1
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Huang P, Wen F, Li Y, Li Q. The tale of SOX2: Focusing on lncRNA regulation in cancer progression and therapy. Life Sci 2024; 344:122576. [PMID: 38492918 DOI: 10.1016/j.lfs.2024.122576] [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: 01/14/2024] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as influential contributors to diverse cellular processes, which regulate gene function and expression via multiple mechanistic pathways. Therefore, it is essential to exploit the structures and interactions of lncRNAs to comprehend their mechanistic functions within cells. A growing body of evidence has revealed that deregulated lncRNAs are involved in multiple regulations of malignant events including cell proliferation, growth, invasion, and metabolism. SRY-related high mobility group box (SOX)2, a well-recognized member of the SOX family, is commonly overexpressed in various types of cancer, contributing to tumor progression and maintenance of stemness. Emerging studies have shown that lncRNAs interact with SOX2 to remarkably contribute to carcinogenesis and disease states. This review elaborates on the crosstalk between the intricate and complicated functions of lncRNAs and SOX2 in the context of malignant diseases. We elucidate distinct molecular mechanisms that contribute to the onset/advancement of cancer, indicating that lncRNAs/SOX2 axes hold immense promise for potential therapeutic targets. Furthermore, we delve into the modalities of emerging feasible treatment options for targeting lncRNAs, highlighting the limitations of such therapies and providing novel insights into further ameliorations of targeted strategies of lncRNAs to promote the clinical implications. Translating current discoveries into clinical applications could ultimately boost improved survival and prognosis of cancer patients.
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Affiliation(s)
- Peng Huang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng Wen
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - YiShan Li
- Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, West China School of Nursing, Chengdu, Sichuan 610041, China
| | - Qiu Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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2
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Huang LA, Lin C, Yang L. Plumbing mysterious RNAs in "dark genome" for the conquest of human diseases. Mol Ther 2023; 31:1577-1595. [PMID: 37165619 PMCID: PMC10278048 DOI: 10.1016/j.ymthe.2023.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Next-generation sequencing has revealed that less than 2% of transcribed genes are translated into proteins, with a large portion transcribed into noncoding RNAs (ncRNAs). Among these, long noncoding RNAs (lncRNAs) represent the largest group and are pervasively transcribed throughout the genome. Dysfunctions in lncRNAs have been found in various diseases, highlighting their potential as therapeutic, diagnostic, and prognostic targets. However, challenges, such as unknown molecular mechanisms and nonspecific immune responses, and issues of drug specificity and delivery present obstacles in translating lncRNAs into clinical applications. In this review, we summarize recent publications that have explored lncRNA functions in human diseases. We also discuss challenges and future directions for developing lncRNA treatments, aiming to bridge the gap between functional studies and clinical potential and inspire further exploration in the field.
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Affiliation(s)
- Lisa A Huang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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3
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Shabna A, Bindhya S, Sidhanth C, Garg M, Ganesan TS. Long non-coding RNAs: Fundamental regulators and emerging targets of cancer stem cells. Biochim Biophys Acta Rev Cancer 2023; 1878:188899. [PMID: 37105414 DOI: 10.1016/j.bbcan.2023.188899] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
Cancer is one of the leading causes of death worldwide, primarily due to the dearth of efficient therapies that result in long-lasting remission. This is especially true in cases of metastatic cancer where drug resistance causes the disease to recur after treatment. One of the factors contributing to drug resistance, metastasis, and aggressiveness of the cancer is cancer stem cells (CSCs) or tumor-initiating cells. As a result, CSCs have emerged as a potential target for drug development. In the present review, we have examined and highlighted the lncRNAs with their regulatory functions specific to CSCs. Moreover, we have discussed the difficulties and various methods involved in identifying lncRNAs that can play a particular role in regulating and maintaining CSCs. Interestingly, this review only focuses on those lncRNAs with strong functional evidence for CSC specificity and the mechanistic role that allows them to be CSC regulators and be the focus of CSC-specific drug development.
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Affiliation(s)
- Aboo Shabna
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India; Laboratory for Cancer Biology, Department of Medical Oncology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 610016, India; Department of Endocrinology, Indian Council of Medical Research - National Institute of Nutrtion, Tarnaka, Hyderabad 50007, India
| | - Sadanadhan Bindhya
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India
| | - Chirukandath Sidhanth
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Sector-125, Noida 201301, India
| | - Trivadi S Ganesan
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India; Laboratory for Cancer Biology, Department of Medical Oncology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 610016, India.
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4
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The Intricate Interplay between the ZNF217 Oncogene and Epigenetic Processes Shapes Tumor Progression. Cancers (Basel) 2022; 14:cancers14246043. [PMID: 36551531 PMCID: PMC9776013 DOI: 10.3390/cancers14246043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
The oncogenic transcription factor ZNF217 orchestrates several molecular signaling networks to reprogram integrated circuits governing hallmark capabilities within cancer cells. High levels of ZNF217 expression provide advantages to a specific subset of cancer cells to reprogram tumor progression, drug resistance and cancer cell plasticity. ZNF217 expression level, thus, provides a powerful biomarker of poor prognosis and a predictive biomarker for anticancer therapies. Cancer epigenetic mechanisms are well known to support the acquisition of hallmark characteristics during oncogenesis. However, the complex interactions between ZNF217 and epigenetic processes have been poorly appreciated. Deregulated DNA methylation status at ZNF217 locus or an intricate cross-talk between ZNF217 and noncoding RNA networks could explain aberrant ZNF217 expression levels in a cancer cell context. On the other hand, the ZNF217 protein controls gene expression signatures and molecular signaling for tumor progression by tuning DNA methylation status at key promoters by interfering with noncoding RNAs or by refining the epitranscriptome. Altogether, this review focuses on the recent advances in the understanding of ZNF217 collaboration with epigenetics processes to orchestrate oncogenesis. We also discuss the exciting burgeoning translational medicine and candidate therapeutic strategies emerging from those recent findings connecting ZNF217 to epigenetic deregulation in cancer.
