Shin-Ru Shih

Chang Gung Memorial Hospital, T’ai-pei, Taipei, Taiwan

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Publications (127)490.77 Total impact

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    ABSTRACT: The role of virus-derived small RNAs (vsRNAs) has been identified as an antiviral mechanism in plants, arthropods, and nematodes. Although mammalian DNA viruses have been observed to encode functional miRNAs, whether RNA virus infection generates functional vsRNAs remains under discussion. This article reviews the most recent reports regarding pathways for generating vsRNAs and the identified vsRNA activity in mammalian cells infected with RNA viruses. We also discuss several hypotheses regarding the roles of mammalian vsRNAs and comment on the potential directions for this research field. Copyright © 2015. Published by Elsevier Masson SAS.
    Microbes and Infection 05/2015; 391. DOI:10.1016/j.micinf.2015.04.005 · 2.73 Impact Factor
  • Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi 04/2015; 48(2):S35-S36. DOI:10.1016/j.jmii.2015.02.050 · 2.08 Impact Factor
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    ABSTRACT: Enterovirus 71 (EV71) is a human enterovirus that has seriously affected the Asia-Pacific area for the past two decades. EV71 infection can result in mild hand-foot-and-mouth disease and herpangina and may occasionally lead to severe neurological complications in children. However, the specific biological processes that become altered during EV71 infection remain unclear. To further explore host responses upon EV71 infection, we identified proteins differentially expressed in EV71-infected human glioblastoma SF268 cells using isobaric mass tag (iTRAQ) labeling coupled with multidimensional liquid chromatography-mass spectrometry (LC-MS/MS). Network analysis of proteins altered in cells infected with EV71 revealed that the changed biological processes are related to protein and ion transport, regulation of protein degradation, and homeostatic processes. We confirmed that the levels of NEDD4L and PSMF1 were increased and reduced, respectively, in EV71-infected cells compared to mock-infected control cells. To determine the physiological relevance of our findings, we investigated the consequences of EV71 infection in cells with NEDD4L or PSMF1 depletion. We found that the depletion of NEDD4L significantly reduced the replication of EV71, whereas PSMF1 knockdown enhanced EV71 replication. Collectively, our findings provide the first evidence of proteome-wide dysregulation by EV71 infection and suggest a novel role for the host protein NEDD4L in the replication of this virus.
    Journal of Proteome Research 03/2015; 14(4). DOI:10.1021/pr501199h · 5.00 Impact Factor
  • Guang-Wu Chen · Yu-Nong Gong · Shin-Ru Shih
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    ABSTRACT: An influenza A pandemic occurred in 2009-2010. A novel H1N1 virus (hereafter H1N1pdm) was responsible for this outbreak. H1N1pdm viruses have been largely seen in recent human influenza A viruses. This virus was descended from a triple-reassorted swine virus consisting of human, avian, and swine origins. As a result, the previously established species-associated signatures could be in jeopardy. We analyzed all influenza A sequences in the past 5 years after the inclusion of H1N1pdm into human viruses since 2009, and examined how human signatures may lose their distinctness by mixing with avian residues that H1N1pdm have brought in. In particular, we compared how those signatures were changed/shifted in the past 5 years for human-isolated avian influenza A viruses and discussed their implications. Only eight out of 47 signatures remained human-like for human influenza A viruses in the past 5 years. They are PB2 271A; PB1 336I; PA 356R and 409N; NP 33I, 305K, and 357K; and NS1 227R. Although most avian-like residues were preserved in human-isolated avian influenza A viruses, a number of them were found to have become or on the verge of becoming human-like, including PB2 627, PA 100, 356, 404, 409, NP 33, 61, 305, 357, M2 20, and NS1 81. Analyzing how species-associated signatures are becoming human-like in human-isolated avian influenza A viruses helps in assessing their potential to go pandemic as well as providing insights into host adaptation. Copyright © 2015. Published by Elsevier B.V.
