Centre for Cancer Research

Innate immunity & protein kinase R publications

2010
Gantier MP, Irving AT, Kaparakis-Liaskos M, Xu D, Evans VA, Cameron PU, Bourne JA, Ferrero RL, John M, Behlke MA, Williams BRG (2010) Genetic modulation of TLR8 response following bacterial phagocytosis. Hum Mutat 31:1069-1079.

Halili MA, Andrews MR, Labzin LI, Schroder K, Matthias G, Cao C, Lovelace E, Reid RC, Le GT, Hume DA, Irvine KM, Matthias P, Fairlie DP, Sweet MJ (2010) Differential effects of selective HDAC inhibitors on macrophage inflammatory responses to the Toll-like receptor 4 agonist LPS. J Leukoc Biol 87:1103-1114.

Kubosaki A, Lindgren G, Tagami M, Simon C, Tomaru Y, Miura H, Suzuki T, Arner E, Forrest ARR, Irvine KM, Schroder K, Hasegawa Y, Kanamori-Katayama M, Rehli M, Hume DA, Kawai J, Suzuki M, Suzuki H, Hayashizaki Y (2010) The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. Mol Immunol 47:2295-2302.

Low PC, Misaki R, Schroder K, Stanley AC, Sweet MJ, Teasdale RD, Vanhaesebroeck B, Meunier FA, Taguchi T, Stow JL (2010) Phosphoinositide 3-kinase d regulates membrane fission of Golgi carriers for selective cytokine secretion. J Cell Biol 190:1053-1065.

Nakayama Y, Plisch EH, Sullivan J, Thomas C, Czuprynski CJ, Williams BRG, Suresh M (2010) Role of PKR and type I IFNs in viral control during primary and secondary infection. PLoS Pathogens 6:e1000966.

Sadler AJ (2010) Orchestration of the activation of protein kinase R by the RNA-binding motif. J Interferon Cytokine Res 30:195-204.

Schroder K, Tschopp J (2010) The inflammasomes. Cell 140:821-832.

Schroder K, Zhou R, Tschopp J (2010) The NLRP3 inflammasome: a sensor for metabolic danger? Science 327:296-300.

Tschopp J, Schroder K (2010) NLRP3 inflammasome activation: the convergence of multiple signaling pathways on ROS production? Nat Rev Immunol 10:210-215.

Wei J, Waithman J, Lata R, Mifsud NA, Cebon J, Kay T, Smyth MJ, Sadler AJ, Chen W (2010) Influenza A infection enhances cross-priming of CD8⁺ T cells to cell-associated antigens in a TLR7- and type I IFN-dependent fashion. J Immunol 185:6013-6022.

2009
Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41:563-571.

Irvine KM, Andrews MR, Fernandez-Rojo MA, Schroder K, Burns CJ, Su S, Wilks AF, Parton RG, Hume DA, Sweet MJ (2009) Colony-stimulating factor-1 (CSF-1) delivers a proatherogenic signal to human macrophages. J Leukoc Biol 85:278-288.

Irving A, Williams BRG (2009) Latest advances in innate antiviral defence. F1000 Biology Reports 1:22.

Lynch HE, Ray CA, Oie KL, Pollara JJ, Petty ITD, Sadler AJ, Williams BRG, Pickup DJ (2009) Modified vaccinia virus Ankara can activate NF-κB transcription factors through a double-stranded RNA-activated protein kinase (PKR)-dependent pathway during the early phase of virus replication. Virology 391:177-186

Mar JC, Kimura Y, Schroder K, Irvine KM, Hayashizaki Y, Suzuki H, Hume D, Quackenbush J (2009) Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics 10:110.

McCoy CE, O'Neill LAJ, editors (2009) Toll-Like Receptors: Methods and Protocols. Methods in Molecular Biology, Vol 517. New York, USA: Humana Press. 447 pp.

Rebsamen M, Heinz LX, Meylan E, Michallet M-C, Schroder K, Hofmann K, Vazquez J, Benedict CA, Tschopp J (2009) DAI/ZBP1 recruits RIP1 and RIP3 through RIP homotypic interaction motifs to activate NF-kB. EMBO Rep 10:916-922.

Sadler AJ, Latchoumanin O, Hawkes D, Mak J, Williams BRG (2009) An antiviral response directed by PKR phosphorylation of the RNA helicase A. PLoS Pathog 5:e1000311.

Schroder K, Muruve DA, Tschopp J (2009) Innate immunity: cytoplasmic DNA sensing by the AIM2 inflammasome. Curr Biol 19:R262-R265.

Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest ARR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS (2009) Tiny RNAs associated with transcription start sites in animals. Nat Genet 41:572-578.

The FANTOM Consortium and the Riken Omics Science Center (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41:553-562.

Thompson MR, Xu D, Williams BRG (2009) ATF3 transcription factor and its emerging roles in immunity and cancer. J Mol Med 87:1053-1060.

2008
Chakrabarti A, Sadler AJ, Kar N, Young HA, Silverman RH, Williams BRG (2008) Protein kinase R-dependent regulation of interleukin-10 in response to double-stranded RNA. J Biol Chem 283:25132-25139.

Gantier MP, Tong S, Behlke MA, Xu D, Phipps S, Foster PS and Williams BRG (2008)TLR7 is involved in sequence-specific sensing of single-stranded RNAs in human macrophages. J Immunol 180(4):2117-2124.

Lim W-S, Timmins JM, Seimon TA, Sadler A, Kolodgie FD, Virmani R, Tabas I (2008) Signal transducer and activator of transcription-1 is critical for apoptosis in macrophages subjected to endoplasmic reticulum stress in vitro and in advanced atherosclerotic lesions in vivo. Circulation 117:940-951.

Marques J, Anwar J, Eskildsen-Larsen S, Rebouillat D, Paludan SR, Sen G, Williams BRG, Hartmann R (2008) The p59 oligoadenylate synthetase-like protein possesses antiviral activity that requires the C-terminal ubiquitin-like domain. J Gen Virol 89:2767-2772.

Marques JT, White CL, Peters GA, Williams BRG, Sen GC (2008) The role of PACT in mediating gene induction, PKR activation, and apoptosis in response to diverse stimuli. J Interferon Cytokine Res 28:469-476.

2007
Alirezaei M, Watry DD, Flynn CF, Kiosses WB, Masliah E, Williams BRG, Kaul M, Lipton SA and Fox HS (2007) Human immunodeficiency virus-1/surface glycoprotein 120 induces apoptosis through RNA-activated protein kinase signaling in neurons. J Neurosci 27(41):11047-11055.

Austin BA, Halford WP, Williams BRG and Carr DJJ (2007) Oligoadenylate synthetase/protein kinase R pathways and a/ß TCR+ T cells are required for adenovirus vector: IFN-? inhibition of Herpes simplex virus-1 in cornea. J Immunol 178(8):5166-5172.

Carpentier PA, Williams BR and Miller SD (2007) Distinct roles of protein kinase R and toll-like receptor 3 in the activation of astrocytes by viral stimuli.   Glia 55(3):239-252.

Gantier MP, Baugh JA and Donnelly SC (2007) Nuclear transcription of long hairpin RNA triggers innate immune responses. J Interferon Cytokine Res 27(9):789-797.

Gantier MP, Sadler AJ and Williams BRG (2007) Fine-tuning of the innate immune response by microRNAs. Immunol Cell Biol 85(6):458-462.

Sadler AJ and Williams BRG (2007) Structure and function of the protein kinase R. In: Current Topics in Microbiology and Immunology, Vol 316: Interferon: The 50^th Anniversary. PM Pitha, ed. Springer, Berlin, pp 253-292.

Silva AM, Wang D, Komar AA, Castilho BA and Williams BRG (2007) Salicylates trigger protein synthesis inhibition in a protein kinase R-like endoplasmic reticulum kinase-dependent manner. J Biol Chem 282(14):10164-10171.

White CL, Whitmore MM and Williams BRG (2007) Enlarged spleens without enlarged lymph nodes in tlr3-/- pkr-/- mice. J Interferon Cytokine Res 27(1):6-12.

Whitmore MM, Iparraguirre A, Kubelka L, Weninger W, Hai T and Williams BRG (2007) Negative regulation of TLR-signaling pathways by activating transcription factor-3. J Immunol 179(6):3622-3630.

2006
Austin BA, Halford W, Silverman RH, Williams BRG and Carr DJJ (2006) OAS and PKR are not required for the antiviral effect of Ad:IFN-γ against acute HSV-1 in primary trigeminal ganglia cultures. J Interferon Cytokine Res 26:220-225.

Bakheet T, Williams BRG and Khabar KSA (2006) ARED 3.0: The large and diverse AU-rich transcriptome. Nucleic Acids Res 34:D111-D114.