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Chellini L, Pieraccioli M, Sette C, Paronetto MP. The DNA/RNA helicase DHX9 contributes to the transcriptional program of the androgen receptor in prostate cancer. J Exp Clin Cancer Res 2022; 41:178. [PMID: 35590370 PMCID: PMC9118622 DOI: 10.1186/s13046-022-02384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Prostate cancer (PC) is the most commonly diagnosed male malignancy and an important cause of mortality. Androgen deprivation therapy is the first line treatment but, unfortunately, a large part of patients evolves to a castration-resistant stage, for which no effective cure is currently available. The DNA/RNA helicase DHX9 is emerging as an important regulator of cellular processes that are often deregulated in cancer.
Methods
To investigate whether DHX9 modulates PC cell transcriptome we performed RNA-sequencing analyses upon DHX9 silencing in the androgen-responsive cell line LNCaP. Bioinformatics and functional analyses were carried out to elucidate the mechanism of gene expression regulation by DHX9. Data from The Cancer Genome Atlas were mined to evaluate the potential role of DHX9 in PC.
Results
We found that up-regulation of DHX9 correlates with advanced stage and is associated with poor prognosis of PC patients. High-throughput RNA-sequencing analysis revealed that depletion of DHX9 in androgen-sensitive LNCaP cells affects expression of hundreds of genes, which significantly overlap with known targets of the Androgen Receptor (AR). Notably, AR binds to the DHX9 promoter and induces its expression, while Enzalutamide-mediated inhibition of AR activity represses DHX9 expression. Moreover, DHX9 interacts with AR in LNCaP cells and its depletion significantly reduced the recruitment of AR to the promoter region of target genes and the ability of AR to promote their expression in response to 5α-dihydrotestosterone. Consistently, silencing of DXH9 negatively affected androgen-induced PC cell proliferation and migration.
Conclusions
Collectively, our data uncover a new role of DHX9 in the control of the AR transcriptional program and establish the existence of an oncogenic DHX9/AR axis, which may represent a new druggable target to counteract PC progression.
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Pandey GK, Kanduri C. Long Non-Coding RNAs: Tools for Understanding and Targeting Cancer Pathways. Cancers (Basel) 2022; 14:cancers14194760. [PMID: 36230680 PMCID: PMC9564174 DOI: 10.3390/cancers14194760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
The regulatory nature of long non-coding RNAs (lncRNAs) has been well established in various processes of cellular growth, development, and differentiation. Therefore, it is vital to examine their contribution to cancer development. There are ample examples of lncRNAs whose cellular levels are significantly associated with clinical outcomes. However, whether these non-coding molecules can work as either key drivers or barriers to cancer development remains unknown. The current review aims to discuss some well-characterised lncRNAs in the process of oncogenesis and extrapolate the extent of their decisive contribution to tumour development. We ask if these lncRNAs can independently initiate neoplastic lesions or they always need the modulation of well characterized oncogenes or tumour suppressors to exert their functional properties. Finally, we discuss the emerging genetic approaches and appropriate animal and humanised models that can significantly contribute to the functional dissection of lncRNAs in cancer development and progression.
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Affiliation(s)
- Gaurav Kumar Pandey
- Department of Zoology, Banaras Hindu University, Varanasi 221005, India
- Correspondence: (G.K.P.); (C.K.)
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Correspondence: (G.K.P.); (C.K.)
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7
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Eptaminitaki GC, Stellas D, Bonavida B, Baritaki S. Long Non-coding RNAs (lncRNAs) signaling in Cancer Chemoresistance: From Prediction to Druggability. Drug Resist Updat 2022; 65:100866. [DOI: 10.1016/j.drup.2022.100866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/03/2022]
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8
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Wang Y, Xu Y, Zhang Y. A novel ferroptosis-related long noncoding RNA signature for relapse free survival prediction in patients with breast cancer. Medicine (Baltimore) 2022; 101:e29573. [PMID: 35945765 PMCID: PMC9351903 DOI: 10.1097/md.0000000000029573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ferroptosis is the process of cell death dependent on iron. Growing evidence suggests that ferroptosis plays vital roles in the biological process of many cancers. However, just a small number of ferroptosis-related lncRNAs have been explored in depth. Ferroptosis-related lncRNAs in breast cancer (BC) were identified by co-expression analysis based on The Cancer Genome Atlas database (TCGA). The whole set was divided into a training set and a test set with a 1:1 ratio. Univariate Cox regression and LASSO analyses were performed to establish a signature in the 3 sets. Kaplan-Meier analysis and receiver operating characteristic (ROC) for the 3 sets validated the effectiveness and robustness of the signature. Besides, we also explore the relationship between this and clinical characteristics, immune cell infiltration and tumor microenvironment. Meanwhile, the nomogram was drawn by screening indicators of independent recurrent prediction. Finally, we evaluated the relationships between the signature and tumor microenvironment. We identified 391 ferroptosis-related lncRNAs and constructed a 5 lncRNAs-based signature in the training, test, and whole sets, stratifying patients into high-risk and low-risk groups. According to survival analysis, patients in the high-risk groups had worse relapse free survival (RFS) compared to the low risk-groups. The ROC curves indicated that the recurrent signature had a promising predictive capability for BC patients. Moreover, an independent factors-based nomogram model could offer the quantitative prediction and net benefit for the recurrence of BC patients. Finally, the microenvironment, including tumor mutational burden (TMB), immune cell functions and immune checkpoints, showed big differences between the 2 groups. The 5 ferroptosis-related lncRNAs and their signature might be novel promising biomarkers and immunotherapy targets for patients with BC.
