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Farhan SH, Jasim SA, Bansal P, Kaur H, Abed Jawad M, Qasim MT, Jabbar AM, Deorari M, Alawadi A, Hadi A. Exosomal Non-coding RNA Derived from Mesenchymal Stem Cells (MSCs) in Autoimmune Diseases Progression and Therapy; an Updated Review. Cell Biochem Biophys 2024:10.1007/s12013-024-01432-4. [PMID: 39225902 DOI: 10.1007/s12013-024-01432-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2024] [Indexed: 09/04/2024]
Abstract
Inflammation and autoimmune diseases (AD) are common outcomes of an overactive immune system. Inflammation occurs due to the immune system reacting to damaging stimuli. Exosomes are being recognized as an advanced therapeutic approach for addressing an overactive immune system, positioning them as a promising option for treating AD. Mesenchymal stem cells (MSCs) release exosomes that have strong immunomodulatory effects, influenced by their cell of origin. MSCs-exosomes, being a cell-free therapy, exhibit less toxicity and provoke a diminished immune response compared to cell-based therapies. Exosomal non-coding RNAs (ncRNA), particularly microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are intricately linked to various biological and functional aspects of human health. Exosomal ncRNAs can lead to tissue malfunction, aging, and illnesses when they experience tissue-specific alterations as a result of various internal or external problems. In this study, we will examine current trends in exosomal ncRNA researches regarding AD. Then, therapeutic uses of MSCs-exosomal ncRNA will be outlined, with a particle focus on the underlying molecular mechanisms.
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Affiliation(s)
- Shireen Hamid Farhan
- Biotechnology department, College of Applied Science, Fallujah University, Fallujah, Iraq
| | | | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh, India
- Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand, India
| | - Mohammed Abed Jawad
- Department of Medical Laboratories Technology, Al-Nisour University College, Baghdad, Iraq.
| | - Maytham T Qasim
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar, Iraq
| | - Abeer Mhussan Jabbar
- College of Pharmacy, National University of Science and Technology, Dhi Qar, Iraq.
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Ahmed Alawadi
- College of technical engineering, the Islamic University, Najaf, Iraq
- College of technical engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of technical engineering, the Islamic University of Babylon, Babylon, Iraq
| | - Ali Hadi
- Department of medical laboratories techniques, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
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2
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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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3
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Moradimotlagh A, Brar HK, Chen S, Moon KM, Foster LJ, Reiner N, Nandan D. Characterization of Argonaute-containing protein complexes in Leishmania-infected human macrophages. PLoS One 2024; 19:e0303686. [PMID: 38781128 PMCID: PMC11115314 DOI: 10.1371/journal.pone.0303686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
The intracellular protozoan parasite Leishmania causes leishmaniasis in humans, leading to serious illness and death in tropical and subtropical areas worldwide. Unfortunately, due to the unavailability of approved vaccines for humans and the limited efficacy of available drugs, leishmaniasis is on the rise. A comprehensive understanding of host-pathogen interactions at the molecular level could pave the way to counter leishmaniasis. There is growing evidence that several intracellular pathogens target RNA interference (RNAi) pathways in host cells to facilitate their persistence. The core elements of the RNAi system are complexes of Argonaute (Ago) proteins with small non-coding RNAs, also known as RNA-induced silencing complexes (RISCs). Recently, we have shown that Leishmania modulates Ago1 protein of host macrophages for its survival. In this study, we biochemically characterize the Ago proteins' interactome in Leishmania-infected macrophages compared to non-infected cells. For this, a quantitative proteomic approach using stable isotope labelling by amino acids in cell culture (SILAC) was employed, followed by purification of host Ago-complexes using a short TNRC6 protein-derived peptide fused to glutathione S-transferase beads as an affinity matrix. Proteomic-based detailed biochemical analysis revealed Leishmania modulated host macrophage RISC composition during infection. This analysis identified 51 Ago-interacting proteins with a broad range of biological activities. Strikingly, Leishmania proteins were detected as part of host Ago-containing complexes in infected cells. Our results present the first report of comprehensive quantitative proteomics of Ago-containing complexes isolated from Leishmania-infected macrophages and suggest targeting the effector complex of host RNAi machinery. Additionally, these results expand knowledge of RISC in the context of host-pathogen interactions in parasitology in general.
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Affiliation(s)
- Atieh Moradimotlagh
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Harsimran Kaur Brar
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Stella Chen
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, B.C, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, B.C, Canada
| | - Neil Reiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Devki Nandan
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
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4
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Chen H, Zhang CJ, Zhao ZY, Gao YY, Zhao JT, Li XX, Zhang M, Wang H. Mechanisms underlying LncRNA SNHG1 regulation of Alzheimer's disease involve DNA methylation. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2024; 87:428-435. [PMID: 38551404 DOI: 10.1080/15287394.2024.2334248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease associated with long non-coding RNAs and DNA methylation; however, the mechanisms underlying the role of lncRNA small nucleolar RNA host gene 1 (lncRNA SNHG1) and subsequent involvement of DNA methylation in AD development are not known. The aim of this study was to examine the regulatory mechanisms attributed to lncRNA SNHG1 gene utilizing 2 strains of senescence-accelerated mouse prone 8 (SAMP8) model of AD and compared to senescence-accelerated mouse resistant (SAMR) considered a control. Both strains of the mouse were transfected with either blank virus, psLenti-U6-SNHG1(low gene expression) virus, and psLenti-pA-SNHG1(gene overexpression) virus via a single injection into the brains for 2 weeks. At 2 weeks mice were subjected to a Morris water maze to determine any behavioral effects followed by sacrifice to extract hippocampal tissue for Western blotting to measure protein expression of p-tau, DNMT1, DNMT3A, DNMT3B, TET1, and p-Akt. No marked alterations were noted in any parameters following blank virus transfection. In SAMP8 mice, a significant decrease was noted in protein expression of DNMT1, DNMT3A, DNMT3B, and p-Akt associated with rise in p-tau and TET1. Transfection with ps-Lenti-U6-SNHG1 alone in SAMR1 mice resulted in a significant rise in DNMTs and p-Akt and a fall in p-tau and TET1. Transfection of SAMP8 with ps-Lenti-U6-SNHG1 blocked effects on overexpression noted in this mouse strain. However, knockdown of lncRNA SNHG1 yielded the opposite results as found in SAMR1 mice. In conclusion, the knockdown of lncRNA SNHG1 enhanced DNA methylation through the PI3K/Akt signaling pathway, thereby reducing the phosphorylation levels of tau in SAMP8 AD model mice with ameliorating brain damage attributed to p-tau accumulation with consequent neuroprotection.
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Affiliation(s)
- Hong Chen
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - Chun-Jie Zhang
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
- Center of Collaborative Innovation in Translational Medicine, Baotou Medical College, Inner Mongolia, China
| | - Zhi-Ying Zhao
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - Yang-Yang Gao
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - Jian-Tian Zhao
- Institute of Public Health, Baotou Medical College, Inner Mongolia, China
| | - Xiao-Xu Li
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - Ming Zhang
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - He Wang
- School of Health Sciences, University of Newcastle, Newcastle, Australia
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5
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Saikia S, Postwala H, Athilingam VP, Anandan A, Padma VV, Kalita PP, Chorawala M, Prajapati B. Single Nucleotide Polymorphisms (SNPs) in the Shadows: Uncovering their Function in Non-Coding Region of Esophageal Cancer. Curr Pharm Biotechnol 2024; 25:1915-1938. [PMID: 38310451 DOI: 10.2174/0113892010265004231116092802] [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: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 02/05/2024]
Abstract
Esophageal cancer is a complex disease influenced by genetic and environmental factors. Single nucleotide polymorphisms (SNPs) in non-coding regions of the genome have emerged as crucial contributors to esophageal cancer susceptibility. This review provides a comprehensive overview of the role of SNPs in non-coding regions and their association with esophageal cancer. The accumulation of SNPs in the genome has been implicated in esophageal cancer risk. Various studies have identified specific locations in the genome where SNPs are more likely to occur, suggesting a location-specific response. Chromatin conformational studies have shed light on the localization of SNPs and their impact on gene transcription, posttranscriptional modifications, gene expression regulation, and histone modification. Furthermore, miRNA-related SNPs have been found to play a significant role in esophageal squamous cell carcinoma (ESCC). These SNPs can affect miRNA binding sites, thereby altering target gene regulation and contributing to ESCC development. Additionally, the risk of ESCC has been linked to base excision repair, suggesting that SNPs in this pathway may influence disease susceptibility. Somatic DNA segment alterations and modified expression quantitative trait loci (eQTL) have also been associated with ESCC. These alterations can lead to disrupted gene expression and cellular processes, ultimately contributing to cancer development and progression. Moreover, SNPs have been found to be associated with the long non-coding RNA HOTAIR, which plays a crucial role in ESCC pathogenesis. This review concludes with a discussion of the current and future perspectives in the field of SNPs in non-coding regions and their relevance to esophageal cancer. Understanding the functional implications of these SNPs may lead to the identification of novel therapeutic targets and the development of personalized approaches for esophageal cancer prevention and treatment.
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Affiliation(s)
- Surovi Saikia
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Humzah Postwala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad, India
| | - Vishnu Prabhu Athilingam
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Aparna Anandan
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - V Vijaya Padma
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Partha P Kalita
- Program of Biotechnology, Assam Down Town University, Panikhaiti, Guwahati 781026, Assam, India
| | - Mehul Chorawala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad, India
| | - Bhupendra Prajapati
- Department of Pharmaceutics and Pharmaceutical Technology, Shree. S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva, Gujarat, India
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6
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Liu J, Yu Q, Yang X. Circ_0102231 inactivates the PI3K/AKT signaling pathway by regulating the miR-635/NOVA2 pathway to promote the progression of non-small cell lung cancer. Thorac Cancer 2023; 14:3453-3464. [PMID: 37864285 PMCID: PMC10719657 DOI: 10.1111/1759-7714.15138] [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: 09/04/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are involved in the malignant development of tumors. However, the mechanism of circ_0102231 in non-small cell lung cancer (NSCLC) has rarely been discussed and reported. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure the expression of circ_0102231, miR-635 and NOVA alternative splicing regulator 2 (NOVA2) in NSCLC tissues and cells. Western blot was applied to detect the protein expression. Cell proliferation was monitored by cell counting kit-8 (CCK8) and 5-ethynyl-2'-deoxyuridine (EdU) experiments. The angiogenesis ability of cells was tested by angiogenesis assay. Flow cytometry was used to analyze cell apoptosis. The relationship between circ_0102231 and NOVA2 or miR-635 was analyzed by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. An in vivo transplanted tumor model was established to confirm the effect of circ_0102231 on tumor formation. RESULTS Circ_0102231 was abnormally upregulated in NSCLC tissues and correlated with clinical stage. Silencing of circ_0102231 inhibited cell proliferation and angiogenesis but significantly promoted the apoptosis of NSCLC cells. There were target binding sites between circ_0102231 and miR-635, miR-635 and NOVA2. Importantly, circ_0102231 acted as a sponge for miR-635, increased the expression of NOVA2, and activated the PI3K/AKT signaling pathway. Finally, silencing of circ_0102231 also had obvious antitumor effects in vivo. CONCLUSION Circ_0102231 increased the expression of NOVA2 by interacting with miR-635 to promote the malignant progression of NSCLC.
