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Wang T, Zhang C, Xu L, Li X. Roles of circular RNAs in osteogenic/osteoclastogenic differentiation. Biofactors 2024; 50:6-15. [PMID: 37534732 DOI: 10.1002/biof.1994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/09/2023] [Indexed: 08/04/2023]
Abstract
The process of bone remodeling occurs and is regulated through interactions between osteoclasts, which resorb bone, and osteoblasts, which generate bone tissue. When the homeostatic balance between these two cell types is dysregulated, this can contribute to abnormal bone remodeling resulting in a loss of bone mass as is observed in osteoporosis (OP) and other forms of degenerative bone metabolic diseases. At present, details of molecular mechanism underlying the development of bone metabolic diseases such as OP remain to be elucidated. Circular RNAs (circRNAs) are small non-coding RNA molecules with a closed-loop structure that can regulate the differentiation of osteoclasts and osteoblasts. The present review provides a systematic overview of recent literature on the processes through which circRNAs regulate the dynamic balance between osteoblasts and osteoclasts that ultimately preserve bone homeostasis. It will also give insight that can shape current understanding of the pathogenesis of OP and other bone metabolic diseases to better guide diagnostic and treatment strategies for affected patients.
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Affiliation(s)
- Tao Wang
- Key Laboratory of System Bio-Medicine of Jiangxi Province, Jiujiang University, Jiujiang, China
| | - Chao Zhang
- Affiliated Hospital of Jiujiang University, Jiujiang, China
| | - Lin Xu
- Key Laboratory of System Bio-Medicine of Jiangxi Province, Jiujiang University, Jiujiang, China
| | - Xingnuan Li
- Key Laboratory of System Bio-Medicine of Jiangxi Province, Jiujiang University, Jiujiang, China
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2
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Luo L, Zhen Y, Peng D, Wei C, Zhang X, Liu X, Han L, Zhang Z. The role of N6-methyladenosine-modified non-coding RNAs in the pathological process of human cancer. Cell Death Discov 2022; 8:325. [PMID: 35851061 PMCID: PMC9293946 DOI: 10.1038/s41420-022-01113-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) account for the majority of the widespread transcripts of mammalian genomes. They rarely encode proteins and peptides, but their regulatory role is crucial in numerous physiological and pathological processes. The m6A (N6-methyladenosine) modification is one of the most common internal RNA modifications in eukaryotes and is associated with all aspects of RNA metabolism. Accumulating researches have indicated a close association between m6A modification and ncRNAs, and suggested m6A-modified ncRNAs played a crucial role in tumor progression. The correlation between m6A modification and ncRNAs offers a novel perspective for investigating the potential mechanisms of cancer pathological processes, which suggests that both m6A modification and ncRNAs are critical prognostic markers and therapeutic targets in numerous malignancies. In the present report, we summarized the interaction between m6A modification and ncRNA, emphasizing how their interaction regulates pathological processes in cancer.
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Affiliation(s)
- Lin Luo
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.,Academy of medical sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yingwei Zhen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China
| | - Dazhao Peng
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Cheng Wei
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xiaoyang Zhang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.
| | - Lei Han
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China.
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.
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3
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Establishing a Prognostic Model Based on Three Genomic Instability-related LncRNAs for Clear Cell Renal Cell Cancer. Clin Genitourin Cancer 2022; 20:e317-e329. [DOI: 10.1016/j.clgc.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/17/2022]
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4
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Fatmi A, Chabni N, Cernada M, Vento M, González-López M, Aribi M, Pallardó FV, García-Giménez JL. Clinical and immunological aspects of microRNAs in neonatal sepsis. Biomed Pharmacother 2021; 145:112444. [PMID: 34808550 DOI: 10.1016/j.biopha.2021.112444] [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] [Received: 09/23/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022] Open
Abstract
Neonatal sepsis constitutes a highly relevant public health challenge and is the most common cause of infant morbidity and mortality worldwide. Recent studies have demonstrated that during infection epigenetic changes may occur leading to reprogramming of gene expression. Post-transcriptional regulation by short non-coding RNAs (e.g., microRNAs) have recently acquired special relevance because of their role in the regulation of the pathophysiology of sepsis and their potential clinical use as biomarkers. ~22-nucleotide of microRNAs are not only involved in regulating multiple relevant cellular and molecular functions, such as immune cell function and inflammatory response, but have also been proposed as good candidates as biomarkers in sepsis. Nevertheless, establishing clinical practice guidelines based on microRNA patterns as biomarkers for diagnosis and prognosis in neonatal sepsis has yet to be achieved. Given their differential expression across tissues in neonates, the release of specific microRNAs to blood and their expression pattern can differ compared to sepsis in adult patients. Further in-depth research is necessary to fully understand the biological relevance of microRNAs and assess their potential use in clinical settings. This review provides a general overview of microRNAs, their structure, function and biogenesis before exploring their potential clinical interest as diagnostic and prognostic biomarkers of neonatal sepsis. An important part of the review is focused on immune and inflammatory aspects of selected microRNAs that may become biomarkers for clinical use and therapeutic intervention.
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Affiliation(s)
- Ahlam Fatmi
- Laboratory of Applied Molecular Biology and Immunology, University of Tlemcen, W0414100, 13000 Tlemcen, Algeria
| | - Nafissa Chabni
- Faculty of Medicine, Tlemcen Medical Centre University, 13000 Tlemcen, Algeria
| | - María Cernada
- Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain; Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Máximo Vento
- Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain; Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - María González-López
- Department of Pediatrics. Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, University of Tlemcen, W0414100, 13000 Tlemcen, Algeria; Biotechnology Center of Constantine (CRBt), 25000 Constantine, Algeria
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain; INCLIVA Health Research Institute, Mixed Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain; INCLIVA Health Research Institute, Mixed Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain.
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5
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Feng R, Patil S, Zhao X, Miao Z, Qian A. RNA Therapeutics - Research and Clinical Advancements. Front Mol Biosci 2021; 8:710738. [PMID: 34631795 PMCID: PMC8492966 DOI: 10.3389/fmolb.2021.710738] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/07/2021] [Indexed: 12/16/2022] Open
Abstract
RNA therapeutics involve the use of coding RNA such as mRNA as well as non-coding RNAs such as small interfering RNAs (siRNA), antisense oligonucleotides (ASO) to target mRNA, aptamers, ribozymes, and clustered regularly interspaced short palindromic repeats-CRISPR-associated (CRISPR/Cas) endonuclease to target proteins and DNA. Due to their diverse targeting ability and research in RNA modification and delivery systems, RNA-based formulations have emerged as suitable treatment options for many diseases. Therefore, in this article, we have summarized different RNA therapeutics, their targeting strategies, and clinical progress for various diseases as well as limitations; so that it might help researchers formulate new and advanced RNA therapeutics for various diseases. Additionally, U.S. Food and Drug Administration (USFDA)-approved RNA-based therapeutics have also been discussed.
