1
|
Hussain S, Gupta G, Shahwan M, Bansal P, Kaur H, Deorari M, Pant K, Ali H, Singh SK, Rama Raju Allam VS, Paudel KR, Dua K, Kumarasamy V, Subramaniyan V. Non-coding RNA: A key regulator in the Glutathione-GPX4 pathway of ferroptosis. Noncoding RNA Res 2024; 9:1222-1234. [PMID: 39036600 PMCID: PMC11259992 DOI: 10.1016/j.ncrna.2024.05.007] [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: 02/05/2024] [Revised: 04/26/2024] [Accepted: 05/19/2024] [Indexed: 07/23/2024] Open
Abstract
Ferroptosis, a form of regulated cell death, has emerged as a crucial process in diverse pathophysiological states, encompassing cancer, neurodegenerative ailments, and ischemia-reperfusion injury. The glutathione (GSH)-dependent lipid peroxidation pathway, chiefly governed by glutathione peroxidase 4 (GPX4), assumes an essential part in driving ferroptosis. GPX4, as the principal orchestrator of ferroptosis, has garnered significant attention across cancer, cardiovascular, and neuroscience domains over the past decade. Noteworthy investigations have elucidated the indispensable functions of ferroptosis in numerous diseases, including tumorigenesis, wherein robust ferroptosis within cells can impede tumor advancement. Recent research has underscored the complex regulatory role of non-coding RNAs (ncRNAs) in regulating the GSH-GPX4 network, thus influencing cellular susceptibility to ferroptosis. This exhaustive review endeavors to probe into the multifaceted processes by which ncRNAs control the GSH-GPX4 network in ferroptosis. Specifically, we delve into the functions of miRNAs, lncRNAs, and circRNAs in regulating GPX4 expression and impacting cellular susceptibility to ferroptosis. Moreover, we discuss the clinical implications of dysregulated interactions between ncRNAs and GPX4 in several conditions, underscoring their capacity as viable targets for therapeutic intervention. Additionally, the review explores emerging strategies aimed at targeting ncRNAs to modulate the GSH-GPX4 pathway and manipulate ferroptosis for therapeutic advantage. A comprehensive understanding of these intricate regulatory networks furnishes insights into innovative therapeutic avenues for diseases associated with perturbed ferroptosis, thereby laying the groundwork for therapeutic interventions targeting ncRNAs in ferroptosis-related pathological conditions.
Collapse
Affiliation(s)
- Sadique Hussain
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Gaurav Gupta
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, 346, United Arab Emirates
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - Moyad Shahwan
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, 346, United Arab Emirates
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, 346, United Arab Emirates
| | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka, 560069, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh, 247341, India
- Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand, 831001, India
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Kumud Pant
- Graphic Era (Deemed to be University), Clement Town, Dehradun, 248002, India
- Graphic Era Hill University, Clement Town, Dehradun, 248002, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- School of Medical and Life Sciences, Sunway University, 47500 Sunway City, Malaysia
| | | | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW, 2007, Australia
| | - Kamal Dua
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, P.O. Box: 123 Broadway, Ultimo, NSW, 2007, Australia
| | - Vinoth Kumarasamy
- Department of Parasitology and Medical Entomology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia
| |
Collapse
|
2
|
Nejadi Orang F, Abdoli Shadbad M. CircRNA and lncRNA-associated competing endogenous RNA networks in medulloblastoma: a scoping review. Cancer Cell Int 2024; 24:248. [PMID: 39010056 PMCID: PMC11251335 DOI: 10.1186/s12935-024-03427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Medulloblastoma is one of the common primary central nervous system (CNS) malignancies in pediatric patients. The main treatment is surgical resection preceded and/or followed by chemoradiotherapy. However, their serious side effects necessitate a better understanding of medulloblastoma biology to develop novel therapeutic options. MAIN BODY Circular RNA (circRNA) and long non-coding RNA (lncRNA) regulate gene expression via microRNA (miRNA) pathways. Although growing evidence has highlighted the significance of circRNA and lncRNA-associated competing endogenous RNA (ceRNA) networks in cancers, no study has comprehensively investigated them in medulloblastoma. For this aim, the Web of Science, PubMed, Scopus, and Embase were systematically searched to obtain the relevant papers published before 16 September 2023, adhering to the PRISMA-ScR statement. HOTAIR, NEAT1, linc-NeD125, HHIP-AS1, CRNDE, and TP73-AS1 are the oncogenic lncRNAs, and Nkx2-2as is a tumor-suppressive lncRNA that develop lncRNA-associated ceRNA networks in medulloblastoma. CircSKA3 and circRNA_103128 are upregulated oncogenic circRNAs that develop circRNA-associated ceRNA networks in medulloblastoma. CONCLUSION In summary, this study has provided an overview of the existing evidence on circRNA and lncRNA-associated ceRNA networks and their impact on miRNA and mRNA expression involved in various signaling pathways of medulloblastoma. Suppressing the oncogenic ceRNA networks and augmenting tumor-suppressive ceRNA networks can provide ample opportunities for medulloblastoma treatment.
Collapse
Affiliation(s)
| | - Mahdi Abdoli Shadbad
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
3
|
Kong J, Lyu H, Ouyang Q, Shi H, Zhang R, Xiao S, Guo D, Zhang Q, Chen XZ, Zhou C, Tang J. Insights into the Roles of Epigenetic Modifications in Ferroptosis. BIOLOGY 2024; 13:122. [PMID: 38392340 PMCID: PMC10886775 DOI: 10.3390/biology13020122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Ferroptosis is a non-apoptotic mode of cell death driven by membrane lipid peroxidation and is characterized by elevated intracellular levels of Fe2+, ROS, and lipid peroxidation. Studies have shown that ferroptosis is related to the development of multiple diseases, such as cancer, neurodegenerative diseases, and acute myeloid leukemia. Ferroptosis plays a dual role in the occurrence and development of these diseases. Ferroptosis mainly involves iron metabolism, ROS, and lipid metabolism. Various mechanisms, including epigenetic regulation, have been reported to be deeply involved in ferroptosis. Abnormal epigenetic modifications have been reported to promote tumor onset or other diseases and resistance to chemotherapy drugs. In recent years, diversified studies have shown that epigenetic modification is involved in ferroptosis. In this review, we reviewed the current resistance system of ferroptosis and the research progress of epigenetic modification, such as DNA methylation, RNA methylation, non-coding RNAs, and histone modification in cancer and other diseases by regulating ferroptosis.
