1
|
Epp S, Chuah SM, Halasz M. Epigenetic Dysregulation in MYCN-Amplified Neuroblastoma. Int J Mol Sci 2023; 24:17085. [PMID: 38069407 PMCID: PMC10707345 DOI: 10.3390/ijms242317085] [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: 11/07/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Neuroblastoma (NB), a childhood cancer arising from the neural crest, poses significant clinical challenges, particularly in cases featuring amplification of the MYCN oncogene. Epigenetic factors play a pivotal role in normal neural crest and NB development, influencing gene expression patterns critical for tumorigenesis. This review delves into the multifaceted interplay between MYCN and known epigenetic modifications during NB genesis, shedding light on the intricate regulatory networks underlying the disease. We provide an extensive survey of known epigenetic mechanisms, encompassing DNA methylation, histone modifications, non-coding RNAs, super-enhancers (SEs), bromodomains (BET), and chromatin modifiers in MYCN-amplified (MNA) NB. These epigenetic changes collectively contribute to the dysregulated gene expression landscape observed in MNA NB. Furthermore, we review emerging therapeutic strategies targeting epigenetic regulators, including histone deacetylase inhibitors (HDACi), histone methyltransferase inhibitors (HMTi), and DNA methyltransferase inhibitors (DNMTi). We also discuss and summarize current drugs in preclinical and clinical trials, offering insights into their potential for improving outcomes for MNA NB patients.
Collapse
Affiliation(s)
- Soraya Epp
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
| | - Shin Mei Chuah
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
| | - Melinda Halasz
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
| |
Collapse
|
2
|
Long non-coding RNAs involved in retinoblastoma. J Cancer Res Clin Oncol 2023; 149:401-421. [PMID: 36305946 DOI: 10.1007/s00432-022-04398-z] [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: 09/12/2022] [Accepted: 10/05/2022] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Retinoblastoma (RB) is the most common childhood tumor that can occur in the retina and develop in a sporadic or heritable form. Although various traditional treatment options have been used for patients with RB, identifying novel strategies for childhood cancers is necessary. MATERIAL AND METHODS Recently, molecular-based targeted therapies have opened a greater therapeutic window for RB. Long non-coding RNAs (lncRNAs) presented a potential role as a biomarker for the detection of RB in various stages. CONCLUSION LncRNAs by targeting several miRNA/transcription factors play critical roles in the stimulation or suppression of RB. In this review, we summarized recent progress on the functions of tumor suppressors or oncogenes lncRNAs in RB.
Collapse
|
3
|
Tan K, Mo J, Li M, Dong Y, Han Y, Sun X, Ma Y, Zhu K, Wu W, Lu L, Liu J, Zhao K, Zhang L, Tang Y, Lv Z. SMAD9-MYCN positive feedback loop represents a unique dependency for MYCN-amplified neuroblastoma. J Exp Clin Cancer Res 2022; 41:352. [PMID: 36539767 PMCID: PMC9764568 DOI: 10.1186/s13046-022-02563-3] [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: 08/08/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common extracranial solid tumor occurring during childhood and high-risk NB patients have a poor prognosis. The amplified MYCN gene serves as an important determinant of a high risk of NB. METHODS We performed an integrative screen using public NB tissue and cell line data, and identified that SMAD9 played an important role in high-risk NB. An investigation of the super-enhancers database (SEdb) and chromatin immunoprecipitation sequencing (ChIP-seq) dataset along with biological experiments of incorporating gene knockdown and CRISPR interference (CRISPRi) were performed to identify upstream regulatory mechanism of SMAD9. Gene knockdown and rescue, quantitative real-time PCR (Q-RT-PCR), cell titer Glo assays, colony formation assays, a subcutaneous xenograft model and immunohistochemistry were used to determine the functional role of SMAD9 in NB. An integrative analysis of ChIP-seq data with the validation of CRISPRi and dual-luciferase reporter assays and RNA sequencing (RNA-seq) data with Q-RT-PCR validation was conducted to analyze the downstream regulatory mechanism of SMAD9. RESULTS High expression of SMAD9 was specifically induced by the transcription factors including MYCN, PHOX2B, GATA3 and HAND2 at the enhancer region. Genetic suppression of SMAD9 inhibited MYCN-amplified NB cell proliferation and tumorigenicity both in vitro and in vivo. Further studies revealed that SMAD9 bound to the MYCN promoter and transcriptionally regulate MYCN expression, with MYCN reciprocally binding to the SMAD9 enhancer and transactivating SMAD9, thus forming a positive feedback loop along with the MYCN-associated cancer cell cycle. CONCLUSION This study delineates that SMAD9 forms a positive transcriptional feedback loop with MYCN and represents a unique tumor-dependency for MYCN-amplified neuroblastoma.
Collapse
Affiliation(s)
- Kezhe Tan
- Department of General Surgery, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jialin Mo
- Research Center of Translational medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Li
- Research Center of Translational medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Dong
- Shanghai Institute of Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yujie Han
- Research Center of Translational medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Sun
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingxuan Ma
- Department of General Surgery, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Zhu
- Department of General Surgery, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wu
- Department of General Surgery, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li Lu
- Department of General Surgery, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangbin Liu
- Department of General Surgery, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kewen Zhao
- Research Center of Translational medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Zhang
- Research Center of Translational medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yujie Tang
- Research Center of Translational medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
| | - Zhibao Lv
- Department of General Surgery, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
4
|
Bartolucci D, Montemurro L, Raieli S, Lampis S, Pession A, Hrelia P, Tonelli R. MYCN Impact on High-Risk Neuroblastoma: From Diagnosis and Prognosis to Targeted Treatment. Cancers (Basel) 2022; 14:cancers14184421. [PMID: 36139583 PMCID: PMC9496712 DOI: 10.3390/cancers14184421] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Neuroblastoma is one of the most diffuse and the deadliest cancer in children. While many advances have been made in the last few decades to improve patients’ outcome, high-risk neuroblastoma (HR-NB) still shows a very aggressive pattern of development and poor prognosis, with only a 50% chance of 5-year survival. Moreover, while many factors contribute to defining the high-risk condition, MYCN status is well established as the major element in pathology disclosure. The aim of this review is to describe the current knowledge in the diagnosis, prognosis and therapeutic approaches of HR-NB, particularly in relation to MYCN. The review highlights how MYCN influences the HR-NB scenario and the new therapeutic approaches that are currently proposed to target it, in consideration of MYCN as a highly relevant target for HR-NB patient management. Abstract Among childhood cancers, neuroblastoma is the most diffuse solid tumor and the deadliest in children. While to date, the pathology has become progressively manageable with a significant increase in 5-year survival for its less aggressive form, high-risk neuroblastoma (HR-NB) remains a major issue with poor outcome and little survivability of patients. The staging system has also been improved to better fit patient needs and to administer therapies in a more focused manner in consideration of pathology features. New and improved therapies have been developed; nevertheless, low efficacy and high toxicity remain a staple feature of current high-risk neuroblastoma treatment. For this reason, more specific procedures are required, and new therapeutic targets are also needed for a precise medicine approach. In this scenario, MYCN is certainly one of the most interesting targets. Indeed, MYCN is one of the most relevant hallmarks of HR-NB, and many studies has been carried out in recent years to discover potent and specific inhibitors to block its activities and any related oncogenic function. N-Myc protein has been considered an undruggable target for a long time. Thus, many new indirect and direct approaches have been discovered and preclinically evaluated for the interaction with MYCN and its pathways; a few of the most promising approaches are nearing clinical application for the investigation in HR-NB.
