therapeutic strategies.

Shedding light on function of long non-coding RNAs (lncRNAs) in glioblastoma

The brain tumors and especially glioblastoma, are affecting life of many people worldwide and due to their high mortality and morbidity, their treatment is of importance and has gained attention in recent years. The abnormal expression of genes is commonly observed in GBM and long non-coding RNAs (lncRNAs) have demonstrated dysregulation in this tumor. LncRNAs have length more than 200 nucleotides and they have been located in cytoplasm and nucleus. The current review focuses on the role of lncRNAs in GBM. There two types of lncRNAs in GBM including tumor-promoting and tumor-suppressor lncRNAs and overexpression of oncogenic lncRNAs increases progression of GBM. LncRNAs can regulate proliferation, cell cycle arrest and metastasis of GBM cells. Wnt, STAT3 and EZH2 are among the molecular pathways affected by lncRNAs in GBM and for regulating metastasis of GBM cells, these RNA molecules mainly affect EMT mechanism. LncRNAs are involved in drug resistance and can induce resistance of GBM cells to temozolomide chemotherapy. Furthermore, lncRNAs stimulate radio-resistance in GBM cells. LncRNAs increase PD-1 expression to mediate immune evasion. LncRNAs can be considered as diagnostic and prognostic tools in GBM and researchers have developed signature from lncRNAs in GBM.

Techniques for investigating lncRNA transcript functions in neurodevelopment

Long noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are transcribed from a large portion of the mammalian genome. While hypothesized to have a variety of biological roles, many lncRNAs remain largely functionally uncharacterized due to unique challenges associated with their investigation. For example, some lncRNAs overlap with other genomic loci, are expressed in a cell-type-specific manner, and/or are differentially processed at the post-transcriptional level. The mammalian CNS contains a vast diversity of lncRNAs, and lncRNAs are highly abundant in the mammalian brain. However, interrogating lncRNA function in models of the CNS, particularly in vivo, can be complex and challenging. Here we review the breadth of methods used to investigate lncRNAs in the CNS, their merits, and the understanding they can provide with respect to neurodevelopment and pathophysiology. We discuss remaining challenges in the field and provide recommendations to assay lncRNAs based on current methods.

Expression of lncRNAs in glioma: A lighthouse for patients with glioma

Glioma is the most common malignant tumour in the central nervous system, accounting for approximately 30 % of the primary tumours of this system. The World Health Organization grades for glioma include: Grade I (pilocytic astrocytoma), Grade II (astrocytoma, oligodastoma, etc.), Grade III (anaplastic astrocytoma, anaplastic oligodastoma, etc.) and Grade IV (glioblastoma). With grade increases, the proliferation, invasion and other malignant biological properties of the glioma are enhanced, and the treatment results are less satisfactory. The overall survival of patients with glioblastoma is less than 15 months. Recent research has focused on the roles of long non-coding RNAs, previously regarded as "transcriptional noise", in diseases, leading to a new understanding of these roles. Therefore, we conducted this review to explore the progress of research regarding the expression and mechanism of long non-coding RNAs in glioma.

A novel immunogenic cell death-related gene risk signature can identify biomarkers of gliomas and predict the immunotherapeutic response

Immunogenic cell death (ICD) is a type of cell death that plays a pivotal role in immunity. Recent studies have identified the critical role of ICD in glioma treatment. This study aimed to use ICD-associated differentially expressed genes (ICD-DEGs) to predict survival of glioma patients. We investigated the relationship between clinical prognosis and the date-to-clinical prognosis of 1,721 glioma patients by examining the expression, methylation, and mutation status of ICD-related genes (IRGs) in these patients. Our prediction of survival in glioma patients was based on three risk genes, and we explored the association between these genes and clinical outcomes. Additionally, IRG expression was used to stratify glioma patients. We further examined the relationship among the three subgroups in terms of immune microenvironment heterogeneity and immunotherapy response. In addition, this study also included analyses of histograms and sensitivity to antitumor drugs. The expression of these genes was externally validated by RT-qPCR, Western blot (WB), and immunohistochemistry (IHC) in glioma and normal brain tissue. Our findings reveal that most IRGs are overexpressed in glioma tumor tissues, and this high expression was confirmed through histological validation. We successfully developed predictive models for three prognostic genes associated with ICD. These models not only predict survival in glioma but also correlate with the tumor's immune microenvironment. Finally, using consensus clustering, we identified three ICD-associated subtypes. Notably, patients with the C3 subtype showed high levels of immune cell infiltration, whereas those with the C1 subtype exhibited lower levels of immune cell infiltration. We successfully developed an innovative IRG-based systematic approach for evaluating glioma patients. This stratification in experimental studies opens new avenues for prognosis and assessing immunotherapy responses in glioma patients. Our study demonstrates the effectiveness of this approach in treating glioma, potentially paving the way for more promising and effective therapeutic strategies in the future.