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Affiliation(s)
- Rundong Feng
- Shaanxi Institute for Food and Drug Control, Xi'an, China
| | - Suryaji Patil
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xin Zhao
- School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xi'an, China
| | - Zhiping Miao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Airong Qian
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
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6
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Proshkina E, Yushkova E, Koval L, Zemskaya N, Shchegoleva E, Solovev I, Yakovleva D, Pakshina N, Ulyasheva N, Shaposhnikov M, Moskalev A. Tissue-Specific Knockdown of Genes of the Argonaute Family Modulates Lifespan and Radioresistance in Drosophila Melanogaster. Int J Mol Sci 2021; 22:2396. [PMID: 33673647 PMCID: PMC7957547 DOI: 10.3390/ijms22052396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Small RNAs are essential to coordinate many cellular processes, including the regulation of gene expression patterns, the prevention of genomic instability, and the suppression of the mutagenic transposon activity. These processes determine the aging, longevity, and sensitivity of cells and an organism to stress factors (particularly, ionizing radiation). The biogenesis and activity of small RNAs are provided by proteins of the Argonaute family. These proteins participate in the processing of small RNA precursors and the formation of an RNA-induced silencing complex. However, the role of Argonaute proteins in regulating lifespan and radioresistance remains poorly explored. We studied the effect of knockdown of Argonaute genes (AGO1, AGO2, AGO3, piwi) in various tissues on the Drosophila melanogaster lifespan and survival after the γ-irradiation at a dose of 700 Gy. In most cases, these parameters are reduced or did not change significantly in flies with tissue-specific RNA interference. Surprisingly, piwi knockdown in both the fat body and the nervous system causes a lifespan increase. But changes in radioresistance depend on the tissue in which the gene was knocked out. In addition, analysis of changes in retrotransposon levels and expression of stress response genes allow us to determine associated molecular mechanisms.
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Affiliation(s)
- Ekaterina Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Liubov Koval
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Nadezhda Zemskaya
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Evgeniya Shchegoleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Ilya Solovev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Daria Yakovleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Natalya Pakshina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Natalia Ulyasheva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Mikhail Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Laboratory of Post-Genomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia
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7
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Zhang Y, Yu F, Ni B, Li Q, Bae SW, Choi JH, Yang HK, Kong SH, Zhu C. The RNA-Binding Protein DDX18 Promotes Gastric Cancer by Affecting the Maturation of MicroRNA-21. Front Oncol 2021; 10:598238. [PMID: 33489896 PMCID: PMC7821424 DOI: 10.3389/fonc.2020.598238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/06/2020] [Indexed: 12/24/2022] Open
Abstract
Objectives The noncoding RNAs (ncRNAs) play important roles in gastric cancer. Most studies have focused on the functions and influence of ncRNAs, but seldom on their maturation. DEAD box genes are a family of RNA-binding proteins that may influence the development of ncRNAs, which attracted our attention. By combining a small sample for high-throughput gene microarray screening with large samples of The Cancer Genome Atlas (TCGA) data and our cohort, we aimed to find some gastric cancer-related genes. We evaluated the clinical significance and prognostic value of candidate gene DDX18, which is overexpressed in gastric cancer tissues. To provide a theoretical basis for the development of new therapeutic targets for the treatment of gastric cancer, we investigated its effect on the malignant biological behavior of gastric cancer in vitro and in vivo, and also discuss its mechanism of action. Methods (i) The differential profiling of mRNA expression in five pairs of gastric cancer and adjacent normal tissues was studied by Arraystar Human mRNA Microarray. By combining this with TCGA data and our cohort, we finally filtered out DDX18, which was upregulated in gastric cancer tissues, for further investigation. (ii) The protein expression of DDX18 was detected by immunohistochemistry staining. Then the relationship between the DDX18 expression level and the clinicopathological data and prognosis was analyzed. (iii) A CCK-8 assay and colony formation assay were used to evaluate the effect of DDX18 on cell growth and proliferation in vitro. A transwell assay was also performed to examine the migration and invasion of gastric cancer cells. Cell apoptosis was analyzed by using a fluorescein isothiocyanate–annexin V/propidium iodide double-staining assay. To identify the role of DDX18 in the tumorigenic ability of gastric cancer cells in vivo, we also established a subcutaneous gastric cancer xenograft model. Coimmunoprecipitation, small RNAseq, and western blotting were performed to explore the mechanism of action of DDX18 in gastric cancer. A patient-derived xenograft (PDX) model was used to confirm the effect of DDX18 in gastric cancer tissues. Result (i) DDX18 was upregulated in gastric cancer tumor tissues from a TCGA database and our cohort. The expression of DDX18 was also closely related to tumor volume, Borrmann classification, degree of tumor differentiation, cancer embolus, lymph node metastasis, and TNM stage. (ii) DDX18 could promote cell proliferation, migration, and invasion and inhibit cell apoptosis in vivo and in vitro. (iii) DDX18 could promote the maturation of microRNA-21 through direct interaction with Drosha, decreasing PTEN, which could upregulate the AKT signaling pathway. (iv) The PDX model showed that DDX18 could promote the proliferation of gastric cancer tissues by means of the PTEN–AKT signaling pathway. Conclusions (i) DDX18 can be treated as a molecular marker to assess the prognosis of patients with gastric cancer. (ii) DDX18 could be a potential therapeutic target in gastric cancer.
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Affiliation(s)
- Yeqian Zhang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fengrong Yu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Ni
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Seong-Woo Bae
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Jong-Ho Choi
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Han-Kwang Yang
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea.,CancerResearch Institute, Seoul National University, Seoul, South Korea
| | - Seong-Ho Kong
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea.,CancerResearch Institute, Seoul National University, Seoul, South Korea
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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8
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Patil S, Dang K, Zhao X, Gao Y, Qian A. Role of LncRNAs and CircRNAs in Bone Metabolism and Osteoporosis. Front Genet 2020; 11:584118. [PMID: 33281877 PMCID: PMC7691603 DOI: 10.3389/fgene.2020.584118] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023] Open
Abstract
Bone is a mechanosensitive organ that provides strength and support. Many bone cells, various pathways, and signaling molecules coordinate bone metabolism and also determine the course of bone diseases, such as osteoporosis, osteonecrosis, osteopenia, etc. Osteoporosis is caused by increased bone resorption and reduced bone formation due to the changes in the level of different proteins and RNAs in osteoclast or/and osteoblasts. The available therapeutic interventions can significantly reduce bone resorption or enhance bone formation, but their prolonged use has deleterious side effects. Therefore, the use of non-coding RNAs as therapeutics has emerged as an interesting field of research. Despite advancements in the molecular field, not much is known about the role of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in bone homeostasis and osteoporosis. Therefore, in this article, we summarize the role of lncRNAs and circRNAs in different bone cells and osteoporosis so that it might help in the development of osteoporotic therapeutics.
