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Lee YR, Chang CM, Yeh YC, Huang CYF, Lin FM, Huang JT, Hsieh CC, Wang JR, Liu HS. Honeysuckle Aqueous Extracts Induced let-7a Suppress EV71 Replication and Pathogenesis In Vitro and In Vivo and Is Predicted to Inhibit SARS-CoV-2. Viruses 2021; 13:v13020308. [PMID: 33669264 PMCID: PMC7920029 DOI: 10.3390/v13020308] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/17/2022] Open
Abstract
Honeysuckle (Lonicera japonica Thunb) is a traditional Chinese medicine (TCM) with an antipathogenic activity. MicroRNAs (miRNAs) are small non-coding RNA molecules that are ubiquitously expressed in cells. Endogenous miRNA may function as an innate response to block pathogen invasion. The miRNA expression profiles of both mice and humans after the ingestion of honeysuckle were obtained. Fifteen overexpressed miRNAs overlapped and were predicted to be capable of targeting three viruses: dengue virus (DENV), enterovirus 71 (EV71) and SARS-CoV-2. Among them, let-7a was examined to be capable of targeting the EV71 RNA genome by reporter assay and Western blotting. Moreover, honeysuckle-induced let-7a suppression of EV71 RNA and protein expression as well as viral replication were investigated both in vitro and in vivo. We demonstrated that let-7a targeted EV71 at the predicted sequences using luciferase reporter plasmids as well as two infectious replicons (pMP4-y-5 and pTOPO-4643). The suppression of EV71 replication and viral load was demonstrated in two cell lines by luciferase activity, RT-PCR, real-time PCR, Western blotting and plaque assay. Furthermore, EV71-infected suckling mice fed honeysuckle extract or inoculated with let-7a showed decreased clinical scores and a prolonged survival time accompanied with decreased viral RNA, protein expression and virus titer. The ingestion of honeysuckle attenuates EV71 replication and related pathogenesis partially through the upregulation of let-7a expression both in vitro and in vivo. Our previous report and the current findings imply that both honeysuckle and upregulated let-7a can execute a suppressive function against the replication of DENV and EV71. Taken together, this evidence indicates that honeysuckle can induce the expression of let-7a and that this miRNA as well as 11 other miRNAs have great potential to prevent and suppress EV71 replication.
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Affiliation(s)
- Ying-Ray Lee
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chia-Ming Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
| | - Yuan-Chieh Yeh
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Keelung Medical Center, Keelung 204, Taiwan;
- Program in Molecular Medicine, School of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan;
| | - Chi-Ying F. Huang
- Program in Molecular Medicine, School of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan;
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan;
| | - Juan-Ting Huang
- Division of Big Data, Phalanx Biotech Group, Hsinchu 300, Taiwan;
| | - Chang-Chi Hsieh
- Department of Animal Science and Biotechnology, Tunghai University, Taichung 407, Taiwan;
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
| | - Hsiao-Sheng Liu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
- Center for Cancer Research, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- M. Sc. Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-7-3121101 (ext. 2378)
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Kato M, Abdollahi M, Tunduguru R, Tsark W, Chen Z, Wu X, Wang J, Chen ZB, Lin FM, Lanting L, Wang M, Huss J, Fueger PT, Chan D, Natarajan R. Publisher Correction: miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1. Commun Biol 2021; 4:175. [PMID: 33542531 PMCID: PMC7862629 DOI: 10.1038/s42003-021-01691-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s42003-021-01691-4
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Affiliation(s)
- Mitsuo Kato
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
| | - Maryam Abdollahi
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Ragadeepthi Tunduguru
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Walter Tsark
- Transgenic Mouse Facility, Center for Comparative Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Zhuo Chen
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Feng-Mao Lin
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Mei Wang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Janice Huss
- Department of Cellular and Molecular Endocrinology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Patrick T Fueger
- Department of Cellular and Molecular Endocrinology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.,Comprehensive Metabolic Phenotyping Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - David Chan
- Division of Biology and Biological Engineering, Caltech, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA. .,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
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Kato M, Abdollahi M, Tunduguru R, Tsark W, Chen Z, Wu X, Wang J, Chen ZB, Lin FM, Lanting L, Wang M, Huss J, Fueger PT, Chan D, Natarajan R. miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1. Commun Biol 2021; 4:30. [PMID: 33398021 PMCID: PMC7782535 DOI: 10.1038/s42003-020-01516-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/23/2020] [Indexed: 01/29/2023] Open
Abstract
Diabetic kidney disease (DKD) is a major complication of diabetes. Expression of members of the microRNA (miRNA) miR-379 cluster is increased in DKD. miR-379, the most upstream 5'-miRNA in the cluster, functions in endoplasmic reticulum (ER) stress by targeting EDEM3. However, the in vivo functions of miR-379 remain unclear. We created miR-379 knockout (KO) mice using CRISPR-Cas9 nickase and dual guide RNA technique and characterized their phenotype in diabetes. We screened for miR-379 targets in renal mesangial cells from WT vs. miR-379KO mice using AGO2-immunopreciptation and CLASH (cross-linking, ligation, sequencing hybrids) and identified the redox protein thioredoxin and mitochondrial fission-1 protein. miR-379KO mice were protected from features of DKD as well as body weight loss associated with mitochondrial dysfunction, ER- and oxidative stress. These results reveal a role for miR-379 in DKD and metabolic processes via reducing adaptive mitophagy. Strategies targeting miR-379 could offer therapeutic options for DKD.
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Affiliation(s)
- Mitsuo Kato
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
| | - Maryam Abdollahi
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Ragadeepthi Tunduguru
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Walter Tsark
- Transgenic Mouse Facility, Center for Comparative Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Zhuo Chen
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Feng-Mao Lin
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Mei Wang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Janice Huss
- Department of Cellular and Molecular Endocrinology, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Patrick T Fueger
- Department of Cellular and Molecular Endocrinology, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Comprehensive Metabolic Phenotyping Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - David Chan
- Division of Biology and Biological Engineering, Caltech, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
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Tang X, Miao Y, Luo Y, Sriram K, Qi Z, Lin FM, Gu Y, Lai CH, Hsu CY, Peterson KL, Van Keuren-Jensen K, Fueger PT, Yeo GW, Natarajan R, Zhong S, Chen ZB. Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction. Circulation 2020; 142:365-379. [PMID: 32393053 DOI: 10.1161/circulationaha.119.041231] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Metabolic disorders such as obesity and diabetes mellitus can cause dysfunction of endothelial cells (ECs) and vascular rarefaction in adipose tissues. However, the modulatory role of ECs in adipose tissue function is not fully understood. Other than vascular endothelial growth factor-vascular endothelial growth factor receptor-mediated angiogenic signaling, little is known about the EC-derived signals in adipose tissue regulation. We previously identified Argonaute 1 (AGO1; a key component of microRNA-induced silencing complex) as a crucial regulator in hypoxia-induced angiogenesis. In this study, we intend to determine the AGO1-mediated EC transcriptome, the functional importance of AGO1-regulated endothelial function in vivo, and the relevance to adipose tissue function and obesity. METHODS We generated and subjected mice with EC-AGO1 deletion (EC-AGO1-knockout [KO]) and their wild-type littermates to a fast food-mimicking, high-fat high-sucrose diet and profiled the metabolic phenotypes. We used crosslinking immunoprecipitation- and RNA-sequencing to identify the AGO1-mediated mechanisms underlying the observed metabolic phenotype of EC-AGO1-KO. We further leveraged cell cultures and mouse models to validate the functional importance of the identified molecular pathway, for which the translational relevance was explored using human endothelium isolated from healthy donors and donors with obesity/type 2 diabetes mellitus. RESULTS We identified an antiobesity phenotype of EC-AGO1-KO, evident by lower body weight and body fat, improved insulin sensitivity, and enhanced energy expenditure. At the organ level, we observed the most significant phenotype in the subcutaneous and brown adipose tissues of KO mice, with greater vascularity and enhanced browning and thermogenesis. Mechanistically, EC-AGO1 suppression results in inhibition of thrombospondin-1 (THBS1/TSP1), an antiangiogenic and proinflammatory cytokine that promotes insulin resistance. In EC-AGO1-KO mice, overexpression of TSP1 substantially attenuated the beneficial phenotype. In human endothelium isolated from donors with obesity or type 2 diabetes mellitus, AGO1 and THBS1 are expressed at higher levels than the healthy controls, supporting a pathological role of this pathway. CONCLUSIONS Our study suggests a novel mechanism by which ECs, through the AGO1-TSP1 pathway, control vascularization and function of adipose tissues, insulin sensitivity, and whole-body metabolic state.
