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Saxena T, Quan A, Chan E, Kozlova N, Matai L, Lee JD, Rupaimoole R, Beca F, Muranen T, Slack FJ. EGFR-induced lncRNA TRIDENT promotes drug resistance in non-small cell lung cancer via phospho-TRIM28-mediated DNA damage repair. Proc Natl Acad Sci U S A 2025; 122:e2415389122. [PMID: 40030013 PMCID: PMC11912419 DOI: 10.1073/pnas.2415389122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 01/06/2025] [Indexed: 03/19/2025] Open
Abstract
Long noncoding RNAs (lncRNAs) play numerous roles in cellular biology and alterations in lncRNA expression profiles have been implicated in a variety of cancers. Here, we identify and characterize a lncRNA, TRIM28 Interacting DNA damage repair Enhancing Noncoding Transcript (TRIDENT), whose expression is induced upon epithelial growth factor receptor (EGFR) activation, and which exerts pro-oncogenic functions in EGFR-driven non-small cell lung cancer. Knocking down TRIDENT leads to decreased tumor-cell proliferation in both in vitro and in vivo model systems and induces sensitization to chemotherapeutic drugs. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to accumulation of DNA damage in cancer cells via decreased TRIM28 phosphorylation. Altogether, our results reveal a molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance. Our findings suggest that TRIDENT can be developed as a biomarker or therapeutic target for EGFR mutant non-small cell lung cancer.
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Affiliation(s)
- Tanvi Saxena
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Anan Quan
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Erica Chan
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Nina Kozlova
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Latika Matai
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Jonathan D. Lee
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Rajesha Rupaimoole
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Francisco Beca
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Taru Muranen
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Frank J. Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
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2
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Shirani N, Abdi N, Chehelgerdi M, Yaghoobi H, Chehelgerdi M. Investigating the role of exosomal long non-coding RNAs in drug resistance within female reproductive system cancers. Front Cell Dev Biol 2025; 13:1485422. [PMID: 39925739 PMCID: PMC11802832 DOI: 10.3389/fcell.2025.1485422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 01/02/2025] [Indexed: 02/11/2025] Open
Abstract
Exosomes, as key mediators of intercellular communication, have been increasingly recognized for their role in the oncogenic processes, particularly in facilitating drug resistance. This article delves into the emerging evidence linking exosomal lncRNAs to the modulation of drug resistance mechanisms in cancers such as ovarian, cervical, and endometrial cancer. It synthesizes current research findings on how these lncRNAs influence cancer cell survival, tumor microenvironment, and chemotherapy efficacy. Additionally, the review highlights potential therapeutic strategies targeting exosomal lncRNAs, proposing a new frontier in overcoming drug resistance. By mapping the interface of exosomal lncRNAs and drug resistance, this article aims to provide a comprehensive understanding that could pave the way for innovative treatments and improved patient outcomes in female reproductive system cancers.
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Affiliation(s)
- Nooshafarin Shirani
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Neda Abdi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hajar Yaghoobi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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3
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Kilgas S, Syed A, Toolan-Kerr P, Swift ML, Roychoudhury S, Sarkar A, Wilkins S, Quigley M, Poetsch AR, Botuyan MV, Cui G, Mer G, Ule J, Drané P, Chowdhury D. NEAT1 modulates the TIRR/53BP1 complex to maintain genome integrity. Nat Commun 2024; 15:8438. [PMID: 39349456 PMCID: PMC11443056 DOI: 10.1038/s41467-024-52862-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 09/20/2024] [Indexed: 10/02/2024] Open
Abstract
Tudor Interacting Repair Regulator (TIRR) is an RNA-binding protein (RBP) that interacts directly with 53BP1, restricting its access to DNA double-strand breaks (DSBs) and its association with p53. We utilized iCLIP to identify RNAs that directly bind to TIRR within cells, identifying the long non-coding RNA NEAT1 as the primary RNA partner. The high affinity of TIRR for NEAT1 is due to prevalent G-rich motifs in the short isoform (NEAT1_1) region of NEAT1. This interaction destabilizes the TIRR/53BP1 complex, promoting 53BP1's function. NEAT1_1 is enriched during the G1 phase of the cell cycle, thereby ensuring that TIRR-dependent inhibition of 53BP1's function is cell cycle-dependent. TDP-43, an RBP that is implicated in neurodegenerative diseases, modulates the TIRR/53BP1 complex by promoting the production of the NEAT1 short isoform, NEAT1_1. Together, we infer that NEAT1_1, and factors regulating NEAT1_1, may impact 53BP1-dependent DNA repair processes, with implications for a spectrum of diseases.
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Affiliation(s)
- Susan Kilgas
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aleem Syed
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Patrick Toolan-Kerr
- The Francis Crick Institute, 1 Midland Road, London, UK
- UK Dementia Research Institute at King's College London, 5 Cutcombe Rd, London, UK
| | - Michelle L Swift
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Shrabasti Roychoudhury
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aniruddha Sarkar
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah Wilkins
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Yale School of Medicine, 333 Cedar St, New Haven, CT, USA
| | - Mikayla Quigley
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, 300 Longwood Ave, Boston, MA, USA
| | - Anna R Poetsch
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, Dresden, Germany
| | | | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London, UK
- UK Dementia Research Institute at King's College London, 5 Cutcombe Rd, London, UK
| | - Pascal Drané
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Dipanjan Chowdhury
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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4
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Han B, Ma Y, Yang P, Zhao F, Zhu H, Li S, Yu R, Bao S. Novel histone acetylation-related lncRNA signature for predicting prognosis and tumor microenvironment in esophageal carcinoma. Aging (Albany NY) 2024; 16:5163-5183. [PMID: 38478744 PMCID: PMC11006502 DOI: 10.18632/aging.205636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/02/2024] [Indexed: 04/06/2024]
Abstract
Histone acetylation is one of the most common epigenetic modifications and plays a crucial role in tumorigenesis. However, the prognostic significance of histone acetylation-related lncRNAs (HARlncRNAs) in esophageal carcinoma (ESCA) is not well understood. A total of 653 differentially expressed lncRNAs (DElncRNAs) were identified between 162 ESCA tissues and 11 normal tissues in the TCGA database, and 7 of them were correlated with acetylation regulators. We employed univariate Cox regression analysis, combining it with clinical prognosis information, to select 3 prognostic-related HARlncRNAs for further analysis. Subsequently, we used LASSO regression analysis to construct a risk signature for ESCA and identified C21orf62-AS1 and SSTR5.AS1 as potential biomarkers for the prognosis of ESCA patients. Based on the risk score calculated using the risk signature, we categorized patients into high- and low-risk groups. We identified the risk score as an independent risk factor and validated it in the training, test, and GSE53624 datasets. Additionally, patients categorized by their risk scores exhibited distinct immune statuses, tumor mutation burdens, responses to immunotherapy, and drug sensitivities.
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Affiliation(s)
- Batter Han
- Department of Thoracic Surgery, Peking University Cancer Hospital Inner Mongolia Hospital, Hohhot 010010, China
| | - Ying Ma
- Department of Thoracic Surgery, Mongolia Medical University Affiliated Hospital, Hohhot 010050, China
| | - Pengjie Yang
- Department of Thoracic Surgery, Peking University Cancer Hospital Inner Mongolia Hospital, Hohhot 010010, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Haiyong Zhu
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Shujun Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Rong Yu
- Department of Thoracic Surgery, Peking University Cancer Hospital Inner Mongolia Hospital, Hohhot 010010, China
| | - Subudao Bao
- Mongolian Medicine College, Inner Mongolia Medical University, Hohhot 010110, China
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5
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Ghahramani Almanghadim H, Karimi B, Poursalehi N, Sanavandi M, Atefi Pourfardin S, Ghaedi K. The biological role of lncRNAs in the acute lymphocytic leukemia: An updated review. Gene 2024; 898:148074. [PMID: 38104953 DOI: 10.1016/j.gene.2023.148074] [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: 10/10/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
The cause of leukemia, a common malignancy of the hematological system, is unknown. The structure of long non-coding RNAs (lncRNAs) is similar to mRNA but no ability to encode proteins. Numerous malignancies, including different forms of leukemia, are linked to Lnc-RNAs. It is verified that the carcinogenesis and growth of a variety of human malignancies are significantly influenced by aberrant lncRNA expression. The body of evidence linking various types of lncRNAs to the etiology of leukemia has dramatically increased during the past ten years. Some lncRNAs are therefore anticipated to function as novel therapeutic targets, diagnostic biomarkers, and clinical outcome predictions. Additionally, these lncRNAs may provide new therapeutic options and insight into the pathophysiology of diseases, particularly leukemia. Thus, this review outlines the present comprehension of leukemia-associated lncRNAs.
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Affiliation(s)
| | - Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Negareh Poursalehi
- Department of Medical Biotechnology, School of Medicine Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., 81746-73441 Isfahan, Iran.
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Podralska M, Sajek MP, Bielicka A, Żurawek M, Ziółkowska-Suchanek I, Iżykowska K, Kolenda T, Kazimierska M, Kasprzyk ME, Sura W, Pietrucha B, Cukrowska B, Rozwadowska N, Dzikiewicz-Krawczyk A. Identification of ATM-dependent long non-coding RNAs induced in response to DNA damage. DNA Repair (Amst) 2024; 135:103648. [PMID: 38382170 DOI: 10.1016/j.dnarep.2024.103648] [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: 11/20/2023] [Revised: 01/23/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
DNA damage response (DDR) is a complex process, essential for cell survival. Especially deleterious type of DNA damage are DNA double-strand breaks (DSB), which can lead to genomic instability and malignant transformation if not repaired correctly. The central player in DSB detection and repair is the ATM kinase which orchestrates the action of several downstream factors. Recent studies have suggested that long non-coding RNAs (lncRNAs) are involved in DDR. Here, we aimed to identify lncRNAs induced upon DNA damage in an ATM-dependent manner. DNA damage was induced by ionizing radiation (IR) in immortalized lymphoblastoid cell lines derived from 4 patients with ataxia-telangiectasia (AT) and 4 healthy donors. RNA-seq revealed 10 lncRNAs significantly induced 1 h after IR in healthy donors, whereas none in AT patients. 149 lncRNAs were induced 8 h after IR in the control group, while only three in AT patients. Among IR-induced mRNAs, we found several genes with well-known functions in DDR. Gene Set Enrichment Analysis and Gene Ontology revealed delayed induction of key DDR pathways in AT patients compared to controls. The induction and dynamics of selected 9 lncRNAs were confirmed by RT-qPCR. Moreover, using a specific ATM inhibitor we proved that the induction of those lncRNAs is dependent on ATM. Some of the detected lncRNA genes are localized next to protein-coding genes involved in DDR. We observed that induction of lncRNAs after IR preceded changes in expression of adjacent genes. This indicates that IR-induced lncRNAs may regulate the transcription of nearby genes. Subcellular fractionation into chromatin, nuclear, and cytoplasmic fractions revealed that the majority of studied lncRNAs are localized in chromatin. In summary, our study revealed several lncRNAs induced by IR in an ATM-dependent manner. Their genomic co-localization and co-expression with genes involved in DDR suggest that those lncRNAs may be important players in cellular response to DNA damage.