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Affiliation(s)
- Suryaji Patil
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Kai Dang
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xin Zhao
- School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xi'an, China
| | - Yongguang Gao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.,Department of Chemistry, Tangshan Normal University, Tangshan, China
| | - Airong Qian
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
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9
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Akbari A, Majd HM, Rahnama R, Heshmati J, Morvaridzadeh M, Agah S, Amini SM, Masoodi M. Cross-talk between oxidative stress signaling and microRNA regulatory systems in carcinogenesis: Focused on gastrointestinal cancers. Biomed Pharmacother 2020; 131:110729. [PMID: 33152911 DOI: 10.1016/j.biopha.2020.110729] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/30/2020] [Accepted: 09/02/2020] [Indexed: 01/17/2023] Open
Abstract
Molecular mechanisms underlying development and progression of gastrointestinal (GI) cancers are mediated by both oxidative stress (OS) and microRNAs (miRNAs) involvement. Notably, OS signaling may regulate the expression of miRNAs, and miRNAs function as imperative players in OS-initiated tumors. Given the defined biological roles of both OS systems and miRNAs in GI carcinogenesis, a possible interplay between these two key cellular networks is considered. A growing body of evidence has indicated a reciprocal connection between OS signaling pathways and miRNA regulatory machines in GI cancer development and progression. Illumination of the molecular cross-talking between miRNAs and the OS would improve our pathophysiological insight into carcinogens. Also, understanding the molecular mechanisms in which these systems are reciprocally regulated may imply in future medical practice mainly GI cancer therapy. Nowadays, therapeutic strategies focusing on miRNA and OS in GI cancer treatment are increasingly delineated. Since the use of antioxidants is limited owing to the contrasting consequences of OS signaling in cancer, the discovery of OS-responsive miRNAs may provide a potential new strategy to overcome OS-mediated GI carcinogenesis. Given the possible interaction between OS and miRNAs in GI cancers, this review aimed to elucidate the existing evidence on the interaction between OS and miRNA regulatory machinery and its role in GI carcinogenesis. In this regard, we will illustrate the function of miRNAs which target OS systems during homeostasis and tumorigenesis. We also discuss the biological cross-talk between OS systems and miRNAs and corresponding cell signaling pathways.
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Affiliation(s)
- Abolfazl Akbari
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Hassan Mehrad Majd
- Cancer Molecular Pathology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reyhane Rahnama
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Javad Heshmati
- Department of Nutritional Science, School of Nutritional Science and Food Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mojgan Morvaridzadeh
- Department of Nutritional Science, School of Nutritional Science and Food Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shahram Agah
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Amini
- Radiation Biology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Masoodi
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran.
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10
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TCF21: a critical transcription factor in health and cancer. J Mol Med (Berl) 2020; 98:1055-1068. [DOI: 10.1007/s00109-020-01934-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 05/07/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
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11
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Wang L, Shi Z, Wang X, Mu S, Xu X, Shen L, Li P. Protective effects of bovine milk exosomes against oxidative stress in IEC-6 cells. Eur J Nutr 2020; 60:317-327. [PMID: 32328746 DOI: 10.1007/s00394-020-02242-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 03/27/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Bovine milk exosomes, which are enriched with microRNAs (miRNAs) and proteins, regulate immune response and growth. In the present study, we aimed to assess the protective effects of bovine milk exosomes against oxidative stress of intestinal crypt epithelial cells (IEC-6). METHODS Bovine milk exosomes were isolated and characterized. To assess the protective effects of exosomes, IEC-6 cells were pretreated with exosomes, followed by H2O2. Cell viability and levels of superoxide dismutase (SOD), malondialdehyde (MDA), glutathione peroxidase (GPX), reactive oxidative species (ROS), and lactate dehydrogenase (LDH) were measured. The expression levels of nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase 1 (Ho1) genes, and miR-146a, miR-155, and the HO-1 protein were also determined. RESULTS The isolated bovine milk exosome were positive for CD63 and CD9 expression. The exosomes were approximately circular and had a diameter of about 67.23 nm. Pretreatment of IEC-6 cells with bovine milk exosomes enhanced cell viability; increased SOD and GPX activities; and reduced LDH, ROS, and MDA levels after H2O2 challenge. Further analysis showed that exosome pretreatment increased intracellular miR-146a and miR-155 levels. Exosome pretreatment inhibited the elevation of Nrf2 and Ho1 gene expression induced by H2O2, but promoted HO-1 protein expression. CONCLUSION The results indicated that bovine milk exosomes exerted protective effects against oxidative stress in IEC-6 cells.
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Affiliation(s)
- Lanfang Wang
- Research Center for Translational Medicine at Shanghai East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, People's Republic of China.
| | - Zhexi Shi
- Research Center for Translational Medicine at Shanghai East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Xinyan Wang
- The People's Hospital of Zhaoyuan City, Zhaoyuan, 265400, Shandong Province, China
| | - Shu Mu
- Research Center for Translational Medicine at Shanghai East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Xiaoyan Xu
- Research Center for Translational Medicine at Shanghai East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Li Shen
- Department of Pathogen Biology, Tongji University School of Medicine, Shanghai, 200092, China
| | - Ping Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
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12
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Chen L, Qu H, Guo M, Zhang Y, Cui Y, Yang Q, Bai R, Shi D. ANRIL and atherosclerosis. J Clin Pharm Ther 2019; 45:240-248. [PMID: 31703157 DOI: 10.1111/jcpt.13060] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/26/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE The 3.8-kb-long antisense non-coding RNA at the INK4 locus (ANRIL) is transcribed from the short arm of human chromosome 9 on P21 and is associated with malfunction of the vascular endothelium, vascular smooth muscle cell (VSMC) proliferation/migration/senescence/apoptosis, mononuclear cell adhesion and proliferation, glycolipid metabolism disorder and DNA damage. Hence, ANRIL plays an important role in atherogenesis. Moreover, genome-wide association studies (GWAS) have identified ANRIL as a biomarker that is closely related to coronary heart disease (CHD). The objective of this review was to discuss the pathological mechanism of ANRIL in atherosclerotic development and its significance as a predictor of cardiovascular disease. METHODS Review of the PubMed, EMBASE and Cochrane databases for articles demonstrating the roles of ANRIL in the development of atherosclerotic diseases. RESULTS AND DISCUSSION The abnormal expression of ANRIL is linked to vascular endothelium injury; the proliferation, migration, senescence and apoptosis of VSMCs; mononuclear cell adhesion and proliferation; glycolipid metabolism disorder; DNA damage; and competing endogenous RNAs. Moreover, ANRIL accelerates the progression of CHD by regulating its single nucleotide polymorphisms (SNPs). WHAT IS NEW AND CONCLUSION Considering that ANRIL accelerates atherosclerosis (AS) development and is a risk factor for CHD, it is reasonable for us to explore an efficacious ANRIL-based therapy for AS in CHD.