LMNB1 targets FOXD1 to promote progression of prostate cancer

Forkhead box D1 (FOXD1) expression is upregulated in various types of human cancer. To the best of our knowledge, the roles of FOXD1 in prostate cancer (PC) remain largely unknown. The Cancer Genome Atlas dataset was used for the bioinformatics analysis of FOXD1 in PC. FOXD1 expression levels in normal immortalized human prostate epithelial cells (RWPE-1) and prostate cancer cells were detected by reverse transcription-quantitative PCR. PC cell viability was detected using Cell Counting Kit-8 assay. Transwell assays were performed to assess the migration and invasion of PC cells. Luciferase reporter gene assay was used to validate the association between FOXD1 and lamin (LMN)B1. LMNB1 is an important part of the cytoskeleton, which serves an important role in the process of tumor occurrence and development, regulating apoptosis and DNA repair. FOXD1 expression was upregulated in PC tissues, with its high expression being associated with clinical stage and survival in PC. Knockdown of FOXD1 inhibited viability, migration and invasion of PC cells. FOXD1 positively regulated LMNB1 expression. The effect of FOXD1 knockdown on PC cells was reversed by LMNB1 overexpression. In conclusion, FOXD1, positively regulated by LMNB1, served as an oncogene in PC and may be a potential biomarker and treatment target for PC.

Dissecting multifunctional roles of forkhead box transcription factor D1 in cancers

As a member of the forkhead box (FOX) family of transcription factors (TF), FOXD1 has recently been implicated as a crucial regulator in a variety of human cancers. Accumulating evidence has established dysregulated and aberrant FOXD1 signaling as a prominent feature in cancer development and progression. However, there is a lack of systematic review on this topic. Here, we summarized the present understanding of FOXD1 functions in cancer biology and reviewed the downstream targets and upstream regulatory mechanisms of FOXD1 as well as the related signaling pathways within the context of current reports. We highlighted the functional features of FOXD1 in cancers to identify the future research consideration of this multifunctional transcription factor and potential therapeutic strategies targeting its oncogenic activity.

Identification of MIR600HG/hsa-miR-342-3p/ANLN network as a potential prognosis biomarker associated with lmmune infiltrates in pancreatic cancer

Pancreatic cancer is one of the tumors with the worst prognosis, causing serious harm to human health. The RNA network and immune response play an important role in tumor progression. While a systematic RNA network linked to the tumor immune response remains to be further explored in pancreatic cancer. Based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, the MIR600HG/hsa-miR-342-3p/ANLN network was determined. WB and IHC were used to confirm the high expression of ANLN in pancreatic cancer. The prognostic model based on the RNA network could effectively predict the survival prognosis of patients. The analysis of immune infiltration showed that the MIR600HG/hsa-miR-342-3p/ANLN network altered the level of infiltration of T helper 2 (Th2) and effector memory T (Tem) cells. Furthermore, we found that the chemokines chemokine ligand (CCL) 5 and CCL14 may play a key role in immune cell infiltration mediated by the RNA network. In conclusion, this study constructed a prognostic model based on the MIR600HG/hsa-miR-342-3p/ANLN network and found that it may function in tumor immunity.

FOXD1-AS1 upregulates FOXD1 to promote oral squamous cell carcinoma progression

OBJECTIVES

Recently, increasing attention has been concentrated on decrypting the potential of long non-coding RNAs (lncRNAs) in influencing the progression of human tumors, oral squamous cell carcinoma (OSCC) included. The role of a novel lncRNA, forkhead box D1 antisense RNA 1 (FOXD1-AS1), has been discussed in multiple cancers. Nevertheless, its function and relevant mechanism in OSCC have been not probed yet.

MATERIALS AND METHODS

FOXD1-AS1 expression was detected via RT-qPCR. Colony formation, EdU, transwell and Western blot analyses tested the functional role of FOXD1-AS1 in OSCC cells. The relationship between RNAs was assessed by a series of mechanical assays.

RESULTS

FOXD1-AS1 was expressed at a high level in head and neck squamous cell carcinoma (HNSC). Knockdown of FOXD1-AS1 exerted repressive impacts on OSCC cell proliferation, migration, invasion, and EMT. Moreover, FOXD1-AS1 positively regulated its nearby gene FOXD1 via interacting with miR-369-3p. In addition, adenosine deaminase RNA specific (ADAR), known as a RNA-binding protein (RBP), was capable to bind with FOXD1-AS1 and FOXD1 simultaneously, and could regulate the stability of FOXD1 mRNA. Aside from that, rescue assays delineated that FOXD1-AS1 promoted OSCC progression via upregulating FOXD1.

CONCLUSIONS

FOXD1-AS1 elevates FOXD1 expression to promote OSCC malignant phenotypes through miR-369-3p and ADAR.

LncRNA LINC01018/miR-942-5p/KNG1 axis regulates the malignant development of glioma in vitro and in vivo

AIMS

Since the inhibitory effect of KNG1 on glioma has been proved, this study further explores the regulation of the lncRNA/miRNA axis on KNG1 in glioma.