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Affiliation(s)
- Marta Podralska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marcin Piotr Sajek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Antonina Bielicka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Marta Kazimierska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Weronika Sura
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Pietrucha
- Children's Memorial Health Institute, Department of Immunology, Warsaw, Poland
| | - Bożena Cukrowska
- Children's Memorial Health Institute, Department of Pathomorphology, Immunology Laboratorium, Warsaw, Poland
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7
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Liu Y, Huang S, Dong G, Hou C, Zhao Y, Zhang D. Computational identification of DNA damage-relevant lncRNAs for predicting therapeutic efficacy and clinical outcomes in cancer. Comput Biol Med 2024; 171:108107. [PMID: 38412692 DOI: 10.1016/j.compbiomed.2024.108107] [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: 12/12/2023] [Revised: 01/12/2024] [Accepted: 02/04/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES The role of long non-coding RNAs (lncRNAs) in cancer treatment, particularly in modulating DNA repair programs, is an emerging field that warrants systematic exploration. This study aimed to systematically identify the lncRNA regulators that potentially regulate DNA damage response (DDR). METHODS Using genome-wide mRNA and lncRNA expression profiles of the same tumor patients, we proposed a novel computational framework. This framework performed Gene Set Variation Analysis to calculate DDR pathway enrichment score, which relies on weighting by tumor purity to obtain DDR activity score for each patient. Then, an in-depth differential expression profiling was conducted to identify pathway activity lncRNAs between high- and low-activity groups, utilizing a bootstrap-based randomization method. RESULTS We comprehensively charted the landscape of DDR-relevant lncRNAs across 23 epithelial-based cancer types. Its effectiveness was validated by assessing the consistency of these lncRNAs within various datasets of the same cancer type (hypergeometric test P < 0.001), examining the expression perturbation of these lncRNAs in response to treatment and demonstrating its application in prioritizing clinically-related lncRNAs. Furthermore, leveraging 820 epithelial ovarian cancer patients from four public datasets, we applied these lncRNAs identified by DDRLnc to establish and validate a risk stratification model to evaluate the benefits of platinum-based adjuvant chemotherapy for the improvement of clinical treatment outcomes. CONCLUSIONS Comprehensive pan-cancer analysis illustrates the utility of computational framework in identifying potentially lncRNAs involved in DDR, thereby offering novel insights into the complex realm of cancer research, and it will become a valuable tool for identifying potential therapeutic targets for cancer.
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Affiliation(s)
- Yixin Liu
- Modern Education Technology Center, Harbin Medical University, Harbin, 150080, China
| | - Shan Huang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Guanghui Dong
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Chang Hou
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yuming Zhao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China.
| | - Dandan Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150007, China.
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Kang J, Chung A, Suresh S, Bonzi LC, Sourisse JM, Ramirez‐Calero S, Romeo D, Petit‐Marty N, Pegueroles C, Schunter C. Long non-coding RNAs mediate fish gene expression in response to ocean acidification. Evol Appl 2024; 17:e13655. [PMID: 38357358 PMCID: PMC10866067 DOI: 10.1111/eva.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear. To explore the potential role of lncRNAs in fish exposed to ocean acidification (OA), we analyzed publicly available brain RNA-seq data from a coral reef fish Acanthochromis polyacanthus. We annotated the lncRNAs in its genome and examined the expression changes of intergenic lncRNAs (lincRNAs) between A. polyacanthus samples from a natural CO2 seep and a nearby control site. We identified 4728 lncRNAs, including 3272 lincRNAs in this species. Remarkably, 93.03% of these lincRNAs were species-specific. Among the 125 highly expressed lincRNAs and 403 differentially expressed lincRNAs in response to elevated CO2, we observed that lincRNAs were either neighboring or potentially trans-regulating differentially expressed coding genes associated with pH regulation, neural signal transduction, and ion transport, which are known to be important in the response to OA in fish. In summary, lncRNAs may facilitate fish acclimation and mediate the responses of fish to OA by modulating the expression of crucial coding genes, which offers insight into the regulatory mechanisms underlying fish responses to environmental changes.
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Affiliation(s)
- Jingliang Kang
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Arthur Chung
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sneha Suresh
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Lucrezia C. Bonzi
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Jade M. Sourisse
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sandra Ramirez‐Calero
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Daniele Romeo
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Natalia Petit‐Marty
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Cinta Pegueroles
- Department of Genetics, Microbiology and Statistics, Institute for Research on Biodiversity (IRBio)University of BarcelonaBarcelonaSpain
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
- State Key Laboratory of Marine Pollution and Department of ChemistryCity University of Hong KongHong Kong SARChina
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Zhou X, Liu X, Wan X, Xu M, Wang R, Yang D, Peng M, Jin T, Tang R, Liu M, Hou Y. Oxidized ATM governs stemness of breast cancer stem cell through regulating ubiquitylation and acetylation switch. Biochem Biophys Res Commun 2024; 691:149243. [PMID: 38016338 DOI: 10.1016/j.bbrc.2023.149243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023]
Abstract
Cancer stem cells (CSCs), as parts of tumor initiation cells, play a crucial role to tumorigenesis, development and recurrence. However, the complicated mechanisms of CSCs to adapt to tumor microenvironment and its stemness maintenance remains unclear. Here, we show that oxidized ATM, a hypoxia-activated cytoplasm ATM, acts a novel function to maintain CSC stemness in triple-negative breast cancer cells (BCSCs) via regulating histone H4 acetylation. Mechanistically, oxidized ATM phosphorylates TRIM21 (a E3 ubiquitin ligase) serine 80 and serine 469. Serine 80 phosphorylation of TRIM21 is essential for the ubiquitination activity of TRIM21. TRIM21 binds with SIRT1 (one of deacetylase), resulting in ubiquitylation-mediated degradation of SIRT1. The reduced SIRT1 leads to increase of histone H4 acetylation, thus facilitating CSC-related gene expression. Clinical data verify that high level of ATM in breast tumors is positively correlated with malignant grade, and is closely related with low SIRT1, high p-TRIM21, and high CD44 expression. In conclusion, our study provides a novel mechanism by which oxidized ATM governing BCSCs stemness and reveals an important link among oxidized ATM, histone acetylation, and BCSCs maintenance.
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Affiliation(s)
- Xinyue Zhou
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaoqi Liu
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Xueying Wan
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Ming Xu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Rui Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Dan Yang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Meixi Peng
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Ting Jin
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Rui Tang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Manran Liu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yixuan Hou
- Experimental Teaching Center of Basic Medicine Science, Chongqing Medical University, Chongqing, 400016, China.
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10
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Peng PH, Chen JL, Wu HH, Yang WH, Lin LJ, Lai JCY, Chang JS, Syu JL, Wu HT, Hsu FT, Cheng WC, Hsu KW. Interplay between lncRNA RP11-367G18.1 variant 2 and YY1 plays a vital role in hypoxia-mediated gene expression and tumorigenesis. Cancer Cell Int 2023; 23:266. [PMID: 37941005 PMCID: PMC10634066 DOI: 10.1186/s12935-023-03067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 09/15/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The hypoxia-responsive long non-coding RNA, RP11-367G18.1, has recently been reported to induce histone 4 lysine 16 acetylation (H4K16Ac) through its variant 2; however, the underlying molecular mechanism remains poorly understood. METHODS RNA pull-down assay and liquid chromatography-tandem mass spectrometry were performed to identify RP11-367G18.1 variant 2-binding partner. The molecular events were examined utilizing western blot analysis, real-time PCR, luciferase reporter assay, chromatin immunoprecipitation, and chromatin isolation by RNA purification assays. The migration, invasion, soft agar colony formation, and in vivo xenograft experiments were conducted to evaluate the impact of RP11-367G18.1 variant 2-YY1 complex on tumor progression. RESULTS In this study, RNA sequencing data revealed that hypoxia and RP11-367G18.1 variant 2 co-regulated genes were enriched in tumor-related pathways. YY1 was identified as an RP11-367G18.1 variant 2-binding partner that activates the H4K16Ac mark. YY1 was upregulated under hypoxic conditions and served as a target gene for hypoxia-inducible factor-1α. RP11-367G18.1 variant 2 colocalized with YY1 and H4K16Ac in the nucleus under hypoxic conditions. Head and neck cancer tissues had higher levels of RP11-367G18.1 and YY1 which were associated with poor patient outcomes. RP11-367G18.1 variant 2-YY1 complex contributes to hypoxia-induced epithelial-mesenchymal transition, cell migration, invasion, and tumorigenicity. YY1 regulated hypoxia-induced genes dependent on RP11-367G18.1 variant 2. CONCLUSIONS RP11-367G18.1 variant 2-YY1 complex mediates the tumor-promoting effects of hypoxia, suggesting that this complex can be targeted as a novel therapeutic strategy for cancer treatment.
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Affiliation(s)
- Pei-Hua Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, 333, Taiwan
| | - Ji-Lin Chen
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, No. 201, Sec. 2, Shih- Pai Road, Taipei, 112, Taiwan
| | - Heng-Hsiung Wu
- Research Center for Cancer Biology, China Medical University, Taichung, 40402, Taiwan
- Drug Development Center, Program for Cancer Biology and Drug Discovery, China Medical University, Taichung, 40402, Taiwan
| | - Wen-Hao Yang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan
| | - Li-Jie Lin
- Research Center for Cancer Biology, China Medical University, Taichung, 40402, Taiwan
- The PhD Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung, 40402, Taiwan
| | - Joseph Chieh-Yu Lai
- Institute of Biomedical Science, China Medical University, Taichung, 40402, Taiwan
| | - Jeng-Shou Chang
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, 333, Taiwan
| | - Jia-Ling Syu
- Research Center for Cancer Biology, China Medical University, Taichung, 40402, Taiwan
| | - Han-Tsang Wu
- Cancer Research Center, Changhua Christian Hospital, Changhua, 500, Taiwan
| | - Fei-Ting Hsu
- Department of Biological Science and Technology, China Medical University, Taichung, 40402, Taiwan.
| | - Wei-Chung Cheng
- Research Center for Cancer Biology, China Medical University, Taichung, 40402, Taiwan.
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan.
- The PhD Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung, 40402, Taiwan.
| | - Kai-Wen Hsu
- Research Center for Cancer Biology, China Medical University, Taichung, 40402, Taiwan.
- Drug Development Center, Program for Cancer Biology and Drug Discovery, China Medical University, Taichung, 40402, Taiwan.
- Institute of Translational Medicine and New Drug Development, China Medical University, Taichung, 40402, Taiwan.