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Affiliation(s)
- Li Chen
- Peking University Traditional Chinese Medicine Clinical Medical School (Xi yuan), Beijing, China
| | - Hua Qu
- Graduate School of China Academy of Chinese Medical Sciences, Beijing, China
| | - Ming Guo
- Cardiovascular Diseases Center, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Zhang
- Cardiovascular Diseases Center, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuanyuan Cui
- Cardiovascular Diseases Center, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Qiaoning Yang
- Cardiovascular Diseases Center, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Ruina Bai
- Cardiovascular Diseases Center, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Dazhuo Shi
- Cardiovascular Diseases Center, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
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13
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Durut N, Mittelsten Scheid O. The Role of Noncoding RNAs in Double-Strand Break Repair. FRONTIERS IN PLANT SCIENCE 2019; 10:1155. [PMID: 31611891 PMCID: PMC6776598 DOI: 10.3389/fpls.2019.01155] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Genome stability is constantly threatened by DNA lesions generated by different environmental factors as well as endogenous processes. If not properly and timely repaired, damaged DNA can lead to mutations or chromosomal rearrangements, well-known reasons for genetic diseases or cancer in mammals, or growth abnormalities and/or sterility in plants. To prevent deleterious consequences of DNA damage, a sophisticated system termed DNA damage response (DDR) detects DNA lesions and initiates DNA repair processes. In addition to many well-studied canonical proteins involved in this process, noncoding RNA (ncRNA) molecules have recently been discovered as important regulators of the DDR pathway, extending the broad functional repertoire of ncRNAs to the maintenance of genome stability. These ncRNAs are mainly connected with double-strand breaks (DSBs), the most dangerous type of DNA lesions. The possibility to intentionally generate site-specific DSBs in the genome with endonucleases constitutes a powerful tool to study, in vivo, how DSBs are processed and how ncRNAs participate in this crucial event. In this review, we will summarize studies reporting the different roles of ncRNAs in DSB repair and discuss how genome editing approaches, especially CRISPR/Cas systems, can assist DNA repair studies. We will summarize knowledge concerning the functional significance of ncRNAs in DNA repair and their contribution to genome stability and integrity, with a focus on plants.
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14
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Wu J, Chen L, Zheng C, Xu S, Gao Y, Wang J. Co-expression Network Analysis Revealing the Potential Regulatory Roles of lncRNAs in Alzheimer's Disease. Interdiscip Sci 2019; 11:645-654. [PMID: 30715720 DOI: 10.1007/s12539-019-00319-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 01/16/2023]
Abstract
Alzheimer's disease (AD) is one of the most common types of dementia among the elderly. Previous studies had revealed that the dysregulation of lncRNAs played important roles in human diseases, including AD. However, there is still a lack of comprehensive analysis of differently expressed long non-coding RNAs (lncRNAs) in different distinct regions related to AD. In present study, we identified a total of 678, 593, 941, 1445, 1179, 466 differently expressed lncRNAs that were found in entorhinal cortex (EC), middle temporal gyrus(MTG), hippocampus (HIP), superior frontal gyrus (SFG), posterior cingulate (PC), cortex and primary visual cortex (VCX) AD samples, respectively. Furthermore, we constructed lncRNA-mRNA co-expression networks in AD to explore the potential roles of these lncRNAs. Differentially expressed (DE) lncRNAs were involved in regulating metabolic process, respiratory electron transport chain and ATP metabolic process showed by GO analysis. Interestingly, KEGG analysis revealed these lncRNAs were associated with neurodegenerative disorders such as Alzheimer's disease, Huntington's disease and Parkinson's disease. Four lncRNAs (LOC100507557, LOC101929787, NEAT1, and JAZF1-AS1) were identified as key lncRNAs in AD progression and dysregulated in different distinct regions related to AD. Our study has uncovered several key lncRNAs in AD, which would give novel underlying therapeutic and prognostic targets for AD.
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Affiliation(s)
- Jiong Wu
- Department of Neurology, Zhejiang Hospital, Hangzhou, 310000, Zhejiang, China
| | - Linhui Chen
- Department of Neurology, Zhejiang Hospital, Hangzhou, 310000, Zhejiang, China
| | - Chaobo Zheng
- Department of Neurology, Zhejiang Hospital, Hangzhou, 310000, Zhejiang, China
| | - Shanhu Xu
- Department of Neurology, Zhejiang Hospital, Hangzhou, 310000, Zhejiang, China
| | - Yuhai Gao
- Department of Neurology, Zhejiang Hospital, Hangzhou, 310000, Zhejiang, China
| | - Junjun Wang
- Department of Neurology, Zhejiang Hospital, Hangzhou, 310000, Zhejiang, China.
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15
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Norouzitallab P, Baruah K, Vanrompay D, Bossier P. Can epigenetics translate environmental cues into phenotypes? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:1281-1293. [PMID: 30180336 DOI: 10.1016/j.scitotenv.2018.08.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/03/2018] [Accepted: 08/04/2018] [Indexed: 05/17/2023]
Abstract
Living organisms are constantly exposed to wide ranges of environmental cues. They react to these cues by undergoing a battery of phenotypic responses, such as by altering their physiological and behavioral traits, in order to adapt and survive in the changed environments. The adaptive response of a species induced by environmental cues is typically thought to be associated with its genetic diversity such that higher genetic diversity provides increased adaptive potential. This originates from the general consensus that phenotypic traits have a genetic basis and are subject to Darwinian natural selection and Mendelian inheritance. There is no doubt about the validity of these principles, supported by the successful introgression of specific traits during (selective) breeding. However, a range of recent studies provided fascinating evidences suggesting that environmental effects experienced by an organism during its lifetime can have marked influences on its phenotype, and additionally the organism can pass on the acquired phenotypes to its subsequent generations through non-genetic mechanisms (also termed as epigenetic mechanism) - a notion that dates back to Lamarck and has been controversial ever since. In this review, we describe how the epigenetics has reshaped our long perception about the inheritance/development of phenotypes within organisms, contrasting with the classical gene-based view of inheritance. We particularly highlighted recent developments in our understanding of inheritance of parental environmental induced phenotypic traits in multicellular organisms under different environmental conditions, and discuss how modifications of the epigenome contribute to the determination of the adult phenotype of future generations.
