Update tsv, md and png files

Author: actions-user

_data/WP5514-bibliography.tsv

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+ID	Database	Citation
+39326063	Pubmed	"DNAJB1-PRKACA Fusion Drives Fibrolamellar Liver Cancer through Impaired SIK Signaling and CRTC2/p300-Mediated Transcriptional Reprogramming. Gritti I, Wan J, Weeresekara V, Vaz JM, Tarantino G, Bryde TH, et al. Cancer Discov. 2025 Feb 7;15(2):382–400.  <a href=""http://www.ncbi.nlm.nih.gov/pubmed/39326063"" target=""_blank"" class=""external"" rel=""nofollow"">PubMed</a> <a href=""https://europepmc.org/abstract/MED/39326063"" target=""_blank"" class=""external"" rel=""nofollow"">Europe PMC</a> <a href=""https://scholia.toolforge.org/pubmed/39326063"" target=""_blank"" class=""external"" rel=""nofollow"">Scholia</a>"

_data/WP5514-datanodes.tsv

@@ -0,0 +1,12 @@
+Label	Type	Identifier	Comment	Ensembl	NCBI gene	HGNC	UniProt	Wikidata	ChEBI	InChI	PubChem	ChemSpider	HMDB	KEGG	LipidMaps
+GNAS	GeneProduct	ensembl:ENSG00000087460	""	ensembl:ENSG00000087460	ncbigene:2778	hgnc.symbol:GNAS	uniprot:O95467;uniprot:A0A590UJY2;uniprot:A0A590UJF0;uniprot:A0A804HIH4;uniprot:A0A590UJ46;uniprot:A0A590UJ47;uniprot:A2A2S1;uniprot:A0A590UJQ9;uniprot:A0A0A0MR13;uniprot:H0Y7E8;uniprot:A0A590UK28;uniprot:B0AZR9;uniprot:H0Y7Z6;uniprot:P63092;uniprot:A0A590UK00;uniprot:Q5JWE9;uniprot:A0A590UJS2;uniprot:A0A590UJC9;uniprot:A0A0S2Z3H8;uniprot:Q5JWD1;uniprot:Q5JWF2;uniprot:A0A0S2Z3S5;uniprot:A0A7I2V5R6;uniprot:A2A2R6;uniprot:A0A590UJX3;uniprot:A0A590UJX6								
+DNAJB1	GeneProduct	ensembl:ENSG00000132002	""	ensembl:ENSG00000132002	ncbigene:3337	hgnc.symbol:DNAJB1	uniprot:M0R1D6;uniprot:Q6FHS4;uniprot:A0A7I2YQW1;uniprot:M0QZD0;uniprot:M0R128;uniprot:A0A1B0GX60;uniprot:M0R080;uniprot:M0QYT3;uniprot:M0QXK0;uniprot:A0A7I2V3K7;uniprot:P25685								
+PRKACA	GeneProduct	ensembl:ENSG00000072062	""	ensembl:ENSG00000072062	ncbigene:5566	hgnc.symbol:PRKACA	uniprot:A0A024R7J0;uniprot:P17612;uniprot:A0A7I2YQ82;uniprot:K7EMV1;uniprot:K7ERP6;uniprot:Q15136;uniprot:K7ENJ5;uniprot:B7Z708;uniprot:A0A7I2V5J4								
+SIK1	GeneProduct	ensembl:ENSG00000142178	""	ensembl:ENSG00000142178	ncbigene:150094	hgnc.symbol:SIK1	uniprot:A0A2R8Y6E4;uniprot:P57059								
+SIK2	GeneProduct	ensembl:ENSG00000170145	""	ensembl:ENSG00000170145	ncbigene:23235	hgnc.symbol:SIK2	uniprot:Q9H0K1;uniprot:A0A024R3G7								
+SIK3	GeneProduct	ensembl:ENSG00000160584	""	ensembl:ENSG00000160584	ncbigene:23387	hgnc.symbol:SIK3	uniprot:Q9Y2K2;uniprot:H7C038;uniprot:H0Y4E8;uniprot:H7C3X8;uniprot:H7C042								
+HDAC4	GeneProduct	ensembl:ENSG00000068024	""	ensembl:ENSG00000068024	ncbigene:9759	hgnc.symbol:HDAC4	uniprot:H7BZT3;uniprot:C9J481;uniprot:A0A7I2SVS4;uniprot:C9J0X4;uniprot:H7C397;uniprot:P56524								
+HDAC5	GeneProduct	ensembl:ENSG00000108840	""	ensembl:ENSG00000108840	ncbigene:10014	hgnc.symbol:HDAC5	uniprot:K7EJZ7;uniprot:Q9UQL6;uniprot:K7ES01;uniprot:K7EJL4;uniprot:K7EJL6								
+HDAC7	GeneProduct	ensembl:ENSG00000061273	""	ensembl:ENSG00000061273	ncbigene:51564	hgnc.symbol:HDAC7	uniprot:C9JBC2;uniprot:C9J102;uniprot:H0YH91;uniprot:C9JVZ1;uniprot:C9JKN3;uniprot:J3KPH8;uniprot:C9JEB6;uniprot:C9JNI4;uniprot:H0YI41;uniprot:C9JZ79;uniprot:C9JGF5;uniprot:F8VWY3;uniprot:A0A087WYQ4;uniprot:C9JF80;uniprot:H0YI15;uniprot:Q8WUI4;uniprot:C9JH46;uniprot:C9JAH2;uniprot:H0YHJ5								
+CRTC2	GeneProduct	ensembl:ENSG00000160741	""	ensembl:ENSG00000160741	ncbigene:200186	hgnc.symbol:CRTC2	uniprot:Q5T4K5;uniprot:H0YDQ8;uniprot:J3KNE6;uniprot:Q53ET0								
+CREB1	GeneProduct	ensembl:ENSG00000118260	""	ensembl:ENSG00000118260	ncbigene:1385	hgnc.symbol:CREB1	uniprot:C9JBT4;uniprot:C9J276;uniprot:E7EWP8;uniprot:H7C3I0;uniprot:C9JCI4;uniprot:Q5U0J5;uniprot:C9J4L5;uniprot:P16220;uniprot:H7C1R5;uniprot:Q53X93;uniprot:C9J896								