METHODS

The miRNAs that target KNG1 and the lncRNA that targets miR-942-5p were predicted by bioinformatics analysis and verified by experiments. The correlations between miR-942-5p and the survival of patients and between KNG1 and miR-942-5p were analyzed. After transfection, cell migration, invasion, proliferation, and cell cycle were detected through wound healing, Transwell, colony formation, and flow cytometry assays. A mouse subcutaneous xenotransplanted tumor model was established. The expressions of miR-942-5p, KNG1, LINC01018, and related genes were evaluated by quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR), Western blot, or immunohistochemistry.

RESULTS

MiR-942-5p targeted KNG1, and LINC01018 sponged miR-942-5p. The high survival rate of patients was related to low miR-942-5p level. MiR-942-5p was highly expressed, whereas KNG1 was lowly expressed in glioma. MiR-942-5p was negatively correlated with KNG1. Silent LINC01018 or KNG1 and miR-942-5p mimic enhanced the migration, invasion, and proliferation of glioma cells, and regulated the expressions of metastasis-related and proliferation-related genes. LINC01018 knockdown and miR-942-5p mimic promoted glioma tumor growth in mice. The levels of miR-942-5p and KNG1 were decreased by LINC01018 knockdown, and LINC01018 expression was suppressed by miR-942-5p mimic. MiR-942-5p inhibitor, KNG1, and LINC01018 had the opposite effect to miR-942-5p mimic.

CONCLUSION

LINC01018/miR-942-5p/KNG1 pathway regulates the development of glioma cells in vitro and in vivo.

SLC11A1 as a stratification indicator for immunotherapy or chemotherapy in patients with glioma

Background

Glioma is a fatal tumor originating from the brain, which accounts for most intracranial malignancies. Currently, Immunotherapy has turned into a novel and promising treatment in glioma patients. however, there are still few effective biomarkers to mirror the reaction to immunotherapy in patients with glioma. Therefore, we intended to elucidate the evaluable efficacy of SLC11A1 in glioma patients.

Methods

In this study, samples from Shanghai General Hospital and data from TCGA, GEO, CGGA datasets were used to investigate and validate the relationship between SLC11A1 and the progression of glioma. We evaluated the predictive value of SLC11A1 on the prognosis of glioma with cox regression analysis. Then the relationship between immune infiltration and SLC11A1 was also analyzed. Ultimately, we performed the prediction on the immunotherapeutic response and therapeutic drugs according to the expression of SLC11A1.

Results

Expression of SLC11A1 increased with progression and predicted unfavorable prognosis for glioma patients. The hazard ratio for SLC11A1 expression was 2.33 with 95% CI (1.92-2.58) (P < 0.001) in cox analysis. And based on expression, we found SLC11A1 stratified glioma patients into subgroups with different immune activation statuses. Moreover, we observed that patients with higher SLC11A1 levels companied with better immunotherapeutic response, while those with lower SLC11A1 levels may respond better to temozolomide.

Conclusion

This study provided evidence that SLC11A1 was a novel prognostic marker and immunotherapy response indicator for gliomas. In some cases, SLC11A1 could be an effective marker for identifying patients who might benefit from immunotherapy or chemotherapy.

Latest updates on cellular and molecular biomarkers of gliomas

Gliomas are the most common central nervous system malignancies, compromising almost 80% of all brain tumors and is associated with significant mortality. The classification of gliomas has shifted from basic histological perspective to one that is based on molecular biomarkers. Treatment of this type of tumors consists currently of surgery, chemotherapy and radiation therapy. During the past years, there was a limited development of effective glioma diagnostics and therapeutics due to multiple factors including the presence of blood-brain barrier and the heterogeneity of this type of tumors. Currently, it is necessary to highlight the advantage of molecular diagnosis of gliomas to develop patient targeted therapies based on multiple oncogenic pathway. In this review, we will evaluate the development of cellular and molecular biomarkers for the diagnosis of gliomas and the impact of these diagnostic tools for better tailored and targeted therapies.

Transcriptional Factor Forkhead Box D1 Upregulates Sirtuin3 by Activating the Wnt/β-Catenin Pathway to Alleviate HTR-8/Svneo Trophoblast Cell Dysfunction in Preeclampsia