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Affiliation(s)
- Jianhong Liu
- Department of Respiratory MedicineZhejiang Jinhua Guangfu Cancer HospitalJinhuaChina
| | - Qiong Yu
- Department of Respiratory MedicineZhejiang Jinhua Guangfu Cancer HospitalJinhuaChina
| | - Xu Yang
- Department of Respiratory MedicineZhejiang Jinhua Guangfu Cancer HospitalJinhuaChina
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7
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Moradimotlagh A, Chen S, Koohbor S, Moon KM, Foster LJ, Reiner N, Nandan D. Leishmania infection upregulates and engages host macrophage Argonaute 1, and system-wide proteomics reveals Argonaute 1-dependent host response. Front Immunol 2023; 14:1287539. [PMID: 38098491 PMCID: PMC10720368 DOI: 10.3389/fimmu.2023.1287539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/26/2023] [Indexed: 12/17/2023] Open
Abstract
Leishmania donovani, an intracellular protozoan parasite, is the causative agent of visceral leishmaniasis, the most severe form of leishmaniasis in humans. It is becoming increasingly clear that several intracellular pathogens target host cell RNA interference (RNAi) pathways to promote their survival. Complexes of Argonaute proteins with small RNAs are core components of the RNAi. In this study, we investigated the potential role of host macrophage Argonautes in Leishmania pathogenesis. Using Western blot analysis of Leishmania donovani-infected macrophages, we show here that Leishmania infection selectively increased the abundance of host Argonaute 1 (Ago1). This increased abundance of Ago1 in infected cells also resulted in higher levels of Ago1 in active Ago-complexes, suggesting the preferred use of Ago1 in RNAi in Leishmania-infected cells. This analysis used a short trinucleotide repeat containing 6 (TNRC6)/glycine-tryptophan repeat protein (GW182) protein-derived peptide fused to Glutathione S-transferase as an affinity matrix to capture mature Ago-small RNAs complexes from the cytosol of non-infected and Leishmania-infected cells. Furthermore, Ago1 silencing significantly reduced intracellular survival of Leishmania, demonstrating that Ago1 is essential for Leishmania pathogenesis. To investigate the role of host Ago1 in Leishmania pathogenesis, a quantitative whole proteome approach was employed, which showed that expression of several previously reported Leishmania pathogenesis-related proteins was dependent on the level of macrophage Ago1. Together, these findings identify Ago1 as the preferred Argonaute of RNAi machinery in infected cells and a novel and essential virulence factor by proxy that promotes Leishmania survival.
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Affiliation(s)
- Atieh Moradimotlagh
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stella Chen
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sara Koohbor
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Neil Reiner
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Devki Nandan
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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8
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Solati A, Thvimi S, Khatami SH, Shabaninejad Z, Malekzadegan Y, Alizadeh M, Mousavi P, Taheri-Anganeh M, Razmjoue D, Bahmyari S, Ghasemnejad-Berenji H, Vafadar A, Soltani Fard E, Ghasemi H, Movahedpour A. Non-coding RNAs in gynecologic cancer. Clin Chim Acta 2023; 551:117618. [PMID: 38375624 DOI: 10.1016/j.cca.2023.117618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 02/21/2024]
Abstract
The term "gynecologic cancer" pertains to neoplasms impacting the reproductive tissues and organs of women encompassing the endometrium, vagina, cervix, uterus, vulva, and ovaries. The progression of gynecologic cancer is linked to various molecular mechanisms. Historically, cancer research primarily focused on protein-coding genes. However, recent years have unveiled the involvement of non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs (LncRNAs), and circular RNAs, in modulating cellular functions within gynecological cancer. Substantial evidence suggests that ncRNAs may wield a dual role in gynecological cancer, acting as either oncogenic or tumor-suppressive agents. Numerous clinical trials are presently investigating the roles of ncRNAs as biomarkers and therapeutic agents. These endeavors may introduce a fresh perspective on the diagnosis and treatment of gynecological cancer. In this overview, we highlight some of the ncRNAs associated with gynecological cancers.
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Affiliation(s)
- Arezoo Solati
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sina Thvimi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Mehdi Alizadeh
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Damoun Razmjoue
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran; Department of Pharmacognosy, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sedigheh Bahmyari
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hojat Ghasemnejad-Berenji
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Asma Vafadar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elahe Soltani Fard
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
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9
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Hu X, Liu D, Zhang J, Fan Y, Ouyang T, Luo Y, Zhang Y, Deng L. A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations. Brief Bioinform 2023; 24:bbad410. [PMID: 37985451 DOI: 10.1093/bib/bbad410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/07/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
Non-coding RNAs (ncRNAs) play a critical role in the occurrence and development of numerous human diseases. Consequently, studying the associations between ncRNAs and diseases has garnered significant attention from researchers in recent years. Various computational methods have been proposed to explore ncRNA-disease relationships, with Graph Neural Network (GNN) emerging as a state-of-the-art approach for ncRNA-disease association prediction. In this survey, we present a comprehensive review of GNN-based models for ncRNA-disease associations. Firstly, we provide a detailed introduction to ncRNAs and GNNs. Next, we delve into the motivations behind adopting GNNs for predicting ncRNA-disease associations, focusing on data structure, high-order connectivity in graphs and sparse supervision signals. Subsequently, we analyze the challenges associated with using GNNs in predicting ncRNA-disease associations, covering graph construction, feature propagation and aggregation, and model optimization. We then present a detailed summary and performance evaluation of existing GNN-based models in the context of ncRNA-disease associations. Lastly, we explore potential future research directions in this rapidly evolving field. This survey serves as a valuable resource for researchers interested in leveraging GNNs to uncover the complex relationships between ncRNAs and diseases.
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Affiliation(s)
- Xiaowen Hu
- School of Computer Science and Engineering, Central South University,410075 Changsha, China
| | - Dayun Liu
- School of Computer Science and Engineering, Central South University,410075 Changsha, China
| | - Jiaxuan Zhang
- Department of Electrical and Computer Engineering, University of California, San Diego,92093 CA, USA
| | - Yanhao Fan
- School of Computer Science and Engineering, Central South University,410075 Changsha, China
| | - Tianxiang Ouyang
- School of Computer Science and Engineering, Central South University,410075 Changsha, China
| | - Yue Luo
- School of Computer Science and Engineering, Central South University,410075 Changsha, China
| | - Yuanpeng Zhang
- school of software, Xinjiang University, 830046 Urumqi, China
| | - Lei Deng
- School of Computer Science and Engineering, Central South University,410075 Changsha, China
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Mojodi E, Mosadegh Mehrjardi A, Naeimzadeh Y, Ghasemi N, Falahati A, Mohammad Moshtaghioun S. The sequence variation of mitochondrial tRNA tyrosine and cysteine among Iranian women with idiopathic recurrent miscarriage: A case-control study. Int J Reprod Biomed 2023; 21:567-576. [PMID: 37727391 PMCID: PMC10505698 DOI: 10.18502/ijrm.v21i7.13894] [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: 04/24/2022] [Revised: 12/08/2022] [Accepted: 06/07/2023] [Indexed: 09/21/2023] Open
Abstract
Background Recurrent miscarriage is one of the most prevalent reproductive diseases. This phenomenon has several reasons, including maternal, hormonal, immunological, and parental genetic factors. Idiopathic recurrent miscarriage (IRM), with no distinctive etiology, involves about half of the recurrent miscarriage cases. Some mutations in mitochondrial DNA can lead to miscarriage. Mitochondrial tRNA (mt-tRNA) mutations cause nearly half of the mitochondrial disorders. Objective To identify mt- tRNAC y s & T y r gene mutations in Iranian women with IRM. Materials and Methods In this case-control study, 100 Iranian women with IRM and 100 women as control without any history of miscarriage were investigated by polymerase chain reaction-single strand conformation polymorphism technique followed by gene sequencing. Bioinformatics analysis were done using human mitochondrial genome database, molecular evolutionary genetics analysis, mammalian mitochondrial-tRNA, etc. Results Results showed 4 mt-tRNA mutations including 1 cysteine mt-tRNA mutation (5824C> T) and 3 tyrosine mt-tRNA mutations (5868T> A, 5849C> T, and 5836T> C) in our cases. Conclusion Amongst the 4 mutations found, one was novel that is still not reported. Our bioinformatics analysis revealed that these mutations can be pathogenic. They occurred in tRNA-conserved regions and their secondary structure was changed, which can result in mitochondrial dysfunction. Mutations of these genes may help in the assessment of IRM. Further study of all 22 mt-tRNAs possible mutations is recommended to describe their etiologic role in IRM.
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Affiliation(s)
- Elham Mojodi
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - Alimohammad Mosadegh Mehrjardi
- Department of Traditional Pharmacy, Faculty of Traditional Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yasaman Naeimzadeh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasrin Ghasemi
- Abortion Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ali Falahati
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
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11
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Fallet M, Blanc M, Di Criscio M, Antczak P, Engwall M, Guerrero Bosagna C, Rüegg J, Keiter SH. Present and future challenges for the investigation of transgenerational epigenetic inheritance. ENVIRONMENT INTERNATIONAL 2023; 172:107776. [PMID: 36731188 DOI: 10.1016/j.envint.2023.107776] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.
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Affiliation(s)
- Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden; Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, United Kingdom.
| | - Mélanie Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, Palavas, France
| | - Michela Di Criscio
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Philipp Antczak
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
| | - Magnus Engwall
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | | | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
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12
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Singh D, Rai V, Agrawal DK. Non-Coding RNAs in Regulating Plaque Progression and Remodeling of Extracellular Matrix in Atherosclerosis. Int J Mol Sci 2022; 23:13731. [PMID: 36430208 PMCID: PMC9692922 DOI: 10.3390/ijms232213731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Non-coding RNAs (ncRNAs) regulate cell proliferation, migration, differentiation, inflammation, metabolism of clinically important biomolecules, and other cellular processes. They do not encode proteins but are involved in the regulatory network of various proteins that are directly related to the pathogenesis of diseases. Little is known about the ncRNA-associated mechanisms of atherosclerosis and related cardiovascular disorders. Remodeling of the extracellular matrix (ECM) is critical in the pathogenesis of atherosclerosis and related disorders; however, its regulatory proteins are the potential subjects to explore with special emphasis on epigenetic regulatory components. The activity of regulatory proteins involved in ECM remodeling is regulated by various ncRNA molecules, as evident from recent research. Thus, it is important to critically evaluate the existing literature to enhance the understanding of nc-RNAs-regulated molecular mechanisms regulating ECM components, remodeling, and progression of atherosclerosis. This is crucial since deregulated ECM remodeling contributes to atherosclerosis. Thus, an in-depth understanding of ncRNA-associated ECM remodeling may identify novel targets for the treatment of atherosclerosis and other cardiovascular diseases.