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Affiliation(s)
- Xiaofang Tang
- Department of Diabetes Complications and Metabolism (X.T., Y.M., Y.L., K.S., F.L., C.H.L., R.N., Z.C.), City of Hope, Duarte, CA
| | - Yifei Miao
- Department of Diabetes Complications and Metabolism (X.T., Y.M., Y.L., K.S., F.L., C.H.L., R.N., Z.C.), City of Hope, Duarte, CA
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism (X.T., Y.M., Y.L., K.S., F.L., C.H.L., R.N., Z.C.), City of Hope, Duarte, CA
| | - Kiran Sriram
- Department of Diabetes Complications and Metabolism (X.T., Y.M., Y.L., K.S., F.L., C.H.L., R.N., Z.C.), City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (K.S., P.T.F., R.N., Z.C.), City of Hope, Duarte, CA
| | - Zhijie Qi
- Department of Bioengineering (Z.Q., S.Z.), University of California at San Diego, La Jolla
| | - Feng-Mao Lin
- Department of Diabetes Complications and Metabolism (X.T., Y.M., Y.L., K.S., F.L., C.H.L., R.N., Z.C.), City of Hope, Duarte, CA
| | - Yusu Gu
- Department of Medicine (Y.G., K.L.P.), University of California at San Diego, La Jolla
| | - Chih-Hung Lai
- Department of Diabetes Complications and Metabolism (X.T., Y.M., Y.L., K.S., F.L., C.H.L., R.N., Z.C.), City of Hope, Duarte, CA
| | - Chien-Yi Hsu
- Department of Internal Medicine, Taipei Medical University Hospital, Taiwan (C.Y.H)
| | - Kirk L Peterson
- Department of Medicine (Y.G., K.L.P.), University of California at San Diego, La Jolla
| | | | - Patrick T Fueger
- Irell and Manella Graduate School of Biological Sciences (K.S., P.T.F., R.N., Z.C.), City of Hope, Duarte, CA.,Department of Molecular and Cellular Endocrinology (P.T.F.), City of Hope, Duarte, CA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine (G.W.Y.), University of California at San Diego, La Jolla
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism (X.T., Y.M., Y.L., K.S., F.L., C.H.L., R.N., Z.C.), City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (K.S., P.T.F., R.N., Z.C.), City of Hope, Duarte, CA
| | - Sheng Zhong
- Department of Bioengineering (Z.Q., S.Z.), University of California at San Diego, La Jolla
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism (X.T., Y.M., Y.L., K.S., F.L., C.H.L., R.N., Z.C.), City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (K.S., P.T.F., R.N., Z.C.), City of Hope, Duarte, CA
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Lin FM, Yost SE, Wen W, Frankel PH, Schmolze D, Chu PG, Yuan YC, Liu Z, Yim J, Chen Z, Yuan Y. Differential gene expression and AKT targeting in triple negative breast cancer. Oncotarget 2019; 10:4356-4368. [PMID: 31320990 PMCID: PMC6633890 DOI: 10.18632/oncotarget.27026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/30/2019] [Indexed: 02/03/2023] Open
Abstract
Background: Metastatic triple negative breast cancer (mTNBC) is a heterogeneous disease with poor prognosis. Molecular evolution of TNBC through chemotherapy selection pressure is well recognized but poorly understood. PI3K/AKT/mTOR is one of the most commonly identified oncogenic-driver pathways in breast cancer. The current study is designed to understand the genomic and transcriptomic changes, focusing on the PI3K/AKT/mTOR pathway alterations in paired primary and metastatic TNBCs. Results: Genomic analysis of 7 paired specimens identified 67 known mutations including those from the following signaling pathways: cell cycle, p53, PI3K/AKT/mTOR, RAS/MAPK, and RTK/GF. Principle coordinate analysis (PCoA) identified 4 distinctive molecular groups based on the gene expression patterns of PI3K/AKT/mTOR pathway. Key differentially-expressed genes included AKT3, GSK3B, GNA11, PI3KR1, and GNAQ. Importantly, AKT-targeted therapy showed efficacy in a patient-derived xenograft (PDX) model of TNBC in vivo. Conclusion: Genomic discordance of paired primary and metastatic TNBCs was identified, with significant increase in tumor proliferation pathways seen in metastases. Among the differentially expressed genes, AKT3 can potentially serve as a target for novel combination therapy for treatment of metastatic TNBC. Methods: Paired specimens from 10 patients with TNBCs were identified through an IRB-approved protocol (2002-2015). FoundationOneTM sequencing was performed for genomic profiling, and Affymetrix Human Genechip 2.0st was used for mRNA expression profiling. The similarity among samples was calculated based on Pearson correlation coefficients, which were used to construct hierarchical clustering and heat maps.
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Affiliation(s)
- Feng-Mao Lin
- Department of Diabetes Complications and Metabolism, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Susan E. Yost
- Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Wei Wen
- Department of Surgery, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Paul H. Frankel
- Department of Biostatistics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Pei-Guo Chu
- Department of Pathology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Yate-Ching Yuan
- Bioinformatics Core Facility, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Zheng Liu
- Bioinformatics Core Facility, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - John Yim
- Department of Surgery, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Zhen Chen
- Department of Diabetes Complications and Metabolism, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
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Chu SY, Chou CH, Huang HD, Yen MH, Hong HC, Chao PH, Wang YH, Chen PY, Nian SX, Chen YR, Liou LY, Liu YC, Chen HM, Lin FM, Chang YT, Chen CC, Lee OK. Mechanical stretch induces hair regeneration through the alternative activation of macrophages. Nat Commun 2019; 10:1524. [PMID: 30944305 PMCID: PMC6447615 DOI: 10.1038/s41467-019-09402-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/04/2019] [Indexed: 12/28/2022] Open
Abstract
Tissues and cells in organism are continuously exposed to complex mechanical cues from the environment. Mechanical stimulations affect cell proliferation, differentiation, and migration, as well as determining tissue homeostasis and repair. By using a specially designed skin-stretching device, we discover that hair stem cells proliferate in response to stretch and hair regeneration occurs only when applying proper strain for an appropriate duration. A counterbalance between WNT and BMP-2 and the subsequent two-step mechanism are identified through molecular and genetic analyses. Macrophages are first recruited by chemokines produced by stretch and polarized to M2 phenotype. Growth factors such as HGF and IGF-1, released by M2 macrophages, then activate stem cells and facilitate hair regeneration. A hierarchical control system is revealed, from mechanical and chemical signals to cell behaviors and tissue responses, elucidating avenues of regenerative medicine and disease control by demonstrating the potential to manipulate cellular processes through simple mechanical stimulation.
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Affiliation(s)
- Szu-Ying Chu
- Department of Dermatology, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, 112, Taiwan.,Department of Dermatology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chih-Hung Chou
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsien-Da Huang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Sciences and Engineering, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Meng-Hua Yen
- Department of Electronic Engineering, National Chin-Yi University of Technology, Taichung, 411, Taiwan
| | - Hsiao-Chin Hong
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Po-Han Chao
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yu-Hsuan Wang
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, 999077, China.,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Po-Yu Chen
- Department of Dermatology, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,Department of Dermatology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Shi-Xin Nian
- Department of Dermatology, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,Department of Dermatology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yu-Ru Chen
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, 112, Taiwan
| | - Li-Ying Liou
- Department of Dermatology, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,Department of Dermatology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Yu-Chen Liu
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hui-Mei Chen
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Feng-Mao Lin
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yun-Ting Chang
- Department of Dermatology, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,Department of Dermatology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chih-Chiang Chen
- Department of Dermatology, Taipei Veterans General Hospital, Taipei, 112, Taiwan. .,Institute of Clinical Medicine, National Yang-Ming University, Taipei, 112, Taiwan. .,Department of Dermatology, National Yang-Ming University, Taipei, 112, Taiwan.
| | - Oscar K Lee
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, 112, Taiwan. .,Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, 999077, China. .,Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong, 999077, China.
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7
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Chen HM, Chen CC, Chen CC, Wang SC, Wang CL, Huang CH, Liou JS, Liu TW, Peng HL, Lin FM, Liu CY, Weng SL, Cheng CJ, Hung YF, Liao CC, Huang HD. Gut microbiome changes in overweight male adults following bowel preparation. BMC Genomics 2018; 19:904. [PMID: 30598081 PMCID: PMC6311932 DOI: 10.1186/s12864-018-5285-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Human gut microbiome has an essential role in human health and disease. Although the major dominant microbiota within individuals have been reported, the change of gut microbiome caused by external factors, such as antibiotic use and bowel cleansing, remains unclear. We conducted this study to investigate the change of gut microbiome in overweight male adults after bowel preparation, where none of the participants had been diagnosed with any systemic diseases. Methods A total of 20 overweight, male Taiwanese adults were recruited, and all participants were omnivorous. The participants provided fecal samples and blood samples at three time points: prior to bowel preparation, 7 days after colonoscopy, and 28 days after colonoscopy. The microbiota composition in fecal samples was analyzed using 16S ribosome RNA gene amplicon sequencing. Results Our results demonstrated that the relative abundance of the most dominant bacteria hardly changed from prior to bowel preparation to 28 days after colonoscopy. Using the ratio of Prevotella to the sum of Prevotella and Bacteroides in the fecal samples at baseline, the participants were separated into two groups. The fecal samples of the Type 1 group was Bacteroides-dominant, and that of the Type 2 group was Prevotella-dominant with a noticeable presence Bacteroides. Bulleidia appears more in the Type 1 fecal samples, while Akkermensia appears more in the Type 2 fecal samples. Of each type, the gut microbial diversity differed slightly among the three collection times. Additionally, the Type 2 fecal microbiota was temporarily susceptible to bowel cleansing. Predictive functional analysis of microbial community reveals that their activities for the mineral absorption metabolism and arachidonic acid metabolism differed significantly between the two types. Depending on their fecal type, the variance of triglycerides and C-reactive protein also differed between the two types of participants. Conclusions Depending upon the fecal type, the microbial diversity and the predictive functional modules of microbial community differed significantly after bowel preparation. In addition, blood biochemical markers presented somewhat associated with fecal type. Therefore, our results might provide some insights as to how knowledge of the microbial community could be used to promote health through personalized clinical treatment. Electronic supplementary material The online version of this article (10.1186/s12864-018-5285-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui-Mei Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chung-Chu Chen
- Division of Hepatology and Gastroenterology, Department of Internal Medicine, MacKay Memorial Hospital, Hsinchu, 300, Taiwan.,Teaching Center of Natural Science, Minghsin University of Science and Technology, Hsinchu, 300, Taiwan
| | - Chien-Chi Chen
- Food Industry Research and Development Institute, Hsinchu, 300, Taiwan
| | - Shen-Chih Wang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Departmnet of Anesthesiology, Taipei Veterans General Hospital, Taipei, 112, Taiwan.,School of Medicine, National Yang Ming University, Taipei, 112, Taiwan
| | - Chun-Lin Wang
- Food Industry Research and Development Institute, Hsinchu, 300, Taiwan
| | - Chien-Hsun Huang
- Food Industry Research and Development Institute, Hsinchu, 300, Taiwan
| | - Jong-Shian Liou
- Food Industry Research and Development Institute, Hsinchu, 300, Taiwan
| | - Ta-Wei Liu
- Food Industry Research and Development Institute, Hsinchu, 300, Taiwan
| | - Hwei-Ling Peng
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chia-Yuan Liu
- Division of Gastroenterology, Department of Medicine & Department of Medical Research, MacKay Memorial Hospital, Taipei, 112, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei City, 252, Taiwan
| | - Shun-Long Weng
- Department of Medicine, MacKay Medical College, New Taipei City, 252, Taiwan.,Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu, 300, Taiwan.,MacKay Medicine, Nursing and Management College, Taipei, 112, Taiwan
| | - Chieh-Jen Cheng
- Food Industry Research and Development Institute, Hsinchu, 300, Taiwan
| | - Yi-Fang Hung
- Food Industry Research and Development Institute, Hsinchu, 300, Taiwan
| | - Chii-Cherng Liao
- Food Industry Research and Development Institute, Hsinchu, 300, Taiwan.