Collapse
Affiliation(s)
- Jinghua Kong
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Qian Ouyang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Hao Shi
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Rui Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Shuai Xiao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Dong Guo
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Qi Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| |
Collapse
|
4
|
Wang Y, Wang J, Zhang Y, Luo H, Yuan H. LncRNA-MUF: A Novel Oncogenic Star with Potential as a Biological Marker and Therapeutic Target for Gastrointestinal Malignancies. J Cancer 2024; 15:1498-1510. [PMID: 38370364 PMCID: PMC10869981 DOI: 10.7150/jca.91984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/30/2023] [Indexed: 02/20/2024] Open
Abstract
Gastrointestinal (GI) cancers pose a significant global health challenge, characterized by a high incidence and poor prognosis. The delayed detection and occurrence of metastasis contribute to the overall low survival rates associated with these cancers. Therefore, there is an urgent need to identify novel molecular targets for effective GI cancer treatment. Recent research has shed light on the potential of long non-coding RNAs (lncRNAs) as promising targets in cancer therapy, given their strong association with carcinogenesis and profound impact on tumor development. Among these lncRNAs, lncRNA-MUF, also known as LINC00941, has emerged as a key player in oncogenic regulation, specifically implicated in the progression of various GI cancers, including esophageal, gastric, colorectal, hepatic, and pancreatic cancer. This review aims to provide an updated and focused analysis of the regulatory roles of LINC00941 in the initiation and progression of GI cancer. Our objective is to unravel the underlying molecular mechanisms through which LINC00941 influences GI cancer phenotypes both in vivo and in vitro, with a special emphasis on the key molecules and signaling pathways involved. Additionally, LINC00941 has demonstrated clinical significance in terms of clinical pathology, prognosis, and diagnosis in GI tumors, further reinforcing its potential as a novel therapeutic target.
Collapse
Affiliation(s)
- Yang Wang
- Department of Gastroenterology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330008, Jiangxi, China
| | - Jialing Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330008, Jiangxi, China
| | - Yihan Zhang
- Second School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Nanchang 330008, Jiangxi, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330008, Jiangxi, China
| | - Huazhao Yuan
- Department of General Surgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang 332007, Jiangxi, China
| |
Collapse
|
5
|
Saatci O, Alam R, Huynh-Dam KT, Isik A, Uner M, Belder N, Ersan PG, Cetin M, Tokat UM, Gedik ME, Bal H, Sahin OS, Riazalhosseini Y, Thieffry D, Gautheret D, Ogretmen B, Aksoy S, Uner A, Akyol A, Sahin O. Targeting LINC00152 activates cAMP/Ca 2+/ferroptosis axis and overcomes tamoxifen resistance in ER+ breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.05.565697. [PMID: 38496603 PMCID: PMC10942410 DOI: 10.1101/2023.11.05.565697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Tamoxifen has been the mainstay therapy to treat early, locally advanced, and metastatic estrogen receptor-positive (ER+) breast cancer, constituting around 75% of all cases. However, emergence of resistance is common, necessitating the identification of novel therapeutic targets. Here, we demonstrated that long-noncoding RNA LINC00152 confers tamoxifen resistance via blocking tamoxifen-induced ferroptosis, an iron-mediated cell death. Mechanistically, inhibiting LINC00152 reduces the mRNA stability of phosphodiesterase 4D (PDE4D), leading to activation of cAMP/PKA/CREB axis and increased expression of TRPC1 Ca2+ channel. This causes cytosolic Ca2+ overload and generation of reactive oxygen species (ROS) that is, on one hand, accompanied by downregulation of FTH1, a member of the iron sequestration unit, thus increasing intracellular Fe2+ levels; and on the other hand, inhibition of the peroxidase activity upon reduced GPX4 and xCT levels. These ultimately induce lipid peroxidation and ferroptotic cell death in combination with tamoxifen. Overexpressing PDE4D rescues LINC00152 inhibition-mediated tamoxifen sensitization by de-activating the cAMP/Ca2+/ferroptosis axis. Importantly, high LINC00152 expression is significantly correlated with high PDE4D/low ferroptosis and worse survival in multiple cohorts of tamoxifen- or tamoxifen-containing endocrine therapy-treated ER+ breast cancer patients. Overall, we identified LINC00152 inhibition as a novel mechanism of ferroptosis induction and tamoxifen sensitization, thereby revealing LINC00152 and its effectors as actionable therapeutic targets to improve clinical outcome in refractory ER+ breast cancer.
Collapse
Affiliation(s)
- Ozge Saatci
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Rashed Alam
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Kim-Tuyen Huynh-Dam
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Aynur Isik
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, TURKEY
| | - Meral Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, TURKEY
| | - Nevin Belder
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, TURKEY
| | - Pelin Gulizar Ersan
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, TURKEY
| | - Metin Cetin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Unal Metin Tokat
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, TURKEY
| | - Mustafa Emre Gedik
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Hilal Bal
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, TURKEY
| | - Ozlem Sener Sahin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, Quebec, CANADA
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Quebec, CANADA
| | - Denis Thieffry
- Département de biologie de l'Ecole normale supérieure, PSL Université, 75005 Paris, FRANCE
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91190, Gifsur-Yvette, FRANCE
| | - Besim Ogretmen
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Sercan Aksoy
- Department of Medical Oncology, Hacettepe University Cancer Institute, 06100, Ankara, TURKEY
| | - Aysegul Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, TURKEY
| | - Aytekin Akyol
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, TURKEY
| | - Ozgur Sahin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| |
Collapse
|
6
|
Pordel S, Khorrami M, Saadatpour F, Rezaee D, Cho WC, Jahani S, Aghaei-Zarch SM, Hashemi E, Najafi S. The role of microRNA-185 in the pathogenesis of human diseases: A focus on cancer. Pathol Res Pract 2023; 249:154729. [PMID: 37639952 DOI: 10.1016/j.prp.2023.154729] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/29/2023] [Indexed: 08/31/2023]
Abstract
MicroRNAs (miRNAs) are a widely-studied class of non-coding RNAs characterized by their short length (18-25 nucleotides). The precise functions of miRNAs are not well-elucidated; however, an increasing number of studies suggest their involvement in various physiologic processes and deregulation in pathologic conditions. miRNA-185 (miR-185) is among the mostly-studied miRNAs in human diseases, which is found to play putative roles in conditions like metabolic disorders, asthma, frailty, schizophrenia, and hepatitis. Notably, many cancer studies report the downregulation of miR-185 in cell lines, tumor tissues, and plasma specimens of patients, while it demonstrates a suppressing role on the malignant properties of cancer cells in vitro and in vivo. Accordingly, miR-185 can be considered a tumor suppressor miRNA in human malignancies, while a few studies also report inconsistent findings. Being suggested as a prognostic/diagnostic biomarker, mi-185 is also found to offer clinical potentials, particularly for early diagnosis and prediction of the prognosis of cancer patients. In this review, we have outlined the studies that have evaluated the functions and clinical significance of miR-185 in different human diseases with a particular focus on cancer.
Collapse
Affiliation(s)
- Safoora Pordel
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Immunology and Allergy, The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Saadatpour
- Pharmaceutical Biotechnology Lab, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong, China
| | | | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elham Hashemi
- Department of Anatomical Sciences, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
7
|
Yang Q, Wang Y, Liu T, Wu C, Li J, Cheng J, Wei W, Yang F, Zhou L, Zhang Y, Yang S, Dong H. Microneedle Array Encapsulated with Programmed DNA Hydrogels for Rapidly Sampling and Sensitively Sensing of Specific MicroRNA in Dermal Interstitial Fluid. ACS NANO 2022; 16:18366-18375. [PMID: 36326107 DOI: 10.1021/acsnano.2c06261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Author: Please verify that the changes made to improve the English still retain your original meaning.Detection of microRNA (miRNA) in dermal interstitial fluid (ISF) has emerged as clinically useful in health status monitoring. However, it remains a great challenge owing to the difficult sampling and low abundance. Here, we report a DNA hydrogel microneedles (MNs) array to realize rapid enrichment and sensitive detection of miRNA in ISF. The MNs' patch consists of methacrylate hyaluronic acid (MeHA) equipped with a smart DNA circuit hydrogels' system (MeHA/DNA), in which an appropriate miRNA input enables triggering a cascading toehold-mediated DNA displacement reaction to catalytically cleave cross-linking points to generate amplified fluorescence (FL) for miRNA detection. The MeHA/DNA-MNs patch with high mechanical strength can extract adequate ISF in a short time (0.97 ± 0.2 mg in 5 min) in vivo because of its supreme water affinity. Additionally, the cascading toehold-mediated DNA displacement signal amplification reaction allows for sensitive detection of the low-abundant miRNAs down to 241.56 pM. The DNA hydrogels' MNs present potential for minimally invasive personalized diagnosis and real-time health monitoring in clinical applications.