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Affiliation(s)
| | | | - Devendra K. Agrawal
- Department of Translational Research, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
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13
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Baruah C, Nath P, Barah P. LncRNAs in neuropsychiatric disorders and computational insights for their prediction. Mol Biol Rep 2022; 49:11515-11534. [PMID: 36097122 DOI: 10.1007/s11033-022-07819-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/20/2022] [Accepted: 07/24/2022] [Indexed: 12/06/2022]
Abstract
Long non-coding RNAs (lncRNAs) are 200 nucleotide extended transcripts that do not encode proteins or possess limited coding ability. LncRNAs epigenetically control several biological functions such as gene regulation, transcription, mRNA splicing, protein interaction, and genomic imprinting. Over the years, drastic progress in understanding the role of lncRNAs in diverse biological processes has been made. LncRNAs are reported to show tissue-specific expression patterns suggesting their potential as novel candidate biomarkers for diseases. Among all other non-coding RNAs, lncRNAs are highly expressed within the brain-enriched or brain-specific regions of the neural tissues. They are abundantly expressed in the neocortex and pre-mature frontal regions of the brain. LncRNAs are co-expressed with the protein-coding genes and have a significant role in the evolution of functions of the brain. Any deregulation in the lncRNAs contributes to disruptions in normal brain functions resulting in multiple neurological disorders. Neuropsychiatric disorders such as schizophrenia, bipolar disease, autism spectrum disorders, and anxiety are associated with the abnormal expression and regulation of lncRNAs. This review aims to highlight the understanding of lncRNAs concerning normal brain functions and their deregulation associated with neuropsychiatric disorders. We have also provided a survey on the available computational tools for the prediction of lncRNAs, their protein coding potentials, and sub-cellular locations, along with a section on existing online databases with known lncRNAs, and their interactions with other molecules.
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Affiliation(s)
- Cinmoyee Baruah
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India
| | - Prangan Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India
| | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India.
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14
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Nagpal N, Tai AK, Nandakumar J, Agarwal S. Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13. Nucleic Acids Res 2022; 50:9413-9425. [PMID: 36018809 PMCID: PMC9458449 DOI: 10.1093/nar/gkac706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/27/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
Mutations in DKC1 (encoding dyskerin) cause telomere diseases including dyskeratosis congenita (DC) by decreasing steady-state levels of TERC, the non-coding RNA component of telomerase. How DKC1 mutations variably impact numerous other snoRNAs remains unclear, which is a barrier to understanding disease mechanisms in DC beyond impaired telomere maintenance. Here, using DC patient iPSCs, we show that mutations in the dyskerin N-terminal extension domain (NTE) dysregulate scaRNA13. In iPSCs carrying the del37L NTE mutation or engineered to carry NTE mutations via CRISPR/Cas9, but not in those with C-terminal mutations, we found scaRNA13 transcripts with aberrant 3' extensions, as seen when the exoribonuclease PARN is mutated in DC. Biogenesis of scaRNA13 was rescued by repair of the del37L DKC1 mutation by genome-editing, or genetic or pharmacological inactivation of the polymerase PAPD5, which counteracts PARN. Inspection of the human telomerase cryo-EM structure revealed that in addition to mediating intermolecular dyskerin interactions, the NTE interacts with terminal residues of the associated snoRNA, indicating a role for this domain in 3' end definition. Our results provide mechanistic insights into the interplay of dyskerin and the PARN/PAPD5 axis in the biogenesis and accumulation of snoRNAs beyond TERC, broadening our understanding of ncRNA dysregulation in human diseases.
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Affiliation(s)
- Neha Nagpal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children's Hospital; Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; Department of Pediatrics, Harvard Medical School; Manton Center for Orphan Disease Research; Harvard Initiative in RNA Medicine; Boston, MA, USA
| | - Albert K Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
- Data Intensive Studies Center, Tufts University, Medford, MA, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Suneet Agarwal
- To whom correspondence should be addressed. Tel: +1 617 919 4610; Fax: +1 617 919 3359;
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15
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Xu J, Li L, Shi P, Cui H, Yang L. The Crucial Roles of Bmi-1 in Cancer: Implications in Pathogenesis, Metastasis, Drug Resistance, and Targeted Therapies. Int J Mol Sci 2022; 23:ijms23158231. [PMID: 35897796 PMCID: PMC9367737 DOI: 10.3390/ijms23158231] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 12/01/2022] Open
Abstract
B-cell-specific Moloney murine leukemia virus integration region 1 (Bmi-1, also known as RNF51 or PCGF4) is one of the important members of the PcG gene family, and is involved in regulating cell proliferation, differentiation and senescence, and maintaining the self-renewal of stem cells. Many studies in recent years have emphasized the role of Bmi-1 in the occurrence and development of tumors. In fact, Bmi-1 has multiple functions in cancer biology and is closely related to many classical molecules, including Akt, c-MYC, Pten, etc. This review summarizes the regulatory mechanisms of Bmi-1 in multiple pathways, and the interaction of Bmi-1 with noncoding RNAs. In particular, we focus on the pathological processes of Bmi-1 in cancer, and explore the clinical relevance of Bmi-1 in cancer biomarkers and prognosis, as well as its implications for chemoresistance and radioresistance. In conclusion, we summarize the role of Bmi-1 in tumor progression, reveal the pathophysiological process and molecular mechanism of Bmi-1 in tumors, and provide useful information for tumor diagnosis, treatment, and prognosis.
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Affiliation(s)
- Jie Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (J.X.); (L.L.); (P.S.)
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Lin Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (J.X.); (L.L.); (P.S.)
| | - Pengfei Shi
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (J.X.); (L.L.); (P.S.)
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (J.X.); (L.L.); (P.S.)
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
- Correspondence: (H.C.); (L.Y.)
| | - Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China; (J.X.); (L.L.); (P.S.)
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
- Correspondence: (H.C.); (L.Y.)
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16
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Zhang H, Zhou Q, Shen W. Circ-FOXM1 promotes the proliferation, migration and EMT process of osteosarcoma cells through FOXM1-mediated Wnt pathway activation. J Orthop Surg Res 2022; 17:344. [PMID: 35799265 PMCID: PMC9261067 DOI: 10.1186/s13018-022-03207-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Osteosarcoma (OS) is a malignant bone tumor that commonly occurs in adolescents with a high mortality rate and frequent pulmonary metastasis. Emerging evidence has suggested that circular RNAs (circRNAs) are important regulators in multiple biological activities of carcinomas. Nevertheless, the role of circRNAs derived from forkhead box M1 (FOXM1), a well-accepted modulator of OS progression, has not been discussed in OS. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to test circ-FOXM1 (hsa_circ_0025033) expression in OS cell lines. Cell counting kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU), terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL), transwell assays and western blot analysis of epithelial-mesenchymal transition (EMT) markers were conducted to evaluate cell proliferation, apoptosis, migration, and EMT process. Luciferase reporter assay and RNA-binding protein immunoprecipitation (RIP) assay were utilized to detect the interaction of circ-FOXM1 and RNAs. RESULTS High expression of circ-FOXM1 was detected in OS cell lines. Functionally, circ-FOXM1 knockdown inhibited the proliferation, migration and EMT process, whereas induced the apoptosis of OS cells. From the aspect of molecular mechanism, circ-FOXM1 was discovered to upregulate FOXM1 expression via sponging miR-320a and miR-320b, therefore activating Wnt signaling pathway. Besides, rescue experiments elucidated that circ-FOXM1 regulated cellular activities of OS cells via FOXM1. Further, in vivo assays supported that loss of circ-FOXM1 restrained OS tumor growth. CONCLUSION Circ-FOXM1 facilitated the malignant phenotypes of OS cells through FOXM1-mediated Wnt pathway activation, revealing circ-FOXM1 as a potential biomarker for OS treatment.
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Affiliation(s)
- Hao Zhang
- Department of Burn and Plastic Surgery, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, Jiangsu, China
| | - Qiongqiong Zhou
- Department of Otolaryngology, Children's Hospital of Nanjing Medical University, Nanjing, 210008, China
| | - Weimin Shen
- Department of Burn and Plastic Surgery, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210008, Jiangsu, China.
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Castro I, Carvajal P, Jara D, Aguilera S, Heathcote B, Barrera MJ, Aliaga-Tobar V, Maracaja-Coutinho V, Urzúa U, Quest AFG, González S, Molina C, Hermoso M, González MJ. Small RNA Expression Profiling Reveals hsa-miR-181d-5p Downregulation Associated With TNF-α Overexpression in Sjögren’s Syndrome Patients. Front Immunol 2022; 13:870094. [PMID: 35432384 PMCID: PMC9010469 DOI: 10.3389/fimmu.2022.870094] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/14/2022] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (sRNA), that alter gene expression by binding to target messenger RNAs (mRNAs) and repressing translation. Dysregulated miRNA expression has been implicated in the pathogenesis of autoimmune diseases such as Sjögren’s syndrome (SS). The aim of this study was to characterize the global profile of sRNAs in labial salivary glands (LSG) from SS-patients and to validate potential miRNA candidates implicated in glandular inflammation. LSG from 21 SS-patients and 9 sicca controls were analyzed. A global next generation sequencing (NGS)-based sRNA profiling approach was employed to identify direct targets whereby differentially expressed miRNAs were predicted using bioinformatics tools. miRNA levels were validated by TaqMan and target mRNA levels were determined by quantitative real-time PCR. We also performed in vitro assays using recombinant TNF-α. NGS shows that ~30% of sRNAs were miRNAs. In comparison with samples from sicca controls, four miRNAs were found differentially expressed in LSG from SS-patients with low focus score (LFS) and 18 from SS-patients with high focus score (HFS). The miRNA with the most significant changes identified by NGS was hsa-miR-181d-5p and downregulation was confirmed by TaqMan analysis. Levels of TNF-α mRNA, a direct target of hsa-miR-181d-5p, were significantly increased and negatively correlated with hsa-miR-181d-5p presence. Moreover, positive correlations between TNF-α transcript levels, focus score, ESSDAI, and autoantibody levels were also detected. Furthermore, TNF-α stimulation decreased hsa-miR-181d-5p levels in vitro. Downregulation of hsa-miR-181d-5p in LSG from SS-patients could contribute to the glandular pro-inflammatory environment by deregulation of its direct target TNF-α. Further dissection of the pathophysiological mechanisms underlying the hsa-miR-181d-5p-mediated action in inflammatory conditions could be useful to evaluate the benefits of increasing hsa-miR-181d-5p levels for restoration of salivary gland epithelial cell architecture and function.
