gocam-betacat.yaml

input_id: /Users/cjm/repos/semantic-llama/tests/input/cases/gocam-betacat.txt
input_text: "Title: \u03B2-Catenin Is Required for the cGAS/STING Signaling Pathway\
  \ but Antagonized by the Herpes Simplex Virus 1 US3 Protein\nText:\nThe cGAS/STING-mediated\
  \ DNA-sensing signaling pathway is crucial\nfor interferon (IFN) production and\
  \ host antiviral\nresponses. Herpes simplex virus I (HSV-1) is a DNA virus that\
  \ has\nevolved multiple strategies to evade host immune responses. Here,\nwe demonstrate\
  \ that the highly conserved \u03B2-catenin protein in the\nWnt signaling pathway\
  \ is an important factor to enhance the\ntranscription of type I interferon (IFN-I)\
  \ in the cGAS/STING\nsignaling pathway, and the production of IFN-I mediated by\n\
  \u03B2-catenin was antagonized by HSV-1 US3 protein via its kinase\nactivity. Infection\
  \ by US3-deficienct HSV-1 and its kinase-dead\nvariants failed to downregulate IFN-I\
  \ and IFN-stimulated\ngene (ISG) production induced by \u03B2-catenin. Consistent\
  \ with this,\nabsence of \u03B2-catenin enhanced the replication of US3-deficienct\n\
  HSV-1, but not wild-type HSV-1. The underlying mechanism was the\ninteraction of\
  \ US3 with \u03B2-catenin and its hyperphosphorylation of\n\u03B2-catenin at Thr556\
  \ to block its nuclear translocation. For the\nfirst time, HSV-1 US3 has been shown\
  \ to inhibit IFN-I production\nthrough hyperphosphorylation of \u03B2-catenin and\
  \ to subvert host\nantiviral innate immunity.IMPORTANCE Although increasing evidence\n\
  has demonstrated that HSV-1 subverts host immune responses and\nestablishes lifelong\
  \ latent infection, the molecular mechanisms\nby which HSV-1 interrupts antiviral\
  \ innate immunity, especially\nthe cGAS/STING-mediated cellular DNA-sensing signaling\
  \ pathway,\nhave not been fully explored. Here, we show that \u03B2-catenin\npromotes\
  \ cGAS/STING-mediated activation of the IFN pathway, which\nis important for cellular\
  \ innate immune responses and intrinsic\nresistance to DNA virus infection. The\
  \ protein kinase US3\nantagonizes the production of IFN by targeting \u03B2-catenin\
  \ via its\nkinase activity. The findings in this study reveal a novel\nmechanism\
  \ for HSV-1 to evade host antiviral immunity and add new\nknowledge to help in understanding\
  \ the interaction between the\nhost and HSV-1 infection.\n\nKeywords: HSV-1; US3;\
  \ type I IFN; \u03B2-catenin."
input_title: null
named_entities:
- id: HGNC:16289
  label: TRIM31
- id: HGNC:16400
  label: NLRP3
- id: HGNC:5992
  label: "IL-1\u03B2"
- id: CHEBI:CHEBI:16412
  label: LPS
- id: MESH:D006801
  label: Homo sapiens
- id: NCBITaxon:10090
  label: Mus musculus
- id: TRIM31*
  label: TRIM31
- id: MESH:D006801
  label: Homo sapiens
- id: NLRP3*
  label: NLRP3
- id: MESH:D006801
  label: Homo sapiens
- id: "IL-1\u03B2*"
  label: "IL-1\u03B2"
- id: MESH:D006801
  label: Homo sapiens
- id: LPS*
  label: LPS
- id: MESH:D006801
  label: Homo sapiens
- id: GO:0005488
  label: binding
- id: K48-linked polyubiquitination
  label: K48-linked polyubiquitination
- id: proteasomal degradation
  label: Proteasomal Degradation
- id: expression
  label: Expression
- id: secrection
  label: secrection
- id: TRIM31*
  label: TRIM31
- id: GO:0005488
  label: binding
- id: TRIM31*
  label: TRIM31
- id: K48-linked polyubiquitination
  label: K48-linked polyubiquitination
- id: TRIM31*
  label: TRIM31
- id: proteasomal degradation
  label: Proteasomal Degradation
- id: NLRP3*
  label: NLRP3
- id: Expression
  label: Expression
- id: "IL-1\u03B2*"
  label: "IL-1\u03B2"
- id: GO:0046903
