Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| Infection with Mycobacterium tuberculosis Accession ID: Reactome:R-HSA-9635486 |
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Repasy T, Lee J, Marino S, Martinez N, Kirschner DE, Hendricks G, Baker S, Wilson AA, Kotton DN, Kornfeld H. Intracellular Bacillary Burden Reflects a Burst Size for Mycobacterium tuberculosis In Vivo. PLoS Pathog. 2013 Feb 21;9(2):e1003190. doi: 10.1371/journal.ppat.1003190.; Russell DG. Mycobacterium tuberculosis and the intimate discourse of a chronic infection. Immunological Reviews. 2011 Feb 23;240(1):252–68. doi: 10.1111/j.1600-065x.2010.00984.x.; Russell DG, Barry CE, Flynn JL. Tuberculosis: what we don't know can, and does, hurt us. Science. 2010 May 14;328(5980):852–6. PMID: 20466922; PMCID: PMC2872107.; Barry CE, Boshoff HI, Dartois V, Dick T, Ehrt S, Flynn J, Schnappinger D, Wilkinson RJ, Young D. The spectrum of latent tuberculosis: rethinking the biology and intervention strategies. Nature Reviews Microbiology. 2009 Oct 26;7(12):845–55. doi: 10.1038/nrmicro2236.; Boshoff HI, Barry CE. Tuberculosis - metabolism and respiration in the absence of growth. Nat Rev Microbiol. 2005 Jan;3(1):70–80. doi: 10.1038/nrmicro1065. PMID: 15608701. |
| Bacterial Infection Pathways Accession ID: Reactome:R-HSA-9824439 |
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| Disease Accession ID: Reactome:R-HSA-1643685 |
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Javorsky A, Humbert PO, Kvansakul M. Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain. Communications Biology. 2021 Jun 11;4(1):724. doi: 10.1038/s42003-021-02250-7.; Ordonez AA, Bullen CK, Villabona-Rueda AF, Thompson EA, Turner ML, Davis SL, Komm O, Powell JD, D'Alessio FR, Yolken RH, Jain SK, Jones-Brando L. Sulforaphane exhibits in vitro and in vivo antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses. bioRxiv. 2021 Mar 25;(). PMID: 33791708; PMCID: PMC8010735.; Olagnier D, Farahani E, Thyrsted J, Blay-Cadanet J, Herengt A, Idorn M, Hait A, Hernaez B, Knudsen A, Iversen MB, Schilling M, Jørgensen SE, Thomsen M, Reinert LS, Lappe M, Hoang H, Gilchrist VH, Hansen AL, Ottosen R, Nielsen CG, Møller C, van der Horst D, Peri S, Balachandran S, Huang J, Jakobsen M, Svenningsen EB, Poulsen TB, Bartsch L, Thielke AL, Luo Y, Alain T, Rehwinkel J, Alcamí A, Hiscott J, Mogensen TH, Paludan SR, Holm CK. Author Correction: SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate. Nature Communications. 2020 Oct 21;11(1):5419. doi: 10.1038/s41467-020-19363-y.; Wynn D, Lategan TW, Sprague TN, Rousseau FS, Fox EJ. Monomethyl fumarate has better gastrointestinal tolerability profile compared with dimethyl fumarate. Multiple Sclerosis and Related Disorders. 2020 Oct;45():102335. doi: 10.1016/j.msard.2020.102335.; Toto A, Ma S, Malagrinò F, Visconti L, Pagano L, Stromgaard K, Gianni S. Comparing the binding properties of peptides mimicking the Envelope protein of |
| Tolerance by Mtb to nitric oxide produced by macrophages Accession ID: Reactome:R-HSA-1222538 |
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Fang FC. Antimicrobial reactive oxygen and nitrogen species: concepts and controversies. Nat Rev Microbiol. 2004 Oct;2(10):820–32. doi: 10.1038/nrmicro1004. PMID: 15378046. |
| Latent infection - Other responses of Mtb to phagocytosis Accession ID: Reactome:R-HSA-1222499 |