Chang K-S, Cai Z, Zhang C, Sen GC, Williams BRG and Luo G (2006) Replication of hepatitis C virus (HCV) RNA in mouse embryonic fibroblasts: protein kinase R (PKR)-dependent and PKR-independent mechanisms for controlling HCV RNA replication and mediating interferon actions. J Virol 80:7364-7374.

Gabel F, Wang D, Madern D, Sadler A, Dayie K, Zamanian Daryoush M, Schwahn D, Zaccai G, Lee X and Williams BRG (2006) Dynamic flexibility of double-stranded RNA activated PKR in solution. J Mol Biol 359:610-623.

Green J, Khabar KSA, Koo BCA, Williams BRG and Polyak SJ (2006) Stability of CXCL-8 and related AU-rich mRNAs in the context of hepatitis C virus replication in vitro. J Infect Dis 193:802-811.

Samuel MA, Whitby K, Keller BC, Marri A, Barchet W, Williams BRG, Silverman RH, Gale M Jr and Diamond MS (2006) PKR and RNase L contribute to protection against lethal West Nile virus infection by controlling early viral spread in the periphery and replication in neurons. J Virol 80:7009-7019.

2005
Al-khatib K, Williams BRG, Silverman RH, Halford W and Carr DJJ (2005) Dichotomy between survival and lytic gene expression in RNase L- and PKR-deficient mice transduced with an adenoviral vector expressing murine IFN-β following ocular HSV-1 infection. Exp Eye Res 80:167-173.

Carr DJJ, Tomanek L, Silverman RH, Campbell IL and Williams BRG (2005) RNA-dependent protein kinase is required for alpha-1 interferon transgene-induced resistance to genital herpes simplex virus type 2. J Virol 79:9341-9345.

Elco CP, Guenther JM, Williams BR and Sen GC (2005) Analysis of genes induced by Sendai virus infection of mutant cell lines reveals essential roles of interferon regulatory factor 3, NF-κB, and interferon but not toll-like receptor 3. J Virol 79:3920-3929.

Flodström-Tullberg M, Hultcrantz M, Stotland A, Maday A, Tsai D, Fine C, Williams B, Silverman RH and Sarvetnick N (2005) RNase L and double-stranded RNA-dependent protein kinase exert complementary roles in islet cell defense during Coxsackievirus infection. J Immunol 174:1171-1177.

Khabar KSA, Bakheet T and Williams BRG (2005) AU-rich transient response transcripts in the human genome: expressed sequence tag clustering and gene discovery approach. Genomics 85:165-175.

Malathi K, Paranjape JM, Bulanova E, Shim M, Guenther-Johnson JM, Faber PW, Eling TE, Williams BRG and Silverman RH (2005) A transcriptional signaling pathway in the IFN system mediated by 2’-5’-oligoadenylate activation of RNase L. Proc Natl Acad Sci USA 102:14533-14538.

Marques JT, Rebouillat D, Ramana CV, Murakami J, Hill JE, Gudkov A, Silverman RH, Stark GR and Williams BRG (2005) Down-regulation of p53 by double-stranded RNA modulates the antiviral response. J Virol 79:11105-11114.

Smith JA, Schmechel SC, Williams BRG, Silverman RH and Schiff LA (2005) Involvement of the interferon-regulated antiviral proteins PKR and RNase L in reovirus-induced shutoff of cellular translation. J Virol 79:2240-2250.

Zhou Y, Chase BI, Whitmore M, Williams BRG and Zhou A (2005) Double-stranded RNA-dependent protein kinase (PKR) is downregulated by phorbol ester. FEBS J 272:1568-1576.

2004
Al-khatib K, Williams BRG, Silverman RH, Halford W and Carr DJJ (2004) Distinctive roles for 2',5'-oligoadenylate synthetases and double-stranded RNA-dependent protein kinase R in the in vivo antiviral effect of an adenoviral vector expressing murine IFN-β. J Immunol 172:5638-5647.

Chang H-M, Paulson M, Holko M, Rice CM, Williams BRG, Marié I and Levy DE (2004) Induction of interferon-stimulated gene expression and antiviral responses require protein deacetylase activity. Proc Natl Acad Sci USA 101:9578-9583.

Dong B, Zhou Q, Zhao J, Zhou A, Harty RN, Bose S, Banerjee A, Slee R, Guenther J, Williams BRG, Wiedmer T, Sims PJ and Silverman RH (2004) Phospholipid scramblase 1 potentiates the antiviral activity of interferon. J Virol 78:8983-8993.