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Affiliation(s)
- Isabel Castro
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Patricia Carvajal
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Daniela Jara
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sergio Aguilera
- Departamento de Reumatología, Clínica Instituto de Diagnóstico Sociedad Anónima (Indisa), Santiago, Chile
| | - Benjamín Heathcote
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Víctor Aliaga-Tobar
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O’Higgins, Rancagua, Chile
| | - Vinicius Maracaja-Coutinho
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Ulises Urzúa
- Departamento de Oncología Básico-Clínico, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Andrew F. G. Quest
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Centro de Estudios en Ejercicio, Metabolismo y Cáncer (CEMC), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sergio González
- Escuela de Odontología, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | - Claudio Molina
- Facultad de Odontología, Universidad San Sebastián, Santiago, Chile
| | - Marcela Hermoso
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - María-Julieta González
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- *Correspondence: María-Julieta González, ;
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CircPVT1: a pivotal circular node intersecting Long Non-Coding-PVT1 and c-MYC oncogenic signals. Mol Cancer 2022; 21:33. [PMID: 35090471 PMCID: PMC8796571 DOI: 10.1186/s12943-022-01514-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/18/2022] [Indexed: 12/11/2022] Open
Abstract
The role of circular RNAs in oncogenesis has begun to be widely studied in recent years, due to the significant impact that these molecules have in disease pathogenesis, as well as their potential for the future of innovative therapies. Moreover, due to their characteristically circular shape, circular RNAs are very resistant molecules to RNA degradation whose levels are easily assessed in body fluids. Accordingly, they represent an opportunity for the discovery of new diagnostic and prognostic markers in a wide range of diseases. Among circular RNAs, circPVT1 is a rather peculiar one that originates from the circularization of the exon 2 of the PVT1 gene that encodes a pro-tumorigenic long non-coding RNA named lncPVT1. There are a few examples of circular RNAs that derive from a locus producing another non-coding RNA. Despite their apparent transcriptional independence, which occurs using two different promoters, a possible synergistic effect in tumorigenesis cannot be excluded considering that both have been reported to correlate with the oncogenic phenotype. This complex mechanism of regulation appears to also be controlled by c-MYC. Indeed, the PVT1 locus is located only 53 Kb downstream c-MYC gene, a well-known oncogene that regulates the expression levels of about 15% of all genes. Here, we review circPVT1 origin and biogenesis highlighting the most important mechanisms through which it plays a fundamental role in oncogenesis, such as the well-known sponge activity on microRNAs, as well as its paradigmatic interactome link with lncPVT1 and c-MYC expression.
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Minshall N, Chernukhin I, Carroll JS, Git A. ncRNAseq: simple modifications to RNA-seq library preparation allow recovery and analysis of mid-sized non-coding RNAs. Biotechniques 2022; 72:21-28. [PMID: 34841883 DOI: 10.2144/btn-2021-0035] [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] [Indexed: 11/23/2022] Open
Abstract
Despite their abundance, mid-sized RNAs (30-300 nt) have not been extensively studied by high-throughput sequencing, mostly due to selective loss in library preparation. The authors propose simple and inexpensive modifications to the Illumina TruSeq protocol (ncRNAseq), allowing the capture and sequencing of mid-sized non-coding RNAs without detriment to the coverage of coding mRNAs. This protocol is coupled with a two-step alignment: a pre-alignment to a curated non-coding genome, passing only the non-mapping reads to a standard genomic alignment. ncRNAseq correctly assigns the highest read-numbers to established abundant non-coding RNAs and correctly identifies cytosolic and nuclear enrichment of known non-coding RNAs in two cell lines.
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Affiliation(s)
- Nicola Minshall
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Igor Chernukhin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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Sakai K, Hiradate Y, Hara K, Tanemura K. Potential of sperm small non-coding RNAs as biomarkers of testicular toxicity in a doxorubicin-induced mouse model. Biochem Biophys Rep 2021; 28:101160. [PMID: 34729424 PMCID: PMC8545667 DOI: 10.1016/j.bbrep.2021.101160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 11/28/2022] Open
Abstract
Testicular toxicity is a major concern in cancer chemotherapy and drug development as it can result in infertility; however, there are no effective biomarkers for this adverse effect. To identify new biomarkers, we investigated the expression of small non-coding RNAs (sncRNAs) in a mouse model of doxorubicin (DXR)-induced testicular toxicity. First, we performed small RNA-seq analysis of sperm from DXR-treated or control mice and observed differential expression of many genome-derived sequences. We then performed real-time RT-PCR validation of these sequences and discovered that sncRNA detected by one primers, dxRN_3, showed similar differential expression as that seen in the RNA-seq experiment. These findings suggest that the sncRNAs present in sperm have potential as clinically acceptable biomarkers for testicular toxicity. Testicular toxicity is a major concern in cancer chemotherapy and drug development. There is a lack of effective biomarkers to assess testicular toxicity. Small RNA-seq analysis was performed on sperm from doxorubicin-treated mice. Differential RNA expression analyses identified a small non-coding RNA. Small non-coding RNAs in sperm may be useful biomarkers for testicular toxicity.
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Affiliation(s)
- Kazuya Sakai
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yuki Hiradate
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Kenshiro Hara
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Kentaro Tanemura
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
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21
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Dey P, Mattick JS. High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs. Epigenetics Chromatin 2021; 14:45. [PMID: 34579770 PMCID: PMC8477579 DOI: 10.1186/s13072-021-00419-2] [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: 04/19/2021] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND It is established that protein-coding exons are preferentially localized in nucleosomes. To examine whether the same is true for non-coding exons, we analysed nucleosome occupancy in and adjacent to internal exons in genes encoding long non-coding RNAs (lncRNAs) in human CD4+ T cells and K562 cells. RESULTS We confirmed that internal exons in lncRNAs are preferentially associated with nucleosomes, but also observed an elevated signal from H3K4me3-marked nucleosomes in the sequences upstream of these exons. Examination of 200 genomic lncRNA loci chosen at random across all chromosomes showed that high-density regions of H3K4me3-marked nucleosomes, which we term 'slabs', are associated with genomic regions exhibiting intron retention. These retained introns occur in over 50% of lncRNAs examined and are mostly first introns with an average length of just 354 bp, compared to the average length of all human introns of 6355 and 7987 bp in mRNAs and lncRNAs, respectively. Removal of short introns from the dataset abrogated the high upstream H3K4me3 signal, confirming that the association of slabs and short lncRNA introns with intron retention holds genome-wide. The high upstream H3K4me3 signal is also associated with alternatively spliced exons, known to be prominent in lncRNAs. This phenomenon was not observed with mRNAs. CONCLUSIONS There is widespread intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs, which raises intriguing questions about the relationship of IR to lncRNA function and chromatin organization.
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Affiliation(s)
- Pinki Dey
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Sydney, Australia
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Sydney, Australia.
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22
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Mortoglou M, Tabin ZK, Arisan ED, Kocher HM, Uysal-Onganer P. Non-coding RNAs in pancreatic ductal adenocarcinoma: New approaches for better diagnosis and therapy. Transl Oncol 2021; 14:101090. [PMID: 33831655 PMCID: PMC8042452 DOI: 10.1016/j.tranon.2021.101090] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/14/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive malignancies with a 5-year survival rate less than 8%, which has remained unchanged over the last 50 years. Early detection is particularly difficult due to the lack of disease-specific symptoms and a reliable biomarker. Multimodality treatment including chemotherapy, radiotherapy (used sparingly) and surgery has become the standard of care for patients with PDAC. Carbohydrate antigen 19-9 (CA 19-9) is the most common diagnostic biomarker; however, it is not specific enough especially for asymptomatic patients. Non-coding RNAs are often deregulated in human malignancies and shown to be involved in cancer-related mechanisms such as cell growth, differentiation, and cell death. Several micro, long non-coding and circular RNAs have been reported to date which are involved in PDAC. Aim of this review is to discuss the roles and functions of non-coding RNAs in diagnosis and treatments of PDAC.
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Affiliation(s)
- Maria Mortoglou
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - Zoey Kathleen Tabin
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
| | - E Damla Arisan
- Institution of Biotechnology, Gebze Technical University, Gebze, Turkey.
| | - Hemant M Kocher
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University London, London EC1M 6BQ, UK.
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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23
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Sun J, Yin A, Zhang W, Lv J, Liang Y, Li H, Li Y, Li X. CircUBAP2 Inhibits Proliferation and Metastasis of Clear Cell Renal Cell Carcinoma via Targeting miR-148a-3p/FOXK2 Pathway. Cell Transplant 2021; 29:963689720925751. [PMID: 32425115 PMCID: PMC7563813 DOI: 10.1177/0963689720925751] [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] [Indexed: 01/17/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the prominent histological subtype of renal cell carcinoma (RCC) with high incidence of local recurrence and distant metastasis. It has been documented that circular ribonucleic acids (circRNAs) play crucial roles in the development of cancers; however, study on exploring the role of circRNAs in ccRCC still remains limited. In the present study, we aimed to evaluate the biological function of a novel circRNA UBAP2 (circUBAP2) in ccRCC and the underlying mechanism. Our results showed that circUBAP2 expression was significantly down-regulated in ccRCC tissues and cell lines. Overexpression of circUBAP2 significantly inhibited the proliferation, migration, and invasion of ccRCC cells. MiR-148a-3p was a target miRNA of circUBAP2 in ccRCC cells, and its expression levels in ccRCC tissues and cell lines were negatively correlated with circUBAP2 levels. Moreover, miR-148a-3p reversed the inhibitory effects of circUBAP2 on cell proliferation, migration, and invasion in ccRCC cells. Additionally, forkhead box K2 (FOXK2) was found to be a target gene of miR-148a-3p and regulated by miR-148a-3p in ccRCC cells. Furthermore, knockdown of FOXK2 reversed the inhibitory effects of miR-148a-3p inhibitor on ccRCC cells. In conclusion, these findings indicated that circUBAP2 functioned as a novel tumor suppressor in ccRCC through regulating the miR-148a-3p/FOXK2 axis. Therefore, circUBAP2 might serve as a potential therapeutic target for the treatment of ccRCC.
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Affiliation(s)
- Jiping Sun
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China.,Both the authors contributed equally to this article
| | - Aiping Yin
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China.,Both the authors contributed equally to this article
| | - Wenjing Zhang
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Jia Lv
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Yu Liang
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Huixian Li
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Yan Li
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Xudong Li
- Department of Urology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
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24
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Luan T, Zhang TY, Lv ZH, Guan BX, Xu JY, Li J, Li MX, Hu SL. The lncRNA ALMS1-IT1 may promote malignant progression of lung adenocarcinoma via AVL9-mediated activation of the cyclin-dependent kinase pathway. FEBS Open Bio 2021; 11:1504-1515. [PMID: 33683834 PMCID: PMC8091588 DOI: 10.1002/2211-5463.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/23/2021] [Accepted: 03/05/2021] [Indexed: 12/21/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the primary epithelial tumor of the lung. The lack of clinical symptoms and specific molecular diagnostic indicators during the early stages of LUAD mean that the disease may not be detected until late stages, and the 5‐year survival rate is only approximately 15%. Long non‐coding RNA ALMS1 intronic script 1 (ALMS1‐IT1) was previously reported to be correlated with the poor prognosis of head and neck squamous cell carcinoma patients. Here, we investigated whether ALMS1‐IT1 has prognostic potential for LUAD. Bioinformatics analyses were performed to examine the expression and prognostic value of ALMS1 and AVL9 (for which gene expression is positively correlated with ALMS1‐IT1 expression in LUAD) in LUAD based on TCGA and Oncomine databases. We report that ALMS1‐IT1 and AVL9 were both highly expressed in LUAD and correlated with poor outcomes in LUAD patients. Of note, the prognosis of LUAD patients with low expression of both ALMS1‐IT1 and AVL9 was superior to that of other patients. Furthermore, the proliferation, migration and invasion of LUAD cells were decreased in cells lacking ALMS1‐IT1, and this decrease could be almost completely reversed through overexpression of AVL9. Gene set enrichment analysis revealed that expression of genes related to the cell cycle pathway is closely related to both the high expression of ALMS1‐IT1 and AVL9 in LUAD. Finally, up‐regulation of ALMS1‐IT1 can activate the cyclin‐dependent kinase pathway, whereas absence of AVL9 can reverse this activation, as shown by western blotting. In summary, ALMS1‐IT1/AVL9 may promote the malignant progression of LUAD, at least in part by regulating the cyclin‐dependent kinase pathway.