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Russell DG. Mycobacterium tuberculosis and the intimate discourse of a chronic infection. Immunological Reviews. 2011 Feb 23;240(1):252–68. doi: 10.1111/j.1600-065x.2010.00984.x.; Russell DG, Barry CE, Flynn JL. Tuberculosis: what we don't know can, and does, hurt us. Science. 2010 May 14;328(5980):852–6. PMID: 20466922; PMCID: PMC2872107.; de Chastellier C. The many niches and strategies used by pathogenic mycobacteria for survival within host macrophages. Immunobiology. 2009;214(7):526–42. doi: 10.1016/j.imbio.2008.12.005. PMID: 19261352.; Flannagan RS, Cosío G, Grinstein S. Antimicrobial mechanisms of phagocytes and bacterial evasion strategies. Nat Rev Microbiol. 2009 May;7(5):355–66. doi: 10.1038/nrmicro2128. PMID: 19369951. |
| Immune System Accession ID: Reactome:R-HSA-168256 |
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Campbell GR, To RK, Hanna J, Spector SA. SARS-CoV-2, SARS-CoV-1, and HIV-1 derived ssRNA sequences activate the NLRP3 inflammasome in human macrophages through a non-classical pathway. iScience. 2021 Apr 23;24(4):102295. PMID: 33718825; PMCID: PMC7939994.; Moreno-Eutimio MA, López-Macías C, Pastelin-Palacios R. Bioinformatic analysis and identification of single-stranded RNA sequences recognized by TLR7/8 in the SARS-CoV-2, SARS-CoV, and MERS-CoV genomes. Microbes and Infection. 2020 May;22(4-5):226–9. doi: 10.1016/j.micinf.2020.04.009.; Zhang Z, Ohto U, Shibata T, Taoka M, Yamauchi Y, Sato R, Shukla NM, David SA, Isobe T, Miyake K, Shimizu T. Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands. Cell Rep. 2018 Dec 18;25(12):3371–3381.e5. doi: 10.1016/j.celrep.2018.11.081. PMID: 30566863.; Schierhorn KL, Jolmes F, Bespalowa J, Saenger S, Peteranderl C, Dzieciolowski J, Mielke M, Budt M, Pleschka S, Herrmann A, Herold S, Wolff T. Influenza A Virus Virulence Depends on Two Amino Acids in the N-Terminal Domain of Its NS1 Protein To Facilitate Inhibition of the RNA-Dependent Protein Kinase PKR. J Virol. 2017 May 15;91(10). PMID: 28250123; PMCID: PMC5411612.; Zhang Z, Ohto U, Shibata T, Krayukhina E, Taoka M, Yamauchi Y, Tanji H, Isobe T, Uchiyama S, Miyake K, Shimizu T. Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA. Immunity. 2016 Oct 18;45(4):737–48. doi: 10.1016/j.immuni.2016.09.011. PMID: 27742543.; Tanji H, Ohto U, Motoi Y, Shibata T, Miyake K, Shimizu T. Autoinhibition and relief mechanism by the proteolytic processing of Toll-like receptor 8. Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):3012–7. PMID: 26929371; PMCID: PMC4801236.; Scheuplein VA, Seifried J, Malczyk AH, Miller L, Höcker L, Vergara-Alert J, Dolnik O, Zielecki F, Becker B, Spreitzer I, König R, Becker S, Waibler Z, Mühlebach MD. High secretion of interferons by human plasmacytoid dendritic cells upon recognition of Middle East respiratory syndrome coronavirus. J Virol. 2015 Apr;89(7):3859–69. PMID: 25609809; PMCID: PMC4403407.; Costedoat-Chalumeau N, Dunogué B, Morel N, Le Guern V, Guettrot-Imbert G. Hydroxychloroquine: a multifaceted treatment in lupus. Presse Med. 2014 Jun;43(6 Pt 2):e167–80. doi: 10.1016/j.lpm.2014.03.007. PMID: 24855048.; Lester SN, Li K. Toll-Like Receptors in Antiviral Innate Immunity. Journal of Molecular Biology. 2014 Mar;426(6):1246–64. doi: 10.1016/j.jmb.2013.11.024.; Lamphier M, Zheng W, Latz E, Spyvee M, Hansen H, Rose J, Genest M, Yang H, Shaffer C, Zhao Y, Shen Y, Liu C, Liu D, Mempel TR, Rowbottom C, Chow J, Twine NC, Yu M, Gusovsky F, Ishizaka ST. Novel small molecule inhibitors of TLR7 and TLR9: mechanism of action and efficacy in vivo. Mol Pharmacol. 2014 Mar;85(3):429–40. doi: 10.1124/mol.113.089821. PMID: 24342772.; Tanji H, Ohto U, Shibata T, Miyake K, Shimizu T. Structural reorganization of the Toll-like receptor 8 dimer induced by agonistic ligands. Science. 