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Zhang D, Li L, Li M, Cao X. Biological functions and clinic significance of SAF‑A (Review). Biomed Rep 2024; 20:88. [PMID: 38665420 PMCID: PMC11040223 DOI: 10.3892/br.2024.1776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
As one member of the heterogeneous ribonucleoprotein (hnRNP) family, scaffold attachment factor A (SAF-A) or hnRNP U, is an abundant nuclear protein. With RNA and DNA binding activities, SAF-A has multiple functions. The present review focused on the biological structure and different roles of SAF-A and SAF-A-related diseases. It was found that SAF-A maintains the higher-order chromatin organization via RNA and DNA, and regulates transcription at the initiation and elongation stages. In addition to regulating pre-mRNA splicing, mRNA transportation and stabilization, SAF-A participates in double-strand breaks and mitosis repair. Therefore, the aberrant expression and mutation of SAF-A results in tumors and impaired neurodevelopment. Moreover, SAF-A may play a role in the anti-virus system. In conclusion, due to its essential biological functions, SAF-A may be a valuable clinical prediction factor or therapeutic target. Since the role of SAF-A in tumors and viral infections may be controversial, more animal experiments and clinical assays are needed.
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Affiliation(s)
- Daiquan Zhang
- Department of Traditional Chinese Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Li Li
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Mengni Li
- Department of Pediatrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
| | - Xinmei Cao
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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Patty BJ, Hainer SJ. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589208. [PMID: 38659863 PMCID: PMC11042195 DOI: 10.1101/2024.04.12.589208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and noncoding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
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Affiliation(s)
- Benjamin J. Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA USA
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Wu X, Zhao X, Zhou C, Wei N, Xu Z, Zhang X. Prognostic and onco-immunological value of immune-related eRNAs-driven genes in lung adenocarcinoma. J Cancer Res Clin Oncol 2024; 150:188. [PMID: 38602568 PMCID: PMC11008071 DOI: 10.1007/s00432-024-05687-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 03/05/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND We aimed to comprehensively analyze the clinical value of immune-related eRNAs-driven genes in lung adenocarcinoma (LUAD) and find the potential biomarkers for prognosis and therapeutic response to improve the survival of this malignant disease. MATERIALS AND METHODS Pearson's correlation analysis was performed to identify the immune-related eRNAs-driven genes. Cox regression and least absolute shrinkage and selection operator (LASSO) analyses were used to construct this prognostic risk signature. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to investigate the underlying molecular mechanism. The single sample gene set enrichment analysis (ssGSEA) algorithm was conducted to evaluate the immune status based on the signature. The quantitative real-time PCR (qRT-PCR) analysis was performed to evaluate the expression value of the signature genes between LUAD tissues and adjacent lung tissues. RESULTS Five immune-related eRNAs-driven genes (SHC1, GDF10, CCL14, FYN, and NOD1) were identified to construct a prognostic risk signature with favorable predictive capacity. The patients with high-risk scores based on the signature were significantly associated with the malignant clinical features compared with those with low-risk scores. Kaplan-Meier analysis demonstrated that the sample in the low-risk group had a prolonged survival compared with those in the high-risk group. This risk signature was validated to have a promising predictive capacity and reliability in diverse clinical situations and independent cohorts. The functional enrichment analysis demonstrated that humoral immune response and intestinal immune network for IgA production pathway might be the underlying molecular mechanism related to the signature. The proportion of the vast majority of immune infiltrating cells in the high-risk group was significantly lower than that in the low-risk group, and the immunotherapy response rate in the low-risk group was significantly higher than that in the high-risk group. Moreover, BI-2536, sepantronium bromide, and ULK1 were the potential drugs for the treatment of patients with higher risk scores. Finally, the experiment in vivo and database analysis indicated that CCL14, FYN, NOD1, and GDF10 are the potential LUAD suppressor and SHC1 is a potential treatment target for LUAD. CONCLUSION Above all, we constructed a prognostic risk signature with favorable predictive capacity in LUAD, which was significantly associated with malignant features, immunosuppressive tumor microenvironment, and immunotherapy response and may provide clinical benefit in clinical decisions.
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Affiliation(s)
- Xuan Wu
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Xingru Zhao
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Chao Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Nan Wei
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Zhiwei Xu
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
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Liu Y, Zhao Y, Lin L, Yang Q, Zhang L. Differential Expression of Noncoding RNAs Revealed Enhancer RNA AC016735.2 as a Potential Pathogenic Marker of Congenital Microtia Patients. J Craniofac Surg 2024; 35:00001665-990000000-01401. [PMID: 38456687 PMCID: PMC11045553 DOI: 10.1097/scs.0000000000010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 01/11/2024] [Indexed: 03/09/2024] Open
Abstract
PURPOSE Congenital microtia is a complex maxillofacial malformation with various risk factors. This study aimed to find potential pathogenic noncoding RNAs for congenital microtia patients. METHODS We collected 3 pairs of residual ear cartilage samples and corresponding normal ear cartilage samples from nonsyndromic congenital microtia patients for microarray experiments. The differentially expressed RNAs were screened, and enrichment analysis and correlation expression analysis were performed to elucidate the function of the differentially expressed genes (DEGs). We further investigated the most significantly differentially expressed long noncoding RNA (lncRNA), AC016735.2, through follow-up analyses including RT-qPCR and Western blotting, to validate its differential expression in residual ear cartilage compared with normal ear cartilage. SiRNA was designed to study the regulatory role of AC016735.2, and cell proliferation experiments were conducted to explore its impact on residual ear chondrocytes. RESULTS Analysis of the microarray data revealed a total of 1079 differentially expressed RNAs, including 305 mRNAs and x lncRNAs, using a threshold of FC>1.5 and P<0.05 for mRNA, and FC>1.0 and P<0.05 for lncRNA. Enrichment analysis indicated that these genes are mainly involved in extracellular matrix regulation and embryonic development. AC016735.2 showed the highest differential expression among the eRNAs, being upregulated in residual ear cartilage. It acts in cis to regulate the nearby coding gene ZFP36L2, indirectly affecting downstream genes such as BMP4, TWSG1, COL2A1, and COL9A2. CONCLUSION Significant differences were observed in the expression of lncRNAs and mRNAs between residual ear cartilage and normal auricular cartilage tissues in the same genetic background of congenital microtia. These differentially expressed lncRNAs and mRNAs may play crucial roles in the occurrence and development of microtia through pathways associated with extracellular matrix regulation and gastrulation. Particularly, AC016735.2, an eRNA acting in cis, could serve as a potential pathogenic noncoding gene.
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Affiliation(s)
- Ying Liu
- Ear Reconstruction Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Plastic Surgery Department, Beijing Hospital of Integrated Traditional Chinese and Western Medicine, Beijing, China
| | - Yanyong Zhao
- Ear Reconstruction Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lin Lin
- Ear Reconstruction Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qinghua Yang
- Ear Reconstruction Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Ling Zhang
- Laser Treatment Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Li X, Xu SJ, Jin B, Lu HS, Zhao SK, Ding XF, Xu LL, Li HJ, Liu SC, Chen J, Chen G. Heparanase inhibitor OGT 2115 induces prostate cancer cell apoptosis via the downregulation of MCL‑1. Oncol Lett 2024; 27:83. [PMID: 38249815 PMCID: PMC10797316 DOI: 10.3892/ol.2024.14217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/31/2023] [Indexed: 01/23/2024] Open
Abstract
Heparanase (HPSE), an endo-β-D-glucuronidase, cleaves heparan sulfate and serves an important role in the tumor microenvironment and thus in tumorigenesis. HPSE is known to promote tumor cell evasion of apoptosis. However, the underlying mechanism of this requires further study. In the present study, the results demonstrated that myeloid cell leukemia-1 (MCL-1), an antiapoptotic protein, and HPSE were upregulated in prostate cancer tissues compared with adjacent normal tissues. In addition, the HPSE inhibitor, OGT 2115, inhibited PC-3 and DU-145 prostate cancer cell viability in a dose-dependent manner, with IC50 values of 20.2 and 97.2 µM, respectively. Furthermore, annexin V/PI double-staining assays demonstrated that OGT 2115 induced apoptosis in prostate cancer cells. OGT 2115 treatment markedly decreased MCL-1 protein expression levels, whereas RNA interference-mediated downregulation of MCL-1 and OGT 2115 drug treatment synergistically induced apoptosis in PC-3 and DU-145 cells. In vivo, OGT 2115 40 mg/kg (ig) significantly inhibited PC-3 cell xenograft growth in nude mice and increased the positive TUNEL staining rate of xenograft tissues. It was therefore hypothesized that MCL-1 was an important signaling molecule in OGT 2115-induced apoptosis. The results of the present study also demonstrated that the proteasome inhibitor, MG-132, markedly inhibited the downregulation of MCL-1 protein expression levels induced by OGT 2115. However, the protein synthesis inhibitor, cycloheximide, did not affect the role of OGT 2115 in regulating MCL-1. In summary, the results of the present study demonstrated that the proapoptotic activity of OGT 2115 was achieved by downregulating MCL-1.
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Affiliation(s)
- Xin Li
- Department of Urology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang 318000, P.R. China
| | - Shuai-Jun Xu
- Graduate School of Medicine, Hebei North University, Zhangjiakou, Hebei 075000, P.R. China
| | - Bin Jin
- Graduate School of Medicine, Hebei North University, Zhangjiakou, Hebei 075000, P.R. China
| | - Hong-Sheng Lu
- Department of Pathology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang 318000, P.R. China
| | - Shan-Kun Zhao
- Department of Urology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang 318000, P.R. China
| | - Xiao-Fei Ding
- Department of Pharmacology, Taizhou University, Taizhou, Zhejiang 318000, P.R. China
| | - Ling-Long Xu
- Department of Hematology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang 318000, P.R. China
| | - Hai-Jun Li
- Department of Neurology, Taizhou Second People's Hospital, Taizhou University, Taizhou, Zhejiang 318000, P.R. China
| | - Shuang-Chun Liu
- Laboratory Department, Municipal Hospital Affiliated to Taizhou University, Taizhou, Zhejiang 318000, P.R. China
| | - Jie Chen
- Department of Pharmacology, Taizhou University, Taizhou, Zhejiang 318000, P.R. China
| | - Guang Chen
- Department of Pharmacology, Taizhou University, Taizhou, Zhejiang 318000, P.R. China
- Department of Hematology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang 318000, P.R. China
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Chakkarappan SR, Umadharshini KV, Dhamodharan S, Rose MM, Gopu G, Murugan AK, Inoue I, Munirajan AK. Super enhancer loci of EGFR regulate EGFR variant 8 through enhancer RNA and strongly associate with survival in HNSCCs. Mol Genet Genomics 2024; 299:3. [PMID: 38236481 DOI: 10.1007/s00438-023-02089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/21/2023] [Indexed: 01/19/2024]
Abstract
Epidermal growth factor receptor (EGFR) has been shown to be overexpressed in human cancers due to mutation, amplification, and epigenetic hyperactivity, which leads to deregulated transcriptional mechanism. Among the eight different EGFR isoforms, the mechanism of regulation of full-length variant 1 is well-known, no studies have examined the function & factors regulating the expression of variant 8. This study aimed to understand the function of EGFR super-enhancer loci and its associated transcription factors regulating the expression of EGFR variant 8. Our study shows that overexpression of variant 8 and its transcription was more prevalent than variant 1 in many cancers and positively correlated with the EGFR-AS1 expression in oral cancer and HNSCC. Notably, individuals overexpressing variant 8 showed shorter overall survival and had a greater connection with other clinical traits than patients with overexpression of variant 1. In this study, TCGA enhancer RNA profiling on the constituent enhancer (CE1 and CE2) region revealed that the multiple enhancer RNAs formed from CE2 by employing CE1 as a promoter. Our bioinformatic analysis further supports the enrichment of enhancer RNA specific chromatin marks H3K27ac, H3K4me1, POL2 and H2AZ on CE2. GeneHancer and 3D chromatin capture analysis showed clustered interactions between CE1, CE2 loci and this interaction may regulates expression of both EGFR-eRNA and variant 8. Moreover, increased expression of SNAI2 and its close relationship to EGFR-AS1 and variant 8 suggest that SNAI2 could regulates variant 8 overexpression by building a MegaTrans complex with both EGFR-eRNA and EGFR-AS1. Our findings show that EGFR variant 8 and its transcriptional regulation & chromatin modification by eRNAs may provide a rationale for targeting RNA splicing in combination with targeted EGFR therapies in cancer.