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Affiliation(s)
- Yuzhi Wang
- Department of Laboratory Medicine, People’s Hospital of Deyang City, Deyang, Sichuan, P. R. China
| | - Yunfei Xu
- Department of Laboratory Medicine, Chengdu Women’s and Children’s Central Hospital, Chengdu, Sichuan, P. R. China
| | - Yi Zhang
- Department of Blood Transfusion, People’s Hospital of Deyang City, Deyang, Sichuan, P. R. China
- *Correspondence: Yi Zhang, People’s Hospital of Deyang City, No. 173, Section 1, Taishan North Road, Deyang City, Sichuan 618000, China (e-mail: )
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9
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Introduction of long non-coding RNAs to regulate autophagy-associated therapy resistance in cancer. Mol Biol Rep 2022; 49:10761-10773. [PMID: 35810239 DOI: 10.1007/s11033-022-07669-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 12/19/2022]
Abstract
Autophagy is a lysosomal degradation pathway that depends on various evolutionarily conserved autophagy-related genes (ATGs). Dysregulation of autophagy plays an important role in the occurrence and development of cancer. Chemotherapy, targeted therapy, radiotherapy, and immunotherapy are important treatment options for cancer, which can significantly improve the survival rate of cancer patients. However, the occurrence of therapy resistance results in therapeutic failure and poor prognosis of cancer. Accumulating studies have found that long non-coding RNAs (lncRNAs) are well known as crucial regulators to control autophagy through regulating ATGs and autophagy-associated signaling pathways, including the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway, ultimately mediating chemoresistance and radioresistance. Taken together, this review systematically summarizes and elucidates the pivotal role of lncRNAs in cancer chemoresistance and radioresistance via regulating autophagy. Understanding the specific mechanism of which may provide autophagy-related therapeutic targets for cancer in the future.
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10
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Ebrahimi N, Parkhideh S, Samizade S, Esfahani AN, Samsami S, Yazdani E, Adelian S, Chaleshtori SR, Shah-Amiri K, Ahmadi A, Aref AR. Crosstalk between lncRNAs in the apoptotic pathway and therapeutic targets in cancer. Cytokine Growth Factor Rev 2022; 65:61-74. [PMID: 35597701 DOI: 10.1016/j.cytogfr.2022.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/03/2022]
Abstract
The assertion that a significant portion of the mammalian genome has not been translated and that non-coding RNA accounts for over half of polyadenylate RNA have received much attention. In recent years, increasing evidence proposes non-coding RNAs (ncRNAs) as new regulators of various cellular processes, including cancer progression and nerve damage. Apoptosis is a type of programmed cell death critical for homeostasis and tissue development. Cancer cells often have inhibited apoptotic pathways. It has recently been demonstrated that up/down-regulation of various lncRNAs in certain types of tumors shapes cancer cells' response to apoptotic stimuli. This review discusses the most recent studies on lncRNAs and apoptosis in healthy and cancer cells. In addition, the role of lncRNAs as novel targets for cancer therapy is reviewed here. Finally, since it has been shown that lncRNA expression is associated with specific types of cancer, the potential for using lncRNAs as biomarkers is also discussed.
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Affiliation(s)
- Nasim Ebrahimi
- Genetics Division, Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Iran
| | - Sahar Parkhideh
- Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Setare Samizade
- Department of Cellular and molecular, School of Biological Sciences, Islamic Azad University of Falavarjan, Iran
| | - Alireza Nasr Esfahani
- Department of Cellular and molecular, School of Biological Sciences, Islamic Azad University of Falavarjan, Iran
| | - Sahar Samsami
- Biotechnology department of Fasa University of medical science, Fasa, Iran
| | - Elnaz Yazdani
- Department of Biology, Faculty of Science, University Of Isfahan, Isfahan, Iran; Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Samaneh Adelian
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Kamal Shah-Amiri
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Amirhossein Ahmadi
- Department of Biological Science and Technology, Faculty of Nano and Bio Science and Technology, Persian Gulf University, Bushehr 75169, Iran.