Collapse
Affiliation(s)
- Qiqi Yang
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Guangdong 518060, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Yeyu Wang
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Guangdong 518060, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Tengfei Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Chaoxiong Wu
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Guangdong 518060, P.R. China
| | - Jinze Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Jiale Cheng
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Guangdong 518060, P.R. China
| | - Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Fan Yang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Yufan Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Shuangshuang Yang
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Guangdong 518060, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Haifeng Dong
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Guangdong 518060, P.R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Department of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| |
Collapse
|
8
|
Balihodzic A, Prinz F, Dengler MA, Calin GA, Jost PJ, Pichler M. Non-coding RNAs and ferroptosis: potential implications for cancer therapy. Cell Death Differ 2022; 29:1094-1106. [PMID: 35422492 PMCID: PMC9177660 DOI: 10.1038/s41418-022-00998-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022] Open
Abstract
Ferroptosis is a recently defined form of regulated cell death, which is biochemically and morphologically distinct from traditional forms of programmed cell death such as apoptosis or necrosis. It is driven by iron, reactive oxygen species, and phospholipids that are oxidatively damaged, ultimately resulting in mitochondrial damage and breakdown of membrane integrity. Numerous cellular signaling pathways and molecules are involved in the regulation of ferroptosis, including enzymes that control the cellular redox status. Alterations in the ferroptosis-regulating network can contribute to the development of various diseases, including cancer. Evidence suggests that ferroptosis is commonly suppressed in cancer cells, allowing them to survive and progress. However, cancer cells which are resistant to common chemotherapeutic drugs seem to be highly susceptible to ferroptosis inducers, highlighting the great potential of pharmacologic modulation of ferroptosis for cancer treatment. Non-coding RNAs (ncRNAs) are considered master regulators of various cellular processes, particularly in cancer where they have been implicated in all hallmarks of cancer. Recent work also demonstrated their involvement in the molecular control of ferroptosis. Hence, ncRNA-based therapeutics represent an exciting alternative to modulate ferroptosis for cancer therapy. This review summarizes the ncRNAs implicated in the regulation of ferroptosis in cancer and highlights their underlying molecular mechanisms in the light of potential therapeutic applications.
Collapse
Affiliation(s)
- Amar Balihodzic
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria.,Research Unit "Non-Coding RNAs and Genome Editing in Cancer", Division of Oncology, Medical University of Graz, 8036, Graz, Austria
| | - Felix Prinz
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria.,Research Unit "Non-Coding RNAs and Genome Editing in Cancer", Division of Oncology, Medical University of Graz, 8036, Graz, Austria
| | - Michael A Dengler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Philipp J Jost
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria.,Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Pichler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria. .,Research Unit "Non-Coding RNAs and Genome Editing in Cancer", Division of Oncology, Medical University of Graz, 8036, Graz, Austria. .,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| |
Collapse
|
9
|
Zhou R, Luo Z, Yin G, Yu L, Zhong H. MiR-556-5p modulates migration, invasion, and epithelial-mesenchymal transition in breast cancer cells via targeting PTHrP. J Mol Histol 2022; 53:297-308. [PMID: 35000027 DOI: 10.1007/s10735-021-10056-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 12/29/2021] [Indexed: 01/19/2023]
Abstract
Breast cancer bone metastases may block normal bone remodeling and promote bone degradation, during which several signaling pathways and small non-coding miRNAs might all play a role. miRNAs and target mRNAs that might be associated with breast cancer bone metastasis were analyzed and selected using bioinformatics analyses based on online data. The 3' untranslated region of key factors associated with breast cancer metastasis were examined for candidate miRNA binding site using Targetscan. The predicted binding was validated. The specific effects of single miRNA and dynamic effects of the miRNA-mRNA axis on breast cancer cell metastasis were investigated. miR-556-5p was downregulated in breast cancer samples according to online datasets and experimental analyses. In breast cancer cells, miR-556-5p overexpression inhibited, whereas miR-556-5p inhibition promoted cancer cell invasion and migration. Among key factors associated with breast cancer bone metastasis, parathyroid hormone related protein (PTHrP) 3'UTR possessed miR-556-5p binding site. Through direct binding, miR-556-5p negatively regulated PTHrP expression. In breast cancer cell lines, miR-556-5p inhibition promoted, whereas PTHrP silencing suppressed cancer cell migration, invasion, and epithelial-mesenchymal transition; the effects of miR-556-5p inhibition were partially reversed by PTHrP silencing. In summary, miR-556-5p targets PTHrP to modulate the cell migration and invasion of breast cancer.
Collapse
Affiliation(s)
- Rongjun Zhou
- Department of Surgery, Changsha Hospital for Maternal and Child Health Care, No. 416 Chengnan East Road, Yuhua District, Changsha, 410007, Hunan, China.