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Affiliation(s)
- Parisa Norouzitallab
- Laboratory for Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium; Laboratory of Aquaculture &Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium.
| | - Kartik Baruah
- Laboratory of Aquaculture &Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium; Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Daisy Vanrompay
- Laboratory for Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture &Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure 653, Ghent 9000, Belgium
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16
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Cimini S, Gualtieri C, Macovei A, Balestrazzi A, De Gara L, Locato V. Redox Balance-DDR-miRNA Triangle: Relevance in Genome Stability and Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:989. [PMID: 31428113 PMCID: PMC6688120 DOI: 10.3389/fpls.2019.00989] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/15/2019] [Indexed: 05/05/2023]
Abstract
Plants are continuously faced with complex environmental conditions which can affect the oxidative metabolism and photosynthetic efficiency, thus leading to the over-production of reactive oxygen species (ROS). Over a certain threshold, ROS can damage DNA. DNA damage, unless repaired, can affect genome stability, thus interfering with cell survival and severely reducing crop productivity. A complex network of pathways involved in DNA damage response (DDR) needs to be activated in order to maintain genome integrity. The expression of specific genes belonging to these pathways can be used as indicators of oxidative DNA damage and effective DNA repair in plants subjected to stress conditions. Managing ROS levels by modulating their production and scavenging systems shifts the role of these compounds from toxic molecules to key messengers involved in plant tolerance acquisition. Oxidative and anti-oxidative signals normally move among the different cell compartments, including the nucleus, cytosol, and organelles. Nuclei are dynamically equipped with different redox systems, such as glutathione (GSH), thiol reductases, and redox regulated transcription factors (TFs). The nuclear redox network participates in the regulation of the DNA metabolism, in terms of transcriptional events, replication, and repair mechanisms. This mainly occurs through redox-dependent regulatory mechanisms comprising redox buffering and post-translational modifications, such as the thiol-disulphide switch, glutathionylation, and S-nitrosylation. The regulatory role of microRNAs (miRNAs) is also emerging for the maintenance of genome stability and the modulation of antioxidative machinery under adverse environmental conditions. In fact, redox systems and DDR pathways can be controlled at a post-transcriptional level by miRNAs. This review reports on the interconnections between the DDR pathways and redox balancing systems. It presents a new dynamic picture by taking into account the shared regulatory mechanism mediated by miRNAs in plant defense responses to stress.
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Affiliation(s)
- Sara Cimini
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
| | - Carla Gualtieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Laura De Gara
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
| | - Vittoria Locato
- Unit of Food Science and Human Nutrition, Campus Bio-Medico University of Rome, Rome, Italy
- *Correspondence: Vittoria Locato,
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17
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Liu Y, Xu J, Choi HH, Han C, Fang Y, Li Y, Van der Jeught K, Xu H, Zhang L, Frieden M, Wang L, Eyvani H, Sun Y, Zhao G, Zhang Y, Liu S, Wan J, Huang C, Ji G, Lu X, He X, Zhang X. Targeting 17q23 amplicon to overcome the resistance to anti-HER2 therapy in HER2+ breast cancer. Nat Commun 2018; 9:4718. [PMID: 30413718 PMCID: PMC6226492 DOI: 10.1038/s41467-018-07264-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 10/25/2018] [Indexed: 12/26/2022] Open
Abstract
Chromosome 17q23 amplification occurs in ~11% of human breast cancers. Enriched in HER2+ breast cancers, the 17q23 amplification is significantly correlated with poor clinical outcomes. In addition to the previously identified oncogene WIP1, we uncover an oncogenic microRNA gene, MIR21, in a majority of the WIP1-containing 17q23 amplicons. The 17q23 amplification results in aberrant expression of WIP1 and miR-21, which not only promotes breast tumorigenesis, but also leads to resistance to anti-HER2 therapies. Inhibiting WIP1 and miR-21 selectively inhibits the proliferation, survival and tumorigenic potential of the HER2+ breast cancer cells harboring 17q23 amplification. To overcome the resistance of trastuzumab-based therapies in vivo, we develop pH-sensitive nanoparticles for specific co-delivery of the WIP1 and miR-21 inhibitors into HER2+ breast tumors, leading to a profound reduction of tumor growth. These results demonstrate the great potential of the combined treatment of WIP1 and miR-21 inhibitors for the trastuzumab-resistant HER2+ breast cancers. The 17q23 amplicon containing the WIP1 oncogene is frequently amplified in HER2+ breast cancer. Here they find MIR21 to be present in WIP1-containing amplicons, and report nanoparticle based co-delivery of WIP1 and miR-21 inhibitors to be effective in trastuzumab-resistant HER2+ breast cancer.
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Affiliation(s)
- Yunhua Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 200032, Shanghai, China
| | - Jiangsheng Xu
- Department of Biomedical Engineering and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Hyun Ho Choi
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cecil Han
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuanzhang Fang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yujing Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kevin Van der Jeught
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hanchen Xu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lu Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 200032, Shanghai, China
| | - Michael Frieden
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Lifei Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Haniyeh Eyvani
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yifan Sun
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Gang Zhao
- Department of Electronic Science and Technology, School of Information Science and Technology, University of Science and Technology of China, 230027, Hefei, China
| | - Yuntian Zhang
- Department of Biomedical Engineering and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Cheng Huang
- Drug Discovery Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 200032, Shanghai, China
| | - Xiongbin Lu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Xiaoming He
- Department of Biomedical Engineering and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA. .,Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA. .,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD, 20742, USA. .,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD, 21201, USA.
| | - Xinna Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Indiana University Melvin and Bren Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA. .,Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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18
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Melatonin Sensitizes Hepatocellular Carcinoma Cells to Chemotherapy Through Long Non-Coding RNA RAD51-AS1-Mediated Suppression of DNA Repair. Cancers (Basel) 2018; 10:cancers10090320. [PMID: 30201872 PMCID: PMC6162454 DOI: 10.3390/cancers10090320] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/20/2018] [Accepted: 09/07/2018] [Indexed: 12/26/2022] Open
Abstract
DNA repair systems are abnormally active in most hepatocellular carcinoma (HCC) cells due to accumulated mutations, resulting in elevated DNA repair capacity and resistance to chemotherapy and radiotherapy. Thus, targeting DNA repair mechanisms is a common treatment approach in HCC to sensitize cancer cells to DNA damage. In this study, we examined the anti-HCC effects of melatonin and elucidated the regulatory mechanisms. The results of functional assays showed that in addition to inhibiting the proliferation, migration, and invasion abilities of HCC cells, melatonin suppressed their DNA repair capacity, thereby promoting the cytotoxicity of chemotherapy and radiotherapy. Whole-transcriptome and gain- and loss-of-function analyses revealed that melatonin induces expression of the long noncoding RNA RAD51-AS1, which binds to RAD51 mRNA to inhibit its translation, effectively decreasing the DNA repair capacity of HCC cells and increasing their sensitivity to chemotherapy and radiotherapy. Animal models further demonstrated that a combination of melatonin and the chemotherapeutic agent etoposide (VP16) can significantly enhance tumor growth inhibition compared with monotherapy. Our results show that melatonin is a potential adjuvant treatment for chemotherapy and radiotherapy in HCC.