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Affiliation(s)
- Sundaram Reddy Chakkarappan
- Department of Health Research, Multi Disciplinary Research Unit (DHR-MRU), Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | | | - Shankar Dhamodharan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | - Mathew Maria Rose
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | - Govindasamy Gopu
- Department of Surgical Oncology, Rajiv Gandhi Government General Hospital, Madras Medical College, Chennai, 600003, India
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Health Research, Multi Disciplinary Research Unit (DHR-MRU), Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India.
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India.
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Liu D, Wang W, Wu Y, Qiu Y, Zhang L. LINC00887 Acts as an Enhancer RNA to Promote Medullary Thyroid Carcinoma Progression by Binding with FOXQ1. Curr Cancer Drug Targets 2024; 24:519-533. [PMID: 38804344 DOI: 10.2174/0115680096258716231026063704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 05/29/2024]
Abstract
BACKGROUND Medullary thyroid carcinoma (MTC) is a rare but aggressive endocrine malignancy that originates from the parafollicular C cells of the thyroid gland. Enhancer RNAs (eRNAs) are non-coding RNAs transcribed from enhancer regions, which are critical regulators of tumorigenesis. However, the roles and regulatory mechanisms of eRNAs in MTC remain poorly understood. This study aims to identify key eRNAs regulating the malignant phenotype of MTC and to uncover transcription factors involved in the regulation of key eRNAs. METHODS GSE32662 and GSE114068 were used for the identification of differentially expressed genes, eRNAs, enhancers and enhancer-regulated genes in MTC. Metascape and the transcription factor affinity prediction method were used for gene function enrichment and transcription factor prediction, respectively. qRT-PCR was used to detect gene transcription levels. ChIP-qPCR was used to assess the binding of histone H3 lysine 27 acetylation (H3K27ac)-enriched regions to anti- H3K27ac. RIP-qPCR was used to detect the binding between FOXQ1 and LINC00887. CCK8 and Transwell were performed to measure the proliferation and invasion of MTC cells, respectively. Intracellular reactive oxygen species (ROS) levels were quantified using a ROS assay kit. RESULTS Four eRNAs (H1FX-AS1, LINC00887, MCM3AP-AS1 and A1BG-AS1) were screened, among which LINC00887 was the key eRNA promoting the proliferation and invasion of MTC cells. A total of 135 genes controlled by LINC00887-regulated enhancers were identified; among them, BCL2, PRDX1, SFTPD, TPO, GSS, RAD52, ZNF580, and ZFP36L1 were significantly enriched in the "ROS metabolic process" term. As a transcription factor regulating genes enriched in the "ROS metabolic process" term, FOXQ1 could recruit LINC00887. Overexpression of FOXQ1 restored LINC00887 knockdown-induced downregulation of GSS and ZFP36L1 transcription in MTC cells. Additionally, FOXQ1 overexpression counteracted the inhibitory effects of LINC00887 knockdown on the proliferation and invasion of MTC cells and the promotion of intracellular ROS accumulation induced by LINC00887 knockdown. CONCLUSION LINC00887 was identified as a key eRNA promoting the malignant phenotype of MTC cells. The involvement of FOXQ1 was essential for LINC00887 to play a pro-tumorigenic role in MTC. Our findings suggest that the FOXQ1/LINC00887 axis is a potential therapeutic target for MTC.
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Affiliation(s)
- Daxiang Liu
- Department of Otolaryngology & Head and Neck Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China
| | - Wenjing Wang
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035 , China
| | - Yanzhao Wu
- Department of Otolaryngology & Head and Neck Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China
| | - Yongle Qiu
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035 , China
| | - Lan Zhang
- Department of Otolaryngology & Head and Neck Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China
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Luo X, Li Q, Tang Y, Liu Y, Zou Q, Zheng J, Zhang Y, Xu L. Predicting active enhancers with DNA methylation and histone modification. BMC Bioinformatics 2023; 24:414. [PMID: 37919681 PMCID: PMC10621108 DOI: 10.1186/s12859-023-05547-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Enhancers play a crucial role in gene regulation, and some active enhancers produce noncoding RNAs known as enhancer RNAs (eRNAs) bi-directionally. The most commonly used method for detecting eRNAs is CAGE-seq, but the instability of eRNAs in vivo leads to data noise in sequencing results. Unfortunately, there is currently a lack of research focused on the noise inherent in CAGE-seq data, and few approaches have been developed for predicting eRNAs. Bridging this gap and developing widely applicable eRNA prediction models is of utmost importance. RESULTS In this study, we proposed a method to reduce false positives in the identification of eRNAs by adjusting the statistical distribution of expression levels. We also developed eRNA prediction models using joint gene expressions, DNA methylation, and histone modification. These models achieved impressive performance with an AUC value of approximately 0.95 for intra-cell prediction and 0.9 for cross-cell prediction. CONCLUSIONS Our method effectively attenuates the noise generated by stochastic RNA production, resulting in more accurate detection of eRNAs. Furthermore, our eRNA prediction model exhibited significant accuracy in both intra-cell and cross-cell validation, highlighting its robustness and potential application in various cellular contexts.
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Affiliation(s)
- Ximei Luo
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- School of Electronic and Communication Engineering, Shenzhen Polytechnic University, Shenzhen, Guangdong, China
| | - Qun Li
- Department of Pain, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yifan Tang
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yan Liu
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China
| | - Jie Zheng
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Ying Zhang
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic University, Shenzhen, Guangdong, China.
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Li Q, Liu X, Wen J, Chen X, Xie B, Zhao Y. Enhancer RNAs: mechanisms in transcriptional regulation and functions in diseases. Cell Commun Signal 2023; 21:191. [PMID: 37537618 PMCID: PMC10398997 DOI: 10.1186/s12964-023-01206-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/23/2023] [Indexed: 08/05/2023] Open
Abstract
In recent years, increasingly more non-coding RNAs have been detected with the development of high-throughput sequencing technology, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), small nucleolar RNAs (snoRNAs), and piwi-interacting RNA (piRNAs). The discovery of enhancer RNAs (eRNAs) in 2010 has further broadened the range of non-coding RNAs revealed. eRNAs are non-coding RNA molecules produced by the transcription of DNA cis-acting elements, enhancer fragments. Recent studies revealed that the transcription of eRNAs may be a biological marker responding to enhancer activity that can participate in the regulation of coding gene transcription. In this review, we discussed the biological characteristics of eRNAs, their functions in transcriptional regulation, the regulation factors of eRNAs production, and the research progress of eRNAs in different diseases. Video Abstract.
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Affiliation(s)
- Qianhui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Xin Liu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Jingtao Wen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Bumin Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China.
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Jia Q, Tan Y, Li Y, Wu Y, Wang J, Tang F. JUN-induced super-enhancer RNA forms R-loop to promote nasopharyngeal carcinoma metastasis. Cell Death Dis 2023; 14:459. [PMID: 37479693 PMCID: PMC10361959 DOI: 10.1038/s41419-023-05985-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Oncogenic super-enhancers (SEs) generate noncoding enhancer/SE RNAs (eRNAs/seRNAs) that exert a critical function in malignancy through powerful regulation of target gene expression. Herein, we show that a JUN-mediated seRNA can form R-loop to regulate target genes to promote metastasis of nasopharyngeal carcinoma (NPC). A combination of global run-on sequencing, chromatin-immunoprecipitation sequencing, and RNA sequencing was used to screen seRNAs. A specific seRNA associated with NPC metastasis (seRNA-NPCM) was identified as a transcriptional regulator for N-myc downstream-regulated gene 1 (NDRG1). JUN was found to regulate seRNA-NPCM through motif binding. seRNA-NPCM was elevated in NPC cancer tissues and highly metastatic cell lines, and promoted the metastasis of NPC cells in vitro and in vivo. Mechanistically, the 3' end of seRNA-NPCM hybridizes with the SE region to form an R-loop, and the middle segment of seRNA-NPCM binds to heterogeneous nuclear ribonucleoprotein R (hnRNPR) at the promoter of distal gene NDRG1 and neighboring gene tribbles pseudokinase 1 (TRIB1). These structures promote chromatin looping and long-distance chromatin interactions between SEs and promoters, thus facilitating NDRG1 and TRIB1 transcription. Furthermore, the clinical analyses showed that seRNA-NPCM and NDRG1 were independent prognostic factors for NPC patients. seRNA-NPCM plays a critical role in orchestrating target gene transcription to promote NPC metastasis.
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Affiliation(s)
- Qunying Jia
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, 410013, Changsha, China
| | - Yuan Tan
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, 410013, Changsha, China
| | - Yuejin Li
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, 410013, Changsha, China
| | - Yao Wu
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, 410013, Changsha, China
- Department of Ophthalmology and Otolaryngology, The First Hospital of Hunan University of Chinese Medicine, 410208, Changsha, China
| | - Jing Wang
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, 410013, Changsha, China
| | - Faqin Tang
- Hunan Key Laboratory of Oncotarget Gene and Clinical Laboratory, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, 410013, Changsha, China.
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11
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Qiu Y, Feng D, Jiang W, Zhang T, Lu Q, Zhao M. 3D genome organization and epigenetic regulation in autoimmune diseases. Front Immunol 2023; 14:1196123. [PMID: 37346038 PMCID: PMC10279977 DOI: 10.3389/fimmu.2023.1196123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023] Open
Abstract
Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin. Chromatin folding can be studied using chromosome conformation capture (3C) technology and 3C-based derivative sequencing technologies, including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), and high-throughput chromosome conformation capture (Hi-C), which allow scientists to capture 3D conformations from a single site to the entire genome. A comprehensive analysis of the relationships between various regulatory components and gene function also requires the integration of multi-omics data such as genomics, transcriptomics, and epigenomics. 3D genome folding is involved in immune cell differentiation, activation, and dysfunction and participates in a wide range of diseases, including autoimmune diseases. We describe hierarchical 3D chromatin organization in this review and conclude with characteristics of C-techniques and multi-omics applications of the 3D genome. In addition, we describe the relationship between 3D genome structure and the differentiation and maturation of immune cells and address how changes in chromosome folding contribute to autoimmune diseases.