| | - Zhen Luo
- Department of General Surgery, The First Hospital of Changsha, Changsha, 410005, Hunan, China
| | - Guanqun Yin
- Department of Surgery, Changsha Hospital for Maternal and Child Health Care, No. 416 Chengnan East Road, Yuhua District, Changsha, 410007, Hunan, China
| | - Lanting Yu
- Department of Surgery, Changsha Hospital for Maternal and Child Health Care, No. 416 Chengnan East Road, Yuhua District, Changsha, 410007, Hunan, China
| | - Hao Zhong
- Department of Surgery, Changsha Hospital for Maternal and Child Health Care, No. 416 Chengnan East Road, Yuhua District, Changsha, 410007, Hunan, China
| |
Collapse
|
10
|
Cesar ASM, Regitano LCA, Reecy JM, Poleti MD, Oliveira PSN, de Oliveira GB, Moreira GCM, Mudadu MA, Tizioto PC, Koltes JE, Fritz-Waters E, Kramer L, Garrick D, Beiki H, Geistlinger L, Mourão GB, Zerlotini A, Coutinho LL. Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. BMC Genomics 2018; 19:499. [PMID: 29945546 PMCID: PMC6020320 DOI: 10.1186/s12864-018-4871-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/14/2018] [Indexed: 12/21/2022] Open
Abstract
Background Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a whole genome scale. Intramuscular fat (IMF) content and carcass composition play important roles in metabolic and physiological processes in mammals because they influence insulin sensitivity and consequently prevalence of metabolic diseases such as obesity and type 2 diabetes. However, limited information is available on the genetic variants and mechanisms associated with IMF deposition in mammals. Thus, our hypothesis was that eQTL analyses could identify putative regulatory regions and transcription factors (TFs) associated with intramuscular fat (IMF) content traits. Results We performed an integrative eQTL study in skeletal muscle to identify putative regulatory regions and factors associated with intramuscular fat content traits. Data obtained from skeletal muscle samples of 192 animals was used for association analysis between 461,466 SNPs and the transcription level of 11,808 genes. This yielded 1268 cis- and 10,334 trans-eQTLs, among which we identified nine hotspot regions that each affected the expression of > 119 genes. These putative regulatory regions overlapped with previously identified QTLs for IMF content. Three of the hotspots respectively harbored the transcription factors USF1, EGR4 and RUNX1T1, which are known to play important roles in lipid metabolism. From co-expression network analysis, we further identified modules significantly correlated with IMF content and associated with relevant processes such as fatty acid metabolism, carbohydrate metabolism and lipid metabolism. Conclusion This study provides novel insights into the link between genotype and IMF content as evident from the expression level. It thereby identifies genomic regions of particular importance and associated regulatory factors. These new findings provide new knowledge about the biological processes associated with genetic variants and mechanisms associated with IMF deposition in mammals. Electronic supplementary material The online version of this article (10.1186/s12864-018-4871-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Mirele D Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | | | - Gabriel C M Moreira
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Polyana C Tizioto
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Elyn Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Dorian Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Hamid Beiki
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
| |
Collapse
|
11
|
Lerner E, Cordes T, Ingargiol A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 2018; 359:eaan1133. [PMID: 29348210 PMCID: PMC6200918 DOI: 10.1126/science.aan1133] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
Collapse
Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Antonino Ingargiol
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yazan Alhadid
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
12
|
De Lacorte Singulani J, De Fátima Da Silva J, Gullo FP, Costa MC, Fusco-Almeida AM, Enguita FJ, Mendes-Giannini MJS. Preliminary evaluation of circulating microRNAs as potential biomarkers in paracoccidioidomycosis. Biomed Rep 2017; 6:353-357. [PMID: 28451399 DOI: 10.3892/br.2017.849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/09/2017] [Indexed: 01/19/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNAs (length, 19-24 nucleotides) that regulate gene expression by either mRNA degradation or translational inhibition of proteins. Circulating miRNAs, which are extremely stable and protected from RNAse-mediated degradation in body fluids, have appeared as candidate biomarkers for numerous diseases. However, little is known about circulating miRNAs in fungal infections. Paracoccidioidomycosis (PCM) is caused by the Paracoccidioides species, and is endemic in Central and South America, with predominance in adult male workers from rural areas. The current study aimed to identify a serum miRNA expression profile that could serve as a novel diagnostic biomarker for PCM. Total RNA was isolated and the levels of circulating miRNAs were compared between patients with PCM and healthy control subjects using reverse transcription-quantitative polymerase chain reaction. Bioinformatic analysis was used to evaluate the potential roles of these miRNAs in PCM. Eight miRNAs were differentially expressed in serum samples from patients with PCM. These miRNAs are associated with apoptosis and immune response. The identified miRNAs facilitate with understanding the regulatory mechanisms involved in the host-parasite interaction of PCM. Furthermore, considering that the diagnosis of PCM presents difficulties, these miRNAs may serve as novel biomarkers for this disease.
Collapse
Affiliation(s)
- Junya De Lacorte Singulani
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo 14800-901, Brazil
| | - Julhiany De Fátima Da Silva
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo 14800-901, Brazil
| | - Fernanda Patricia Gullo
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo 14800-901, Brazil
| | - Marina Célia Costa
- Faculty of Medicine, Institute of Molecular Medicine, University of Lisbon, 1649-004 Lisbon, Portugal
| | - Ana Marisa Fusco-Almeida
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo 14800-901, Brazil
| | - Francisco Javier Enguita
- Faculty of Medicine, Institute of Molecular Medicine, University of Lisbon, 1649-004 Lisbon, Portugal
| | - Maria José Soares Mendes-Giannini
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo 14800-901, Brazil
| |
Collapse
|
13
|
Abstract
With the impressive advancement in high-throughput 'omics' technologies over the past two decades, epigenetic mechanisms have emerged as the regulatory interface between the genome and environmental factors. These mechanisms include DNA methylation, histone modifications, ATP-dependent chromatin remodeling and RNA-based mechanisms. Their highly interdependent and coordinated action modulates the chromatin structure controlling access of the transcription machinery and thereby regulating expression of target genes. Given the rather limited proliferative capability of human cardiomyocytes, epigenetic regulation appears to play a particularly important role in the myocardium. The highly dynamic nature of the epigenome allows the heart to adapt to environmental challenges and to respond quickly and properly to cardiac stress. It is now becoming evident that histone-modifying and chromatin-remodeling enzymes as well as numerous non-coding RNAs play critical roles in cardiac development and function, while their dysregulation contributes to the onset and development of pathological cardiac remodeling culminating in HF. This review focuses on up-to-date knowledge about the epigenetic mechanisms and highlights their emerging role in the healthy and failing heart. Uncovering the determinants of epigenetic regulation holds great promise to accelerate the development of successful new diagnostic and therapeutic strategies in human cardiac disease.
Collapse
Affiliation(s)
- José Marín-García
- The Molecular Cardiology and Neuromuscular Institute, 75 Raritan Ave., Highland Park, NJ, 08904, USA,
| | | |
Collapse
|
14
|
Vachirayonstien T, Yan B. MicroRNA-30c-1-3p is a silencer of the pregnane X receptor by targeting the 3'-untranslated region and alters the expression of its target gene cytochrome P450 3A4. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1238-1244. [PMID: 27085140 DOI: 10.1016/j.bbagrm.2016.03.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/17/2016] [Accepted: 03/30/2016] [Indexed: 01/07/2023]
Abstract
The pregnane X receptor (PXR) is a master regulator of genes involved in drug elimination. Recently, activation of PXR has also been linked to the development of many disease conditions such as metabolic disorders and malignancies. MicroRNAs (miRs) emerge as important molecular species involved in these conditions. This study was undertaken to test a large number of miRs for their ability to regulate PXR expression. As many as 58 miRs were tested and miR-30c-1-3p was identified to suppress PXR expression. The suppression was achieved by targeting the 3'-untranslated region, 438 nucleotides from the stop codon. The suppression was detected in multiple cell lines from different organ origins. In addition, miR-30c-1-3p altered basal and induced expression of cytochrome P450 3A4 (CYP3A4), a prototypical target gene of PXR. The alteration varied depending on the time and amounts of miR-30c-1-3p. CYP3A4 is responsible for the metabolism of more than 50% medicines. The interconnection between miR-30c-1-3p and PXR signifies a role of miRs in drug-drug interactions and chemosensitivity. This article is part of a Special Issue entitled: Xenobiotic nuclear receptors: New Tricks for An Old Dog, edited by Dr. Wen Xie.