2013 Mar 22;339(6126):1426–9. doi: 10.1126/science.1229159. PMID: 23520111.; Li Y, Chen M, Cao H, Zhu Y, Zheng J, Zhou H. Extraordinary GU-rich single-strand RNA identified from SARS coronavirus contributes an excessive innate immune response. Microbes and Infection. 2013 Feb;15(2):88–95. doi: 10.1016/j.micinf.2012.10.008.; Melén K, Kinnunen L, Fagerlund R, Ikonen N, Twu KY, Krug RM, Julkunen I. Nuclear and nucleolar targeting of influenza A virus NS1 protein: striking differences between different virus subtypes. J Virol. 2007 Jun;81(11):5995–6006. PMID: 17376915; PMCID: PMC1900311.; Dauber B, Schneider J, Wolff T. Double-stranded RNA binding of influenza B virus nonstructural NS1 protein inhibits protein kinase R but is not essential to antagonize production of alpha/beta interferon. J Virol. 2006 Dec;80(23):11667–77. PMID: 16987984; PMCID: PMC1642593.; Cervantes-Barragan L, Züst R, Weber F, Spiegel M, Lang KS, Akira S, Thiel V, Ludewig B. Control of coronavirus infection through plasmacytoid dendritic-cell-derived type I interferon. Blood. 2007 Feb 01;109(3):1131–7. PMID: 16985170; PMCID: PMC8254533.; Li S, Min JY, Krug RM, Sen GC. Binding of the influenza A virus NS1 protein to PKR mediates the inhibition of its activation by either PACT or double-stranded RNA. Virology. 2006 May 25;349(1):13–21. doi: 10.1016/j.virol.2006.01.005. PMID: 16466763.; Gorden KB, Gorski KS, Gibson SJ, Kedl RM, Kieper WC, Qiu X, Tomai MA, Alkan SS, Vasilakos JP. Synthetic TLR agonists reveal functional differences between human TLR7 and TLR8. J Immunol. 2005 Feb 01;174(3):1259–68. doi: 10.4049/jimmunol.174.3.1259. PMID: 15661881.; Cros JF, García-Sastre A, Palese P. An unconventional NLS is critical for the nuclear import of the influenza A virus nucleoprotein and ribonucleoprotein. Traffic. 2005 Mar;6(3):205–13. doi: 10.1111/j.1600-0854.2005.00263.x. PMID: 15702989.; Diebold SS, Kaisho T, Hemmi H, Akira S, Reis e Sousa C. Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA. Science. 2004 Mar 05;303(5663):1529–31. doi: 10.1126/science.1093616. PMID: 14976261.; Heil F, Hemmi H, Hochrein H, Ampenberger F, Kirschning C, Akira S, Lipford G, Wagner H, Bauer S. Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. Science. 2004 Mar 05;303(5663):1526–9. doi: 10.1126/science.1093620. PMID: 14976262.; Jurk M, Heil F, Vollmer J, Schetter C, Krieg AM, Wagner H, Lipford G, Bauer S. Human TLR7 or TLR8 independently confer responsiveness to the antiviral compound R-848. Nat Immunol. 2002 Jun;3(6):499. doi: 10.1038/ni0602-499. PMID: 12032557.; Hemmi H, Kaisho T, Takeuchi O, Sato S, Sanjo H, Hoshino K, Horiuchi T, Tomizawa H, Takeda K, Akira S. Small anti-viral compounds activate immune cells via the TLR7 MyD88-dependent signaling pathway. Nat Immunol. 2002 Feb;3(2):196–200. doi: 10.1038/ni758. PMID: 11812998.; Bergmann M, Garcia-Sastre A, Carnero E, Pehamberger H, Wolff K, Palese P, Muster T. Influenza Virus NS1 Protein Counteracts PKR-Mediated Inhibition of Replication. J Virol. 2000 Jul;74(13):6203–6. doi: 10.1128/jvi.74.13.6203-6206.2000.; Hatada E, Saito S, Fukuda R. Mutant Influenza Viruses with a Defective NS1 Protein Cannot Block the Activation of PKR in Infected Cells. J Virol. 1999 Mar;73(3):2425–33. doi: 10.1128/jvi.73.3.2425-2433.1999.; TAN S, KATZE MG. Biochemical and Genetic Evidence for Complex Formation Between the Influenza A Virus NS1 Protein and the Interferon-induced PKR Protein Kinase. Journal of Interferon & Cytokine Research. 1998 Sep;18(9):757–66. doi: 10.1089/jir.1998.18.757.; O'Neill RE, Jaskunas R, Blobel G, Palese P, Moroianu J. Nuclear Import of Influenza Virus RNA Can Be Mediated by Viral Nucleoprotein and Transport Factors Required for Protein Import. Journal of Biological Chemistry. 1995 Sep;270(39):22701–4. doi: 10.1074/jbc.270.39.22701. |