    Journal of the Formosan Medical Association 03/2015; 114(5). DOI:10.1016/j.jfma.2015.01.015 · 1.70 Impact Factor
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    ABSTRACT: The influenza A virus contains 8 segmented genomic RNAs and was considered to encode 10 viral proteins until investigators identified the 11th viral protein, PB1-F2, which uses an alternative reading frame of the PB1 gene. The recently identified PB1-N40, PA-N155 and PA-N182 influenza A proteins have shown the potential for using a leaking ribosomal scanning mechanism to generate novel open reading frames (ORFs). These novel ORFs provide examples of the manner in which the influenza A virus expands its coding capacity by using overlapping reading frames. In this study, we performed a computational search, based on a ribosome scanning mechanism, on all influenza A coding sequences to identify possible forward-reading ORFs that could be translated into novel viral proteins. We specified that the translated products had a prevalence ≥5% to eliminate sporadic ORFs. A total of 1,982 ORFs were thus identified and presented in terms of their locations, lengths and Kozak sequence strengths. We further provided an abridged list of ORFs by requiring every candidate an upstream start codon (within the upstream third of the primary transcript), a strong Kozak consensus sequence and high prevalence (≥95% and ≥50% for in-frame and alternative-frame ORFs, respectively). The PB1-F2, PB1-N40, PA-N155 and PA-N182 proteins all fulfilled our filtering criteria. Subject to these three stringent settings, we additionally named 16 novel ORFs for all influenza A genomes except for HA and NA, for which 43 HA and 11 NA ORFs from their respective subtypes were also recognized.
    PLoS ONE 12/2014; 9(12):e115016. DOI:10.1371/journal.pone.0115016 · 3.23 Impact Factor
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    ABSTRACT: Enterovirus 71 (EV-A71) is a neurotropic virus that can cause severe complications involving the central nervous system. No effective antiviral therapeutics are available for treating EV-A71 infection and drug discovery efforts are rarely focused to target this disease. Thus, the main goal of this study was to discover existing drugs with novel indications that may effectively inhibit EV-A71 replication and the inflammatory cytokines elevation. In this study, we showed that LiCl, a GSK3β inhibitor, effectively suppressed EV-A71 replication, apoptosis and inflammatory cytokines production (Interleukin 6, Interleukin-1β) in infected cells. Furthermore, LiCl and an immunomodular agent were shown to strongly synergize with each other in suppressing EV-A71 replication. The results highlighted potential new treatment regimens in suppressing sequelae caused by EV-A71 replication.
    PLoS ONE 11/2014; 9(11):e111331. DOI:10.1371/journal.pone.0111331 · 3.23 Impact Factor
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    ABSTRACT: Background Highly pathogenic influenza viruses cause high levels of morbidity, including excessive infiltration of leukocytes into the lungs, high viral loads and a cytokine storm. However, the details of how these pathological features unfold in severe influenza infections remain unclear. Accumulation of Gr1¿+¿CD11b¿+¿myeloid cells has been observed in highly pathogenic influenza infections but it is not clear how and why they accumulate in the severely inflamed lung. In this study, we selected this cell population as a target to investigate the extreme inflammatory response during severe influenza infection.ResultsWe established H1N1 IAV-infected mouse models using three viruses of varying pathogenicity and noted the accumulation of a defined Gr1¿+¿CD11b¿+¿myeloid population correlating with the pathogenicity. Herein, we reported that CCR2+ inflammatory monocytes are the major cell compartments in this population. Of note, impaired clearance of the high pathogenicity virus prolonged IFN expression, leading to CCR2+ inflammatory monocytes amplifying their own recruitment via an interferon-¿/ß receptor 1 (IFNAR1)-triggered chemokine loop. Blockage of IFNAR1-triggered signaling or inhibition of viral replication by Oseltamivir significantly suppresses the expression of CCR2 ligands and reduced the influx of CCR2+ inflammatory monocytes. Furthermore, trafficking of CCR2+ inflammatory monocytes from the bone marrow to the lung was evidenced by a CCR2-dependent chemotaxis. Importantly, leukocyte infiltration, cytokine storm and expression of iNOS were significantly reduced in CCR2¿/¿ mice lacking infiltrating CCR2+ inflammatory monocytes, enhancing the survival of the infected mice.Conclusions Our results indicated that uncontrolled viral replication leads to excessive production of inflammatory innate immune responses by accumulating CCR2+ inflammatory monocytes, which contribute to the fatal outcomes of high pathogenicity virus infections.