Collapse
Affiliation(s)
| | - Luca Montemurro
- Pediatric Oncology and Hematology Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | | | | | - Andrea Pession
- Pediatric Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Roberto Tonelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
- Correspondence:
| |
Collapse
|
5
|
Weisman CM. The Origins and Functions of De Novo Genes: Against All Odds? J Mol Evol 2022; 90:244-257. [PMID: 35451603 PMCID: PMC9233646 DOI: 10.1007/s00239-022-10055-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/29/2022] [Indexed: 01/22/2023]
Abstract
"De novo" genes evolve from previously non-genic DNA. This strikes many of us as remarkable, because it seems extraordinarily unlikely that random sequence would produce a functional gene. How is this possible? In this two-part review, I first summarize what is known about the origins and molecular functions of the small number of de novo genes for which such information is available. I then speculate on what these examples may tell us about how de novo genes manage to emerge despite what seem like enormous opposing odds.
Collapse
Affiliation(s)
- Caroline M Weisman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
6
|
Zhang G, Zheng D, Chen X, Li L, Yu J. miR-152-mediated MKK7 downregulation is attenuated by MYCNOS in ovarian adenocarcinoma. Oncol Lett 2021; 22:841. [PMID: 34733360 PMCID: PMC8561216 DOI: 10.3892/ol.2021.13102] [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: 12/30/2020] [Accepted: 09/07/2021] [Indexed: 12/09/2022] Open
Abstract
MYCN opposite strand (MYCNOS) acts as an oncogenic long non-coding RNA in liver cancer. However, its role in other cancer types is unknown. The aim of the present study was to investigate the function of MYCNOS in ovarian adenocarcinoma (OA). MYCNOS expression in OA was determined using reverse transcription-quantitative PCR (RT-qPCR), and its prognostic value for OA was evaluated in a 5-year follow-up study. The predicted interaction between MYCNOS and microRNA (miR)-152 was confirmed using a dual luciferase reporter assay. The association between MYCNOS and miR-152 was also analyzed in overexpression experiments. The effects of MYCNOS and miR-152 on mitogen-activated protein kinase kinase 7 (MKK7) expression were explored using RT-qPCR and western blotting. Cell proliferation was analyzed using a Cell Counting Kit-8 assay. MYCNOS expression was found to be upregulated in OA and predicted poor survival. In addition, MYCNOS was predicted to interact with miR-152, and a dual luciferase assay confirmed this interaction. However, MYCNOS and miR-152 overexpression did not affect their mutual expression levels. MYCNOS overexpression upregulated MKK7, a target of miR-152. Cell proliferation increased following simultaneous MYCNOS and MKK7 overexpression, but was reduced following miR-152 overexpression. Moreover, MYCNOS overexpression attenuated the effects of miR-152 overexpression. In conclusion, MYCNOS may act by sponging miR-152 to upregulate MKK7 expression in OA, thereby promoting cell proliferation.
Collapse
Affiliation(s)
- Guifang Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Dan Zheng
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Xiaoqing Chen
- Day Operation Center, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330003, P.R. China
| | - Li Li
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Jingrong Yu
- Department of Oncology, The Fourth Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330003, P.R. China
| |
Collapse
|
7
|
Matsuo T, Nakatani K, Setoguchi T, Matsuo K, Tamada T, Suenaga Y. Secondary Structure of Human De Novo Evolved Gene Product NCYM Analyzed by Vacuum-Ultraviolet Circular Dichroism. Front Oncol 2021; 11:688852. [PMID: 34497756 PMCID: PMC8420857 DOI: 10.3389/fonc.2021.688852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/31/2021] [Indexed: 11/29/2022] Open
Abstract
NCYM, a cis-antisense gene of MYCN, encodes a Homininae-specific protein that promotes the aggressiveness of human tumors. Newly evolved genes from non-genic regions are known as de novo genes, and NCYM was the first de novo gene whose oncogenic functions were validated in vivo. Targeting NCYM using drugs is a potential strategy for cancer therapy; however, the NCYM structure must be determined before drug design. In this study, we employed vacuum-ultraviolet circular dichroism to evaluate the secondary structure of NCYM. The SUMO-tagged NCYM and the isolated SUMO tag in both hydrogenated and perdeuterated forms were synthesized and purified in a cell-free in vitro system, and vacuum-ultraviolet circular dichroism spectra were measured. Significant differences between the tagged NCYM and the isolated tag were evident in the wavelength range of 190–240 nm. The circular dichroism spectral data combined with a neural network system enabled to predict the secondary structure of NCYM at the amino acid level. The 129-residue tag consists of α-helices (approximately 14%) and β-strands (approximately 29%), which corresponded to the values calculated from the atomic structure of the tag. The 238-residue tagged NCYM contained approximately 17% α-helices and 27% β-strands. The location of the secondary structure predicted using the neural network revealed that these secondary structures were enriched in the Homininae-specific region of NCYM. Deuteration of NCYM altered the secondary structure at D90 from an α-helix to another structure other than α-helix and β-strand although this change was within the experimental error range. All four nonsynonymous single-nucleotide polymorphisms (SNPs) in human populations were in this region, and the amino acid alteration in SNP N52S enhanced Myc-nick production. The D90N mutation in NCYM promoted NCYM-mediated MYCN stabilization. Our results reveal the secondary structure of NCYM and demonstrated that the Homininae-specific domain of NCYM is responsible for MYCN stabilization.
Collapse
Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Ibaraki, Japan
| | - Kazuma Nakatani
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan.,Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan.,Innovative Medicine CHIBA Doctoral World-leading Innovative & Smart Education (WISE) Program, Chiba University, Chiba, Japan
| | - Taiki Setoguchi
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan.,Department of Neurosurgery, Chiba Cancer Center, Chiba, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Hiroshima, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Ibaraki, Japan
| | - Yusuke Suenaga
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan
| |
Collapse
|
8
|
Yang M, Carter S, Parmar S, Bume DD, Calabrese DR, Liang X, Yazdani K, Xu M, Liu Z, Thiele CJ, Schneekloth JS. Targeting a noncanonical, hairpin-containing G-quadruplex structure from the MYCN gene. Nucleic Acids Res 2021; 49:7856-7869. [PMID: 34289065 DOI: 10.1093/nar/gkab594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/10/2021] [Accepted: 07/20/2021] [Indexed: 11/12/2022] Open
Abstract
The MYCN gene encodes the transcription factor N-Myc, a driver of neuroblastoma (NB). Targeting G-quadruplexes (G4s) with small molecules is attractive strategy to control the expression of undruggable proteins such as N-Myc. However, selective binders to G4s are challenging to identify due to the structural similarity of many G4s. Here, we report the discovery of a small molecule ligand (4) that targets the noncanonical, hairpin containing G4 structure found in the MYCN gene using small molecule microarrays (SMMs). Unlike many G4 binders, the compound was found to bind to a pocket at the base of the hairpin region of the MYCN G4. This compound stabilizes the G4 and has affinity of 3.5 ± 1.6 μM. Moreover, an improved analog, MY-8, suppressed levels of both MYCN and MYCNOS (a lncRNA embedded within the MYCN gene) in NBEB neuroblastoma cells. This work indicates that the approach of targeting complex, hybrid G4 structures that exist throughout the human genome may be an applicable strategy to achieve selectivity for targeting disease-relevant genes including protein coding (MYCN) as well as non-coding (MYCNOS) gene products.