| Innate Immune System Accession ID: Reactome:R-HSA-168249 |
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| ROS and RNS production in phagocytes Accession ID: Reactome:R-HSA-1222556 |
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Erard M, Dupré-Crochet S, Nüße O. Biosensors for spatiotemporal detection of reactive oxygen species in cells and tissues. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology. 2018 May 01;314(5):R667–83. doi: 10.1152/ajpregu.00140.2017.; Winterbourn CC, Kettle AJ, Hampton MB. Reactive Oxygen Species and Neutrophil Function. Annu Rev Biochem. 2016 Jun 02;85():765–92. doi: 10.1146/annurev-biochem-060815-014442. PMID: 27050287.; Levine AP, Duchen MR, de Villiers S, Rich PR, Segal AW. Alkalinity of Neutrophil Phagocytic Vacuoles Is Modulated by HVCN1 and Has Consequences for Myeloperoxidase Activity. PLoS ONE. 2015 Apr 17;10(4):e0125906. doi: 10.1371/journal.pone.0125906.; Weidinger A, Kozlov AV. Biological Activities of Reactive Oxygen and Nitrogen Species: Oxidative Stress versus Signal Transduction. Biomolecules. 2015 Apr 15;5(2):472–84. PMID: 25884116; PMCID: PMC4496681.; Vatansever F, de Melo WC, Avci P, Vecchio D, Sadasivam M, Gupta A, Chandran R, Karimi M, Parizotto NA, Yin R, Tegos GP, Hamblin MR. Antimicrobial strategies centered around reactive oxygen species--bactericidal antibiotics, photodynamic therapy, and beyond. FEMS Microbiol Rev. 2013 Nov;37(6):955–89. PMID: 23802986; PMCID: PMC3791156.; Gostner JM, Becker K, Fuchs D, Sucher R. Redox regulation of the immune response. Redox Report. 2013 May;18(3):88–94. doi: 10.1179/1351000213y.0000000044.; Yang Y, Bazhin AV, Werner J, Karakhanova S. Reactive Oxygen Species in the Immune System. International Reviews of Immunology. 2013 Apr 25;32(3):249–70. doi: 10.3109/08830185.2012.755176.; Flannagan RS, Jaumouillé V, Grinstein S. The Cell Biology of Phagocytosis. Annu. Rev. Pathol. Mech. Dis. 2012 Feb 28;7(1):61–98. doi: 10.1146/annurev-pathol-011811-132445.; Nordenfelt P, Tapper H. Phagosome dynamics during phagocytosis by neutrophils. J Leukoc Biol. 2011 Aug;90(2):271–84. doi: 10.1189/jlb.0810457. PMID: 21504950.; Nüsse O. Biochemistry of the phagosome: the challenge to study a transient organelle. ScientificWorldJournal. 2011;11():2364–81. PMID: 22194668; PMCID: PMC3236389.; Attia SM. Deleterious Effects of Reactive Metabolites. Oxidative Medicine and Cellular Longevity. 2010 Jan;3(4):238–53. doi: 10.4161/oxim.3.4.13246.; Flannagan RS, Cosío G, Grinstein S. Antimicrobial mechanisms of phagocytes and bacterial evasion strategies. Nat Rev Microbiol. 2009 May;7(5):355–66. doi: 10.1038/nrmicro2128. PMID: 19369951.; Kohchi C, Inagawa H, Nishizawa T, Soma G. ROS and innate immunity. Anticancer Res. 2009 Mar;29(3):817–21. PMID: 19414314.; Robinson JM. Reactive oxygen species in phagocytic leukocytes. Histochemistry and Cell Biology. 2008 Jul 03;130(2):281. doi: 10.1007/s00418-008-0461-4.; Savina A, Amigorena S. Phagocytosis and antigen presentation in dendritic cells. Immunol Rev. 2007 Oct;219():143–56. doi: 10.1111/j.1600-065x.2007.00552.x. PMID: 17850487.; Stuart LM, Ezekowitz RA. Phagocytosis: elegant complexity. Immunity. 2005 May;22(5):539–50. doi: 10.1016/j.immuni.2005.05.002. PMID: 15894272.; Fang FC. Antimicrobial reactive oxygen and nitrogen species: concepts and controversies. Nat Rev Microbiol. 