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,School of Science and Engineering, The Chinese University of Hong Kong, Guangdong Province, Shenzhen, 518172, China. .,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Guangdong Province, Shenzhen, 518172, China.
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8
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Chen HM, Chang TH, Lin FM, Liang C, Chiu CM, Yang TL, Yang T, Huang CY, Cheng YN, Chang YA, Chang PY, Weng SL. Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis. BMC Genomics 2018; 19:876. [PMID: 30598080 PMCID: PMC6311936 DOI: 10.1186/s12864-018-5284-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the “normal” vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel criteria and Nugent score test are widely used for diagnosing BV; however, these tests are based on different criteria, and so may indicate distinct changes in the vaginal microbial community. Nevertheless, few studies have compared the results of these test against metagenomics analysis. Methods Vaginal flora samples from 77 participants were classified according to the Amsel criteria and Nugent score test. The microbiota composition was analyzed using 16S ribosome RNA gene amplicon sequencing. Bioinformatics analysis and multivariate statistical analysis were used to evaluate the microbial diversity and function. Results Only 3 % of the participants diagnosed BV negative using the Amsel criteria (A−) were BV-positive according to the Nugent score test (N+), while over half of the BV-positive patients using the Amsel criteria (A+) were BV-negative according to the Nugent score test (N−). Thirteen genera showed significant differences in distribution among BV status defined by BV tests (e.g., A − N−, A + N− and A + N+). Variations in the four most abundant taxa, Lactobacillus, Gardnerella, Prevotella, and Escherichia, were responsible for most of this dissimilarity. Furthermore, vaginal microbial diversity differed significantly among the three groups classified by the Nugent score test (N−, N+, and intermediate flora), but not between the Amsel criteria groups. Numerous predictive microbial functions, such as bacterial chemotaxis and bacterial invasion of epithelial cells, differed significantly among multiple BV test, but not between the A− and A+ groups. Conclusions Metagenomics analysis can greatly expand our current understanding of vaginal microbial diversity in health and disease. Metagenomics profiling may also provide more reliable diagnostic criteria for BV testing. Electronic supplementary material The online version of this article (10.1186/s12864-018-5284-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui-Mei Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan.,Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chih-Min Chiu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Tzu-Ling Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ting Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chia-Yen Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, Taiwan
| | - Yeong-Nan Cheng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yi-An Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Medical Research, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Po-Ya Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Medical Research, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Shun-Long Weng
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan. .,Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan. .,MacKay Junior College of Medicine, Nursing and Management, Taipei, Taiwan.
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9
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Nieminen T, Scott TA, Lin FM, Chen Z, Yla-Herttuala S, Morris KV. Long Non-Coding RNA Modulation of VEGF-A during Hypoxia. Noncoding RNA 2018; 4:ncrna4040034. [PMID: 30463374 PMCID: PMC6315885 DOI: 10.3390/ncrna4040034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022] Open
Abstract
The role and function of long non-coding RNAs (lncRNAs) in modulating gene expression is becoming apparent. Vascular endothelial growth factor A (VEGF-A) is a key regulator of blood vessel formation and maintenance making it a promising therapeutic target for activation in ischemic diseases. In this study, we uncover a functional role for two antisense VEGF-A lncRNAs, RP1-261G23.7 and EST AV731492, in transcriptional regulation of VEGF-A during hypoxia. We find here that both lncRNAs are polyadenylated, concordantly upregulated with VEGF-A, localize to the VEGF-A promoter and upstream elements in a hypoxia dependent manner either as a single-stranded RNA or DNA bound RNA, and are associated with enhancer marks H3K27ac and H3K9ac. Collectively, these data suggest that VEGF-A antisense lncRNAs, RP1-261G23.7 and EST AV731492, function as VEGF-A promoter enhancer-like elements, possibly by acting as a local scaffolding for proteins and also small RNAs to tether.
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Affiliation(s)
- Tiina Nieminen
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - Tristan A Scott
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Feng-Mao Lin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Zhen Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Seppo Yla-Herttuala
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, FI-70211 Kuopio, Finland.
| | - Kevin V Morris
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
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10
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Cai Q, Qiao L, Wang M, He B, Lin FM, Palmquist J, Huang SD, Jin H. Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes. Science 2018; 360:1126-1129. [PMID: 29773668 DOI: 10.1126/science.aar4142] [Citation(s) in RCA: 546] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/12/2018] [Indexed: 01/01/2023]
Abstract
Some pathogens and pests deliver small RNAs (sRNAs) into host cells to suppress host immunity. Conversely, hosts also transfer sRNAs into pathogens and pests to inhibit their virulence. Although sRNA trafficking has been observed in a wide variety of interactions, how sRNAs are transferred, especially from hosts to pathogens and pests, is still unknown. Here, we show that host Arabidopsis cells secrete exosome-like extracellular vesicles to deliver sRNAs into fungal pathogen Botrytis cinerea These sRNA-containing vesicles accumulate at the infection sites and are taken up by the fungal cells. Transferred host sRNAs induce silencing of fungal genes critical for pathogenicity. Thus, Arabidopsis has adapted exosome-mediated cross-kingdom RNA interference as part of its immune responses during the evolutionary arms race with the pathogen.
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Affiliation(s)
- Qiang Cai
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Lulu Qiao
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.,Department of Plant Protection, Nanjing Agriculture University, Nanjing, 210095, China
| | - Ming Wang
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Baoye He
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Feng-Mao Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Jared Palmquist
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Sienna-Da Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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11
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Chen Z, Miao Y, Lin FM. Abstract 250: Endothelial functional Regulation by Enhancer-Associated Long Non-Coding RNAs. Arterioscler Thromb Vasc Biol 2018. [DOI: 10.1161/atvb.38.suppl_1.250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Vascular endothelium constitutes the critical interface between circulating blood and vessel wall. Long non-coding RNAs (lncRNAs) are important regulators in gene expression and chromotin remodeling. We recently identified a
l
ncRNA that
e
nhances
e
ndothelial
n
itric oxide synthase (eNOS)
e
xpression (LEENE), that is encoded in a distal enhancer region and mediates long-range DNA interaction to promote the eNOS expression. We now extend from this prototype using a systematic approach to identify enhancer-associated lncRNAs and their molecular and functional regulation of endothelial gene expression. We integrate a variety of publicly available high-throughput sequencing datasets (including various chromatin immunoprecipitation-sequencing) that provide information on histone modifications and transcriptional activity and high-resolution chromatin conformation capture combined with sequencing (4C-seq) profiles generated in our own lab. From these analyses, we identified over 200 enhancer-associated lncRNA candidates with high potential to regulate endothelial gene expression. Quantitative PCR analysis verified that 7 out of the top 10 ranked candidates are differentially regulated by stimuli that alter endothelial gene expression and functions, including high-glucose, TNFα, atorvastatin, and metformin. Using CRISPR-cas9 gene editing to delete these lncRNA-associated enhancer regions and locked nucleic acid-mediated lncRNA inhibition, we demonstrated that the loss-of-function of these lncRNAs lead to significant alteration of endothelial gene expression, including those involved in angiogenesis and eNOS signaling. Collectively, these lncRNAs play an essential role in epigenetic regulation of endothelial functions; the identification of these lncRNAs can have significant impacts on understanding of endothelial homeostasis and dysfunction.
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12
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Wang M, Weiberg A, Lin FM, Thomma B, Huang HD, Jin H. Bidirectional cross-kingdom RNAi and fungal uptake of external RNAs confer plant protection. Nat Plants 2016; 2:16151. [PMID: 27643635 PMCID: PMC5040644 DOI: 10.1038/nplants.2016.151] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 09/01/2016] [Indexed: 05/17/2023]
Abstract
Aggressive fungal pathogens such as Botrytis and Verticillium spp. cause severe crop losses worldwide. We recently discovered that Botrytis cinerea delivers small RNAs (Bc-sRNAs) into plant cells to silence host immunity genes. Such sRNA effectors are mostly produced by Botrytis cinerea Dicer-like protein 1 (Bc-DCL1) and Bc-DCL2. Here we show that expressing sRNAs that target Bc-DCL1 and Bc-DCL2 in Arabidopsis and tomato silences Bc-DCL genes and attenuates fungal pathogenicity and growth, exemplifying bidirectional cross-kingdom RNAi and sRNA trafficking between plants and fungi. This strategy can be adapted to simultaneously control multiple fungal diseases. We also show that Botrytis can take up external sRNAs and double-stranded RNAs (dsRNAs). Applying sRNAs or dsRNAs that target Botrytis DCL1 and DCL2 genes on the surface of fruits, vegetables and flowers significantly inhibits grey mould disease. Such pathogen gene-targeting RNAs represent a new generation of environmentally friendly fungicides.
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Affiliation(s)
- Ming Wang
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Arne Weiberg
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Bart Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
- Correspondence to Hailing Jin.
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13
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Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, Liu CC, Huang HD. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res 2016. [PMID: 26450965 DOI: 10.1093/nargkv940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA-miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.
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Affiliation(s)
- Yu-Chen Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Jian-Rong Li
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Chuan-Hu Sun
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Erik Andrews
- Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
| | - Rou-Fang Chao
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan Mackay Medicine, Nursing and Management College, Taipei, Taiwan Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chao Cheng
- Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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14
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Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, Liu CC, Huang HD. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res 2015; 44:D209-15. [PMID: 26450965 PMCID: PMC4702939 DOI: 10.1093/nar/gkv940] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/08/2015] [Indexed: 01/26/2023] Open
Abstract
Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA–miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.