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Oxidative stress-modulating drugs have preferential anticancer effects - involving the regulation of apoptosis, DNA damage, endoplasmic reticulum stress, autophagy, metabolism, and migration. Semin Cancer Biol 2018; 58:109-117. [PMID: 30149066 DOI: 10.1016/j.semcancer.2018.08.010] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/19/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023]
Abstract
To achieve preferential effects against cancer cells but less damage to normal cells is one of the main challenges of cancer research. In this review, we explore the roles and relationships of oxidative stress-mediated apoptosis, DNA damage, ER stress, autophagy, metabolism, and migration of ROS-modulating anticancer drugs. Understanding preferential anticancer effects in more detail will improve chemotherapeutic approaches that are based on ROS-modulating drugs in cancer treatments.
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20
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Vieweger M, Nesbitt DJ. Synergistic SHAPE/Single-Molecule Deconvolution of RNA Conformation under Physiological Conditions. Biophys J 2018; 114:1762-1775. [PMID: 29694857 PMCID: PMC5937115 DOI: 10.1016/j.bpj.2018.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/06/2018] [Accepted: 02/20/2018] [Indexed: 11/24/2022] Open
Abstract
Structural RNA domains are widely involved in the regulation of biological functions, such as gene expression, gene modification, and gene repair. Activity of these dynamic regions depends sensitively on the global fold of the RNA, in particular, on the binding affinity of individual conformations to effector molecules in solution. Consequently, both the 1) structure and 2) conformational dynamics of noncoding RNAs prove to be essential in understanding the coupling that results in biological function. Toward this end, we recently reported observation of three conformational states in the metal-induced folding pathway of the tRNA-like structure domain of Brome Mosaic Virus, via single-molecule fluorescence resonance energy transfer studies. We report herein selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE)-directed structure predictions as a function of metal ion concentrations ([Mn+]) to confirm the three-state folding model, as well as test 2° structure models from the literature. Specifically, SHAPE reactivity data mapped onto literature models agrees well with the secondary structures observed at 0-10 mM [Mg2+], with only minor discrepancies in the E hairpin domain at low [Mg2+]. SHAPE probing and SHAPE-directed structure predictions further confirm the stepwise unfolding pathway previously observed in our single-molecule studies. Of special relevance, this means that reduction in the metal-ion concentration unfolds the 3' pseudoknot interaction before unfolding the long-range stem interaction. This work highlights the synergistic power of combining 1) single-molecule Förster resonance energy transfer and 2) SHAPE-directed structure-probing studies for detailed analysis of multiple RNA conformational states. In particular, single-molecule guided deconvolution of the SHAPE reactivities permits 2° structure predictions of isolated RNA conformations, thereby substantially improving on traditional limitations associated with current structure prediction algorithms.
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Affiliation(s)
- Mario Vieweger
- JILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - David J Nesbitt
- JILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado; Department of Physics, University of Colorado, Boulder, Colorado.
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21
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Chiarelli N, Carini G, Zoppi N, Ritelli M, Colombi M. Transcriptome analysis of skin fibroblasts with dominant negative COL3A1 mutations provides molecular insights into the etiopathology of vascular Ehlers-Danlos syndrome. PLoS One 2018; 13:e0191220. [PMID: 29346445 PMCID: PMC5773204 DOI: 10.1371/journal.pone.0191220] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/29/2017] [Indexed: 01/20/2023] Open
Abstract
Vascular Ehlers-Danlos syndrome (vEDS) is a dominantly inherited connective tissue disorder caused by mutations in the COL3A1 gene that encodes type III collagen (COLLIII), which is the major expressed collagen in blood vessels and hollow organs. The majority of disease-causing variants in COL3A1 are glycine substitutions and in-frame splice mutations in the triple helix domain that through a dominant negative effect are associated with the severe clinical spectrum potentially lethal of vEDS, characterized by fragility of soft connective tissues with arterial and organ ruptures. To shed lights into molecular mechanisms underlying vEDS, we performed gene expression profiling in cultured skin fibroblasts from three patients with different structural COL3A1 mutations. Transcriptome analysis revealed significant changes in the expression levels of several genes involved in maintenance of cell redox and endoplasmic reticulum (ER) homeostasis, COLLs folding and extracellular matrix (ECM) organization, formation of the proteasome complex, and cell cycle regulation. Protein analyses showed that aberrant COLLIII expression is associated with the disassembly of many structural ECM constituents, such as fibrillins, EMILINs, and elastin, as well as with the reduction of the proteoglycans perlecan, decorin, and versican, all playing an important role in the vascular system. Furthermore, the altered distribution of the ER marker protein disulfide isomerase PDI and the strong reduction of the COLLs-modifying enzyme FKBP22 are consistent with the disturbance of ER-related homeostasis and COLLs biosynthesis and post-translational modifications, indicated by microarray analysis. Our findings add new insights into the pathophysiology of this severe vascular disorder, since they provide a picture of the gene expression changes in vEDS skin fibroblasts and highlight that dominant negative mutations in COL3A1 also affect post-translational modifications and deposition into the ECM of several structural proteins crucial to the integrity of soft connective tissues.
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Affiliation(s)
- Nicola Chiarelli
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Giulia Carini
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Nicoletta Zoppi
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Marco Ritelli
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Marina Colombi
- Department of Molecular and Translational Medicine, Division of Biology and Genetics, University of Brescia, Brescia, Italy
- * E-mail:
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22
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Fu Q, Liu CJ, Zhai ZS, Zhang X, Qin T, Zhang HW. Single-Cell Non-coding RNA in Embryonic Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:19-32. [DOI: 10.1007/978-981-13-0502-3_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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23
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Abstract
In modern molecular biology, RNA has emerged as a versatile macromolecule capable of mediating an astonishing number of biological functions beyond its role as a transient messenger of genetic information. The recent discovery and functional analyses of new classes of noncoding RNAs (ncRNAs) have revealed their widespread use in many pathways, including several in the nucleus. This Review focuses on the mechanisms by which nuclear ncRNAs directly contribute to the maintenance of genome stability. We discuss how ncRNAs inhibit spurious recombination among repetitive DNA elements, repress mobilization of transposable elements (TEs), template or bridge DNA double-strand breaks (DSBs) during repair, and direct developmentally regulated genome rearrangements in some ciliates. These studies reveal an unexpected repertoire of mechanisms by which ncRNAs contribute to genome stability and even potentially fuel evolution by acting as templates for genome modification.
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24
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Yang Y, Zhao L, Lei L, Lau WB, Lau B, Yang Q, Le X, Yang H, Wang C, Luo Z, Xuan Y, Chen Y, Deng X, Xu L, Feng M, Yi T, Zhao X, Wei Y, Zhou S. LncRNAs: the bridge linking RNA and colorectal cancer. Oncotarget 2017; 8:12517-12532. [PMID: 27888635 PMCID: PMC5355361 DOI: 10.18632/oncotarget.13573] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/12/2016] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcribed by genomic regions (exceeding 200 nucleotides in length) that do not encode proteins. While the exquisite regulation of lncRNA transcription can provide signals of malignant transformation, lncRNAs control pleiotropic cancer phenotypes through interactions with other cellular molecules including DNA, protein, and RNA. Recent studies have demonstrated that dysregulation of lncRNAs is influential in proliferation, angiogenesis, metastasis, invasion, apoptosis, stemness, and genome instability in colorectal cancer (CRC), with consequent clinical implications. In this review, we explicate the roles of different lncRNAs in CRC, and the potential implications for their clinical application.