The proliferation, invasion, migration and apoptosis of trophoblast cells in preeclampsia are closely related to the occurrence and development of preeclampsia. Transcription factors forkhead box D1 and Sirtuin3 are abnormally expressed in preeclampsia, and Sirtuin3 plays a regulatory role in cell proliferation, invasion and apoptosis in related diseases. However, the studies on forkhead box D1 and Sirtuin3 in preeclampsia and their specific mechanisms have not been reported so far. In this study, the expression of Sirtuin3 in Human chorionic trophoblast cells HTR-8/Svneo was inhibited by cell transfection, and then the effects of Sirtuin3 expression in interfering cells on cell invasion, migration and apoptosis were detected by MTT, TUNEL, Western blot, wound healing and Transwell techniques. Subsequently, the binding between forkhead box D1 and Sirtuin3 was predicted by JASPAR website and verified by luciferase assay and ChIP assay. Finally, cell invasion, migration and apoptosis were detected after overexpression of forkhead box D1 and interference with Sirtuin3, and the Wnt/β-catenin signaling pathway was detected to explore the mechanism. We found that interfering with Sirtuin3 induced apoptosis of HTR-8/Svneo cells and inhibited cell invasion and migration. Forkhead box D1 transcriptional activation of Sirtuin3 alleviated HTR-8/SVneo cell dysfunction through activation of the Wnt/β-catenin signaling pathway. Overall, transcriptional factor forkhead box D1 can upregulate Sirtuin3 by activating the Wnt/β-catenin pathway to alleviate HTR-8/Svneo trophoblast cell dysfunction in preeclampsia.

Evolving Insights Into the Biological Function and Clinical Significance of Long Noncoding RNA in Glioblastoma

Glioblastoma (GBM) is one of the most prevalent and aggressive cancers worldwide. The overall survival period of GBM patients is only 15 months even with standard combination therapy. The absence of validated biomarkers for early diagnosis mainly accounts for worse clinical outcomes of GBM patients. Thus, there is an urgent requirement to characterize more biomarkers for the early diagnosis of GBM patients. In addition, the detailed molecular basis during GBM pathogenesis and oncogenesis is not fully understood, highlighting that it is of great significance to elucidate the molecular mechanisms of GBM initiation and development. Recently, accumulated pieces of evidence have revealed the central roles of long noncoding RNAs (lncRNAs) in the tumorigenesis and progression of GBM by binding with DNA, RNA, or protein. Targeting those oncogenic lncRNAs in GBM may be promising to develop more effective therapeutics. Furthermore, a better understanding of the biological function and underlying molecular basis of dysregulated lncRNAs in GBM initiation and development will offer new insights into GBM early diagnosis and develop novel treatments for GBM patients. Herein, this review builds on previous studies to summarize the dysregulated lncRNAs in GBM and their unique biological functions during GBM tumorigenesis and progression. In addition, new insights and challenges of lncRNA-based diagnostic and therapeutic potentials for GBM patients were also introduced.

GDF15 expression in glioma is associated with malignant progression, immune microenvironment, and serves as a prognostic factor

Aims

Growth differentiation factor 15 (GDF15) is involved in lots of crucial inflammatory and immune response. The clinical and immune features for GDF15 in glioma have not been specifically investigated so far.

Methods

Gene expression profiles obtained from public glioma datasets were used to explore the biological function of GDF15 and its impact on immune microenvironment. Interference with GDF15 in several glioma cell lines to verify its functions in vitro. Survival data were used for the survival analysis and establishment of a nomogram predictive model.

Results

GDF15 was up‐regulated in various malignant phenotypes of glioma. Function analysis and in vitro experiments revealed that GDF15 was associated with malignant progression and NF‐κB pathway. GDF15 was closely correlated to inflammatory response, infiltrating immune cells, and immune checkpoint molecules, especially in lower grade glioma (LGG). High expression level of GDF15 predicted poor survival in LGG, while the effect on glioblastoma (GBM) was not significant. A nomogram predictive model combining GDF15 and other prognostic factors was constructed and showed ideal predictive performance.

Conclusions

GDF15 could serve as an interesting prognostic biomarker for LGG. Regulating the expression of GDF15 may help solve the dilemma of immunotherapy in glioma.

FOXD1-AS1 promotes malignant behaviours of prostate cancer cells via the miR-3167/YWHAZ axis

Herein, the effect of long noncoding RNA forkhead box D1 antisense RNA 1 (FOXD1-AS1) on malignant phenotypes of prostate cancer (PCa) cells was investigated. FOXD1-AS1 presented high expression in PCa cells according to the results of RT-qPCR. As shown by cell counting kit-8 assays, colony formation assays, wound-healing assays, Transwell assays and flow cytometry analyses, silenced FOXD1-AS1 suppressed PCa cell viability, proliferation, migration and invasion and enhanced cell apoptosis. Additionally, FOXD1-AS1 was primarily localised in cytoplasm of PCa cells. RNA immunoprecipitation assays and luciferase reporter assays revealed that FOXD1-AS1 interacted with miR-3167 in PCa cells. MiR-3167 functioned as an anti-oncogene in PCa and miR-3167 overexpression suppressed cell proliferation while promoted cell apoptosis. Moreover, the downstream target of miR-3167 is mRNA YWHAZ. FOXD1-AS1 elevated the expression of YWHAZ by binding with miR-3167. The suppressive effect of miR-3167 on YWHAZ expression was reversed by FOXD1-AS1 overexpression. Furthermore, overexpressed YWHAZ reversed the suppressive effect of FOXD1-AS1 deficiency on malignant behaviours of PCa cells. Overall, FOXD1-AS1 facilitates malignant phenotypes of PCa cells by up-regulating YWHAZ via miR-3167. The study first reveals the molecular mechanism of FOXD1-AS1 in PCa, suggesting that FOXD1-AS1 and its downstream molecules might be prognostic biomarkers before medical treatment.