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Affiliation(s)
- Yu-Chen Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Jian-Rong Li
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Chuan-Hu Sun
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Erik Andrews
- Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
| | - Rou-Fang Chao
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan Mackay Medicine, Nursing and Management College, Taipei, Taiwan Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chao Cheng
- Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
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15
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Belay TA, Lin FM, Lin CY, Hsiao HM, Chang MF, Liu JC. Reduction of concentrated nitrate by using in situ synthesized zero-valent copper. Water Sci Technol 2015; 72:960-965. [PMID: 26360756 DOI: 10.2166/wst.2015.287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although zero-valent iron represents a promising approach for reduction of nitrate (NO(3)(-)) in water, its application in concentrated nitrate is limited by surface passivation. In this study, an alternative approach using in situ synthesized zero-valent copper (Cu(0)) produced by borohydride (NaBH(4)) was investigated. Complete reduction was observed within 55 min by reacting 677 mg-N/L of NO(3)(-) with CuO (0.312 g/L) and NaBH(4) (4.16 g/L) at 60 °C. The pseudo-first-order rate constant was 0.059 min(-1), and it increased threefold when the CuO dose was increased to 1.24 g/L. Increasing the NaBH(4) dose produced less nitrite (NO(2)(-)) throughout the experiments, indicating that it is the primary agent for reducing NO(2)(-). The initial pH exerted a significant effect on the reaction rate, and NO(3)(-) was rapidly reduced when the initial pH was less than 4. Based on the research findings, possible reaction pathways for NO(3)(-) reduction by Cu(0) are proposed in this work.
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Affiliation(s)
- Tihitinna Asmellash Belay
- Department of Chemical Engineering, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei 106, Taiwan E-mail:
| | - F M Lin
- Department of Chemical Engineering, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei 106, Taiwan E-mail:
| | - C Y Lin
- Institute of Nuclear Energy Research, 1000 Wen-Hua Road, Chia-An Village, Lung-Tan District, Tao-Yuan City 32546, Taiwan
| | - H M Hsiao
- Institute of Nuclear Energy Research, 1000 Wen-Hua Road, Chia-An Village, Lung-Tan District, Tao-Yuan City 32546, Taiwan
| | - M F Chang
- Institute of Nuclear Energy Research, 1000 Wen-Hua Road, Chia-An Village, Lung-Tan District, Tao-Yuan City 32546, Taiwan
| | - J C Liu
- Department of Chemical Engineering, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei 106, Taiwan E-mail:
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Chen Z, Wen L, Martin M, Hsu CY, Fang L, Lin FM, Lin TY, Geary MJ, Geary GG, Zhao Y, Johnson DA, Chen JW, Lin SJ, Chien S, Huang HD, Miller YI, Huang PH, Shyy JYJ. Oxidative stress activates endothelial innate immunity via sterol regulatory element binding protein 2 (SREBP2) transactivation of microRNA-92a. Circulation 2014; 131:805-14. [PMID: 25550450 DOI: 10.1161/circulationaha.114.013675] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Oxidative stress activates endothelial innate immunity and disrupts endothelial functions, including endothelial nitric oxide synthase-derived nitric oxide bioavailability. Here, we postulated that oxidative stress induces sterol regulatory element-binding protein 2 (SREBP2) and microRNA-92a (miR-92a), which in turn activate endothelial innate immune response, leading to dysfunctional endothelium. METHODS AND RESULTS Using cultured endothelial cells challenged by diverse oxidative stresses, hypercholesterolemic zebrafish, and angiotensin II-infused or aged mice, we demonstrated that SREBP2 transactivation of microRNA-92a (miR-92a) is oxidative stress inducible. The SREBP2-induced miR-92a targets key molecules in endothelial homeostasis, including sirtuin 1, Krüppel-like factor 2, and Krüppel-like factor 4, leading to NOD-like receptor family pyrin domain-containing 3 inflammasome activation and endothelial nitric oxide synthase inhibition. In endothelial cell-specific SREBP2 transgenic mice, locked nucleic acid-modified antisense miR-92a attenuates inflammasome, improves vasodilation, and ameliorates angiotensin II-induced and aging-related atherogenesis. In patients with coronary artery disease, the level of circulating miR-92a is inversely correlated with endothelial cell-dependent, flow-mediated vasodilation and is positively correlated with serum level of interleukin-1β. CONCLUSIONS Our findings suggest that SREBP2-miR-92a-inflammasome exacerbates endothelial dysfunction during oxidative stress. Identification of this mechanism may help in the diagnosis or treatment of disorders associated with oxidative stress, innate immune activation, and endothelial dysfunction.
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Affiliation(s)
- Zhen Chen
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.).
| | - Liang Wen
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Marcy Martin
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Chien-Yi Hsu
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Longhou Fang
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Feng-Mao Lin
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Ting-Yang Lin
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - McKenna J Geary
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Greg G Geary
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Yongli Zhao
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - David A Johnson
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Jaw-Wen Chen
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Shing-Jong Lin
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Shu Chien
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Hsien-Da Huang
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Yury I Miller
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - Po-Hsun Huang
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.)
| | - John Y-J Shyy
- From Department of Medicine, School of Medicine (Z.C., L.W., M.M., L.F., T.-Y.L., M.J.C., Y.I.M., J.Y.-J.S.) and Department of Bioengineering (S.C.), University of California, San Diego; Department of Cardiovascular Sciences, Houston Methodist Medical Institute, Houston (L.F.); Biochemistry and Molecular Biology Graduate Program (M.M.) and Division of Biomedical Sciences, School of Medicine (D.A.J.), University of California, Riverside; Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan (C.-Y.H., J.-W.C., S.-J.L., P.-H.H.); Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan (F.-M.L., H.-D.H.); Department of Kinesiology and Health Sciences, California State University, San Bernardino (G.G.); and Cardiovascular Research Center, Medical School, Xi'an Jiaotong University, Xi'an, China (Y.Z., J.Y.-J.S.).
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Weng SL, Chiu CM, Lin FM, Huang WC, Liang C, Yang T, Yang TL, Liu CY, Wu WY, Chang YA, Chang TH, Huang HD. Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality. PLoS One 2014; 9:e110152. [PMID: 25340531 PMCID: PMC4207690 DOI: 10.1371/journal.pone.0110152] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 08/21/2014] [Indexed: 12/12/2022] Open
Abstract
Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA), Atypical, and leukocytes). Computer-assisted semen analysis (CASA) was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%), Pseudomonas (9.85%), Prevotella (8.51%) and Gardnerella (4.21%). The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6%) were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.
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Affiliation(s)
- Shun-Long Weng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Chih-Min Chiu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ting Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Tzu-Ling Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chia-Yu Liu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wei-Yun Wu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yi-An Chang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Health GeneTech Corporation, Taoyuan, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Bioinformatics Research, National Chiao Tung University, HsinChu, Taiwan
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Hsieh WJ, Lin FM, Huang HD, Wang H. Investigating microRNA-target interaction-supported tissues in human cancer tissues based on miRNA and target gene expression profiling. PLoS One 2014; 9:e95697. [PMID: 24756070 PMCID: PMC3995724 DOI: 10.1371/journal.pone.0095697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/28/2014] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Recent studies have revealed that a small non-coding RNA, microRNA (miRNA) down-regulates its mRNA targets. This effect is regarded as an important role in various biological processes. Many studies have been devoted to predicting miRNA-target interactions. These studies indicate that the interactions may only be functional in some specific tissues, which depend on the characteristics of an miRNA. No systematic methods have been established in the literature to investigate the correlation between miRNA-target interactions and tissue specificity through microarray data. In this study, we propose a method to investigate miRNA-target interaction-supported tissues, which is based on experimentally validated miRNA-target interactions. The tissue specificity results by our method are in accordance with the experimental results in the literature. AVAILABILITY AND IMPLEMENTATION Our analysis results are available at http://tsmti.mbc.nctu.edu.tw/ and http://www.stat.nctu.edu.tw/hwang/tsmti.html.
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Affiliation(s)
- Wan J. Hsieh
- Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan
| | - Feng-Mao Lin
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hsien-Da Huang
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- * E-mail: (HW); (H-DH)
| | - Hsiuying Wang
- Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan
- * E-mail: (HW); (H-DH)
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Chiu CM, Lin FM, Chang TH, Huang WC, Liang C, Yang T, Wu WY, Yang TL, Weng SL, Huang HD. Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing. J Clin Bioinforma 2014; 4:1. [PMID: 24418497 PMCID: PMC3901789 DOI: 10.1186/2043-9113-4-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 12/13/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The human body plays host to a vast array of bacteria, found in oral cavities, skin, gastrointestinal tract and the vagina. Some bacteria are harmful while others are beneficial to the host. Despite the availability of many methods to identify bacteria, most of them are only applicable to specific and cultivable bacteria and are also tedious. Based on high throughput sequencing technology, this work derives 16S rRNA sequences of bacteria and analyzes probiotics and pathogens species. RESULTS We constructed a database that recorded the species of probiotics and pathogens from literature, along with a modified Smith-Waterman algorithm for assigning the taxonomy of the sequenced 16S rRNA sequences. We also constructed a bacteria disease risk model for seven diseases based on 98 samples. Applicability of the proposed platform is demonstrated by collecting the microbiome in human gut of 13 samples. CONCLUSIONS The proposed platform provides a relatively easy means of identifying a certain amount of bacteria and their species (including uncultivable pathogens) for clinical microbiology applications. That is, detecting how probiotics and pathogens inhabit humans and how affect their health can significantly contribute to develop a diagnosis and treatment method.
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Affiliation(s)
- Chih-Min Chiu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Feng-Mao Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Ting Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Wei-Yun Wu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Tzu-Ling Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Shun-Long Weng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.,Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan.,Mackay Medicine, Nursing and Management College, Taipei, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
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Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel A, Chou CH, Chu CF, Huang HY, Lin CM, Ho SY, Jian TY, Lin FM, Chang TH, Weng SL, Liao KW, Liao IE, Liu CC, Huang HD. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res 2013; 42:D78-85. [PMID: 24304892 PMCID: PMC3965058 DOI: 10.1093/nar/gkt1266] [Citation(s) in RCA: 539] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database (http://mirtarbase.mbc.nctu.edu.tw/) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for >100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system.