    Journal of Biomedical Science 11/2014; 21(1):99. DOI:10.1186/s12929-014-0099-6 · 2.74 Impact Factor
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    ABSTRACT: The roles of virus-derived small RNAs (vsRNAs) have been studied in plants and insects. However, the generation and function of small RNAs from cytoplasmic RNA viruses in mammalian cells remain unexplored. This study describes four vsRNAs that were detected in enterovirus 71-infected cells using next-generation sequencing and northern blots. Viral infection produced substantial levels (>105 copy numbers per cell) of vsRNA1, one of the four vsRNAs. We also demonstrated that Dicer is involved in vsRNA1 generation in infected cells. vsRNA1 overexpression inhibited viral translation and internal ribosomal entry site (IRES) activity in infected cells. Conversely, blocking vsRNA1 enhanced viral yield and viral protein synthesis. We also present evidence that vsRNA1 targets stem-loop II of the viral 5′ untranslated region and inhibits the activity of the IRES through this sequence-specific targeting. Our study demonstrates the ability of a cytoplasmic RNA virus to generate functional vsRNA in mammalian cells. In addition, we also demonstrate a potential novel mechanism for a positive-stranded RNA virus to regulate viral translation: generating a vsRNA that targets the IRES.
    Nucleic Acids Research 10/2014; 42(20). DOI:10.1093/nar/gku952 · 9.11 Impact Factor
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    ABSTRACT: Enterovirus 71 (EV71) infections can cause hand, foot, and mouth disease with severe neurological complications. Because no clinical drug is available for treating EV71 infections, developing an efficient antiviral medication against EV71 infection is crucial. This study indicated that 6-bromo-2-[1-(2,5-dimethylphenyl)-5-methyl-1H-pyrazol-4-yl] quinoline-4-carboxylic acid (BPR-3P0128) exhibits excellent antiviral activity against EV71 (EC50=0.0029μM). BPR-3P0128 inhibits viral replication during the early post infection stage, targets EV71 RNA-dependent RNA polymerase and VPg uridylylation, and also reduces viral RNA accumulation levels and inhibits viral replication of EV71. Copyright © 2014 Elsevier B.V. All rights reserved.
    Antiviral Research 10/2014; 112C:18-25. DOI:10.1016/j.antiviral.2014.10.003 · 3.94 Impact Factor
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    ABSTRACT: Neural progenitor cells (NPCs) are stem cells that can differentiate into various neural lineage cells. The damage and loss of NPCs are associated with neurological conditions such as cognitive deficits and memory impairment. In a long-term study of patients with EV71, cognitive disorders were observed. Therefore, we hypothesized that NPCs may be permissive to EV71 infection. We demonstrated that NPCs are prone to EV71 infection and that these stem cells can support the active replication of this virus. Furthermore, EV71 infection triggers apoptosis, resulting in significant cell death in infected NPCs. However, EV71 did not replicate in the differentiated cell types that were tested. Our findings suggest that EV71 can infect NPCs and cause the depletion of these cells.
    Virology 10/2014; 468-470C:592-600. DOI:10.1016/j.virol.2014.09.017 · 3.28 Impact Factor
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    ABSTRACT: Infections of the novel avian influenza A H7N9 virus cause severe respiratory diseases and death. In this study, to develop highly sensitive methods for differentially detecting the H7N9 virus, multiplex and singular real-time reverse transcription polymerase chain reaction (RT-PCR) assays were established and examined by targeting the H7 and N9 genes of the H7N9 virus. Furthermore, an additional multiplex assay combining previous real-time RT-PCR designs was established to subtype the pandemic H1N1, H3, and H5 influenza viruses. Applying the proposed assay system to analyze 100 clinical specimens collected from respiratory infection cases identified influenza A viruses (pandemic H1N1 and H3) in 23 samples. It has been demonstrated that other common respiratory viruses will not be detected by using this platform.
    Journal of Virological Methods 07/2014; 208. DOI:10.1016/j.jviromet.2014.07.020 · 1.88 Impact Factor
  • Yu-An Kung · Chuan-Tien Hung · Yen-Chin Liu · Shin-Ru Shih
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    ABSTRACT: Introduction: Enterovirus 71 (EV71) is an etiological agent that causes severe neurological complications in children. EV71 outbreaks have occurred throughout the Asia-Pacific region, posing a severe global public health threat; however, no specific therapeutic strategy exists for treating EV71-infected children. Areas covered: Five manufacturers have produced inactivated EV71 whole virus vaccines in mainland China, Taiwan, and Singapore, which have completed Phase III (mainland China) and Phase I (Taiwan and Singapore) clinical trials. Various EV71 vaccine candidates are being researched in animal models, including live-attenuated virus vaccine, recombinant VP1 vaccine, VP1-based DNA vaccine, synthetic peptide vaccine and virus-like particle vaccine. In this review, the present situation is summarized, and feasible improvements to the EV71 vaccine are explored. Expert opinion: Although inactivated EV71 vaccines are safe, efficient and elicit strong immune responses to protect adults, children and infants against infection, the quality control of production is critical.