Collapse
Affiliation(s)
- Thaveechai Vachirayonstien
- Department of Biomedical and Pharmaceutical Sciences, Center for Integrated Drug Development, University of Rhode Island, Kingston, RI 02881, United States
| | - Bingfang Yan
- Department of Biomedical and Pharmaceutical Sciences, Center for Integrated Drug Development, University of Rhode Island, Kingston, RI 02881, United States.
| |
Collapse
|
15
|
Abstract
Hematopoiesis is a dynamic process in which blood cells are continuously generated from hematopoietic stem cells (HSCs). The regulatory mechanisms controlling HSC fate have been studied extensively over the past several decades. Although many protein-coding genes have been shown to regulate hematopoietic differentiation, additional levels of HSC regulation are not well studied. Advances in deep sequencing have revealed many new classes of regulatory noncoding RNAs (ncRNAs), such as enhancer RNAs and antisense ncRNAs. Functional analysis of some of these ncRNAs has provided insights into the molecular mechanisms that regulate hematopoietic development and disease. In this review, we summarize recent advances in our understanding of functional regulatory ncRNAs associated with hematopoietic self-renewal and differentiation, as well as those dysregulated ncRNAs involved in hematologic malignancies.
Collapse
|
16
|
Langie SAS, Koppen G, Desaulniers D, Al-Mulla F, Al-Temaimi R, Amedei A, Azqueta A, Bisson WH, Brown DG, Brunborg G, Charles AK, Chen T, Colacci A, Darroudi F, Forte S, Gonzalez L, Hamid RA, Knudsen LE, Leyns L, Lopez de Cerain Salsamendi A, Memeo L, Mondello C, Mothersill C, Olsen AK, Pavanello S, Raju J, Rojas E, Roy R, Ryan EP, Ostrosky-Wegman P, Salem HK, Scovassi AI, Singh N, Vaccari M, Van Schooten FJ, Valverde M, Woodrick J, Zhang L, van Larebeke N, Kirsch-Volders M, Collins AR. Causes of genome instability: the effect of low dose chemical exposures in modern society. Carcinogenesis 2015; 36 Suppl 1:S61-88. [PMID: 26106144 DOI: 10.1093/carcin/bgv031] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus, genome instability can be defined as an enhanced tendency for the genome to acquire mutations; ranging from changes to the nucleotide sequence to chromosomal gain, rearrangements or loss. This review raises the hypothesis that in addition to known human carcinogens, exposure to low dose of other chemicals present in our modern society could contribute to carcinogenesis by indirectly affecting genome stability. The selected chemicals with their mechanisms of action proposed to indirectly contribute to genome instability are: heavy metals (DNA repair, epigenetic modification, DNA damage signaling, telomere length), acrylamide (DNA repair, chromosome segregation), bisphenol A (epigenetic modification, DNA damage signaling, mitochondrial function, chromosome segregation), benomyl (chromosome segregation), quinones (epigenetic modification) and nano-sized particles (epigenetic pathways, mitochondrial function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make scientists aware of the increasing need to unravel the underlying mechanisms via which chemicals at low doses can induce genome instability and thus promote carcinogenesis.
Collapse
Affiliation(s)
- Sabine A S Langie
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium, Health Canada, Environmental Health Sciences and Research Bureau, Environmental Health Centre, Ottawa, Ontario K1A0K9, Canada, Department of Pathology, Kuwait University, Safat 13110, Kuwait, Department of Experimental and Clinical Medicine, University of Firenze, Florence 50134, Italy, Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Navarra, Pamplona 31009, Spain, Environmental and Molecular Toxicology, Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA, Department of Environmental and Radiological Health Sciences/Food Science and Human Nutrition, College of Veterinary Medicine and Biomedical Sciences, Colorado State University/Colorado School of Public Health, Fort Collins, CO 80523-1680, USA, Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, PO Box 4404, N-0403 Oslo, Norway, Hopkins Building, School of Biological Sciences, University of Reading, Reading, Berkshire RG6 6UB, UK, Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA, Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, Bologna 40126, Italy, Human and Environmental Safety Research, Department of Health Sciences, College of North Atlantic, Doha, State of Qatar, Mediterranean Institute of Oncology, 95029 Viagrande, Italy, Laboratory for Cell Genetics, Vrije Universiteit Brussel, Brussels 1050, Belgium, Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra, Serdang 43400, Selangor, Malaysia, University of Copenhagen, Department of Public Health, Copenhagen 1353, Denmark, Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy, Medical Phys
| | - Gudrun Koppen
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium, Health Canada, Environmental Health Sciences and Research Bureau, Environmental Health Centre, Ottawa, Ontario K1A0K9, Canada, Department of Pathology, Kuwait University, Safat 13110, Kuwait, Department of Experimental and Clinical Medicine, University of Firenze, Florence 50134, Italy, Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Navarra, Pamplona 31009, Spain, Environmental and Molecular Toxicology, Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA, Department of Environmental and Radiological Health Sciences/Food Science and Human Nutrition, College of Veterinary Medicine and Biomedical Sciences, Colorado State University/Colorado School of Public Health, Fort Collins, CO 80523-1680, USA, Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, PO Box 4404, N-0403 Oslo, Norway, Hopkins Building, School of Biological Sciences, University of Reading, Reading, Berkshire RG6 6UB, UK, Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA, Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, Bologna 40126, Italy, Human and Environmental Safety Research, Department of Health Sciences, College of North Atlantic, Doha, State of Qatar, Mediterranean Institute of Oncology, 95029 Viagrande, Italy, Laboratory for Cell Genetics, Vrije Universiteit Brussel, Brussels 1050, Belgium, Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra, Serdang 43400, Selangor, Malaysia, University of Copenhagen, Department of Public Health, Copenhagen 1353, Denmark, Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy, Medical Phys
| | - Daniel Desaulniers
- Health Canada, Environmental Health Sciences and Research Bureau, Environmental Health Centre, Ottawa, Ontario K1A0K9, Canada
| | - Fahd Al-Mulla
- Department of Pathology, Kuwait University, Safat 13110, Kuwait
| | | | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Firenze, Florence 50134, Italy
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Navarra, Pamplona 31009, Spain
| | - William H Bisson
- Environmental and Molecular Toxicology, Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA
| | - Dustin G Brown
- Department of Environmental and Radiological Health Sciences/Food Science and Human Nutrition, College of Veterinary Medicine and Biomedical Sciences, Colorado State University/Colorado School of Public Health, Fort Collins, CO 80523-1680, USA
| | - Gunnar Brunborg
- Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, PO Box 4404, N-0403 Oslo, Norway
| | - Amelia K Charles
- Hopkins Building, School of Biological Sciences, University of Reading, Reading, Berkshire RG6 6UB, UK
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Annamaria Colacci
- Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, Bologna 40126, Italy
| | - Firouz Darroudi
- Human and Environmental Safety Research, Department of Health Sciences, College of North Atlantic, Doha, State of Qatar
| | - Stefano Forte
- Mediterranean Institute of Oncology, 95029 Viagrande, Italy
| | - Laetitia Gonzalez
- Laboratory for Cell Genetics, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Roslida A Hamid
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, University Putra, Serdang 43400, Selangor, Malaysia
| | - Lisbeth E Knudsen
- University of Copenhagen, Department of Public Health, Copenhagen 1353, Denmark
| | - Luc Leyns