| | - Amir Reza Aref
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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11
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Maki RG, Grohar PJ, Antonescu CR. Ewing sarcoma and related FET family translocation-associated round cell tumors: a century of clinical and scientific progress. Genes Chromosomes Cancer 2022; 61:509-517. [PMID: 35443099 PMCID: PMC9197982 DOI: 10.1002/gcc.23050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
The year 2021 marked the centenary of the first publication of a cancer termed diffuse endothelioma of bone by James Ewing. Its unique features were apparent even in the first case series he described. This new diagnosis was clearly distinct from osteogenic sarcoma and myeloma, which were already well recognized at the time. We undertake this summary to better understanding Ewing sarcoma, contrasting the logarithmic evolution of the standard of care of systemic therapy for this and related diagnoses to the exponential understanding of the molecular biology of this family of tumors. We also outline in this manuscript how the finding of genomic relatives within Ewing sarcoma itself and related tumors, first noted nearly 40 years ago, helps us appreciate the need to find therapeutic plans that are specific for each small round blue cell tumor subtype. The advent of next generation sequencing regarding previously unknown small round blue cell tumor subtypes in many ways puts us back in the shoes of James Ewing in 1921, searching anew for clues leading to better treatments for increasingly rare cancer subsets. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Robert G Maki
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, US.,Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, US.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, US
| | - Patrick J Grohar
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, US.,Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, US.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, US
| | - Cristina R Antonescu
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, US.,Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, US.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, US
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12
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Zooming in on Long Non-Coding RNAs in Ewing Sarcoma Pathogenesis. Cells 2022; 11:cells11081267. [PMID: 35455947 PMCID: PMC9032025 DOI: 10.3390/cells11081267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
Ewing sarcoma (ES) is a rare aggressive cancer of bone and soft tissue that is mainly characterized by a reciprocal chromosomal translocation. As a result, about 90% of cases express the EWS-FLI1 fusion protein that has been shown to function as an aberrant transcription factor driving sarcomagenesis. ES is the second most common malignant bone tumor in children and young adults. Current treatment modalities include dose-intensified chemo- and radiotherapy, as well as surgery. Despite these strategies, patients who present with metastasis or relapse still have dismal prognosis, warranting a better understanding of treatment resistant-disease biology in order to generate better prognostic and therapeutic tools. Since the genomes of ES tumors are relatively quiet and stable, exploring the contributions of epigenetic mechanisms in the initiation and progression of the disease becomes inevitable. The search for novel biomarkers and potential therapeutic targets of cancer metastasis and chemotherapeutic drug resistance is increasingly focusing on long non-coding RNAs (lncRNAs). Recent advances in genome analysis by high throughput sequencing have immensely expanded and advanced our knowledge of lncRNAs. They are non-protein coding RNA species with multiple biological functions that have been shown to be dysregulated in many diseases and are emerging as crucial players in cancer development. Understanding the various roles of lncRNAs in tumorigenesis and metastasis would determine eclectic avenues to establish therapeutic and diagnostic targets. In ES, some lncRNAs have been implicated in cell proliferation, migration and invasion, features that make them suitable as relevant biomarkers and therapeutic targets. In this review, we comprehensively discuss known lncRNAs implicated in ES that could serve as potential biomarkers and therapeutic targets of the disease. Though some current reviews have discussed non-coding RNAs in ES, to our knowledge, this is the first review focusing exclusively on ES-associated lncRNAs.
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Dey S, Misra A, Selvi Bharathavikru R. Long Non-coding RNAs, Lnc (ing) RNA Metabolism to Cancer Biology. Subcell Biochem 2022; 100:175-199. [PMID: 36301495 DOI: 10.1007/978-3-031-07634-3_6] [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] [Indexed: 06/16/2023]
Abstract
The eukaryotic genome is represented by a vast proportion of non-coding regions, which in recent years have been attributed to have important functional roles in gene regulation through a myriad of processes, ranging from proper localization, correct folding and, most importantly, spatial and temporally regulated expression of genes. One of the major contributing factors in these processes is ribonucleic acid (RNA) metabolism, which comprises the RNA-nucleoprotein (RNP) complexes that interact with and instruct the genome to function. Long non-coding RNAs are an integral component of several RNPs, and herein we provide an overview of the understanding of the long non-coding RNAs, their characteristics, their function and their balancing act as dual modulators in cancer manifestation and progression.
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Affiliation(s)
- Sourav Dey
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India
| | - Arushi Misra
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India
| | - R Selvi Bharathavikru
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India.
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14
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miRNA- and lncRNA-Based Therapeutics for Non-Hodgkin’s Lymphoma: Moving towards an RNA-Guided Precision Medicine. Cancers (Basel) 2021; 13:cancers13246324. [PMID: 34944942 PMCID: PMC8699447 DOI: 10.3390/cancers13246324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Non-Hodgkin’s lymphoma (NHL) is a very heterogenous class of hematological cancers, with variable patient outcomes. Therefore, there is an urgent need to develop new and more effective therapeutic approaches. MiRNAs and lncRNAs have emerged as the central gene expression regulators, and their deregulation has been reported to be involved in lymphomagenesis. Given their ability to simultaneously modulate multiple targets, they provide an attractive therapeutic approach to treat NHL patients. In this review, we discuss the scientific rationale behind miRNA/lncRNA-based therapies in NHL and the different targeting technologies, such as antisense oligonucleotides, CRISPR-Cas9, and nanomedicines. Abstract Increasing evidence has demonstrated the functional roles of miRNAs and lncRNAs in lymphoma onset and progression, either by acting as tumor-promoting ncRNAs or as tumor suppressors, emphasizing their appeal as lymphoma therapeutics. In fact, their intrinsic ability to modulate multiple dysregulated genes and/or signaling pathways makes them an attractive therapeutic approach for a multifactorial pathology like lymphoma. Currently, the clinical application of miRNA- and lncRNA-based therapies still faces obstacles regarding effective delivery systems, off-target effects, and safety, which can be minimized with the appropriate chemical modifications and the development of tumor site-specific delivery approaches. Moreover, miRNA- and lncRNA-based therapeutics are being studied not only as monotherapies but also as complements of standard treatment regimens to provide a synergic effect, improving the overall treatment efficacy and reducing the therapeutic resistance. In this review, we summarize the fundamentals of miRNA- and lncRNA-based therapeutics by discussing the different types of delivery systems, with a focus on those that have been investigated in lymphoma in vitro and in vivo. Moreover, we described the ongoing clinical trials of novel miRNA- and lncRNA-based therapeutics in lymphoma.