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11
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Veschetti L, Treccani M, De Tomi E, Malerba G. Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects? Int J Mol Sci 2023; 24:11437. [PMID: 37511197 PMCID: PMC10380557 DOI: 10.3390/ijms241411437] [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: 05/11/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
In this work, we propose a comprehensive perspective on genomic instability comprising not only the accumulation of mutations but also telomeric shortening, epigenetic alterations and other mechanisms that could contribute to genomic information conservation or corruption. First, we present mechanisms playing a role in genomic instability across the kingdoms of life. Then, we explore the impact of genomic instability on the human being across its evolutionary history and on present-day human health, with a particular focus on aging and complex disorders. Finally, we discuss the role of non-coding RNAs, highlighting future approaches for a better living and an expanded healthy lifespan.
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Affiliation(s)
| | | | | | - Giovanni Malerba
- GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (M.T.); (E.D.T.)
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12
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Franco PIR, Neto JRDC, de Menezes LB, Machado JR, Miguel MP. Revisiting the hallmarks of cancer: A new look at long noncoding RNAs in breast cancer. Pathol Res Pract 2023; 243:154381. [PMID: 36857948 DOI: 10.1016/j.prp.2023.154381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
Breast cancer is one of the leading causes of death in women worldwide. The increasing understanding of the molecular mechanisms underlying its heterogeneity favors a better understanding of tumor biology and consequently the development of better diagnostic and treatment techniques. The advent of tumor genome sequencing techniques has highlighted more participants in the process, in addition to protein-coding genes. Thus, it is now known that long noncoding RNAs, previously described as transcriptional noise with no biological function, are intimately associated with tumor development. In breast cancer, they are abnormally expressed and closely associated with tumor progression, which makes them attractive diagnostic biomarkers and prognostic and specific therapeutic targets. Therefore, a thorough understanding of the regulatory mechanisms of long noncoding RNAs in breast cancer is essential for the search for new treatment strategies. In this review, we summarize the major long noncoding RNAs and their association with the cancer characteristics of the ability to sustain proliferative signaling, evasion of growth suppressors, replicative immortality, activation of invasion and metastasis, induction of angiogenesis, resistance to cell death, reprogramming of energy metabolism, genomic instability and sustained mutations, promotion of tumor inflammation, and evasion of the immune system. In addition, we report and suggest how they can be used as prognostic biomarkers and possible therapeutic targets.
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Affiliation(s)
- Pablo Igor Ribeiro Franco
- Instituto de Patologia Tropical e Saúde Pública, Programa de Pós-Graduação em Medicina Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil.
| | - José Rodrigues do Carmo Neto
- Instituto de Patologia Tropical e Saúde Pública, Programa de Pós-Graduação em Medicina Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Liliana Borges de Menezes
- Setor de Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil; Escola de Veterinária e Zootecnia, Programa de Pós-Graduação em Ciência Animal, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Juliana Reis Machado
- Instituto de Patologia Tropical e Saúde Pública, Programa de Pós-Graduação em Medicina Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil; Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Marina Pacheco Miguel
- Setor de Patologia Geral, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil; Escola de Veterinária e Zootecnia, Programa de Pós-Graduação em Ciência Animal, Universidade Federal de Goiás, Goiânia, GO, Brazil
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13
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Liu J, Yang X, Gao S, Wen M, Yu Q. DDX11-AS1 modulates DNA damage repair to enhance paclitaxel resistance of lung adenocarcinoma cells. Pharmacogenomics 2023; 24:163-172. [PMID: 36779347 DOI: 10.2217/pgs-2022-0121] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Aim: To investigate the influence of DDX11-AS1 on paclitaxel (PTX) resistance in lung adenocarcinoma (LUAD). Methods: LncRNA expression and functional enrichment analyses were processed via bioinformatics methods. DDX11-AS1 expression was detected via quantitative real-time PCR. Cell counting kit-8, colony formation, flow cytometry and comet assays were manipulated to measure cell proliferation, apoptosis, cell cycle and DNA damage repair, respectively. Western blot was used to assess DNA damage-related protein expression. Results: DDX11-AS1 was in a high expression status in LUAD, and could promote LUAD cell proliferation and PTX resistance, while suppressing cell apoptosis. DNA damage repairing ability was also modulated by the change of DDX11-AS1 expression. Conclusion: LncRNA DDX11-AS1 promotes DNA damage repair to enhance PTX resistance in LUAD.
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Affiliation(s)
- Jianhong Liu
- Department of Respiratory Medicine, Zhejiang Jinhua Guangfu Cancer Hospital, Jinhua City, Zhejiang Province, 321000, China
| | - Xu Yang
- Department of Respiratory Medicine, Zhejiang Jinhua Guangfu Cancer Hospital, Jinhua City, Zhejiang Province, 321000, China
| | - Shasha Gao
- Department of Respiratory Medicine, Zhejiang Jinhua Guangfu Cancer Hospital, Jinhua City, Zhejiang Province, 321000, China
| | - Minya Wen
- Department of Laboratory, Jinhua Wenrong Hospital, Jinhua City, Zhejiang Province, 322118, China
| | - Qiong Yu
- Department of Respiratory Medicine, Zhejiang Jinhua Guangfu Cancer Hospital, Jinhua City, Zhejiang Province, 321000, China
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14
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Lai Y, Lin H, Chen M, Lin X, Wu L, Zhao Y, Lin F, Lin C. Integration of bulk RNA sequencing and single-cell analysis reveals a global landscape of DNA damage response in the immune environment of Alzheimer's disease. Front Immunol 2023; 14:1115202. [PMID: 36895559 PMCID: PMC9989175 DOI: 10.3389/fimmu.2023.1115202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Background We developed a novel system for quantifying DNA damage response (DDR) to help diagnose and predict the risk of Alzheimer's disease (AD). Methods We thoroughly estimated the DDR patterns in AD patients Using 179 DDR regulators. Single-cell techniques were conducted to validate the DDR levels and intercellular communications in cognitively impaired patients. The consensus clustering algorithm was utilized to group 167 AD patients into diverse subgroups after a WGCNA approach was employed to discover DDR-related lncRNAs. The distinctions between the categories in terms of clinical characteristics, DDR levels, biological behaviors, and immunological characteristics were evaluated. For the purpose of choosing distinctive lncRNAs associated with DDR, four machine learning algorithms, including LASSO, SVM-RFE, RF, and XGBoost, were utilized. A risk model was established based on the characteristic lncRNAs. Results The progression of AD was highly correlated with DDR levels. Single-cell studies confirmed that DDR activity was lower in cognitively impaired patients and was mainly enriched in T cells and B cells. DDR-related lncRNAs were discovered based on gene expression, and two different heterogeneous subtypes (C1 and C2) were identified. DDR C1 belonged to the non-immune phenotype, while DDR C2 was regarded as the immune phenotype. Based on various machine learning techniques, four distinctive lncRNAs associated with DDR, including FBXO30-DT, TBX2-AS1, ADAMTS9-AS2, and MEG3 were discovered. The 4-lncRNA based riskScore demonstrated acceptable efficacy in the diagnosis of AD and offered significant clinical advantages to AD patients. The riskScore ultimately divided AD patients into low- and high-risk categories. In comparison to the low-risk group, high-risk patients showed lower DDR activity, accompanied by higher levels of immune infiltration and immunological score. The prospective medications for the treatment of AD patients with low and high risk also included arachidonyltrifluoromethane and TTNPB, respectively. Conclusions In conclusion, immunological microenvironment and disease progression in AD patients were significantly predicted by DDR-associated genes and lncRNAs. A theoretical underpinning for the individualized treatment of AD patients was provided by the suggested genetic subtypes and risk model based on DDR.
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Affiliation(s)
- Yongxing Lai
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Han Lin
- Department of Gastroenterology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Manli Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Xin Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Lijuan Wu
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Yinan Zhao
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Fan Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Chunjin Lin
- Department of Geriatric Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian, China.,Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, Fujian, China
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15
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Arman W, Munger K. Mechanistic Contributions of lncRNAs to Cellular Signaling Pathways Crucial to the Lifecycle of Human Papillomaviruses. Viruses 2022; 14:2439. [PMID: 36366537 PMCID: PMC9697900 DOI: 10.3390/v14112439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Papillomaviruses are ubiquitous epitheliotropic viruses with double-stranded circular DNA genomes of approximately 8000 base pairs. The viral life cycle is somewhat unusual in that these viruses can establish persistent infections in the mitotically active basal epithelial cells that they initially infect. High-level viral genome replication ("genome amplification"), the expression of capsid proteins, and the formation of infectious progeny are restricted to terminally differentiated cells where genomes are synthesized at replication factories at sites of double-strand DNA breaks. To establish persistent infections, papillomaviruses need to retain the basal cell identity of the initially infected cells and restrain and delay their epithelial differentiation program. To enable high-level viral genome replication, papillomaviruses also need to hold the inherently growth-arrested terminally differentiated cells in a replication-competent state. To provide ample sites for viral genome synthesis, they target the DNA damage and repair machinery. Studies focusing on delineating cellular factors that are targeted by papillomaviruses may aid the development of antivirals. Whilst most of the current research efforts focus on protein targets, the majority of the human transcriptome consists of noncoding RNAs. This review focuses on one specific class of noncoding RNAs, long noncoding RNAs (lncRNAs), and summarizes work on lncRNAs that may regulate the cellular processes that are subverted by papillomavirus to enable persistent infections and progeny synthesis.
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Affiliation(s)
- Warda Arman
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
- Molecular Microbiology Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Karl Munger
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
- Molecular Microbiology Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
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16
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Cheng T, Bai Y, Huang S, Wang Y, Zhou S, Liu H, Zhang R, Luo X, Yu P. Estrogen receptor 1 inhibits the progression of hepatocellular carcinoma via positively regulating lncRNA maternally expressed gene 3 under high glucose conditions. J Gastrointest Oncol 2022; 13:2485-2496. [PMID: 36388662 PMCID: PMC9660067 DOI: 10.21037/jgo-22-825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND Long noncoding RNA (lncRNA) maternally expressed gene 3 (MEG3) is crucial in the association of diabetes mellitus (DM) and hepatocellular carcinoma (HCC), and estrogen receptor 1 (ESR1) plays an essential role in various cancers. However, the underlying regulatory effect of ESR1/lncRNA MEG3 on HCC with DM remains unclear. This study explored the regulatory effect of ESR1/lncRNA MEG3 on HCC cell progression. METHODS Bioinformatics analysis was used to predict the promoter sequence of lncRNA MEG3 using UCSC (http://genome.ucsc.edu/), followed by luciferase reporter and RNA immunoprecipitation (RIP) assays to verify the specific combination between ESR1 and lncRNA MEG3 promoter. After cotransfection with ESR1, ESR1 siRNA or lncRNA MEG3 RNA, CCK-8, 5-ethynyl-2'-deoxyuridine (EdU) and colony formation assays were used to evaluate the cell proliferation capacity. Cell apoptosis was assessed using flow cytometry analysis. Next, wound healing and Transwell assays were conducted to examine cell invasiveness and migration. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot analysis were performed to quantify the expression of ESR1 or lncRNA MEG3. RESULTS ESR1 might be the transcription factor (TF) of lncRNA MEG3, and ESR1 bound with lncRNA MEG3 promoter. Overexpression of ESR1 repressed the proliferation, migration and invasion of HepG2 cells, and promoted apoptosis of HepG2 cells under high glucose conditions. Silencing ESR1 decreased lncRNA MEG3 expression in HepG2 cells but enhanced proliferation, migration and invasion. Meanwhile, a rescue assay demonstrated that silencing lncRNA MEG3 reversed the inhibitory effect of ESR1 on HepG2 cell progression. CONCLUSIONS ESR1 inhibits HCC cell progression through positively regulating lncRNA MEG3, and the results provide a promising strategy for HCC management.