- Laboratory for Cell Genetics, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | | | - Lorenzo Memeo
- Mediterranean Institute of Oncology, 95029 Viagrande, Italy
| | - Chiara Mondello
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - Carmel Mothersill
- Medical Physics & Applied Radiation Sciences, McMaster University, Hamilton, Ontario L8S4L8, Canada
| | - Ann-Karin Olsen
- Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, PO Box 4404, N-0403 Oslo, Norway
| | - Sofia Pavanello
- Department of Cardiac, Thoracic and Vascular Sciences, Unit of Occupational Medicine, University of Padova, Padova 35128, Italy
| | - Jayadev Raju
- Toxicology Research Division, Bureau of Chemical Safety Food Directorate, Health Products and Food Branch Health Canada, Ottawa, Ontario K1A0K9, Canada
| | - Emilio Rojas
- Departamento de Medicina Genomica y Toxicologia Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de México, México CP 04510, México
| | - Rabindra Roy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences/Food Science and Human Nutrition, College of Veterinary Medicine and Biomedical Sciences, Colorado State University/Colorado School of Public Health, Fort Collins, CO 80523-1680, USA
| | - Patricia Ostrosky-Wegman
- Departamento de Medicina Genomica y Toxicologia Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de México, México CP 04510, México
| | - Hosni K Salem
- Urology Department, kasr Al-Ainy School of Medicine, Cairo University, El Manial, Cairo 12515, Egypt
| | - A Ivana Scovassi
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - Neetu Singh
- Centre for Advanced Research, King George's Medical University, Chowk, Lucknow 226003, Uttar Pradesh, India
| | - Monica Vaccari
- Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, Bologna 40126, Italy
| | - Frederik J Van Schooten
- Department of Toxicology, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht University, 6200MD, PO Box 61, Maastricht, The Netherlands
| | - Mahara Valverde
- Departamento de Medicina Genomica y Toxicologia Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de México, México CP 04510, México
| | - Jordan Woodrick
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720-7360, USA
| | - Nik van Larebeke
- Laboratory for Analytical and Environmental Chemistry, Vrije Universiteit Brussel, Brussels 1050, Belgium, Study Centre for Carcinogenesis and Primary Prevention of Cancer, Ghent University, Ghent 9000, Belgium
| | | | | |
Collapse
|
17
|
Zhang Q, Xu M, Qu Y, Li Z, Zhang Q, Cai X, Lu L. Analysis of the differential expression of circulating microRNAs during the progression of hepatic fibrosis in patients with chronic hepatitis B virus infection. Mol Med Rep 2015; 12:5647-54. [PMID: 26299203 PMCID: PMC4581744 DOI: 10.3892/mmr.2015.4221] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 05/08/2015] [Indexed: 01/06/2023] Open
Abstract
Considering the limitations of liver biopsy, reliable non‑invasive serum biomarkers of liver fibrosis are required for early diagnosis. The present study analyzed the expression profile of circulating micro (mi)RNAs during the development and progression of hepatic fibrosis in patients with chronic hepatitis B virus (HBV) infection, aiming to identify novel earlier diagnostic biomarkers. Fresh plasma samples were collected from 50 patients diagnosed with chronic HBV infection and hepatic fibrosis. These patients were classified into five groups (S0, S1, S2, S3 and S4; n=10 per group) based on Scheuer's staging criteria. The differential expression of the circulating miRNAs was determined by performing miRNA microarray hybridization. Finally, the target genes of the miRNAs were predicted and classified using gene ontology analysis. A total of 140 miRNAs were detected in the S1‑S4 patient groups, and their expression levels were >2‑fold higher compared with those in the S0 group. The numbers of miRNAs differentially expressed in the S1‑S4 patient groups were 48, 97, 84 and 56, respectively, with 12 miRNAs differentially expressed at all stages, 10 of which were upregulated and two of which were downregulated. The target genes of the miRNAs identified were found to be involved in 100 signal transduction pathways, the majority of which affected hepatic fibrosis via the TGF‑/Smad, Wnt, MAPK, Jak/STAT and VEGF pathways. The differential expression levels of miRNAs were closely associated with the staging of hepatic fibrosis. The results of the present study provide evidence to facilitate the development and application of non‑invasive biomarkers for earlier diagnosis of hepatic fibrosis.
Collapse
Affiliation(s)
- Qingqing Zhang
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Mingyi Xu
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Ying Qu
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Zhenghong Li
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Qidi Zhang
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Xiaobo Cai
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Lungen Lu
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| |
Collapse
|
18
|
Khorkova O, Hsiao J, Wahlestedt C. Basic biology and therapeutic implications of lncRNA. Adv Drug Deliv Rev 2015; 87:15-24. [PMID: 26024979 PMCID: PMC4544752 DOI: 10.1016/j.addr.2015.05.012] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 05/11/2015] [Accepted: 05/21/2015] [Indexed: 12/11/2022]
Abstract
Long non-coding RNAs (lncRNA), a class of non-coding RNA molecules recently identified largely due to the efforts of FANTOM, and later GENCODE and ENCODE consortia, have been a subject of intense investigation in the past decade. Extensive efforts to get deeper understanding of lncRNA biology have yielded evidence of their diverse structural and regulatory roles in protecting chromosome integrity, maintaining genomic architecture, X chromosome inactivation, imprinting, transcription, translation and epigenetic regulation. Here we will briefly review the recent studies in the field of lncRNA biology focusing mostly on mammalian species and discuss their therapeutic implications.
Collapse
MESH Headings
- Animals
- Chromosomal Instability
- Epigenesis, Genetic
- Evolution, Molecular
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/genetics
- Genetic Diseases, Inborn/diagnosis
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/therapy
- Humans
- Neoplasms/diagnosis
- Neoplasms/genetics
- Neoplasms/therapy
- Oligonucleotides, Antisense/administration & dosage
- Oligonucleotides, Antisense/therapeutic use
- RNA Processing, Post-Transcriptional
- RNA, Long Noncoding/blood
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/urine
- Species Specificity
- Telomere/genetics
Collapse
Affiliation(s)
- O Khorkova
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - J Hsiao
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - C Wahlestedt
- Center for Therapeutic Innovation and the Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami 33136, FL, USA.
| |
Collapse
|
19
|
Circulating microRNAs: emerging biomarkers for diagnosis and prognosis in patients with gastrointestinal cancers. Clin Sci (Lond) 2014; 128:1-15. [PMID: 25168167 DOI: 10.1042/cs20140089] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To identify novel non-invasive biomarkers for improved detection, risk assessment and prognostic evaluation of cancer, expression profiles of circulating microRNAs are currently under evaluation. Circulating microRNAs are highly promising candidates in this context, as they present some key characteristics for cancer biomarkers: they are tissue-specific with reproducible expression and consistency among individuals from the same species, they are potentially derived directly from the tumour and therefore might correlate with tumour progression and recurrence, and they are bound to proteins or contained in subcellular particles, such as microvesicles or exosomes, making them highly stable and resistant to degradation. The present review highlights the origin of circulating microRNAs, their stability in blood samples, and techniques to isolate exosomal microRNAs, and then addresses the current evidence supporting potential clinical applications of circulating miRNAs for diagnostic and prognostic purposes.
