Mutant SF3B1 promotes malignancy in PDAC
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Switzerland
- Institute of Pharmacology and Toxicology, University of Zurich, Switzerland
- Department of Computer Science, Biomedical Informatics Group, ETH Zurich, Switzerland
- Swiss Institute of Bioinformatics, Switzerland
- Department of Biology, ETH Zurich, Switzerland
- Biomedical Informatics Research, University Hospital Zurich, Switzerland
Figures
Figure 1 with 1 supplement
Sf3b1K700E increases aggressiveness of murine PDAC.
(A) Schematic overview of the Sf3b1K700E/+ knockin model. Arrows indicate direction of the translatable code of the gene. An A to G conversion at base position 2098, induced by Cre-recombination, …
Figure 1—figure supplement 1
Sf3b1K700E increases aggressiveness of murine PDAC.
(A) Incidence of mutations in splicing factors in PDAC patients derived from the ICGC database (PACA-AU, n=391 and PACA-CA, n=268). (B) Incidence of SF3B1 missense mutations in PDAC patients derived …
Figure 2 with 1 supplement
Sf3b1K700E induces downregulation of EMT.
(A) Gene-set enrichment analysis (GSEA) enrichment plot of epithelial-mesenchymal transition (EMT), representing the most deregulated pathway of the GSEA-Hallmark pathways when comparing KPC (n=3) …
Figure 2—figure supplement 1
Sf3b1K700E induces downregulation of EMT.
(A) Integrated genome viewer (IGV) displaying RNA-seq reads of Trp53 of sorted KPC and KPC-Sf3b1K700E/+ cells. (B) Principal component analysis showing the variance in two dimensions in relation to …
Figure 3 with 1 supplement
Sf3b1K700E reduces TGF-β-induced apoptosis.
(A) Representative microscopy images of E-Cadherin (green) and CC3 (red) in murine PDAC samples. Scale bar is 50 μm. (B) Quantification of CC3 positive cells in KPC (n=8) and KPC-Sf3b1K700E/+ (n=7) …
Figure 3—figure supplement 1
Sf3b1K700E reduces TGF-β-induced apoptosis.
(A) Representative microscopy images of CC3 (red) in KPC tumor samples. Scale bar is 50 μm. (B) Quantification of CC3 positive cells according to location (inside of PanIN lumen or outside of lumen) …
Figure 4 with 1 supplement
SF3B1-K700E induces aberrant splicing of MAP3K7 in human and mouse PDAC.
(A) Summary of alternative splice events detected in KPC-Sf3b1K700E/+ sorted tumor cells (PSI > 0.1, p<0.01). (B) Histogram displaying the distance of cryptic 3’splice-site (ss) from the adjacent …
Figure 4—figure supplement 1
SF3B1-K700E induces aberrant splicing of MAP3K7 in human and mouse PDAC.
(A) Pan-cancer analysis of alternative splice-events identified in solid tumors carrying the SF3B1K700E mutation (PSI >0.05, FDR <1–10). (B) Histogram displaying the distance of cryptic 3’ss from …
Figure 5 with 1 supplement
Reduction in Map3k7 lowers sensitivity to TGF-β1.
(A–C) RT-qPCR data showing Map3k7 expression in KPC (n=13) and KPC-Sf3b1K700E/+ (n=12) ex vivo tumor cultures (A), as well as WT (n=3) and Sf3b1K700E/+ (n=4) pancreata (B) and organoid lines (C). …
Figure 5—figure supplement 1
Reduction in Map3k7 lowers sensitivity to TGF-β1.
(A) Western blot gel-image of MAP3K7 (molecular weight 78 kDa) and GAPDH (molecular weight 37 kDa) in a KPC cell line transduced with a control shRNA (shCtrl) or a shRNA targeting Map3k7 (shMap3k7). …
Author response image 1
Impact of altered Map3k7 levels in an orthotopic PDAC model.
(A) Relative gene expression of Map3k7 in KPC cells transduced with shRNA targeting Map3k7 (shMap3k7), normalized to KPC cells transduced with scrambled control shRNA (shCtrl). 3 biological …
Tables
Author response table 1
Mutual exclusivity analysis of public PDAC databases (ICGC, CPTAC, QCMG, TCGA, UTSW), including 910 patients.
Mutation frequency is 25% for SMAD4, 5% for TGF-ΒR2, 3% for SMAD2, 2.6% for TGF-ΒR1, 1.4% for SMAD3, 0.7% for SF3B1-K700E, 0.7% for TGF-ΒR3, 0.4% for SMAD1. Analysis was performed on cbioportal.org.
| A | B | p-Value | q-Value | Tendency |
|---|---|---|---|---|
| SF3B1: MUT=K700E | SMAD1 | 0.974 | 0.974 | Mutual exclusivity |
| SF3B1: MUT=K700E | SMAD2 | 0.823 | 0.974 | Mutual exclusivity |
| SF3B1: MUT=K700E | SMAD3 | 0.917 | 0.974 | Mutual exclusivity |
| SF3B1: MUT=K700E | SMAD4 | 0.524 | 0.974 | Mutual exclusivity |
| SF3B1: MUT=K700E | TGF-ΒR1 | 0.851 | 0.974 | Mutual exclusivity |
| SF3B1: MUT=K700E | TGF-ΒR2 | 0.268 | 0.682 | Co-occurrence |
| SF3B1: MUT=K700E | TGF-ΒR3 | 0.961 | 0.974 | Mutual exclusivity |
Additional files
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Supplementary file 1
Differential gene expression analysis of sorted KPC and KPC-Sf3b1K700E tumor cells, displaying logFC, logCPM, P-Value, False discovery rate (FDR) and EntrezID.
- https://cdn.elifesciences.org/articles/80683/elife-80683-supp1-v3.xlsx
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Supplementary file 2
Splicing analysis of indicated alternative splice events in sorted KPC and KPC-Sf3b1K700E tumor cells, displaying Ensembl ID, gene name, event positions, percent spliced in (delta psi), standard deviation, p-value and FDR.
- https://cdn.elifesciences.org/articles/80683/elife-80683-supp2-v3.xlsx
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Supplementary file 3
Name and nucleotide sequence of all primers used in the study.
- https://cdn.elifesciences.org/articles/80683/elife-80683-supp3-v3.xlsx
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Source data 1
Uncropped gel images of Western blot an RT-PCR experiments.
- https://cdn.elifesciences.org/articles/80683/elife-80683-data1-v3.zip
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MDAR checklist
- https://cdn.elifesciences.org/articles/80683/elife-80683-mdarchecklist1-v3.docx