2004 Oct;2(10):820–32. doi: 10.1038/nrmicro1004. PMID: 15378046.; Robinson JM, Ohira T, Badwey JA. Regulation of the NADPH-oxidase complex of phagocytic leukocytes. Recent insights from structural biology, molecular genetics, and microscopy. Histochem Cell Biol. 2004 Oct;122(4):293–304. doi: 10.1007/s00418-004-0672-2. PMID: 15365846.; Vieira OV, Botelho RJ, Grinstein S. Phagosome maturation: aging gracefully. Biochem J. 2002 Sep 15;366(Pt 3):689–704. PMID: 12061891; PMCID: PMC1222826.; Nauclér C, Grinstein S, Sundler R, Tapper H. Signaling to localized degranulation in neutrophils adherent to immune complexes. J Leukoc Biol. 2002 Apr;71(4):701–10. PMID: 11927658.; Jankowski A, Scott CC, Grinstein S. Determinants of the Phagosomal pH in Neutrophils. Journal of Biological Chemistry. 2002 Feb;277(8):6059–66. doi: 10.1074/jbc.m110059200.; Karlsson A, Dahlgren C. Assembly and activation of the neutrophil NADPH oxidase in granule membranes. Antioxid Redox Signal. 2002 Feb;4(1):49–60. doi: 10.1089/152308602753625852. PMID: 11970843.; Nathan C, Shiloh MU. Reactive oxygen and nitrogen intermediates in the relationship between mammalian hosts and microbial pathogens. Proc Natl Acad Sci U S A. 2000 Aug 01;97(16):8841–8. PMID: 10922044; PMCID: PMC34021.; Tapper H, Grinstein S. Fc receptor-triggered insertion of secretory granules into the plasma membrane of human neutrophils: selective retrieval during phagocytosis. 1997 Jul 01;159(1):409–18. doi: 10.4049/jimmunol.159.1.409.; Evans TJ, Buttery LD, Carpenter A, Springall DR, Polak JM, Cohen J. Cytokine-treated human neutrophils contain inducible nitric oxide synthase that produces nitration of ingested bacteria. Proc. Natl. Acad. Sci. U.S.A. 1996 Sep 03;93(18):9553–8. doi: 10.1073/pnas.93.18.9553.; Zimmerli S, Majeed M, Gustavsson M, Stendahl O, Sanan DA, Ernst JD. Phagosome-lysosome fusion is a calcium-independent event in macrophages. J Cell Biol. 1996 Jan;132(1-2):49–61. PMID: 8567729; PMCID: PMC2120694.; Segal AW, Geisow M, Garcia R, Harper A, Miller R. The respiratory burst of phagocytic cells is associated with a rise in vacuolar pH. Nature. 1981 Apr 02;290(5805):406–9. doi: 10.1038/290406a0. PMID: 7219526. |
| Infectious disease Accession ID: Reactome:R-HSA-5663205 |
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Javorsky A, Humbert PO, Kvansakul M. Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain. Communications Biology. 2021 Jun 11;4(1):724. doi: 10.1038/s42003-021-02250-7.; Ordonez AA, Bullen CK, Villabona-Rueda AF, Thompson EA, Turner ML, Davis SL, Komm O, Powell JD, D'Alessio FR, Yolken RH, Jain SK, Jones-Brando L. Sulforaphane exhibits in vitro and in vivo antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses. bioRxiv. 2021 Mar 25;(). PMID: 33791708; PMCID: PMC8010735.; Olagnier D, Farahani E, Thyrsted J, Blay-Cadanet J, Herengt A, Idorn M, Hait A, Hernaez B, Knudsen A, Iversen MB, Schilling M, Jørgensen SE, Thomsen M, Reinert LS, Lappe M, Hoang H, Gilchrist VH, Hansen AL, Ottosen R, Nielsen CG, Møller C, van der Horst D, Peri S, Balachandran S, Huang J, Jakobsen M, Svenningsen EB, Poulsen TB, Bartsch L, Thielke AL, Luo Y, Alain T, Rehwinkel J, Alcamí A, Hiscott J, Mogensen TH, Paludan SR, Holm CK. Author Correction: SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate. Nature Communications. 2020 Oct 21;11(1):5419. doi: 10.1038/s41467-020-19363-y.; Wynn D, Lategan TW, Sprague TN, Rousseau FS, Fox EJ. Monomethyl fumarate has better gastrointestinal tolerability profile compared with dimethyl fumarate. Multiple Sclerosis and Related Disorders. 2020 Oct;45():102335. doi: 10.1016/j.msard.2020.102335.; Toto A, Ma S, Malagrinò F, Visconti L, Pagano L, Stromgaard K, Gianni S. Comparing the binding properties of peptides mimicking the Envelope protein of |