Collapse
|
20
|
Matuszcak C, Haier J, Hummel R, Lindner K. MicroRNAs: Promising chemoresistance biomarkers in gastric cancer with diagnostic and therapeutic potential. World J Gastroenterol 2014; 20:13658-13666. [PMID: 25320504 PMCID: PMC4194550 DOI: 10.3748/wjg.v20.i38.13658] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/29/2014] [Accepted: 05/26/2014] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is the fourth most common cancer worldwide and ranks second in global cancer mortality statistics. Perioperative chemotherapy plays an important role in the management and treatment of advanced stage disease. However, response to chemotherapy varies widely, with some patients presenting no or only minor response to treatment. Hence, chemotherapy resistance is a major clinical problem that impacts on outcome. Unfortunately, to date there are no reliable biomarkers available that predict response to chemotherapy before the start of the treatment, or that allow modification of chemotherapy resistance. MicroRNAs (miRNAs) could provide an answer to this problem. miRNAs are involved in the initiation and progression of a variety of cancer types, and there is evidence that miRNAs impact on resistance towards chemotherapeutic drugs as well. This current review aims to provide an overview about the potential clinical applicability of miRNAs as biomarkers for chemoresistance in GC. The authors focus in this context on the potential of miRNAs to predict sensitivity towards different chemotherapeutics, and on the potential of miRNAs to modulate sensitivity and resistance towards chemotherapy in GC.
Collapse
|
21
|
Gupta Y, Witte M, Möller S, Ludwig RJ, Restle T, Zillikens D, Ibrahim SM. ptRNApred: computational identification and classification of post-transcriptional RNA. Nucleic Acids Res 2014; 42:e167. [PMID: 25303994 PMCID: PMC4267668 DOI: 10.1093/nar/gku918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED Non-coding RNAs (ncRNAs) are known to play important functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as classification tools, offer a fast and reliable way for such screening and multiple classifiers have already been developed to predict well-defined subfamilies of RNA. So far, however, out of all the ncRNAs, only tRNA, miRNA and snoRNA can be predicted with a satisfying sensitivity and specificity. We here present ptRNApred, a tool to detect and classify subclasses of non-coding RNA that are involved in the regulation of post-transcriptional modifications or DNA replication, which we here call post-transcriptional RNA (ptRNA). It (i) detects RNA sequences coding for post-transcriptional RNA from the genomic sequence with an overall sensitivity of 91% and a specificity of 94% and (ii) predicts ptRNA-subclasses that exist in eukaryotes: snRNA, snoRNA, RNase P, RNase MRP, Y RNA or telomerase RNA. AVAILABILITY The ptRNApred software is open for public use on http://www.ptrnapred.org/.
Collapse
Affiliation(s)
- Yask Gupta
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Mareike Witte
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Steffen Möller
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Ralf J Ludwig
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Tobias Restle
- Institute for Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Saleh M Ibrahim
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| |
Collapse
|
22
|
Dorweiler JE, Ni T, Zhu J, Munroe SH, Anderson JT. Certain adenylated non-coding RNAs, including 5' leader sequences of primary microRNA transcripts, accumulate in mouse cells following depletion of the RNA helicase MTR4. PLoS One 2014; 9:e99430. [PMID: 24926684 PMCID: PMC4057207 DOI: 10.1371/journal.pone.0099430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/14/2014] [Indexed: 12/30/2022] Open
Abstract
RNA surveillance plays an important role in posttranscriptional regulation. Seminal work in this field has largely focused on yeast as a model system, whereas exploration of RNA surveillance in mammals is only recently begun. The increased transcriptional complexity of mammalian systems provides a wider array of targets for RNA surveillance, and, while many questions remain unanswered, emerging data suggest the nuclear RNA surveillance machinery exhibits increased complexity as well. We have used a small interfering RNA in mouse N2A cells to target the homolog of a yeast protein that functions in RNA surveillance (Mtr4p). We used high-throughput sequencing of polyadenylated RNAs (PA-seq) to quantify the effects of the mMtr4 knockdown (KD) on RNA surveillance. We demonstrate that overall abundance of polyadenylated protein coding mRNAs is not affected, but several targets of RNA surveillance predicted from work in yeast accumulate as adenylated RNAs in the mMtr4KD. microRNAs are an added layer of transcriptional complexity not found in yeast. After Drosha cleavage separates the pre-miRNA from the microRNA's primary transcript, the byproducts of that transcript are generally thought to be degraded. We have identified the 5′ leading segments of pri-miRNAs as novel targets of mMtr4 dependent RNA surveillance.
Collapse
Affiliation(s)
- Jane E. Dorweiler
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - Ting Ni
- DNA Sequencing and Genomics Core, Genetics and Development Biology Center, National Institutes of Health, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Jun Zhu
- DNA Sequencing and Genomics Core, Genetics and Development Biology Center, National Institutes of Health, National Heart Lung and Blood Institute, Bethesda, Maryland, United States of America
| | - Stephen H. Munroe
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
- * E-mail: (JTA); (SHM)
| | - James T. Anderson
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
- * E-mail: (JTA); (SHM)
| |
Collapse
|
23
|
Kentwell J, Gundara JS, Sidhu SB. Noncoding RNAs in endocrine malignancy. Oncologist 2014; 19:483-91. [PMID: 24718512 PMCID: PMC4012972 DOI: 10.1634/theoncologist.2013-0458] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/05/2014] [Indexed: 01/22/2023] Open
Abstract
Only recently has it been uncovered that the mammalian transcriptome includes a large number of noncoding RNAs (ncRNAs) that play a variety of important regulatory roles in gene expression and other biological processes. Among numerous kinds of ncRNAs, short noncoding RNAs, such as microRNAs, have been extensively investigated with regard to their biogenesis, function, and importance in carcinogenesis. Long noncoding RNAs (lncRNAs) have only recently been implicated in playing a key regulatory role in cancer biology. The deregulation of ncRNAs has been demonstrated to have important roles in the regulation and progression of cancer development. In this review, we describe the roles of both short noncoding RNAs (including microRNAs, small nuclear RNAs, and piwi-interacting RNAs) and lncRNAs in carcinogenesis and outline the possible underlying genetic mechanisms, with particular emphasis on clinical applications. The focus of our review includes studies from the literature on ncRNAs in traditional endocrine-related cancers, including thyroid, parathyroid, adrenal gland, and gastrointestinal neuroendocrine malignancies. The current and potential future applications of ncRNAs in clinical cancer research is also discussed, with emphasis on diagnosis and future treatment.
Collapse
|
24
|
Shi C, Liu Q, Ma C, Zhong W. Exponential strand-displacement amplification for detection of microRNAs. Anal Chem 2013; 86:336-9. [PMID: 24345199 DOI: 10.1021/ac4038043] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNAs) are promising targets for disease diagnosis. However, miRNA detection requires rapid, sensitive, and selective detection to be effective as a diagnostic tool. Herein, a miRNA-initiated exponential strand-displacement amplification (SDA) assay was reported. With the Klenow fragment, nicking enzyme Nt.AlwI, and two primers, the miRNA target can trigger two cycles of nicking, polymerization, and displacement reactions. These reaction cycles amplified the target miRNA exponentially and generated dsDNAs detectable with SYBR Green I in real-time PCR. As low as 16 zmol of the target miRNA was detected by this one-pot assay within 90 min, and the dynamic range spanned over 9 orders of magnitude. Negligible impact from the complex biological matrix was observed on the amplification reaction, indicating the assay's capability to directly detect miRNAs in biofluids.