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Affiliation(s)
- Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan, Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan, Department of Computer Science and Engineering, National Chung Hsing University, Taichung 402, Taiwan, Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Molecular Bioinformatics Center, National Chiao Tung University, Hsinchu 300, Taiwan, Graduate Department of Clinical Pharmacy, Taipei Medical University, Taipei 110, Taiwan, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan, Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 110, Taiwan, Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu 300, Taiwan, Mackay Medicine, Nursing and Management College, Taipei 112, Taiwan, Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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21
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Weiberg A, Wang M, Lin FM, Zhao H, Zhang Z, Kaloshian I, Huang HD, Jin H. Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science 2013; 342:118-23. [PMID: 24092744 PMCID: PMC4096153 DOI: 10.1126/science.1239705] [Citation(s) in RCA: 715] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Botrytis cinerea, the causative agent of gray mold disease, is an aggressive fungal pathogen that infects more than 200 plant species. Here, we show that some B. cinerea small RNAs (Bc-sRNAs) can silence Arabidopsis and tomato genes involved in immunity. These Bc-sRNAs hijack the host RNA interference (RNAi) machinery by binding to Arabidopsis Argonaute 1 (AGO1) and selectively silencing host immunity genes. The Arabidopsis ago1 mutant exhibits reduced susceptibility to B. cinerea, and the B. cinerea dcl1 dcl2 double mutant that can no longer produce these Bc-sRNAs displays reduced pathogenicity on Arabidopsis and tomato. Thus, this fungal pathogen transfers "virulent" sRNA effectors into host plant cells to suppress host immunity and achieve infection, which demonstrates a naturally occurring cross-kingdom RNAi as an advanced virulence mechanism.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Ming Wang
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Feng-Mao Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Hongwei Zhao
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Zhihong Zhang
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Isgouhi Kaloshian
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Nematology, University of California, Riverside, CA 92521, USA
| | - Hsien-Da Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Teng YC, Lee CF, Li YS, Chen YR, Hsiao PW, Chan MY, Lin FM, Huang HD, Chen YT, Jeng YM, Hsu CH, Yan Q, Tsai MD, Juan LJ. Histone demethylase RBP2 promotes lung tumorigenesis and cancer metastasis. Cancer Res 2013; 73:4711-21. [PMID: 23722541 DOI: 10.1158/0008-5472.can-12-3165] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The retinoblastoma binding protein RBP2 (KDM5A) is a histone demethylase that promotes gastric cancer cell growth and is enriched in drug-resistant lung cancer cells. In tumor-prone mice lacking the tumor suppressor gene RB or MEN1, genetic ablation of RBP2 can suppress tumor initiation, but the pathogenic breadth and mechanistic aspects of this effect relative to human tumors have not been defined. Here, we approached this question in the context of lung cancer. RBP2 was overexpressed in human lung cancer tissues where its depletion impaired cell proliferation, motility, migration, invasion, and metastasis. RBP2 oncogenicity relied on its demethylase and DNA-binding activities. RBP2 upregulated expression of cyclins D1 and E1 while suppressing the expression of cyclin-dependent kinase inhibitor p27 (CDKN1B), each contributing to RBP2-mediated cell proliferation. Expression microarray analyses revealed that RBP2 promoted expression of integrin-β1 (ITGB1), which is implicated in lung cancer metastasis. Mechanistic investigations established that RBP2 bound directly to the p27, cyclin D1, and ITGB1 promoters and that exogenous expression of cyclin D1, cyclin E1, or ITGB1 was sufficient to rescue proliferation or migration/invasion, respectively. Taken together, our results establish an oncogenic role for RBP2 in lung tumorigenesis and progression and uncover novel RBP2 targets mediating this role.
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Affiliation(s)
- Yu-Ching Teng
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang, Taipei, 115, Taiwan
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23
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Chen Z, Lai TC, Jan YH, Lin FM, Wang WC, Xiao H, Wang YT, Sun W, Cui X, Li YS, Fang T, Zhao H, Padmanabhan C, Sun R, Wang DL, Jin H, Chau GY, Huang HD, Hsiao M, Shyy JYJ. Hypoxia-responsive miRNAs target argonaute 1 to promote angiogenesis. J Clin Invest 2013; 123:1057-67. [PMID: 23426184 DOI: 10.1172/jci65344] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 01/03/2013] [Indexed: 12/14/2022] Open
Abstract
Despite a general repression of translation under hypoxia, cells selectively upregulate a set of hypoxia-inducible genes. Results from deep sequencing revealed that Let-7 and miR-103/107 are hypoxia-responsive microRNAs (HRMs) that are strongly induced in vascular endothelial cells. In silico bioinformatics and in vitro validation showed that these HRMs are induced by HIF1α and target argonaute 1 (AGO1), which anchors the microRNA-induced silencing complex (miRISC). HRM targeting of AGO1 resulted in the translational desuppression of VEGF mRNA. Inhibition of HRM or overexpression of AGO1 without the 3' untranslated region decreased hypoxia-induced angiogenesis. Conversely, AGO1 knockdown increased angiogenesis under normoxia in vivo. In addition, data from tumor xenografts and human cancer specimens indicate that AGO1-mediated translational desuppression of VEGF may be associated with tumor angiogenesis and poor prognosis. These findings provide evidence for an angiogenic pathway involving HRMs that target AGO1 and suggest that this pathway may be a suitable target for anti- or proangiogenesis strategies.
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Affiliation(s)
- Zhen Chen
- Division of Biomedical Sciences, University of California, Riverside, California, USA
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Chou CH, Lin FM, Chou MT, Hsu SD, Chang TH, Weng SL, Shrestha S, Hsiao CC, Hung JH, Huang HD. A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics 2013; 14 Suppl 1:S2. [PMID: 23368412 PMCID: PMC3549799 DOI: 10.1186/1471-2164-14-s1-s2] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background MicroRNAs (miRNAs) play a critical role in down-regulating gene expression. By coupling with Argonaute family proteins, miRNAs bind to target sites on mRNAs and employ translational repression. A large amount of miRNA-target interactions (MTIs) have been identified by the crosslinking and immunoprecipitation (CLIP) and the photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP) along with the next-generation sequencing (NGS). PAR-CLIP shows high efficiency of RNA co-immunoprecipitation, but it also lead to T to C conversion in miRNA-RNA-protein crosslinking regions. This artificial error obviously reduces the mappability of reads. However, a specific tool to analyze CLIP and PAR-CLIP data that takes T to C conversion into account is still in need. Results We herein propose the first CLIP and PAR-CLIP sequencing analysis platform specifically for miRNA target analysis, namely miRTarCLIP. From scratch, it automatically removes adaptor sequences from raw reads, filters low quality reads, reverts C to T, aligns reads to 3'UTRs, scans for read clusters, identifies high confidence miRNA target sites, and provides annotations from external databases. With multi-threading techniques and our novel C to T reversion procedure, miRTarCLIP greatly reduces the running time comparing to conventional approaches. In addition, miRTarCLIP serves with a web-based interface to provide better user experiences in browsing and searching targets of interested miRNAs. To demonstrate the superior functionality of miRTarCLIP, we applied miRTarCLIP to two public available CLIP and PAR-CLIP sequencing datasets. miRTarCLIP not only shows comparable results to that of other existing tools in a much faster speed, but also reveals interesting features among these putative target sites. Specifically, we used miRTarCLIP to disclose that T to C conversion within position 1-7 and that within position 8-14 of miRNA target sites are significantly different (p value = 0.02), and even more significant when focusing on sites targeted by top 102 highly expressed miRNAs only (p value = 0.01). These results comply with previous findings and further suggest that combining miRNA expression and PAR-CLIP data can improve accuracy of the miRNA target prediction. Conclusion To sum up, we devised a systematic approach for mining miRNA-target sites from CLIP-seq and PAR-CLIP sequencing data, and integrated the workflow with a graphical web-based browser, which provides a user friendly interface and detailed annotations of MTIs. We also showed through real-life examples that miRTarCLIP is a powerful tool for understanding miRNAs. Our integrated tool can be accessed online freely at http://miRTarCLIP.mbc.nctu.edu.tw.
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Affiliation(s)
- Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
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25
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Wang HM, Chang TH, Lin FM, Chao TH, Huang WC, Liang C, Chu CF, Chiu CM, Wu WY, Chen MC, Weng CT, Weng SL, Chiang FF, Huang HD. A new method for post Genome-Wide Association Study (GWAS) analysis of colorectal cancer in Taiwan. Gene 2012; 518:107-13. [PMID: 23262349 DOI: 10.1016/j.gene.2012.11.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/27/2012] [Indexed: 01/09/2023]
Abstract
Recently, single nucleotide polymorphisms (SNPs) located in specific loci or genes have been identified associated with susceptibility to colorectal cancer (CRC) in Genome-Wide Association Studies (GWAS). However, in different ethnicities and regions, the genetic variations and the environmental factors can widely vary. Therefore, here we propose a post-GWAS analysis method to investigate the CRC susceptibility SNPs in Taiwan by conducting a replication analysis and bioinformatics analysis. One hundred and forty-four significant SNPs from published GWAS results were collected by a literature survey, and two hundred and eighteen CRC samples and 385 normal samples were collected for post-GWAS analysis. Finally, twenty-six significant SNPs were identified and reported as associated with susceptibility to colorectal cancer, other cancers, obesity, and celiac disease in a previous GWAS study. Functional analysis results of 26 SNPs indicate that most biological processes identified are involved in regulating immune responses and apoptosis. In addition, an efficient prediction model was constructed by applying Jackknife feature selection and ANOVA testing. As compared to another risk prediction model of CRC for European Caucasians population, which performs 0.616 of AUC by using 54 SNPs, the proposed model shows good performance in predicting CRC risk within the Taiwanese population, i.e., 0.724 AUC by using 16 SNPs. We believe that the proposed risk prediction model is highly promising for predicting CRC risk within the Taiwanese population. In addition, the functional analysis results could be helpful to explore the potential associated regulatory mechanisms that may be involved in CRC development.