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15
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Lu Q, Lou J, Cai R, Han W, Pan H. Emerging roles of a pivotal lncRNA SBF2-AS1 in cancers. Cancer Cell Int 2021; 21:417. [PMID: 34372871 PMCID: PMC8351094 DOI: 10.1186/s12935-021-02123-3] [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: 05/07/2021] [Accepted: 07/29/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs refer to transcripts over 200 nt in length that lack the ability to encode proteins, which occupy the majority of the genome and play a crucial role in the occurrence and development of human diseases, especially cancers. SBF2-AS1, a newly identified long non-coding RNA, has been verified to be highly expressed in diversiform cancers, and is involved in processes promoting tumorigenesis, tumor progression and tumor metastasis. Moreover, upregulation of SBF2-AS1 expression was significantly related to disadvantageous clinicopathologic characteristics and indicated poor prognosis. In this review, we comprehensively summarize the up-to-date knowledge of the detailed mechanisms and underlying functions of SBF2-AS1 in diverse cancer types, highlighting the potential of SBF2-AS1 as a diagnostic and prognostic biomarker and even a therapeutic target.
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Affiliation(s)
- Qian Lu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jun Lou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ruyun Cai
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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16
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The Landscape of Regulatory Noncoding RNAs in Ewing's Sarcoma. Biomedicines 2021; 9:biomedicines9080933. [PMID: 34440137 PMCID: PMC8391329 DOI: 10.3390/biomedicines9080933] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Ewing’s sarcoma (ES) is a pediatric sarcoma caused by a chromosomal translocation. Unlike in most cancers, the genomes of ES patients are very stable. The translocation product of the EWS-FLI1 fusion is most often the predominant genetic driver of oncogenesis, and it is pertinent to explore the role of epigenetic alterations in the onset and progression of ES. Several types of noncoding RNAs, primarily microRNAs and long noncoding RNAs, are key epigenetic regulators that have been shown to play critical roles in various cancers. The functions of these epigenetic regulators are just beginning to be appreciated in ES. Here, we performed a comprehensive literature review to identify these noncoding RNAs. We identified clinically relevant tumor suppressor microRNAs, tumor promoter microRNAs and long noncoding RNAs. We then explored the known interplay between different classes of noncoding RNAs and described the currently unmet need for expanding the noncoding RNA repertoire of ES. We concluded the review with a discussion of epigenetic regulation of ES via regulatory noncoding RNAs. These noncoding RNAs provide new avenues of exploration to develop better therapeutics and identify novel biomarkers.
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Singh N. Role of mammalian long non-coding RNAs in normal and neuro oncological disorders. Genomics 2021; 113:3250-3273. [PMID: 34302945 DOI: 10.1016/j.ygeno.2021.07.015] [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: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes but have a crucial role in gene regulation. LncRNA is distinct, they are being transcribed using RNA polymerase II, and their functionality depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer. To date, ~40% of lncRNAs have been reported in the nervous system (NS) and are involved in the early development/differentiation of the NS to synaptogenesis. LncRNA expression patterns in the most common adult and pediatric tumor suggest them as potential biomarkers and provide a rationale for targeting them pharmaceutically. Here, we discuss the mechanisms of lncRNA synthesis, localization, and functions in transcriptional, post-transcriptional, and other forms of gene regulation, methods of lncRNA identification, and their potential therapeutic applications in neuro oncological disorders as explained by molecular mechanisms in other malignant disorders.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Department of Centre for Advance Research, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
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18
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Sellitto A, Pecoraro G, Giurato G, Nassa G, Rizzo F, Saggese P, Martinez CA, Scafoglio C, Tarallo R. Regulation of Metabolic Reprogramming by Long Non-Coding RNAs in Cancer. Cancers (Basel) 2021; 13:cancers13143485. [PMID: 34298698 PMCID: PMC8308086 DOI: 10.3390/cancers13143485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 01/10/2023] Open
Abstract
Metabolic reprogramming is a well described hallmark of cancer. Oncogenic stimuli and the microenvironment shape the metabolic phenotype of cancer cells, causing pathological modifications of carbohydrate, amino acid and lipid metabolism that support the uncontrolled growth and proliferation of cancer cells. Conversely, metabolic alterations in cancer can drive changes in genetic programs affecting cell proliferation and differentiation. In recent years, the role of non-coding RNAs in metabolic reprogramming in cancer has been extensively studied. Here, we review this topic, with a focus on glucose, glutamine, and lipid metabolism and point to some evidence that metabolic alterations occurring in cancer can drive changes in non-coding RNA expression, thus adding an additional level of complexity in the relationship between metabolism and genetic programs in cancer cells.
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Affiliation(s)
- Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
- Genome Research Center for Health—CRGS, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
- Genome Research Center for Health—CRGS, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
- Genome Research Center for Health—CRGS, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
| | - Pasquale Saggese
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.S.); (C.A.M.); (C.S.)
| | - Cesar A. Martinez
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.S.); (C.A.M.); (C.S.)
| | - Claudio Scafoglio
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.S.); (C.A.M.); (C.S.)
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Italy; (A.S.); (G.P.); (G.G.); (G.N.); (F.R.)