Collapse
Affiliation(s)
- Mo Yang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Sakereh Carter
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Desta D Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - David R Calabrese
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Xiao Liang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Kamyar Yazdani
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Man Xu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| |
Collapse
|
9
|
Saengwimol D, Chittavanich P, Laosillapacharoen N, Srimongkol A, Chaitankar V, Rojanaporn D, Aroonroch R, Suktitipat B, Saisawang C, Svasti S, Hongeng S, Kaewkhaw R. Silencing of the Long Noncoding RNA MYCNOS1 Suppresses Activity of MYCN-Amplified Retinoblastoma Without RB1 Mutation. Invest Ophthalmol Vis Sci 2021; 61:8. [PMID: 33270844 PMCID: PMC7718827 DOI: 10.1167/iovs.61.14.8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Purpose MYCNOS (MYCN opposite strand) is co-amplified with MYCN in pediatric cancers, including retinoblastoma. MYCNOS encodes several RNA variants whose functions have not been elucidated in retinoblastoma. Thus, we attempted to identify MYCNOS variants in retinoblastoma and aimed to decipher the role of MYCNOS variant 1 (MYCNOS1) on the activity of MYCN-amplified retinoblastoma. Methods The profiles of MYCNOS variants and MYCN status were determined in 17 retinoblastoma tissues, cell lines, retinas, and retinal organoids. A functional study of MYCNOS1 expression was conducted in patient-derived tumor cells and in retinoblastoma cell lines via short hairpin RNA-mediated gene silencing. We carried out MYCN expression, cell viability, cell cycle, apoptosis, soft agar colony formation, and transwell assays to examine the role of MYCNOS1 in MYCN and cell behaviors. We analyzed a transcriptome of MYCN-amplified retinoblastoma cells deficient for MYCNOS1 and, finally, tested the responses of these cells to chemotherapeutic agents. Results Expression of MYCNOS1 was associated with the expression and copy number of MYCN. Knockdown of MYCNOS1 caused instability of the MYCN protein, leading to cell cycle arrest and impaired proliferation and chemotaxis-directed migration in MYCN-amplified retinoblastoma cells in which RB1 was intact. MYCNOS1 expression was associated with gene signatures of photoreceptor cells and epithelial–mesenchymal transition. MYCNOS1 silencing enhanced the response of retinoblastoma cells to topotecan but not carboplatin. Conclusions MYCNOS1 supports progression of retinoblastoma. Inhibition of MYCNOS1 expression may be necessary to suppress MYCN activity when treating MYCN-amplified cancers without RB1 mutation.
Collapse
Affiliation(s)
- Duangporn Saengwimol
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pamorn Chittavanich
- Section of Translational Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Natanan Laosillapacharoen
- Section of Translational Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Atthapol Srimongkol
- Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Vijender Chaitankar
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Duangnate Rojanaporn
- Department of Ophthalmology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rangsima Aroonroch
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Bhoom Suktitipat
- Department of Biochemistry, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Integrative Computational BioScience Center, Mahidol University, Nakhon Pathom, Thailand
| | - Chonticha Saisawang
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Saovaros Svasti
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.,Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rossukon Kaewkhaw
- Section of Translational Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
10
|
Rezaei O, Honarmand Tamizkar K, Hajiesmaeili M, Taheri M, Ghafouri-Fard S. Non-Coding RNAs Participate in the Pathogenesis of Neuroblastoma. Front Oncol 2021; 11:617362. [PMID: 33718173 PMCID: PMC7945591 DOI: 10.3389/fonc.2021.617362] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Neuroblastoma is one of the utmost frequent neoplasms during the first year of life. This pediatric cancer is believed to be originated during the embryonic life from the neural crest cells. Previous studies have detected several types of chromosomal aberrations in this tumor. More recent studies have emphasized on expression profiling of neuroblastoma samples to identify the dysregulated genes in this type of cancer. Non-coding RNAs are among the mostly dysregulated genes in this type of cancer. Such dysregulation has been associated with a number of chromosomal aberrations that are frequently detected in neuroblastoma. In this study, we explain the role of non-coding transcripts in the malignant transformation in neuroblastoma and their role as biomarkers for this pediatric cancer.
Collapse
Affiliation(s)
- Omidvar Rezaei
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mohammadreza Hajiesmaeili
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
11
|
Poon E, Liang T, Jamin Y, Walz S, Kwok C, Hakkert A, Barker K, Urban Z, Thway K, Zeid R, Hallsworth A, Box G, Ebus ME, Licciardello MP, Sbirkov Y, Lazaro G, Calton E, Costa BM, Valenti M, De Haven Brandon A, Webber H, Tardif N, Almeida GS, Christova R, Boysen G, Richards MW, Barone G, Ford A, Bayliss R, Clarke PA, De Bono J, Gray NS, Blagg J, Robinson SP, Eccles SA, Zheleva D, Bradner JE, Molenaar J, Vivanco I, Eilers M, Workman P, Lin CY, Chesler L. Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma. J Clin Invest 2020; 130:5875-5892. [PMID: 33016930 PMCID: PMC7598076 DOI: 10.1172/jci134132] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/29/2020] [Indexed: 01/23/2023] Open
Abstract
The undruggable nature of oncogenic Myc transcription factors poses a therapeutic challenge in neuroblastoma, a pediatric cancer in which MYCN amplification is strongly associated with unfavorable outcome. Here, we show that CYC065 (fadraciclib), a clinical inhibitor of CDK9 and CDK2, selectively targeted MYCN-amplified neuroblastoma via multiple mechanisms. CDK9 - a component of the transcription elongation complex P-TEFb - bound to the MYCN-amplicon superenhancer, and its inhibition resulted in selective loss of nascent MYCN transcription. MYCN loss led to growth arrest, sensitizing cells for apoptosis following CDK2 inhibition. In MYCN-amplified neuroblastoma, MYCN invaded active enhancers, driving a transcriptionally encoded adrenergic gene expression program that was selectively reversed by CYC065. MYCN overexpression in mesenchymal neuroblastoma was sufficient to induce adrenergic identity and sensitize cells to CYC065. CYC065, used together with temozolomide, a reference therapy for relapsed neuroblastoma, caused long-term suppression of neuroblastoma growth in vivo, highlighting the clinical potential of CDK9/2 inhibition in the treatment of MYCN-amplified neuroblastoma.
