A novel liquid biopsy could help predict which patients with breast cancer will respond to immunotherapy

Immunotherapy has already rewritten the treatment playbook for high-risk, early-stage breast cancer. Since the landmark KEYNOTE-522 trial demonstrated that adding Keytruda (pembrolizumab) to neoadjuvant chemotherapy improved event-free survival, and, more recently, overall survival by a clinically meaningful 5% absolute gain at five years, perioperative pembrolizumab has become an established standard of care for stage 2 and 3 triple-negative breast cancer (TNBC). But a critical problem remains unsolved: Clinicians do not have a reliable way to know, at the start of treatment, which patients will actually respond.

Now, a study published in Science Translational Medicine from researchers at the Vanderbilt-Ingram Cancer Center may offer a way forward, not by looking at the tumor itself, but at the blood.

The study, led by corresponding author Justin Balko, Ph.D., Pharm.D., professor of medicine and pathology, microbiology and immunology at Vanderbilt Health, took a fundamentally different approach to biomarker discovery. Rather than relying on tumor tissue biopsies, an inherently invasive procedure that provides only a frozen-in-time snapshot of tumor biology, the team performed RNA sequencing on serial peripheral blood samples collected longitudinally throughout treatment.

The cohort included 160 patients with high-risk, stage 2 or 3 HER2-negative breast cancer enrolled in the I-SPY2 adaptive clinical trial, a pioneering 42-site national platform designed to match patients to novel treatment regimens based on their tumor's molecular characteristics. Patients received either chemotherapy alone or in combination with Keytruda. Across the full cohort, 546 blood samples were collected and analyzed, yielding what the investigators describe as a comprehensive peripheral transcriptomic roadmap of the immune response to therapy.

The core analytical focus was the T cell compartment. By profiling T cell receptor (TCR) clonality, diversity, and activation markers captured in circulating blood, the team tracked whether and how each patient's immune system was engaging the tumor over the course of treatment. The signal was clear as patients who responded to pembrolizumab looked immunologically different in their blood, and they looked different early.

Among the study's key findings, TNBC patients exhibited notably higher baseline TCR clonality and immune activation signatures in peripheral blood compared with hormone receptor-positive patients. Critically, among Keytruda responders, the team observed T cell clonal expansion and activation after treatment initiation, a dynamic shift not seen in nonresponders or in patients receiving chemotherapy alone.

Translating these observations into a clinical decision tool, the researchers built a logistic regression model incorporating immunological features assessed both at baseline and early in treatment. The model predicted response to Keytruda with strong accuracy and was subsequently validated in an independent cohort of patients treated with Jemperli (dostarlimab), another PD-1 inhibitor, in the neoadjuvant setting. That cross-drug validation is a meaningful signal since the predictive signature may reflect a broader, mechanism-driven immune phenomenon rather than a pembrolizumab-specific artifact.

Balko and his colleagues characterized the approach as a novel form of liquid biopsy, one that captures systemic immune dynamics rather than circulating tumor DNA (ctDNA) or somatic mutations. Although cell-free DNA testing has become a standard clinical liquid biopsy tool for detection and therapeutic monitoring across multiple malignancies, this study expands the concept into a new dimension: gene expression from immune cells in circulation, providing real-time readout of whether the immune system is mounting an antitumor attack.

“This study shows that a new form of liquid biopsy — measuring immune-related gene expression in a routine blood sample — may provide an accessible way to monitor how patients respond to immune-based cancer therapies such as checkpoint inhibitors,” Balko wrote in an email to Managed Healthcare Executive. “Although further validation in larger and more diverse patient cohorts is needed, these findings suggest that blood-based immune profiling could eventually help guide treatment decisions and longitudinal monitoring for patients with breast cancer and potentially other cancers.”