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Affiliation(s)
- Yueqi Qiu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Delong Feng
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wenjuan Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Tingting Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ming Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
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12
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Chen Q, Zeng Y, Kang J, Hu M, Li N, Sun K, Zhao Y. Enhancer RNAs in transcriptional regulation: recent insights. Front Cell Dev Biol 2023; 11:1205540. [PMID: 37266452 PMCID: PMC10229774 DOI: 10.3389/fcell.2023.1205540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023] Open
Abstract
Enhancers are a class of cis-regulatory elements in the genome that instruct the spatiotemporal transcriptional program. Last decade has witnessed an exploration of non-coding transcripts pervasively transcribed from active enhancers in diverse contexts, referred to as enhancer RNAs (eRNAs). Emerging evidence unequivocally suggests eRNAs are an important layer in transcriptional regulation. In this mini-review, we summarize the well-established regulatory models for eRNA actions and highlight the recent insights into the structure and chemical modifications of eRNAs underlying their functions. We also explore the potential roles of eRNAs in transcriptional condensates.
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Affiliation(s)
- Qi Chen
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yaxin Zeng
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jinjin Kang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Minghui Hu
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Nianle Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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13
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Di Giorgio E, Benetti R, Kerschbamer E, Xodo L, Brancolini C. Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:97-148. [PMID: 37657861 DOI: 10.1016/bs.ircmb.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Super-enhancers evolve as elements at the top of the hierarchical control of gene expression. They are important end-gatherers of signaling pathways that control stemness, differentiation or adaptive responses. Many epigenetic regulations focus on these regions, and not surprisingly, during the process of tumorigenesis, various alterations can account for their dysfunction. Super-enhancers are emerging as key drivers of the aberrant gene expression landscape that sustain the aggressiveness of cancer cells. In this review, we will describe and discuss about the structure of super-enhancers, their epigenetic regulation, and the major changes affecting their functionality in cancer.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Roberta Benetti
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Emanuela Kerschbamer
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Luigi Xodo
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy.
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14
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Diao P, Huang R, Shi Y, Yao Q, Dai Y, Yuan H, Wang Y, Cheng J. Development of a novel prognostic signature derived from enhancer RNA-regulated genes in head neck squamous cell carcinoma. Head Neck 2023; 45:900-912. [PMID: 36786387 DOI: 10.1002/hed.27316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/21/2023] [Accepted: 01/29/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Enhancer RNAs (eRNAs) are increasingly recognized as prognostic biomarkers-across human cancers. Here, we sought to develop a novel eRNA-regulated genes (ERGs)-derived prognostic signature for head neck squamous cell carcinoma (HNSCC). METHODS Candidate ERGs were identified via co-expression between individual survival-related eRNAs and their putative targets by Spearman's correlation analyses. The ERG signature was developed by univariate Cox regression, Kaplan-Meier survival analysis and maximum AUC in 1000 iterations of LASSO-penalized multivariate Cox regression. An ERG nomogram incorporating ERG signature and selected clinicopathological parameters were constructed by multivariate Cox regression. Biological roles of eRNA of interest were further explored in vitro. RESULTS The ERG signature successfully stratified patients into subgroups with distinct survival in multiple cohorts. An ERG nomogram was developed with satisfactory performance in prognostication. Inhibition of ENSR00000165816 significantly reduced transcript level of SLC2A9 and impaired cell proliferation and invasion. CONCLUSION Our results establish ERG signature and nomogram as powerful prognostic predictors for HNSCC.
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Affiliation(s)
- Pengfei Diao
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Province Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
| | - Rong Huang
- School of Medical Technology, Taizhou Polytechnic College, Taizhou, China
| | - Yawei Shi
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
| | - Qin Yao
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
| | - Yibin Dai
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
| | - Hua Yuan
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Province Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
| | - Yanling Wang
- Jiangsu Province Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
| | - Jie Cheng
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Province Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
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15
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Yang Y, Yuan F, Zhou H, Quan J, Liu C, Wang Y, Xiao F, Liu Q, Liu J, Zhang Y, Yu X. Potential roles of heparanase in cancer therapy: Current trends and future direction. J Cell Physiol 2023; 238:896-917. [PMID: 36924082 DOI: 10.1002/jcp.30995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/17/2023]
Abstract
Heparanase (HPSE; heparanase-1) is an endo-β-glucuronidase capable of degrading the carbohydrate moiety of heparan sulfate proteoglycans, thus modulating and facilitating the remodeling of the extracellular matrix and basement membrane. HPSE activity is strongly associated with major human pathological complications, including but not limited to tumor progress and angiogenesis. Several lines of literature have shown that overexpression of HPSE leads to enhanced tumor growth and metastatic transmission, as well as poor prognosis. Gene silencing of HPSE or treatment of tumor with compounds that block HPSE activity are shown to remarkably attenuate tumor progression. Therefore, targeting HPSE is considered as a potential therapeutical strategy for the treatment of cancer. Intriguingly, recent findings disclose that heparanase-2 (HPSE-2), a close homolog of HPSE but lacking enzymatic activity, can also regulate antitumor mechanisms. Given the pleiotropic roles of HPSE, further investigation is in demand to determine the precise mechanism of regulating action of HPSE in different cancer settings. In this review, we first summarize the current understanding of HPSE, such as its structure, subcellular localization, and tissue distribution. Furthermore, we systematically review the pro- and antitumorigenic roles and mechanisms of HPSE in cancer progress. In addition, we delineate HPSE inhibitors that have entered clinical trials and their therapeutic potential.
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Affiliation(s)
- Yiyuan Yang
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Fengyan Yuan
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Huiqin Zhou
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Jing Quan
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Chongyang Liu
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Yi Wang
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Fen Xiao
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Qiao Liu
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Jie Liu
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Yujing Zhang
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Xing Yu
- Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
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16
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Yeo SJ, Ying C, Fullwood MJ, Tergaonkar V. Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains. Trends Genet 2023; 39:217-232. [PMID: 36642680 DOI: 10.1016/j.tig.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.
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Affiliation(s)
- Samuel Jianjie Yeo
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), Singapore 308232, Singapore
| | - Chen Ying
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Pathology and the Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore.
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17
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Zhuang HH, Qu Q, Teng XQ, Dai YH, Qu J. Superenhancers as master gene regulators and novel therapeutic targets in brain tumors. Exp Mol Med 2023; 55:290-303. [PMID: 36720920 PMCID: PMC9981748 DOI: 10.1038/s12276-023-00934-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/27/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Transcriptional deregulation, a cancer cell hallmark, is driven by epigenetic abnormalities in the majority of brain tumors, including adult glioblastoma and pediatric brain tumors. Epigenetic abnormalities can activate epigenetic regulatory elements to regulate the expression of oncogenes. Superenhancers (SEs), identified as novel epigenetic regulatory elements, are clusters of enhancers with cell-type specificity that can drive the aberrant transcription of oncogenes and promote tumor initiation and progression. As gene regulators, SEs are involved in tumorigenesis in a variety of tumors, including brain tumors. SEs are susceptible to inhibition by their key components, such as bromodomain protein 4 and cyclin-dependent kinase 7, providing new opportunities for antitumor therapy. In this review, we summarized the characteristics and identification, unique organizational structures, and activation mechanisms of SEs in tumors, as well as the clinical applications related to SEs in tumor therapy and prognostication. Based on a review of the literature, we discussed the relationship between SEs and different brain tumors and potential therapeutic targets, focusing on glioblastoma.
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Affiliation(s)
- Hai-Hui Zhuang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410007, PR China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410007, PR China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China
| | - Ying-Huan Dai
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, 410011, PR China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China.
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18
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Hu Y, Yang Q, Cai S, Wang W, Fu S. The integrative analysis based on super-enhancer related genes for predicting different subtypes and prognosis of patient with lower-grade glioma. Front Genet 2023; 14:1085584. [PMID: 37091789 PMCID: PMC10119407 DOI: 10.3389/fgene.2023.1085584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Objective: Emerging evidence revealed that super-enhancer plays a crucial role in the transcriptional reprogramming for many cancers. The purpose aimed to explored how the super-enhancer related genes affects the prognosis and tumor immune microenvironment (TIME) of patients with low-grade glioma (LGG). Methods: In this study, the differentially expressed genes (DEGs) between LGG cohorts and normal brain tissue cohort were identified by the comprehensive analysis of the super-enhancer (SE) related genes. Then non-negative matrix factorization was performed to seek the optimal classification based on the DEGs, while investigating prognostic and clinical differences between different subtypes. Subsequently, a prognostic related signature (SERS) was constructed for the comprehensive evaluation in term of individualized prognosis, clinical characteristics, cancer markers, genomic alterations, and immune microenvironment of patients with LGG. Results: Based on the expression profiles of 170 DEGs, we identified three SE subtypes, and the three subtypes showed significant differences in prognostic, clinicopathological features. Then, nine optimal SE-related genes were selected to construct the SERS through the least absolute shrinkage and selection operator Cox regression analysis. Survival analysis showed that SERS had strong and stable predictive ability for the prognosis of LGG patients in the The Cancer Genome Atlas, China Glioma Genome Atlas, and Remdrandt cohorts, respectively. We also found that SERS was highly correlated with clinicopathological features, tumor immune microenvironment, cancer hallmarks, and genomic alterations in LGG patients. In addition, the predictive power of SERS for immune checkpoint inhibitor treatment is also superior. The qRT-PCR results and immunohistochemical results also confirmed the difference in the expression of four key genes in normal cells and tumors, as well as in normal tissues and tumor tissues. Conclusion: The SERS could be suitable to utilize individualized prognosis prediction and immunotherapy options for LGG patients in clinical application.
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Affiliation(s)
- Yungang Hu
- Department of Neurosurgery, Wuhan University of Science and Technology Affiliated Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Qingqing Yang
- Department of Thyroid and Breast Surgery, Wuhan University of Science and Technology Affiliated Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Shuzhou Cai
- Department of Neurosurgery, Wuhan University of Science and Technology Affiliated Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Wei Wang
- Department of Neurosurgery, Wuhan University of Science and Technology Affiliated Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Shiyin Fu
- Department of Pediatric, Jinchu University of Technology Affiliated Central Hospital, Jingmen, Hubei, China
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19
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Circulating Exosomal miR-493-3p Affects Melanocyte Survival and Function by Regulating Epidermal Dopamine Concentration in Segmental Vitiligo. J Invest Dermatol 2022; 142:3262-3273.e11. [PMID: 35690140 DOI: 10.1016/j.jid.2022.05.1086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/12/2022] [Accepted: 05/05/2022] [Indexed: 01/05/2023]
Abstract
Circulating exosomal microRNAs have been used as potential biomarkers for various disorders. However, to date, the microRNA expression profile of circulating exosomes in patients with segmental vitiligo (SV) has not been identified. Thus, we aimed to identify the expression profile of circulating exosomal microRNAs and investigate their role in the pathogenesis of SV. Our study identified the expression profile of circulating exosomal microRNAs in SV and selected miR-493-3p as a candidate biomarker whose expression is significantly increased in circulating exosomes and perilesions in patients with SV. Circulating exosomes were internalized by human primary keratinocytes and increased dopamine secretion in vitro. Furthermore, miR-493-3p overexpression in keratinocytes increased dopamine concentration in the culture supernatant, which led to a significant increase in ROS and melanocyte apoptosis as well as a decrease in melanocyte proliferation and melanin synthesis in the coculture system by targeting HNRNPU. We also confirmed that HNRNPU could bind to and regulate COMT, a major degradative enzyme of dopamine. Hence, circulating exosomal miR-493-3p is a biomarker for SV, and the miR-493-3p/HNRNPU/COMT/dopamine axis may contribute to melanocyte dysregulation in the pathogenesis of SV.