Aberrant hypermethylation induced downregulation of antisense lncRNA STXBP5-AS1 and its sense gene STXBP5 correlate with tumorigenesis of glioma

AIMS

The expression of antisense lncRNA STXBP5-AS1 and its sense gene STXBP5 were found to be downregulated in glioma by RNA sequencing; however, the function and mechanism of both two genes in the development of glioma have not been studied.

MATERIALS AND METHODS

QRT-PCR and western blot were used to determine the transcriptional and translational levels of moleculars. MSP and BSP assays were used to evaluate the methylation status of promoter CpG island. MTT, EdU, flow cytometry, and transwell assays were used to reveal biological effects. The in vivo mice model was used to validate the role of target genes in tumorigenesis.

KEY FINDINGS

The mRNA and protein expression of STXBP5 was significantly downregulated in glioma tissues and positively correlated with prognosis. STXBP5-AS1 was downregulated in glioma cells and tissues, and associated with tumor size and clinical stages. Both of two genes were significantly restored in cells treatment with 5-Aza. The promoter CpG island of STXBP5/STXBP5-AS1 was hypermethylated in glioma cells, but partially methylated in NHA cells. We found that promoter methylation frequency was significantly higher in glioma tissues. Functionally, overexpression of STXBP5 and STXBP5-AS1 inhibited cell proliferation, migration, and invasion and promoted apoptosis in vitro, whereas depletion of STXBP5 and STXBP5-AS1 showed opposite effects. Both the mRNA and protein expression of STXBP5 were positively regulated by STXBP5-AS1. Ectopic expression of STXBP5 and STXBP5-AS1 suppressed tumor formation in vivo.

SIGNIFICANCE

Our findings suggested that epigenetically silenced STXBP5-AS1 and STXBP5 might act as novel tumor suppressors of glioma.

Long Noncoding RNA AATBC Promotes the Proliferation and Migration of Prostate Cancer Cell Through miR-1245b-5p/CASK Axis

Introduction

Long noncoding RNAs (lncRANs) as suppressive or oncogenic genes have been substantiated in prostate cancer (PCa). In the current study, the role and molecular mechanism of lncRNA AATBC in the progression of PCa was evaluated.

Methods

LncRNA AATBC and miR-1245b-5p expression were evaluated using RT-qPCR. CCK-8, colony-formation, apoptosis and transwell assay were used to analyze the in vitro role. The xenograft model was used to explore the in vivo role. Bioinformatics analysis and a dual luciferase assay, RIP and RNA pull down were used to confirm the interaction between lncRNA AATBC and 1245b-5p, as well as 1245b-5p and CASK.

Results

Firstly, we certified that the expression of AATBC was augmented in PCa, and knockdown of AATBC could significantly inhibit the growth of PCa in vitro and in vivo. Mechanistically, our results manifested that AATBC could directly bind to miR-1245b-5p. In addition, miR-1245b-5p played cancer-suppressive role in PCa cells. Moreover, CASK was attested as the target of miR-1245b-5p, and CASK was demonstrated to exert as oncogene in the progression of PCa. Finally, rescue assays illustrated that miR-1245b-5p downregulation or CASK restoration could greatly resist the restrained effects of AATBC knockdown on PCa progression.

Conclusion

AATBC could accelerate the progression of PCa through regulating miR-1245b-5p/CASK axis, which provided a potential therapeutic target for PCa treatment.

Roles of Long Noncoding RNAs in Conferring Glioma Progression and Treatment

Accompanying the development of biomedicine, our knowledge of glioma, one of the most common primary intracranial carcinomas, is becoming more comprehensive. Unfortunately, patients with glioblastoma (GBM) still have a dismal prognosis and a high relapse rate, even with standard combination therapy, namely, surgical resection, postoperative radiotherapy and chemotherapy. The absence of validated biomarkers is responsible for the majority of these poor outcomes, and reliable therapeutic targets are indispensable for improving the prognosis of patients suffering from gliomas. Identification of both precise diagnostic and accurate prognostic markers and promising therapeutic targets has therefore attracted considerable attention from researchers. Encouragingly, accumulating evidence has demonstrated that long noncoding RNAs (lncRNAs) play important roles in the pathogenesis and oncogenesis of various categories of human tumors, including gliomas. Nevertheless, the underlying mechanisms by which lncRNAs regulate diverse biological behaviors of glioma cells, such as proliferation, invasion and migration, remain poorly understood. Consequently, this review builds on previous studies to further summarize the progress in the field of lncRNA regulation of gliomas over recent years and addresses the potential of lncRNAs as diagnostic and prognostic markers and therapeutic targets.

