title: An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer.
abstract: Lineage-restricted transcription factors (TFs) are frequently mutated or overexpressed in cancer and contribute toward malignant behaviors; however, the molecular bases of their oncogenic properties are largely unknown. As TF activities are difficult to inhibit directly with small molecules, the genes and pathways they regulate might represent more tractable targets for drug therapy. We studied GATA6, a TF gene that is frequently amplified or overexpressed in gastric, esophageal and pancreatic adenocarcinomas. GATA6-overexpressing gastric cancer cell lines cluster in gene expression space, separate from non-overexpressing lines. This expression clustering signifies a shared pathogenic group of genes that GATA6 may regulate through direct cis-element binding. We used chromatin immunoprecipitation and sequencing (ChIP-seq) to identify GATA6-bound genes and considered TF occupancy in relation to genes that respond to GATA6 depletion in cell lines and track with GATA6 mRNA (synexpression groups) in primary gastric cancers. Among other cellular functions, GATA6-occupied genes control apoptosis and govern the M-phase of the cell cycle. Depletion of GATA6 reduced the levels of the latter transcripts and arrested cells in G2 and M phases of the cell cycle. Synexpression in human tumor samples identified likely direct transcriptional targets substantially better than consideration only of transcripts that respond to GATA6 loss in cultured cells. Candidate target genes responded to the loss of GATA6 or its homolog GATA4 and even more to the depletion of both proteins. Many GATA6-dependent genes lacked nearby binding sites but several strongly dependent, synexpressed and GATA6-bound genes encode TFs such as MYC, HES1, RARB and CDX2. Thus, many downstream effects occur indirectly through other TFs and GATA6 activity in gastric cancer is partially redundant with GATA4. This integrative analysis of locus occupancy, gene dependency and synexpression provides a functional signature of GATA6-overexpressing gastric cancers, revealing both limits and new therapeutic directions for a challenging and frequently fatal disease.
authors: 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Medicine, Harvard Medical School, Boston, MA, USA.
authors: R
authors: R
authors: Sulahian
authors: Novartis Institutes for Biomedical Research, Emeryville, CA, USA.
authors: F
authors: F
authors: Casey
authors: Novartis Institutes for Biomedical Research, Emeryville, CA, USA.
authors: J
authors: J
authors: Shen
authors: 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Pathology, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA.
authors: Z R
authors: ZR
authors: Qian
authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
authors: H
authors: H
authors: Shin
authors: 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Pathology, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA.
authors: S
authors: S
authors: Ogino
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
authors: B A
authors: BA
authors: Weir
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
authors: F
authors: F
authors: Vazquez
authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
authors: X S
authors: XS
authors: Liu
authors: 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Medicine, Harvard Medical School, Boston, MA, USA [3] Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA.
authors: W C
authors: WC
authors: Hahn
authors: 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Medicine, Harvard Medical School, Boston, MA, USA [3] Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA.
authors: A J
authors: AJ
authors: Bass
authors: Novartis Institutes for Biomedical Research, Emeryville, CA, USA.
authors: V
authors: V
authors: Chan
authors: 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Medicine, Harvard Medical School, Boston, MA, USA [3] Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA.
authors: R A
authors: RA
authors: Shivdasani
mesh_terms: D017209:Apoptosis; D001665:Binding Sites; D002453:Cell Cycle; D045744:Cell Line, Tumor; D019070:Cell Lineage; D049109:Cell Proliferation; D044127:Epigenesis, Genetic; D050991:GATA4 Transcription Factor / Q000235:genetics / Q000378:metabolism; D050993:GATA6 Transcription Factor / Q000235:genetics* / Q000502:physiology*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006657:Histones / Q000378:metabolism; D006801:Humans; D012333:RNA, Messenger / Q000235:genetics; D015398:Signal Transduction; D013274:Stomach Neoplasms / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D050991:GATA4 Transcription Factor; C484170:GATA4 protein, human; D050993:GATA6 Transcription Factor; C494759:GATA6 protein, human; D006657:Histones; D012333:RNA, Messenger; D014157:Transcription Factors