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Affiliation(s)
- Ting Cheng
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Yu Bai
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Shuai Huang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Yao Wang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Saijun Zhou
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Hongyan Liu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Rui Zhang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Xi Luo
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Pei Yu
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
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17
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Singh D, Assaraf YG, Gacche RN. Long Non-coding RNA Mediated Drug Resistance in Breast Cancer. Drug Resist Updat 2022; 63:100851. [DOI: 10.1016/j.drup.2022.100851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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The Breast Cancer Protooncogenes HER2, BRCA1 and BRCA2 and Their Regulation by the iNOS/NOS2 Axis. Antioxidants (Basel) 2022; 11:antiox11061195. [PMID: 35740092 PMCID: PMC9227079 DOI: 10.3390/antiox11061195] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
The expression of inducible nitric oxide synthase (iNOS; NOS2) and derived NO in various cancers was reported to exert pro- and anti-tumorigenic effects depending on the levels of expression and the tumor types. In humans, the breast cancer level of iNOS was reported to be overexpressed, to exhibit pro-tumorigenic activities, and to be of prognostic significance. Likewise, the expression of the oncogenes HER2, BRCA1, and BRCA2 has been associated with malignancy. The interrelationship between the expression of these protooncogenes and oncogenes and the expression of iNOS is not clear. We have hypothesized that there exist cross-talk signaling pathways between the breast cancer protooncogenes, the iNOS axis, and iNOS-mediated NO mutations of these protooncogenes into oncogenes. We review the molecular regulation of the expression of the protooncogenes in breast cancer and their interrelationships with iNOS expression and activities. In addition, we discuss the roles of iNOS, HER2, BRCA1/2, and NO metabolism in the pathophysiology of cancer stem cells. Bioinformatic analyses have been performed and have found suggested molecular alterations responsible for breast cancer aggressiveness. These include the association of BRCA1/2 mutations and HER2 amplifications with the dysregulation of the NOS pathway. We propose that future studies should be undertaken to investigate the regulatory mechanisms underlying the expression of iNOS and various breast cancer oncogenes, with the aim of identifying new therapeutic targets for the treatment of breast cancers that are refractory to current treatments.
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19
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Zhu YS, Zhu J. Molecular and cellular functions of long non-coding RNAs in prostate and breast cancer. Adv Clin Chem 2022; 106:91-179. [PMID: 35152976 DOI: 10.1016/bs.acc.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) are defined as noncoding RNA transcripts with a length greater than 200 nucleotides. Research over the last decade has made great strides in our understanding of lncRNAs, especially in the biology of their role in cancer. In this article, we will briefly discuss the biogenesis and characteristics of lncRNAs, then review their molecular and cellular functions in cancer by using prostate and breast cancer as examples. LncRNAs are abundant, diverse, and evolutionarily, less conserved than protein-coding genes. They are often expressed in a tumor and cell-specific manner. As a key epigenetic factor, lncRNAs can use a wide variety of molecular mechanisms to regulate gene expression at each step of the genetic information flow pathway. LncRNAs display widespread effects on cell behavior, tumor growth, and metastasis. They act intracellularly and extracellularly in an autocrine, paracrine and endocrine fashion. Increased understanding of lncRNA's role in cancer has facilitated the development of novel biomarkers for cancer diagnosis, led to greater understanding of cancer prognosis, enabled better prediction of therapeutic responses, and promoted identification of potential targets for cancer therapy.
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Affiliation(s)
- Yuan-Shan Zhu
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States.
| | - Jifeng Zhu
- Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States
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20
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Cheng L, Hu S, Ma J, Shu Y, Chen Y, Zhang B, Qi Z, Wang Y, Zhang Y, Zhang Y, Cheng P. Long noncoding RNA RP11-241J12.3 targeting pyruvate carboxylase promotes hepatocellular carcinoma aggressiveness by disrupting pyruvate metabolism and the DNA mismatch repair system. MOLECULAR BIOMEDICINE 2022; 3:4. [PMID: 35122182 PMCID: PMC8816999 DOI: 10.1186/s43556-021-00065-w] [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: 08/08/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
Accumulating evidence indicates that hepatitis B virus X protein (HBx) plays a key role in HBV-related hepatocellular carcinoma (HCC) aggressiveness; however, the underlying mechanisms are not entirely clear. Long non-coding RNAs (lncRNAs), which participate in the regulation of diverse biological processes, may be critical for the function of HBx. Our research indicated that HBx induced changes in the expression of numerous lncRNAs and implicated the novel lncRNA RP11-241J12.3 in HBx-mediated HCC aggressiveness. Although RP11-241J12.3 expression was downregulated in transient HBx-expressing HCC cells (similar to the early stage of HBV infection), its oncogenic properties remained. The results showed that RP11-241J12.3 not only accelerated DNA synthesis and upregulated the expression of pyruvate carboxylase (PC) and MSH3, which is a key protein in pyruvate metabolism and DNA mismatch repair (MMR), but also promoted tumor growth in vitro and in vivo, thus promoting HCC aggressiveness. More importantly, we revealed that RP11-241J12.3 may interact with PC and identified its location in the cytoplasm close to the nucleus using fluorescence in situ hybridization (FISH). We also observed RP11-241J12.3 expression was upregulated in HCC tissues compared with the paracarcinomatous tissues. Furthermore, RP11-241J12.3 expression levels showed a close relationship with clinical stage and tumor size and that low RP11-241J12.3 expression was significantly correlated with longer HCC patient survival. These results further our understanding of the lncRNAs regulated by HBx in HCC, and provide evidence that dysregulation of RP11-241J12.3 contributes to HCC aggressiveness.
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Affiliation(s)
- Liuliu Cheng
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China
| | - Shichuan Hu
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China
| | - Jinhu Ma
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China
| | - Yongheng Shu
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China
| | - Yanwei Chen
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China
| | - Bin Zhang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China
| | - Zhongbing Qi
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China
| | - Yunmeng Wang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China
| | - Yan Zhang
- Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Yuwei Zhang
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Ping Cheng
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, 17 People's South Road, Chengdu, 610041, Sichuan, PR China.
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21
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García-Padilla C, Dueñas Á, García-López V, Aránega A, Franco D, Garcia-Martínez V, López-Sánchez C. Molecular Mechanisms of lncRNAs in the Dependent Regulation of Cancer and Their Potential Therapeutic Use. Int J Mol Sci 2022; 23:764. [PMID: 35054945 PMCID: PMC8776057 DOI: 10.3390/ijms23020764] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/31/2021] [Accepted: 01/08/2022] [Indexed: 12/16/2022] Open
Abstract
Deep whole genome and transcriptome sequencing have highlighted the importance of an emerging class of non-coding RNA longer than 200 nucleotides (i.e., long non-coding RNAs (lncRNAs)) that are involved in multiple cellular processes such as cell differentiation, embryonic development, and tissue homeostasis. Cancer is a prime example derived from a loss of homeostasis, primarily caused by genetic alterations both in the genomic and epigenetic landscape, which results in deregulation of the gene networks. Deregulation of the expression of many lncRNAs in samples, tissues or patients has been pointed out as a molecular regulator in carcinogenesis, with them acting as oncogenes or tumor suppressor genes. Herein, we summarize the distinct molecular regulatory mechanisms described in literature in which lncRNAs modulate carcinogenesis, emphasizing epigenetic and genetic alterations in particular. Furthermore, we also reviewed the current strategies used to block lncRNA oncogenic functions and their usefulness as potential therapeutic targets in several carcinomas.
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Affiliation(s)
- Carlos García-Padilla
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Ángel Dueñas
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Virginio García-López
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Amelia Aránega
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Fundación Medina, 18016 Granada, Spain
| | - Diego Franco
- Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain; (Á.D.); (A.A.); (D.F.)
- Fundación Medina, 18016 Granada, Spain
| | - Virginio Garcia-Martínez
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
| | - Carmen López-Sánchez
- Department of Human Anatomy and Embryology, University of Extremadura, 06006 Badajoz, Spain; (V.G.-L.); (V.G.-M.)
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006 Badajoz, Spain
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22
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Crosstalk between non-coding RNAs expression profile, drug resistance and immune response in breast cancer. Pharmacol Res 2021; 176:106041. [PMID: 34952200 DOI: 10.1016/j.phrs.2021.106041] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/15/2021] [Accepted: 12/19/2021] [Indexed: 12/18/2022]
Abstract
Drug resistance is one of the most critical challenges facing researchers in treating breast cancer. Despite numerous treatments for breast cancer, including conventional chemical drugs, monoclonal antibodies, and immunotherapeutic drugs known as immune checkpoint inhibitors (ICI), many patients resist various approaches. In recent years, the relationship between gene expression profiles and drug resistance phenotypes has attracted much attention. Non-coding RNAs (ncRNAs) are regulatory molecules that have been shown to regulate gene expression and cell transcriptome. Two categories, microRNAs and long non-coding RNAs have been more considered and studied among these ncRNAs. Studying the role of different ncRNAs in chemical drug resistance and ICI resistance together can be beneficial in selecting more effective treatments for breast cancer. Changing the expression and action mechanism of these regulatory molecules on drug resistance phenotypes is the main topic of this review article.
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23
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Comprehensive Analysis of Acetylation-Related lncRNAs and Identified AC099850.3 as Prognostic Biomarker in Non-Small Cell Lung Cancer. JOURNAL OF ONCOLOGY 2021; 2021:4405697. [PMID: 34675976 PMCID: PMC8526274 DOI: 10.1155/2021/4405697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/09/2021] [Accepted: 09/27/2021] [Indexed: 12/01/2022]
Abstract
The present study aimed to analyze the effects of acetylation-related lncRNAs in non-small-cell lung cancer (NSCLC). A total of 399 differentially expressed lncRNAs (DElncRNAs) have been identified between 497 NSCLC tissues and 54 normal tissues in the TCGA database, and 105 of which were correlated with acetylation regulators. By using univariate cox regression analysis and combining it with clinical prognosis information, 12 prognostic-related lncRNAs were selected for the subsequent analysis. The NSCLC patients were divided into two subgroups (cluster 1 and cluster 2) by clustering software, and immunocyte infiltration analysis, microenvironmental analysis, and clinical relevance analysis were performed between the two subgroups. A risk model was also built to further assess the prognosis value of prognostic-related lncRNAs in NSCLC patients. We found that AC099850.3 was significantly higher in both cluster 1 and high-risk subgroups, which may serve as a potential biomarker for the prognosis of NSCLC patients. Then, based on ceRNA competition mechanisms, the pathway enrichment of 105 acetylation-related lncRNAs was conducted by GO and KEGG analyses. We found the acetylation-related lncRNAs were primarily enriched in MAPK and EGFR signaling pathways, which were closely associated with NSCLC development. Finally, we validated the expression levels of AC099850.3 in NSCLC tissues and adjacent non-cancerous tissues and confirmed that AC099850.3 was significantly highly expressed in NSCLC tissues and cells. These results may provide clues for our understanding of the role of acetylation-related lncRNAs and valuable information for future clinical diagnosis and prognosis in NSCLC patients.
