Super-enhancer-associated long noncoding RNA AC005592.2 promotes tumor progression by regulating OLFM4 in colorectal cancer

SE-lncRNAs in Cancer: Classification, Subcellular Localisation, Function and Corresponding TFs

Emerging evidence highlights certain long noncoding RNAs (lncRNAs) transcribed from or interacting with super-enhancer (SE) regulatory elements. These lncRNAs, known as SE-lncRNAs, are strongly linked to cancer and regulate cancer progression through multiple interactions with downstream targets. The expression of SE-lncRNAs is controlled by various transcription factors (TFs), and dysregulation of these TFs can contribute to cancer development. In this review, we discuss the characteristics, classification and subcellular distribution of SE-lncRNAs and summarise the role of key TFs in the transcription and regulation of SE-lncRNAs. Moreover, we examine the distinct functions and potential mechanisms of SE-lncRNAs in cancer progression.

Pathogenic role of super-enhancers as potential therapeutic targets in lung cancer

Lung cancer is still one of the deadliest malignancies today, and most patients with advanced lung cancer pass away from disease progression that is uncontrollable by medications. Super-enhancers (SEs) are large clusters of enhancers in the genome's non-coding sequences that actively trigger transcription. Although SEs have just been identified over the past 10 years, their intricate structure and crucial role in determining cell identity and promoting tumorigenesis and progression are increasingly coming to light. Here, we review the structural composition of SEs, the auto-regulatory circuits, the control mechanisms of downstream genes and pathways, and the characterization of subgroups classified according to SEs in lung cancer. Additionally, we discuss the therapeutic targets, several small-molecule inhibitors, and available treatment options for SEs in lung cancer. Combination therapies have demonstrated considerable advantages in preclinical models, and we anticipate that these drugs will soon enter clinical studies and benefit patients.

Super enhancer lncRNAs: a novel hallmark in cancer

Super enhancers (SEs) consist of clusters of enhancers, harboring an unusually high density of transcription factors, mediator coactivators and epigenetic modifications. SEs play a crucial role in the maintenance of cancer cell identity and promoting oncogenic transcription. Super enhancer lncRNAs (SE-lncRNAs) refer to either transcript from SEs locus or interact with SEs, whose transcriptional activity is highly dependent on SEs. Moreover, these SE-lncRNAs can interact with their associated enhancer regions in cis and modulate the expression of oncogenes or key signal pathways in cancers. Inhibition of SEs would be a promising therapy for cancer. In this review, we summarize the research of SE-lncRNAs in different kinds of cancers so far and decode the mechanism of SE-lncRNAs in carcinogenesis to provide novel ideas for the cancer therapy.

Effects of BRD4 inhibitor JQ1 on the expression profile of super-enhancer related lncRNAs and mRNAs in cervical cancer HeLa cells

Objective

To investigate the effects of bromine domain protein 4 (BRD4) inhibitor JQ1 on the expression profile of super-enhancer-related lncRNAs (SE-lncRNAs) and mRNAs in cervical cancer (CC) HeLa-cells.

Methods

The CCK8 method was implemented to detect the inhibitory effect of JQ1 on HeLa cells and explore the best inhibitory concentration. Whole transcriptome sequencing was performed to detect the changes of lncRNAs and mRNAs expression profiles in cells of the JQ1 treatment group and control group, respectively. The differentially expressed SE-lncRNAs were obtained by matching, while the co-expressed mRNAs were obtained by Pearson correlation analysis.

Results

The inhibitory effect of JQ1 on HeLa cell proliferation increased significantly with increasing concentration and treatment time (P < 0.05). Under the experimental conditions of three concentrations of 0.01, 0.1 and 1 μmol/L of JQ1 on HeLa cells at 24, 48, 72 and 120 h, 1 μmol/L of JQ1 at 72 and 120 h had the same cell viability and the strongest cell proliferation inhibition. In order to understand the inhibitory mechanism of JQ1 on HeLa cells, this study analyzed the expression profile differences from the perspective of SE-lncRNAs and mRNAs. A total of 162 SE-lncRNAs were identified, of which 8 SE-lncRNAs were down-regulated and seven SE-lncRNAs were up-regulated. A total of 418 differentially expressed mRNAs related to SE-lncRNAs were identified, of which 395 mRNAs had positive correlation with 12 SE-lncRNAs and 408 mRNAs had negative correlation with 15 SE-lncRNAs.

