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Ngum JA, Tatang FJ, Toumeni MH, Nguengo SN, Simo USF, Mezajou CF, Kameni C, Ngongang NN, Tchinda MF, Dongho Dongmo FF, Akami M, Ngane Ngono AR, Tamgue O. An overview of natural products that modulate the expression of non-coding RNAs involved in oxidative stress and inflammation-associated disorders. Front Pharmacol 2023; 14:1144836. [PMID: 37168992 PMCID: PMC10165025 DOI: 10.3389/fphar.2023.1144836] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Oxidative stress is a state in which oxidants are produced in excess in the body's tissues and cells, resulting in a biological imbalance amid the generation of reactive oxygen and nitrogen species (RONS) from redox reactions. In case of insufficient antioxidants to balance, the immune system triggers signaling cascades to mount inflammatory responses. Oxidative stress can have deleterious effects on major macromolecules such as lipids, proteins, and nucleic acids, hence, Oxidative stress and inflammation are among the multiple factors contributing to the etiology of several disorders such as diabetes, cancers, and cardiovascular diseases. Non-coding RNAs (ncRNAs) which were once referred to as dark matter have been found to function as key regulators of gene expression through different mechanisms. They have dynamic roles in the onset and development of inflammatory and oxidative stress-related diseases, therefore, are potential targets for the control of those diseases. One way of controlling those diseases is through the use of natural products, a rich source of antioxidants that have drawn attention with several studies showing their involvement in combating chronic diseases given their enormous gains, low side effects, and toxicity. In this review, we highlighted the natural products that have been reported to target ncRNAs as mediators of their biological effects on oxidative stress and several inflammation-associated disorders. Those natural products include Baicalein, Tanshinone IIA, Geniposide, Carvacrol/Thymol, Triptolide, Oleacein, Curcumin, Resveratrol, Solarmargine, Allicin, aqueous extract or pulp of Açai, Quercetin, and Genistein. We also draw attention to some other compounds including Zanthoxylum bungeanum, Canna genus rhizome, Fuzi-ganjiang herb pair, Aronia melanocarpa, Peppermint, and Gingerol that are effective against oxidative stress and inflammation-related disorders, however, have no known effect on ncRNAs. Lastly, we touched on the many ncRNAs that were found to play a role in oxidative stress and inflammation-related disorders but have not yet been investigated as targets of a natural product. Shedding more light into these two last points of shadow will be of great interest in the valorization of natural compounds in the control and therapy of oxidative stress- and inflammation-associated disorders.
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Zou L, Bao W, Gao Y, Chen M, Wu Y, Wang S, Li C, Zhang J, Zhang D, Wang Q, Zhu A. Integrated Analysis of Transcriptome and microRNA Profile Reveals the Toxicity of Euphorbia Factors toward Human Colon Adenocarcinoma Cell Line Caco-2. Molecules 2022; 27:molecules27206931. [PMID: 36296525 PMCID: PMC9608949 DOI: 10.3390/molecules27206931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022] Open
Abstract
Euphorbia factors, lathyrane-type diterpenoids isolated from the medical herb Euphorbia lathyris L. (Euphorbiaceae), have been associated with intestinal irritation toxicity, but the mechanisms underlying this phenomenon are still unknown. The objective of this study was to evaluate the transcriptome and miRNA profiles of human colon adenocarcinoma Caco-2 cells in response to Euphorbia factors L1 (EFL1) and EFL2. Whole transcriptomes of mRNA and microRNA (miRNA) were obtained using second generation high-throughput sequencing technology in response to 200 μM EFL treatment for 72 h, and the differentially expressed genes and metabolism pathway were enriched. Gene structure changes were analyzed by comparing them with reference genome sequences. After 72 h of treatment, 16 miRNAs and 154 mRNAs were differently expressed between the EFL1 group and the control group, and 47 miRNAs and 1101 mRNAs were differentially expressed between the EFL2 group and the control. Using clusters of orthologous protein enrichment, the sequenced mRNAs were shown to be mainly involved in transcription, post-translational modification, protein turnover, chaperones, signal transduction mechanisms, intracellular trafficking, secretion, vesicular transport, and the cytoskeleton. The differentially expressed mRNA functions and pathways were enriched in transmembrane transport, T cell extravasation, the IL-17 signaling pathway, apoptosis, and the cell cycle. The differentially expressed miRNA EFLs caused changes in the structure of the gene, including alternative splicing, insertion and deletion, and single nucleotide polymorphisms. This study reveals the underlying mechanism responsible for the toxicity of EFLs in intestinal cells based on transcriptome and miRNA profiles of gene expression and structure.
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Affiliation(s)
- Lingyue Zou
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China
| | - Wenqiang Bao
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China
| | - Yadong Gao
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, China
- Fujian Provincial Key Laboratory of Zoonosis Research, Fujian Center for Disease Control and Prevention, Fuzhou 350001, China
| | - Mengting Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China
| | - Yajiao Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China
| | - Shuo Wang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, China
| | - Chutao Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China
| | - Jian Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China
| | - Dongcheng Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China
| | - Qi Wang
- Department of Toxicology, School of Public Health, Peking University, Beijing 100191, China
- Key Laboratory of State Administration of Traditional Chinese Medicine for Compatibility Toxicology, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing 100191, China
- Correspondence: (Q.W.); (A.Z.)
| | - An Zhu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China
- Correspondence: (Q.W.); (A.Z.)