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24
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Jin H, Du W, Huang W, Yan J, Tang Q, Chen Y, Zou Z. lncRNA and breast cancer: Progress from identifying mechanisms to challenges and opportunities of clinical treatment. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:613-637. [PMID: 34589282 PMCID: PMC8463317 DOI: 10.1016/j.omtn.2021.08.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Breast cancer is a malignant tumor that has a high mortality rate and mostly occurs in women. Although significant progress has been made in the implementation of personalized treatment strategies for molecular subtypes in breast cancer, the therapeutic response is often not satisfactory. Studies have reported that long non-coding RNAs (lncRNAs) are abnormally expressed in breast cancer and closely related to the occurrence and development of breast cancer. In addition, the high tissue and cell-type specificity makes lncRNAs particularly attractive as diagnostic biomarkers, prognostic factors, and specific therapeutic targets. Therefore, an in-depth understanding of the regulatory mechanisms of lncRNAs in breast cancer is essential for developing new treatment strategies. In this review, we systematically elucidate the general characteristics, potential mechanisms, and targeted therapy of lncRNAs and discuss the emerging functions of lncRNAs in breast cancer. Additionally, we also highlight the advantages and challenges of using lncRNAs as biomarkers for diagnosis or therapeutic targets for drug resistance in breast cancer and present future perspectives in clinical practice.
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Affiliation(s)
- Huan Jin
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, China.,MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Wei Du
- Department of Neurosurgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, China
| | - Wentao Huang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Jiajing Yan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Qing Tang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yibing Chen
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, China
| | - Zhengzhi Zou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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25
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Price RL, Bhan A, Mandal SS. HOTAIR beyond repression: In protein degradation, inflammation, DNA damage response, and cell signaling. DNA Repair (Amst) 2021; 105:103141. [PMID: 34183273 PMCID: PMC10426209 DOI: 10.1016/j.dnarep.2021.103141] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 05/13/2021] [Accepted: 05/21/2021] [Indexed: 01/17/2023]
Abstract
Long noncoding RNAs (lncRNAs) are pervasively transcribed from the mammalian genome as transcripts that are usually >200 nucleotides long. LncRNAs generally do not encode proteins but are involved in a variety of physiological processes, principally as epigenetic regulators. HOX transcript antisense intergenic RNA (HOTAIR) is a well-characterized lncRNA that has been implicated in several cancers and in various other diseases. HOTAIR is a repressor lncRNA and regulates various repressive chromatin modifications. However, recent studies have revealed additional functions of HOTAIR in regulation of protein degradation, microRNA (miRNA) sponging, NF-κB activation, inflammation, immune signaling, and DNA damage response. Herein, we have summarized the diverse functions and modes of action of HOTAIR in protein degradation, inflammation, DNA repair, and diseases, beyond its established functions in gene silencing.
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Affiliation(s)
- Rachel L Price
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, United States
| | - Arunoday Bhan
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, United States
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, United States.
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26
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Rusek M, Krasowska D. Non-Coding RNA in Systemic Sclerosis: A Valuable Tool for Translational and Personalized Medicine. Genes (Basel) 2021; 12:1296. [PMID: 34573278 PMCID: PMC8471866 DOI: 10.3390/genes12091296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
Epigenetic factors are heritable and ultimately play a role in modulating gene expression and, thus, in regulating cell functions. Non-coding RNAs have growing recognition as novel biomarkers and crucial regulators of pathological conditions in humans. Their characteristic feature is being transcribed in a tissue-specific pattern. Now, there is emerging evidence that lncRNAs have been identified to be involved in the differentiation of human skin, wound healing, fibrosis, inflammation, and immunological response. Systemic sclerosis (SSc) is a heterogeneous autoimmune disease characterized by fibrosis, vascular abnormalities, and immune system activation. The pathogenesis remains elusive, but clinical manifestations reveal autoimmunity with the presence of specific autoantibodies, activation of innate and adaptive immunity, vascular changes, and active deposition of extracellular matrix components leading to fibrosis. The use of multi-omics studies, including NGS, RNA-seq, or GWAS, has proposed that the non-coding genome may be a significant player in its pathogenesis. Moreover, it may unravel new therapeutic targets in the future. The aim of this review is to show the pathogenic role of long non-coding RNAs in systemic sclerosis. Investigation of these transcripts' functions has the potential to elucidate the molecular pathology of SSc and provide new opportunities for drug-targeted therapy for this disorder.
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Affiliation(s)
- Marta Rusek
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
- Department of Pathophysiology, Medical University of Lublin, 20-090 Lublin, Poland
| | - Dorota Krasowska
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
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27
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Cheng C, Liu F, Tian N, Mensah RA, Sun X, Liu J, Wu J, Wang B, Li D, Lai Z. Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing. Sci Rep 2021; 11:16363. [PMID: 34381122 PMCID: PMC8358008 DOI: 10.1038/s41598-021-95832-8] [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: 03/14/2021] [Accepted: 07/29/2021] [Indexed: 12/03/2022] Open
Abstract
Fusarium wilt disease, caused by Fusarium oxysporum f.sp. cubense (Foc), has been recognized as the most devastating disease to banana. The regulatory role of long non-coding RNAs (lncRNAs) in plant defense has been verified in many plant species. However, the understanding of their role during early FocTR4 (Foc tropical race 4) infection stage is very limited. In this study, lncRNA sequencing was used to reveal banana root transcriptome profile changes during early FocTR4 infection stages. Quantitative real time PCR (qRT-PCR) was performed to confirm the expression of eight differentially expressed (DE) lncRNAs (DELs) and their predicted target genes (DETs), and three DE genes (DEGs). Totally, 12,109 lncRNAs, 36,519 mRNAs and 2642 novel genes were obtained, of which 1398 (including 78 DELs, 1220 DE known genes and 100 DE novel genes) were identified as FocTR4 responsive DE transcripts. Gene function analysis revealed that most DEGs were involved in biosynthesis of secondary metabolites, plant–pathogen interaction, plant hormone signal transduction, phenylalanine metabolism, phenylpropanoid biosynthesis, alpha-linolenic acid metabolism and so on. Coincidently, many DETs have been identified as DEGs in previous transcriptome studies. Moreover, many DETs were found to be involved in ribosome, oxidative phosphorylation, lipoic acid metabolism, ubiquitin mediated proteolysis, N-glycan biosynthesis, protein processing in endoplasmic reticulum and DNA damage response pathways. QRT-PCR result showed the expression patterns of the selected transcripts were mostly consistent with our lncRNA sequencing data. Our present study showed the regulatory role of lncRNAs on known biotic and abiotic stress responsive genes and some new-found FocTR4 responsive genes, which can provide new insights into FocTR4-induced changes in the banana root transcriptome during the early pathogen infection stage.
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Affiliation(s)
- Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China.
| | - Fan Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Na Tian
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Raphael Anue Mensah
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueli Sun
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiapeng Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Junwei Wu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bin Wang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dan Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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28
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Regulatory and Functional Involvement of Long Non-Coding RNAs in DNA Double-Strand Break Repair Mechanisms. Cells 2021; 10:cells10061506. [PMID: 34203749 PMCID: PMC8232683 DOI: 10.3390/cells10061506] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Protection of genome integrity is vital for all living organisms, particularly when DNA double-strand breaks (DSBs) occur. Eukaryotes have developed two main pathways, namely Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR), to repair DSBs. While most of the current research is focused on the role of key protein players in the functional regulation of DSB repair pathways, accumulating evidence has uncovered a novel class of regulating factors termed non-coding RNAs. Non-coding RNAs have been found to hold a pivotal role in the activation of DSB repair mechanisms, thereby safeguarding genomic stability. In particular, long non-coding RNAs (lncRNAs) have begun to emerge as new players with vast therapeutic potential. This review summarizes important advances in the field of lncRNAs, including characterization of recently identified lncRNAs, and their implication in DSB repair pathways in the context of tumorigenesis.
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29
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Wang MQ, Zhu WJ, Gao P. New insights into long non-coding RNAs in breast cancer: Biological functions and therapeutic prospects. Exp Mol Pathol 2021; 120:104640. [PMID: 33878314 DOI: 10.1016/j.yexmp.2021.104640] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/24/2021] [Accepted: 04/16/2021] [Indexed: 11/29/2022]
Abstract
Breast cancer (BC) has become one of the most common malignant tumors in the world, seriously endangering women's health and life. However, the underlying molecular mechanisms of BC remain unclear. Over the past decade, long non-coding RNAs (lncRNAs) were gradually discovered and appreciated to play pivotal regulatory role in the progression of BC. It has been demonstrated that lncRNAs are implicated in regulating plenty of biological phenomena including cell proliferation, apoptosis, invasion and metastasis by interacting with DNA, RNA or proteins. In addition to these, the function of lncRNAs in tumor resistance has increasingly attracted more attention. In this review, we summarized the emerging impact of lncRNAs on the occurrence and progression of human BC, specifically focusing on the functions and mechanisms of them, with the aim of exploring the potential value of lncRNAs as oncogenic drivers or tumor suppressors. Furthermore, the potential clinical application of lncRNAs as diagnostic biomarkers and therapeutic targets in BC was also discussed.
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Affiliation(s)
- Meng-Qi Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, CheeLoo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pathology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, China
| | - Wen-Jie Zhu
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, CheeLoo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pathology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, China.
| | - Peng Gao
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, CheeLoo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pathology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, China.