Collapse
Affiliation(s)
- Evon Poon
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Tong Liang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Yann Jamin
- Division of Radiotherapy and Imaging, ICR, London, United Kingdom
| | - Susanne Walz
- Core Unit Bioinformatics, Comprehensive Cancer Center Mainfranken and Theodor Boveri Institute, Biocenter, University of Wurzburg, Wurzburg, Germany
| | - Colin Kwok
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Anne Hakkert
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Karen Barker
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Zuzanna Urban
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Khin Thway
- Division of Molecular Pathology, ICR, London, and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Albert Hallsworth
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Gary Box
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Marli E. Ebus
- Prinses Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Marco P. Licciardello
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Yordan Sbirkov
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Glori Lazaro
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Elizabeth Calton
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Barbara M. Costa
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Melanie Valenti
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Alexis De Haven Brandon
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Hannah Webber
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Nicolas Tardif
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Gilberto S. Almeida
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Division of Radiotherapy and Imaging, ICR, London, United Kingdom
| | | | | | - Mark W. Richards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Giuseppe Barone
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Anthony Ford
- Division of Molecular Pathology, ICR, London, and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Richard Bayliss
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Paul A. Clarke
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | | | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Julian Blagg
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | | | - Suzanne A. Eccles
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | | | - James E. Bradner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan Molenaar
- Prinses Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Igor Vivanco
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Martin Eilers
- Comprehensive Cancer Center Mainfranken and Theodor Boveri Institute, Biocenter, University of Wurzburg, Wurzburg, Germany
| | - Paul Workman
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
- Cancer Research UK, Cancer Therapeutics Unit, ICR, London, United Kingdom
| | - Charles Y. Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Louis Chesler
- Division of Clinical Studies and
- Division of Cancer Therapeutics, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| |
Collapse
|
12
|
Suenaga Y, Nakatani K, Nakagawara A. De novo evolved gene product NCYM in the pathogenesis and clinical outcome of human neuroblastomas and other cancers. Jpn J Clin Oncol 2020; 50:839-846. [PMID: 32577751 DOI: 10.1093/jjco/hyaa097] [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: 03/21/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022] Open
Abstract
NCYM is an antisense transcript of MYCN oncogene and promotes tumor progression. NCYM encodes a de novo protein whose open reading frame evolved from noncoding genomic regions in the ancestor of Homininae. Because of its topology, NCYM is always co-amplified with MYCN oncogene, and the mutual regulations between NCYM and MYCN maintain their expressions at high levels in MYCN-amplified tumors. NCYM stabilizes MYCN by inhibiting GSK3β, whereas MYCN stimulates transcription of both NCYM and MYCN. NCYM mRNA and its noncoding transcript variants MYCNOS have been shown to stimulate MYCN expression via direct binding to MYCN promoter, indicating that both coding and noncoding transcripts of NCYM induce MYCN expression. In contrast to the noncoding functions of NCYM, NCYM protein also promotes calpain-mediated cleavage of c-MYC. The cleaved product called Myc-nick inhibits cell death and promotes cancer cell migration. Furthermore, NCYM-mediated inhibition of GSK3β results in the stabilization of β-catenin, which promotes aggressiveness of bladder cancers. These MYCN-independent functions of NCYM showed their clinical significance in MYCN-non-amplified tumors, including adult tumors. This year is the 30th anniversary of the identification of NCYM/MYCNOS gene. On this special occasion, we summarize the current understanding of molecular functions and the clinical significance of NCYM and discuss future directions to achieve therapeutic strategies targeting NCYM.
Collapse
|
13
|
Dysregulated Pyrimidine Biosynthesis Contributes to 5-FU Resistance in SCLC Patient-Derived Organoids but Response to a Novel Polymeric Fluoropyrimidine, CF10. Cancers (Basel) 2020; 12:cancers12040788. [PMID: 32224870 PMCID: PMC7226016 DOI: 10.3390/cancers12040788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 02/08/2023] Open
Abstract
Chemo-immunotherapy is central to the treatment of small cell lung cancer (SCLC). Despite modest progress made with the addition of immunotherapy, current cytotoxic regimens display minimal survival benefit and new treatments are needed. Thymidylate synthase (TS) is a well-validated anti-cancer drug target, but conventional TS inhibitors display limited clinical efficacy in refractory or recurrent SCLC. We performed RNA-Seq analysis to identify gene expression changes in SCLC biopsy samples to provide mechanistic insight into the potential utility of targeting pyrimidine biosynthesis to treat SCLC. We identified systematic dysregulation of pyrimidine biosynthesis, including elevated TYMS expression that likely contributes to the lack of efficacy for current TS inhibitors in SCLC. We also identified E2F1-3 upregulation in SCLC as a potential driver of TYMS expression that may contribute to tumor aggressiveness. To test if TS inhibition could be a viable strategy for SCLC treatment, we developed patient-derived organoids (PDOs) from human SCLC biopsy samples and used these to evaluate both conventional fluoropyrimidine drugs (e.g., 5-fluorouracil), platinum-based drugs, and CF10, a novel fluoropyrimidine polymer with enhanced TS inhibition activity. PDOs were relatively resistant to 5-FU and while moderately sensitive to the front-line agent cisplatin, were relatively more sensitive to CF10. Our studies demonstrate dysregulated pyrimidine biosynthesis contributes to drug resistance in SCLC and indicate that a novel approach to target these pathways may improve outcomes.