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Zhang H, Liu X, Liu Y, Liu J, Gong X, Li G, Tang M. Crosstalk between regulatory non-coding RNAs and oxidative stress in Parkinson’s disease. Front Aging Neurosci 2022; 14:975248. [PMID: 36016854 PMCID: PMC9396353 DOI: 10.3389/fnagi.2022.975248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson’s disease is the second most common neurodegenerative disease after Alzheimer’s disease, which imposes an ever-increasing burden on society. Many studies have indicated that oxidative stress may play an important role in Parkinson’s disease through multiple processes related to dysfunction or loss of neurons. Besides, several subtypes of non-coding RNAs are found to be involved in this neurodegenerative disorder. However, the interplay between oxidative stress and regulatory non-coding RNAs in Parkinson’s disease remains to be clarified. In this article, we comprehensively survey and overview the role of regulatory ncRNAs in combination with oxidative stress in Parkinson’s disease. The interaction between them is also summarized. We aim to provide readers with a relatively novel insight into the pathogenesis of Parkinson’s disease, which would contribute to the development of pre-clinical diagnosis and treatment.
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Affiliation(s)
- Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- *Correspondence: Gang Li Min Tang
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Gang Li Min Tang
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LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants. Funct Integr Genomics 2021; 21:195-204. [PMID: 33635499 DOI: 10.1007/s10142-021-00769-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/09/2022]
Abstract
Following the elucidation of the critical roles they play in numerous important biological processes, long noncoding RNAs (lncRNAs) have gained vast attention in recent years. Manual annotation of lncRNAs is restricted by known gene annotations and is prone to false prediction due to the incompleteness of available data. However, with the advent of high-throughput sequencing technologies, a magnitude of high-quality data has become available for annotation, especially for plant species such as wheat. Here, we compared prediction accuracies of several machine learning algorithms using a 10-fold cross-validation. This study includes a comprehensive feature selection step to refine irrelevant and repeated features. We present a crop-specific, alignment-free coding potential prediction tool, LncMachine, that performs at higher prediction accuracies than the currently available popular tools (CPC2, CPAT, and CNIT) when used with the Random Forest algorithm. Further, LncMachine with Random Forest performed well on human and mouse data, with an average accuracy of 92.67%. LncMachine only requires either a FASTA file or a TAB separated CSV file containing features as input files. LncMachine can deploy several user-provided algorithms in real time and therefore be effortlessly applied to a wide range of studies.
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Chen L, Bao Y, Jiang S, Zhong XB. The Roles of Long Noncoding RNAs HNF1α-AS1 and HNF4α-AS1 in Drug Metabolism and Human Diseases. Noncoding RNA 2020; 6:ncrna6020024. [PMID: 32599764 PMCID: PMC7345002 DOI: 10.3390/ncrna6020024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNAs with a length of over 200 nucleotides that do not have protein-coding abilities. Recent studies suggest that lncRNAs are highly involved in physiological functions and diseases. lncRNAs HNF1α-AS1 and HNF4α-AS1 are transcripts of lncRNA genes HNF1α-AS1 and HNF4α-AS1, which are antisense lncRNA genes located in the neighborhood regions of the transcription factor (TF) genes HNF1α and HNF4α, respectively. HNF1α-AS1 and HNF4α-AS1 have been reported to be involved in several important functions in human physiological activities and diseases. In the liver, HNF1α-AS1 and HNF4α-AS1 regulate the expression and function of several drug-metabolizing cytochrome P450 (P450) enzymes, which also further impact P450-mediated drug metabolism and drug toxicity. In addition, HNF1α-AS1 and HNF4α-AS1 also play important roles in the tumorigenesis, progression, invasion, and treatment outcome of several cancers. Through interacting with different molecules, including miRNAs and proteins, HNF1α-AS1 and HNF4α-AS1 can regulate their target genes in several different mechanisms including miRNA sponge, decoy, or scaffold. The purpose of the current review is to summarize the identified functions and mechanisms of HNF1α-AS1 and HNF4α-AS1 and to discuss the future directions of research of these two lncRNAs.
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Affiliation(s)
- Liming Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
| | - Yifan Bao
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
| | - Suzhen Jiang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 51006, China
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
- Correspondence: ; Tel.: +01-860-486-3697
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Feng Y, Ge Y, Wu M, Xie Y, Wang M, Chen Y, Shi X. Long Non‑Coding RNAs Regulate Inflammation in Diabetic Peripheral Neuropathy by Acting as ceRNAs Targeting miR-146a-5p. Diabetes Metab Syndr Obes 2020; 13:413-422. [PMID: 32110074 PMCID: PMC7035891 DOI: 10.2147/dmso.s242789] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs), as competing endogenous RNAs (ceRNAs), can regulate various pathophysiological processes by binding competitively to microRNAs at the post-transcription level. Our previous work demonstrated that miR-146a-5p was lowly expressed in diabetic peripheral neuropathy (DPN) rats. However, the ceRNA network in DPN mediated by lncRNAs and miR-146a-5p remains to be explored. METHODS Two groups of rats (n=4 per group), a type 2 diabetes (T2DM) group and a DPN group, were used in this study. Sciatic nerve conduction velocity (NCV) of each rat was determined at the 6th and the 12th week. LncRNA microarray analysis was performed in the sciatic nerve of DPN and T2DM rats. Based on the TargetScan algorithm and the miRanda database, we determined the differentially expressed (DE) lncRNAs bound to miR-146a-5p. Furthermore, we verified the DE lncRNAs potentially bound to miR-146a-5p by qRT-PCR. The genes targeted by miR-146a-5p were identified by bioinformatics prediction and experimental techniques. RESULTS We found 413 DE lncRNAs between DPN and T2DM rats (|log2FC| ≥ 2 and adjust P ≤ 0.05). Eight DE lncRNAs were predicted to bind to miR-146a-5p by both algorithms, of which four were verified by qRT-PCR. TRAF6, IRAK1, and SMAD4 were identified as miR-146a-5p targeted genes and were predominantly enriched in the inflammatory signaling pathway. CONCLUSION LncRNAs may contribute to the pathogenesis of DPN by regulating inflammation through functioning as ceRNAs of miR-146a-5p.