- Genome Research Center for Health—CRGS, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
- Correspondence: ; Tel.: +39-089-965067
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Ye WC, Huang SF, Hou LJ, Long HJ, Yin K, Hu CY, Zhao GJ. Potential Therapeutic Targeting of lncRNAs in Cholesterol Homeostasis. Front Cardiovasc Med 2021; 8:688546. [PMID: 34179148 PMCID: PMC8224755 DOI: 10.3389/fcvm.2021.688546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/19/2021] [Indexed: 12/19/2022] Open
Abstract
Maintaining cholesterol homeostasis is essential for normal cellular and systemic functions. Long non-coding RNAs (lncRNAs) represent a mechanism to fine-tune numerous biological processes by controlling gene expression. LncRNAs have emerged as important regulators in cholesterol homeostasis. Dysregulation of lncRNAs expression is associated with lipid-related diseases, suggesting that manipulating the lncRNAs expression could be a promising therapeutic approach to ameliorate liver disease progression and cardiovascular disease (CVD). However, given the high-abundant lncRNAs and the poor genetic conservation between species, much work is required to elucidate the specific role of lncRNAs in regulating cholesterol homeostasis. In this review, we highlighted the latest advances in the pivotal role and mechanism of lncRNAs in regulating cholesterol homeostasis. These findings provide novel insights into the underlying mechanisms of lncRNAs in lipid-related diseases and may offer potential therapeutic targets for treating lipid-related diseases.
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Affiliation(s)
- Wen-Chu Ye
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Shi-Feng Huang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Lian-Jie Hou
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Hai-Jiao Long
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China.,Xiangya Hospital, Central South University, Changsha, China
| | - Kai Yin
- Guangxi Key Laboratory of Diabetic Systems Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Ching Yuan Hu
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Guo-Jun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
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20
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Chen Y, Li Z, Chen X, Zhang S. Long non-coding RNAs: From disease code to drug role. Acta Pharm Sin B 2021; 11:340-354. [PMID: 33643816 PMCID: PMC7893121 DOI: 10.1016/j.apsb.2020.10.001] [Citation(s) in RCA: 253] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Enormous studies have corroborated that long non-coding RNAs (lncRNAs) extensively participate in crucial physiological processes such as metabolism and immunity, and are closely related to the occurrence and development of tumors, cardiovascular diseases, nervous system disorders, nephropathy, and other diseases. The application of lncRNAs as biomarkers or intervention targets can provide new insights into the diagnosis and treatment of diseases. This paper has focused on the emerging research into lncRNAs as pharmacological targets and has reviewed the transition of lncRNAs from the role of disease coding to acting as drug candidates, including the current status and progress in preclinical research. Cutting-edge strategies for lncRNA modulation have been summarized, including the sources of lncRNA-related drugs, such as genetic technology and small-molecule compounds, and related delivery methods. The current progress of clinical trials of lncRNA-targeting drugs is also discussed. This information will form a latest updated reference for research and development of lncRNA-based drugs.
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Key Words
- AD, Alzheimer's disease
- ANRIL, antisense noncoding RNA gene at the INK4 locus
- ASO, antisense oligonucleotide
- ASncmtRNA
- ASncmtRNA, antisense noncoding mitochondrial RNA
- BCAR4, breast cancer anti-estrogen resistance 4
- BDNF-AS, brain-derived neurotrophic factor antisense
- CASC9, cancer susceptibility candidate 9
- CDK, cyclin dependent kinase 1
- CHRF, cardiac hypertrophy related factor
- CRISPR, clustered regularly interspaced short palindromic repeats
- Clinical trials
- DACH1, dachshund homolog 1
- DANCR, differentiation antagonizing non-protein coding RNA
- DKD, diabetic kidney disease
- DPF, diphenyl furan
- Delivery
- EBF3-AS, early B cell factor 3-antisense
- ENE, element for nuclear expression
- Erbb4-IR, Erb-B2 receptor tyrosine kinase 4-immunoreactivity
- FDA, U.S. Food and Drug Administration
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GAS5, growth arrest specific 5
- Gene therapy
- HISLA, HIF-1α-stabilizing long noncoding RNA
- HOTAIR, HOX transcript antisense intergenic RNA
- HULC, highly upregulated in liver cancer
- LIPCAR, long intergenic noncoding RNA predicting cardiac remodeling
- LNAs, locked nucleic acids
- LncRNAs
- MALAT1, metastasis associated lung adenocarcinoma transcript 1
- MEG3, maternally expressed gene 3
- MHRT, myosin heavy chain associated RNA transcripts
- MM, multiple myeloma
- NEAT1, nuclear enriched abundant transcript 1
- NKILA, NF-kappaB interacting lncRNA
- NPs, nanoparticles
- Norad, non-coding RNA activated by DNA damage
- OIP5-AS1, opa-interacting protein 5 antisense transcript 1
- PD, Parkinson's disease
- PEG, polyethylene glycol
- PNAs, peptide nucleic acids
- PTO, phosphorothioate
- PVT1, plasmacytoma variant translocation 1
- RGD, arginine-glycine-aspartic acid peptide
- RISC, RNA-induced silencing complex
- SALRNA1, senescence associated long non-coding RNA 1
- SNHG1, small nucleolar RNA host gene 1
- Small molecules
- SncmtRNA, sense noncoding mitochondrial RNA
- THRIL, TNF and HNRNPL related immunoregulatory
- TTTY15, testis-specific transcript, Y-linked 15
- TUG1, taurine-upregulated gene 1
- TWIST1, twist family BHLH transcription factor 1
- Targeted drug
- TncRNA, trophoblast-derived noncoding RNA
- Translational medicine
- UCA1, urothelial carcinoma-associated 1
- UTF1, undifferentiated transcription factor 1
- XIST, X-inactive specific transcript
- lincRNA-p21, long intergenic noncoding RNA p21
- lncRNAs, long non-coding RNAs
- mtlncRNA, mitochondrial long noncoding RNA
- pHLIP, pH-low insertion peptide
- sgRNA, single guide RNA