Collapse
|
14
|
Zhao Z, Shelton SD, Oviedo A, Baker AL, Bryant CP, Omidvarnia S, Du L. The PLAGL2/MYCN/miR-506-3p interplay regulates neuroblastoma cell fate and associates with neuroblastoma progression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:41. [PMID: 32087738 PMCID: PMC7036248 DOI: 10.1186/s13046-020-1531-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/21/2020] [Indexed: 12/17/2022]
Abstract
Background The oncogene MYCN is critical for tumorigenesis of several types of cancers including neuroblastoma. We previously reported that miR-506-3p repressed MYCN expression in neuroblastoma cells. However, the mechanism underlying such regulation was undetermined since there is no miR-506-3p target site in MYCN 3’UTR. Methods By a systematic investigation combining microarray, informatics and luciferase reporter assay, we identified that the transcriptional factor pleiomorphic adenoma gene-like 2 (PLAGL2) is a direct target of miR-506-3p that mediates its regulation on MYCN expression. Using CHIP-PCR and luciferase reporter assay, we validated the transcriptional regulation of MYCN by PLAGL2 and we further demonstrated the transcriptional regulation of PLAGL2 by MYCN. We examined the function of PLAGL2 in regulating neuroblastoma cell fate by cell viability assay, colony formation and Western blotting of differentiation markers. We examined the effect of retinoic acid, the differentiation agent used in neuroblastoma therapy, on miR-506-3p, PLAGL2 and MYCN expressions by quantitative PCR and Western blots. We investigated the clinical relevance of PLAGL2 expression by examining the correlation of tumor PLAGL2 mRNA levels with MYCN mRNA expression and patient survival using public neuroblastoma patient datasets. Results We found that miR-506-3p directly down-regulated PLAGL2 expression, and we validated a PLAGL2 binding site in the MYCN promoter region responsible for promoting MYCN transcription, thereby establishing a mechanism through which miR-506-3p regulates MYCN expression. Conversely, we discovered that MYCN regulated PLAGL2 transcription through five N-Myc-binding E-boxes in the PLAGL2 promoter region. We further confirmed the reciprocal regulation between endogenous PLAGL2 and MYCN in multiple neuroblastoma cell lines. Moreover, we found that PLAGL2 knockdown induced neuroblastoma cell differentiation and reduced cell proliferation, and combined knockdown of PLAGL2 and MYCN showed a synergistic effect. More strikingly, we found that high tumor PLAGL2 mRNA levels were significantly correlated with high MYCN mRNA levels and poor patient survival in neuroblastoma patients. Furthermore, we found that retinoic acid increased expression of miR-506-3p and repressed expression of MYCN and PLAGL2. Conclusions Our findings altogether suggest that the interplay network formed by PLAGL2, MYCN and miR-506-3p is an important mechanism in regulating neuroblastoma cell fate, determining neuroblastoma prognosis, and mediating the therapeutic function of retinoic acid.
Collapse
Affiliation(s)
- Zhenze Zhao
- Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Spencer D Shelton
- Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Alejandro Oviedo
- Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Amy L Baker
- Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Collin P Bryant
- Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Soroush Omidvarnia
- Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Liqin Du
- Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA.
| |
Collapse
|
15
|
LncRNA MYCNOS facilitates proliferation and invasion in hepatocellular carcinoma by regulating miR-340. Hum Cell 2019; 33:148-158. [PMID: 31776854 DOI: 10.1007/s13577-019-00303-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) remains one of the most common and aggressive human cancers worldwide. Accumulating evidences indicate that non-coding RNAs are critical regulators implicated in various physiological processes including HCC development. Long non-coding RNA (lncRNA) MYCN opposite-strand (MYCNOS) was reported to be up-regulated in several human cancers, yet its role in HCC progression is still elusive. In the present study, MYCNOS was up-regulated in both HCC tissues and cell lines, and elevated MYCNOS expression was correlated to shorter survival time of HCC patients. We knocked down MYCNOS expression using short hairpin RNAs specifically targeting MYCNOS. MYCNOS knockdown significantly inhibited proliferation in HCC cells in vitro accompanied by exacerbated cell apoptosis; it also suppressed tumor growth in mouse model in vivo. Besides, the migration and invasion of HCC cells were remarkably inhibited after MYCNOS knockdown. In addition, MYCNOS acted as a negative regulator of miR-340 in HCC cells, and all effects of MYCNOS knockdown were abrogated by further miR-340 inhibition. We also discovered that oncogene phosphatidylinositol-3, 4, 5-trisphosphate-dependent Rac exchange factor 2 (PREX2) was a downstream target of miR-340, and PREX2 expression was positively correlated to that of MYCNOS in HCC tissues. In conclusion, our findings demonstrated that MYCNOS knockdown inhibited HCC progression through regulating miR-340.
Collapse
|
16
|
Mühling J, Eberherr C, Müller Höcker J, Grote V, von Schweinitz D, Kappler R, Fröba-Pohl A. Vessel adherent growth represents a major challenge in the surgical resection of neuroblastoma and Is associated with adverse outcome. J Pediatr Surg 2019; 54:2336-2342. [PMID: 31402147 DOI: 10.1016/j.jpedsurg.2019.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 01/02/2023]
Abstract
PURPOSE Neuroblastoma (NB) is the most common extracranial, solid tumor in childhood, with a peak incidence in children under 6 years of age. Due to its variable course of disease, which ranges from spontaneous regression to metastatic spread, NB still represents a significant therapeutic challenge. Strikingly, a certain number of NBs intraoperatively show vessel adhesion and/or infiltrative growth, which is often not visible in pre-operative imaging. We proposed the term unexpected vessel infiltration of NB (UVIN) to denote this phenomenon. UVIN represents a major surgical challenge. METHODS In this study, we determined frequency and clinical relevance of UVIN in a cohort of 100 NB-patients with subsequent correlation to several unfavorable characteristics of disease. RNA expression levels of MYCN and its co-regulated antisense transcript MYCNOS to identify markers was measured by PCR. RESULTS We found UVIN to be present in 34% of cases and significantly correlated with incomplete resection, MYCN amplification, complications, neoadjuvant therapy, tumor grade and MYCNOS expression levels. MYCN expression levels showed no significant results with UVIN. CONCLUSION Collectively, our data show that UVIN represents a frequent surgical problem associated with a poor outcome in NB patients. MYCN and MYCNOS seem to be no appropriate markers for UVIN. TYPE OF STUDY Prognosis study. LEVEL OF EVIDENCE Level III.
Collapse
Affiliation(s)
- Jakob Mühling
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany.
| | - Corinna Eberherr
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | | | - Veit Grote
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Dietrich von Schweinitz
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Roland Kappler
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Alexandra Fröba-Pohl
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| |
Collapse
|
17
|
Utnes P, Løkke C, Flægstad T, Einvik C. Clinically Relevant Biomarker Discovery in High-Risk Recurrent Neuroblastoma. Cancer Inform 2019; 18:1176935119832910. [PMID: 30886518 PMCID: PMC6413431 DOI: 10.1177/1176935119832910] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/27/2018] [Indexed: 12/28/2022] Open
Abstract
Neuroblastoma is a pediatric cancer of the developing sympathetic nervous system.
High-risk neuroblastoma patients typically undergo an initial remission in
response to treatment, followed by recurrence of aggressive tumors that have
become refractory to further treatment. The need for biomarkers that can select
patients not responding well to therapy in an early phase is therefore needed.
In this study, we used next generation sequencing technology to determine the
expression profiles in high-risk neuroblastoma cell lines established before and
after therapy. Using partial least squares-discriminant analysis (PLS-DA) with
least absolute shrinkage and selection operator (LASSO) and leave-one-out
cross-validation, we identified a panel of 55 messenger RNAs and 17 long
non-coding RNAs (lncRNAs) which were significantly altered in the expression
between cell lines isolated from primary and recurrent tumors. From a
neuroblastoma patient cohort, we found 20 of the 55 protein-coding genes to be
differentially expressed in patients with unfavorable compared with favorable
outcome. We further found a twofold increase or decrease in hazard ratios in
these genes when comparing patients with unfavorable and favorable outcome. Gene
set enrichment analysis (GSEA) revealed that these genes were involved in
proliferation, differentiation and regulated by Polycomb group (PcG) proteins.