Ferroptosis-related gene signature predicts prognosis and immunotherapy in glioma

Aims

Glioma is a highly invasive brain tumor, which makes prognosis challenging and renders patients resistant to various treatments. Induction of cell death is promising in cancer therapy. Ferroptosis, a recently discovered regulated cell death, can be induced for killing glioma cells. However, the prognostic prediction of ferroptosis‐related genes (FRGs) in glioma remains elusive.

Methods

The mRNA expression profiles and gene variation and corresponding clinical data of glioma patients and NON‐TUMOR control were downloaded from public databases. Risk score based on a FRGs signature was constructed in REMBRANDT cohort and validated in other datasets including CGGA‐693, CGGA‐325, and TCGA.

Results

Our results demonstrated that the majority of FRGs was differentially expressed among GBM, LGG, and NON‐TUMOR groups (96.6%). Furthermore, the glioma patients with low‐risk score exhibited a more satisfactory clinical outcome. The better prognosis was also validated in the glioma patients with low‐risk score no matter to which grade they were affiliated. Functional analysis revealed that the high‐risk score group was positively correlated with the enrichment scores for immune checkpoint blockade‐related positive signatures, indicating the critical role of glioma immunotherapy via risk score.

Conclusion

A novel FRGs‐related risk score can predict prognosis and immunotherapy in glioma patients.

The role of M6A modification in the regulation of tumor-related lncRNAs

N⁶-methyladenosine (m⁶A) is the most abundant modification in eukaryotic cells, and it regulates RNA transcription, processing, splicing, degradation, and translation. Long non-coding RNAs (lncRNAs), as transcriptional products with no or limited protein coding ability more than 200 nt in length, play an important role in epigenetic modification, mRNA transcription, splicing, stability, translation, and other biological functions. Extensive studies have shown that both m⁶A modification and lncRNAs are involved in the pathogenesis of various diseases, such as kinds of cancers, heart failure, Alzheimer’s disease, periodontitis, human abdominal aortic aneurysm, and obesity. To date, m⁶A modification has been identified as an important biological function in enrichment and regulation of lncRNAs. In this review, we summarize the role of m⁶A modification in the regulation and function of tumor-related lncRNAs. Moreover, we discuss the potential applications and possible future directions in the field.

The Role of LncRNAs in Translation

Long non-coding RNAs (lncRNAs), a group of non-protein coding RNAs with lengths of more than 200 nucleotides, exert their effects by binding to DNA, mRNA, microRNA, and proteins and regulate gene expression at the transcriptional, post-transcriptional, translational, and post-translational levels. Depending on cellular location, lncRNAs are involved in a wide range of cellular functions, including chromatin modification, transcriptional activation, transcriptional interference, scaffolding and regulation of translational machinery. This review highlights recent studies on lncRNAs in the regulation of protein translation by modulating the translational factors (i.e, eIF4E, eIF4G, eIF4A, 4E-BP1, eEF5A) and signaling pathways involved in this process as wells as their potential roles as tumor suppressors or tumor promoters.

FOXD1-AS1 regulates FOXD1 translation and promotes gastric cancer progression and chemoresistance by activating the PI3K/AKT/mTOR pathway

Gastric cancer (GC) is a common gastrointestinal cancer with a high global mortality. Recent reports have suggested that long noncoding RNA (lncRNA) are implicated in multiple aspects of GC, including pathogenesis, progression, and therapeutic response. Herein, we investigated the function of FOXD1-AS1 in GC progression and chemoresistance. Expression of FOXD1-AS1 was low in normal stomach tissues but was upregulated in GC cell lines. Silencing of FOXD1-AS1 impaired GC cell proliferation and motility in vitro, and repressed tumor growth and metastasis in vivo. Importantly, FOXD1-AS1 upregulation increased the resistance of GC cells to cisplatin. Moreover, we found that FOXD1-AS1 promoted FOXD1 protein translation through the eIF4G-eIF4E-eIF4A translational complex. We also demonstrated that FOXD1-AS1 released eIF4E from phosphorylated 4E-BP1 and thereby strengthened the interaction of eIF4E with eIF4G by activating the PI3K/AKT/mTOR pathway. Activation of the PI3K/AKT/mTOR pathway was due to the post-transcriptional upregulation of PIK3CA, in turn induced by FOXD1-AS1-mediated sequestering of microRNA (miR)-466. Furthermore, we verified that FOXD1-AS1 facilitated GC progression and cisplatin resistance in a FOXD1-dependent manner. In conclusion, FOXD1-AS1 aggravates GC progression and chemoresistance by promoting FOXD1 translation via PIK3CA/PI3K/AKT/mTOR signaling. These findings highlight a novel target for treatment of patients GC, particularly patients with cisplatin resistance.