    Expert Opinion on Biological Therapy 07/2014; 14(10):1-10. DOI:10.1517/14712598.2014.935330 · 3.65 Impact Factor
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    ABSTRACT: Author Summary RNA-dependent RNA polymerase (RdRp) is an enzyme that catalyzes the replication from an RNA template and is encoded in the genomes of all RNA viruses. RNA viruses in general replicate in cytoplasm and interfere host cellular gene expression by utilizing proteolytic destruction of cellular targets as the primary mechanism. However, several cytoplasmic RNA viral proteins have been found in the nucleus. What do they do in the nucleus? This study utilized picornaviral polymerase to probe the function of RdRp in the nucleus. Our findings reveal a novel mechanism of viruses attacking hosts whereby picornaviral 3D polymerase (3Dpol) enters the nucleus and targets the central pre-mRNA processing factor 8 (Prp8) to block pre-mRNA splicing and mRNA synthesis. The 3Dpol inhibits the second catalytic step of the splicing process, resulting in the accumulation of the lariat-form and the reduction of the mRNA. These results provide new insights into the strategy of a cytoplasmic RNA virus attacking host cell, that differs from viral shutting off cellular transcription and translation which contributes to the viral pathogenesis. To our knowledge, this study shows for the first time that a cytoplasmic RNA virus uses its polymerase to alter cellular gene expression by hijacking the splicing machinery.
    PLoS Pathogens 06/2014; 10(6):e1004199. DOI:10.1371/journal.ppat.1004199 · 8.14 Impact Factor
  • Peng-Nien Huang · Shin-Ru Shih
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    ABSTRACT: Human enterovirus type 71 (EV71) has emerged as a major cause of viral encephalitis in children worldwide. The identified EV71 receptors provide useful information for understanding EV71replication and tissue tropism. Host factors interact with the internal ribosome entry site (IRES) of EV71 to regulate viral translation. However, the specific molecular features of the EV71 genome that determine virulence remain unclear. The EV71 capsid protein VP1 region might contribute to virulence and neurotropism. Transgenic mice expressing the EV71 receptor that were infected with the virus exhibited a disease similar to that observed in infected humans. Antiviral drug and vaccine development is urgently required to prevent EV71 epidemics. Delineating viral host interactions and identifying specific mechanisms that might control the neural tropism of EV71 pathogenesis would be substantial advances.
    04/2014; 5C(1):98-104. DOI:10.1016/j.coviro.2014.03.007
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    Jing-Yi Lin · Shin-Ru Shih
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    ABSTRACT: Enterovirus 71 (EV71) is a member of Picornaviridae that causes mild and self-limiting hand, foot, and mouth disease (HFMD). However, EV71 infections can progress to polio-like paralysis, neurogenic pulmonary edema, and fatal encephalitis in infants and young children. Large EV71 outbreaks have been reported in Taiwan, China, Japan, Malaysia, Singapore, and Australia. This virus is considered a critical emerging public health threat. EV71 is an important crucial neurotropic enterovirus for which there is currently no effective antiviral drug or vaccine. The mechanism by which EV71 causes severe central nervous system complications remains unclear. The interaction between the virus and the host is vital for viral replication, virulence, and pathogenicity. SCARB2 or PSGL-1 receptor binding is the first step in the development of viral infections, and viral factors (e.g., 5[prime] UTR, VPI, 3A, 3C, 3D), host factors and environments (e.g., ITAFs, type I IFN) are also involved in viral infections. The tissue tropism and pathogenesis of viruses are determined by a combination of several factors. This review article provides a summary of host and virus factors affecting cell and tissue tropism and the pathogenesis of enteroviruses.
