35P - Whole exome sequencing reveals high frequency of Notch pathway mutations in Indian breast cancer cases

Background

Breast cancer (BC) is a leading global malignancy, responsible for 11.7% of all cancer cases worldwide and 13.5% in India. The Notch signaling pathway, known for its role in cell proliferation and apoptosis, often undergoes genetic alterations. However, the prevalence of these mutations in the Indian BC population remains unclear. This study aims to delineate the mutation profile of genes associated with the Notch pathway using whole exome sequencing (WES) followed by Sanger sequencing validation.

Methods

Postoperative tumor and adjacent normal tissue samples were collected from 47 BC patients. Genomic DNA was extracted using the salting-out method, and libraries were prepared following the manufacturer's instructions. WES was performed on the Illumina platform, achieving an average depth coverage of 100X. Data analysis was conducted using an in-house pipeline. MAML3 and NOTCH4 deletions were further validated by Sanger sequencing. Quantitative PCR was employed to assess mRNA expression levels of MAML3 and NOTCH4.

Results

The Notch pathway exhibited the highest mutation frequency among the ten canonical pathways analyzed, with mutations detected in all 23 patients. A total of 47 mutated genes were identified, including 16 tumor suppressors, 3 oncogenes, and 28 passenger genes. Specifically, MAML3 and NOTCH4 had somatic mutation rates of 17.5% and 20%, respectively. MAML3 mutations comprised missense and frameshift deletions, while NOTCH4 mutations included in-frame deletions and missense mutations. These mutations were confirmed by Sanger sequencing. Both MAML3 and NOTCH4 showed significantly decreased mRNA expression in tumor tissues compared to normal tissues.

Conclusions

This study offers a comprehensive analysis of frequently mutated genes within the Notch pathway in Indian BC patients, highlighting MAML3 and NOTCH4 as prominently mutated genes. These findings suggest the potential of these genes in risk assessment, screening, diagnosis, and early prognosis of BC. The study enhances the understanding of the genetic landscape of BC in the Indian population.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

The authors.

Funding

Has not received any funding.

Disclosure

All authors have declared no conflicts of interest.