Genomic stratification based on SMAD4 in pancreatic cancer reveals biological implications of aberrant TGFβ signaling and susceptibility to TGFβ inhibition
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ABSTRACT:
PROVIDER: PRJNA1257770 | ENA |
REPOSITORIES: ENA
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Project description:Only 13% of newly diagnosed pancreatic cancer cases are surgically resectable, emphasizing the importance of systemic therapy. Yet, the 5-year overall survival rate for pancreatic cancer remains ~13%, underscoring the urgent need for new treatment strategies. TGFβ is a promising target due to its significant involvement in the desmoplasia, immune suppression, and chemoresistance characteristic of pancreatic cancer. Over 300 clinical trials targeting TGFβ have been conducted in unselected patient cohorts; however, none have gained FDA approval. Nevertheless, TGFβ blockade may hold promise for a subset of cancers with non-functional TGFβ signaling. Greater than 25% of pancreatic cancers carry mutations in SMAD4, a key component of canonical TGFβ signaling. In this study, we investigate the potential for stratifying patients based on SMAD4 mutational status to identify tumors susceptible to TGFβ inhibition. Analysis of SMAD4 expression in human pancreatic tumors reveals that SMAD4 mutation or loss is associated with worse disease-free survival. Intriguingly, we observe heterogeneity in intratumoral SMAD4 expression among human pancreatic cancer samples. To investigate the consequences of SMAD4 mutation, we employed SMAD4-deficient genetically engineered mouse models and orthotopic SMAD4 knockout models, which exhibited reduced survival, increased metastasis, and alterations in the tumor microenvironment compared to SMAD4 wildtype controls, consistent with gene and protein expression changes in the absence of functional SMAD4. Importantly, mice bearing SMAD4-deficient tumors treated with a blocking TGFβ antibody exhibited reduced tumor weight and improved survival. These findings suggest that targeting TGFβ signaling in TGFβ-deficient tumors has potential utility in pancreatic cancer.
2025-05-15 | GSE296094 | GEO
Project description:Deregulation of the transforming growth factor-β (TGFβ) signaling pathway in epithelial ovarian cancer has been reported, but the precise mechanism underlying disrupted TGFβ signaling in the disease remains unclear. We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate genome-wide screening of TGFβ-induced SMAD4 binding in epithelial ovarian cancer. Following TGFβ stimulation of the A2780 epithelial ovarian cancer cell line, we identified 2,362 SMAD4 binding loci and 318 differentially expressed SMAD4 target genes. Comprehensive examination of SMAD4-bound loci, revealed four distinct binding patterns: 1) Basal; 2) Shift; 3) Stimulated Only; 4) Unstimulated Only. SMAD4-bound loci were primarily classified as either Stimulated only (74%) or Shift (25%), indicating that TGFβ-stimulation alters SMAD4 binding patterns in epithelial ovarian cancer cells compared to normal epithelial cells. Furthermore, based on gene regulatory network analysis, we determined that the TGFβ-induced SMAD4-dependent regulatory network was strikingly different in ovarian cancer compared to normal cells. Importantly, the TGFβ/SMAD4 target genes identified in the A2780 epithelial ovarian cancer cell line were predictive of patient survival, based on in silico mining of publically available patient data bases. In conclusion, our data highlight the utility of next generation sequencing technology to identify genome-wide SMAD4 target genes in epithelial ovarian cancer. The results link aberrant TGFβ/SMAD signaling to ovarian tumorigenesis. Furthermore, the identified SMAD4 binding loci, combined with gene expression profiling and in silico data mining of patient cohorts, may provide a powerful approach to determine potential gene signatures with biological and future translational research in ovarian and other cancers.
2011-07-01 | GSE27526 | GEO
Project description:TGFβ is known to be a potent inducer of EMT, a process involved in tumor invasion. TIF1γ has been reported to participate to TGFβ signaling. In order to understand the role of TIF1γ in TGFβ signaling and its requirement for EMT, we analyzed the TGFβ1 response of human mammary epithelial cell lines. A strong EMT increase was observed in TIF1γ-silenced cells after TGFβ1 treatment, whereas Smad4 inactivation completely blocked this process. In support of these observations, microarray data show that the functions of several TIF1γ target genes can be linked to EMT. As a negative regulator of Smad4, TIF1γ could be critical for the regulation of TGFβ signaling. This work highlights the molecular relationship between TIF1γ and Smad4 in TGFβ1 signaling and EMT. Total mRNA extractions were performed for 11 samples from transfected HMEC-TR. Replicates are rimo1, 6; rimo3, 9; rimo2, 7; rimo 4, 10 and rimo 5, 11. Rimo 8 is a single experiment. All RNA extractions were obtained from two independent cell cultures excepted for rimo8. Rimo 1, 6 are replicate for ctrl-; Rimo 3, 9 are replicate for ctrl+; Rimo 2, 7 are replicate for SiTIF-; Rimo 4, 10 are replicate for SiTIF+; Rimo8 is SiSmad4-; and Rimo5, 11 are replicate for SiSmad4+. ctrl means that HMEC-TR were transfected with an SiRNA scramble. "siSmad4" means that HMEC-TR were transfected with an SiRNA anti Smad4. "siTIF" means that HMEC-TR were transfected with an SiRNA anti TIF1γ. "-" means that cells were grown without TGFβ. "+" means that cells were treated with 5 ng/ml TGFβ1 for 24h.