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Affiliation(s)
- Hwei-Ming Wang
- Division of Colorectal Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan.
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Hsu CH, Peng KL, Kang ML, Chen YR, Yang YC, Tsai CH, Chu CS, Jeng YM, Chen YT, Lin FM, Huang HD, Lu YY, Teng YC, Lin ST, Lin RK, Tang FM, Lee SB, Hsu H, Yu JC, Hsiao PW, Juan LJ. TET1 Suppresses Cancer Invasion by Activating the Tissue Inhibitors of Metalloproteinases. Cell Rep 2012; 2:568-79. [DOI: 10.1016/j.celrep.2012.08.030] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Revised: 07/12/2012] [Accepted: 08/31/2012] [Indexed: 11/25/2022] Open
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Chen HY, Lin YM, Chung HC, Lang YD, Lin CJ, Huang J, Wang WC, Lin FM, Chen Z, Huang HD, Shyy JYJ, Liang JT, Chen RH. miR-103/107 promote metastasis of colorectal cancer by targeting the metastasis suppressors DAPK and KLF4. Cancer Res 2012; 72:3631-41. [PMID: 22593189 DOI: 10.1158/0008-5472.can-12-0667] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metastasis is the major cause of poor prognosis in colorectal cancer (CRC), and increasing evidence supports the contribution of miRNAs to cancer progression. Here, we found that high expression of miR-103 and miR-107 (miR-103/107) was associated with metastasis potential of CRC cell lines and poor prognosis in patients with CRC. We showed that miR-103/107 targeted the known metastasis suppressors death-associated protein kinase (DAPK) and Krüppel-like factor 4 (KLF4) in CRC cells, resulting in increased cell motility and cell-matrix adhesion and decreased cell-cell adhesion and epithelial marker expression. miR-103/107 expression was increased in the presence of hypoxia, thereby potentiating DAPK and KLF4 downregulation and hypoxia-induced motility and invasiveness. In mouse models of CRC, miR-103/107 overexpression potentiated local invasion and liver metastasis effects, which were suppressed by reexpression of DAPK or KLF4. miR-103/107-mediated downregulation of DAPK and KLF4 also enabled the colonization of CRC cells at a metastatic site. Clinically, the signature of a miR-103/107 high, DAPK low, and KLF4 low expression profile correlated with the extent of lymph node and distant metastasis in patients with CRC and served as a prognostic marker for metastasis recurrence and poor survival. Our findings therefore indicate that miR-103/107-mediated repression of DAPK and KLF4 promotes metastasis in CRC, and this regulatory circuit may contribute in part to hypoxia-stimulated tumor metastasis. Strategies that disrupt this regulation might be developed to block CRC metastasis.
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Affiliation(s)
- Hsin-Yi Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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Lee TY, Hsu JBK, Lin FM, Chang WC, Hsu PC, Huang HD. N-Ace: using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. J Comput Chem 2010; 31:2759-71. [PMID: 20839302 DOI: 10.1002/jcc.21569] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein acetylation, which is catalyzed by acetyltransferases, is a type of post-translational modification and crucial to numerous essential biological processes, including transcriptional regulation, apoptosis, and cytokine signaling. As the experimental identification of protein acetylation sites is time consuming and laboratory intensive, several computational approaches have been developed for identifying the candidates of experimental validation. In this work, solvent accessibility and the physicochemical properties of proteins are utilized to identify acetylated alanine, glycine, lysine, methionine, serine, and threonine. A two-stage support vector machine was applied to learn the computational models with combinations of amino acid sequences, and the accessible surface area and physicochemical properties of proteins. The predictive accuracy thus achieved is 5% to 14% higher than that of models trained using only amino acid sequences. Additionally, the substrate specificity of the acetylated site was investigated in detail with reference to the subcellular colocalization of acetyltransferases and acetylated proteins. The proposed method, N-Ace, is evaluated using independent test sets in various acetylated residues and predictive accuracies of 90% were achieved, indicating that the performance of N-Ace is comparable with that of other acetylation prediction methods. N-Ace not only provides a user-friendly input/output interface but also is a creative method for predicting protein acetylation sites. This novel analytical resource is now freely available at http://N-Ace.mbc.NCTU.edu.tw/.
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Affiliation(s)
- Tzong-Yi Lee
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li 320, Taiwan
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Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 2010; 39:D163-9. [PMID: 21071411 PMCID: PMC3013699 DOI: 10.1093/nar/gkq1107] [Citation(s) in RCA: 938] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs), i.e. small non-coding RNA molecules (∼22 nt), can bind to one or more target sites on a gene transcript to negatively regulate protein expression, subsequently controlling many cellular mechanisms. A current and curated collection of miRNA–target interactions (MTIs) with experimental support is essential to thoroughly elucidating miRNA functions under different conditions and in different species. As a database, miRTarBase has accumulated more than 3500 MTIs by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs. miRTarBase curates 3576 experimentally verified MTIs between 657 miRNAs and 2297 target genes among 17 species. miRTarBase contains the largest amount of validated MTIs by comparing with other similar, previously developed databases. The MTIs collected in the miRTarBase can also provide a large amount of positive samples to develop computational methods capable of identifying miRNA–target interactions. miRTarBase is now available on http://miRTarBase.mbc.nctu.edu.tw/, and is updated frequently by continuously surveying research articles.
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Affiliation(s)
- Sheng-Da Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
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Chevillotte M, von Einem J, Meier BM, Lin FM, Kestler HA, Mertens T. A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes. Antiviral Res 2010; 85:318-27. [DOI: 10.1016/j.antiviral.2009.10.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 10/02/2009] [Accepted: 10/10/2009] [Indexed: 11/25/2022]
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Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS. miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics 2009; 10:328. [PMID: 19821977 PMCID: PMC2767369 DOI: 10.1186/1471-2105-10-328] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 10/12/2009] [Indexed: 12/27/2022] Open
Abstract
Background MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and robust method for detecting miRNA expression. However, the approach is restricted to detecting the expression of known miRNAs. Second-generation sequencing is an inexpensive and high-throughput sequencing method. This new method is a promising tool with high sensitivity and specificity and can be used to measure the abundance of small-RNA sequences in a sample. Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs. Results This work presents a systematic approach, miRExpress, for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. A stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation. Moreover, we demonstrate the utility of miRExpress in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species. Conclusion We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs.
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Affiliation(s)
- Wei-Chi Wang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China.
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Abstract
Viral infection poses a major problem for public health, horticulture, and animal husbandry, possibly causing severe health crises and economic losses. Viral infections can be identified by the specific detection of viral sequences in many ways. The microarray approach not only tolerates sequence variations of newly evolved virus strains, but can also simultaneously diagnose many viral sequences. Many chips have so far been designed for clinical use. Most are designed for special purposes, such as typing enterovirus infection, and compare fewer than 30 different viral sequences. None considers primer design, increasing the likelihood of cross hybridization to similar sequences from other viruses. To prevent this possibility, this work establishes a platform and database that provides users with specific probes of all known viral genome sequences to facilitate the design of diagnostic chips. This work develops a system for designing probes online. A user can select any number of different viruses and set the experimental conditions such as melting temperature and length of probe. The system then returns the optimal sequences from the database. We have also developed a heuristic algorithm to calculate the probe correctness and show the correctness of the algorithm. (The system that supports probe design for identifying viruses has been published on our web page http://bioinfo.csie.ncu.edu.tw/.)
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Affiliation(s)
- Feng-Mao Lin
- Department of Computer Science and Information Engineering, National Central University, Jhongli City, Taiwan, ROC.
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Abstract
We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5′-alternative splicing, 3′-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein sequences available for a given gene for evidence of AS. Additional features such as the tissue specificity of the mRNA, the protein domain contained by exons, the GC-ratio of exons, the repeats contained within the exons, and the Gene Ontology are annotated computationally for each exonic region that is alternatively spliced. Motivated by a previous investigation of AS-related motifs such as exonic splicing enhancer and exonic splicing silencer, this resource also provides a means of identifying motifs candidates and this should help to identify potential regulatory mechanisms within a particular exonic sequence set and its two flanking intronic sequence sets. This is carried out using motif discovery tools to identify motif candidates related to alternative splicing regulation and together with a secondary structure prediction tool, will help in the identification of the structural properties of such regulatory motifs. The integrated resource is now available on http://SpliceInfo.mbc.NCTU.edu.tw/.
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Affiliation(s)
- Hsien-Da Huang
- Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan
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Huang HD, Lee TY, Wu LC, Lin FM, Juan HF, Horng JT, Tsou AP. MultiProtIdent: Identifying Proteins Using Database Search and Protein−Protein Interactions. J Proteome Res 2005; 4:690-7. [PMID: 15952715 DOI: 10.1021/pr0498335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein identification is important in proteomics. Proteomic analyses based on mass spectra (MS) constitute innovative ways to identify the components of protein complexes. Instruments can obtain the mass spectrum to an accuracy of 0.01 Da or better, but identification errors are inevitable. This study shows a novel tool, MultiProtIdent, which can identify proteins using additional information about protein-protein interactions and protein functional associations. Both single and multiple Peptide Mass Fingerprints (PMFs) are input to MultiProtIdent, which matches the PMFs to a theoretical peptide mass database. The relationships or interactions among proteins are considered to reduce false positives in PMF matching. Experiments to identify protein complexes reveal that MultiProtIdent is highly promising. The website associated with this study is http://dbms104.csie.ncu.edu.tw/.
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Affiliation(s)
- Hsien-Da Huang
- Department of Biological Science and Technology and Institute of Bioinformatics, National Chiao-Tung University, Hsin-Chu 300, Taiwan
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Horng JT, Hu KC, Wu LC, Huang HD, Lin FM, Huang SL, Lai HC, Chu TY. Identifying the combination of genetic factors that determine susceptibility to cervical cancer. ACTA ACUST UNITED AC 2004; 8:59-66. [PMID: 15055802 DOI: 10.1109/titb.2004.824738] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cervical cancer is common among women all over the world. Although infection with high-risk types of human papillomavirus (HPV) has been identified as the primary cause of cervical cancer, only some of those infected go on to develop cervical cancer. Obviously, the progression from HPV infection to cancer involves other environmental and host factors. Recent population-based twin and family studies have demonstrated the importance of the hereditary component of cervical cancer, associated with genetic susceptibility. Consequently, single-nucleotide polymorphism (SNP) markers and microsatellites should be considered genetic factors for determining what combinations of genetic factors are involved in precancerous changes to cervical cancer. This study employs a Bayesian network and four different decision tree algorithms, and compares the performance of these learning algorithms. The results of this study raise the possibility of investigations that could identify combinations of genetic factors, such as SNPs and microsatellites, that influence the risk associated with common complex multifactorial diseases, such as cervical cancer.
