Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases

Biology Biology
Cancer Cancer
Genomics Genomics
Immunology Immunology
Medicine Medicine
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Jay Prakadan Jay Prakadan
Kellie Kolb Kellie Kolb
Marc Wadsworth II Marc Wadsworth II

Prakadan et al.▾ Prakadan, S.M., Alvarez-Breckenridge, C.A., Markson, S.C., Kim, A.E., Klein, R.H., Nayyar, N., Navia, A.W., Kuter, B.M., Kolb, K.E., Bihun, I., Mora, J.L., Bertalan, M.S., Shaw, B., White, M., Kaplan, A., Stocking, J.H., Wadsworth II, M.H., Lee, E.Q., Chukwueke, U., Wang, N., Subramanian, M., Rotem, D., Cahill, D.P., Adalsteinsson, V.A., Miller, J.W., Sullivan, R.J., Carter, S.L., Brastianos, P.K., Shalek, A.K.

Nature Communications , Volume 12

October, 2021


Leptomeningeal disease (LMD) is a devastating complication of solid tumor malignancies, with dire prognosis and no effective systemic treatment options. Over the past decade, the incidence of LMD has steadily increased due to therapeutics that have extended the survival of cancer patients, highlighting the need for new interventions. To examine the efficacy of immune checkpoint inhibitors (ICI) in patients with LMD, we completed two phase II clinical trials. Here, we investigate the cellular and molecular features underpinning observed patient trajectories in these trials by applying single-cell RNA and cell-free DNA profiling to longitudinal cerebrospinal fluid (CSF) draws from enrolled patients. We recover immune and malignant cell types in the CSF, characterize cell behavior changes following ICI, and identify genomic features associated with relevant clinical phenomena. Overall, our study describes the liquid LMD tumor microenvironment prior to and following ICI treatment and demonstrates clinical utility of cell-free and single-cell genomic measurements for LMD research.