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20
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Liu L, Hu L, Long H, Zheng M, Hu Z, He Y, Gao X, Du P, Zhao H, Yu D, Lu Q, Zhao M. LncRNA IL21-AS1 interacts with hnRNPU protein to promote IL21 overexpression and aberrant differentiation of Tfh cells in systemic lupus erythematosus. Clin Transl Med 2022; 12:e1117. [PMID: 36447054 PMCID: PMC9708910 DOI: 10.1002/ctm2.1117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The aberrant differentiation of T follicular helper (Tfh) cells plays an important role in the pathogenesis of systemic lupus erythematosus (SLE). However, the mechanism of regulating Tfh cells differentiation remains unclear. Long noncoding RNAs (lncRNAs) act as important regulators in the processes of innate and adaptive immune response. Whether lncRNAs are involved in regulating Tfh cell differentiation and autoimmune responses need to be further identified. METHODS The characters and functions of human IL21-AS1 and its mouse homologous lncRNA (mIl21-AS) were investigated by a series of biochemical assays and cell transfection assay. mIl21-AS1 regulating humoral immune response in vivo was explored by keyhole limpet haemocyanin (KLH) and chronic graft versus host disease (cGVHD) model. RESULTS Human IL21-AS1 and its mouse homologous lncRNA (mIl21-AS) were identified and cloned. We uncovered that IL21-AS1 was highly expressed in CD4+ T cells of SLE patients and Tfh cells, which promoted differentiation of Tfh cells. Mechanistically, IL21-AS1 bound heterogeneous nuclear ribonucleoprotein U and recruited acetyltransferases CREB-binding protein to the promoter of IL21, leading to the transcriptional activation of IL21 and Tfh cells differentiation through increasing Histone H3 acetylation level on IL21 promoter. Moreover, Tfh proportion and antibodies production were significantly increased in mIl21-AS knock-in mice immunized with KLH. mIl21-AS1 overexpression also exacerbated the lupus-like phenotype in cGVHD mice model. CONCLUSIONS Our results demonstrate that IL21-AS1 activates IL21 transcription via epigenetic mechanism to promote germinal centre response, adding insight into the molecular regulation of autoimmune pathogenesis and providing a novel target for SLE treatment.
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Affiliation(s)
- Limin Liu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
- Department of Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Longyuan Hu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Haojun Long
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Meiling Zheng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Zhi Hu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Ye He
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Xiaofei Gao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Pei Du
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Hongjun Zhao
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China
| | - Di Yu
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
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21
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Xiao W, Wang J, Wang X, Cai S, Guo Y, Ye L, Li D, Hu A, Jin S, Yuan B, Zhou Y, Li Q, Tong Q, Zheng L. Therapeutic targeting of the USP2-E2F4 axis inhibits autophagic machinery essential for zinc homeostasis in cancer progression. Autophagy 2022; 18:2615-2635. [PMID: 35253629 PMCID: PMC9629121 DOI: 10.1080/15548627.2022.2044651] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Macroautophagy/autophagy is a conserved cellular process associated with tumorigenesis and aggressiveness, while mechanisms regulating expression of autophagic machinery genes in cancers still remain elusive. Herein, we identified E2F4 (E2F transcription factor 4) as a novel transcriptional activator of cytoprotective autophagy crucial for zinc homeostasis in cancer cells. Gain- and loss-of-function studies showed that E2F4 promoted autophagy in a cell cycle-dependent manner, resulting in facilitated degradation of MT (metallothionein) proteins, elevated distribution of Zn2+ within autophagosomes, decreased labile intracellular zinc ions, and increased growth, invasion, and metastasis of gastric cancer cells. Mechanistically, E2F4 directly regulated the transcription of ATG2A (autophagy related 2A) and ULK2 (unc-51 like autophagy activating kinase 2), leading to autophagic degradation of MT1E, MT1M, and MT1X, while USP2 (ubiquitin specific peptidase 2) stabilized E2F4 protein to induce its transactivation via physical interaction and deubiquitination in cancer cells. Rescue experiments revealed that USP2 harbored oncogenic properties via E2F4-facilitated autophagy and zinc homeostasis. Emetine, a small chemical inhibitor of autophagy, was able to block interaction between UPS2 and E2F4, increase labile intracellular zinc ions, and suppress tumorigenesis and aggressiveness. In clinical gastric cancer specimens, both USP2 and E2F4 were upregulated and associated with poor outcome of patients. These findings indicate that therapeutic targeting of the USP2-E2F4 axis inhibits autophagic machinery essential for zinc homeostasis in cancer progression.Abbreviations: 3-MA: 3-methyladenine; ANOVA: analysis of variance; ATG2A: autophagy related 2A; ATG5: autophagy related 5; ATP: adenosine triphosphate; BECN1: beclin 1; BiFC: bimolecular fluorescence complementation; CCND1: cyclin D1; CDK: cyclin dependent kinase; ChIP: chromatin immunoprecipitation; CHX: cycloheximide; Co-IP: co-immunoprecipitation; DAPI: 4',6-diamidino-2-phenylindole; E2F4: E2F transcription factor 4; eATP: extracellular adenosine triphosphate; EBSS: Earle's balanced salt solution; FP: first progression; FRET: fluorescence resonance energy transfer; FUCCI: fluorescent ubiquitination-based cell cycle indicator; GFP: green fluorescent protein; GST: glutathione S-transferase; HA: hemagglutinin; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MDM2: MDM2 proto-oncogene; MKI67/Ki-67: marker of proliferation Ki-67; MT: metallothionein; MT1E: metallothionein 1E; MT1M: metallothionein 1M; MT1X: metallothionein 1X; MTT: 3-(4,5-dimethyltriazol-2-yl)-2,5-diphenyl tetrazolium bromide; OS: overall survival; PECAM1/CD31: platelet and endothelial cell adhesion molecule 1; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; qPCR: quantitative PCR; RFP: red fluorescent protein; SQSTM1/p62: sequestosome 1; UBXN1: UBX domain protein 1; Ub: ubiquitin; ULK2: unc-51 like autophagy activating kinase 2; USP14: ubiquitin specific peptidase 14; USP2: ubiquitin specific peptidase 2; USP5: ubiquitin specific peptidase 5; USP7: ubiquitin specific peptidase 7; ZnCl2: zinc chloride.
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Affiliation(s)
- Wenjing Xiao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jianqun Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiaojing Wang
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Shuang Cai
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yanhua Guo
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Lin Ye
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Anpei Hu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Shikai Jin
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Boling Yuan
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yi Zhou
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Qilan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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22
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Panahi-Moghadam S, Hassani S, Farivar S, Vakhshiteh F. Emerging Role of Enhancer RNAs as Potential Diagnostic and Prognostic Biomarkers in Cancer. Noncoding RNA 2022; 8:ncrna8050066. [PMID: 36287118 PMCID: PMC9607539 DOI: 10.3390/ncrna8050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Enhancers are distal cis-acting elements that are commonly recognized to regulate gene expression via cooperation with promoters. Along with regulating gene expression, enhancers can be transcribed and generate a class of non-coding RNAs called enhancer RNAs (eRNAs). The current discovery of abundant tissue-specific transcription of enhancers in various diseases such as cancers raises questions about the potential role of eRNAs in disease diagnosis and therapy. This review aimed to demonstrate the current understanding of eRNAs in cancer research with a focus on the potential roles of eRNAs as prognostic and diagnostic biomarkers in cancers.
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Affiliation(s)
- Somayeh Panahi-Moghadam
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Shokoufeh Hassani
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences (TUMS), Tehran 1417614411, Iran
| | - Shirin Farivar
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Faezeh Vakhshiteh
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran 1449614535, Iran
- Correspondence:
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23
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3D chromatin remodeling potentiates transcriptional programs driving cell invasion. Proc Natl Acad Sci U S A 2022; 119:e2203452119. [PMID: 36037342 PMCID: PMC9457068 DOI: 10.1073/pnas.2203452119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The contribution of deregulated chromatin architecture, including topologically associated domains (TADs), to cancer progression remains ambiguous. CCCTC-binding factor (CTCF) is a central regulator of higher-order chromatin structure that undergoes copy number loss in over half of all breast cancers, but the impact of this defect on epigenetic programming and chromatin architecture remains unclear. We find that under physiological conditions, CTCF organizes subTADs to limit the expression of oncogenic pathways, including phosphatidylinositol 3-kinase (PI3K) and cell adhesion networks. Loss of a single CTCF allele potentiates cell invasion through compromised chromatin insulation and a reorganization of chromatin architecture and histone programming that facilitates de novo promoter-enhancer contacts. However, this change in the higher-order chromatin landscape leads to a vulnerability to inhibitors of mTOR. These data support a model whereby subTAD reorganization drives both modification of histones at de novo enhancer-promoter contacts and transcriptional up-regulation of oncogenic transcriptional networks.
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[Clinical significance and pathogenesis analysis of heterogeneous nuclear ribonucleoprotein U in acute myeloid leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2022; 43:745-752. [PMID: 36709168 PMCID: PMC9613492 DOI: 10.3760/cma.j.issn.0253-2727.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Objective: To investigate the clinical significance and pathogenesis of heterogeneous nuclear ribonucleoprotein U (hnRNP U) in acute myeloid leukemia (AML) . Methods: The expression of hnRNP U, an RNA binding protein, in patients with AML and healthy controls was compared based on the Gene Expression Profiling Interactive Analysis database and the data of the center. The Beat AML Dataset (n=158) was downloaded from the cBioPortal database. The hnRNP U expression level was divided into the high-expression group (n=89) and low-expression group (n=69) , and patients' clinical characteristics were compared. The effect of hnRNP U on the biological behavior of human AML cell lines was studied by Cell Counting Kit-8 assay to detect cell proliferation. Annexin Ⅴ-APC/7-AAD antibodies were used to detect cell apoptosis. DNA content (PI staining) was quantitatively analyzed to detect cell cycle changes, and colony formation experiments were performed to detect cell cloning formation ability after hnRNP U knockdown in Kasumi-1 and MOLM-13 cells. To study the effect of hnRNP U knockdown on the DNA damage response (DDR) pathway proteins of cleaved-PARP, immunoblot analysis using p-H2A.X was conducted. Results: ①Pan-cancer analysis showed that hnRNP U was highly expressed in patients with AML, and the expression level of hnRNP U mRNA in peripheral blood mononuclear cells was significantly higher in patients with AML than in healthy controls (0.0315±0.0042 vs 0.0195±0.0006, respectively, P<0.01) . ②The age of onset was 56 (2-87) years in the high-expression group and 65 (8-85) years in the low-expression group (t=-2.681, P=0.007) . Moreover, the high-expression group had a higher proportion of combined FLT3 mutations than the low-expression group (χ(2)=4.069, P=0.044) . ③Compared with the negative control, hnRNP U knockdown inhibited the proliferation (P<0.001 and P<0.001) , promoted the apoptosis (P<0.01 and P<0.001) , decreased the colony formation ability (P<0.001 and P<0.001) , and arrested the cell cycles in the G(2)/M phase (P<0.05 and P<0.01) of Kasumi-1 and MOLM-13 cells, respectively. ④hnRNP U knockdown could increase the protein expression of cleaved-PARP and p-H2A.X on the DDR pathway. Conclusion: hnRNP U is highly expressed in AML, and hnRNP U knockdown can inhibit the occurrence and development of AML possibly through the activation of the DDR pathway.