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Affiliation(s)
- Tian Luan
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tian-Ye Zhang
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Zhong-Hua Lv
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bi-Xi Guan
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jian-Yu Xu
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jian Li
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ming-Xu Li
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Song-Liu Hu
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, China
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25
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Yu K, Cui S, Xue T. LncRNA MIR22HG is downregulated in adenomyosis and upregulates miR-2861 through demethylation to inhibit endometrial cell proliferation. J Obstet Gynaecol Res 2021; 47:1837-1845. [PMID: 33624428 DOI: 10.1111/jog.14665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/05/2020] [Accepted: 12/31/2020] [Indexed: 01/21/2023]
Abstract
AIM Endometrial cell proliferation plays a critical role in adenomyosis. It has been reported that MIR22HG and miR-2861 play similar roles in regulating endometrial cell proliferation, indicating their involvement in adenomyosis. This study aimed to investigate the potential involvement of MIR22HG and miR-2861 in adenomyosis. METHODS Endometrial biopsy was collected from both adenomyosis (n = 45) and the healthy controls (n = 45). The expression of MIR22HG and miR-2861 in biopsies were determined by quantitative reverse transcription polymerase chain reaction (RT-qPCR). The relationship between MIR22HG and miR-2861 in endometrial cells was analyzed by RT-qPCR. Methylation-specific PCR (MSP) was performed to analyze the effects of overexpression of MIR22HG on the expression of miR-2861. Western-blot assays were performed to illustrate the effect of MIR22HG, miR-2861, STAT3, and MMP2 on adenomyosis. Luciferase report assay was performed to analyze the interactions among miR-2861, STAT3, and MMP2. The role of MIR22HG and miR-2861 in regulating the proliferation of endometrial cells was analyzed by cell proliferation assay. RESULTS The expression of MIR22HG and miR-2861 in adenomyosis did not change with menstrual cycle. MIR22HG and miR-2861 were significantly downregulated in adenomyosis and they were significantly and positively correlated with each other. In endometrial cells, overexpression of MIR22HG upregulated the expression of miR-2861 and decreased methylation of miR-2861 gene. MIR22HG and miR-2861 downregulated STAT3 and MMP2 to inhibit the proliferation of endometrial cells. In addition, overexpression of both MIR22HG and miR-2861 showed stronger effects. CONCLUSION MIR22HG is downregulated in adenomyosis and upregulates miR-2861 through demethylation to inhibit endometrial cell proliferation.
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Affiliation(s)
- Ke Yu
- Department of Gynecology and Obstetrics, Affiliated Hospital of Yangzhou University, Yangzhou City, PR China
| | - Shuna Cui
- Medical College of Yangzhou University, Yangzhou City, PR China
| | - Tongmin Xue
- Nanjing Medical University, Nanjing City, PR China
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26
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The neglected nutrigenomics of milk: What is the role of inter-species transfer of small non-coding RNA? FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2020.100796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Hahne JC, Lampis A, Valeri N. Vault RNAs: hidden gems in RNA and protein regulation. Cell Mol Life Sci 2021; 78:1487-1499. [PMID: 33063126 PMCID: PMC7904556 DOI: 10.1007/s00018-020-03675-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/27/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs are important regulators of differentiation during embryogenesis as well as key players in the fine-tuning of transcription and furthermore, they control the post-transcriptional regulation of mRNAs under physiological conditions. Deregulated expression of non-coding RNAs is often identified as one major contribution in a number of pathological conditions. Non-coding RNAs are a heterogenous group of RNAs and they represent the majority of nuclear transcripts in eukaryotes. An evolutionary highly conserved sub-group of non-coding RNAs is represented by vault RNAs, named since firstly discovered as component of the largest known ribonucleoprotein complexes called "vault". Although they have been initially described 30 years ago, vault RNAs are largely unknown and their molecular role is still under investigation. In this review we will summarize the known functions of vault RNAs and their involvement in cellular mechanisms.
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Affiliation(s)
- Jens Claus Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, UK
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28
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Fu Y, Sun C, Li Q, Qian F, Li C, Xi X, Shang D, Wang C, Peng X, Piao M, Qu W, Tian J, Yu B, Gu X, Tian J. Differential RNA expression profiles and competing endogenous RNA-associated regulatory networks during the progression of atherosclerosis. Epigenomics 2021; 13:99-112. [PMID: 33406894 DOI: 10.2217/epi-2020-0252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: To identify differential mRNA and ncRNA expression profiles and competing endogenous RNA-associated regulatory networks during the progression of atherosclerosis (AS). Materials & methods: We systematically analyzed whole-transcriptome sequencing of samples from different stages of AS to evaluate their long noncoding RNA (lncRNA), circular RNA (circRNA), miRNA and mRNA profiles. Results: We constructed three AS-related competing endogenous RNA regulatory networks of differentially expressed circRNAs, lncRNAs, miRNAs and mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that the circRNAs in the network were enriched in lipid metabolic processes and participated in the PPAR signaling pathway. Furthermore, lncRNAs were related to receptor activity, myofibrils and cardiovascular system development. Conclusion: The current findings further clarified the regulatory mechanisms at different stages of AS and may provide new ideas and targets for AS.
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Affiliation(s)
- Yahong Fu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China.,Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, 541004, Guangxi, China
| | - Changbin Sun
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Qi Li
- Department of Pathology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Fengcui Qian
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, Heilongjiang, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, Heilongjiang, China
| | - Xiangwen Xi
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Desi Shang
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Chuhan Wang
- Department of Pathology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xiang Peng
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Minghui Piao
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Wenbo Qu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Jinwei Tian
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China.,Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, 541004, Guangxi, China
| | - Bo Yu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
| | - Xia Gu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China.,Heilongjiang Provincial Hospital, Harbin, 150030, Heilongjiang, China
| | - Jiangtian Tian
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, Heilongjiang, China.,The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, 150086, Heilongjiang, China
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29
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Li H, An X, Li Q, Yu H, Li Z. Construction and analysis of competing endogenous RNA network of MCF-7 breast cancer cells based on the inhibitory effect of 6-thioguanine on cell proliferation. Oncol Lett 2020; 21:104. [PMID: 33376537 PMCID: PMC7751352 DOI: 10.3892/ol.2020.12365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022] Open
Abstract
Previous research has proven that 6-thioguanine (6-TG) inhibits the growth of MCF-7 breast cancer cells. Accumulating evidence indicates that long non-coding (lnc)RNAs are involved in the development of various cancer types as competitive endogenous (ce)RNA molecules. The present study was conducted to investigate the regulatory mechanism underlying the function of lncRNAs as ceRNA molecules in MCF-7 cells and to identify more effective prognostic biomarkers for breast cancer treatment. The expression profiles of lncRNAs in untreated MCF-7 cells and 6-TG-treated MCF-7 cells were compared by RNA-seq. The regulatory associations among lncRNAs, micro (mi)RNAs and mRNAs were analyzed and verified by the TargetScan, miRDB and miRTarBas databases. The ceRNA networks were constructed by Cytoscape. The expression levels of two lncRNAs and two miRNAs in the ceRNA network were measured by reverse transcription-quantitative PCR. The OncoLnc and Kaplan-Meier plotter network databases were utilized to determine the effects of lncRNA and miRNA expression on the survival of patients with breast cancer. A ceRNA network was constructed for MCF-7 breast cancer cells treated with 6-TG, and this network may provide valuable information for further research elucidating the molecular mechanism underlying the effects of 6-TG on breast cancer. Moreover, LINC00324, MIR22HG, miR-370-3p and miR-424-5p were identified as potential prognostic and therapeutic biomarkers for breast cancer.
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Affiliation(s)
- Hao Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hao Yu
- College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, Jilin 130021, P.R. China
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30
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The Importance of AGO 1 and 4 in Post-Transcriptional Gene Regulatory Function of tRF5-GluCTC, an Respiratory Syncytial Virus-Induced tRNA-Derived RNA Fragment. Int J Mol Sci 2020; 21:ijms21228766. [PMID: 33233493 PMCID: PMC7699471 DOI: 10.3390/ijms21228766] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in infants, the elderly, and immune-compromised patients. It is also a significant contributor to upper respiratory tract infection in the pediatric population. However, its disease mechanisms are still largely unknown. We have recently shown that a tRNA-derived RNA fragment (tRF) from the 5′-end of mature tRNA encoding GluCTC (tRF5-GluCTC), a recently discovered non-coding RNA, is functionally important for RSV replication and host gene regulation at the post-transcriptional level. However, how tRF5-GluCTC carries out the gene regulation is not fully known. In this study, we found that tRF5-GluCTC has impaired gene trans-silencing function in cells deficient of AGO1 or 4, while AGO2 and 3 seem not involved in tRF5-GluCTC-mediated gene regulation. By pulling down individual AGO protein, we discovered that tRF5-GluCTC is detectable only in the AGO4 complex, confirming the essential role of AGO4 in gene regulation and also suggesting that AGO1 contributes to the gene trans-silencing activity of tRF5-GluCTC in an atypical way. We also found that the P protein of RSV is associated with both AGO1 and 4 and AGO4 deficiency leads to reduced infectious viral particles. In summary, this study demonstrates the importance of AGO1 and 4 in mediating the gene trans-silencing function of tRF5-GluCTC.
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31
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Xie H, Gao YM, Zhang YC, Jia MW, Peng F, Meng QH, Wang YC. Low let-7d exosomes from pulmonary vascular endothelial cells drive lung pericyte fibrosis through the TGFβRI/FoxM1/Smad/β-catenin pathway. J Cell Mol Med 2020; 24:13913-13926. [PMID: 33179861 PMCID: PMC7753874 DOI: 10.1111/jcmm.15989] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/08/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
The pathogenesis of pulmonary fibrosis (PF) was mediated by the progressive deposition of excessive extracellular matrix, but little is known about the regulatory mechanisms of fibrogenesis by lung pericytes. The mouse PF model was established by treatment with bleomycin, followed by isolation of exosomes from mouse broncho‐alveolar lavage fluids by the centrifuge method. Relative mRNA/microRNA levels and protein expression were assessed by qRT‐PCR and Western blotting, respectively. The binding of let‐7d with gene promoter was validated by dual‐luciferase reporter assay. Protein interactions were verified via GST pull‐down and co‐immunoprecipitation. Nuclear retention of Smad3 was analysed by extraction of cytoplasmic and nuclear fraction of pericytes followed by Western blotting. Association of FoxM1 with gene promoter was detected by EMSA and ChIP‐PCR methods. FoxM1 expression is significantly elevated in human lung fibroblasts of PF patients and mouse PF model. The expression of let‐7d is repressed in exosomes derived from broncho‐alveolar lavage fluids of PF mice. Let‐7d or FoxM1 knockdown suppressed the expression of FoxM1, Smad3, β‐catenin, Col1A and α‐SMA expression in mouse lung pericytes under TGF‐β1 treatment. FoxM1 overexpression elevated above gene expression in mouse lung pericytes under TGF‐β1 treatment. Let‐7d directly targets TGFβRI to regulate FoxM1 and downstream gene expression in mouse lung pericytes. FoxM1 directly interacts with Smad3 proteins to promote Smad3 nuclear retention and binds with β‐catenin promoter sequence to promote fibrogenesis. Exosomes with low let‐7d from pulmonary vascular endothelial cells drive lung pericyte fibrosis through activating the TGFβRI/FoxM1/Smad/β‐catenin signalling pathway.