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Affiliation(s)
- Yonghao Feng
- Department of Endocrinology, Jinshan Hospital, Fudan University, Shanghai201508, People’s Republic of China
| | - Ying Ge
- Department of General Medicine, Community Health Service Center of Shanghai Jinshan Industrial Zone, Shanghai201506, People’s Republic of China
| | - Men Wu
- Department of Endocrinology, Jinshan Hospital, Fudan University, Shanghai201508, People’s Republic of China
| | - Yangmei Xie
- Department of Neurology, Jinshan Hospital, Fudan University, Shanghai201508, People’s Republic of China
| | - Ming Wang
- Department of Neurology, Jinshan Hospital, Fudan University, Shanghai201508, People’s Republic of China
| | - Yinghui Chen
- Department of Neurology, Jinshan Hospital, Fudan University, Shanghai201508, People’s Republic of China
| | - Xiaohong Shi
- Department of Endocrinology, Jinshan Hospital, Fudan University, Shanghai201508, People’s Republic of China
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Xu L, Zhu H, Gao F, Tang Y, Zhu Y, Sun Z, Wang J. Upregulation of the long non-coding RNA CBR3-AS1 predicts tumor prognosis and contributes to breast cancer progression. Gene 2019; 2:100014. [PMID: 32550547 PMCID: PMC7285981 DOI: 10.1016/j.gene.2019.100014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 03/13/2019] [Accepted: 03/16/2019] [Indexed: 01/14/2023]
Abstract
Breast cancer is the most common female malignancy and the major cause of cancer-related death in women. Long non-coding RNAs (lncRNAs), as oncogenic or tumor suppressor factor, involved in the development and progression of various cancers. In this study, we sought to investigate the function of lncRNA CBR3-AS1 in breast cancer. We evaluated the expression pattern of CBR3-AS1 in breast cancer tissues and cell lines, explored the correlation between CBR3-AS1 expression and the survival time of breast cancer patients, and probed the effect of CBR3-AS1 on tumor progression of breast cancer through loss-of-function and gain-of-function strategies. Our results showed that CBR3-AS1 was overexpressed in breast cancer tissues and cell lines and predicted the prognosis of breast cancer patients. And CBR3-AS1 exerted biological function as an oncogenic lncRNA, involved in the regulation of cell proliferation, colony formation, apoptosis and tumor growth in breast cancer. Taken together, CBR3-AS1 was up-regulated in breast cancer and promoted the risk of breast cancer. It may be a novel therapeutic target and potential prognostic marker for breast cancer.
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Affiliation(s)
- Lingyun Xu
- Department of Breast Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou 213001, China
| | - Hong Zhu
- Department of Radiation Oncology, Minhang Branch of Cancer Hospital of Fudan University, Shanghai 200240, China
| | - Fei Gao
- Family Planning Department, The Affiliated Changzhou Maternal and Child Health Care Hospital of Nanjing Medical University, Changzhou 213001, China
| | - Yinghua Tang
- Breast Surgery Department, The Affiliated Changzhou Maternal and Child Health Care Hospital of Nanjing Medical University, Changzhou 213001, China
| | - Yajun Zhu
- Department of Radiation Oncology, Changzhou Jintan District People's Hospital of Jiangsu University, Changzhou 213200, China
| | - Zhiqiang Sun
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou 213001, China
| | - Jian Wang
- Department of Radiotherapy, Jiangyin People's Hospital, Affiliated Hospital of Southeast University, Jiangyin, 214400, China
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Chen L, Bao Y, Piekos SC, Zhu K, Zhang L, Zhong XB. A Transcriptional Regulatory Network Containing Nuclear Receptors and Long Noncoding RNAs Controls Basal and Drug-Induced Expression of Cytochrome P450s in HepaRG Cells. Mol Pharmacol 2018; 94:749-759. [PMID: 29691280 DOI: 10.1124/mol.118.112235] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/18/2018] [Indexed: 12/20/2022] Open
Abstract
Cytochrome P450 (P450) enzymes are responsible for metabolizing drugs. Expression of P450s can directly affect drug metabolism, resulting in various outcomes in therapeutic efficacy and adverse effects. Several nuclear receptors are transcription factors that can regulate expression of P450s at both basal and drug-induced levels. Some long noncoding RNAs (lncRNAs) near a transcription factor are found to participate in the regulatory functions of the transcription factors. The aim of this study is to determine whether there is a transcriptional regulatory network containing nuclear receptors and lncRNAs controlling both basal and drug-induced expression of P450s in HepaRG cells. Small interfering RNAs or small hairpin RNAs were applied to knock down four nuclear receptors [hepatocyte nuclear factor 1α (HNF1α), hepatocyte nuclear factor 4α (HNF4α), pregnane X receptor (PXR), and constitutive androstane receptor (CAR)] as well as two lncRNAs [HNF1α antisense RNA 1 (HNF1α-AS1) and HNF4α antisense RNA 1 (HNF4α-AS1)] in HepaRG cells with or without treatment of phenobarbital or rifampicin. Expression of eight P450 enzymes was examined in both basal and drug-induced levels. CAR and PXR mainly regulated expression of specific P450s. HNF1α and HNF4α affected expression of a wide range of P450s as well as other transcription factors. HNF1α and HNF4α controlled the expression of their neighborhood lncRNAs, HNF1α-AS1 and HNF4α-AS1, respectively. HNF1α-AS1 and HNF4α-AS1 was also involved in the regulation of P450s and transcription factors in diverse manners. Altogether, our study concludes that a transcription regulatory network containing the nuclear receptors and lncRNAs controls both basal and drug-induced expression of P450s in HepaRG cells.