_pathways/WP5078.md

@@ -1,20 +1,20 @@
 ---
 annotations:
-- id: PW:0000023
-  parent: regulatory pathway
+- id: PW:0000013
+  parent: disease pathway
   type: Pathway Ontology
-  value: immune response pathway
-- id: CL:0000084
-  parent: native cell
-  type: Cell Type Ontology
-  value: T cell
-- id: CL:0001064
-  type: Cell Type Ontology
-  value: malignant cell
+  value: disease pathway
 - id: CL:0002410
   parent: animal cell
   type: Cell Type Ontology
   value: pancreatic stellate cell
+- id: DOID:1793
+  parent: disease of cellular proliferation
+  type: Disease Ontology
+  value: pancreatic cancer
+- id: CL:0001064
+  type: Cell Type Ontology
+  value: malignant cell
 - id: CL:0000889
   parent: native cell
   type: Cell Type Ontology
@@ -23,18 +23,18 @@ annotations:
   parent: native cell
   type: Cell Type Ontology
   value: CD8-positive, alpha-beta T cell
-- id: DOID:1793
-  parent: disease of cellular proliferation
-  type: Disease Ontology
-  value: pancreatic cancer
-- id: PW:0000013
-  parent: disease pathway
-  type: Pathway Ontology
-  value: disease pathway
 - id: PW:0000626
   parent: disease pathway
   type: Pathway Ontology
   value: pancreatic cancer pathway
+- id: PW:0000023
+  parent: regulatory pathway
+  type: Pathway Ontology
+  value: immune response pathway
+- id: CL:0000084
+  parent: native cell
+  type: Cell Type Ontology
+  value: T cell
 - id: CL:0000145
   parent: native cell
   type: Cell Type Ontology
@@ -53,15 +53,15 @@ description: T cells are important effector cells in pancreatic cancer. Their fu
   is inhibited by various cellular interactions and secreted factors in the tumor
   microenvironment (TME). Both immune cells and pancreatic cancer cells are able to
   modulate T cell activation.
-last-edited: 2024-07-22
+last-edited: 2025-02-23
 ndex: null
 organisms:
 - Homo sapiens
 redirect_from:
 - /index.php/Pathway:WP5078
 - /instance/WP5078
-- /instance/WP5078_r134371
-revision: r134371
+- /instance/WP5078_r136810
+revision: r136810
 schema-jsonld:
 - '@context': https://schema.org/
   '@id': https://wikipathways.github.io/pathways/WP5078.html