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Affiliation(s)
- Han Xie
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Changsha, China
| | - Yuan-Mei Gao
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yong-Chang Zhang
- Department of Lung Cancer and Gastroenterology, Hunan Cancer Hospital, Changsha, China
| | - Ming-Wang Jia
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Fang Peng
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qing-He Meng
- Department of Surgery, SUNY Upstate Medical University, Syracuse, U.S.A
| | - Yi-Chun Wang
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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32
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Zhu Z, Wang H, Pang Y, Hu H, Zhang H, Wang W. Exosomal long non-coding RNA UCA1 functions as growth inhibitor in esophageal cancer. Aging (Albany NY) 2020; 12:20523–20539. [PMID: 33122449 PMCID: PMC7655204 DOI: 10.18632/aging.103911] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE Esophageal cancer is a highly lethal and broad-spreading malignant tumor worldwide. Exosome-carrying lncRNAs play an essential role in the pathogenesis of various cancers. RESULTS The results revealed that the expression of UCA1 was decreased in esophageal cancer tissues and plasma exosomes. UCA1 was enriched in exosomes, and exosomal UCA1 was a promising biomarker for the diagnosis of esophageal cancer with 86.7% sensitivity and 70.2% specificity. Overexpression of UCA1 played anticancer roles in esophageal cancer cells through inhibiting cell proliferation, invasion and migration, and colony formation. Also, exosomal UCA1 was taken up by esophageal cancer cells and inhibited the progression of esophageal cancer in vitro and tumor growth in vivo. Furthermore, exosomal UCA1 could directly target miRNA-613 in esophageal cancer cells. CONCLUSIONS The results suggested that exosomal UCA1 inhibits tumorigenesis and progression of esophageal cancer in vitro and in vivo, and might be a promising biomarker for esophageal cancer. PATIENT AND METHODS In this study, we determined the expression of UCA1 in esophageal cancer tissues, plasma exosomes of patients with esophageal cancer. We determined the potential of exosomal UCA1 as a biomarker and its effect on the pathogenesis and progression of esophageal cancer in vitro and in vivo.
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Affiliation(s)
- Zijiang Zhu
- Department of Thoracic Surgery, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Huilin Wang
- Department of Thoracic Surgery, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Yao Pang
- Department of Thoracic Surgery, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Hongxia Hu
- Department of Thoracic Surgery, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Hongyi Zhang
- Department of Thoracic Surgery, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Wenhao Wang
- Department of Thoracic Surgery, Gansu Provincial Hospital, Lanzhou, Gansu, China
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Kyriazi AA, Papiris E, Kitsos Kalyvianakis K, Sakellaris G, Baritaki S. Dual Effects of Non-Coding RNAs (ncRNAs) in Cancer Stem Cell Biology. Int J Mol Sci 2020; 21:ijms21186658. [PMID: 32932969 PMCID: PMC7556003 DOI: 10.3390/ijms21186658] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of cancer stem cells (CSCs) as initiators of carcinogenesis has revolutionized the era of cancer research and our perception for the disease treatment options. Additional CSC features, including self-renewal and migratory and invasive capabilities, have further justified these cells as putative diagnostic, prognostic, and therapeutic targets. Given the CSC plasticity, the identification of CSC-related biomarkers has been a serious burden in CSC characterization and therapeutic targeting. Over the past decades, a compelling amount of evidence has demonstrated critical regulatory functions of non-coding RNAs (ncRNAs) on the exclusive features of CSCs. We now know that ncRNAs may interfere with signaling pathways, vital for CSC phenotype maintenance, such as Notch, Wnt, and Hedgehog. Here, we discuss the multifaceted contribution of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), as representative ncRNA classes, in sustaining the CSC-like traits, as well as the underlying molecular mechanisms of their action in various CSC types. We further discuss the use of CSC-related ncRNAs as putative biomarkers of high diagnostic, prognostic, and therapeutic value.
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Affiliation(s)
- Athina A. Kyriazi
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - Efstathios Papiris
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - Konstantinos Kitsos Kalyvianakis
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - George Sakellaris
- Surgery Unit, University General Hospital, 71500 Heraklion (PAGNH), Greece;
| | - Stavroula Baritaki
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
- Correspondence: ; Tel.: +30-2810394727
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Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene. PLoS One 2020; 15:e0235655. [PMID: 32628740 PMCID: PMC7337319 DOI: 10.1371/journal.pone.0235655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022] Open
Abstract
Biallelic variants in RNU4ATAC, a non-coding gene transcribed into the minor spliceosome component U4atac snRNA, are responsible for three rare recessive developmental diseases, namely Taybi-Linder/MOPD1, Roifman and Lowry-Wood syndromes. Next-generation sequencing of clinically heterogeneous cohorts (children with either a suspected genetic disorder or a congenital microcephaly) recently identified mutations in this gene, illustrating how profoundly these technologies are modifying genetic testing and assessment. As RNU4ATAC has a single non-coding exon, the bioinformatic prediction algorithms assessing the effect of sequence variants on splicing or protein function are irrelevant, which makes variant interpretation challenging to molecular diagnostic laboratories. In order to facilitate and improve clinical diagnostic assessment and genetic counseling, we present i) an update of the previously reported RNU4ATAC mutations and an analysis of the genetic variations affecting this gene using the Genome Aggregation Database (gnomAD) resource; ii) the pathogenicity prediction performances of scores computed based on an RNA structure prediction tool and of those produced by the Combined Annotation Dependent Depletion tool for the 285 RNU4ATAC variants identified in patients or in large-scale sequencing projects; iii) a method, based on a cellular assay, that allows to measure the effect of RNU4ATAC variants on splicing efficiency of a minor (U12-type) reporter intron. Lastly, the concordance of bioinformatic predictions and cellular assay results was investigated.
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Boukelia A, Boucheham A, Belguidoum M, Batouche M, Zehraoui F, Tahi F. A Novel Integrative Approach for Non-coding RNA Classification Based on Deep Learning. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191105160633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background:
Molecular biomarkers show new ways to understand many disease
processes. Noncoding RNAs as biomarkers play a crucial role in several cellular activities, which
are highly correlated to many human diseases especially cancer. The classification and the
identification of ncRNAs have become a critical issue due to their application, such as biomarkers
in many human diseases.
Objective:
Most existing computational tools for ncRNA classification are mainly used for
classifying only one type of ncRNA. They are based on structural information or specific known
features. Furthermore, these tools suffer from a lack of significant and validated features.
Therefore, the performance of these methods is not always satisfactory.
Methods:
We propose a novel approach named imCnC for ncRNA classification based on
multisource deep learning, which integrates several data sources such as genomic and epigenomic
data to identify several ncRNA types. Also, we propose an optimization technique to visualize the
extracted features pattern from the multisource CNN model to measure the epigenomics features
of each ncRNA type.
Results:
The computational results using a dataset of 16 human ncRNA classes downloaded from
RFAM show that imCnC outperforms the existing tools. Indeed, imCnC achieved an accuracy of
94,18%. In addition, our method enables to discover new ncRNA features using an optimization
technique to measure and visualize the features pattern of the imCnC classifier.
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Affiliation(s)
- Abdelbasset Boukelia
- Computer Science Department, Faculty NTIC, University Abdelhamid Mehri Constantine 2, Constantine 25000, Algeria
| | - Anouar Boucheham
- University Salah Boubnider Constantine 3, Constantine 25000, Algeria
| | - Meriem Belguidoum
- Computer Science Department, Faculty NTIC, University Abdelhamid Mehri Constantine 2, Constantine 25000, Algeria
| | - Mohamed Batouche
- IT Department, CCIS - RC, Princess Nourah University, Riyadh, Saudi Arabia
| | - Farida Zehraoui
- IBISC, University Evry, University Paris-Saclay, Evry, France
| | - Fariza Tahi
- IBISC, University Evry, University Paris-Saclay, Evry, France
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Tan Z, Cao F, Jia B, Xia L. Circ_0072088 promotes the development of non-small cell lung cancer via the miR-377-5p/NOVA2 axis. Thorac Cancer 2020; 11:2224-2236. [PMID: 32524752 PMCID: PMC7396390 DOI: 10.1111/1759-7714.13529] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/22/2023] Open
Abstract
Background Non‐small cell lung cancer (NSCLC) is one of the leading causes of cancer‐related death globally. This study aimed to disclose the role of circular RNA circ_0072088 in NSCLC and illustrate its potential mechanism. Methods Quantitative real‐time polymerase chain reaction (qRT‐PCR) was applied to detect the expression of circ_0072088, zinc finger RNA binding protein (ZFR), microRNA‐377‐5p (miR‐377‐5p) and NOVA alternative splicing regulator 2 (NOVA2). The viability, colony formation, cell cycle, migration and invasion of NSCLC cells were measured by cell counting kit‐8 (CCK8) assay, colony formation assay, flow cytometry, wound healing assay and transwell invasion assay. Western blot assay was employed to examine the protein levels of proliferating cell nuclear antigen (PCNA), Cyclin D1, matrix metallopeptidase 2 (MMP2), MMP9 and NOVA2. The downstream targets of circ_0072088 and miR‐377‐5p were searched through using circular RNA Interactome and TargetScan databases, and the interaction between miR‐377‐5p and circ_0072088 or NOVA2 was confirmed by dual‐luciferase reporter assay and RNA immunoprecipitation (RIP) assay. in vivo tumor growth assay was used to evaluate the functions of circ_0072088 in the progression of NSCLC in vivo. Results GSE101586 dataset and the analysis of tissue specimens showed that circ_0072088 was aberrantly upregulated in tumor tissues of lung cancer and NSCLC. Circ_0072088 interference caused marked suppression on the proliferation and motility of NSCLC cells. Circ_0072088 could negatively regulate miR‐377‐5p through direct combination. Circ_0072088 contributed to the progression of NSCLC through sponging miR‐377‐5p. MiR‐377‐5p could directly interact with NOVA2, and the overexpression of NOVA2 overturned miR‐377‐5p‐mediated influence on NSCLC cells. Circ_0072088 facilitated the progression of NSCLC in vivo. Conclusions Circ_0072088 facilitated the proliferation and metastasis of NSCLC cells through upregulating NOVA2 via functioning as a competitive endogenous RNA (ceRNA) for miR‐377‐5p.