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Affiliation(s)
- Liming Chen
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Yifan Bao
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Stephanie C Piekos
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Kexin Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Lirong Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy (L.C., Y.B., S.C.P., X.-b.Z.), and Department of Physiology and Neurobiology (K.Z.), University of Connecticut, Storrs, Connecticut; and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (L.Z.)
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Lee ES, Won YJ, Kim BC, Park D, Bae JH, Park SJ, Noh SJ, Kang YR, Choi SH, Yoon JH, Heo K, Yang K, Son TG. Low-dose irradiation promotes Rad51 expression by down-regulating miR-193b-3p in hepatocytes. Sci Rep 2016; 6:25723. [PMID: 27225532 PMCID: PMC4880923 DOI: 10.1038/srep25723] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/21/2016] [Indexed: 12/28/2022] Open
Abstract
Current evidence indicates that there is a relationship between microRNA (miRNA)-mediated gene silencing and low-dose irradiation (LDIR) responses. Here, alterations of miRNA expression in response to LDIR exposure in male BALB/c mice and three different types of hepatocytes were investigated. The miRNome of the LDIR-exposed mouse spleens (0.01 Gy, 6.5 mGy/h) was analyzed, and the expression of miRNA and mRNA was validated by qRT-PCR. Western blotting, chromatin immunoprecipitation (ChIP), and luciferase assays were also performed to evaluate the interaction between miRNAs and their target genes and to gain insight into the regulation of miRNA expression. The expression of miRNA-193b-3p was down-regulated in the mouse spleen and liver and in various hepatocytes (NCTC, Hepa, and HepG2 cell lines) in response to LDIR. The down-regulation of miR-193b-3p expression was caused by histone deacetylation on the miR-193b-3p promoter in the HepG2 cells irradiated with 0.01 Gy. However, the alteration of histone deacetylation and miR-193b-3p and Rad51 expression in response to LDIR was restored by pretreatment with N-acetyl-cyctein. In conclusion, we provide evidence that miRNA responses to LDIR include the modulation of cellular stress responses and repair mechanisms.
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Affiliation(s)
- Eon-Seok Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
| | - Yeo Jin Won
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
| | - Byoung-Chul Kim
- In silico Toxicology Research Center, Korea Insititute of Toxciology, Daejeon 305-343, Republic of Korea
| | - Daeui Park
- In silico Toxicology Research Center, Korea Insititute of Toxciology, Daejeon 305-343, Republic of Korea
| | - Jin-Han Bae
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
| | - Seong-Joon Park
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
| | - Sung Jin Noh
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
| | - Yeong-Rok Kang
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
| | - Si Ho Choi
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kyu Heo
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
| | - Kwangmo Yang
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea.,Department of Radiation Oncology, Korea Institute of Radiological and Medical Sciences, Seoul 139-709, Republic of Korea
| | - Tae Gen Son
- Research Center, Dongnam Institute of Radiological and Medical Science, 40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 46033, Republic of Korea
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Kohan-Ghadr HR, Kadam L, Jain C, Armant DR, Drewlo S. Potential role of epigenetic mechanisms in regulation of trophoblast differentiation, migration, and invasion in the human placenta. Cell Adh Migr 2016; 10:126-35. [PMID: 26745760 PMCID: PMC4853046 DOI: 10.1080/19336918.2015.1098800] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The proper establishment and organogenesis of the placenta is crucial for intrauterine fetal growth and development. Endometrial invasion by the extravillous trophoblast cells, as well as formation of the syncytiotrophoblast (STB), are of vital importance for placental function. Trophoblast migration and invasion is often compared to tumor metastasis, which uses many of the same molecular mechanisms. However, unlike cancer cells, both initiation and the extent of trophoblast invasion are tightly regulated by feto-maternal cross-talk, which when perturbed, results in a wide range of abnormalities. Multiple factors control the trophoblast, including cytokines and hormones, which are subject to transcriptional regulatory networks. The relevance of epigenetics in transcriptional regulation of trophoblast differentiation and invasion, as well as in the onset of placenta-related pregnancy disorders, became recognized decades ago. Although, there has been tremendous progress in uncovering the molecular foundation of placental development, there is still much to be learned about the epigenetic machinery, and its role in trophoblast differentiation and invasion. This review will provide an overview of the epigenetic control of trophoblast differentiation and invasion. It will also highlight the major epigenetic mechanisms involved in pregnancy complications related to placental deficiencies.