- siRNAs, small interfering RNAs
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21
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Chen M, Zhang R, Lu L, Du J, Chen C, Ding K, Wei X, Zhang G, Huang Y, Hou J. LncRNA PVT1 accelerates malignant phenotypes of bladder cancer cells by modulating miR-194-5p/BCLAF1 axis as a ceRNA. Aging (Albany NY) 2020; 12:22291-22312. [PMID: 33188158 PMCID: PMC7695393 DOI: 10.18632/aging.202203] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023]
Abstract
Background: Numerous studies proved that long non-coding RNA (lncRNA) is involved in the progression of multifarious diseases, especially in some carcinomas. As a potential tumor biomarker, plasmacytoma variant translocation 1 gene (PVT1) is involved in the development and progression of multifarious cancers. Nevertheless, the intrinsic and concrete molecular mechanism of PVT1 in bladder cancer still remained unclear, which is also the dilemma faced in many non-coding RNA studies. Results: Our research revealed that PVT1 was significantly higher expression in bladder carcinoma specimens and cell lines. Further experiments indicated that knockdown or overexpression of PVT1 restrained or promoted the malignant phenotype and WNT/β-catenin signaling in bladder cancer cells. Meanwhile miR-194-5p was in contrast and miR-194-5p could partially reverse the function of PVT1 in malignant bladder tumor cells. As a microRNA sponge, PVT1 actively promotes the expression of b-cells lymphoma-2-associated transcription factor 1 (BCLAF1) to sponge miR-194-5p and subsequently increases malignant phenotypes of bladder cancer cells. Therefore, it performs a carcinogenic effect and miR-194-5p as the opposite function, and serves as an antioncogene in the bladder carcinomas pathogenesis. Conclusion: PVT1-miR-194-5p-BCLAF1 axis is involved in the malignant progression and development of bladder carcinomas. Experiments revealed that PVT1 has a significant regulatory effect on bladder cancer (BC) and can be used as a clinical diagnostic marker and a therapeutic molecular marker for patients suffering from BC. Methods: In urothelial bladder carcinoma specimens and cell lines, the relative expression levels of PVT1 and miR-194-5p were detected by quantitative reverse transcription PCR (RT-qPCR). Through experiments such as loss-function and over-expression, the biological effects of PVT1 and miR-194-5p on the proliferation, migration, apoptosis and tumorigenicity were explored in bladder cancer cells. Co-immunoprecipitation, proteomics experiments, dual luciferase reporter gene analysis, western blot and other methods were adopted to investigate the PVT1 potential mechanism in bladder carcinomas.
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Affiliation(s)
- Mingwei Chen
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China.,Department of Urology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, Zhejiang Province, China
| | - Rongyuan Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China
| | - Le Lu
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China
| | - Jian Du
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China
| | - Chunyang Chen
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China
| | - Keke Ding
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China
| | - Xuedong Wei
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China
| | - Guangbo Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Jiangsu Key Laboratory of Gastrointestinal Tumor Immunology, Suzhou 215006, Jiangsu Province, China
| | - Yuhua Huang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, China
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Regulatory Mechanisms of Epigenetic miRNA Relationships in Human Cancer and Potential as Therapeutic Targets. Cancers (Basel) 2020; 12:cancers12102922. [PMID: 33050637 PMCID: PMC7600069 DOI: 10.3390/cancers12102922] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary By the virtue of targeting multiple genes, a microRNA (miRNA) can infer variable consequences on tumorigenesis by appearing as both a tumour suppressor and oncogene. miRNAs can regulate gene expression by modulating genome-wide epigenetic status of genes that are involved in various cancers. These miRNAs perform direct inhibition of key mediators of the epigenetic machinery, such as DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) genes. Along with miRNAs gene expression, similar to other protein-coding genes, miRNAs are also controlled by epigenetic mechanisms. Overall, this reciprocal interaction between the miRNAs and the epigenetic architecture is significantly implicated in the aberrant expression of miRNAs detected in various human cancers. Comprehensive knowledge of the miRNA-epigenetic dynamics in cancer is essential for the discovery of novel anticancer therapeutics. Abstract Initiation and progression of cancer are under both genetic and epigenetic regulation. Epigenetic modifications including alterations in DNA methylation, RNA and histone modifications can lead to microRNA (miRNA) gene dysregulation and malignant cellular transformation and are hereditary and reversible. miRNAs are small non-coding RNAs which regulate the expression of specific target genes through degradation or inhibition of translation of the target mRNA. miRNAs can target epigenetic modifier enzymes involved in epigenetic modulation, establishing a trilateral regulatory “epi–miR–epi” feedback circuit. The intricate association between miRNAs and the epigenetic architecture is an important feature through which to monitor gene expression profiles in cancer. This review summarises the involvement of epigenetically regulated miRNAs and miRNA-mediated epigenetic modulations in various cancers. In addition, the application of bioinformatics tools to study these networks and the use of therapeutic miRNAs for the treatment of cancer are also reviewed. A comprehensive interpretation of these mechanisms and the interwoven bond between miRNAs and epigenetics is crucial for understanding how the human epigenome is maintained, how aberrant miRNA expression can contribute to tumorigenesis and how knowledge of these factors can be translated into diagnostic and therapeutic tool development.