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Affiliation(s)
- Zhaofeng Tan
- Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Fang Cao
- Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Bin Jia
- Department of Digestive Endoscopy, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lei Xia
- Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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Ahmadi S, Zobeiri M, Bradburn S. Molecular mechanisms underlying actions of certain long noncoding RNAs in Alzheimer's disease. Metab Brain Dis 2020; 35:681-693. [PMID: 32185592 DOI: 10.1007/s11011-020-00564-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/05/2020] [Indexed: 01/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a group of non-protein coding RNAs that have more than 200 nucleotides. LncRNAs play an important role in the regulation of protein-coding genes at the transcriptional and post-transcriptional levels. They are found in most organs, with a high prevalence in the central nervous system. Accumulating data suggests that lncRNAs are involved in various neurodegenerative disorders, including the onset and progression of Alzheimer's disease (AD). Recent insights suggest lncRNAs, such as BACE1-AS, 51A, 17A, NDM29 and AS-UCHL1, are dysregulated in AD tissues. Furthermore, there are ongoing efforts to explore the clinical usability of lncRNAs as biomarkers in the disease. In this review, we explore the mechanisms by which aberrant expressions of the most studied lncRNAs contribute to the neuropathologies associated with AD, including amyloid β plaques and neurofibrillary tangles. Understanding the molecular mechanisms of lncRNAs in patients with AD will reveal novel diagnosis strategies and more effective therapeutic targets.
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Affiliation(s)
- Shamseddin Ahmadi
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran.
| | - Mohammad Zobeiri
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Steven Bradburn
- Bioscience Research Centre, Manchester Metropolitan University, Manchester, UK
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Ratti M, Lampis A, Ghidini M, Salati M, Mirchev MB, Valeri N, Hahne JC. MicroRNAs (miRNAs) and Long Non-Coding RNAs (lncRNAs) as New Tools for Cancer Therapy: First Steps from Bench to Bedside. Target Oncol 2020; 15:261-278. [PMID: 32451752 PMCID: PMC7283209 DOI: 10.1007/s11523-020-00717-x] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs represent a significant proportion of the human genome. After having been considered as 'junk' for a long time, non-coding RNAs are now well established as playing important roles in maintaining cellular homeostasis and functions. Some non-coding RNAs show cell- and tissue-specific expression patterns and are specifically deregulated under pathological conditions (e.g. cancer). Therefore, non-coding RNAs have been extensively studied as potential biomarkers in the context of different diseases with a focus on microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for several years. Since their discovery, miRNAs have attracted more attention than lncRNAs in research studies; however, both families of non-coding RNAs have been established to play an important role in gene expression control, either as transcriptional or post-transcriptional regulators. Both miRNAs and lncRNAs can regulate key genes involved in the development of cancer, thus influencing tumour growth, invasion, and metastasis by increasing the activation of oncogenic pathways and limiting the expression of tumour suppressors. Furthermore, miRNAs and lncRNAs are also emerging as important mediators in drug-sensitivity and drug-resistance mechanisms. In the light of these premises, a number of pre-clinical and early clinical studies are exploring the potential of non-coding RNAs as new therapeutics. The aim of this review is to summarise the latest knowledge of the use of miRNAs and lncRNAs as therapeutic tools for cancer treatment.
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Affiliation(s)
- Margherita Ratti
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Medical Department, Division of Oncology, ASST di Cremona, Ospedale di Cremona, Cremona, Italy
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Michele Ghidini
- Division of Medical Oncology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Massimiliano Salati
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Milko B Mirchev
- Clinic of Gastroenterology, Medical University, Varna, Bulgaria
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, UK
| | - Jens C Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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Tian J, Fu Y, Li Q, Xu Y, Xi X, Zheng Y, Yu L, Wang Z, Yu B, Tian J. Differential Expression and Bioinformatics Analysis of CircRNA in PDGF-BB-Induced Vascular Smooth Muscle Cells. Front Genet 2020; 11:530. [PMID: 32547599 PMCID: PMC7272660 DOI: 10.3389/fgene.2020.00530] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022] Open
Abstract
Atherosclerosis is mediated by various factors and plays an important pathological foundation for cardiovascular and cerebrovascular diseases. Abnormal vascular smooth muscle cells (VSMCs) proliferation and migration have an essential role in atherosclerotic lesion formation. Circular RNAs (circRNA) have been widely detected in different species and are closely related to various diseases. However, the expression profiles and molecular regulatory mechanisms of circRNAs in VSMCs are still unknown. We used high-throughput RNA-seq as well as bioinformatics tools to systematically analyze circRNA expression profiles in samples from different VSMC phenotypes. Polymerase chain reaction (PCR), Sanger sequencing, and qRT-PCR were performed for circRNA validation. A total of 22191 circRNAs corresponding to 6273 genes (host genes) in the platelet-derived growth factor (PDGF-BB) treated group, the blank control group or both groups, were detected, and 112 differentially expressed circRNAs were identified between the PDGF-BB treated and control groups, of which 59 were upregulated, and 53 were downregulated. We selected 9 circRNAs for evaluation of specific head-to-tail splicing, and 10 differentially expressed circRNAs between the two groups for qRT-PCR validation. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses enrichment analyses revealed that the parental genes of the circRNAs mainly participated in cardiac myofibril assembly and positive regulation of DNA-templated transcription, indicating that they might be involved in cardiovascular diseases. Finally, we constructed a circRNA-miRNA network based on the dysregulated circRNAs and VSMC-related microRNAs. Our study is the first to show the differential expression of circRNAs in PDGF-BB-induced VSMCs and may provide new ideas and targets for the prevention and therapy of vascular diseases.
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Affiliation(s)
- Jiangtian Tian
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yahong Fu
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qi Li
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Pathology, Harbin Medical University, Harbin, China
| | - Ying Xu
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Basic Medical College of Mudanjiang Medical College, Mudanjiang, China
| | - Xiangwen Xi
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuqi Zheng
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Li Yu
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhuozhong Wang
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China.,Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bo Yu
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jinwei Tian
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Bartoszewski R, Sikorski AF. Editorial focus: understanding off-target effects as the key to successful RNAi therapy. Cell Mol Biol Lett 2019; 24:69. [PMID: 31867046 PMCID: PMC6902517 DOI: 10.1186/s11658-019-0196-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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Ke XL, Zhang DF, Li QY, Liu ZG, Gao FY, Lu MX, Yang H. Digital gene expression analysis in the liver of ScpB-vaccinated and Streptococcus agalactiae-challenged Nile tilapia. FISH & SHELLFISH IMMUNOLOGY 2019; 94:249-257. [PMID: 31470139 DOI: 10.1016/j.fsi.2019.08.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/09/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
In recent years, streptococcal diseases have severely threatened the development of tilapia aquaculture, but effective prevention and control methods have not yet been established. To understand the immune responses of vaccinated Nile tilapia (Oreochromis niloticus), digital gene expression (DGE) technology was applied in this study to detect the gene expression profile of the Nile tilapia (O. niloticus) liver in response to ScpB (Streptococcal C5a peptidase from group B Streptococcus, ScpB) vaccination and a Streptococcus agalactiae-challenge. The control and the ScpB-vaccinated Nile tilapia yielded a total of 25,788,734 and 27,088,598 clean reads, respectively. A total of 1234 significant differentially expressed unigenes were detected (P < 0.05), of which 236 were significantly up-regulated, and 269 were significantly down-regulated (P < 0.05, |fold|>2, FDR<0.05). Of the differentially expressed gene, the identified genes which were enriched using databases of GO and KEGG could be categorized into a total of 67 functional groups and were mapped to 153 signaling pathways including 15 immune-related pathways. The differentially expressed genes (TLR1, TLR2, TLR3, TLR5, TLR9, MyD88, C3, IL-1β, IL-10) were detected in the expression profiles, and this was subsequently verified via quantitative real-time PCR (qPCR). The results of this study can serve as a basis for future research not only on the molecular mechanism of S. agalactiae invasion, but also on the anti-S. agalactiae mechanism in targeted tissues of Nile tilapia.
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Affiliation(s)
- Xiao-Li Ke
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China
| | - De-Feng Zhang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China
| | - Qing-Yong Li
- Fisheries Research & Extension Center of Huizhou, Huizhou, 516002, China
| | - Zhi-Gang Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China
| | - Feng-Ying Gao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China
| | - Mai-Xin Lu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China.
| | - Hong Yang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi, 214081, China.
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Mitochondrial Damage Mediated by miR-1 Overexpression in Cancer Stem Cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:938-953. [PMID: 31765945 PMCID: PMC6883328 DOI: 10.1016/j.omtn.2019.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023]
Abstract
It is well known that cells rely on mitochondrial respiration for survival. However, the effect of microRNAs (miRNAs) on mitochondria of cells has not been extensively explored. Our results indicated that the overexpression of a miRNA (miR-1) could destroy mitochondria of cancer stem cells. miR-1 was downregulated in melanoma stem cells (MSCs) and breast cancer stem cells (BCSCs) compared with cancer non-stem cells. However, the upregulation of miR-1 in cancer non-stem cells did not induce mitochondrial damage. miR-1 overexpression caused mitochondrial damage of cancer stem cells by directly targeting the 3′ UTRs of MINOS1 (mitochondrial inner membrane organizing system 1) and GPD2 (glycerol-3-phosphate dehydrogenase 2) genes and interacting with LRPPRC (leucine-rich pentatricopeptide-repeat containing) protein, a protein localized in mitochondria. MINOS1, GPD2, and LRPPRC in mitochondria were required for mitochondrial inner membrane. The results of in vitro and in vivo assays demonstrated that miR-1 overexpression induced mitophagy of cancer stem cells. Therefore, our study contributed novel insights into the mechanism of miRNA-mediated regulation of mitochondria morphology of cancer stem cells.
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Cui J, Li W, Liu G, Chen X, Gao X, Lu H, Lin D. A novel circular RNA, hsa_circ_0043278, acts as a potential biomarker and promotes non-small cell lung cancer cell proliferation and migration by regulating miR-520f. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:810-821. [PMID: 30873868 DOI: 10.1080/21691401.2019.1575847] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
More and more circular RNAs (circRNAs) revealed to play a critical role in the initiation and progression of cancer, however, the effects of circRNAs on non-small cell lung cancer (NSCLC) remain largely undetermined. In the present study, we screened the dysregulated circRNAs in paired NSCLC and normal samples from GEO database and identified circ_0043278 was to be significantly up-regulated in NSCLC and demonstrated it promotes NSCLC progression in vitro and in vivo. Then, we revealed the expression of miR-520f, a downstream factor of circ_0043278, was significantly down-regulated in NSCLC and acted as a tumor inhibitor. In addition, we revealed that circ_0043278 sponged miR-520f, which was demonstrated to target ROCK1, CDKN1B, and AKT3 in NSCLC cells. In conclusion, circ_0043278 promoted NSCLC cell proliferation, invasion, and migration by increasing ROCK1, CDKN1B, and AKT3 expressions through direct inhibition of miR-520f.