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30
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Xu A, Huang MF, Zhu D, Gingold JA, Bazer DA, Chang B, Wang D, Lai CC, Lemischka IR, Zhao R, Lee DF. LncRNA H19 Suppresses Osteosarcomagenesis by Regulating snoRNAs and DNA Repair Protein Complexes. Front Genet 2021; 11:611823. [PMID: 33519915 PMCID: PMC7844330 DOI: 10.3389/fgene.2020.611823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022] Open
Abstract
Osteosarcoma is one of the most frequent common primary malignant tumors in childhood and adolescence. Long non-coding RNAs (lncRNAs) have been reported to regulate the initiation and progression of tumors. However, the exact molecular mechanisms involving lncRNA in osteosarcomagenesis remain largely unknown. Li-Fraumeni syndrome (LFS) is a familial cancer syndrome caused by germline p53 mutation. We investigated the tumor suppressor function of lncRNA H19 in LFS-associated osteosarcoma. Analyzing H19-induced transcriptome alterations in LFS induced pluripotent stem cell (iPSC)-derived osteoblasts, we unexpectedly discovered a large group of snoRNAs whose expression was significantly affected by H19. We identified SNORA7A among the H19-suppressed snoRNAs. SNORA7A restoration impairs H19-mediated osteogenesis and tumor suppression, indicating an oncogenic role of SNORA7A. TCGA analysis indicated that SNORA7A expression is associated with activation of oncogenic signaling and poor survival in cancer patients. Using an optimized streptavidin-binding RNA aptamer designed from H19 lncRNA, we revealed that H19-tethered protein complexes include proteins critical for DNA damage response and repair, confirming H19's tumor suppressor role. In summary, our findings demonstrate a critical role of H19-modulated SNORA7A expression in LFS-associated osteosarcomas.
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Affiliation(s)
- An Xu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Dandan Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Julian A Gingold
- Department of Obstetrics and Gynecology and Women's Health, Einstein/Montefiore Medical Center, Bronx, NY, United States
| | - Danielle A Bazer
- Department of Neurology, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, United States
| | - Betty Chang
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Donghui Wang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States.,Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Precision Health, School of Biomedical Informatics and School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
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31
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Li G, Deng L, Huang N, Sun F. The Biological Roles of lncRNAs and Future Prospects in Clinical Application. Diseases 2021; 9:diseases9010008. [PMID: 33450825 PMCID: PMC7838801 DOI: 10.3390/diseases9010008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Chemo and radiation therapies are the most commonly used therapies for cancer, but they can induce DNA damage, resulting in the apoptosis of host cells. DNA double-stranded breaks (DSBs) are the most lethal form of DNA damage in cells, which are constantly caused by a wide variety of genotoxic agents, both environmentally and endogenously. To maintain genomic integrity, eukaryotic organisms have developed a complex mechanism for the repair of DNA damage. Researches reported that many cellular long noncoding RNAs (lncRNAs) were involved in the response of DNA damage. The roles of lncRNAs in DNA damage response can be regulated by the dynamic modification of N6-adenosine methylation (m6A). The cellular accumulation of DNA damage can result in various diseases, including cancers. Additionally, lncRNAs also play roles in controlling the gene expression and regulation of autophagy, which are indirectly involved with individual development. The dysregulation of these functions can facilitate human tumorigenesis. In this review, we summarized the origin and overview function of lncRNAs and highlighted the roles of lncRNAs involved in the repair of DNA damage.
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Affiliation(s)
- Guohui Li
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China; (G.L.); (L.D.)
| | - Liang Deng
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China; (G.L.); (L.D.)
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
| | - Nan Huang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
- Correspondence: ; Tel.: +86-021-6630-6909
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32
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Zhang Y, Sun Z, Jia J, Du T, Zhang N, Tang Y, Fang Y, Fang D. Overview of Histone Modification. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:1-16. [PMID: 33155134 DOI: 10.1007/978-981-15-8104-5_1] [Citation(s) in RCA: 252] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics is the epi-information beyond the DNA sequence that can be inherited from parents to offspring. From years of studies, people have found that histone modifications, DNA methylation, and RNA-based mechanism are the main means of epigenetic control. In this chapter, we will focus on the general introductions of epigenetics, which is important in the regulation of chromatin structure and gene expression. With the development and expansion of high-throughput sequencing, various mutations of epigenetic regulators have been identified and proven to be the drivers of tumorigenesis. Epigenetic alterations are used to diagnose individual patients more accurately and specifically. Several drugs, which are targeting epigenetic changes, have been developed to treat patients regarding the awareness of precision medicine. Emerging researches are connecting the epigenetics and cancers together in the molecular mechanism exploration and the development of druggable targets.
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Affiliation(s)
- Yanjun Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
| | - Zhongxing Sun
- Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
| | - Junqi Jia
- Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
| | - Tianjiao Du
- Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
| | - Nachuan Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
| | - Yin Tang
- Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
| | - Yuan Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China
| | - Dong Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, P.R. China.
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33
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Johnson SJ, Cooper TA. Overlapping mechanisms of lncRNA and expanded microsatellite RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1634. [PMID: 33191580 PMCID: PMC7880542 DOI: 10.1002/wrna.1634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022]
Abstract
RNA has major regulatory roles in a wide range of biological processes and a surge of RNA research has led to the classification of numerous functional RNA species. One example is long noncoding RNAs (lncRNAs) that are structurally complex transcripts >200 nucleotides (nt) in length and lacking a canonical open reading frame (ORF). Despite a general lack of sequence conservation and low expression levels, many lncRNAs have been shown to have functionality in diverse biological processes as well as in mechanisms of disease. In parallel with the growing understanding of lncRNA functions, there is a growing subset of microsatellite expansion disorders in which the primary mechanism of pathogenesis is an RNA gain of function arising from RNA transcripts from the mutant allele. Microsatellite expansion disorders are caused by an expansion of short (3-10 nt) repeats located within coding genes. Expanded repeat-containing RNA mediates toxicity through multiple mechanisms, the details of which remain only partially understood. The purpose of this review is to highlight the links between functional mechanisms of lncRNAs and the potential pathogenic mechanisms of expanded microsatellite RNA. These shared mechanisms include protein sequestration, peptide translation, micro-RNA (miRNA) processing, and miRNA sequestration. Recognizing the parallels between the normal functions of lncRNAs and the negative impact of expanded microsatellite RNA on biological processes can provide reciprocal understanding to the roles of both RNA species. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Sara J Johnson
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Thomas A Cooper
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
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Wu C, Chen W, Yu F, Yuan Y, Chen Y, Hurst DR, Li Y, Li L, Liu Z. Long Noncoding RNA HITTERS Protects Oral Squamous Cell Carcinoma Cells from Endoplasmic Reticulum Stress-Induced Apoptosis via Promoting MRE11-RAD50-NBS1 Complex Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002747. [PMID: 33240783 PMCID: PMC7675039 DOI: 10.1002/advs.202002747] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Indexed: 02/05/2023]
Abstract
Recent studies have proven that long noncoding RNAs (lncRNAs) exhibit regulatory functions of both DNA damage response (DDR) and endoplasmic reticulum (ER) stress. Herein, ER stress-induced lncRNA transcriptomic changes are reported in human oral squamous cell carcinoma (OSCC) cells and a novel lncRNA HITTERS ( H ERPUD1 intronic transcript of ER stress) is identified as the most significantly upregulated lncRNA. It is shown that HITTERS is a nucleus-located lncRNA including two transcript variants. HITTERS lacks an independent promoter but shares the same promoter with HERPUD1. HITTERS is transcriptionally regulated by Activating Transcription Factor (ATF) 6, ATF4, X-Box Binding Protein 1 (XBP1), and DNA methylation. In human OSCC tissues, HITTERS is significantly correlated with OSCC clinicopathological features and prognosis. Gain- and loss-of-function studies reveal that HITTERS promotes OSCC proliferation and invasion via influencing the expression of growth factor receptors and the downstream pathways. Once ER stress is triggered, HITTERS significantly attenuates ER stress-induced apoptosis both in vivo and in vitro. Mechanically, HITTERS functions as RNA scaffold to promote MRE11-RAD50-NBS1 complex formation in the repair of ER stress-induced DNA damage. To sum up, this study presents a novel lncRNA, namely HITTERS, which links ER stress and DDR together in OSCC.
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Affiliation(s)
- Chenzhou Wu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Head and Neck OncologyWest China Hospital of StomatologySichuan UniversityNumber 14, Unit 3, Renmin Nan RoadChengduSichuan610041China
| | - Wen Chen
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Head and Neck OncologyWest China Hospital of StomatologySichuan UniversityNumber 14, Unit 3, Renmin Nan RoadChengduSichuan610041China
| | - Fanyuan Yu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of EndodonticsWest China Hospital of StomatologySichuan UniversityNumber 14, Unit 3, Renmin Nan RoadChengduSichuan610041China
| | - Yihang Yuan
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Head and Neck OncologyWest China Hospital of StomatologySichuan UniversityNumber 14, Unit 3, Renmin Nan RoadChengduSichuan610041China
| | - Yafei Chen
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Head and Neck OncologyWest China Hospital of StomatologySichuan UniversityNumber 14, Unit 3, Renmin Nan RoadChengduSichuan610041China
| | - Douglas R. Hurst
- Department of PathologyUniversity of Alabama at BirminghamBirminghamAL35294USA
| | - Yi Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Head and Neck OncologyWest China Hospital of StomatologySichuan UniversityNumber 14, Unit 3, Renmin Nan RoadChengduSichuan610041China
| | - Longjiang Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Head and Neck OncologyWest China Hospital of StomatologySichuan UniversityNumber 14, Unit 3, Renmin Nan RoadChengduSichuan610041China
| | - Zhe Liu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Head and Neck OncologyWest China Hospital of StomatologySichuan UniversityNumber 14, Unit 3, Renmin Nan RoadChengduSichuan610041China
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Peng L, Jiang J, Tang B, Nice EC, Zhang YY, Xie N. Managing therapeutic resistance in breast cancer: from the lncRNAs perspective. Theranostics 2020; 10:10360-10377. [PMID: 32929354 PMCID: PMC7482807 DOI: 10.7150/thno.49922] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/04/2020] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is the most common female malignancy and the second leading cause of cancer-related death worldwide. In spite of significant advances in clinical management, the mortality of BC continues to increase due to the frequent occurrence of treatment resistance. Intensive studies have been conducted to elucidate the molecular mechanisms underlying BC therapeutic resistance, including increased drug efflux, altered drug targets, activated bypass signaling pathways, maintenance of cancer stemness, and deregulated immune response. Emerging evidence suggests that long noncoding RNAs (lncRNAs) are intimately involved in BC therapy resistance through multiple modes of action. Therefore, an in-depth understanding of the implication of lncRNAs in resistance to clinical therapies may improve the clinical outcome of BC patients. Here, we highlight the role and underlying mechanisms of lncRNAs in regulating BC treatment resistance with an emphasis on lncRNAs-mediated resistance in different clinical scenarios, and discuss the potential of lncRNAs as novel biomarkers or therapeutic targets to improve BC therapy response.
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Affiliation(s)
- Liyuan Peng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Bo Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, P.R. China
| | - Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
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Yuan C, Ning Y, Pan Y. Emerging roles of HOTAIR in human cancer. J Cell Biochem 2020; 121:3235-3247. [PMID: 31943306 DOI: 10.1002/jcb.29591] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
Abstract
Long noncoding RNA HOX antisense intergenic RNA (HOTAIR) is overexpressed in many types of cancers, and substantial evidence has suggested a link between cancers and HOTAIR. In the present study, we reviewed the structure and the corresponding biologic function of HOTAIR to clarify its molecular mechanism in cancer progression. HOTAIR promotes proliferation, invasion, and migration, and inhibits apoptosis in cancer cells. HOTAIR also participates in the pathogenesis and progression of cancer by regulating inflammation and immune signaling. These findings suggested that HOTAIR is a novel biomarker in human cancers.