    Journal of Biomedical Science 03/2014; 21(1):18. DOI:10.1186/1423-0127-21-18 · 2.74 Impact Factor
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    ABSTRACT: There are no antivirals or vaccines available to treat Enterovirus 71 (EV71) infections. Although the type I interferon response, elicited upon virus infection, is critical to establishing host antiviral innate immunity, EV71 fails to induce this response efficiently. Here we provide new insights into potential anti-EV71 therapy by showing that neutralization of EV71-induced miR-146a prevents death in mice by restarting the production of type I interferon. EV71 infection upregulates miR-146a, which targets IRAK1 and TRAF6 involved in TLR signalling and type I interferon production. We further identify AP1 as being responsible for the EV71-induced expression of miR-146a. Surprisingly, knocking out miR-146a or neutralizing virus-induced miR-146a by specific antagomiR restores expressions of IRAK1 and TRAF6, augments IFNβ production, inhibits viral propagation and improves survival in the mouse model. Our results suggest that enterovirus-induced miR-146a facilitates viral pathogenesis by suppressing IFN production and provide a clue to developing preventive and therapeutic strategies for enterovirus infections.
    Nature Communications 02/2014; 5:3344. DOI:10.1038/ncomms4344 · 10.74 Impact Factor
  • Guang-Wu Chen · Shin-Ru Shih
    01/2014; 37(1):1-2. DOI:10.4103/2319-4170.125882
  • Peng-Nien Huang · Shin-Ru Shih
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    ABSTRACT: Human enterovirus type 71 (EV71) has emerged as a major cause of viral encephalitis in children worldwide. The identified EV71 receptors provide useful information for understanding EV71replication and tissue tropism. Host factors interact with the internal ribosome entry site (IRES) of EV71 to regulate viral translation. However, the specific molecular features of the EV71 genome that determine virulence remain unclear. The EV71 capsid protein VP1 region might contribute to virulence and neurotropism. Transgenic mice expressing the EV71 receptor that were infected with the virus exhibited a disease similar to that observed in infected humans. Antiviral drug and vaccine development is urgently required to prevent EV71 epidemics. Delineating viral host interactions and identifying specific mechanisms that might control the neural tropism of EV71 pathogenesis would be substantial advances.
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    ABSTRACT: Neuraminidase (NA) is a homotetramer viral surface glycoprotein that is essential for virus release during influenza virus infections. Previous studies have not explored why influenza NA forms a tetramer when the bacterial monomer NA already exhibits excellent NA enzymatic activity levels. In this study, we focused on 28 highly conserved residues among all NA subtypes, identifying 21 of 28 positions as crucial residues for viral survival by using reverse genetics. Maintaining NA enzymatic activity levels is critical and numerous conserved residues were located at the oligomerization interface; however, these mutations did not affect NA enzymatic activity levels or NA cellular localization, but rather affected the stability of NA oligomerization, suggesting that the oligomerization of NA is essential for viral viability. An increased understanding of the biological functions of NA, in particular NA oligomerization, could facilitate an alternative design for antivirals to combat influenza virus infections.
    Virology 12/2013; 447(1-2):32-44. DOI:10.1016/j.virol.2013.08.012 · 3.28 Impact Factor
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    ABSTRACT: Prompt diagnosis of an oseltamivir-resistant marker is important for patient management, in particular to prevent the spread of resistant strains in the recent human H7N9 outbreak. We tailored a pyrosequencing assay to reveal neuraminidase R292K, a resistant marker found in one isolate from China, and demonstrated its performance in both sensitivity and specificity. In addition, a semi-nested polymerase chain reaction was applied, which enhanced the detection rate by at least 10-fold. We validated this assay by examining the marker in Taiwan's first imported human case and found R and K in quasispecies.
    Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi 12/2013; 13. DOI:10.1016/j.jmii.2013.09.010 · 2.08 Impact Factor

Publication Stats

3k Citations
490.77 Total Impact Points

Institutions

  • 2004–2015
    • Chang Gung Memorial Hospital
      T’ai-pei, Taipei, Taiwan
  • 2000–2015
    • Chang Gung University
      • • Department of Medical Biotechnology and Laboratory Science
      • • Division of Biotechnology
      • • Graduate Institute of Clinical Medicine Sciences
      Hsin-chu-hsien, Taiwan, Taiwan
  • 2012
    • National Cheng Kung University
      臺南市, Taiwan, Taiwan
  • 2011
    • French National Centre for Scientific Research
      Lutetia Parisorum, Île-de-France, France
  • 2009
    • National Tsing Hua University
      • Institute of Molecular Medicine
      Hsin-chu-hsien, Taiwan, Taiwan
  • 2008
    • Academia Sinica
      • Institute of Biological Chemistry
      T’ai-pei, Taipei, Taiwan
  • 2002
    • Harvard University
      Cambridge, Massachusetts, United States