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Affiliation(s)
- Hamid-Reza Kohan-Ghadr
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Leena Kadam
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chandni Jain
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - D. Randall Armant
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sascha Drewlo
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
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11
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MicroRNA-Specificity Protein (Sp) Transcription Factor Interactions and Significance in Carcinogenesis. ACTA ACUST UNITED AC 2015; 1:73-78. [PMID: 26457240 DOI: 10.1007/s40495-014-0012-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Specificity protein (Sp) transcription factors (TFs) such as Sp1, Sp3 and Sp4 are overexpressed in tumors and Sp1 is a negative prognostic factor for multiple tumor types. Sp TFs regulate expression of pro-oncogenic factors important for cell proliferation, survival, angiogenesis, migration/invasion and inflammation and the high expression of Sp TFs in tumors is primarily due to miRNAs. For example, expression of tumor-suppressor-like miRNAs such as miR-200b/c, miR-335, miR-22, miR-149 and others that inactivate Sp1 expression is low in many tumor types. Research in our laboratory has also demonstrated that high expression of Sp TFs is also due to miRNA-dependent inhibition of the transcriptional repressors ZBTB10 and ZBTB4 by miR-27a and miR-20a/miR-17p, respectively. Thus, miRNAs play a critical role in maintaining high levels of Sp1, Sp3, Sp4 and pro-oncogenic Sp-regulated genes in tumors and cancer cells, and there is ample evidence that anticancer agents targeting the miRNASp TF axis can be highly effective for cancer chemotherapy.
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12
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Ranganathan K, Sivasankar V. MicroRNAs - Biology and clinical applications. J Oral Maxillofac Pathol 2014; 18:229-34. [PMID: 25328304 PMCID: PMC4196292 DOI: 10.4103/0973-029x.140762] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/02/2014] [Indexed: 01/27/2023] Open
Abstract
MicroRNAs are a highly conserved group of small, non-coding RNA molecules, which are 19-25 nucleotides in size. Previously thought to be evolutionary debris with no evident function, these small RNAs have been found to control gene expression primarily by silencing the gene. MicroRNAs are critical to cell physiology and development. They are also implicated in pathological processes such as autoimmune diseases, viral infections and carcinogenesis.
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Affiliation(s)
- Kannan Ranganathan
- Department of Oral and Maxillofacial Pathology, Ragas Dental College and Hospital, Uthandi, Chennai, Tamil Nadu, India
| | - Vaishnavi Sivasankar
- Department of Oral and Maxillofacial Pathology, Ragas Dental College and Hospital, Uthandi, Chennai, Tamil Nadu, India
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13
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Wang CM, Wu QQ, Li SQ, Chen FJ, Tuo L, Xie HW, Tong YS, Ji L, Zhou GZ, Cao G, Wu M, Lv J, Shi WH, Cao XF. Upregulation of the long non-coding RNA PlncRNA-1 promotes esophageal squamous carcinoma cell proliferation and correlates with advanced clinical stage. Dig Dis Sci 2014; 59:591-7. [PMID: 24337686 DOI: 10.1007/s10620-013-2956-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 11/13/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND Recent studies revealed that long noncoding RNAs (lncRNAs) play critical regulatory roles in cancer biology. PlncRNA-1 is one of lncRNAs that is associated with cell apoptosis and proliferation of prostate cancer. AIM This study aimed to assess the potential role of PlncRNA-1 in the pathogenesis of esophageal squamous cell carcinoma (ESCC). MATERIALS AND METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression level of PlncRNA-1 in 73 pairs of ESCC and their matched normal tissues. The correlation of PlncRNA-1 with clinicopathological features and clinical stages was also analyzed. Cancer cell proliferation and apoptosis were assessed following knock-down of PlncRNA-1 by MTT, colony formation assay, and flow cytometry. RESULTS The expression of PlncRNA-1 was significantly higher in human ESCC compared with the adjacent noncancerous tissues (69.8 %, p < 0.05), and the high level of PlncRNA-1 expression was significantly correlated with advanced clinical stage (p < 0.01) and lymph node metastasis (p < 0.05). Furthermore, knockdown of PlncRNA-1 reduced cell proliferation and increased the apoptosis in vitro. CONCLUSIONS PlncRNA-1 plays an important role in ESCC cell proliferation. Overexpression of PlncRNA-1 is correlated with advanced tumor stage and lymph node metastasis, and may serve as a potential prognostic marker and therapeutic target for ESCC.
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Affiliation(s)
- Chun-Mei Wang
- Department of Surgical Oncology, Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, Jiangsu, China,
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14
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Mitchell JA, Clay I, Umlauf D, Chen CY, Moir CA, Eskiw CH, Schoenfelder S, Chakalova L, Nagano T, Fraser P. Nuclear RNA sequencing of the mouse erythroid cell transcriptome. PLoS One 2012; 7:e49274. [PMID: 23209567 PMCID: PMC3510205 DOI: 10.1371/journal.pone.0049274] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/08/2012] [Indexed: 12/31/2022] Open
Abstract
In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq) in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq) of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A)-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs.
