The synthetic lethal effect observed with the use of PARP inhibitors (PARPi) in tumors characterized by deficiencies in key components in the homologous recombination (HR) pathway, commonly referred to as "BRCAness", continues to be of significant interest in oncology. This synthetic lethality arises because PARPi exploit the vulnerability of HR-deficient tumor cells, which are heavily reliant on the PARP enzyme for DNA repair. Inhibition of PARP activity leads to an accumulation of unrepaired DNA damage, ultimately resulting in cell death.

BRCAness is a well-established feature in several types of cancer, including breast, ovarian, prostate, and pancreatic carcinomas. In these cancers, the presence of BRCAness is frequently associated with mutations in the BRCA1 and BRCA2 genes, which are essential for HR-mediated DNA repair. The loss of function in these genes sensitizes tumor cells to PARPi, thereby providing a therapeutic advantage in treating these malignancies.

Our recent findings reveal that up to 15% of colorectal cancers (CRC) also exhibit defects in the HR pathway (PMID 31831554), expanding the potential application of PARPi beyond the cancers traditionally associated with BRCA-mediated homologous recombination deficiency (HRD). The identification of HR deficiencies in a subset of CRC patients opens up new avenues for innovative therapeutic strategies. By targeting HR-deficient CRCs with PARPi inhibitors, we could potentially exploit the same synthetic lethal effect observed in breast, ovarian, prostate, and pancreatic cancers.

The clinical implications of these findings are substantial. For patients with HR-deficient CRC, PARPi (not yet approved in the CRC clinical practice) could offer a more personalized and effective treatment option, potentially improving clinical outcomes. Moreover, the identification of HR defects in CRC can serve as a predictive biomarker for selecting patients likely to benefit from PARPi therapy, including those that, by carrying BRAF and KRAS mutations, would be resistant to conventional targeted therapies.

In the pursuit of enhancing cancer diagnostics, we have developed a novel tool called HRDirect (https://doi.org/10.1038/s41698-024-00706-7). This innovative tool builds upon the foundations laid by the HRDetect algorithm and is designed to predict HRD from reference-free tumor samples. The development of HRDirect marks a significant advancement in cancer diagnostics, as it offers a more precise approach to identifying HRD without the need for matched normal tissue samples. This feature is particularly advantageous in clinical settings where obtaining reference samples may be challenging.

We performed a comprehensive validation process for HRDirect using matched breast cancer and colorectal cancer (CRC) patient samples. This process demonstrated that our tool is reliable and accurate in a clinical context. By validating HRDirect with these diverse cancer types, we show its versatility and broad potential applicability across different tumor types.

To further assess the efficacy of HRDirect, we conducted a comparative analysis with two other commercial HRD assays: AmoyDx HRD by Amoy Diagnostics and the TruSight Oncology 500 HRD (TSO500-HRD) panel by Illumina NGS technology. These assays are known in the field for their ability to identify HRD and predict response to PARPi, making them ideal benchmarks for comparison with HRDirect.

In our comparative analysis, all three assays successfully identified the CRC models most sensitive to the PARPi olaparib. However, HRDirect demonstrated superior precision in distinguishing resistant models compared to AmoyDx and TSO500-HRD, which exhibited overlapping scores between sensitive and resistant models.

The implications of our findings are significant. HRDirect offers a robust tool for accurately identifying HRD without the need for reference samples, and its ability to distinguish between sensitive and resistant models with greater precision could improve the selection of patients for PARPi therapy in the context of a more precise personalized medicine context

Finally, to further improve the accuracy of HRD tumor detection, we suggest combining HRDirect scoring with ATM and RAD51C immunohistochemical analysis. This combination is the foundation of our "composite biomarker approach" (PMID 35881546) that aims to offer a more precise HRD identification method. By integrating these techniques, we might enhance the reliability of tumor diagnosis as we hope to further validate in our future studies.

by Giorgio Corti and prof. Sabrina Arena