Of the 17 lncRNAs, 3 upregulated (NEAT1, SH3BP5-AS1, NORAD) and
3 downregulated lncRNAs (DUBR, MEG3, DHRS4-AS1) were also found
to be differentially expressed in favorable compared with unfavorable outcome.
Moreover, using expression profiles on both miRNAs and mRNAs in the same cohort
of cell lines, we found 13 downregulated and 18 upregulated experimentally
observed miRNA target genes targeted by miR-21, -424 and
-30e, -29b, -138, -494, -181a, -34a, -29b,
respectively. The advantage of analyzing biomarkers in a clinically relevant
neuroblastoma model system enables further studies on the effect of individual
genes upon gene perturbation. In summary, this study identified several genes,
which may aid in the prediction of response to therapy and tumor recurrence.
Collapse
Affiliation(s)
- Peter Utnes
- Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, Tromsø, Norway
| | - Cecilie Løkke
- Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, Tromsø, Norway
| | - Trond Flægstad
- Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, Tromsø, Norway.,Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, Tromsø, Norway
| | - Christer Einvik
- Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, Tromsø, Norway.,Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, Tromsø, Norway
| |
Collapse
|
18
|
Eberherr C, Beck A, Vokuhl C, Becker K, Häberle B, Von Schweinitz D, Kappler R. Targeting excessive MYCN expression using MLN8237 and JQ1 impairs the growth of hepatoblastoma cells. Int J Oncol 2019; 54:1853-1863. [PMID: 30864675 DOI: 10.3892/ijo.2019.4741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/23/2019] [Indexed: 11/06/2022] Open
Abstract
Hepatoblastoma (HB) is the most common liver tumor in children under the age of 3 years worldwide. While many patients achieve good outcomes with surgical resection and conventional chemotherapy, there is still a high‑risk population that exhibits a poor treatment response and unfavorable prognosis, which warrants the search for novel treatment options. In recent years, it has become clear that genetic events alone are not sufficient to explain the aggressive phenotype of this embryonal malignancy. Instead, epigenetic modifications and aberrant gene expression seem to be key drivers of HB. In the present study, expression analyses such as reverse transcription‑quantitative polymerase chain reaction revealed that the oncogene, MYCN proto‑oncogene basic‑helix‑loop‑helix transcription factor (MYCN) was upregulated in HB and other pediatric liver tumors, due to the transcriptional activity of its antisense transcript MYCN opposite strand (MYCNOS). Pyrosequencing demonstrated the hypomethylated regions in the promoter of MYCN and MYCNOS, suggesting that an epigenetic mechanism may underlie the induction of aberrant expression. Transient MYCN knockdown in HB cells resulted in growth inhibition over time. In addition, treating HB cells with the MYCN inhibitors JQ1 and MLN8237 led to the significant downregulation of MYCN either at the mRNA or protein levels, respectively. The underlying mechanism of action of the two inhibitors was revealed to be associated with the induction of dose‑dependent growth arrest, by arresting cells at either the G1/G0 or G2 phase. Furthermore, MLN8237 and JQ1 were able to cause spindle disturbances and/or apoptosis in HB cells. The present results suggest that MYCN may be a promising biomarker for HB and a potential therapeutic target in patients with tumors overexpressing MYCN.
Collapse
Affiliation(s)
- Corinna Eberherr
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, D‑80337 Munich, Germany
| | - Alexander Beck
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, D‑80337 Munich, Germany
| | - Christian Vokuhl
- Institute of Paidopathology, Pediatric Tumor Registry, Christian‑Albrecht's‑University Kiel, D‑24105 Kiel, Germany
| | - Kristina Becker
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, D‑80337 Munich, Germany
| | - Beate Häberle
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, D‑80337 Munich, Germany
| | - Dietrich Von Schweinitz
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, D‑80337 Munich, Germany
| | - Roland Kappler
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, D‑80337 Munich, Germany
| |
Collapse
|
19
|
Nieminen T, Scott TA, Lin FM, Chen Z, Yla-Herttuala S, Morris KV. Long Non-Coding RNA Modulation of VEGF-A during Hypoxia. Noncoding RNA 2018; 4:ncrna4040034. [PMID: 30463374 PMCID: PMC6315885 DOI: 10.3390/ncrna4040034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022] Open
Abstract
The role and function of long non-coding RNAs (lncRNAs) in modulating gene expression is becoming apparent. Vascular endothelial growth factor A (VEGF-A) is a key regulator of blood vessel formation and maintenance making it a promising therapeutic target for activation in ischemic diseases. In this study, we uncover a functional role for two antisense VEGF-A lncRNAs, RP1-261G23.7 and EST AV731492, in transcriptional regulation of VEGF-A during hypoxia. We find here that both lncRNAs are polyadenylated, concordantly upregulated with VEGF-A, localize to the VEGF-A promoter and upstream elements in a hypoxia dependent manner either as a single-stranded RNA or DNA bound RNA, and are associated with enhancer marks H3K27ac and H3K9ac. Collectively, these data suggest that VEGF-A antisense lncRNAs, RP1-261G23.7 and EST AV731492, function as VEGF-A promoter enhancer-like elements, possibly by acting as a local scaffolding for proteins and also small RNAs to tether.
Collapse
Affiliation(s)
- Tiina Nieminen
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - Tristan A Scott
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Feng-Mao Lin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Zhen Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Seppo Yla-Herttuala
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, FI-70211 Kuopio, Finland.
| | - Kevin V Morris
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| |
Collapse
|
20
|
Singh AS, Heery R, Gray SG. In Silico and In Vitro Analyses of LncRNAs as Potential Regulators in the Transition from the Epithelioid to Sarcomatoid Histotype of Malignant Pleural Mesothelioma (MPM). Int J Mol Sci 2018; 19:ijms19051297. [PMID: 29701689 PMCID: PMC5983793 DOI: 10.3390/ijms19051297] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare malignancy, with extremely poor survival rates. At present, treatment options are limited, with no second line chemotherapy for those who fail first line therapy. Extensive efforts are ongoing in a bid to characterise the underlying molecular mechanisms of mesothelioma. Recent research has determined that between 70–90% of our genome is transcribed. As only 2% of our genome is protein coding, the roles of the remaining proportion of non-coding RNA in biological processes has many applications, including roles in carcinogenesis and epithelial–mesenchymal transition (EMT), a process thought to play important roles in MPM pathogenesis. Non-coding RNAs can be separated loosely into two subtypes, short non-coding RNAs (<200 nucleotides) or long (>200 nucleotides). A significant body of evidence has emerged for the roles of short non-coding RNAs in MPM. Less is known about the roles of long non-coding RNAs (lncRNAs) in this disease setting. LncRNAs have been shown to play diverse roles in EMT, and it has been suggested that EMT may play a role in the aggressiveness of MPM histological subsets. In this report, using both in vitro analyses on mesothelioma patient material and in silico analyses of existing RNA datasets, we posit that various lncRNAs may play important roles in EMT within MPM, and we review the current literature regarding these lncRNAs with respect to both EMT and MPM.