Conclusion

JQ1 can significantly inhibit the proliferation of HeLa cells and affect the expression profile of SE-lncRNAs and mRNAs.

Integrative analysis of a novel super-enhancer-associated lncRNA prognostic signature and identifying LINC00945 in aggravating glioma progression

BACKGROUND

Super-enhancers (SEs), driving high-level expression of genes with tumor-promoting functions, have been investigated recently. However, the roles of super-enhancer-associated lncRNAs (SE-lncRNAs) in tumors remain undetermined, especially in gliomas. We here established a SE-lncRNAs expression-based prognostic signature to choose the effective treatment of glioma and identify a novel therapeutic target.

METHODS

Combined analysis of RNA sequencing (RNA-seq) data and ChIP sequencing (ChIP-seq) data of glioma patient-derived glioma stem cells (GSCs) screened SE-lncRNAs. Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets served to construct and validate SE-lncRNA prognostic signature. The immune profiles and potential immuno- and chemotherapies response prediction value of the signature were also explored. Moreover, we verified the epigenetic activation mechanism of LINC00945 via the ChIP assay, and its effect on glioma was determined by performing the functional assay and a mouse xenograft model.

RESULTS

6 SE-lncRNAs were obtained and identified three subgroups of glioma patients with different prognostic and clinical features. A risk signature was further constructed and demonstrated to be an independent prognostic factor. The high-risk group exhibited an immunosuppressive microenvironment and was higher enrichment of M2 macrophage, regulatory T cells (Tregs), and Cancer-associated fibroblasts (CAFs). Patients in the high-risk group were better candidates for immunotherapy and chemotherapeutics. The SE of LINC00945 was further verified via ChIP assay. Mechanistically, BRD4 may mediate epigenetic activation of LINC00945. Additionally, overexpression of LINC00945 promoted glioma cell proliferation, EMT, migration, and invasion in vitro and xenograft tumor formation in vivo.

CONCLUSION

Our study constructed the first prognostic SE-lncRNA signature with the ability to optimize the choice of patients receiving immuno- and chemotherapies and provided a potential therapeutic target for glioma.

E2F1 combined with LINC01004 super-enhancer to promote hepatocellular carcinoma cell proliferation and metastasis

INTRODUCTION

Super-enhancer-associated lncRNAs play important roles in the occurrence and development of malignant tumors, including hepatocellular carcinoma (HCC).

OBJECTIVES

The current work aimed to identify and characterize super-enhancer-associated lncRNAs in the pathogenesis of HCC.

METHODS

H3K27ac ChIP-seq data from HepG2 cell line and two HCC tissues were used to identify super-enhancer-associated lncRNAs in HCC. JQ-1 treatment and CRISPR-dCas9 system were performed to confirm super-enhancer activity. Quantitative real-time PCR (qPCR), ChIP-qPCR, and dual-luciferase reporter system assay demonstrated the regulation of E2F1 on super-enhancer. Functional loss experiment was used to identify the function of LINC01004.

RESULTS

In this study, we identified and characterized LINC01004, a novel super-enhancer-associated lncRNA, as a crucial oncogene in HCC. LINC01004 was upregulated in liver cancer tissues and was associated with poor patient prognosis. Moreover, LINC01004 promoted cell proliferation and metastasis of HCC. The binding of E2F1 to the super-enhancer could promote the transcription of LINC01004, while the inhibition of super-enhancer activity decreased LINC01004 expression.

CONCLUSION

This finding might provide mechanistic insights into the molecular mechanisms underlying hepatocarcinogenesis and the biological function of super-enhancer. LINC01004 can serve as a potential therapeutic target for HCC patient.