Collapse
Affiliation(s)
- Chao Shi
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, Shandong 266042, P. R. China
| | | | | | | |
Collapse
|
25
|
Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS. Biases in small RNA deep sequencing data. Nucleic Acids Res 2013; 42:1414-26. [PMID: 24198247 PMCID: PMC3919602 DOI: 10.1093/nar/gkt1021] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
High-throughput RNA sequencing (RNA-seq) is considered a powerful tool for novel gene discovery and fine-tuned transcriptional profiling. The digital nature of RNA-seq is also believed to simplify meta-analysis and to reduce background noise associated with hybridization-based approaches. The development of multiplex sequencing enables efficient and economic parallel analysis of gene expression. In addition, RNA-seq is of particular value when low RNA expression or modest changes between samples are monitored. However, recent data uncovered severe bias in the sequencing of small non-protein coding RNA (small RNA-seq or sRNA-seq), such that the expression levels of some RNAs appeared to be artificially enhanced and others diminished or even undetectable. The use of different adapters and barcodes during ligation as well as complex RNA structures and modifications drastically influence cDNA synthesis efficacies and exemplify sources of bias in deep sequencing. In addition, variable specific RNA G/C-content is associated with unequal polymerase chain reaction amplification efficiencies. Given the central importance of RNA-seq to molecular biology and personalized medicine, we review recent findings that challenge small non-protein coding RNA-seq data and suggest approaches and precautions to overcome or minimize bias.
Collapse
Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Strasse 56, 48149 Muenster, Germany and Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Penang, Malaysia
| | | | | | | |
Collapse
|
26
|
Sandoval J, Peiró-Chova L, Pallardó FV, García-Giménez JL. Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Rev Mol Diagn 2013; 13:457-71. [PMID: 23782253 DOI: 10.1586/erm.13.37] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics has emerged as a new and promising field in recent years. Lifestyle, stress, drugs, physiopathological situations and pharmacological interventions have a great impact on the epigenetic code of the cells by altering the methylome, miRNA expression and the covalent histone modifications. Since there exists a need to find new biomarkers and improve diagnosis for several diseases, the research on epigenetic biomarkers for molecular diagnostics encourages the translation of this field from the bench to clinical practice. In this context, deciphering intricate epigenetic modifications involved in several molecular processes is a challenge that will be solved in the near future. In this review, the authors present an overview of the high-throughput technologies and laboratory techniques available for epigenetic studies, and also discuss which of them are more reliable to be used in a clinical diagnostic laboratory. In addition, the authors describe the most promising epigenetic biomarkers in lung, colorectal and prostate cancer, in which most advances have been achieved. Finally, the authors describe epigenetic biomarkers in some rare diseases; these rare syndromes are paradigms for a specific impaired molecular pathway, thus providing valuable information on the discovery of new epigenetic biomarkers.
Collapse
Affiliation(s)
- Juan Sandoval
- Epigenetics and Cancer Biology, Institut d'Investigació Biomèdica de Bellvitge IDIBELL, Barcelona, Spain
| | | | | | | |
Collapse
|
27
|
MiR-205 is progressively down-regulated in lymph node metastasis but fails as a prognostic biomarker in high-risk prostate cancer. Int J Mol Sci 2013; 14:21414-34. [PMID: 24173237 PMCID: PMC3856012 DOI: 10.3390/ijms141121414] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/01/2013] [Accepted: 10/09/2013] [Indexed: 01/07/2023] Open
Abstract
The treatment of high-risk prostate cancer (HRPCa) is a tremendous challenge for uro-oncologists. The identification of predictive moleculobiological markers allowing risk assessment of lymph node metastasis and systemic progression is essential in establishing effective treatment. In the current study, we investigate the prognostic potential of miR-205 in HRPCa study and validation cohorts, setting defined clinical endpoints for both. We demonstrate miR-205 to be significantly down-regulated in over 70% of the HRPCa samples analysed and that reconstitution of miR-205 causes inhibition of proliferation and invasiveness in prostate cancer (PCa) cell lines. Additionally, miR-205 is increasingly down-regulated in lymph node metastases compared to the primary tumour indicating that miR-205 plays a role in migration of PCa cells from the original location into extraprostatic tissue. Nevertheless, down-regulation of miR-205 in primary PCa was not correlated to the synchronous presence of metastasis and failed to predict the outcome for HRPCa patients. Moreover, we found a tendency for miR-205 up-regulation to correlate with an adverse outcome of PCa patients suggesting a pivotal role of miR-205 in tumourigenesis. Overall, we showed that miR-205 is involved in the development and metastasis of PCa, but failed to work as a useful clinical biomarker in HRPCa. These findings might have implications for the use of miR-205 as a prognostic or therapeutic target in HRPCa.
Collapse
|
28
|
Li S, Ma D, Yi L, Mei S, Ouyang D, Xi Z. Terminal dual-labeling of a transcribed RNA. Bioorg Med Chem Lett 2013; 23:6304-6. [PMID: 24135725 DOI: 10.1016/j.bmcl.2013.09.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 09/09/2013] [Accepted: 09/24/2013] [Indexed: 12/22/2022]
Abstract
We report here a site-specific terminal dual-labeling strategy for a transcribed RNA. The combination of 5'-thiophosphoryl and 3'-amino functionalities enables efficient RNA dual labeling with different fluorophores at both 5'- and 3'-terminal positions specifically. This dual-labeling strategy is applied to pre-miRNA for construction of molecular beacons. The RNA beacons in their native hairpin formation bring the fluorophore and quencher groups into close proximity, leading to fluorescence quenching by FRET effect. Ribonuclease (dicer enzyme or micrococcal nuclease) can efficiently cleave RNA beacons leading to concentration- and time-dependent fluorescence increase. The dual-labeling strategy for transcribed RNAs involves only commercially available reagents, enzymes and native RNA, making it more accessible for general applications.
Collapse
Affiliation(s)
- Shibo Li
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, Nankai University, Tianjin 300071, PR China
| | | | | | | | | | | |
Collapse
|
29
|
Regulation of breast cancer and bone metastasis by microRNAs. DISEASE MARKERS 2013; 35:369-87. [PMID: 24191129 PMCID: PMC3809754 DOI: 10.1155/2013/451248] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/17/2013] [Accepted: 08/27/2013] [Indexed: 01/05/2023]
Abstract
Breast cancer progression including bone metastasis is a complex process involving numerous changes in gene expression and function. MicroRNAs (miRNAs) are small endogenous noncoding RNAs that regulate gene expression by targeting protein-coding mRNAs posttranscriptionally, often affecting a number of gene targets simultaneously. Alteration in expression of miRNAs is common in human breast cancer, possessing with either oncogenic or tumor suppressive activity. The expression and the functional role of several miRNAs (miR-206, miR-31, miR-27a/b, miR-21, miR-92a, miR-205, miR-125a/b, miR-10b, miR-155, miR-146a/b, miR-335, miR-204, miR-211, miR-7, miR-22, miR-126, and miR-17) in breast cancer has been identified. In this review we summarize the experimentally validated targets of up- and downregulated miRNAs and their regulation in breast cancer and bone metastasis for diagnostic and therapeutic purposes.
Collapse
|