Breast cancer (BC) has become a severe public health concern, and its burden impacts the financial, psychological, and physical facets of human life. In women, it is the most frequent cancer, and along with lung and colorectal cancers, it is one of the three most prevalent malignancies worldwide in both sexes. According to a report published by the IARC, BC accounts for over 25% of all new malignancies in women, with 2.3 million women diagnosed globally in 2020. The incidence of BC in 2020 was 0.18 million, with a mortality rate of approximately 51%, and BC is the primary cause of cancer incidence and fatalities among the Indian population 9. Over the past few years, the age-related incidence pattern has significantly shifted. India's BC cases present with a diagnosis at a younger median age (49 years) than the Western population, where the median age at diagnosis is 62 years 10. A similar pattern of median age-related incidence (48 years) was observed in our BC cohort.
According to recent research, ethnicity may significantly influence the genetic propensity to breast cancer. The genetic variants may vary by ethnicity and can be ethnic or race-specific 11–13. However, most of today's understanding of the disease's predisposition comes from Western populations. To our knowledge, this is the first study that comprehensively outlines the somatic variants discovered in Indian BC cases. We reported several altered canonical and non-canonical genes. In our cohort, TP53, PIK3CA, KMT2C and ZFHX3 were found to be mutated in 59%, 34%, 30%, and 29% of samples, respectively, compared with 26%, 29%, 12%, and 12% of BC samples in the COSMIC database. Detailed variants of the above mentioned genes are listed in Table S2.
TP53 is a tumor suppressor gene, and its genetic variants (mainly due to frameshift or missense mutations) lead to human malignancies 14. Under normal physiological conditions, it acts as a transcription factor with a pro-apoptotic function, while in diseased conditions, mutational inactivation makes it dysfunctional 15. In our study, the mutation was mainly confined to the kinase region. Mutations in these regions disrupt its configuration and help to gain kinase activity. Thus, in the presence of damaged DNA, it could not arrest the cell cycle and prevent apoptosis, promoting oncogenesis. PIK3CA is an oncogene that plays a significant role in cell signaling, particularly in the phosphoinositide 3-kinase (PI3K) pathway 16. Under normal physiological conditions, PIK3CA regulates various cellular processes, including cell growth, survival, and metabolism. However, when mutated, it can lead to the development of human malignancies 17. PIK3CA mutations are also found in other cancers, such as colorectal cancers (10–15%) and lung cancers (4%) 18,19. Overall, mutations in PIK3CA contribute to the promotion of oncogenesis by driving aberrant cell growth, evading cell death, and enhancing cell survival 20. ZFHX3 is a zinc finger transcription factor-encoding gene that plays a significant role in various cellular processes, including cell differentiation, proliferation, and apoptosis 21. Under normal circumstances, ZFHX3 acts as a tumor suppressor gene, regulates cell growth, prevents the formation of cancerous cells, and modulates the expression of genes involved in key cellular pathways. In diseased conditions, mutational inactivation or loss of ZFHX3 function can occur, disrupting its tumor-suppressive capabilities 22. Mutations in the ZFHX3 gene can lead to increased activity of the protein, which can promote cell growth and proliferation 23. KMT2C is a gene that encodes a histone methyltransferase and plays a crucial role in gene regulation and chromatin remodeling 24. In its normal state, KMT2C helps maintain genomic stability and prevents uncontrolled cell growth by regulating the expression of specific genes involved in cell cycle control and DNA repair 25. Mutations in KMT2C have been identified in various cancers, including gastrointestinal, breast, and ovarian cancers 26. These mutations can lead to functional alterations, affecting the ability of KMT2C to regulate gene expression and chromatin remodeling 27. TMB is the genetic feature of tumorous tissue that varies among patients and tumor types. TMB across 33 different tumor types, including BC (named BRCA), was retrieved from the TCGA database and compared with our cohort. High TMB in the AIIMS cohort correlates with various tumoral immunogenicity and could be a clinical biomarker for immunotherapy response 28,29.
Cancer-causing altered genes show a significant pattern in their co-occurrence and exclusiveness. We performed interaction analysis to test this concurrent and exclusive mutation interaction among the top most altered genes. PIK3CA is one of the driver genes found in our study and was found to be only mutually exclusive with the CCDC168 gene (p < 0.05). CCDC168 (Coiled-Coil Domain Containing 168) is significantly mutated and upregulated in various tumor types, including colorectal cancer and Paget's disease, and is associated with poor prognosis 30,31. The PI3K, NOTCH, and RTK-RAS pathways were the most frequently influenced oncogenic pathways in neuroendocrine breast tumors, while the RTK-RAS, Hippo, and WNT pathways were reported in gastric cancer 32,33. However, in regard to our investigation, the RTK-RAS, WNT, and NOTCH pathways were the most often impacted. Receptor tyrosine kinase (RTK) is one of the most common intracellular signaling pathways that plays an essential role in cell growth, differentiation, and survival 34,35. On the other hand, WNT is a canonical pathway primarily engaged in cell proliferation. In contrast, the Notch pathway is one such juxtacrine signaling pathway that plays a significant role in maintaining progenitor cells, the fate of the cell, differentiation, and cell death 36,37. From a therapeutic perspective, the RTK-RAS and NOTCH pathways are well targeted and can be modulated with FDA-approved drugs 38,39. Conversely, there are no approved chemical compounds that target WNT signaling 40. However, many repurposed drugs or natural compounds are currently in the clinical trial phase 41.
During the tumor formation and development period, multiple mutational events occur, which may contribute to the set of mutational signatures 42. Each signature reveals its mutation etiology, which can be a potential genomic biomarker for personalized therapy. Additionally, it also opens up opportunities for the individual's stratification and for predicting cancer predisposition 43. The vast majority of malignancies are thought to be triggered by somatic mutations 44 acquired either through endogenous (failure of repair mechanism, SBS13 & SBS6) or exogenous (exposure to mutagen, SBS29) mechanisms. Dysregulation of repair machinery or APOBEC activity can lead to hyper-mutation of the DNA that can be linked with the emergence of cancer 45,46. Genomic evidence of SBS13, 6 &29 was also found in various other malignancies, including BC (Figure S6). Finally, we could not undertake a survival analysis in this cohort due to the patients' short follow-up duration. Future research will address these issues, and the understanding gained from the present study will assist us in achieving appropriate patient stratification. In summary, we performed WES on 97 BC cases along with matched blood samples from an Indian population and characterized genes with high somatic mutation frequencies. We also identified several genes with increased mutational frequency in contrast with other BC cases in the COSMIC database. Furthermore, several top mutated genes were enriched in different oncogenic signaling pathways that were primarily responsible for the pathogenesis and development of BC. Mutational signatures SBS13, SBS6 and SBS29 were predominantly observed in our cohort. Moreover, these findings encourage additional investigation to determine the functional significance of altered genes in the development of BC.