Tumor Analysis of BRCA Carriers Reveals Genomic Similarities Despite Temporal Separation

Biochemistry Genetics Basic Medical Sciences Life Sciences Immunology Oncology Medicine Cell Biology
BRCA breast cancer genomic profile molecular analysis early life events genetic modifiers preventive medicine

Tumor Analysis of BRCA1/2 Carriers: Genomic Similarities Evident Across Different Time Points

Breast cancer (BC) is the most common malignant tumor among women globally, with its pathogenesis predominantly sporadic, while familial hereditary cases account for only 5% to 10%. Among various pathogenic molecules, mutations in the BRCA1/2 genes (Pathogenic Gene, PG) have become a focus due to their high penetrance, significantly increasing the lifetime risk for women of developing breast cancer and ovarian cancer, up to 38%-87% and 16.5%-73%, respectively. These gene mutations are also associated with other cancer types, including pancreatic cancer, stomach cancer, and prostate cancer.

The research team, including Tal Falick Michaeli, Avital Granit Mizrahi, and others from the Hebrew University and Hadassah Medical Center in Israel, published their study in the journal “Discover Oncology” in 2024. Their study aims to explore the relative contributions of genetic modifiers and environmental factors to the development of breast cancer in BRCA1/2 mutation carriers, with a particular focus on the impact of early life events.

Background and Objectives

BRCA1/2 mutation carriers often exhibit unique molecular characteristics in breast cancer (such as mutational signature 3). However, it remains unclear how genetic modifiers and external environmental factors interact to influence tumor characteristics and risk. This study aims to reveal the roles of genetic and environmental factors in tumor formation by comparing the molecular characteristics of primary breast cancer (BC) at different time points in the same patient. Additionally, the study analyzed primary lung cancer samples from two patients to explore cross-organ tumor molecular characteristic differences.

Methods

The study involved whole-exome sequencing (WES) of tumor samples from three female BRCA1/2 mutation patients. It analyzed six primary breast cancer samples (two from each patient) and lung cancer samples from two patients. The experimental process primarily included the following steps:

  1. DNA Extraction and Quality Control: DNA was extracted from formalin-fixed paraffin-embedded (FFPE) sections, with its quality and integrity assessed using a NanoDrop spectrophotometer, Qubit dsdna HS Assay, and Agilent 2100 Bioanalyzer.

  2. Library Construction and Sequencing: Exome libraries were constructed using the KAPA HyperPrep kit, captured with the Roche MedExome Nimblegen kit, and sequenced on the Illumina NextSeq 500 platform.

  3. Data Processing and Variance Detection:

    • Filtered Fastq files were aligned to the human genome GRCh38 using the BWA-MEM2 software.
    • Duplicate sequences were removed using the Picard tool.
    • Somatic single nucleotide variations (SNVs) were detected with the GATK Mutect2 tool and compared with the COSMIC mutational signature database.

  4. Copy Number Variation (CNV) Analysis: CNVs were detected using CNVkit, with gene enrichment pathways analyzed using tools such as Enrichr.

  5. Statistical Analysis and Visualization: The significance of genomic overlaps was calculated using hypergeometric distribution, with results presented using Venn diagrams and bar charts.

Results

Similarities in Tumor Molecular Characteristics

The study found significant molecular similarities in breast cancer occurring at different time points in the same patient (both primary and second primary cancer). Key findings include:

  1. Similar Genomic Features:

    • CNV analysis of primary breast cancer samples (Group A) and second breast cancer samples (Group B) revealed 941 and 448 related genes, respectively.
    • The commonality of 56 shared genes between the two groups further supports the similarity in tumor characteristics.

  2. Mutational Signature Analysis:

    • Both Group A and Group B samples exhibited similar mutational signature characteristics, including typical BRCA1/2 mutations (e.g., signature 3).
    • Breast cancer samples across different patients showed significant consistency, while lung cancer samples presented markedly different molecular characteristics.

  3. Differences in Tumor Characteristics Across Organs:

    • Lung cancer samples from two patients exhibited entirely different genomic characteristics from breast cancer samples, including distinct mutational signatures and enrichment pathways.

Impact of External Factors

Despite the years-long interval and different treatments or external exposures (such as hormonal therapy and chemotherapy) between two breast cancers, no significant environmental impacts on tumor characteristics were observed. This finding supports the hypothesis that genetic modifiers and early life events play a leading role in tumor characteristics.

Discussion and Significance

The study demonstrates that secondary primary breast tumors share significant genomic similarities with the initial tumors, indicating limited impact from life events occurring after the first tumor development. This might be attributed to the following factors:

  1. Role of Genetic Modifiers: The genetic uniformity of BRCA1/2 mutation carriers may play a dominant role in tumor formation.
  2. Long-term Impact of Early Life Events: Early environmental exposures may leave lasting imprints on the genome, significantly influencing subsequent tumor development.

Additionally, the study highlights significant genomic characteristic differences between tumors of different organs (e.g., breast cancer vs. lung cancer), underscoring the importance of organ microenvironment in tumor formation.

Highlights and Limitations

Highlights

  1. By comparing multiple primary tumors in the same patient, the study eliminates the interference of other genetic backgrounds on tumor characteristics, providing a new perspective for understanding the roles of environmental factors and genetic modifiers.
  2. The comprehensive application of CNV, SNV, mutational signature, and pathway analysis methods provides a systematic framework for tumor molecular characteristic research.

Limitations

  1. The small sample size (only three patients) may limit the generalizability of the conclusions.
  2. The study did not further explore the specific mechanisms of early life events’ impact.

Conclusion

This study reveals the stability of molecular characteristics in breast cancer among BRCA1/2 mutation carriers, emphasizing the critical roles of genetic modifiers and early environmental factors in tumor formation. This finding provides a theoretical basis for developing personalized screening and prevention strategies and guides future research exploring genotype-phenotype interactions.