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Cai Y, Li Y, Sun B, Wang H, Zhang W, Zhao Y, Zhao H, Zhang J, Xu J, Wang Y. LncRNA PTCSC3 and lncRNA HULC Negatively Affect Each Other to Regulate Cancer Cell Invasion and Migration in Gastric Cancer. Cancer Manag Res 2020; 12:8535-8543. [PMID: 32982446 PMCID: PMC7502400 DOI: 10.2147/cmar.s254944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/13/2020] [Indexed: 11/23/2022] Open
Abstract
Background LncRNA PTCSC3 (PTCSC3) inhibits thyroid cancer cervical carcinoma and glioma, while its roles in gastric cancer are unknown. Studies have reported that HULC could serve as a potential biomarker for the diagnosis and prognosis of gastric cancer (GC). Our study aimed to investigate the potential interaction between PTCSC3 and HULC in gastric cancer. Methods This study enrolled 77 gastric cancer patients at the First Affiliated Hospital of Anhui Medical University from January 2016 to January 2018. RT-qPCR was performed to analyze gene expression levels. Cell transfections were carried out to evaluate gene interactions. Transwell assays and wound healing assays were used to analyze the effects of transfection on cell invasion and migration. Western blotting was also used to illustrate the possibility that lncRNA PTCSC3 and lncRNA HULC negatively affected each other through WNT signal path. Results We showed that PTCSC3 was downregulated in tumor tissues of gastric cancer patients in comparison to that in adjacent healthy tissues, and an inverse correlation between the expression levels of PTCSC3 and AJCC stage was observed. LncRNA HULC (HULC) was upregulated in tumor and inversely correlated with PTCSC3 in tumor tissues. Overexpression of PTCSC3 mediated the inhibition of HULC, while overexpression of HULC also mediated the inhibition of PTCSC3. PTCSC3 inhibited, while HULC promoted invasion and migration of gastric cancer cells. In addition, overexpression of HULC attenuated the effects of overexpression of PTCSC3. However, overexpression of PTCSC3 showed no significant effects on cell proliferation. We also found that PTCSC3/HULC affected each other to regulate cell invasion and migration through the Wnt/β-catenin signaling. Conclusion Therefore, overexpression of PTCSC3 inhibited the invasion and migration of gastric cancer cells, and the function of PTCSC3 is associated with HULC.
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Affiliation(s)
- Yi Cai
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Yang Li
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Bin Sun
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Hugen Wang
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Weiping Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Yuanyuan Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Haodong Zhao
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Jianlin Zhang
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Jianming Xu
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
| | - Yalei Wang
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province 230032, People's Republic of China
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24
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Zhou Y, Sun W, Qin Z, Guo S, Kang Y, Zeng S, Yu L. LncRNA regulation: New frontiers in epigenetic solutions to drug chemoresistance. Biochem Pharmacol 2020; 189:114228. [PMID: 32976832 DOI: 10.1016/j.bcp.2020.114228] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/09/2023]
Abstract
Long-noncoding RNAs (lncRNAs) have been shown to participate in sensitizing or de-sensitizing cancer cells to chemical drugs during cancer therapeutics. Notably, a plethora of lncRNAs have been confirmed to be associated with epigenetic controllers and regulate histone protein modification or DNA methylation states in the process of gene transcription. This correlation between lncRNAs and epigenetic regulators can induce the expression of core genes to trigger drug resistance. In addition, epigenetic signatures are considered to be effective and attractive biomarkers for monitoring drug therapeutic effects because they are inheritable, dynamic, and reversible. Therefore, the regulatory mechanism between lncRNAs and epigenetic machinery can serve as a novel indicator and target to overcome or reverse drug resistance in cancer therapy. In this review, we also presented a curated selection of computational tools (including online databases and network analysis) in the area of epigenetics. A classic workflow for lncRNA expression network analysis is presented, providing guidance for non-bioinformaticians to identify significant correlation between lncRNAs and other biomolecules.
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Affiliation(s)
- Ying Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Wen Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhiyuan Qin
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Suhang Guo
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
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25
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Palombo R, Verdile V, Paronetto MP. Poison-Exon Inclusion in DHX9 Reduces Its Expression and Sensitizes Ewing Sarcoma Cells to Chemotherapeutic Treatment. Cells 2020; 9:cells9020328. [PMID: 32023846 PMCID: PMC7072589 DOI: 10.3390/cells9020328] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing is a combinatorial mechanism by which exons are joined to produce multiple mRNA variants, thus expanding the coding potential and plasticity of eukaryotic genomes. Defects in alternative splicing regulation are associated with several human diseases, including cancer. Ewing sarcoma is an aggressive tumor of bone and soft tissue, mainly affecting adolescents and young adults. DHX9 is a key player in Ewing sarcoma malignancy, and its expression correlates with worse prognosis in patients. In this study, by screening a library of siRNAs, we have identified splicing factors that regulate the alternative inclusion of a poison exon in DHX9 mRNA, leading to its downregulation. In particular, we found that hnRNPM and SRSF3 bind in vivo to this poison exon and suppress its inclusion. Notably, DHX9 expression correlates with that of SRSF3 and hnRNPM in Ewing sarcoma patients. Furthermore, downregulation of SRSF3 or hnRNPM inhibited DHX9 expression and Ewing sarcoma cell proliferation, while sensitizing cells to chemotherapeutic treatment. Hence, our study suggests that inhibition of hnRNPM and SRSF3 expression or activity could be exploited as a therapeutic tool to enhance the efficacy of chemotherapy in Ewing sarcoma.
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Affiliation(s)
- Ramona Palombo
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
| | - Veronica Verdile
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy; (R.P.); (V.V.)
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
- Correspondence: ; Tel.:+39-0636733576
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