Collapse
Affiliation(s)
- Anand S Singh
- Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital, Dublin D08 W9RT, Ireland.
- MSc in Translational Oncology Program, Trinity College Dublin, Dublin 2, Ireland.
| | - Richard Heery
- Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital, Dublin D08 W9RT, Ireland.
- MSc in Translational Oncology Program, Trinity College Dublin, Dublin 2, Ireland.
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital, Dublin D08 W9RT, Ireland.
- HOPE Directorate, St. James's Hospital, Dublin 8, Ireland.
- Department of Clinical Medicine, Trinity College Dublin, Dublin 8, Ireland.
- Labmed Directorate, St. James's Hospital, Dublin 8, Ireland.
| |
Collapse
|
21
|
O'Brien EM, Selfe JL, Martins AS, Walters ZS, Shipley JM. The long non-coding RNA MYCNOS-01 regulates MYCN protein levels and affects growth of MYCN-amplified rhabdomyosarcoma and neuroblastoma cells. BMC Cancer 2018; 18:217. [PMID: 29466962 PMCID: PMC5822637 DOI: 10.1186/s12885-018-4129-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/13/2018] [Indexed: 12/02/2022] Open
Abstract
Background MYCN is amplified in small cell lung cancers and several pediatric tumors, including alveolar rhabdomyosarcomas and neuroblastomas. MYCN protein is known to play a key oncogenic role in both alveolar rhabdomyosarcomas and neuroblastomas. MYCN opposite strand (MYCNOS) is a gene located on the antisense strand to MYCN that encodes alternatively spliced transcripts, two of which (MYCNOS-01 and MYCNOS-02) are known to be expressed in neuroblastoma and small cell lung cancer with reciprocal regulation between MYCNOS-02 and MYCN reported for neuroblastomas. We sought to determine a functional role for MYCNOS-01 in alveolar rhabdomyosarcoma and neuroblastoma cells and identify any associated regulatory effects between MYCN and MYCNOS-01. Methods MYCNOS-01, MYCNOS-02 and MYCN expression levels were assessed in alveolar rhabdomyosarcoma and neuroblastoma cell lines and tumor samples from patients using Affymetrix microarray data and quantitative RT-PCR. Following MYCNOS-01 or MYCN siRNA knockdown and MYCNOS-01 overexpression, transcript levels were assayed by quantitative RT-PCR and MYCN protein expression assessed by Western blot and immunofluorescence. Additionally, effects on cell growth, apoptosis and cell cycle profiles were determined by a metabolic assay, caspase activity and flow cytometry, respectively. Results MYCNOS-01 transcript levels were generally higher in NB and RMS tumor samples and cell lines with MYCN genomic amplification. RNA interference of MYCNOS-01 expression did not alter MYCN transcript levels but decreased MYCN protein levels. Conversely, MYCN reduction increased MYCNOS-01 transcript levels, creating a negative feedback loop on MYCN protein levels. Reduction of MYCNOS-01 or MYCN expression decreased cell growth in MYCN-amplified alveolar rhabdomyosarcoma and neuroblastoma cell lines. This is consistent with MYCNOS-01-mediated regulation of MYCN contributing to the phenotype observed. Conclusions An alternative transcript of MYCNOS, MYCNOS-01, post-transcriptionally regulates MYCN levels and affects growth in MYCN-amplified rhabdomyosarcoma and neuroblastoma cells. Electronic supplementary material The online version of this article (10.1186/s12885-018-4129-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Eleanor M O'Brien
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK
| | - Joanna L Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK
| | - Ana Sofia Martins
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK
| | - Zoë S Walters
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK
| | - Janet M Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK.
| |
Collapse
|
22
|
Magnani E, Macchi F, Mancini M, Lomazzi V, Cogliati S, Pistore C, Mandruzzato M, Dock-Bregeon AC, Bonapace IM. UHRF1 regulates CDH1 via promoter associated non-coding RNAs in prostate cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:258-270. [PMID: 29466696 DOI: 10.1016/j.bbagrm.2018.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/01/2018] [Accepted: 02/15/2018] [Indexed: 01/07/2023]
Abstract
Non-coding RNAs (ncRNAs) transcribed from the promoter and the downstream region can affect the expression of the corresponding coding genes. It has been shown that sense-directed ncRNAs arising from the promoter region of the E-cadherin gene (CDH1) mediate its repression. Here, we show that an antisense-directed ncRNA (paRCDH1-AS) transcribed from the CDH1 promoter is necessary for its expression. paRCDH1-AS acts as a hooking scaffold by recruiting the epigenetic regulators, UHRF1, DNMT3A, SUV39H1 and SUZ12, involved in CDH1 repression. The binding of epigenetic regulators to paCRDH1-AS, indeed, prevents their localization to the chromatin on CDH1 promoter. Moreover, paRCDH1-AS silencing induces CDH1 repression and a switch of the epigenetic profile on the promoter towards a more closed chromatin. Using bioinformatic and experimental approaches we defined that the promoter of the paRCDH1-AS is shared with the E-cadherin gene, showing a bidirectional promoter activity. We found that UHRF1 controls both CDH1 and paRCDH1-AS by directly binding this bidirectional promoter region. Our study provides evidences, for the first time, that UHRF1 recruitment can be affected by promoter-associated non-coding RNAs, opening new perspective regarding the role of UHRF1 in these complex regulatory networks.
Collapse
Affiliation(s)
- Elena Magnani
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Filippo Macchi
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Vanessa Lomazzi
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Sara Cogliati
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy; IGBMC, BP10142, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Christian Pistore
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | - Martina Mandruzzato
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy
| | | | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, 21052 Busto Arsizio, VA, Italy.
| |
Collapse
|
23
|
lncRNAs and MYC: An Intricate Relationship. Int J Mol Sci 2017; 18:ijms18071497. [PMID: 28704924 PMCID: PMC5535987 DOI: 10.3390/ijms18071497] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 01/27/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important regulators of gene expression networks, acting either at the transcriptional level, by influencing histone modifications, or at the post-transcriptional level, by controlling mRNA stability and translation. Among the gene expression networks known to influence the process of oncogenic transformation, the one controlled by the proto-oncogene MYC is one of the most frequently deregulated in cancer. In B-cell lymphomas, the MYC gene is subject to chromosomal rearrangements that result in MYC overexpression. In many other cancers, the region surrounding MYC is subject to gene amplification. MYC expression is also controlled at the level of protein and mRNA stability. Neoplastic lesions affecting MYC expression are responsible for a drastic change in the number and the type of genes that are transcriptionally controlled by MYC, depending on differential promoter affinities. Transcriptome profiling of tumor samples has shown that several lncRNAs can be found differentially regulated by MYC in different cancer types and many of them can influence cancer cell viability and proliferation. At the same time, lncRNAs have been shown to be able to control the expression of MYC itself, both at transcriptional and post-transcriptional levels. Given that targeting the MYC-dependent transcriptional program has the potential to reach broad anticancer activity, molecular dissection of the complex regulatory mechanisms governing MYC expression will be crucial in the future for the identification of novel therapeutic strategies.