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25
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Yang M, Tang B, Wang S, Tang L, Wen D, Vlodavsky I, Yang SM. Non-enzymatic heparanase enhances gastric tumor proliferation via TFEB-dependent autophagy. Oncogenesis 2022; 11:49. [PMID: 35970822 PMCID: PMC9378687 DOI: 10.1038/s41389-022-00424-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 11/08/2022] Open
Abstract
Heparanase (HPA) is the predominant enzyme that cleaves heparan sulfate and plays a critical role in a variety of pathophysiological processes. HPA activity has been traditionally correlated with tumor metastasis due to participation in the cleavage and remodeling of the extracellular matrix (ECM). Apart from its well-characterized catalytic properties, HPA was noticed to exert biological functions not rely on its enzymatic activity. This feature is supported by studies showing induction of signaling events, such as Src and AKT, by nonenzymatic HPA mutant. We provide evidence here that active HPA and inactive HPA mutant proteins enhance gastric cancer cell growth, possibly attributed to TFEB-mediated autophagy. Similarly, HPA gene silencing resulted in decreased gastric cancer cell proliferation and autophagy. Besides, TFEB inhibition reduced cell growth and autophagy induced by nonenzymatic HPA. Notably, HPA and TFEB were significantly elevated in gastric carcinomas compared with the adjacent gastric tissue. Moreover, the elevation of HPA gene expression and upregulation of TFEB levels have been associated with advanced clinical stage and poor prognosis of gastric cancer, providing strong clinical support for a connection between TFEB and HPA. Thus, neutralizing the nonenzymatic function of HPA and the related TFEB-driven autophagy may profoundly impact gastric cancer progression.
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Affiliation(s)
- Min Yang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Sumin Wang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Li Tang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Dalin Wen
- Wound Trauma Medical Center, State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Israel Vlodavsky
- Cancer and Vascular Biology Research Center, the Bruce Rappaport Faculty of Medicine, Technion, Haifa, 31096, Israel.
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China.
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26
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Abstract
Enhancers confer precise spatiotemporal patterns of gene expression in response to developmental and environmental stimuli. Over the last decade, the transcription of enhancer RNAs (eRNAs) – nascent RNAs transcribed from active enhancers – has emerged as a key factor regulating enhancer activity. eRNAs are relatively short-lived RNA species that are transcribed at very high rates but also quickly degraded. Nevertheless, eRNAs are deeply intertwined within enhancer regulatory networks and are implicated in a number of transcriptional control mechanisms. Enhancers show changes in function and sequence over evolutionary time, raising questions about the relationship between enhancer sequences and eRNA function. Moreover, the vast majority of single nucleotide polymorphisms associated with human complex diseases map to the non-coding genome, with causal disease variants enriched within enhancers. In this Primer, we survey the diverse roles played by eRNAs in enhancer-dependent gene expression, evaluating different models for eRNA function. We also explore questions surrounding the genetic conservation of enhancers and how this relates to eRNA function and dysfunction. Summary: This Primer evaluates the ideas that underpin developing models for eRNA function, exploring cases in which perturbed eRNA function contributes to disease.
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Affiliation(s)
- Laura J. Harrison
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
| | - Daniel Bose
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
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27
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Li Y, Wang H, Wan J, Ma Q, Qi Y, Gu Z. The hnRNPK/A1/R/U Complex Regulates Gene Transcription and Translation and is a Favorable Prognostic Biomarker for Human Colorectal Adenocarcinoma. Front Oncol 2022; 12:845931. [PMID: 35875075 PMCID: PMC9301189 DOI: 10.3389/fonc.2022.845931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are emerging as a crucially important protein family in tumors. However, it is unclear which family members are essential for cancer progression, and their diverse expression patterns and prognostic values are rarely reported. In this work, we found that the expression levels of hnRNPs were all upregulated in colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) tissues. Immunohistochemical staining revealed that hnRNPA1, hnRNPA2B1, hnRNPC, hnRNPK, hnRNPR, and hnRNPU are overexpressed in colorectal adenocarcinoma. Additionally, the promoter methylation levels of hnRNPs were significantly elevated or decreased, and multiple genetic alterations of hnRNPs were found in colorectal adenocarcinoma patients. Correlation analysis showed that the expression levels of hnRNPs were positively correlated with each other. Furthermore, we demonstrated that high expressions of hnRNPA1, hnRNPK, hnRNPR, and hnRNPU were associated with better overall survival rates for colorectal adenocarcinoma patients. The co-expression network and functional prediction analysis indicated that hnRNPK/A1/R/U was involved in cellular gene transcription and translation. Moreover, hnRNPK/A1/R/U complex was identified and confirmed by mass spectrometry and co-immunoprecipitation. RNA sequencing analysis revealed that the transcription factor hnRNPK regulated transcription and translation of related genes. Finally, through establishment of stable cell lines in vitro, we verified that hnRNPK was a favorable factor in human colorectal adenocarcinoma which promoted immune cell infiltration and inhibited tumor growth. Our findings illustrate that the hnRNPK/A1/R/U complex is a favorable prognostic biomarker for human colorectal adenocarcinoma. Targeting hnRNPK during transcription and translation could be a promising therapeutic strategy for colorectal adenocarcinoma treatment.
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Affiliation(s)
- Yixin Li
- Department of Clinical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Hui Wang
- Department of Clinical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Jiajia Wan
- Post-Doctoral Station of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Qian Ma
- Post-Doctoral Station of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Qian Ma, ; Yu Qi, ; Zhuoyu Gu,
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Qian Ma, ; Yu Qi, ; Zhuoyu Gu,
| | - Zhuoyu Gu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Qian Ma, ; Yu Qi, ; Zhuoyu Gu,
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28
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Mo J, Zhang L, Li H, Duan H, Wang D, Zhao X, Xie Y. The enhancer RNA ADCY10P1 is associated with the progression of ovarian cancer. J Ovarian Res 2022; 15:61. [PMID: 35568893 PMCID: PMC9107640 DOI: 10.1186/s13048-022-00987-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 04/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Emerging evidence identifies enhancer RNAs (eRNAs) as a class of regulatory ncRNAs that can contribute to the transcription of target genes. In this study, we used an integrated data analysis method to identify the important role of eRNAs in ovarian cancer (OC). METHODS Gene expression profiles and clinical information from The Cancer Genome Atlas (TCGA) database were used for this study. Based on expression analysis using GEPIA2 gene and Kaplan-Meier survival was performed to ensure the significance of the selected enhancer RNA ADCY10P1 in OC. Next, we explored the correlation and clinical significance between ADCY10P1 and target gene NFYA. Furthermore, we evaluated the effects of overexpression of ADCY10P1 on the proliferation, migration, invasion and epithelial-mesenchymal transformation (EMT) of OC cell lines. We also investigated the biological function enrichment score of ADCY10P1 and verified it with OC cell lines. Finally, external validation was conducted, and the prognostic value of the ADCY10P1 in different tumors was demonstrated. RESULTS We selected the eRNA ADCY10P1 associated with OC prognosis, with NFYA as its predicted target gene. Low ADCY10P1 expression was found to be associated with poor overall survival, high histological grade, and advanced stage of OC. Additionally, overexpression of ADCY10P1 inhibited the proliferation, migration, invasion and EMT phenotype of OC cell lines. Furthermore, ADCY10P1 was observed to inhibit glycolysis and fatty acid metabolism, thereby affecting OC progression. Meanwhile, OC tissue samples were externally validated. In addition, the pan-cancer analysis revealed that ADCY10P1 had prognostic value in other cancers. CONCLUSIONS This study showed that ADCY10P1 plays a key role in OC progression and may facilitate prognosis prediction.
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Affiliation(s)
- Jiaya Mo
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lianghao Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Huiqing Li
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haoran Duan
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Dong Wang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaolei Zhao
- Department of Information, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ya Xie
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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29
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Wan L, Li W, Meng Y, Hou Y, Chen M, Xu B. Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects. Front Immunol 2022; 13:849451. [PMID: 35514959 PMCID: PMC9063412 DOI: 10.3389/fimmu.2022.849451] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of multiple high-throughput sequencing technologies has made it possible to explore the critical roles and mechanisms of functional enhancers and enhancer RNAs (eRNAs). The inflammatory immune response, as a fundamental pathological process in infectious diseases, cancers and immune disorders, coordinates the balance between the internal and external environment of the organism. It has been shown that both active enhancers and intranuclear eRNAs are preferentially expressed over inflammation-related genes in response to inflammatory stimuli, suggesting that enhancer transcription events and their products influence the expression and function of inflammatory genes. Therefore, in this review, we summarize and discuss the relevant inflammatory roles and regulatory mechanisms of eRNAs in inflammatory immune cells, non-inflammatory immune cells, inflammatory immune diseases and tumors, and explore the potential therapeutic effects of enhancer inhibitors affecting eRNA production for diseases with inflammatory immune responses.
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Affiliation(s)
- Lilin Wan
- Medical School, Southeast University, Nanjing, China
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Yuan Meng
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yue Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
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30
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Super enhancers as master gene regulators in the pathogenesis of hematologic malignancies. Biochim Biophys Acta Rev Cancer 2022; 1877:188697. [PMID: 35150791 DOI: 10.1016/j.bbcan.2022.188697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/20/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
Transcriptional deregulation of multiple oncogenes, tumor suppressors and survival pathways is a cancer cell hallmark. Super enhancers (SE) are long stretches of active enhancers in close linear proximity that ensure extraordinarily high expression levels of key genes associated with cell lineage, function and survival. SE landscape is intrinsically prone to changes and reorganization during the course of normal cell differentiation. This functional plasticity is typically utilized by cancer cells, which remodel their SE landscapes to ensure oncogenic transcriptional reprogramming. Multiple recent studies highlighted structural genetic mechanisms in non-coding regions that create new SE or hijack already existing ones. In addition, alterations in abundance/activity of certain SE-associated proteins or certain viral infections can elicit new super enhancers and trigger SE-driven transcriptional changes. For these reasons, SE profiling emerged as a powerful tool for discovering the core transcriptional regulatory circuits in tumor cells. This, in turn, provides new insights into cancer cell biology, and identifies main nodes of key cellular pathways to be potentially targeted. Since SEs are susceptible to inhibition, their disruption results in exponentially amassing 'butterfly' effect on gene expression and cell function. Moreover, many of SE elements are druggable, opening new therapeutic opportunities. Indeed, SE targeting drugs have been studied preclinically in various hematologic malignancies with promising effects. Herein, we review the unique features of SEs, present different cis- and trans-acting mechanisms through which hematologic tumor cells acquire SEs, and finally, discuss the potential of SE targeting in the therapy of hematologic malignancies.
