Priming Agents Transiently Reduce the Clearance of Cell-Free DNA to Improve Liquid Biopsies

Key Takeaways

• ctDNA shows promise for non-invasive cancer detection and monitoring through standard blood tests, but its effectiveness is limited by degradation and clearance mechanisms.
• A novel approach using DNA-binding monoclonal antibodies with blocked FcγR-binding improves cfDNA recovery by delaying ctDNA clearance.
• DNA-binding mAbs boosted ctDNA recovery in tumor-bearing mice by more than 10-fold, enhancing liquid biopsy sensitivity and ctDNA detection capabilities.

Summary

Circulating tumor DNA (ctDNA), released into the bloodstream by tumor cells, is a promising biomarker for cancer detection, providing a non-invasive means for diagnosis and monitoring of disease via standard blood tests. However, the utility of cell-free DNA (cfDNA) is limited by its scarcity, attributed to degradation by circulating nucleases and organ-mediated clearance. In oncology, ctDNA-based screening tests exhibit low sensitivity (~20 to 40% for Stage I cancer) and can yield inconclusive results in up to 40% of patients with advanced cancer. To enhance the sensitivity of liquid biopsies for ctDNA detection, mitigating ctDNA clearance from the bloodstream presents a viable strategy.

Researchers from the Tabrizi and Adalsteinsson labs at the Koch Institute For Integrative Cancer Research and the Broad Institute of MIT and Harvard aimed to develop a universal strategy to improve cfDNA recovery from blood samples.  Their method involved the utilization of intravenous priming agents to momentarily stall ctDNA clearance. They identified DNA-binding monoclonal antibodies (mAbs) capable of binding to both free and histone-bound DNA, thereby protecting the DNA from nucleases. However, they encountered challenges as FcγR-mediated clearance of dsDNA bound to mAbs offset the benefits of extended dsDNA stabilization.

To address issues associated with FcγR-mediated clearance, they elucidated the complete amino acid sequence using Rapid Novor’s REmAb® de novo monoclonal antibody sequencing service. This enabled Fc engineering of the DNA-binding mAb, abrogating FcγR binding and enhanced ctDNA recovery. 

Administering the engineered DNA-binding mAb at various doses 2 hours before blood collection led to a significant increase in ctDNA recovery by more than 10-fold in tumor-bearing mice. This breakthrough effectively addresses the challenge of low ctDNA quantities, which frequently limits the sensitivity of liquid biopsies for oncological purposes. Moreover, it enables non-invasive cancer diagnosis and monitoring, potentially improving patient care and treatment outcomes.

Graphical Abstract

REmAb® de novo monoclonal antibody sequencing service was employed to derive the complete amino acid sequence of the DNA-binding antibody. This information facilitated Fc engineering to obstruct FcγR-binding, making it suitable as a DNA-priming agent for the development of in vitro diagnostics for ctDNA detection in oncology applications.