  label: secretion
- id: inflammasome activation
  label: inflammasome activation
- id: immune homeostasis
  label: Immune Homeostasis
- id: NLRP3 inflammasome
  label: NLRP3 inflammasome
- id: TRIM31*
  label: TRIM31
- id: HGNC:16400
  label: NLRP3
- id: "IL-1\u03B2*"
  label: "IL-1\u03B2"
- id: CHEBI:CHEBI:16412
  label: LPS
- id: TRIM31*
  label: TRIM31
- id: GO:0005737
  label: cytoplasm
- id: HGNC:16400
  label: NLRP3
- id: GO:0005739
  label: mitochondrion
- id: HGNC:5992
  label: Il1b
- id: HGNC:5993
  label: Il1r1
- id: HGNC:16400
  label: NLRP3
- id: HGNC:1499
  label: caspase-1
- id: F4/80
  label: F4/80
- id: NCBITaxon:10090
  label: Mus Musculus
- id: HGNC:5992
  label: Il1b
- id: NCBITaxon:10090
  label: Mus Musculus
- id: HGNC:5993
  label: Il1r1
- id: NCBITaxon:10090
  label: Mus Musculus
- id: HGNC:16400
  label: NLRP3
- id: NCBITaxon:10090
  label: Mus Musculus
- id: HGNC:1499
  label: caspase-1
- id: NCBITaxon:10090
  label: Mus Musculus
- id: F4/80
  label: F4/80
- id: NCBITaxon:10090
  label: Mus Musculus
- id: targeting
  label: Targeting
- id: suppressing
  label: suppressing
- id: validating
  label: validating
- id: HGNC:5992
  label: Il1b
- id: targeting
  label: Targeting
- id: HGNC:5993
  label: Il1r1
- id: targeting
  label: Targeting
- id: HGNC:16400
  label: NLRP3
- id: targeting
  label: Targeting
- id: HGNC:1499
  label: caspase-1
- id: targeting
  label: Targeting
- id: F4/80
  label: F4/80
- id: Targeting
  label: Targeting
- id: MESH:C529594
  label: rytvela
- id: suppressing
  label: suppressing
- id: Kineret
  label: Kineret
- id: suppressing
  label: suppressing
- id: neuro-retinal degeneration
  label: Neuro-retinal Degeneration
- id: neuronal ativation
  label: Neuronal Activation
- id: macrophage-induced photoreceptor death
  label: Macrophage-induced Photoreceptor Death
- id: interleukin-1 pathway
  label: interleukin-1 pathway
- id: HGNC:5992
  label: Il1b
- id: HGNC:5993
  label: Il1r1
- id: HGNC:16400
  label: NLRP3
- id: HGNC:1499
  label: caspase-1
- id: HGNC:5992
  label: Il1b
- id: Perivascular Macrophages
  label: Perivascular Macrophages
- id: HGNC:5993
  label: Il1r1
- id: astrocytes, bipolar, and vascular cells
  label: null
- id: HGNC:16400
  label: NLRP3
- id: subretinal space
  label: subretinal space
- id: HGNC:1499
  label: caspase-1
- id: subretinal space
  label: subretinal space
- id: F4/80
  label: F4/80
- id: mononuclear phagocytes
  label: Mononuclear Phagocytes
- id: HGNC:21367
  label: cGAS
- id: HGNC:27962
  label: STING
- id: HGNC:2514
  label: "\u03B2-catenin"
- id: US3
  label: US3
- id: FPLX:Interferon
  label: IFN
- id: ISG
  label: ISG
- id: Thr556
  label: Thr556
- id: MESH:D006801
  label: Homo sapiens
- id: MESH:D018259
  label: Herpes simplex virus I
- id: HGNC:21367
  label: cGAS
- id: MESH:D006801
  label: Homo sapiens
- id: HGNC:27962
  label: STING
- id: MESH:D006801
  label: Homo sapiens
- id: HGNC:2514
  label: "\u03B2-catenin"
- id: MESH:D006801
  label: Homo sapiens
- id: US3
  label: US3
- id: MESH:D018259
  label: Herpes simplex virus I
- id: FPLX:Interferon
  label: IFN
- id: MESH:D006801
  label: Homo sapiens
- id: ISG
  label: ISG
- id: MESH:D006801
  label: Homo sapiens
- id: Thr556
  label: Thr556
- id: MESH:D006801
  label: Homo sapiens
- id: GO:0006351
  label: transcription
- id: replication
  label: Replication
- id: production
  label: production
- id: nuclear translocation
  label: Nuclear Translocation
- id: HGNC:21367
  label: cGAS
- id: activate type I IFN
  label: activate
- id: HGNC:27962
  label: STING
- id: activate type I IFN
  label: activate
- id: HGNC:2514
  label: "\u03B2-catenin"
- id: enhance transcription of type I IFN