The Emerging Role of Super-enhancers as Therapeutic Targets in The Digestive System Tumors

Digestive system tumors include malignancies of the stomach, pancreas, colon, rectum, and the esophagus, and are associated with high morbidity and mortality. Aberrant epigenetic modifications play a vital role in the progression of digestive system tumors. The aberrant transcription of key oncogenes is driven by super-enhancers (SEs), which are characterized by large clusters of enhancers with significantly high density of transcription factors, cofactors, and epigenetic modulatory proteins. The SEs consist of critical epigenetic regulatory elements, which modulate the biological characteristics of digestive system tumors including tumor cell identity and differentiation, tumorigenesis, environmental response, immune response, and chemotherapeutic resistance. The core transcription regulatory loop of the digestive system tumors is complex and a high density of transcription regulatory complexes in the SEs and the crosstalk between SEs and the noncoding RNAs. In this review, we summarized the known characteristics and functions of the SEs in the digestive system tumors. Furthermore, we discuss the oncogenic roles and regulatory mechanisms of SEs in the digestive system tumors. We highlight the role of SE-driven genes, enhancer RNAs (eRNAs), lncRNAs, and miRNAs in the digestive system tumor growth and progression. Finally, we discuss clinical significance of the CRISPR-Cas9 gene editing system and inhibitors of SE-related proteins such as BET and CDK7 as potential cancer therapeutics.

Significance of differential expression of OLFM4 in the development of endometrial adenocarcinoma

The incidence of endometrial adenocarcinoma (EA) has increased worldwide in recent years due to the widespread use of estrogen therapy and the overall increase in life expectancy. However, we know of no sensitive molecular index that can be used to predict the onset of EA, evaluate the therapeutic effects of treatment agents, or provide prognostic benefit in post-treatment follow-up. To explore the correlation between human olfactomedin 4 (OLFM4) and the clinicopathologic parameters of EA, and to determine the precise involvement of OLFM4 as a related factor in the occurrence and development of EA. We enrolled 61 gynecologic patients for a retrospective study at the Tai'an Central Hospital of Shandong Province from January 1, 2016, to June 30, 2022. We determined the expression levels of estrogen receptor α (ERα), progesterone receptor (PR), and OLFM4 proteins in endometrial tissue with the immunohistochemical S-P staining method, and analyzed the correlations among ERα, PR, and OLFM4 protein expression levels and with the pathologic stage, histologic grade, myometrial invasiveness, and lymphatic metastasis of EA. The expression levels of OLFM4 in EA were higher than in normal endometrium (P = .036). The expression level of OLFM4 protein in stage II-III patients was higher than that in stage I patients (P = .034), and the expression levels of ERα and PR proteins in EA were lower than those in normal endometrial tissue (P = .014 and P = .0005). While we observed no correlation in endometrial tissues of disparate pathologic types between OLFM4 and the expression levels of ERα and PR proteins, we noted a positive correlation between the expression levels of ERα and PR protein. The expression level of OLFM4 protein increased with the malignant degree of endometrial lesions and OLFM4 protein expression was related to the FIGO stage of EA. And OLFM4 protein can be used as 1 of the potential diagnostic factors for endometrial lesions, which is worthy of further study.

Identification of lncRNAs Associated with the Pathogenesis of Diabetic Retinopathy: From Sequencing Analysis to Validation via In Vivo and In Vitro Experiments

This study is aimed at screening for differentially expressed long noncoding RNAs (lncRNAs) associated with the pathogenesis of diabetic retinopathy and verifying the role of lncZNRD1 in high glucose-induced injury of retinal microvascular endothelial cells. The retinal tissues of normal and diabetic rats were collected for high-throughput sequencing of differentially expressed lncRNAs. Retinal microvascular endothelial cells were treated with 50 mM glucose for 4 h, 8 h, 24 h, 48 h, and 72 h. Our results showed that compared with the control group, there were 736 differentially expressed lncRNAs in the retina tissue of the model group, including 226 upregulated genes and 736 downregulated genes. Based on the differentially expressed lncRNAs, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the ErbB signaling pathway, transforming growth factor- (TGF-) β signaling pathway, PI3K − Akt signaling pathway, cyclic adenosine 3,5-monophosphate (cAMP) signaling pathway, mitogen-activated protein kinase (MAPK) signaling pathway, and hypoxia-inducible factor-1 (HIF-1) signaling pathway were likely involved in the regulation of diabetic retinopathy. Compared with the control group, the expression of lncZNRD1-AS1 was significantly increased in retinal microvascular endothelial cells after treatment with high glucose for 24 h. Silencing lncZNRD1 promoted high glucose-induced apoptosis of microvascular endothelial cells. Additionally, silencing lncZNRD1 increased the expression levels of ALDH7A1 and ALDH3A2. In conclusion, lncZNRD1-AS1 demonstrated potentially beneficial function against high glucose-induced retina cell injury by regulating ALDH7A1 and ALDH3A2 expressions.