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Affiliation(s)
- Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
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15
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Guleria P, Mahajan M, Bhardwaj J, Yadav SK. Plant small RNAs: biogenesis, mode of action and their roles in abiotic stresses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2011; 9:183-99. [PMID: 22289475 PMCID: PMC5054152 DOI: 10.1016/s1672-0229(11)60022-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 10/21/2011] [Indexed: 01/01/2023]
Abstract
Small RNAs (sRNAs) are 18-30 nt non-coding regulatory elements found in diverse organisms, which were initially identified as small double-stranded RNAs in Caenorhabditis elegans. With the development of new and improved technologies, sRNAs have also been identified and characterized in plant systems. Among them, micro RNAs (miRNAs) and small interfering RNAs (siRNAs) are found to be very important riboregulators in plants. Various types of sRNAs differ in their mode of biogenesis and in their function of gene regulation. sRNAs are involved in gene regulation at both transcriptional and post-transcriptional levels. They are known to regulate growth and development of plants. Furthermore, sRNAs especially plant miRNAs have been found to be involved in various stress responses, such as oxidative, mineral nutrient deficiency, dehydration, and even mechanical stimulus. Therefore, in the present review, we focus on the current understanding of biogenesis and regulatory mechanisms of plant sRNAs and their responses to various abiotic stresses.
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Affiliation(s)
- Praveen Guleria
- Plant Metabolic Engineering, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, CSIR, Palampur 176061 (HP), India
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16
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Amarante MK, Oda JMM, Reiche EMV, Morimoto HK, Aoki MN, Watanabe MAE. Human endogenous RNAs: Implications for the immunomodulation of Toll-like receptor 3. Exp Ther Med 2011; 2:925-929. [PMID: 22977599 DOI: 10.3892/etm.2011.303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 05/24/2011] [Indexed: 02/07/2023] Open
Abstract
Toll-like receptors (TLRs), a family of mammalian receptors, are able to recognize nucleic acids. TLR3 recognizes double-stranded (ds)RNA, a product of the replication of certain viruses. Polyinosinic-polycytidylic acid, referred to as poly(I:C), an analog of viral dsRNA, interacts with TLR3 thereby eliciting immunoinflammatory responses characteristic of viral infection or down-regulating the expression of chemokine receptor CXCR4. It is known that dsRNA also directly activates interferon (IFN)-induced enzymes, such as the RNA-dependent protein kinase (PKR). In the present study, the mRNA expression of TLR3, CXCR4, IFNγ and PKR was investigated in a culture of peripheral blood mononuclear cells (PBMCs) stimulated with poly(I:C) and endogenous RNA from human PBMCs. No cytotoxic effect on the cells or on the proliferation of CD3(+), CD4(+) and CD8(+) cells was observed. TLR3 expression in the PBMCs in the presence of poly(I:C) was up-regulated 9.5-fold, and TLR3 expression in the PBMCs treated with endogenous RNA was down-regulated 1.8-fold (p=0.002). The same trend was observed for IFNγ where in the presence of poly(I:C) an 8.7-fold increase was noted and in the presence of endogenous RNA a 3.1-fold decrease was observed. In the culture activated with poly(I:C), mRNA expression of CXCR4 increased 8.0-fold and expression of PKR increased 33.0-fold. Expression of these genes decreased in the culture treated with endogenous RNA when compared to the culture without stimulus. Thus, high expression of mRNA for TLR3, IFNγ, CXCR4 and PKR was observed in the presence of poly(I:C) and low expression was observed in the cells cultured with endogenous RNA. In conclusion, TLR3 may play major physiological roles that are not in the context of viral infection. It is possible that RNA released from cells could contain enough double-stranded structures to regulate cell activation. The involvement of endogenous RNA in endogenous gene expression and its implications in the regulation thereof, are still being studied, and will have significant implications in the future.
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Galiveti CR, Rozhdestvensky TS, Brosius J, Lehrach H, Konthur Z. Application of housekeeping npcRNAs for quantitative expression analysis of human transcriptome by real-time PCR. RNA (NEW YORK, N.Y.) 2010; 16:450-61. [PMID: 20040593 PMCID: PMC2811673 DOI: 10.1261/rna.1755810] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 11/09/2009] [Indexed: 05/22/2023]
Abstract
In recent years the improvements in high-throughput gene expression analysis have led to the discovery of numerous non-protein-coding RNA (npcRNA) molecules. They form an abundant class of untranslated RNAs that have shown to play a crucial role in different biochemical pathways in the cell. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an efficient tool to measure RNA abundance and gene expression levels in tiny amounts of material. Despite its sensitivity, the lack of appropriate internal controls necessary for accurate data analysis is a limiting factor for its application in npcRNA research. Common internal controls applied are protein-coding reference genes, also termed "housekeeping" genes (HKGs). However, their expression levels reportedly vary among tissues and different experimental conditions. Moreover, application of HKGs as reference in npcRNA expression analyses is questionable, due to the differences in biogenesis. To address the issue of optimal RT-qPCR normalizers in npcRNA analysis, we performed a systematic evaluation of 18 npcRNAs along with four common HKGs in 20 different human tissues. To determine the most suitable internal control with least expression variance, four evaluation strategies, geNORM, NormFinder, BestKeeper, and the comparative delta C(q) method, were applied. Our data strongly suggest that five npcRNAs, which we term housekeeping RNAs (HKRs), exhibit significantly better constitutive expression levels in 20 different human tissues than common HKGs. Determined HKRs are ideal candidates for RT-qPCR data normalization in human transcriptome analysis, and might also be used as reference genes irrespective of the nature of the genes under investigation.