_pathways/WP5514.md

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+---
+annotations:
+- id: CL:0000182
+  parent: native cell
+  type: Cell Type Ontology
+  value: hepatocyte
+- id: DOID:5015
+  parent: disease of cellular proliferation
+  type: Disease Ontology
+  value: fibrolamellar carcinoma
+- id: CL:0001063
+  type: Cell Type Ontology
+  value: neoplastic cell
+authors:
+- Eweitz
+citedin: ''
+communities: []
+description: '"Fibrolamellar carcinoma (FLC) is a liver cancer of adolescents and
+  young adults characterized by fusions of the genes encoding the protein kinase A
+  catalytic subunit, PRKACA, and heat shock protein, DNAJB1. The chimeric DNAJB1-PRKACA
+  protein has increased kinase activity and is essential for FLC xenograft growth....
+  a core function of DNAJB1-PRKACA is the phosphorylation and inactivation of salt-inducible
+  kinases (SIKs). This leads to deregulation of the CRTC2 transcriptional coactivator
+  and p300 acetyltransferase, resulting in transcriptional reprogramming and increased
+  global histone acetylation, driving malignant growth. Our studies establish a central
+  oncogenic mechanism of DNAJB1-PRKACA and suggest the potential of targeting CRTC2/p300
+  in FLC. Notably, these findings link this rare cancer’s signature fusion oncoprotein
+  to more common cancer gene alterations involving STK11 and GNAS, which also function
+  via SIK suppression."  Diagram inspired by figure 1H in Gritti, Wan et al. (2025),
+  https://pmc.ncbi.nlm.nih.gov/articles/PMC11803398.'
+last-edited: 2025-02-23
+ndex: null
+organisms:
+- Homo sapiens
+redirect_from:
+- /index.php/Pathway:WP5514
+- /instance/WP5514
+- /instance/WP5514_r136808
+revision: r136808
+schema-jsonld:
+- '@context': https://schema.org/
+  '@id': https://wikipathways.github.io/pathways/WP5514.html
+  '@type': Dataset
+  creator:
+    '@type': Organization
+    name: WikiPathways
+  description: '"Fibrolamellar carcinoma (FLC) is a liver cancer of adolescents and
+    young adults characterized by fusions of the genes encoding the protein kinase
+    A catalytic subunit, PRKACA, and heat shock protein, DNAJB1. The chimeric DNAJB1-PRKACA
+    protein has increased kinase activity and is essential for FLC xenograft growth....
+    a core function of DNAJB1-PRKACA is the phosphorylation and inactivation of salt-inducible
+    kinases (SIKs). This leads to deregulation of the CRTC2 transcriptional coactivator
+    and p300 acetyltransferase, resulting in transcriptional reprogramming and increased
+    global histone acetylation, driving malignant growth. Our studies establish a
+    central oncogenic mechanism of DNAJB1-PRKACA and suggest the potential of targeting
+    CRTC2/p300 in FLC. Notably, these findings link this rare cancer’s signature fusion
+    oncoprotein to more common cancer gene alterations involving STK11 and GNAS, which
+    also function via SIK suppression."  Diagram inspired by figure 1H in Gritti,
+    Wan et al. (2025), https://pmc.ncbi.nlm.nih.gov/articles/PMC11803398.'
+  keywords:
+  - CREB1
+  - CRTC2
+  - DNAJB1
+  - GNAS
+  - HDAC4
+  - HDAC5
+  - HDAC7
+  - PRKACA
+  - SIK1
+  - SIK2
+  - SIK3
+  license: CC0
+  name: DNAJB1-PRKACA fusion in fibrolamellar liver cancer
+seo: CreativeWork
+title: DNAJB1-PRKACA fusion in fibrolamellar liver cancer
+wpid: WP5514
+---