Gorchakov R, Frolova E, Williams BRG, Rice CM and Frolov I (2004) PKR-dependent and -independent mechanisms are involved in translational shutoff during Sindbis virus infection. J Virol 78:8455-8467.

Raghavan A, Dhalla M, Bakheet T, Ogilvie RL, Vlasova IA, Khabar KSA, Williams BRG and Bohjanen PR (2004) Patterns of coordinate down-regulation of ARE-containing transcripts following immune cell activation. Genomics 84:1002-1013.

Silva AM, Whitmore M, Xu Z, Jiang Z, Li X and Williams BRG (2004) Protein kinase R (PKR) interacts with and activates mitogen-activated protein kinase kinase 6 (MKK6) in response to double-stranded RNA stimulation. J Biol Chem 279:37670-37676.

Whitmore MM, DeVeer MJ, Edling A, Oates RK, Simons B, Lindner D and Williams BRG (2004) Synergistic activation of innate immunity by double-stranded RNA and CpG DNA promotes enhanced antitumor activity. Cancer Res 64:5850-5860.

Xu Z, Wang D, Lee X and Williams BRG (2004) Biochemical analyses of multiple fractions of PKR purified from Escherichia coli. J Interferon Cytokine Res 24:522-535.

2003   
Al-khatib K, Williams BRG, Silverman RH, Halford W and Carr DJJ (2003) The murine double-stranded RNA-dependent protein kinase PKR and the murine 2’, 5’-oligoadenylate synthetase-dependent RNase L are required for IFN-b-mediated resistance against herpes simplex virus type 1 in primary trigeminal ganglion culture. Virology 313:126-135.

Bakheet T, Williams BR and Khabar KS (2003) ARED 2.0: an update of AU-rich element mRNA database. Nucleic Acids Res 31:421-423.

Frevel MAE, Bakheet T, Silva AM, Hissong JG, Khabar KSA and Williams BRG (2003) p38 mitogen-activated protein kinase-dependent and -independent signaling of mRNA stability of AU-rich element-containing transcripts. Mol Cell Biol 23:425-436.

Jiang Z, Zamanian-Daryoush M, Nie H, Silva AM, Williams BRG and Li X (2003) Poly(dI·dC)-induced Toll-like receptor 3 (TLR3)-mediated activation of NFκB and MAP kinase is through an interleukin-1 receptor-associated kinase (IRAK)-independent pathway employing the signaling components TLR3-TRAF6-TAK1-TAB2-PKR. J Biol Chem 278:16713-16719.

Khabar KSA, Siddiqui YM, al-Zoghaibi F, al-Haj L, Dhalla M, Zhou A, Dong B, Whitmore M, Paranjape J, Al-Ahdal MN, Al-Mohanna F, Williams BRG and Silverman RH (2003) RNase L mediates transient control of interferon response through modulation of the double-stranded RNA-dependent protein kinase PKR. J Biol Chem 278:20124-20132.

Leitner WW, Hwang LN, de Veer MJ, Zhou A, Silverman RH, Williams BRG, Dubensky TW, Ying H and Restifo NP (2003) Alphavirus-based DNA vaccine breaks immunological tolerance by activating innate antiviral pathways. Nat Med 9:33-39.

López CB, García-Sastre A, Williams BRG and Moran TM (2003) Type I IFN induction pathway, but not released interferon, participates in the maturation of dendritic cells induced by negative-strand RNA viruses. J Infect Dis 187:1126-1136.

Navarro A, Frevel M, Gamero AM, Williams BRG, Feldman G and Larner AC (2003) Thrombomodulin RNA is destabilized through its 3’-untranslated element in cells exposed to IFN-γ. J Interferon Cytokine Res 23:723-728.

Sawicki DL, Silverman RH, Williams BRG and Sawicki SG (2003) Alphavirus minus-strand synthesis and persistence in mouse embryo fibroblasts derived from mice lacking RNase L and protein kinase R. J Virol 77:1801-1811.

Tebo J, Der S, Frevel M, Khabar KSA, Williams BRG and Hamilton TA (2003) Heterogeneity in control of mRNA stability by AU-rich elements. J Biol Chem 278:12085-12093.

Williams BRG and Sen GC (2003) A viral on/off switch for interferon. Science 300:1100-1101.

Yin Z, Haynie J, Williams BRG and Yang Y-C (2003) C114 is a novel IL-11-inducible nuclear double-stranded RNA-binding protein that inhibits protein kinase R. J Biol Chem 278:22838-22845.