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Affiliation(s)
- Yanfei Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Linjie Zhao
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Lingzi Lei
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Wayne Bond Lau
- Department of Emergency Medicine, Thomas Jefferson University Hospital, U.S.A
| | - Bonnie Lau
- Department of Emergency Medicine, Kaiser Permanente Santa Clara Medical Center, Affiliate of Stanford University, U.S.A
| | - Qilian Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Xiaobing Le
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Huiliang Yang
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Chenlu Wang
- College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - Zhongyue Luo
- College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - Yu Xuan
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yi Chen
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xiangbing Deng
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Lian Xu
- Department of Pathology, West China Second Hospital, Sichuan University, Chengdu, P. R. China
| | - Min Feng
- Department of Pathology, West China Second Hospital, Sichuan University, Chengdu, P. R. China
| | - Tao Yi
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Xia Zhao
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Yuquan Wei
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second Hospital and State Key Laboratory of Biotherapy/Collaborative Innovation Center, West China Hospital, Sichuan University, Chengdu, P. R. China
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25
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Antoniali G, Malfatti MC, Tell G. Unveiling the non-repair face of the Base Excision Repair pathway in RNA processing: A missing link between DNA repair and gene expression? DNA Repair (Amst) 2017. [DOI: 10.1016/j.dnarep.2017.06.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Asha S, Soniya EV. Transfer RNA Derived Small RNAs Targeting Defense Responsive Genes Are Induced during Phytophthora capsici Infection in Black Pepper (Piper nigrum L.). FRONTIERS IN PLANT SCIENCE 2016; 7:767. [PMID: 27313593 PMCID: PMC4887504 DOI: 10.3389/fpls.2016.00767] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 05/17/2016] [Indexed: 05/09/2023]
Abstract
Small RNAs derived from transfer RNAs were recently assigned as potential gene regulatory candidates for various stress responses in eukaryotes. In this study, we report on the cloning and identification of tRNA derived small RNAs from black pepper plants in response to the infection of the quick wilt pathogen, Phytophthora capsici. 5'tRFs cloned from black pepper were validated as highly expressed during P. capsici infection. A high-throughput systematic analysis of the small RNAome (sRNAome) revealed the predominance of 5'tRFs in the infected leaf and root. The abundance of 5'tRFs in the sRNAome and the defense responsive genes as their potential targets indicated their regulatory role during stress response in black pepper. The 5'Ala(CGC) tRF mediated cleavage was experimentally mapped at the tRF binding sites on the mRNA targets of Non-expresser of pathogenesis related protein (NPR1), which was down-regulated during pathogen infection. Comparative sRNAome further demonstrated sequence conservation of 5'Ala tRFs across the angiosperm plant groups, and many important genes in the defense response were identified in silico as their potential targets. Our findings uncovered the diversity, differential expression and stress responsive functional role of tRNA-derived small RNAs during Phytophthora infection in black pepper.
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27
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Sharma V, Khurana S, Kubben N, Abdelmohsen K, Oberdoerffer P, Gorospe M, Misteli T. A BRCA1-interacting lncRNA regulates homologous recombination. EMBO Rep 2015; 16:1520-34. [PMID: 26412854 DOI: 10.15252/embr.201540437] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/25/2015] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are important players in diverse biological processes. Upon DNA damage, cells activate a complex signaling cascade referred to as the DNA damage response (DDR). Using a microarray screen, we identify here a novel lncRNA, DDSR1 (DNA damage-sensitive RNA1), which is induced upon DNA damage. DDSR1 induction is triggered in an ATM-NF-κB pathway-dependent manner by several DNA double-strand break (DSB) agents. Loss of DDSR1 impairs cell proliferation and DDR signaling and reduces DNA repair capacity by homologous recombination (HR). The HR defect in the absence of DDSR1 is marked by aberrant accumulation of BRCA1 and RAP80 at DSB sites. In line with a role in regulating HR, DDSR1 interacts with BRCA1 and hnRNPUL1, an RNA-binding protein involved in DNA end resection. Our results suggest a role for the lncRNA DDSR1 in modulating DNA repair by HR.
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Affiliation(s)
- Vivek Sharma
- National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Nard Kubben
- National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
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28
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Dicks N, Gutierrez K, Michalak M, Bordignon V, Agellon LB. Endoplasmic reticulum stress, genome damage, and cancer. Front Oncol 2015; 5:11. [PMID: 25692096 PMCID: PMC4315039 DOI: 10.3389/fonc.2015.00011] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/12/2015] [Indexed: 01/30/2023] Open
Abstract
Endoplasmic reticulum (ER) stress has been linked to many diseases, including cancer. A large body of work has focused on the activation of the ER stress response in cancer cells to facilitate their survival and tumor growth; however, there are some studies suggesting that the ER stress response can also mitigate cancer progression. Despite these contradictions, it is clear that the ER stress response is closely associated with cancer biology. The ER stress response classically encompasses activation of three separate pathways, which are collectively categorized the unfolded protein response (UPR). The UPR has been extensively studied in various cancers and appears to confer a selective advantage to tumor cells to facilitate their enhanced growth and resistance to anti-cancer agents. It has also been shown that ER stress induces chromatin changes, which can also facilitate cell survival. Chromatin remodeling has been linked with many cancers through repression of tumor suppressor and apoptosis genes. Interplay between the classic UPR and genome damage repair mechanisms may have important implications in the transformation process of normal cells into cancer cells.
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Affiliation(s)
- Naomi Dicks
- Department of Animal Science, McGill University , Montréal, QC , Canada
| | - Karina Gutierrez
- Department of Animal Science, McGill University , Montréal, QC , Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta , Edmonton, AB , Canada
| | - Vilceu Bordignon
- Department of Animal Science, McGill University , Montréal, QC , Canada
| | - Luis B Agellon
- School of Dietetics and Human Nutrition, McGill University , Montréal, QC , Canada
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29
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Enterococcus faecalis Infection and Reactive Oxygen Species Down-Regulates the miR-17-92 Cluster in Gastric Adenocarcinoma Cell Culture. Genes (Basel) 2014; 5:726-38. [PMID: 25170597 PMCID: PMC4198927 DOI: 10.3390/genes5030726] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 07/14/2014] [Accepted: 08/13/2014] [Indexed: 12/15/2022] Open
Abstract
Chronic inflammation due to bacterial overgrowth of the stomach predisposes to the development of gastric cancer and is also associated with high levels of reactive oxygen species (ROS). In recent years increasing attention has been drawn to microRNAs (miRNAs) due to their role in the pathogenesis of many human diseases including gastric cancer. Here we studied the impact of infection by the gram-positive bacteria Enterococcus faecalis (E. faecalis) on global miRNA expression as well as the effect of ROS on selected miRNAs. Human gastric adenocarcinoma cell line MKN74 was infected with living E. faecalis for 24 h or for 5 days or with E. faecalis lysate for 5 days. The miRNA expression was examined by microarray analysis using Affymetrix GeneChip miRNA Arrays. To test the effect of ROS, MKN74 cells were treated with 100 mM tert-Butyl hydroperoxide (TBHP). Following 5 days of E. faecalis infection we found 91 differentially expressed miRNAs in response to living bacteria and 2 miRNAs responded to E. faecalis lysate. We verified the down-regulation of the miR-17-92 and miR-106-363 clusters and of other miRNAs involved in the oxidative stress-response by qRT-PCR. We conclude that only infection by living E. faecalis bacteria caused a significant global response in miRNA expression in the MKN74 cell culture. E. faecalis infection as well as ROS stimulation down-regulated the expression of the miR-17-92 cluster. We believe that these changes could reflect a general response of gastric epithelial cells to bacterial infections.