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Affiliation(s)
- Jorng-Tzong Horng
- Department of Life Science, National Central University, Jhongli City 320, Taiwan, ROC.
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Siu LK, Lu PL, Chen JY, Lin FM, Chang SC. High-level expression of ampC beta-lactamase due to insertion of nucleotides between -10 and -35 promoter sequences in Escherichia coli clinical isolates: cases not responsive to extended-spectrum-cephalosporin treatment. Antimicrob Agents Chemother 2003; 47:2138-44. [PMID: 12821459 PMCID: PMC161857 DOI: 10.1128/aac.47.7.2138-2144.2003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two Escherichia coli isolates were recovered from the blood of two cancer patients and were demonstrated to produce high levels of the AmpC beta-lactamase with isoelectric points of >9.0. The hypertranscription of ampC RNA was observed by Northern blot hybridization in both isolates. One isolate (isolate EC44) had a point mutation (G-->A at position -28) and insertion of thymidine between positions -20 and -19 of the ampC promoter gene (GenBank accession no. AE000487). The single nucleotide insertion of T between positions -19 and -20 created an optimal distance (17 bp) in the Pribnow box for ampC hyperproduction. The other isolate (isolate EC38) had two point mutations (G-->A at position -28 and C-->T at position +58) and a 2-base (GT) insertion between positions -14 and -15. Although the insertion of GT between positions -14 and -15 may create a new promoter next to the original promoter, cloning of the ampC region with truncated nucleotides of the original -35 region of EC38 failed to verify the hypothesis that a new promoter would be created by such a nucleotide insertion. Instead, multiple start sites for ampC transcription at -1, +1, +2, and +3 were observed in an S1 nuclease protection assay. These results suggest that the RNA polymerase is flexible in the selection of a start site in ampC hypertranscription. In conclusion, nucleotide insertions between the -35 and -10 ampC promoter sequences was the mechanism for the hyperproduction of AmpC beta-lactamase and resistance to oxyimino-cephalosporins. The failure of the two patients to respond to treatment with oxyimino-cephalosporins highlights the important role of such a resistance mechanism in the clinical setting.
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Affiliation(s)
- L K Siu
- Division of Clinical Research, National Health Research Institutes, National Taiwan University Hospital, Taipei, Taiwan.
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Horng JT, Lin FM, Lin JH, Huang HD, Liu BJ. Database of repetitive elements in complete genomes and data mining using transcription factor binding sites. IEEE Trans Inf Technol Biomed 2003; 7:93-100. [PMID: 12834164 DOI: 10.1109/titb.2003.811878] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Approximately 43% of the human genome is occupied by repetitive elements. Even more, around 51% of the rice genome is occupied by repetitive elements. The analysis presented here indicates that repetitive elements in complete genomes may have been very important in the evolutionary genomics. In this study, a database, called the Repeat Sequence Database, is first designed and implemented to store complete and comprehensive repetitive sequences. See http://rsdb.csie.ncu.edu.tw for more information. The database contains direct, inverted and palindromic repetitive sequences, and each repetitive sequence has a variable length ranging from seven to many hundred nucleotides. The repetitive sequences in the database are explored using a mathematical algorithm to mine rules on how combinations of individual binding sites are distributed among repetitive sequences in the database. Combinations of transcription factor binding sites in the repetitive sequences are obtained and then data mining techniques are applied to mine association rules from these combinations. The discovered associations are further pruned to remove insignificant associations and obtain a set of associations. The mined association rules facilitate efforts to identify gene classes regulated by similar mechanisms and accurately predict regulatory elements. Experiments are performed on several genomes including C. elegans, human chromosome 22, and yeast.
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Affiliation(s)
- Jorng-Tzong Horng
- Department of Computer Science and Information Engineering, National Central University, Jung-li City 320, Taiwan, ROC.
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Chyan CL, Tang TC, Chen Y, Liu H, Lin FM, Liu CK, Hsieh MJ, Shiao MS, Huang H, Lin TH. Letter to the editor: backbone 1H, 15N, and 13C resonance assignments of inhibitor-1--a protein inhibitor of protein phosphatase-1. J Biomol NMR 2001; 21:287-288. [PMID: 11775747 DOI: 10.1023/a:1012968805525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Wu TL, Siu LK, Su LH, Lauderdale TL, Lin FM, Leu HS, Lin TY, Ho M. Outer membrane protein change combined with co-existing TEM-1 and SHV-1 beta-lactamases lead to false identification of ESBL-producing Klebsiella pneumoniae. J Antimicrob Chemother 2001; 47:755-61. [PMID: 11389107 DOI: 10.1093/jac/47.6.755] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nine isolates of Klebsiella pneumoniae, obtained from one colonized and eight bacteraemic patients on a paediatric ward, were shown to be identical by PFGE, indicating an outbreak. Screening for extended-spectrum beta-lactamase (ESBL) production using the double-disc synergy test, Etest for ESBLs and agar diffusion tests indicated ESBL production. The isolates showed reduced susceptibility to cefotaxime but not to other third-generation cephalosporins. Molecular studies revealed production of TEM-1 and SHV-1 but no ESBLs were identified. Deficiency in expression of an outer membrane protein (OmpK35) was also observed. These observations led us to postulate that the extremely low level of OmpK35 expression and the co-existence of TEM-1 and SHV-1 resulted in an increased MIC of cefotaxime and the false designation of the isolates as ESBL producers. All the infected infants were treated with either third-generation cephalosporins alone or multiple antibiotics including a third-generation cephalosporin, and recovered and were discharged without sequelae.
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Affiliation(s)
- T L Wu
- Department of Clinical Pathology, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taipei 11529, Taiwan
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Huang HB, Chen YC, Horiuchi A, Tsai LH, Liu HT, Chyan CL, Hsieh MJ, Liu CK, Lin FM, Greengard P, Nairn AC, Shiao MS, Lin TH. Backbone 1H, 15N, and 13C resonance assignments of ARPP-19. J Biomol NMR 2001; 19:383-384. [PMID: 11370788 DOI: 10.1023/a:1011214512601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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42
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Wang CC, Siu LK, Chen MK, Yu YL, Lin FM, Ho M, Chu ML. Use of automated riboprinter and pulsed-field gel electrophoresis for epidemiological studies of invasive Haemophilus influenzae in Taiwan. J Med Microbiol 2001; 50:277-283. [PMID: 11232775 DOI: 10.1099/0022-1317-50-3-277] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 87 invasive isolates of Haemophilus influenzae isolated throughout Taiwan from 1994 to 1998 was collected; 57 were from children <14 years old. In all, 60.9% of isolates were resistant to ampicillin and produced beta-lactamase. Ribotyping revealed six different profiles in 55 isolates of type b, nine profiles in 10 isolates of non-type b and 12 profiles in 22 isolates of non-typable H. influenzae. Among isolates from 35 cases of meningitis, 30 (86%) were in ribogroups 1, 2 and 3 with >90% genetic similarity. Compared with all the other ribogroups, ribogroups 1, 2 and 3, which encompassed all H. influenzae type b, were significantly more prevalent as a cause of meningitis in children <14 years old. Further subtyping of the predominant ribogroup by pulsed-field gel electrophoresis (PFGE) identified differences of 0-6 bands among these isolates of ribogroup 1, which indicated distant relatedness. Automated ribotyping was found to be a useful method and was less time-consuming for molecular epidemiology studies of H. influenzae. PFGE is suggested as an addition to ribotyping to improve discrimination if H. influenzae type b is involved. Differentiating ribogroups between type b and non-type b H. influenzae by genotyping may help to understand the molecular characteristics of outbreaks, endemicity and value of vaccination. According to the results of ribotyping and PFGE, it seems possible that spread of invasive H. influenzae type b had occurred and ribotyping confirmed that there was no clonal spread of non-type b H. influenzae in Taiwan.
