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Updated: Aug 4, 2025
Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies
Published on: September 15, 2023
The targeted next-generation sequence revealed SMAD4, AKT1, and TP53 mutations from circulating cell-free DNA of
Ambritha Balasundaram1, Udhaya Kumar S1, Thirumal Kumar D2
1Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
Abstract:
Breast cancer biomarkers that detect marginally advanced stages are still challenging. The detection of specific abnormalities, targeted therapy selection, prognosis, and monitoring of treatment effectiveness over time are all made possible by circulating free DNA (cfDNA) analysis. The proposed study will detect specific genetic abnormalities from the plasma cfDNA of a female breast cancer patient by sequencing a cancer-related gene panel (MGM455 - Oncotrack Ultima), including 56 theranostic genes (SNVs and small INDELs). Initially, we determined the pathogenicity of the observed mutations using PredictSNP, iStable, Align-GVGD, and ConSurf servers. As a next step, molecular dynamics (MD) was implemented to determine the functional significance of SMAD4 mutation (V465M). Lastly, the mutant gene relationships were examined using the Cytoscape plug-in GeneMANIA. Using ClueGO, we determined the gene's functional enrichment and integrative analysis. The structural characteristics of SMAD4 V465M protein by MD simulation analysis further demonstrated that the mutation was deleterious. The simulation showed that the native structure was more significantly altered by the SMAD4 (V465M) mutation. Our findings suggest that SMAD4 V465M mutation might be significantly associated with breast cancer, and other patient-found mutations (AKT1-E17K and TP53-R175H) are synergistically involved in the process of SMAD4 translocate to nuclease, which affects the target gene translation. Therefore, this combination of gene mutations could alter the TGF-β signaling pathway in BC. We further proposed that the SMAD4 protein loss may contribute to an aggressive phenotype by inhibiting the TGF-β signaling pathway. Thus, breast cancer's SMAD4 (V465M) mutation might increase their invasive and metastatic capabilities.Communicated by Ramaswamy H. Sarma.
Insights
Circulating free DNA (cfDNA) analysis identified a SMAD4 (V465M) mutation linked to aggressive breast cancer. This mutation, alongside AKT1-E17K and TP53-R175H, may disrupt the TGF-β pathway, increasing invasiveness.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Detecting advanced breast cancer stages remains challenging.
- Circulating free DNA (cfDNA) analysis aids in identifying abnormalities, guiding therapy, and monitoring treatment.
- Targeted gene panels are crucial for comprehensive cancer profiling.
Purpose of the Study:
- To detect and analyze genetic abnormalities in plasma cfDNA from breast cancer patients.
- To determine the pathogenicity and functional significance of identified mutations, particularly SMAD4 (V465M).
- To investigate the synergistic effects of mutations on signaling pathways and their association with aggressive breast cancer phenotypes.
Main Methods:
- Sequencing of a 56-gene cancer-related panel (MGM455 - Oncotrack Ultima) from plasma cfDNA.
- In silico pathogenicity prediction using PredictSNP, iStable, Align-GVGD, and ConSurf servers.
- Molecular dynamics (MD) simulations to assess the functional impact of SMAD4 (V465M) mutation.
- Network analysis (GeneMANIA) and functional enrichment (ClueGO) for mutant gene interactions and pathway analysis.
Main Results:
- The SMAD4 (V465M) mutation was predicted to be deleterious, significantly altering protein structure.
- MD simulations confirmed the detrimental structural impact of the SMAD4 (V465M) mutation.
- Co-occurring mutations (AKT1-E17K, TP53-R175H) were found to synergistically affect SMAD4 translocation and target gene translation, potentially altering the TGF-β signaling pathway.
Conclusions:
- The SMAD4 (V465M) mutation is strongly associated with breast cancer, potentially contributing to an aggressive phenotype.
- Inhibition of the TGF-β signaling pathway due to SMAD4 protein loss may enhance breast cancer invasiveness and metastasis.
- Combined mutations may represent a novel mechanism driving breast cancer progression and therapeutic resistance.