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Tang WQ, Hei Y, Lin J. Heparanase-1 is downregulated in chemoradiotherapy orbital rhabdomyosarcoma and relates with tumor growth as well as angiogenesis. Int J Ophthalmol 2022; 15:31-39. [PMID: 35047353 DOI: 10.18240/ijo.2022.01.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/20/2021] [Indexed: 11/23/2022] Open
Abstract
AIM To determine the role of heparanase-1 (HPSE-1) in orbital rhabdomyosarcoma (RMS), and to investigate the feasibility of HPSE-1 targeted therapy for RMS. METHODS Immunohistochemistry was performed to analyze HPSE-1 expression in 51 cases of orbital RMS patients (including 28 cases of embryonal RMS and 23 cases of alveolar RMS), among whom there were 27 treated and 24 untreated with preoperative chemoradiotherapy. In vitro, studies were conducted to examine the effect of HPSE-1 silencing on RMS cell proliferation and tube formation of human umbilical vein endothelial cells (HUVECs). RD cells (an RMS cell line) and HUVECs were infected with HPSE-1 shRNA lentivirus at a multiplicity of infection (MOI) of 10 and 30 separately. Real-time PCR and Western blot were applied to detect the mRNA and protein expression levels of HPSE-1. Cell viability of treated or control RD cells was evaluated by cell counting kit-8 (CCK-8) assay. Matrigel tube formation assay was used to evaluate the effect of HPSE-1 RNAi on the tube formation of HUVECs. RESULTS Immunohistochemistry showed that the expression rate of HPSE-1 protein was 92.9% in orbital embryonal RMS and 91.3% in orbital alveolar RMS. Tissue from alveolar orbital RMS did not show relatively stronger staining than that from the embryonal orbital RMS. However, despite the types of RMS, comparing the cases treated chemoradiotherapy with those untreated, we have observed that chemoradiotherapy resulted in weaker staining in patients' tissues. The expression levels of HPSE-1 declined significantly in both the mRNA and protein levels in HPSE-1 shRNA transfected RD cells. The CCK-8 assay showed that lentivirus-mediated HPSE-1 silencing resulted in significantly reduced RD cells viability in vitro. Silencing HPSE-1 expression also inhibited VEGF-induced tube formation of HUVECs in Matrigel. CONCLUSION HPSE-1 silencing may be a promising therapy for the inhibition of orbital RMS progression.
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Affiliation(s)
- Wei-Qiang Tang
- Department of Ophthalmology, the Fourth Medical Centre, Chinese PLA General Hospital, Beijing 100048, China
| | - Yan Hei
- Department of Ophthalmology, the Third Medical Centre, Chinese PLA General Hospital, Beijing 100039, China
| | - Jing Lin
- Department of Clinical Laboratory, the Fourth Medical Centre, Chinese PLA General Hospital, Beijing 100048, China
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Choi HI, An GY, Yoo E, Baek M, Chai JC, Binas B, Lee YS, Jung KH, Chai YG. Targeting of noncoding RNAs encoded by a novel MYC enhancers inhibits the proliferation of human hepatic carcinoma cells in vitro. Sci Rep 2022; 12:855. [PMID: 35039581 PMCID: PMC8764030 DOI: 10.1038/s41598-022-04869-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
The proto-oncogene MYC is important for development and cell growth, however, its abnormal regulation causes cancer. Recent studies identified distinct enhancers of MYC in various cancers, but any MYC enhancer(s) in hepatocellular carcinoma (HCC) remain(s) elusive. By analyzing H3K27ac enrichment and enhancer RNA (eRNA) expression in cultured HCC cells, we identified six putative MYC enhancer regions. Amongst these, two highly active enhancers, located ~ 800 kb downstream of the MYC gene, were identified by qRT-PCR and reporter assays. We functionally confirmed these enhancers by demonstrating a significantly reduced MYC expression and cell proliferation upon CRISPR/Cas9-based deletion and/or antisense oligonucleotide (ASO)-mediated inhibition. In conclusion, we identified potential MYC enhancers of HCC and propose that the associated eRNAs may be suitable targets for HCC treatment.
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Affiliation(s)
- Hae In Choi
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Ga Yeong An
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Eunyoung Yoo
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Mina Baek
- Department of Molecular & Life Science, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
- Institute of Natural Science and Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Jin Choul Chai
- College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bert Binas
- Department of Molecular & Life Science, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Young Seek Lee
- College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyoung Hwa Jung
- Convergence Technology Campus of Korea Polytechnic II, Incheon, 21417, Republic of Korea.
- Department of Biopharmaceutical Systems, Gwangmyeong Convergence Technology Campus of Korea Polytechnic II, Gwangmyeong-si, Gyeonggi-do, 14222, Republic of Korea.
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea.
- Department of Molecular & Life Science, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
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A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions. Methods Mol Biol 2021. [PMID: 34382181 DOI: 10.1007/978-1-0716-1597-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Knowledge in gene transcription and chromatin regulation has been intensely studied for decades, but thanks to next-generation sequencing (NGS) techniques there has been a major leap forward in the last few years. Historically, identification of specific enhancer elements has led to the identification of master transcription factors (TFs) in the 1990s. Genetic and biochemical experiments have identified the key regulators controlling RNA polymerase II (RNAPII) transcription and structurally analyses have elucidated detailed mechanisms. NGS and the development of chromatin immunoprecipitation (ChIP) have accelerated the gain of knowledge in the recent years. By now, we have a dazzling wealth of techniques that are currently used to put gene expression into a genome-wide context. This book is an attempt to assemble useful protocols for many researchers within and nearby research areas. In general, these innovative techniques focus on enhancer and promoter studies. The techniques should also be of interest for related fields such as DNA repair and replication.
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Wang L, Liu J, Tai J, Zhou N, Huang T, Xue Y, Quan Z. A prospective study revealing the role of an immune-related eRNA, WAKMAR2, in breast cancer. Sci Rep 2021; 11:15328. [PMID: 34321580 PMCID: PMC8319425 DOI: 10.1038/s41598-021-94784-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/16/2021] [Indexed: 12/26/2022] Open
Abstract
Enhancer RNAs (eRNAs) are a subclass of non-coding RNAs that are generated during the transcription of enhancer regions and play an important role in tumourigenesis. In this study, we focused on the crucial eRNAs that participate in immune responses in invasive breast cancer (IBC). We first used The Cancer Genome Atlas and Human enhancer RNA Atlas to screen for tissue-specific eRNAs and their target genes. Through Pearson correlation analysis with immune genes, the eRNA WAKMAR2 was identified as a key candidate involved in IBC. Our further research suggested that WAKMAR2 is crucial in regulating the tumour microenvironment and may function by regulating immune-related genes, including IL27RA, RAC2, FABP7, IGLV1-51, IGHA1, and IGHD. Quantitative reverse transcription-polymerase chain reaction was used to detect the expression of WAKMAR2 in IBC and normal tissues, and the effect of WAKMAR2 on the regulation of downstream genes in MB-231 and MCF7 cells was studied in vitro. WAKMAR2 was found to be highly involved in tumour immunity and was downregulated in IBC tissues. Furthermore, the expression of WAKMAR2 and its target genes was observed at the pan-cancer level. This study provides evidence to suggest new potential targets for the treatment of breast cancer.
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Affiliation(s)
- Linbang Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Jingkun Liu
- Honghui Hospital, Xian Jiaotong University, Xi'an, 710072, China
| | - Jiaojiao Tai
- Honghui Hospital, Xian Jiaotong University, Xi'an, 710072, China
| | - Nian Zhou
- Department of Orthopedic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Tianji Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yuzhou Xue
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Zhengxue Quan
- Department of Orthopedic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
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35
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Enhancer RNA: biogenesis, function, and regulation. Essays Biochem 2021; 64:883-894. [PMID: 33034351 DOI: 10.1042/ebc20200014] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022]
Abstract
Enhancers are noncoding DNA elements that are present upstream or downstream of a gene to control its spatial and temporal expression. Specific histone modifications, such as monomethylation on histone H3 lysine 4 (H3K4me1) and H3K27ac, have been widely used to assign enhancer regions in mammalian genomes. In recent years, emerging evidence suggests that active enhancers are bidirectionally transcribed to produce enhancer RNAs (eRNAs). This finding not only adds a new reliable feature to define enhancers but also raises a fundamental question of how eRNAs function to activate transcription. Although some believe that eRNAs are merely transcriptional byproducts, many studies have demonstrated that eRNAs execute crucial tasks in regulating chromatin conformation and transcription activation. In this review, we summarize the current understanding of eRNAs from their biogenesis, functions, and regulation to their pathological significance. Additionally, we discuss the challenges and possible mechanisms of eRNAs in regulated transcription.
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Cheng L, Han T, Chen B, Nie K, Peng W. TBX5-AS1, an enhancer RNA, is a potential novel prognostic biomarker for lung adenocarcinoma. BMC Cancer 2021; 21:794. [PMID: 34238250 PMCID: PMC8268367 DOI: 10.1186/s12885-021-08517-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Enhancer RNAs (eRNAs) are demonstrated to be closely associated with tumourigenesis and cancer progression. However, the role of eRNAs in lung adenocarcinoma (LUAD) remains largely unclear. Thus, a comprehensive analysis was constructed to identify the key eRNAs, and to explore the clinical utility of the identified eRNAs in LUAD. METHODS First, LUAD expression profile data from the Cancer Genome Atlas (TCGA) dataset and eRNA-relevant information were integrated for Kaplan-Meier survival analysis and Spearman's correlation analysis to filtered the key candidate eRNAs that was associated with survival rate and their target genes in LUAD. Then, the key eRNA was selected for subsequent clinical correlation analysis. KEGG pathway enrichment analyses were undertaken to explore the potential signaling pathways of the key eRNA. Data from the human protein atlas (HPA) database were used to validate the outcomes and the quantitative real time-polymerase chain reaction (qRT-PCR) analysis was conducted to measure eRNA expression levels in tumor tissues and paired normal adjacent tissues from LUAD patients. Finally, the eRNAs were validated in pan-cancer. RESULTS As a result, TBX5-AS1 was identified as the key eRNA, which has T-box transcription factor 5 (TBX5) as its regulatory target. KEGG analysis indicated that TBX5-AS1 may exert a vital role via the PI3K/AKT pathway, Ras signaling pathway, etc. Additionally, the qRT-PCR results and the HPA database indicated that TBX5-AS1 and TBX5 were significantly downregulated in tumour samples compared to matched-adjacent pairs. The pan-cancer validation results showed that TBX5-AS1 was associated with survival in four tumors, namely, adrenocortical carcinoma (ACC), LUAD, lung squamous cell carcinoma (LUSC), and uterine corpus endometrial carcinoma (UCEC). Correlations were found between TBX5-AS1 and its target gene, TBX5, in 26 tumor types. CONCLUSION Collectively, our results indicated that TBX5-AS1 may be a potential prognostic biomarker for LUAD patients and promote the targeted therapy of LUAD.