Collapse
|
24
|
Insights into the Function of Long Noncoding RNAs in Sepsis Revealed by Gene Co-Expression Network Analysis. Noncoding RNA 2017; 3:ncrna3010005. [PMID: 29657277 PMCID: PMC5831999 DOI: 10.3390/ncrna3010005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/20/2017] [Indexed: 12/18/2022] Open
Abstract
Sepsis is a major cause of death and its incidence and mortality increase exponentially with age. Most gene expression studies in sepsis have focused in protein-coding genes and the expression patterns, and potential roles of long noncoding RNAs (lncRNAs) have not been investigated yet. In this study, we performed co-expression network analysis of protein-coding and lncRNAs measured in neutrophil granulocytes from adult and elderly septic patients, along with age-matched healthy controls. We found that the genes displaying highest network similarity are predominantly differently expressed in sepsis and are enriched in loci encoding proteins with structural or regulatory functions related to protein translation and mitochondrial energetic metabolism. A number of lncRNAs are strongly connected to genes from these pathways and may take part in regulatory loops that are perturbed in sepsis. Among those, the ribosomal pseudogenes RP11-302F12.1 and RPL13AP7 are differentially expressed and appear to have a regulatory role on protein translation in both the elderly and adults, and lncRNAs MALAT1, LINC00355, MYCNOS, and AC010970.2 display variable connection strength and inverted expression patterns between adult and elderly networks, suggesting that they are the best candidates to be further studied to understand the mechanisms by which the immune response is impaired by age. In summary, we report the expression of lncRNAs that are deregulated in patients with sepsis, including subsets that display hub properties in molecular pathways relevant to the disease pathogenesis and that may participate in gene expression regulatory circuits related to the poorer disease outcome observed in elderly subjects.
Collapse
|
25
|
Trakman L, Hewson C, Burdach J, Morris KV. RNA Directed Modulation of Phenotypic Plasticity in Human Cells. PLoS One 2016; 11:e0152424. [PMID: 27082860 PMCID: PMC4833343 DOI: 10.1371/journal.pone.0152424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/14/2016] [Indexed: 11/18/2022] Open
Abstract
Natural selective processes have been known to drive phenotypic plasticity, which is the emergence of different phenotypes from one genome following environmental stimulation. Long non-coding RNAs (lncRNAs) have been observed to modulate transcriptional and epigenetic states of genes in human cells. We surmised that lncRNAs are governors of phenotypic plasticity and drive natural selective processes through epigenetic modulation of gene expression. Using heat shocked human cells as a model we find several differentially expressed transcripts with the top candidates being lncRNAs derived from retro-elements. One particular retro-element derived transcripts, Retro-EIF2S2, was found to be abundantly over-expressed in heat shocked cells. Over-expression of Retro-EIF2S2 significantly enhanced cell viability and modulated a predisposition for an adherent cellular phenotype upon heat shock. Mechanistically, we find that this retro-element derived transcript interacts directly with a network of proteins including 40S ribosomal protein S30 (FAU), Eukaryotic translation initiation factor 5A (EIF5A), and Ubiquitin-60S ribosomal protein L40 (UBA52) to affect protein modulated cell adhesion pathways. We find one motif in Retro-EIF2S2 that exhibits binding to FAU and modulates phenotypic cell transitions from adherent to suspension states. The observations presented here suggest that retroviral derived transcripts actively modulate phenotypic plasticity in human cells in response to environmental selective pressures and suggest that natural selection may play out through the action of retro-elements in human cells.
Collapse
Affiliation(s)
- Laura Trakman
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052, Australia
| | - Chris Hewson
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052, Australia
| | - Jon Burdach
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052, Australia
| | - Kevin V. Morris
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052, Australia
- City of Hope – Beckman Research Institute, Center for Gene Therapy, Duarte, California, 91010, United States of America
- * E-mail:
| |
Collapse
|
26
|
Weinberg MS, Morris KV. Transcriptional gene silencing in humans. Nucleic Acids Res 2016; 44:6505-17. [PMID: 27060137 PMCID: PMC5001580 DOI: 10.1093/nar/gkw139] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/23/2016] [Indexed: 01/21/2023] Open
Abstract
It has been over a decade since the first observation that small non-coding RNAs can functionally modulate epigenetic states in human cells to achieve functional transcriptional gene silencing (TGS). TGS is mechanistically distinct from the RNA interference (RNAi) gene-silencing pathway. TGS can result in long-term stable epigenetic modifications to gene expression that can be passed on to daughter cells during cell division, whereas RNAi does not. Early studies of TGS have been largely overlooked, overshadowed by subsequent discoveries of small RNA-directed post-TGS and RNAi. A reappraisal of early work has been brought about by recent findings in human cells where endogenous long non-coding RNAs function to regulate the epigenome. There are distinct and common overlaps between the proteins involved in small and long non-coding RNA transcriptional regulatory mechanisms, suggesting that the early studies using small non-coding RNAs to modulate transcription were making use of a previously unrecognized endogenous mechanism of RNA-directed gene regulation. Here we review how non-coding RNA plays a role in regulation of transcription and epigenetic gene silencing in human cells by revisiting these earlier studies and the mechanistic insights gained to date. We also provide a list of mammalian genes that have been shown to be transcriptionally regulated by non-coding RNAs. Lastly, we explore how TGS may serve as the basis for development of future therapeutic agents.
Collapse
Affiliation(s)
- Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, WITS 2050, South Africa HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS 2050, South Africa
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA Center for Gene Therapy, City of Hope - BeckmanResearch Institute; Duarte, CA 91010, USA School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, 2033 Australia
| |
Collapse
|
27
|
Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA molecules that are changing how researchers view eukaryotic gene regulation. Once considered to be non-functional products of low-level aberrant transcription from non-coding regions of the genome, lncRNAs are now viewed as important epigenetic regulators and several lncRNAs have now been demonstrated to be critical players in the development and/or maintenance of cancer. Similarly, the emerging variety of interactions between lncRNAs and MYC, a well-known oncogenic transcription factor linked to most types of cancer, have caught the attention of many biomedical researchers. Investigations exploring the dynamic interactions between lncRNAs and MYC, referred to as the lncRNA-MYC network, have proven to be especially complex. Genome-wide studies have shown that MYC transcriptionally regulates many lncRNA genes. Conversely, recent reports identified lncRNAs that regulate MYC expression both at the transcriptional and post-transcriptional levels. These findings are of particular interest because they suggest roles of lncRNAs as regulators of MYC oncogenic functions and the possibility that targeting lncRNAs could represent a novel avenue to cancer treatment. Here, we briefly review the current understanding of how lncRNAs regulate chromatin structure and gene transcription, and then focus on the new developments in the emerging field exploring the lncRNA-MYC network in cancer.
Collapse
Affiliation(s)
- Michael J. Hamilton
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Matthew D. Young
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Silvia Sauer
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| |
Collapse
|