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Affiliation(s)
- Chunjue Yuan
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Yong Ning
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Yunbao Pan
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
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Advances in DNA Repair-Emerging Players in the Arena of Eukaryotic DNA Repair. Int J Mol Sci 2020; 21:ijms21113934. [PMID: 32486270 PMCID: PMC7313471 DOI: 10.3390/ijms21113934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA is constantly damaged by factors produced during natural metabolic processes as well as agents coming from the external environment. Considering such a wide array of damaging agents, eukaryotic cells have evolved a DNA damage response (DRR) that opposes the influence of deleterious factors. Despite the broad knowledge regarding DNA damage and repair, new areas of research are emerging. New players in the field of DDR are constantly being discovered. The aim of this study is to review current knowledge regarding the roles of sirtuins, heat shock proteins, long-noncoding RNAs and the circadian clock in DDR and distinguish new agents that may have a prominent role in DNA damage response and repair.
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Shen A, Ma J, Hu X, Cui X. High expression of lncRNA-SNHG7 is associated with poor prognosis in hepatocellular carcinoma. Oncol Lett 2020; 19:3959-3963. [PMID: 32382340 PMCID: PMC7202315 DOI: 10.3892/ol.2020.11490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/13/2019] [Indexed: 12/16/2022] Open
Abstract
Expression of long non-coding RNA SNHG7 (lncRNA-SNHG7) and its clinical significance in hepatocellular carcinoma (HCC) were explored. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression level of lncRNA-SNHG7 in cancer tissues. Kaplan-Meier curves and multivariate Cox proportional models were used to study the impact on clinical outcome. Expression of lncRNA-SNHG7 was much higher in cancer tissues than that in para-cancer tissues. The lncRNA-SNHG7 expression was correlated with tumor number, lymph node metastasis and clinical stage (P<0.05). In addition, HCC patients with higher lncRNA-SNHG7 expression had significantly poorer progression-free survival time and overall survival time (P<0.001). Both univariate analysis and multivariate analysis indicated that high expression of lncRNA-SNHG7 was an independent predictor of poor prognosis in HCC. LncRNA-SNHG7 might contribute to the development of HCC and serve as a clinical biomarker and a therapeutic target for HCC patients.
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Affiliation(s)
- An Shen
- Department of Hepatological Surgery, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261041, P.R. China
| | - Jinping Ma
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261041, P.R. China
| | - Xiaolin Hu
- Department of General Surgery, Shouguang People's Hospital, Shouguang, Shandong 262700, P.R. China
| | - Xinjiang Cui
- Department of Interventional Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261041, P.R. China
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Zhang X, Yang H. Research Progress on Long Non-coding RNAs and Drug Resistance of Breast Cancer. Clin Breast Cancer 2020; 20:275-282. [PMID: 32414649 DOI: 10.1016/j.clbc.2019.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/23/2019] [Accepted: 11/06/2019] [Indexed: 01/02/2023]
Abstract
Breast cancer, as the foremost cause of women's death in the world, is highly metastatic and mutable. Resistance to drugs for chemotherapies, endocrine therapies, and targeted therapies is an important factor that impacts the prognosis of breast cancer. Long non-coding ribonucleic acids (LncRNAs) are crucial regulators of intracellular gene expressions. Some researchers have suggested that expression level of several types of LncRNAs were closely related to the prognosis of patients with breast cancer. LncRNAs significantly impact biological processes such as drug transport, detoxication, apoptosis, epithelial to mesenchymal transition (EMT), and autophagy by regulating intracellular signaling pathways such as multi-drug resistance gene 1 (MDR1), nuclear factor erythroid 2-related factor 2 (NRF2), phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR), transforming growth factor-β (TGF-β), BRCA1/2, and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). This paper will summarize research progress on correlations between LncRNA and drug resistance of breast cancer. It will particularly expound molecular mechanisms through which LncRNAs regulate drug resistance of breast cancer. It will further discuss the feasibility as molecular markers for forecasting drug resistance of breast cancer and may be becoming new targets for treating breast cancer in the future.
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Affiliation(s)
- Xiping Zhang
- Department of Breast Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, China
| | - Hongjian Yang
- Department of Breast Surgery, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, China.
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Zhang Z, Hu X, Kuang J, Liao J, Yuan Q. LncRNA DRAIC inhibits proliferation and metastasis of gastric cancer cells through interfering with NFRKB deubiquitination mediated by UCHL5. Cell Mol Biol Lett 2020; 25:29. [PMID: 32351584 PMCID: PMC7183705 DOI: 10.1186/s11658-020-00221-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/13/2020] [Indexed: 12/24/2022] Open
Abstract
Background Long non-coding RNA (lncRNA) as a widespread and pivotal epigenetic molecule participates in the occurrence and progression of malignant tumors. DRAIC, a kind of lncRNA whose coding gene location is on 15q23 chromatin, has been found to be weakly expressed in a variety of malignant tumors and acts as a suppressor, but its characteristics and role in gastric cancer (GC) remain to be elucidated. Methods Sixty-seven primary GC tissues and paired paracancerous normal tissues were collected. Bioinformatics is used to predict the interaction molecules of DRAIC. DRAIC and NFRKB were overexpressed or interfered exogenously in GC cells by lentivirus or transient transfection. Quantitative real-time PCR (qPCR) and western blotting were used to evaluate the expression of DRAIC, UCHL5 and NFRKB. The combinations of DRAIC and NFRKB or UCHL5 and NFRKB were verified by RNA-IP and Co-IP assays. Ubiquitination-IP and the treatment of MG132 and CHX were used to detect the ubiquitylation level of NFRKB. The CCK-8 and transwell invasion and migration assays measured the proliferation, migration and invasion of GC cells. Results DRAIC is down-regulated in GC tissues and cell lines while its potential interacting molecules UCHL5 and NFRKB are up-regulated, and DRAIC is positively correlated with NFRKB protein instead of mRNA. Lower DRAIC and higher UCHL5 and NFRKB indicated advanced progression of GC patients. DRAIC could increase NFRKB protein significantly instead of NFRKB mRNA and UCHL5, and bind to UCHL5. DRAIC combined with UCHL5 and attenuated binding of UCHL5 and NFRKB, meanwhile promoting the degradation of NFRKB via ubiquitination, and then inhibited the proliferation and metastasis of GC cells, which can be rescued by oeNFRKB. Conclusion DRAIC suppresses GC proliferation and metastasis via interfering with the combination of UCHL5 and NFRKB and mediating ubiquitination degradation.
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Affiliation(s)
- Zheng Zhang
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
| | - Xiaoxuan Hu
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
| | - Jia Kuang
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
| | - Jinmao Liao
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
| | - Qi Yuan
- Department of Hepatopathy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000 Hunan Province China
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Zhou Y, Zhou Z, Ji Z, Yan W, Li H, Yu X. Tetramethylpyrazine reduces prostate cancer malignancy through inactivation of the DPP10‑AS1/CBP/FOXM1 signaling pathway. Int J Oncol 2020; 57:314-324. [PMID: 32319592 DOI: 10.3892/ijo.2020.5036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 02/06/2020] [Indexed: 11/05/2022] Open
Abstract
Tetramethylpyrazine (TMP), a Chinese herbal medicine, has been reported to possess anticancer effects. Emerging evidence suggests that various long noncoding RNAs (lncRNAs) serve important roles in cancer initiation and progression. In the present study, the tumor‑suppressive effects of TMP in human PCa cells was examined and the underlying mechanisms of its actions were determined. The data showed that TMP treatment reduced cell viability and increased apoptosis in a dose‑dependent manner. Reverse transcription‑quantitative PCR showed TMP treatment increased the expression of lncRNA DPP10‑AS1 in PCa cells. Furthermore, DPP10‑AS1 was also upregulated in TMP‑resistant PCa cells. Knockdown of DPP10‑AS1 reversed TMP resistance, whereas increased expression of DPP10‑AS1 abrogated the TMP‑mediated cytotoxicity in PCa cells. In addition, forkhead box M1 (FOXM1) was verified as the functional target of DPP10‑AS1, and knockdown of FOXM1 reversed the TMP/DPP10‑AS1‑induced cell cytotoxicity. Mechanistically, DPP10‑AS1 was associated with CREB binding protein, thereby induced H3K27ac enrichment at the promoter region of the FOXM1 gene. In conclusion, the present study showed that TMP may be a promising treatment agent for PCa and lncRNA DPP10‑AS1 may be a promising therapeutic target for TMP treatment.
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Affiliation(s)
- Yi Zhou
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100000, P.R. China
| | - Zhien Zhou
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100000, P.R. China
| | - Zhigang Ji
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100000, P.R. China
| | - Weigang Yan
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100000, P.R. China
| | - Hanzhong Li
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100000, P.R. China
| | - Xiao Yu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100000, P.R. China
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Durut N, Mittelsten Scheid O. The Role of Noncoding RNAs in Double-Strand Break Repair. FRONTIERS IN PLANT SCIENCE 2019; 10:1155. [PMID: 31611891 PMCID: PMC6776598 DOI: 10.3389/fpls.2019.01155] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Genome stability is constantly threatened by DNA lesions generated by different environmental factors as well as endogenous processes. If not properly and timely repaired, damaged DNA can lead to mutations or chromosomal rearrangements, well-known reasons for genetic diseases or cancer in mammals, or growth abnormalities and/or sterility in plants. To prevent deleterious consequences of DNA damage, a sophisticated system termed DNA damage response (DDR) detects DNA lesions and initiates DNA repair processes. In addition to many well-studied canonical proteins involved in this process, noncoding RNA (ncRNA) molecules have recently been discovered as important regulators of the DDR pathway, extending the broad functional repertoire of ncRNAs to the maintenance of genome stability. These ncRNAs are mainly connected with double-strand breaks (DSBs), the most dangerous type of DNA lesions. The possibility to intentionally generate site-specific DSBs in the genome with endonucleases constitutes a powerful tool to study, in vivo, how DSBs are processed and how ncRNAs participate in this crucial event. In this review, we will summarize studies reporting the different roles of ncRNAs in DSB repair and discuss how genome editing approaches, especially CRISPR/Cas systems, can assist DNA repair studies. We will summarize knowledge concerning the functional significance of ncRNAs in DNA repair and their contribution to genome stability and integrity, with a focus on plants.