2011-05-26 | E-GEOD-28448 | biostudies-arrayexpress
Project description:RNA-sequencing of TGFβ treated empty vector (EV) or Smad4-expressing AKPS lines followed by GSEA revealed a number of gene sets overlapping with those obtained from analyses in reactive cholangiocytes. Hallmark gene sets MYC, E2F, G2M checkpoint, and oxidative phosphorylation were enriched with loss of Smad4, while TGFβ signaling, EMT, and TNFα were enriched with intact Smad4 signaling, suggesting conserved growth suppressive functions of Smad4 in primary cholangiocytes and advanced cancer.
2023-12-07 | GSE237679 | GEO
Project description:Transforming growth factor β (TGFβ) signaling is essential in cell growth and differentiation. Yet, the role of the individual TGFβ signaling components in human tissue homeostasis and transformation is still incompletely understood. Here we dissected the importance of the core components in the TGFβ signaling pathway by CRISPR/Cas9 genome editing of human keratinocytes. The edited keratinocytes were used for human organotypic skin cultures and global quantitative proteomics and phosphoproteomics by mass spectrometry. Characterization of cells and human organotypic skin tissues showed control of epithelial differentiation by Smad4-dependent TGF signaling through cell cycle regulation and ECM expression. In contrast, we found that the combined Smad4 dependent and independent pathways, governed by TGFβRII, controls epithelial homeostasis and prevents invasive growth by blocking epithelial inflammation and activation of p38 and ERK signaling. The study provides a framework for exploration of signaling pathways in human 3D tissue models and with global phosphoproteomics.
2023-02-09 | PXD024935 | Pride
Project description:Reduced representation bisulfite sequencing (RRBS) on the same TGFβ-treated AKPS lines (with EV or Smad4) revealed that Smad4 impacts DNA methylation (DNAme), with decreases in intergenic DNAme as the most impacted in our CCA models.
2023-12-07 | GSE237680 | GEO
Project description:TGFβ is known to be a potent inducer of EMT, a process involved in tumor invasion. TIF1γ has been reported to participate to TGFβ signaling. In order to understand the role of TIF1γ in TGFβ signaling and its requirement for EMT, we analyzed the TGFβ1 response of human mammary epithelial cell lines. A strong EMT increase was observed in TIF1γ-silenced cells after TGFβ1 treatment, whereas Smad4 inactivation completely blocked this process. In support of these observations, microarray data show that the functions of several TIF1γ target genes can be linked to EMT. As a negative regulator of Smad4, TIF1γ could be critical for the regulation of TGFβ signaling. This work highlights the molecular relationship between TIF1γ and Smad4 in TGFβ1 signaling and EMT.
2011-05-26 | GSE28448 | GEO
Project description:Transforming growth factor β (TGFβ) is a morphogenic protein that augments antiviral immunity by altering the functional properties of pathogen-specific memory CD8 T cells. During infection, TGFβ inhibits formation of effector (TEFF) and circulating memory CD8 T cells, while encouraging tissue-resident memory CD8 T cells (TRM) to settle in peripheral tissues. SMAD proteins are signaling intermediates that are used by members of the TGF cytokine family to modify gene expression. Using RNA-sequencing we determined that SMAD4 altered the transcriptional profile of antiviral CTLs during respiratory infection. Our data show that SMAD4 and TGFβ use alternate signaling pathways to cooperatively regulate a collection of genes that determine whether pathogen-specific memory CD8 T cells localize in peripheral or lymphoid tissues. During infection, SMAD4 acts independently of TGF to inhibit TRM development, while inducing genes that support formation of circulating memory CD8 T cells. The genes that are modulated by SMAD4 include several homing receptors (CD103, KLRG1 and CD62L) and transcription factors (Hobit and EOMES) that support memory formation.
2021-12-22 | GSE151637 | GEO
Project description:DNMT3b mediates TGFβ-Smad2/3 action to maintain Epiblast homeostasis upon Smad4 Loss
| PRJNA1005240 | ENA
Project description:Deregulation of the transforming growth factor-? (TGF?) signaling pathway in epithelial ovarian cancer has been reported, but the precise mechanism underlying disrupted TGF? signaling in the disease remains unclear. We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate genome-wide screening of TGF?-induced SMAD4 binding in epithelial ovarian cancer. Following TGF? stimulation of the A2780 epithelial ovarian cancer cell line, we identified 2,362 SMAD4 binding loci and 318 differentially expressed SMAD4 target genes. Comprehensive examination of SMAD4-bound loci, revealed four distinct binding patterns: 1) Basal; 2) Shift; 3) Stimulated Only; 4) Unstimulated Only. SMAD4-bound loci were primarily classified as either Stimulated only (74%) or Shift (25%), indicating that TGF?-stimulation alters SMAD4 binding patterns in epithelial ovarian cancer cells compared to normal epithelial cells. Furthermore, based on gene regulatory network analysis, we determined that the TGF?-induced SMAD4-dependent regulatory network was strikingly different in ovarian cancer compared to normal cells. Importantly, the TGF?/SMAD4 target genes identified in the A2780 epithelial ovarian cancer cell line were predictive of patient survival, based on in silico mining of publically available patient data bases. In conclusion, our data highlight the utility of next generation sequencing technology to identify genome-wide SMAD4 target genes in epithelial ovarian cancer. The results link aberrant TGF?/SMAD signaling to ovarian tumorigenesis. Furthermore, the identified SMAD4 binding loci, combined with gene expression profiling and in silico data mining of patient cohorts, may provide a powerful approach to determine potential gene signatures with biological and future translational research in ovarian and other cancers. ChIP-Seq: 1 control lane. 4 unstimulated lanes 4 stimulated lanes Gene expression: 3 technical replicates each of SMAD4 stimulated and SMAD4 unstimulated cells
2011-06-30 | E-GEOD-27526 | biostudies-arrayexpress