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Affiliation(s)
- Chenna R Galiveti
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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18
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Ramírez-Gómez F, Ortiz-Pineda PA, Rivera-Cardona G, García-Arrarás JE. LPS-induced genes in intestinal tissue of the sea cucumber Holothuria glaberrima. PLoS One 2009; 4:e6178. [PMID: 19584914 PMCID: PMC2702171 DOI: 10.1371/journal.pone.0006178] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 06/16/2009] [Indexed: 01/16/2023] Open
Abstract
Metazoan immunity is mainly associated with specialized cells that are directly involved with the immune response. Nevertheless, both in vertebrates and invertebrates other organs might respond to immune activation and participate either directly or indirectly in the ongoing immune process. However, most of what is known about invertebrate immunity has been restricted to immune effector cells and little information is available on the immune responses of other tissues or organs. We now focus on the immune reactions of the intestinal tissue of an echinoderm. Our study employs a non-conventional model, the echinoderm Holothuria glaberrima, to identify intestinal molecules expressed after an immune challenge presented by an intra-coelomic injection of lipopolysaccharides (LPS). The expression profiles of intestinal genes expressed differentially between LPS-injected animals and control sea water-injected animals were determined using a custom-made Agilent microarray with 7209 sea cucumber intestinal ESTs. Fifty (50) unique sequences were found to be differentially expressed in the intestine of LPS-treated sea cucumbers. Seven (7) of these sequences represented homologues of known proteins, while the remaining (43) had no significant similarity with any protein, EST or RNA database. The known sequences corresponded to cytoskeletal proteins (Actin and alpha-actinin), metabolic enzymes (GAPDH, Ahcy and Gnmt), metal ion transport/metabolism (major yolk protein) and defense/recognition (fibrinogen-like protein). The expression pattern of 11 genes was validated using semi-quantitative RT-PCR. Nine of these corroborated the microarray results and the remaining two showed a similar trend but without statistical significance. Our results show some of the molecular events by which the holothurian intestine responds to an immune challenge and provide important information to the study of the evolution of the immune response.
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Affiliation(s)
| | - Pablo A. Ortiz-Pineda
- Department of Biology, University of Puerto Rico, Río Piedras, San Juan, Puerto Rico
| | | | - José E. García-Arrarás
- Department of Biology, University of Puerto Rico, Río Piedras, San Juan, Puerto Rico
- * E-mail:
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19
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Sarcinella E, Brown M, Tellier R, Petric M, Mazzulli T. Detection of RNA in purified cytomegalovirus virions. Virus Res 2004; 104:129-37. [PMID: 15246650 DOI: 10.1016/j.virusres.2004.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Revised: 03/15/2004] [Accepted: 03/15/2004] [Indexed: 11/22/2022]
Abstract
Five viral RNA transcripts have recently been detected in purified virions of human cytomegalovirus (HCMV) strain AD169, a well-characterized member of the family Herpesviridae [Science 288 (2000) 2373]. While the function of these transcripts and/or the proteins they encode remains to be elucidated, it is not known whether these transcripts are unique to strain AD169 or are present in other HCMV strains. The objective of this study was to determine if these RNAs are present in other HCMV laboratory strains (Towne and Davis), and a low passage clinical isolate (CL203). These strains of CMV were purified by sequential ultracentrifugation through 20% D-sorbitol and glycerol-potassium tartarate gradients and the morphology and infectivity of the virions confirmed by electron microscopy and inoculation into cell culture. When RNA extracted from the purified virions was amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) the UL 21.5 and TRL/IRL 2-5 transcripts were detected in virions of HCMV strains AD169, Davis, Towne and CL203. The presence of the UL 21.5 and TRL/IRL 2-5 RNA transcripts in all strains tested demonstrates that the packaged transcripts occurs in all strains of HCMV suggesting that they may have a relevant role in the biology of this virus.
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Affiliation(s)
- Elizabeth Sarcinella
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ont., Canada.