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Xie L, Huang R, Liu S, Wu W, Su A, Li R, Liu X, Lei Y, Sun H, Liu X, Xu S. A positive feedback loop of SIRT1 and miR17HG promotes the repair of DNA double-stranded breaks. Cell Cycle 2019; 18:2110-2123. [PMID: 31290724 DOI: 10.1080/15384101.2019.1641388] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as critical regulators for gene expression in multiple levels and thus are involved in various physiological and pathological processes. Sirtuin 1 (SIRT1) has been established to exert key roles in the diverse biological process through deacetylation of substrates, including DNA damage repair. Nevertheless, the regulatory relationship between SIRT1 and lncRNAs, and the effect of lncRNA on SIRT1-mediated functions were still far to be elucidated. We herein uncovered that lncRNA miR17HG was notably down-regulated in SIRT1-deficient cells, and significantly up-regulated after ectopic expression of SIRT1. Subsequently, the results of dual luciferase reporter (DLR) showed that SIRT1 dramatically enhanced the promoter activity of the miR-17-92 cluster. Furthermore, we specifically knocked down the previous demonstrated transcription factor for the miR-17-92 cluster, C-Myc, which was the validated substrate of SIRT1. As expected, miR17HG and miR-17-92 miRNAs were evidently down-regulated after silencing of C-Myc; and silencing of C-Myc significantly reversed the effect of SIRT1 on miR17HG expression, suggesting that SIRT1 endowed cells with elevated miR17HG expression through stabilization of C-Myc. What is more, silencing of miR17HG significantly inhibited the repair of DNA DSBs, while enforced expression of miR17HG promoted DSBs repair. Fascinatingly, overexpression of miR17HG evidently enhanced the deacetylation activity of SIRT1, while silencing of miR17HG conferred diminished deacetylation activity. In addition, the results of RIP unraveled the physical interaction between miR17HG and SIRT1. Taken together, we presented evidences that miR17HG and SIRT1 probably formed a positive feedback loop, which exerted a crucial effect on DSBs repair.
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Affiliation(s)
- Luoyijun Xie
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Ruxiao Huang
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Shuang Liu
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Weijia Wu
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Ailing Su
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Runkai Li
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Xu Liu
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Yiting Lei
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Huidi Sun
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Xinguang Liu
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
| | - Shun Xu
- a Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, the Scientific Research Center of Dongguan, Guangdong Medical University , Dongguan , P.R.China
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Hu R, Zhu Z. ELK1‐activated GPC3‐AS1/GPC3 axis promotes the proliferation and migration of cervical cancer cells. J Gene Med 2019; 21:e3099. [DOI: 10.1002/jgm.3099] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/21/2019] [Accepted: 05/30/2019] [Indexed: 11/10/2022] Open
Affiliation(s)
- Rong Hu
- Department of Obstetrics and Gynecology, Xiangya HospitalCentral South University Changsha Hunan Province China
| | - Zongming Zhu
- Changsha University Changsha Hunan Province China
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Yang M, Sun Y, Xiao C, Ji K, Zhang M, He N, Wang J, Wang Q, Sun Z, Wang Y, Du L, Liu Y, Xu C, Liu Q. Integrated Analysis of the Altered lncRNAs and mRNAs Expression in 293T Cells after Ionizing Radiation Exposure. Int J Mol Sci 2019; 20:ijms20122968. [PMID: 31216644 PMCID: PMC6627384 DOI: 10.3390/ijms20122968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 02/07/2023] Open
Abstract
Tissue and cell damage caused by ionizing radiation is often highly genotoxic. The swift repair of DNA damage is crucial for the maintenance of genomic stability and normal cell fitness. Long noncoding RNAs (lncRNAs) have been reported to play an important role in many physiological and pathological processes in cells. However, the exact function of lncRNAs in radiation-induced DNA damage has yet to be elucidated. Therefore, this study aimed to analyze the potential role of lncRNAs in radiation-induced DNA damage. We examined the expression profiles of lncRNAs and mRNAs in 293T cells with or without 8 Gy irradiation using high-throughput RNA sequencing. We then performed comprehensive transcriptomic and bioinformatic analyses of these sequencing results. A total of 18,990 lncRNAs and 16,080 mRNAs were detected in all samples. At 24 h post irradiation, 49 lncRNAs and 323 mRNAs were differentially expressed between the irradiation group and the control group. qRT-PCR was used to verify the altered expression of six lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that the predicted genes were mainly involved in the histone mRNA metabolic process and Wnt signaling pathways. This study may provide novel insights for the study of lncRNAs in radiation-induced DNA damage.
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Affiliation(s)
- Mengmeng Yang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Yuxiao Sun
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Changyan Xiao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Kaihua Ji
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Manman Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Ningning He
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Jinhan Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Qin Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Zhijuan Sun
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Yan Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Liqing Du
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Yang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
| | - Qiang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.
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Huang C, Leng D, Lei KC, Sun S, Zhang XD. Transcriptome analysis reveals lncRNA-mediated complex regulatory network response to DNA damage in the liver tissue of Rattus norvegicus. J Cell Physiol 2019; 234:23216-23231. [PMID: 31140619 DOI: 10.1002/jcp.28889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022]
Abstract
DNA is prone to damages, which would result in genetic disorders and enhance risk of tumorigenesis. Hence, understanding the molecular mechanisms of DNA damage and repair will provide deep insights into tumorigenesis, carcinogenesis as well as the corresponding treatments. Aiming at investigating potential long noncoding RNAs (lncRNAs) response against DNA damage, we performed a comprehensive transcriptomic analysis based on RNA sequencing data of the liver tissue from Rattus norvegicus, in which DNA damage was induced using aflatoxin B1, ifosfamide and N-nitrosodimethylamine. Through our analyses, numerous novel lncRNAs are identified for the first time, and differential network analysis discloses lncRNA-mediated regulatory networks related to DNA-damage response. The result shows that these DNA-damage-inducing chemicals might disrupt many lncRNA-mediated interactions involved in diverse biological processes and pathways, for example, immune function and cell adhesion. In contrast, the host might also activate a few RNA interactions in response to DNA damage, involving response to drug and regulation of cell cycle.
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Affiliation(s)
- Chen Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dongliang Leng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Kuan Cheok Lei
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Shixue Sun
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
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Wei L, Li J, Han Z, Chen Z, Zhang Q. Silencing of lncRNA MALAT1 Prevents Inflammatory Injury after Lung Transplant Ischemia-Reperfusion by Downregulation of IL-8 via p300. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:285-297. [PMID: 31604167 PMCID: PMC6796730 DOI: 10.1016/j.omtn.2019.05.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
Ischemia-reperfusion injury is a common early complication after lung transplantation. It was reported that long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is involved in ischemia-reperfusion injury and regulates inflammation. This study aimed to explore the role of MALAT1 in inflammatory injury following lung transplant ischemia-reperfusion (LTIR). A LTIR rat model was successfully established, with the expression of MALAT1 and interleukin-8 (IL-8) in lung tissues detected. Then, in vitro loss- and gain-of-function investigations were conducted to evaluate the effect of MALAT1 on pulmonary epithelial cell apoptosis and IL-8 expression. The relationship among MALAT1, p300, and IL-8 was tested. Moreover, a sh-MALAT1-mediated model of LTIR was established in vivo to examine inflammatory injury and chemotaxis infiltration. Both IL-8 and MALAT1 were highly expressed in LTIR. MALAT1 interacted with p300 to regulate the IL-8 expression by recruiting p300. Importantly, silencing of MALAT1 inhibited the chemotaxis of neutrophils by downregulating IL-8 expression via binding to p300. Besides, MALAT1 silencing alleviated the inflammatory injury after LTIR by downregulating IL-8 and inhibiting infiltration and activation of neutrophils. Collectively, these results demonstrated that silencing of MALAT1 ameliorated the inflammatory injury after LTIR by inhibiting chemotaxis of neutrophils through p300-mediated downregulation of IL-8, providing clinical insight for LTIR injury.
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Affiliation(s)
- Li Wei
- Department of Thoracic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou 450003, P.R. China
| | - Jiwei Li
- Department of Thoracic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou 450003, P.R. China.
| | - Zhijun Han
- Department of Thoracic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou 450003, P.R. China
| | - Zhong Chen
- Department of Thoracic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou 450003, P.R. China
| | - Quan Zhang
- Department of Thoracic Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou 450003, P.R. China
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Shaddel S, Ucar S, Andreassen JP, Østerhus SW. Enhancing efficiency and economics of phosphorus recovery process by customizing the product based on sidestream characteristics - an alternative phosphorus recovery strategy. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 79:1777-1789. [PMID: 31241483 DOI: 10.2166/wst.2019.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The enhanced biological phosphorus removal process makes the phosphorus recovery feasible from the dewatering streams of biological sludge. The physicochemical properties of these sidestreams, as an input to a crystallizer, are different before and after anaerobic digestion. In this study, phosphorus recovery by calcium phosphate is proposed for pre-digestion sidestreams and by struvite precipitation for post-digestion sidestreams. The thermodynamic modeling followed by experimental tests was performed to evaluate the recovery efficiency and product properties of struvite and calcium phosphates. The variations in phosphorus recovery potential, reaction kinetics and particle size distribution emphasize the importance of the adjustment of initial supersaturation and pH of the reaction. The optimum pH, considering the economics and recovery efficiency, for both calcium phosphate and struvite precipitation was found to be pH = 8.5, whereas further increase of pH will not improve the overall efficiency of the process. In the case of calcium phosphate precipitation, it was shown that possible phase transformations should be considered and controlled as they affect both process efficiency and product properties. The economic evaluation indicated that the optimized operational condition should be determined for the phosphorus recovery process and that chemical costs for the production of calcium phosphates is lower than for struvite.
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Affiliation(s)
- Sina Shaddel
- Department of Civil and Environmental Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway E-mail:
| | - Seniz Ucar
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jens-Petter Andreassen
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Stein W Østerhus
- Department of Civil and Environmental Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway E-mail:
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49
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Gao S, Lin H, Yu W, Zhang F, Wang R, Yu H, Qian B. LncRNA LCPAT1 is involved in DNA damage induced by CSE. Biochem Biophys Res Commun 2018; 508:512-515. [PMID: 30509493 DOI: 10.1016/j.bbrc.2018.11.171] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/27/2018] [Indexed: 11/30/2022]
Abstract
Cigarette smoking plays an important role in the process of lung cancer, during which DNA damage is proved to be involved. Non-coding RNAs are found to be involved in the DNA damage and repair processes induced by cigarette smoke. In the present study, we investigated the role of lncRNA LCPAT1 in DNA damage caused by CSE in Beas-2B cells. Our results indicate that LCPAT1, through RCC2 is involved in the CSE-induced DNA damage providing new insight into the lung carcinogenesis related to cigarette smoking.
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Affiliation(s)
- Sumeng Gao
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hongyan Lin
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wang Yu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fangfang Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ruoyang Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, USA
| | - Biyun Qian
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Faculty of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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50
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Thapar R. Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs. Molecules 2018; 23:molecules23112789. [PMID: 30373256 PMCID: PMC6278438 DOI: 10.3390/molecules23112789] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 01/12/2023] Open
Abstract
DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer. Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs. Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated. This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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