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Affiliation(s)
- Lin Cheng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011 People’s Republic of China
| | - Tong Han
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011 Hunan China
| | - Bolin Chen
- Department of Thoracic Medical Oncology, Hunan Cancer Hospital/the affiliated Cancer Hospital of Xiangya school of Medicine, Central South University, Changsha, 410013 Hunan China
| | - Kechao Nie
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011 People’s Republic of China
- Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405 Guangdong China
| | - Weijun Peng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011 People’s Republic of China
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37
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Napoli S, Cascione L, Rinaldi A, Spriano F, Guidetti F, Zhang F, Cacciapuoti MT, Mensah AA, Sartori G, Munz N, Forcato M, Bicciato S, Chiappella A, Ghione P, Elemento O, Cerchietti L, Inghirami G, Bertoni F. Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B-cell lymphoma. Haematologica 2021; 107:1131-1143. [PMID: 34162177 PMCID: PMC9052922 DOI: 10.3324/haematol.2020.267096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Enhancers are regulatory regions of DNA, which play a key role in cell-type specific differentiation and development. Most active enhancers are transcribed into enhancer RNA (eRNA) that can regulate transcription of target genes by means of in cis as well as in trans action. eRNA stabilize contacts between distal genomic regions and mediate the interaction of DNA with master transcription factors. Here, we characterized an enhancer eRNA, GECPAR (germinal center proliferative adapter RNA), which is specifically transcribed in normal and neoplastic germinal center B cells from the super-enhancer of POU2AF1, a key regulatory gene of the germinal center reaction. Using diffuse large B-cell lymphoma cell line models, we demonstrated the tumor suppressor activity of GECPAR, which is mediated via its transcriptional regulation of proliferation and differentiation genes, particularly MYC and the Wnt pathway.
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Affiliation(s)
- Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,SARA NAPOLI
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Francesca Guidetti
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Fangwen Zhang
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | - Afua Adjeiwaa Mensah
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Nicolas Munz
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Mattia Forcato
- Center for Genome Research, Department of Life Sciences University of Modena and Reggio, Modena, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Life Sciences University of Modena and Reggio, Modena, Italy
| | - Annalisa Chiappella
- Ematologia, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Paola Ghione
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Leandro Cerchietti
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, NY, USA
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland,FRANCESCO BERTONI
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Xiao S, Huang Q, Ren H, Yang M. The mechanism and function of super enhancer RNA. Genesis 2021; 59:e23422. [PMID: 34028961 DOI: 10.1002/dvg.23422] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022]
Abstract
Super enhancer (SE) is a cluster of enhancers that has a stronger ability to promote transcription compared to the typical enhancer (TE). Similar to TE, which can transcribe enhancer RNA (eRNA), SE produces super enhancer RNA (seRNA). The activation of SE is cell and tissue-specific, and the SE-associated genes are mostly linked to the cell fate. This is demonstrated by the important role-played by SE in the embryonic stem cell (ESC) and multiple cancer development. SeRNA regulates transcription in both cis and trans configuration, and those located in the cytoplasm mediates various cell activities. However, the functions of seRNAs are unclear, and most of them have a synergistic effect with SE and SE-associated genes. In this mini review, we summarized the mechanisms of seRNA and functions of both SE and seRNA.
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Affiliation(s)
- Shibai Xiao
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qin Huang
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Ren
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Min Yang
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Adhikary S, Roy S, Chacon J, Gadad SS, Das C. Implications of Enhancer Transcription and eRNAs in Cancer. Cancer Res 2021; 81:4174-4182. [PMID: 34016622 DOI: 10.1158/0008-5472.can-20-4010] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/03/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022]
Abstract
Despite extensive progress in developing anticancer therapies, therapy resistance remains a major challenge that promotes disease relapse. The changes that lead to therapy resistance can be intrinsically present or may be initiated during treatment. Genetic and epigenetic heterogeneity in tumors make it more challenging to deal with therapy resistance. Recent advances in genome-wide analyses have revealed that the deregulation of distal gene regulatory elements, such as enhancers, appears in several pathophysiological conditions, including cancer. Beyond the conventional function of enhancers in recruiting transcription factors to gene promoters, enhancer elements are also transcribed into noncoding RNAs known as enhancer RNAs (eRNA). Accumulating evidence suggests that uncontrolled enhancer activity with aberrant eRNA expression promotes oncogenesis. Interestingly, tissue-specific, transcribed eRNAs from active enhancers can serve as potential therapeutic targets or biomarkers in several cancer types. This review provides a comprehensive overview of the mechanisms of enhancer transcription and eRNAs as well as their potential roles in cancer and drug resistance.
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Affiliation(s)
- Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jessica Chacon
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas
| | - Shrikanth S Gadad
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas. .,Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas.,Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, Texas.,Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynaecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India. .,Homi Bhaba National Institute, Mumbai, Maharashtra, India
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Li GH, Qu Q, Qi TT, Teng XQ, Zhu HH, Wang JJ, Lu Q, Qu J. Super-enhancers: a new frontier for epigenetic modifiers in cancer chemoresistance. J Exp Clin Cancer Res 2021; 40:174. [PMID: 34011395 PMCID: PMC8132395 DOI: 10.1186/s13046-021-01974-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
Although new developments of surgery, chemotherapy, radiotherapy, and immunotherapy treatments for cancer have improved patient survival, the emergence of chemoresistance in cancer has significant impacts on treatment effects. The development of chemoresistance involves several polygenic, progressive mechanisms at the molecular and cellular levels, as well as both genetic and epigenetic heterogeneities. Chemotherapeutics induce epigenetic reprogramming in cancer cells, converting a transient transcriptional state into a stably resistant one. Super-enhancers (SEs) are central to the maintenance of identity of cancer cells and promote SE-driven-oncogenic transcriptions to which cancer cells become highly addicted. This dependence on SE-driven transcription to maintain chemoresistance offers an Achilles' heel for chemoresistance. Indeed, the inhibition of SE components dampens oncogenic transcription and inhibits tumor growth to ultimately achieve combined sensitization and reverse the effects of drug resistance. No reviews have been published on SE-related mechanisms in the cancer chemoresistance. In this review, we investigated the structure, function, and regulation of chemoresistance-related SEs and their contributions to the chemotherapy via regulation of the formation of cancer stem cells, cellular plasticity, the microenvironment, genes associated with chemoresistance, noncoding RNAs, and tumor immunity. The discovery of these mechanisms may aid in the development of new drugs to improve the sensitivity and specificity of cancer cells to chemotherapy drugs.
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Affiliation(s)
- Guo-Hua Li
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Ting-Ting Qi
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Hai-Hong Zhu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Jiao-Jiao Wang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiong Lu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
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Agelidis A, Turturice BA, Suryawanshi RK, Yadavalli T, Jaishankar D, Ames J, Hopkins J, Koujah L, Patil CD, Hadigal SR, Kyzar EJ, Campeau A, Wozniak JM, Gonzalez DJ, Vlodavsky I, Li JP, Perkins DL, Finn PW, Shukla D. Disruption of innate defense responses by endoglycosidase HPSE promotes cell survival. JCI Insight 2021; 6:144255. [PMID: 33621216 PMCID: PMC8119219 DOI: 10.1172/jci.insight.144255] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/18/2021] [Indexed: 01/03/2023] Open
Abstract
The drive to withstand environmental stresses and defend against invasion is a universal trait extant in all forms of life. While numerous canonical signaling cascades have been characterized in detail, it remains unclear how these pathways interface to generate coordinated responses to diverse stimuli. To dissect these connections, we followed heparanase (HPSE), a protein best known for its endoglycosidic activity at the extracellular matrix but recently recognized to drive various forms of late-stage disease through unknown mechanisms. Using herpes simplex virus-1 (HSV-1) infection as a model cellular perturbation, we demonstrate that HPSE acts beyond its established enzymatic role to restrict multiple forms of cell-intrinsic defense and facilitate host cell reprogramming by the invading pathogen. We reveal that cells devoid of HPSE are innately resistant to infection and counteract viral takeover through multiple amplified defense mechanisms. With a unique grasp of the fundamental processes of transcriptional regulation and cell death, HPSE represents a potent cellular intersection with broad therapeutic potential.
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Affiliation(s)
- Alex Agelidis
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
| | - Benjamin A. Turturice
- Department of Microbiology and Immunology
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | | | | | - Dinesh Jaishankar
- Department of Ophthalmology and Visual Sciences, and
- Department of Dermatology, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Joshua Ames
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
| | - James Hopkins
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
| | - Lulia Koujah
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
| | | | | | - Evan J. Kyzar
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Anaamika Campeau
- Department of Pharmacology and
- Skaggs School of Pharmacy, UCSD, San Diego, La Jolla, California, USA
| | - Jacob M. Wozniak
- Department of Pharmacology and
- Skaggs School of Pharmacy, UCSD, San Diego, La Jolla, California, USA
| | - David J. Gonzalez
- Department of Pharmacology and
- Skaggs School of Pharmacy, UCSD, San Diego, La Jolla, California, USA
| | - Israel Vlodavsky
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Jin-ping Li
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Uppsala, Sweden
| | - David L. Perkins
- Division of Nephrology, Department of Medicine, and
- Department of Surgery, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Patricia W. Finn
- Department of Microbiology and Immunology
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Deepak Shukla
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
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Zhang Z, Hong W, Ruan H, Jing Y, Li S, Liu Y, Wang J, Li W, Diao L, Han L. HeRA: an atlas of enhancer RNAs across human tissues. Nucleic Acids Res 2021; 49:D932-D938. [PMID: 33119754 PMCID: PMC7779069 DOI: 10.1093/nar/gkaa940] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/06/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022] Open
Abstract
Enhancer RNA (eRNA) is a type of long non-coding RNA transcribed from DNA enhancer regions. Despite critical roles of eRNA in gene regulation, the expression landscape of eRNAs in normal human tissue remains unexplored. Using numerous samples from the Genotype-Tissue Expression project, we characterized 45 411 detectable eRNAs and identified tens of thousands of associations between eRNAs and traits, including gender, race, and age. We constructed a co-expression network to identify millions of putative eRNA regulators and target genes across different tissues. We further constructed a user-friendly data portal, Human enhancer RNA Atlas (HeRA, https://hanlab.uth.edu/HeRA/). In HeRA, users can search, browse, and download the eRNA expression profile, trait-related eRNAs, and eRNA co-expression network by searching the eRNA ID, gene symbol, and genomic region in one or multiple tissues. HeRA is the first data portal to characterize eRNAs from 9577 samples across 54 human tissues and facilitates functional and mechanistic investigations of eRNAs.
