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Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer
Haruna Takeda1, Alistair G Rust2, Jerrold M Ward3
1Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673; Department of Pathology, School of Medicine, Kanazawa Medical University, Ishikawa 920-0293, Japan;
Abstract:
Mutations in SMAD4 predispose to the development of gastrointestinal cancer, which is the third leading cause of cancer-related deaths. To identify genes driving gastric cancer (GC) development, we performed a Sleeping Beauty (SB) transposon mutagenesis screen in the stomach of Smad4(+/-) mutant mice. This screen identified 59 candidate GC trunk drivers and a much larger number of candidate GC progression genes. Strikingly, 22 SB-identified trunk drivers are known or candidate cancer genes, whereas four SB-identified trunk drivers, including PTEN, SMAD4, RNF43, and NF1, are known human GC trunk drivers. Similar to human GC, pathway analyses identified WNT, TGF-β, and PI3K-PTEN signaling, ubiquitin-mediated proteolysis, adherens junctions, and RNA degradation in addition to genes involved in chromatin modification and organization as highly deregulated pathways in GC. Comparative oncogenomic filtering of the complete list of SB-identified genes showed that they are highly enriched for genes mutated in human GC and identified many candidate human GC genes. Finally, by comparing our complete list of SB-identified genes against the list of mutated genes identified in five large-scale human GC sequencing studies, we identified LDL receptor-related protein 1B (LRP1B) as a previously unidentified human candidate GC tumor suppressor gene. In LRP1B, 129 mutations were found in 462 human GC samples sequenced, and LRP1B is one of the top 10 most deleted genes identified in a panel of 3,312 human cancers. SB mutagenesis has, thus, helped to catalog the cooperative molecular mechanisms driving SMAD4-induced GC growth and discover genes with potential clinical importance in human GC.
Insights
This study used Sleeping Beauty transposon mutagenesis in mice to identify genes driving gastric cancer (GC) development. It revealed key pathways and identified LDL receptor-related protein 1B (LRP1B) as a novel GC tumor suppressor gene.
Area of Science:
- Oncogenomics
- Cancer Biology
- Molecular Genetics
Background:
- Mutations in SMAD4 are linked to gastrointestinal cancer, the third leading cause of cancer deaths.
- Gastric cancer (GC) development is driven by complex genetic alterations.
- Understanding these drivers is crucial for developing effective cancer therapies.
Purpose of the Study:
- To identify novel genes and pathways that drive gastric cancer (GC) development in the context of SMAD4 mutations.
- To compare findings from a mouse model with human GC genomic data.
- To discover new candidate tumor suppressor genes for GC.
Main Methods:
- Utilized Sleeping Beauty (SB) transposon mutagenesis in Smad4(+/-) mutant mice to screen for GC drivers.
- Performed pathway analysis on identified genes.
- Conducted comparative oncogenomic filtering against human GC mutation data.
Main Results:
- Identified 59 candidate GC trunk drivers and numerous progression genes.
- Found that SB-identified drivers include known human GC genes like PTEN, SMAD4, RNF43, and NF1.
- Pathway analysis revealed deregulation in WNT, TGF-β, PI3K-PTEN signaling, and chromatin organization.
- Identified LDL receptor-related protein 1B (LRP1B) as a novel candidate GC tumor suppressor gene, with frequent mutations and deletions in human GC samples.
Conclusions:
- SB mutagenesis is effective in cataloging cooperative molecular mechanisms in SMAD4-induced GC.
- The study identified LRP1B as a significant, previously unrecognized GC tumor suppressor.
- Findings highlight potential new therapeutic targets and diagnostic markers for human GC.
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