Long non-coding RNA FOXD1-AS1 promotes the progression and glycolysis of nasopharyngeal carcinoma by sustaining FOXD1 expression

Long non-coding RNAs (lncRNAs) play a vital role in the progression of several cancers, including nasopharyngeal carcinoma (NPC). However, the mechanism of lncRNA involvement in the progression of NPC remains to be elucidated. Hence, we conducted in vivo and in vitro experiments to determine the molecular mechanism of FOXD1-AS1. We found that FOXD1-AS1 was over-expressed in NPC cells and tissues, and was significantly associated with poor survival rate in patients with NPC. We also found that FOXD1-AS1 promotes cellular proliferation, migration, invasion, and glycolysis, and inhibits apoptosis by upregulating the expression of FOXD1. Furthermore, FOXD1 could transcriptionally up-regulate the expression of key glycolytic genes to promote the glycolysis levels of NPC. The identified FOXD1-AS1 may serve as a potential prognostic biomarker and therapeutic target for patients with NPC.

Eukaryotic translation initiation factor 5A in the pathogenesis of cancers

Cancer is the leading cause of death worldwide. The absence of obvious symptoms and insufficiently sensitive biomarkers in early stages of carcinoma limits early diagnosis. Cancer therapy agents and targeted therapy have been used extensively against tissues or organs of specific cancers. However, the intrinsic and/or acquired resistance to the agents or targeted drugs as well as the serious toxic side effects of the drugs would limit their use. Therefore, identifying biomarkers involved in tumorigenesis and progression represents a challenge for cancer diagnosis and therapeutic strategy development. The eukaryotic translation factor 5A (eIF5A), originally identified as an initiation factor, was later shown to promote translation elongation of iterated proline sequences. There are two eIF5A isoforms (eIF5A1 and eIF5A2). eIF5A2 protein consists of 153 residues, and shares 84% amino acid identity with eIF5A1. However, the biological functions of these two isoforms may be significantly different. Recently, it was demonstrated that eIF5Ais widely involved in the pathogenesis of a number of diseases, including cancers. In particular, eIF5A plays an important role in regulating tumor growth, invasion, metastasis and tumor microenvironment. It was also shown to serve as a potential biomarker and target for the diagnosis and treatment of cancers. The present review briefly discusses the latest findings of eIF5A in the pathogenesis of certain malignant cancers and evolving clinical applications.

LncRNA NFIA-AS2 promotes glioma progression through modulating the miR-655-3p/ZFX axis

Long non-coding RNAs (lncRNAs) are closely associated with tumorigenesis of various malignancies, including glioma. However, the roles of most lncRNAs in glioma remain undiscovered. The present study for the first time explored the roles of NFIA-AS2 in glioma. Based on informatic analyses by online database, lncRNA NFIA-AS2 in glioma tissues was overexpressed and further confirmed in glioma tissues and cells by quantitative real-time PCR (qRT-PCR). High expression of NFIA-AS2 was closely correlated with poor prognosis and might be an independent prognostic factor for PFS and OS. Functionally, silenced NFIA-AS2 could remarkably hinder glioma cell proliferation, migration and invasion, and cause the apoptosis. Mechanistic investigation disclosed that NFIA-AS2 interacted with miR-655-3p and inversely connected with miR-655-3p in glioma. Additionally, miR-655-3p was proved to regulate the expression of ZFX. Final rescue assay demonstrated that ZFX overexpression or miR-655-3p downregulation could neutralize the suppressive effects of NFIA-AS2 knockdown on glioma progression. In conclusion, this study firstly reported that NFIA-AS2 could promote the progression of glioma by targeting the miR-665-3p/ZFX axis, which highlighted that NFIA-AS2 could be a novel biomarker and therapeutic target for glioma patients.

Avasimibe inhibits the proliferation, migration and invasion of glioma cells by suppressing linc00339

Glioma is one of the most destructive human tumours. Although standard treatment has improved the prognosis for glioma patients, the survival of glioma patients is still unsatisfactory. Avasimibe, an effective inhibitor of cholesterol acyltransferase 1 (ACAT1), has shown anti-tumour efficacy in many kinds of tumours. However, its role and related mechanism in glioma has not been fully elucidated. In the present study, we show that avasimibe effectively inhibits the proliferation, migration and invasion of glioma cell lines. Through LncRNA microarrays, we found that linc00339 levels were closely related to the anti-tumour effect of avasimibe. With the help of a series of functional assays, we show that avasimibe inhibits the proliferation, migration and invasion of glioma cell lines by suppressing linc00339 in vitro and in vivo. Our findings may provide a new approach for glioma therapy.