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20
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Shirasawa S, Harada H, Furugaki K, Akamizu T, Ishikawa N, Ito K, Ito K, Tamai H, Kuma K, Kubota S, Hiratani H, Tsuchiya T, Baba I, Ishikawa M, Tanaka M, Sakai K, Aoki M, Yamamoto K, Sasazuki T. SNPs in the promoter of a B cell-specific antisense transcript, SAS-ZFAT, determine susceptibility to autoimmune thyroid disease. Hum Mol Genet 2004; 13:2221-31. [PMID: 15294872 DOI: 10.1093/hmg/ddh245] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Autoimmune thyroid disease (AITD) is caused by an immune response to self-thyroid antigens and has a significant genetic component. Antisense RNA transcripts have been implicated in gene regulation. Here we have identified a novel zinc-finger gene, designated ZFAT (zinc-finger gene in AITD susceptibility region), as one of the susceptibility genes in 8q23-q24 through an initial association analysis using the probands in the previous linkage analysis and a subsequent association analysis of the samples from a total of 515 affected individuals and 526 controls. The T allele of the single-nucleotide polymorphism (SNP), Ex9b-SNP10 located in the intron 9 of ZFAT, is associated with increased risk for AITD (dominant model: odds ratio = 1.7, P = 0.000091). The Ex9b-SNP10 falls into the 3'-UTR of truncated-ZFAT (TR-ZFAT) and the promoter region of the small antisense transcript of ZFAT (SAS-ZFAT). In peripheral blood lymphocytes, SAS-ZFAT is exclusively expressed in CD19+ B cells and expression levels of SAS-ZFAT and TR-ZFAT seemed to correlate with the Ex9b-SNP10-T-associated ZFAT-allele, inversely and positively, respectively. The Ex9b-SNP10 is critically involved in the regulation of SAS-ZFAT expression in vitro and this expression results in a decreased expression of TR-ZFAT. These results suggested that the SNP-associated ZFAT-allele plays a critical role in B cell function by affecting the expression level of TR-ZFAT through regulating SAS-ZFAT expression and that this novel regulatory mechanism of SNPs might be involved in controlling susceptibility or resistance to human disease.
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Affiliation(s)
- Senji Shirasawa
- Department of Pathology, Research Institute, International Medical Center of Japan, Toyama 1-21-1, Shinjuku-ku, Tokyo 162-8655, Japan
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21
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Martin S, Pombo A. Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Res 2004; 11:461-70. [PMID: 12971722 DOI: 10.1023/a:1024926710797] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Transcription by the three nuclear RNA polymerases is carried out in transcription factories. This conclusion has been drawn from estimates of the total number of nascent transcripts or active polymerase molecules and the number of transcription sites within a cell. Here we summarise the variety of methods used to determine these parameters, discuss their associated problems and outline future prospects.
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Affiliation(s)
- Sonya Martin
- MRC-Clinical Sciences Centre, Faculty of Medicine, Imperial College School of Science, Technology and Medicine, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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22
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Petrovics G, Zhang W, Makarem M, Street JP, Connelly R, Sun L, Sesterhenn IA, Srikantan V, Moul JW, Srivastava S. Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients. Oncogene 2004; 23:605-11. [PMID: 14724589 DOI: 10.1038/sj.onc.1207069] [Citation(s) in RCA: 200] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
PCGEM1 is a novel, highly prostate tissue-specific, androgen-regulated gene. Here, we demonstrate that PCGEM1 expression is significantly higher in prostate cancer (CaP) cells of African-American men than in Caucasian-American men (P=0.0002). Further, increased PCGEM1 expression associates with normal prostate epithelial cells of CaP patients with a family history of CaP (P=0.0400). PCGEM1 overexpression in LNCaP and in NIH3T3 cells promotes cell proliferation and a dramatic increase in colony formation, suggesting a biological role of PCGEM1 in cell growth regulation. Taken together, the cell proliferation/colony formation-promoting functions of PCGEM1 and the association of its increased expression with high-risk CaP patients suggest the potential roles of PCGEM1 in CaP onset/progression, especially in these high-risk groups.
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Affiliation(s)
- Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research, US Military Cancer Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4799, USA.
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23
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Nikaido I, Saito C, Mizuno Y, Meguro M, Bono H, Kadomura M, Kono T, Morris GA, Lyons PA, Oshimura M, Hayashizaki Y, Okazaki Y. Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res 2003; 13:1402-9. [PMID: 12819139 PMCID: PMC403673 DOI: 10.1101/gr.1055303] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Candidate imprinted transcriptional units in the mouse genome were identified systematically from 27,663 FANTOM2 full-length mouse cDNA clones by expression profiling. Large-scale cDNA microarrays were used to detect differential expression dependent upon chromosomal parent of origin by comparing the mRNA levels in the total tissue of 9.5 dpc parthenogenote and androgenote mouse embryos. Of the FANTOM2 transcripts, 2114 were identified as candidates on the basis of the array data. Of these, 39 mapped to known imprinted regions of the mouse genome, 56 were considered as nonprotein-coding RNAs, and 159 were natural antisense transcripts. The imprinted expression of two transcripts located in the mouse chromosomal region syntenic to the human Prader-Willi syndrome region was confirmed experimentally. We further mapped all candidate imprinted transcripts to the mouse and human genome and were shown in correlation with the imprinting disease loci. These data provide a major resource for understanding the role of imprinting in mammalian inherited traits.
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Affiliation(s)
- Itoshi Nikaido
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan
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Abstract
The noncoding RNAs database is a collection of currently available sequence data on RNAs, which have no protein-coding capacity and have been implicated in regulation of cellular processes. The RNAs included in the database form very heterogenous group of molecules that act on different levels of information transmission in the cell. It includes RNAs acting on the level of chromatin structure, transcriptional and translational regulation of gene expression, modulation of protein function and regulation of subcellular distribution of RNAs and proteins. Those RNAs, with potential regulatory functions have been identified in prokaryotic, animal and plant cells. The database can be accessed at http://biobases.ibch.poznan.pl/ncRNA/.
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Affiliation(s)
- Maciej Szymański
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
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