A Practical Approach to Tumor-Specific Aptamers for B-Cell Hematologic Malignancies

Personalized medicine will greatly improve the effectiveness of cancer care; however, the development of practically attainable patient-specific strategies has remained challenging. One unique opportunity exists with B cell-derived malignancies, which often express surface immunoglobulins (sIgs) with variable regions (idiotypes, Ids) within their B-cell receptors (BCRs). As malignant cells originate from a single clone, such sIg-Id molecules are specific to the tumor and unique to each patient. Targeting sIg-Ids can hence enable personalized disease identification and treatment strategies. Early studies using patient-specific anti-sIg-Id antibodies yielded promising results but were deemed unsustainable. A technology to generate personalized ligands in a time- efficient and cost-effective manner remains an unmet need in sIg-Id-based diagnostics and therapeutics. Aptamers, i.e., single-stranded oligonucleotides that specifically bind to biological targets, offer an attractive solution to this unmet need. Aptamers are isolated from a randomized oligonucleotide library via an in vitro process known as SELEX, which is traditionally labor-intensive, time-consuming (up to a month), and impractical for personalized aptamer generation. In contrast, we have developed a microfluidic platform, called microSELEX (μSELEX), which has been used to isolate aptamers for protein biomarkers, including Id regions of monoclonal antibodies from patients with multiple myeloma and COVID-19. Given a monoclonal protein from a patient sample, the platform is capable of rapidly isolating personalized anti-Id aptamers within ~10 hours. We propose to explore time-efficient and cost-effective μSELEX isolation of patient-specific DNA aptamers targeting sIg-Ids of tumor B cells for B-cell hematologic malignancies. We will first establish an optimal μSELEX protocol using B cell-derived cell lines, then isolate anti-sIg aptamers against tumor B cells obtained from peripheral blood samples of B cell lymphoma patients, and finally demonstrate noninvasive peripheral blood- based monitoring of minimal residual disease by using the aptamers to detect circulating tumor B cells. In addition to enabling timely identification of minimal residual disease for more precise clinical decision making, anti-sIg-Id aptamers can also be used as therapeutic ligands to enable personalized and precisely targeted therapy for more effective disease treatment. Such personalized aptamers can hence potentially lead to transformative changes in the care of patients with B-cell hematologic malignancies.