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Affiliation(s)
- Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wei Hong
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hang Ruan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Shengli Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yaoming Liu
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Abstract
Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
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Gao N, Li Y, Li J, Gao Z, Yang Z, Li Y, Liu H, Fan T. Long Non-Coding RNAs: The Regulatory Mechanisms, Research Strategies, and Future Directions in Cancers. Front Oncol 2020; 10:598817. [PMID: 33392092 PMCID: PMC7775490 DOI: 10.3389/fonc.2020.598817] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
The development and application of whole genome sequencing technology has greatly broadened our horizons on the capabilities of long non-coding RNAs (lncRNAs). LncRNAs are more than 200 nucleotides in length and lack protein-coding potential. Increasing evidence indicates that lncRNAs exert an irreplaceable role in tumor initiation, progression, as well as metastasis, and are novel molecular biomarkers for diagnosis and prognosis of cancer patients. Furthermore, lncRNAs and the pathways they influence might represent promising therapeutic targets for a number of tumors. Here, we discuss the recent advances in understanding of the specific regulatory mechanisms of lncRNAs. We focused on the signal, decoy, guide, and scaffold functions of lncRNAs at the epigenetic, transcription, and post-transcription levels in cancer cells. Additionally, we summarize the research strategies used to investigate the roles of lncRNAs in tumors, including lncRNAs screening, lncRNAs characteristic analyses, functional studies, and molecular mechanisms of lncRNAs. This review will provide a short but comprehensive description of the lncRNA functions in tumor development and progression, thus accelerating the clinical implementation of lncRNAs as tumor biomarkers and therapeutic targets.
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Affiliation(s)
- Na Gao
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Yueheng Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Jing Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhengfan Gao
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhenzhen Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
- Translational Medicine Research Center, People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Yong Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
- Faculty of Medicine, St George and Sutherland Clinical School, St George Hospital, The University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
| | - Hongtao Liu
- Laboratory for Cell Biology, College of Life Sciences of Zhengzhou University, Zhengzhou, China
| | - Tianli Fan
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
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Fang K, Huang W, Sun YM, Chen TQ, Zeng ZC, Yang QQ, Pan Q, Han C, Sun LY, Luo XQ, Wang WT, Chen YQ. Cis-acting lnc-eRNA SEELA directly binds histone H4 to promote histone recognition and leukemia progression. Genome Biol 2020; 21:269. [PMID: 33143730 PMCID: PMC7607629 DOI: 10.1186/s13059-020-02186-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Long noncoding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from annotated lncRNAs. They might act as enhancer activity-related therapeutic targets in cancer. However, the underlying mechanism of epigenetic activation and their function in cancer initiation and progression remain largely unknown. Results We identify a set of lncRNAs as lnc-eRNAs according to the epigenetic signatures of enhancers. We show that these lnc-eRNAs are broadly activated in MLL-rearranged leukemia (MLL leukemia), an aggressive leukemia caused by a chromosomal translocation, through a mechanism by which the HOXA cluster initiates enhancer activity, and the epigenetic reader BRD4 cooperates with the coregulator MLL fusion oncoprotein to induce transcriptional activation. To demonstrate the functional roles of lnc-eRNAs, two newly identified lnc-eRNAs transcribed from the SEELA eRNA cluster (SEELA), SEELA1 and SEELA2, are chosen for further studies. The results show that SEELA mediated cis-activated transcription of the nearby oncogene Serine incorporate 2 (SERINC2) by directly binding to the K31 amino acid (aa) of histone H4. Chromatin-bound SEELA strengthens the interaction between chromatin and histone modifiers to promote histone recognition and oncogene transcription. Further studies show that the SEELA-SERINC2 axis regulated aspects of cancer metabolism, such as sphingolipid synthesis, to affect leukemia progression. Conclusions This study shows that lnc-eRNAs are epigenetically activated by cancer-initiating oncoproteins and uncovers a cis-activating mechanism of oncogene transcription control based on lnc-eRNA-mediated epigenetic regulation of enhancer activity, providing insights into the critical roles of lnc-eRNAs in cancer initiation and progression. Supplementary information Supplementary information accompanies this paper at 10.1186/s13059-020-02186-x.
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Affiliation(s)
- Ke Fang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Tian-Qi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhan-Cheng Zeng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qian-Qian Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qi Pan
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xue-Qun Luo
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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Wang Y, Nie H, He X, Liao Z, Zhou Y, Zhou J, Ou C. The emerging role of super enhancer-derived noncoding RNAs in human cancer. Theranostics 2020; 10:11049-11062. [PMID: 33042269 PMCID: PMC7532672 DOI: 10.7150/thno.49168] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023] Open
Abstract
Super enhancers (SEs) are large clusters of adjacent enhancers that drive the expression of genes which regulate cellular identity; SE regions can be enriched with a high density of transcription factors, co-factors, and enhancer-associated epigenetic modifications. Through enhanced activation of their target genes, SEs play an important role in various diseases and conditions, including cancer. Recent studies have shown that SEs not only activate the transcriptional expression of coding genes to directly regulate biological functions, but also drive the transcriptional expression of non-coding RNAs (ncRNAs) to indirectly regulate biological functions. SE-derived ncRNAs play critical roles in tumorigenesis, including malignant proliferation, metastasis, drug resistance, and inflammatory response. Moreover, the abnormal expression of SE-derived ncRNAs is closely related to the clinical and pathological characterization of tumors. In this review, we summarize the functions and roles of SE-derived ncRNAs in tumorigenesis and discuss their prospective applications in tumor therapy. A deeper understanding of the potential mechanism underlying the action of SE-derived ncRNAs in tumorigenesis may provide new strategies for the early diagnosis of tumors and targeted therapy.
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47
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Wu Y, Yang Y, Gu H, Tao B, Zhang E, Wei J, Wang Z, Liu A, Sun R, Chen M, Fan Y, Mao R. Multi-omics analysis reveals the functional transcription and potential translation of enhancers. Int J Cancer 2020; 147:2210-2224. [PMID: 32573785 DOI: 10.1002/ijc.33132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Abstract
Enhancer can transcribe RNAs, however, most of them were neglected in traditional RNA-seq analysis workflow. Here, we developed a Pipeline for Enhancer Transcription (PET, http://fun-science.club/PET) for quantifying enhancer RNAs (eRNAs) from RNA-seq. By applying this pipeline on lung cancer samples and cell lines, we showed that the transcribed enhancers are enriched with histone marks and transcription factor motifs (JUNB, Hand1-Tcf3 and GATA4). By training a machine learning model, we demonstrate that enhancers can predict prognosis better than their nearby genes. Integrating the Hi-C, ChIP-seq and RNA-seq data, we observe that transcribed enhancers associate with cancer hallmarks or oncogenes, among which LcsMYC-1 (Lung cancer-specific MYC eRNA-1) potentially supports MYC expression. Surprisingly, a significant proportion of transcribed enhancers contain small protein-coding open reading frames (sORFs) and can be translated into microproteins. Our study provides a computational method for eRNA quantification and deepens our understandings of the DNA, RNA and protein nature of enhancers.
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Affiliation(s)
- Yingcheng Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China.,Department of Pathophysiology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yang Yang
- Department of Thoracic Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongyan Gu
- Department of Respiratory Medicine, Nantong Sixth People's Hospital, Nantong, Jiangsu, China
| | - Baorui Tao
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Erhao Zhang
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Jinhuan Wei
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Zhou Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Aifen Liu
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Rong Sun
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Miaomiao Chen
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yihui Fan
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China.,Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Renfang Mao
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, Jiangsu, China.,Department of Pathophysiology, School of Medicine, Nantong University, Nantong, Jiangsu, China
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48
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Noncoding RNAs Set the Stage for RNA Polymerase II Transcription. Trends Genet 2020; 37:279-291. [PMID: 33046273 DOI: 10.1016/j.tig.2020.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/24/2022]
Abstract
Effective synthesis of mammalian messenger (m)RNAs depends on many factors that together direct RNA polymerase II (pol II) through the different stages of the transcription cycle and ensure efficient cotranscriptional processing of mRNAs. In addition to the many proteins involved in transcription initiation, elongation, and termination, several noncoding (nc)RNAs also function as global transcriptional regulators. Understanding the mode of action of these non-protein regulators has been an intense area of research in recent years. Here, we describe how these ncRNAs influence key regulatory steps of the transcription process, to affect large numbers of genes. Through direct association with pol II or by modulating the activity of transcription or RNA processing factors, these regulatory RNAs perform critical roles in gene expression.
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49
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Li H, Liu J, Shen S, Dai D, Cheng S, Dong X, Sun L, Guo X. Pan-cancer analysis of alternative splicing regulator heterogeneous nuclear ribonucleoproteins (hnRNPs) family and their prognostic potential. J Cell Mol Med 2020; 24:11111-11119. [PMID: 32915499 PMCID: PMC7576281 DOI: 10.1111/jcmm.15558] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/23/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
As the most critical alternative splicing regulator, heterogeneous nuclear ribonucleoproteins (hnRNPs) have been reported to be implicated in various aspects of cancer. However, the comprehensive understanding of hnRNPs in cancer is still lacking. The molecular alterations and clinical relevance of hnRNP genes were systematically analysed in 33 cancer types based on next-generation sequence data. The expression, mutation, copy number variation, functional pathways, immune cell correlations and prognostic value of hnRNPs were investigated across different cancer types. HNRNPA1 and HNRNPAB were highly expressed in most tumours. HNRNPM, HNRNPUL1, and HNRNPL showed high mutation frequencies, and most hnRNP genes were frequently mutated in uterine corpus endometrial carcinoma (UCEC). HNRNPA2B1 showed widespread copy number amplification across various cancer types. HNRNPs participated in cancer-related pathways including protein secretion, mitotic spindle, G2/M checkpoint, DNA repair, IL6/JAK/STAT3 signal and coagulation, of which hnRNP genes of HNRNPF, HNRNPH2, HNRNPU and HNRNPUL1 are more likely to be implicated. Significant correlation of hnRNP genes with T help cells, NK cells, CD8 positive T cells and neutrophils was identified. Most hnRNPs were associated with worse survival of adrenocortical carcinoma (ACC), liver hepatocellular carcinoma (LIHC) and lung adenocarcinoma (LUAD), whereas hnRNPs predicted better prognosis in kidney renal clear cell carcinoma (KIRC) and thymoma (THYM). The prognosis analysis of KIRC suggested that hnRNPs gene cluster was significantly associated with overall survival (HR = 0.5, 95% CI = 0.35-0.73, P = 0.003). These findings provide novel evidence for further investigation of hnRNPs in the development and therapy of cancer in the future.
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Affiliation(s)
- Hao Li
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Jingwei Liu
- Department of Anorectal Surgerythe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Shixuan Shen
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryKey Laboratory of Cancer Etiology and PreventionThe First Hospital of China Medical UniversityChina Medical UniversityShenyangChina
| | - Di Dai
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Shitong Cheng
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Xiaolong Dong
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Liping Sun
- Tumor Etiology and Screening Department of Cancer Institute and General SurgeryKey Laboratory of Cancer Etiology and PreventionThe First Hospital of China Medical UniversityChina Medical UniversityShenyangChina
| | - Xiaolin Guo
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangChina
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50
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Sun YM, Chen YQ. Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application. J Hematol Oncol 2020; 13:109. [PMID: 32778133 PMCID: PMC7416809 DOI: 10.1186/s13045-020-00945-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including disease pathogenesis. With the development of innovative technologies, an increasing number of novel ncRNAs have been uncovered; information about their prominent tissue-specific expression patterns, various interaction networks, and subcellular locations will undoubtedly enhance our understanding of their potential functions. Here, we summarized the principles and innovative methods for identifications of novel ncRNAs that have potential functional roles in cancer biology. Moreover, this review also provides alternative ncRNA databases based on high-throughput sequencing or experimental validation, and it briefly describes the current strategy for the clinical translation of cancer-associated ncRNAs to be used in diagnosis.
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Affiliation(s)
- Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
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