Research Report on CDK12 Structural Rearrangements in Brain Metastases of Breast Cancer

Background and Purpose

Breast Cancer (BC) is the second most common solid tumor involving the Central Nervous System (CNS). Brain Metastases from Breast Cancer (BCBMs) are becoming increasingly common among patients with metastatic breast cancer. Patients with active brain metastases are often excluded from clinical trials, putting this field at a disadvantage in clinical research. The application of Next-Generation Sequencing (NGS) technology has enabled characterization of brain metastases and comparison with primary tumors, revealing their genomic differences. Moreover, previous studies have shown that BCBMs harbor genomic features and alterations associated with immune checkpoints and Poly(ADP-ribose) Polymerase (PARP) inhibitors, suggesting potential applications of these therapies in BCBMs.

This study aims to explore the role and clinical significance of large-scale structural rearrangements in BCBMs by comparing their frequency in local breast cancer (local BC) and non-CNS metastases (non-CNS M), with a detailed focus on the rearrangements of the CDK12 (Cyclin-Dependent Kinase 12) gene.

Source and Authors

This research was conducted by Talvinder Bhogal, Athina Giannoudis, Ethan Sokol, Simak Ali, and Carlo Palmieri, from the University of Liverpool, Cambridge Foundation Medicine, and Imperial College London. The paper was published in the June 5, 2024, issue of JCO Precision Oncology.

Study Procedure

Subjects and Samples

The study included three different cohorts: 822 BCBMs, 11,988 local breast cancer samples, and 15,516 non-CNS metastases samples. All samples were formalin-fixed, paraffin-embedded materials, analyzed for their genomic characteristics using targeted capture sequencing technology.

Genomic Analysis Methods

The study employed hybrid capture-based NGS technology to analyze genetic variations in at least 324 genes, including short variations (substitutions/insertions/deletions), copy number variations (CNVs, gain/loss), and large-scale structural abnormalities. Genomic rearrangements were identified by analyzing chimeric read pairs, defined as reads mapping to different chromosomes or separated by more than 10Mb. Qualifying rearrangement candidate events were further evaluated for pathogenicity by human reviewers.

Ethical Approval and Statistical Analysis

The study received approval from the Western Institutional Review Board, including waiver of informed consent and Health Insurance Portability and Accountability Act (HIPAA) waiver authorization. Fisher’s exact test was used for statistical comparison of genomic features between different groups, and the Benjamini-Hochberg method was used to adjust P-values for multiple comparisons.

Main Findings

Eighteen genes showed structural rearrangement frequencies exceeding 0.5% in any of the cohorts. Of these, nine genes had significantly higher rearrangement frequencies in BCBMs compared to local breast cancer and non-CNS metastases samples. The most commonly rearranged gene in BCBMs was CDK12, with a rearrangement frequency of 3.53%, significantly higher than in local breast cancer (0.86%) and non-CNS metastases samples (0.68%). CDK12 rearrangements were more frequent in HER2 (Human Epidermal Growth Factor Receptor 2)-positive BCBMs, at 14.59%, significantly higher than in HER2-positive local breast cancer (7.80%) and HER2-positive non-CNS metastases samples (7.87%).

Specifically, 29 CDK12 encoding rearrangement events were identified, including 12 translocations, 9 inversions, 7 deletions, and 1 duplication. Among them, 27 resulted in premature termination or frameshift of the CDK12 protein, suggesting that these rearrangements likely lead to loss of function of CDK12.

Discussion

This study used a large, carefully selected genomic data set to identify significant rearranged genes in BCBMs using targeted NGS technology. Although structural genomic rearrangements are less common in NGS panels than single nucleotide variants (SNVs) and CNVs, the identified rearranged genes involved cell cycle regulation, transcription regulation, and DNA repair pathways, which are critical for targeted therapy. Notably, CDK12, a transcription-related kinase, has tumor suppressor functions in regulating transcription of DNA repair genes and maintaining genomic stability but can act as an oncogene in certain contexts. The frequent CDK12 rearrangements in HER2-positive BCBMs might be related to promoting CNS dissemination phenotype.

CDK12 rearrangements leading to loss of function might promote genomic instability and are associated with homologous recombination and DNA damage repair defects. This defect makes cancer cells more susceptible to platinum-based therapies and PARP inhibitors, while potentially generating fusion-induced neoantigens. Therefore, CDK12 alterations might serve as potential biomarkers for evaluating sensitivity to PARP inhibitors and immune checkpoint inhibitors.

Significance and Value

Using a large BCBMs data set, this study uniquely demonstrates the significant increase in CDK12 rearrangements in HER2-positive BCBMs. These findings support further research to understand the mechanistic basis of this phenomenon and conduct clinical studies to explore the efficacy of PARP inhibitors and immune checkpoint inhibitors in treating HER2-positive BCBMs with CDK12 rearrangements.

Conclusion

This study reveals significant genomic rearrangements of several important genes in BCBMs, particularly the high-frequency CDK12 rearrangements in HER2-positive BCBMs, providing scientific evidence for future targeted therapies and new treatment strategies. These findings provide crucial information for understanding the genomic characteristics of breast cancer brain metastases and developing new clinical treatment strategies.