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30
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Han C, Liu Y, Wan G, Choi HJ, Zhao L, Ivan C, He X, Sood AK, Zhang X, Lu X. The RNA-binding protein DDX1 promotes primary microRNA maturation and inhibits ovarian tumor progression. Cell Rep 2014; 8:1447-60. [PMID: 25176654 DOI: 10.1016/j.celrep.2014.07.058] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/26/2014] [Accepted: 07/30/2014] [Indexed: 12/23/2022] Open
Abstract
Posttranscriptional maturation is a critical step in microRNA (miRNA) biogenesis that determines mature miRNA levels. In addition to core components (Drosha and DGCR8 [DiGeorge syndrome critical region gene 8]) in the microprocessor, regulatory RNA-binding proteins may confer the specificity for recruiting and processing of individual primary miRNAs (pri-miRNAs). Here, we identify DDX1 as a regulatory protein that promotes the expression of a subset of miRNAs, including five members in the microRNA-200 (miR-200) family and four miRNAs in an eight-miRNA signature of a mesenchymal ovarian cancer subtype. A majority of DDX1-dependent miRNAs are induced after DNA damage. This induction is facilitated by the ataxia telangiectasia mutated (ATM)-mediated phosphorylation of DDX1. Inhibiting DDX1 promotes ovarian tumor growth and metastasis in a syngeneic mouse model. Analysis of The Cancer Genome Atlas (TCGA) reveals that low DDX1 levels are associated with poor clinical outcome in patients with serous ovarian cancer. These findings suggest that DDX1 is a key modulator in miRNA maturation and ovarian tumor suppression.
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Affiliation(s)
- Cecil Han
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yunhua Liu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guohui Wan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hyun Jin Choi
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luqing Zhao
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cristina Ivan
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoming He
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Xinna Zhang
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Xiongbin Lu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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31
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Emmrich S, Streltsov A, Schmidt F, Thangapandi VR, Reinhardt D, Klusmann JH. LincRNAs MONC and MIR100HG act as oncogenes in acute megakaryoblastic leukemia. Mol Cancer 2014; 13:171. [PMID: 25027842 PMCID: PMC4118279 DOI: 10.1186/1476-4598-13-171] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/03/2014] [Indexed: 12/02/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are recognized as pivotal players during developmental ontogenesis and pathogenesis of cancer. The intronic microRNA (miRNA) clusters miR-99a ~ 125b-2 and miR-100 ~ 125b-1 promote progression of acute megakaryoblastic leukemia (AMKL), an aggressive form of hematologic cancers. The function of the lncRNA hostgenes MIR99AHG (alias MONC) and MIR100HG within this ncRNA ensemble remained elusive. Results Here we report that lncRNAs MONC and MIR100HG are highly expressed in AMKL blasts. The transcripts were mainly localized in the nucleus and their expression correlated with the corresponding miRNA clusters. Knockdown of MONC or MIR100HG impeded leukemic growth of AMKL cell lines and primary patient samples. The development of a lentiviral lncRNA vector to ectopically express lncRNAs without perturbing their secondary structure due to improper termination of the viral transcript, allowed us to study the function of MONC independent of the miRNAs in cord blood hematopoietic stem and progenitor cells (HSPCs). We could show that MONC interfered with hematopoietic lineage decisions and enhanced the proliferation of immature erythroid progenitor cells. Conclusions Our study reveals an unprecedented function of lncRNAs MONC and MIR100HG as regulators of hematopoiesis and oncogenes in the development of myeloid leukemia.
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Affiliation(s)
| | | | | | | | | | - Jan-Henning Klusmann
- Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
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Abstract
This perspective reviews the many dimensions of base excision repair from a 10,000 foot vantage point and provides one person's view on where the field is headed. Enzyme function is considered under the lens of X-ray diffraction and single molecule studies. Base excision repair in chromatin and telomeres, regulation of expression and the role of posttranslational modifications are also discussed in the context of enzyme activities, cellular localization and interacting partners. The specialized roles that base excision repair play in transcriptional activation by active demethylation and targeted oxidation as well as how base excision repair functions in the immune processes of somatic hypermutation and class switch recombination and its possible involvement in retroviral infection are also discussed. Finally the complexities of oxidative damage and its repair and its link to neurodegenerative disorders, as well as the role of base excision repair as a tumor suppressor are examined in the context of damage, repair and aging. By outlining the many base excision repair-related mysteries that have yet to be unraveled, hopefully this perspective will stimulate further interest in the field.
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Affiliation(s)
- Susan S Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, 95 Carrigan Drive, Stafford Hall, Burlington, VT 05405-0084, USA.
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Abstract
The ability to repair damaged DNA and to maintain genome stability is the utmost importance for the survival of any species. Hence, it is not surprising to find that DNA repair mechanisms are evolutionarily conserved and are expected to evolve to maintain the existence of species. In the last few years, there has been an exponential increase in the evidence linking RNA processing with DNA repair programs. For instance, the well-studied DNA base excision repair (BER) enzyme apurinic/apyrimidinic endonuclease 1 can cleave RNA molecules, regulate mRNA levels, and associate physically with proteins involved in RNA processing. It is now clear that not only the expression of noncoding RNAs are changed upon DNA damage, they can modulate the expression of genes involved in the genome stability programs. The five reviews in this Forum provide the up-to-date knowledge on DNA repair, with a focus on BER, and a perspective on how the two ancient biochemical pathways are linked. The contributions demonstrate the complexity of such interactions, but also pointed out the opportunities for new therapeutic interventions. Future in vivo studies on the link between DNA repair processes and RNA metabolism should contribute to our basic understanding of physiology, disease, and treatment strategies.
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Affiliation(s)
- Chow H Lee
- Chemistry Program, University of Northern British Columbia , Prince George, Canada
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