  label: transcription of type I IFN
- id: US3
  label: US3
- id: FPLX:Interferon
  label: IFN
- id: produce type I IFN
  label: produce type I IFN
- id: ISG
  label: ISG
- id: produce type I IFN
  label: produce type I IFN
- id: Thr556
  label: Thr556
- id: block nuclear translocation
  label: block nuclear translocation
- id: DNA-sensing
  label: DNA-sensing
- id: GO:0001816
  label: interferon production
- id: host antiviral responses
  label: Host antiviral responses
- id: Wnt signaling
  label: Wnt signaling
- id: GO:0048151
  label: hyperphosphorylation
- id: cGAS/STING signaling
  label: cGAS/STING Signaling
- id: Wnt signaling
  label: Wnt signaling
- id: US3
  label: US3
- id: HGNC:2514
  label: "\u03B2-catenin"
- id: HGNC:21367
  label: cGAS
- id: HGNC:27962
  label: STING
- id: HGNC:2514
  label: "\u03B2-catenin"
- id: nuclear
  label: Nuclear
- id: US3
  label: US3
- id: FPLX:Interferon
  label: IFN
- id: ISG
  label: ISG
- id: Thr556
  label: Thr556
prompt: 'Split the following piece of text into fields in the following format:


  label: <The label of the named thing>

  '
raw_completion_output: "genes: cGAS; STING; \u03B2-catenin; US3; IFN; ISG; Thr556\n\
  organisms: Homo sapiens; Herpes simplex virus I\ngene_organisms: cGAS/Homo sapiens;\
  \ STING/Homo sapiens; \u03B2-catenin/Homo sapiens; US3/Herpes simplex virus I; IFN/Homo\
  \ sapiens; ISG/Homo sapiens; Thr556/Homo sapiens\nactivities: transcription; replication;\
  \ production; nuclear translocation\ngene_functions: cGAS/activate type I IFN; STING/activate\
  \ type I IFN; \u03B2-catenin/enhance transcription of type I IFN; US3/antagonize\
  \ production of IFN; IFN/produce type I IFN; ISG/produce type I IFN; Thr556/block\
  \ nuclear translocation\ncellular_processes: DNA-sensing; interferon production;\
  \ host antiviral responses; Wnt signaling; hyperphosphorylation\npathways: cGAS/STING\
  \ signaling; Wnt signaling\ngene_gene_interactions: US3/\u03B2-catenin\ngene_localizations:\
  \ cGAS/--; STING/--; \u03B2-catenin/nuclear; US3/--; IFN/--; ISG/--; Thr556/--"
results:
  activities:
  - GO:0006351
  - replication
  - production
  - nuclear translocation
  cellular_processes:
  - DNA-sensing
  - GO:0001816
  - host antiviral responses
  - Wnt signaling
  - GO:0048151
  gene_functions:
  - gene: HGNC:21367
    molecular_activity: activate type I IFN
  - gene: HGNC:27962
    molecular_activity: activate type I IFN
  - gene: HGNC:2514
    molecular_activity: enhance transcription of type I IFN
  - gene: US3
    molecular_activity: antagonize production of IFN
  - gene: FPLX:Interferon
    molecular_activity: produce type I IFN
  - gene: ISG
    molecular_activity: produce type I IFN
  - gene: Thr556
    molecular_activity: block nuclear translocation
  gene_gene_interactions:
  - gene1: US3
    gene2: HGNC:2514
  gene_localizations:
  - gene: HGNC:21367
    location: --
  - gene: HGNC:27962
    location: --
  - gene: HGNC:2514
    location: nuclear
  - gene: US3
    location: --
  - gene: FPLX:Interferon
    location: --
  - gene: ISG
    location: --
  - gene: Thr556
    location: --
  gene_organisms:
  - gene: HGNC:21367
    organism: MESH:D006801
  - gene: HGNC:27962
    organism: MESH:D006801
  - gene: HGNC:2514
    organism: MESH:D006801
  - gene: US3
    organism: MESH:D018259
  - gene: FPLX:Interferon
    organism: MESH:D006801
  - gene: ISG
    organism: MESH:D006801
  - gene: Thr556
    organism: MESH:D006801
  genes:
  - HGNC:21367
  - HGNC:27962
  - HGNC:2514
  - US3
  - FPLX:Interferon
  - ISG
  - Thr556
  organisms:
  - MESH:D006801
  - MESH:D018259
  pathways:
  - cGAS/STING signaling
  - Wnt signaling