LncRNA CCAT2 promotes angiogenesis in glioma through activation of VEGFA signalling by sponging miR-424

Glioma is characterized by high morbidity, high mortality and poor prognosis. Recent studies exhibited that lncRNA CCAT2 is overexpressed in glioma and promotes glioma progression, but the specific molecular biological mechanism remains to be determined. We performed qRT-PCR to evaluate the expression of related genes, Western blotting analysis to measure protein levels, colony formation assay to detect the proliferative ability of glioma cells, flow cytometry to measure cell apoptosis, bioinformatics analysis and dual luciferase assay to verify the binding sites and the targeted regulatory relationship in A172 and U251 cell lines and tube formation assay to determine endothelial angiogenesis. LncRNA CCAT2 and VEGFA were highly expressed, while miR-424 was expressed at low levels in NHA cells. Furthermore, knockdown of lncRNA CCAT2 decreased cell proliferation, increased cell apoptosis and inhibited endothelial angiogenesis in glioma. Moreover, lncRNA CCAT2 shared a complementary sequence with miR-424 which in turn directly bound to the 3'-UTR of VEGFA. Further investigation indicated that lncRNA CCAT2 promoted cell proliferation and endothelial angiogenesis by inducing the PI3K/AKT signalling pathway in glioma. The oncogenic lncRNA CCAT2 is highly associated with the development of glioma and exerts its function by upregulating VEGFA via miR-424.

Long non-coding RNA LEF1-AS1 is involved in the progression of retinoblastoma through regulating the Wnt/β-catenin pathway

The lymphoid enhancer binding factor 1 antisense RNA 1 (LEF1-AS1) has been suggested to function as a tumour-associated lncRNA in several types of human cancers, but there is no study to date about the role of LEF1-AS1 in retinoblastoma. In our study, LEF1-AS1 expression was increased in retinoblastoma tissues and cell lines compared with paired adjacent normal tissues and the retinal pigment epithelial cell line, respectively. Meanwhile, we found that patients with retinoblastoma with IIRC D-E or undifferentiated type had notably higher levels of LEF1-AS1 expression than those with IIRC A-C or differentiated type. High LEF1-AS1 expression predicted poor disease-free survival in patients with retinoblastoma. The in vitro assays suggested that silencing of LEF1-AS1 suppressed retinoblastoma cell proliferation, migration, and invasion through regulating the Wnt/β-catenin pathway. In conclusion, LEF1-AS1 functions as an oncogenic lncRNA in retinoblastoma.

Unveiling ncRNA regulatory axes in atherosclerosis progression

Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non-coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non-coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3'UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non-coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti-ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.

Recent insights into eukaryotic translation initiation factors 5A1 and 5A2 and their roles in human health and disease

The eukaryotic translation initiation factor 5A1 (eIF5A1) and its homolog eIF5A2 are the only two human proteins containing the unique post-translational modification-hypusination, which is essential for the function of these two proteins. eIF5A1 was initially identified as a translation initiation factor by promoting the first peptide bond formation of protein during translation; however, recent results suggest that eIF5A1 also functions as a translation elongation factor. It has been shown that eIF5A1 is implicated in certain human diseases, including diabetes, several human cancer types, viral infections and diseases of neural system. Meanwhile, eIF5A2 is overexpressed in many cancers, and plays an important role in the development and progression of cancers. As multiple roles of these two factors were observed among these studies, therefore, it remains unclear whether they act as oncogene or tumor suppressor. In this review, the recent literature of eIF5As and their roles in human diseases, especially in human cancers, will be discussed.

LncRNA FOXD1-AS1 acts as a potential oncogenic biomarker in glioma

AIMS

Altered activities of long noncoding RNAs (lncRNAs) have been associated with cancer development, and lncRNA FOXD1-AS1 (FOXD1-AS1) is the antisense transcript of the gene encoding for FOXD1, known for its role as an oncogene in several tumor types including glioma. However, the role of FOXD1-AS1 in the differentiation and progression of glioma is not well known.

METHODS

Expression profile chip and qPCR were used to screen and identify FOXD1-AS1. Glioma cells were transfected with siRNA or eukaryotic expression vector to observe FOXD1-AS1 function in vitro and in vivo. Dual luciferase reporter gene analysis, Western blot, and ChIRP-MS were used to detect microRNAs and protein that combine with FOXD1-AS1.

RESULTS

FOXD1-AS1 was upregulated and directly correlated with the glioma grade, and it was localized in both the nucleus and the cytoplasm of the glioma cell. FOXD1-AS1 silencing caused tumor suppressive effects via inhibiting cell proliferation, migration, and apoptosis, while FOXD1-AS1 overexpression resulted in opposite effects. Additionally, in vivo experiments showed that FOXD1-AS1 knockdown reduced tumor volume and weight. More importantly, mechanical studies revealed that FOXD1-AS1 targeted both miR339-5p and miR342-3p (miR339/342). Furthermore, protein eukaryotic translation initiation factor 5 subunit A (eIF5a) resulted a direct target of FOXD1-AS1.

CONCLUSIONS

These data indicated that FOXD1-AS1, a miR339/342 target, affected biological processes via protein eIF5a; thus, it might be considered as a new therapeutic target for glioblastoma.