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Affiliation(s)
- Jinggang Cui
- a Department of Respiratory Medicine , Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University , Suzhou , China
| | - Wei Li
- a Department of Respiratory Medicine , Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University , Suzhou , China
| | - Guohua Liu
- a Department of Respiratory Medicine , Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University , Suzhou , China
| | - Xiaojun Chen
- a Department of Respiratory Medicine , Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University , Suzhou , China
| | - Xiaolai Gao
- a Department of Respiratory Medicine , Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University , Suzhou , China
| | - Huiling Lu
- a Department of Respiratory Medicine , Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University , Suzhou , China
| | - Dang Lin
- a Department of Respiratory Medicine , Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University , Suzhou , China
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Wong WK, Jiang G, Sørensen AE, Chew YV, Lee-Maynard C, Liuwantara D, Williams L, O'Connell PJ, Dalgaard LT, Ma RC, Hawthorne WJ, Joglekar MV, Hardikar AA. The long noncoding RNA MALAT1 predicts human pancreatic islet isolation quality. JCI Insight 2019; 5:129299. [PMID: 31361602 DOI: 10.1172/jci.insight.129299] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human islet isolation is a cost-/resource-intensive program generating islets for cell therapy in Type 1 diabetes. However, only a third of cadaveric pancreas get to clinical transplantation due to low quality/number of islets. There is a need to identify biomarker(s) that predict the quality of islets, prior to initiating their isolation. Here, we sequenced transcriptome from 18 human islet preparations stratified into three groups (Gr.1: Best quality/transplantable islets, Gr.2: Intermediary quality, Gr.3: Inferior quality/non-transplantable islets) based on routine measurements including islet purity/viability. Machine-learning algorithms involving penalized regression analyses identified 10 long-non-coding(lnc)RNAs significantly different across all group-wise comparisons (Gr1VsGr2, Gr2vsGr3, Gr1vsGr3). Two variants of Metastasis-Associated Lung Adenocarcinoma Transcript-1(MALAT1) lncRNA were common across all comparisons. We confirmed RNA-seq findings in a "validation set" of 75 human islet preparations. Finally, in 19 pancreas samples, we demonstrate that assessing the levels of MALAT1 variants alone (ROC curve AUC: 0.83) offers highest specificity in predicting post-isolation islet quality and improves the predictive potential for clinical islet transplantation when combined with Edmonton Donor Points/Body Mass Index(BMI)/North American Islet Donor Score(NAIDS). We present this resource of islet-quality-stratified lncRNA transcriptome data and identify MALAT1 as a biomarker that significantly enhances current selection methods for clinical (GMP)-grade islet isolation.
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Affiliation(s)
- Wilson Km Wong
- Diabetes and Islet Biology Group, National Health and Medical Research Council (NHMRC) Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Anja E Sørensen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Yi Vee Chew
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Cody Lee-Maynard
- Diabetes and Islet Biology Group, National Health and Medical Research Council (NHMRC) Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - David Liuwantara
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Lindy Williams
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Philip J O'Connell
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Louise T Dalgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Ronald C Ma
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Wayne J Hawthorne
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Mugdha V Joglekar
- Diabetes and Islet Biology Group, National Health and Medical Research Council (NHMRC) Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, National Health and Medical Research Council (NHMRC) Clinical Trials Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
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Zhu K, Niu L, Wang J, Wang Y, Zhou J, Wang F, Cheng Y, Zhang Q, Li H. Circular RNA hsa_circ_0000885 Levels are Increased in Tissue and Serum Samples from Patients with Osteosarcoma. Med Sci Monit 2019; 25:1499-1505. [PMID: 30802235 PMCID: PMC6400018 DOI: 10.12659/msm.914899] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background Circular RNAs (circRNAs) are novel non-coding RNAs that have important roles in tumor progression. This study aimed to measure the levels of hsa_circ_0000885 in serum samples and tumor tissue from patients with osteosarcoma compared with controls and to evaluate the findings with disease-free survival and overall survival. Material/Methods Fifty pairs of osteosarcoma tissues and matched adjacent normal tissue were obtained from patients who underwent the same chemotherapy regimen before surgery. Blood samples were obtained from 30 patients with osteosarcoma before and after chemotherapy, 25 patients with osteosarcoma before and after surgery, 27 patients with benign bone tumors, and 25 age-matched and sex-matched healthy controls. Circular RNA sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) were used to analyze hsa_circ_0000885 expression. Results Hsa_circ_0000885 expression was significantly increased in tissue and serum samples from patients with osteosarcoma, compared with controls, with significantly increased expression levels in patients with Enneking stage IIB and III osteosarcoma, compared with early-stage osteosarcoma. Patients with high serum and tumor levels of hsa_circ_0000885 had lower rates of disease-free survival and overall survival. The serum expression levels of hsa_circ_0000885 were significantly higher in patients with osteosarcoma compared with patients with benign bone tumors or healthy controls. Conclusions Hsa_circ_0000885 was upregulated in osteosarcoma, and it could serve as a good prognostic biomarker indicating poor clinical outcomes of osteosarcoma. Hsa_circ_0000885 was upregulated in serum of osteosarcoma patients and could serve as a good diagnostic biomarker for osteosarcoma.
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Affiliation(s)
- Kai Zhu
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Liang Niu
- Department of Anesthesiology, The Qingdao Women and Children's Hospital, Qingdao, Shandong, China (mainland)
| | - Jun Wang
- Supply Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Yan Wang
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Jianrui Zhou
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Fang Wang
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Yanqin Cheng
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Qian Zhang
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Haiyan Li
- Department of Orthopedics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
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Wong WKM, Sørensen AE, Joglekar MV, Hardikar AA, Dalgaard LT. Non-Coding RNA in Pancreas and β-Cell Development. Noncoding RNA 2018; 4:E41. [PMID: 30551650 PMCID: PMC6315983 DOI: 10.3390/ncrna4040041] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
In this review, we provide an overview of the current knowledge on the role of different classes of non-coding RNAs for islet and β-cell development, maturation and function. MicroRNAs (miRNAs), a prominent class of small RNAs, have been investigated for more than two decades and patterns of the roles of different miRNAs in pancreatic fetal development, islet and β-cell maturation and function are now emerging. Specific miRNAs are dynamically regulated throughout the period of pancreas development, during islet and β-cell differentiation as well as in the perinatal period, where a burst of β-cell replication takes place. The role of long non-coding RNAs (lncRNA) in islet and β-cells is less investigated than for miRNAs, but knowledge is increasing rapidly. The advent of ultra-deep RNA sequencing has enabled the identification of highly islet- or β-cell-selective lncRNA transcripts expressed at low levels. Their roles in islet cells are currently only characterized for a few of these lncRNAs, and these are often associated with β-cell super-enhancers and regulate neighboring gene activity. Moreover, ncRNAs present in imprinted regions are involved in pancreas development and β-cell function. Altogether, these observations support significant and important actions of ncRNAs in β-cell development and function.
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Affiliation(s)
- Wilson K M Wong
- NHMRC Clinical Trials Center, University of Sydney, Camperdown NSW 2050, Sydney, Australia.
| | - Anja E Sørensen
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark.
| | - Mugdha V Joglekar
- NHMRC Clinical Trials Center, University of Sydney, Camperdown NSW 2050, Sydney, Australia.
| | - Anand A Hardikar
- NHMRC Clinical Trials Center, University of Sydney, Camperdown NSW 2050, Sydney, Australia.
| | - Louise T Dalgaard
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark.
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The Interaction of lncRNA-HEIH and lncRNA-HULC with HBXIP in Hepatitis B Patients. Gastroenterol Res Pract 2018; 2018:9187316. [PMID: 30622563 PMCID: PMC6304880 DOI: 10.1155/2018/9187316] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/06/2018] [Accepted: 10/23/2018] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) infection is a major risk factor for the development of hepatic cirrhosis (HC) and hepatocellular carcinoma (HCC), which are associated with very high morbidity and mortality rates worldwide. Many studies have shown that long noncoding RNAs (lncRNAs) that are highly expressed in HCC (lncRNA-HEIH) and highly upregulated in liver cancer (lncRNA-HULC) have been implicated in the development and progression of hepatitis B-related HC and HCC. In this study, reverse transcription and quantitative PCR were used to detect the expression of lncRNA-HEIH and lncRNA-HULC and western blot analysis to detect the expression of hepatitis B X-interacting protein (HBXIP). RNA immunoprecipitation was used to detect the interaction of HBXIP with lncRNA-HULC and lncRNA-HEIH. The results showed that lncRNA-HEIH, lncRNA-HULC, and HBXIP were upregulated in hepatitis B patients, particularly those with hepatitis B-related HCC. Both lncRNA-HEIH and lncRNA-HULC interacted with HBXIP. These results suggest that lncRNA-HEIH and lncRNA-HULC interact with HBXIP in hepatitis B-related diseases.
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Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis. Sci Rep 2018; 8:16638. [PMID: 30413775 PMCID: PMC6226517 DOI: 10.1038/s41598-018-35086-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/29/2018] [Indexed: 12/26/2022] Open
Abstract
The discovery of thousands of non-coding RNAs has revolutionized molecular biology, being implicated in several biological processes and diseases. To clarify oxidative stress role on Retinitis pigmentosa, a very heterogeneous and inherited ocular disorder group characterized by progressive retinal degeneration, we realized a comparative transcriptome analysis of human retinal pigment epithelium cells, comparing two groups, one treated with oxLDL and one untreated, in four time points (1 h, 2 h, 4 h, 6 h). Data analysis foresaw a complex pipeline, starting from CLC Genomics Workbench, STAR and TopHat2/TopHat-Fusion alignment comparisons, followed by transcriptomes assembly and expression quantification. We then filtered out non-coding RNAs and continued the computational analysis roadmap with specific tools and databases for long non-coding RNAs (FEELnc), circular RNAs (CIRCexplorer, UROBORUS, CIRI, KNIFE, CircInteractome) and piwi-interacting RNAs (piRNABank, piRNA Cluster, piRBase, PILFER). Finally, all detected non-coding RNAs underwent pathway analysis by Cytoscape software. Eight-hundred and fifty-four non-coding RNAs, between long non-coding RNAs and PIWI-interacting, were differentially expressed throughout all considered time points, in treated and untreated samples. These non-coding RNAs target host genes involved in several biochemical pathways are related to compromised response to oxidative stress, visual functions, synaptic impairment of retinal neurotransmission, impairment of the interphotoreceptor matrix and blood – retina barrier, all leading to retinal cell death. These data suggest that non-coding RNAs could play a relevant role in Retinitis pigmentosa etiopathogenesis.
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Maternally inherited 133kb deletion of 14q32 causing Kagami–Ogata syndrome. J Hum Genet 2018; 63:1231-1239. [DOI: 10.1038/s10038-018-0506-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/01/2018] [Accepted: 08/15/2018] [Indexed: 11/09/2022]
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Bartoszewski R, Sikorski AF. Editorial focus: entering into the non-coding RNA era. Cell Mol Biol Lett 2018; 23:45. [PMID: 30250489 PMCID: PMC6145373 DOI: 10.1186/s11658-018-0111-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Recent developments in high-throughput genotyping technologies have revealed the existence of several new classes of RNA that do not encode proteins but serve other cellular roles. To date, these non-coding RNAs (ncRNAs) have been shown to modulate both gene expression and genome remodeling, thus contributing to the control of both normal and disease-related cellular processes. The attraction of this research topic can be seen in the increasing number of submissions on ncRNAs to molecular biology journals, including Cellular Molecular Biology Letters (CMBL). As researchers attempt to deepen the understanding of the role of ncRNAs in cell biology, it is worth discussing the broader importance of this research.
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Affiliation(s)
- Rafal Bartoszewski
- 1Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F Sikorski
- 2Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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