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Affiliation(s)
| | - L K Siu
- Department of Paediatrics, Tri-Service General Hospital, National Defense Medical Center, *Division of Clinical Research, National Health Research Institute, †Department of Paediatrics, Taichung Provincial Hospital and ‡Center for Diseases Control, Department of Health, Taiwan
| | - Min-Kung Chen
- Department of Paediatrics, Tri-Service General Hospital, National Defense Medical Center, *Division of Clinical Research, National Health Research Institute, †Department of Paediatrics, Taichung Provincial Hospital and ‡Center for Diseases Control, Department of Health, Taiwan
| | - Yen-Ling Yu
- Department of Paediatrics, Tri-Service General Hospital, National Defense Medical Center, *Division of Clinical Research, National Health Research Institute, †Department of Paediatrics, Taichung Provincial Hospital and ‡Center for Diseases Control, Department of Health, Taiwan
| | - F M Lin
- Department of Paediatrics, Tri-Service General Hospital, National Defense Medical Center, *Division of Clinical Research, National Health Research Institute, †Department of Paediatrics, Taichung Provincial Hospital and ‡Center for Diseases Control, Department of Health, Taiwan
| | - Monto Ho
- Department of Paediatrics, Tri-Service General Hospital, National Defense Medical Center, *Division of Clinical Research, National Health Research Institute, †Department of Paediatrics, Taichung Provincial Hospital and ‡Center for Diseases Control, Department of Health, Taiwan
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Huang HB, Chen YC, Tsai LH, Wang H, Lin FM, Horiuchi A, Greengard P, Nairn AC, Shiao MS, Lin TH. Backbone 1H, 15N, and 13C resonance assignments of inhibitor-2 -- a protein inhibitor of protein phosphatase-1. J Biomol NMR 2000; 17:359-360. [PMID: 11014604 DOI: 10.1023/a:1008355428294] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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44
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Siu LK, Lu PL, Hsueh PR, Lin FM, Chang SC, Luh KT, Ho M, Lee CY. Bacteremia due to extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in a pediatric oncology ward: clinical features and identification of different plasmids carrying both SHV-5 and TEM-1 genes. J Clin Microbiol 2000; 37:4020-7. [PMID: 10565924 PMCID: PMC85870 DOI: 10.1128/jcm.37.12.4020-4027.1999] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirteen patients who had 16 episodes of bacteremia were observed between 1993 and 1997 in a pediatric oncology ward with a high background isolation rate of cefotaxime- or aztreonam-resistant gram-negative bacteria. Four blood isolates were Escherichia coli and 12 were Klebsiella pneumoniae, and these isolates harbored extended-spectrum beta-lactamases (ESBLs). All episodes of bacteremia were nosocomial, all except one of the episodes occurred in neutropenic patients, and all patients were treated with piperacillin or ceftazidime with amikacin and cefazolin prior to the onset of bacteremia. Nine of 13 patients were receiving extended-spectrum beta-lactam treatment when the bacteremias caused by ESBL producers occurred. Molecular studies revealed that four K. pneumoniae SHV-2-producing isolates from 1994 were of the same clone. Other ESBL producers, including six that carried both TEM-1 and SHV-5, five that carried SHV-5, and one that carried SHV-2 alone, were unrelated. In conclusion, SHV-5 was present in 11 of the 16 isolates and coexisted with TEM-1 in 6 isolates. Acquisition of resistance genes probably occurred under antibiotic selection pressure. This study highlights the importance of routine checks for and detection of ESBL producers. Effective therapy against ESBL producers should be considered early for children who have malignancies and neutropenia and who are septic, despite treatment with a regimen that includes an extended-spectrum beta-lactam, in a clinical setting of an increased incidence of ESBL-producing bacteria.
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Affiliation(s)
- L K Siu
- Division of Clinical Research, National Health Research Institute, National Taiwan University Hospital, Taipei, Taiwan
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Lin FM, Sabbahi M. Correlation of spasticity with hyperactive stretch reflexes and motor dysfunction in hemiplegia. Arch Phys Med Rehabil 1999; 80:526-30. [PMID: 10326915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
OBJECTIVES To study the correlation between spasticity and motor dysfunction in the wrist-hand unit of adult hemiplegic patients, and to investigate the correlation between clinical spasticity and hyperactive stretch reflexes. STUDY DESIGN A survey study with a sequential case series of subjects. SETTING Neuromuscular Research Laboratory, School of Physical Therapy, Texas Woman's University, Houston, TX. SUBJECTS Sequential sample recruited from local stroke support groups: 10 patients with chronic hemiplegia caused by cerebral vascular accident who had various degrees of spasticity in the wrist joint. OUTCOME MEASURES Modified Ashworth Scale, amplitudes of stretch reflexes for wrist flexors, grip strength, active range of motion of the wrist joint, and Fugl-Meyer test. RESULTS Strong reverse correlation was found between spasticity and grip strength, the Fugl-Meyer test scores, and the Box and Blocks test scores (p = .001 to .005). Results also indicated a strong and consistent correlation between spasticity and reflexive electromyographic activities of the stretch reflex recorded from active muscles (p = .005 and .007), but not between spasticity and torque response of the stretch reflex. CONCLUSIONS The degree of wrist spasticity is associated with impaired hand function in hemiplegic patients, and hyperactive electromyographic response of the stretch reflex, recorded from active muscles, is a valid indicator of spasticity.
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Affiliation(s)
- F M Lin
- School of Physical Therapy, Texas Woman's University, Houston 77030, USA
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Lin FM, Sabbahi M. The aging effects on the EMG and mechanical responses of the human wrist flexor stretch reflexes. Electromyogr Clin Neurophysiol 1998; 38:323-31. [PMID: 9783117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The purpose of this study is to investigate the effects of aging on the human stretch reflexes. The EMG and torque responses of the stretch reflex of the wrist flexors were evoked by ramp-and-hold mechanical perturbations. The stretch reflexes were recorded at seven test conditions with different stretch velocity and muscle preload. The test results from young and older healthy adult subjects were compared. In average, the absolute amplitude of the short-latency (20-40 ms) EMG (recorded from flexor carpi radialis) reflex response was significantly lower in the older group. If the data were normalized and expressed in percentage of the maximal voluntary EMG activity, however, this group difference was not significant. There was no change in the reflex gain of the short-latency reflex with aging. For the long-latency (50-90 ms) EMG reflex response, both the normalized amplitude and the reflex gain were significantly enhanced with aging, probably through supraspinal mechanisms. There was no significant difference in the threshold velocity for the evoked EMG reflexive activities between age groups. There were also no changes in the reflexive wrist flexion torque with aging. These results suggested that the number of motor units recruited during the stretch reflex activity declined with aging although the percentage of motor units recruited was not affected by aging. It is concluded that the central regulating mechanisms of the spinal motoneuron excitability are not compromised by aging. The automatic gain compensation phenomenon is also preserved with aging.
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Affiliation(s)
- F M Lin
- School of Physical Therapy, Texas Woman's University, Houston, USA
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Chiu CF, Chow KC, Lin FM, Lin CK, Liu SM, Chen KY. Expression of DNA topoisomerase II alpha and multidrug resistance p-glycoprotein in acute leukemia. Zhonghua Yi Xue Za Zhi (Taipei) 1997; 60:184-90. [PMID: 9439046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Drug resistance is a major cause of treatment failure in acute leukemia. Overexpression of multidrug resistance gene and decreased activity of topoisomerase II alpha are suggested as two important mechanisms for this resistance. METHODS We used immunohistochemical method to determine the expressions of both topoisomerase II alpha (topo II alpha) and p-glycoprotein (gp-170) in bone marrow biopsy specimens from 68 cases of acute leukemia. Patients were divided into four groups: (1) leukemia cells with high score for topo II alpha and negative for gp-170; (2) leukemia cells with high score for topo II alpha and positive for gp-170; (3) leukemia cells with low score for topo II alpha and negative for gp-170; and (4) leukemia cells with low score for topo II alpha and positive for gp-170. The clinical responses were then followed as routine, and the clinical correlation was evaluated by analysis of variance and Pearson Chi-Square test. RESULTS The measure of the single parameter (either topo II alpha or gp-170 alone) did not show a significant difference in the overall survival. However, the complete response rate was much higher in the first group patients whose bone marrow reading score was high in topo II alpha and negative for gp-170 expression. Survival duration increased with the increase in the complete response rate. CONCLUSIONS Combined parameters of topo II alpha and gp-170 are more useful than any individual parameter for the prognosis of acute leukemia.
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Affiliation(s)
- C F Chiu
- Department of Internal Medicine, Veterans General Hospital-Taipei, Taiwan, R.O.C
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Lin FM, Pan YC, Dinh TA, Sabbahi M, Shenaq S. Functional assessment of tibial-nerve recovery in the cat using gait analysis: preliminary study. J Reconstr Microsurg 1997; 13:177-83. [PMID: 9101447 DOI: 10.1055/s-2007-1006402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The purpose of this study was to investigate gait-pattern changes after complete tibial nerve lesion in the cat, and to observe whether nerve repair could reverse some of the changes. In six cats, a 5-cm segment of the tibial nerve was transected. The nerve gap was then repaired with nerve autograft in three animals and was unrepaired in three as controls. The walking patterns of the cats were videotaped, and the hip, knee, ankle, and metatarsophalangeal joint angles were measured at the beginnings of the F, E1, E2, and E3 phases of the step cycle. Two weeks after surgery, abnormal gait patterns were observed, and four gait parameters (E3.Hip, E3.Ankle, E3.M-P, and F.Ankle) were found to be statistically significantly different from normal. Six months after surgery, the nerve-graft group had gait-parameter values approaching normal, while the control group showed no measurable improvement. Correspondingly, electrophysiologic testing revealed considerable nerve regeneration in the nerve-graft group but not in the control group. It was concluded that these gait parameters can be used as valid functional indices to evaluate the degree of tibial nerve recovery in the cat model.
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Affiliation(s)
- F M Lin
- Division of Plastic Surgery, Baylor College of Medicine, Houston, Texas, USA
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Zhang YJ, Su RK, Song H, Lin FM. Thermodynamical properties and Coulomb instabilities in hot nuclear systems with the Gogny interaction. Phys Rev C Nucl Phys 1996; 54:1137-1143. [PMID: 9971447 DOI: 10.1103/physrevc.54.1137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Lin FM, Pan YC, Hom C, Sabbahi M, Shenaq S. Ankle stance angle: a functional index for the evaluation of sciatic nerve recovery after complete transection. J Reconstr Microsurg 1996; 12:173-7. [PMID: 8726337 DOI: 10.1055/s-2007-1006472] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This study attempted to develop a motor functional index, ankle stance angle (ASA), to assess rat sciatic nerve regeneration subsequent to autografting. ASA, 50 degrees in normal rats, is the ankle joint angle at the mid-stance phase of the gait cycle. In a nerve graft group, a 1-cm segment of the right sciatic nerve was transected and then repaired with nerve autograft. In an ungrafted group, the nerve gap was left unrepaired. ASA measured 4 months after surgery was statistically significantly larger in the nerve graft group (36 degrees) than in the ungrafted group (22 degrees). The results suggest that ASA is more sensitive than sciatic function index in detecting functional recovery after a complete sciatic nerve lesion. ASA also showed a significant correlation with the passive range of ankle joint motion and gastrocnemius muscle weight. The study concluded that ASA is a reliable index for assessment of regeneration of rat sciatic nerve after a complete lesion. The intra-rater reliability (r = 0.97 and 0.90) and inter-rater reliability (r = 0.85) tests performed support the conclusions.
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Affiliation(s)
- F M Lin
- Division of Plastic Surgery, Baylor College of Medicine, Houston, Texas, USA
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