Authors: Christopher Alvarez-Breckenridge, MD; Christopher Alvarez-Breckenride; Sanjay Prakadan; Anita Giobbie-Hurder; Donald Lawrence; Kevin Oh; Elizabeth Gerstner; Daniel Cahill; Alex Shalek; Scott Carter; Ryan Sullivan; Priscilla Brastianos (Boston, MA)


Approximately 8% of patients with cancer develop leptomeningeal carcinomatosis (LMD). LMD is associated with approximately 4 week median survival and limited treatment options. We performed single cell RNA sequencing of CSF from longitudinally collected patients enrolled in a phase II study of the PD-1 inhibitor pembrolizumab in LMD (NCT02886585) in order to identify cellular states and genetic programs associated with response to immune checkpoint blockade.


The primary endpoint is the rate of overall survival at 3 months (OS3). A Simon two-stage design was used to compare a null hypothesis OS3 of 18% against an alternative of 43%.  Serial CSF, blood samples and tumor samples were collected to elucidate the genomic and transcriptional determinants of response to immunotherapy in CNS lesions. 


Eighteen patients were accrued and the median follow-up of patients still alive was 6.8 months (range: 2.2 to 7.6 months).  At the time of data retrieval, 11 patients (61%) were alive at three months after enrollment (OS3). Therefore, the study met its primary endpoint. Whole exome sequencing of tissue samples and cell-free DNA from CSF and blood, as well as single-cell RNA sequencing of CSF, were carried out to decipher tumor evolution, track immune cell recruitment, and identify biomarkers of response. Analysis of 7877 tumor and immune cells across 6 patients demonstrated patient-specific tumor clustering and evidence of T cell and antigen presenting cells recruited to the CSF following pembrolizumab treatment. Genetic and transcriptomic differences of tumor and immune cells within the CSF were detected longitudinally during therapy and in patients that reached OS3 compared with those that did not.


Pembrolizumab has activity in LMD and single cell sequencing of CSF provides a window in which to monitor the evolution of the tumor and immune microenvironment in response to immune checkpoint blockade.

Journal of Neuro-Oncology Award