Studies by researchers at the Vall d’Hebron Institute of Oncology (VHIO), and the National Centre for Genomic Analysis-Centre for Genomic Regulation (CNAG-CRG), Barcelona, have demonstrated how immune cells that access the cerebrospinal fluid (CSF) of patients with brain metastases faithfully recapitulate the characteristics of the brain tumor immune cells, and could represent novel biomarkers of response to immune checkpoint inhibitor (ICI) therapy.
The team used single-cell RNA sequencing combined with T cell receptor genotyping to characterize immune cells in brain lesions and matched CSF. The single-cell profiling allowed them to chart the major cell types and transient tumor-sepcific states in the brain metastasis (BrM) tumor microenvironment (TME). Describing their results in Nature Communications, the team, led by co-corresponding author, Joan Seoane, PhD, Director of Preclinical and Translational Research co-program at VHIO and ICREA professor, reported that the phenotype of the cytotoxic lymphocytes in the CSF was effectively the same as that of the same cell type observed in the tumor, providing what they suggested is “ … a relatively non-invasive tool to characterize and assess the degree of inflammation in brain lesions that in turn could be used to predict response to ICIs … as well as identify the T cell receptor clonotypes present in brain metastasis.”
Co-corresponding author, Holger Heyn, PhD, Head of CNAG-CRG’s Single Cell Genomics Team, further stated, “The identification of clonal T-cells in both metastasis and liquid biopsy is of particular interest. We have shown that the sequencing of T-cell receptors provides a cellular barcode that can be assessed outside of the tumor. Importantly, this approach opens up new avenues for the detection of systemic disease.”
The researchers’ paper is titled, “Immune cell profiling of cerebrospinal fluid enables the characterization of the brain metastasis microenvironment.”
Brain metastases represent the most prevalent form of brain tumor, with a “dismal prognosis,” the authors wrote. “Brain metastases are the most common tumor of the brain and a devastating complication of cancer with unmet therapeutic needs.” Immune checkpoint inhibitors, including anti-PD1, anti-PD-L1, and anti-CTLA4, have shown significant clinical benefits for patients with progressive or metastatic solid tumors, including some brain metastasis. Notably, these immune-based therapies have improved outcomes for some patients suffering from lung cancer and melanoma. Together, these tumor types (representing between 30-40% of all cancers), along with breast cancer, are three common malignancies that lead to brain metastases, the VHIO team noted. “One of the major challenges in improving outcomes for patients suffering from brain metastases caused by these cancers is that new lesions can differ immensely from the primary tumor, and thus respond in a different way to immune-based therapies,” commented Seoane.
And while some patients with brain metastases benefit from treatment with immune checkpoint inhibitors, the majority do not. “Still, only a fraction of patients responds to ICI, urging for therapy predictive biomarkers,” the team continued. “The nature of the TME can dictate the biology of tumors and determine the tumor sensitivity to immune therapies,” they continued. And importantly, the brain TME has unique characteristics. Predicting tumor response to ICI treatment thus requires characterization of tumor specimens, but the anatomical location of brain tumors and the risk of surgical procedures means that accessing samples from brain malignancies to characterize the immune phenotype is challenging.
Prior studies by Seoane, and by other groups, have suggested that cerebrospinal fluid can provide vital insights into the genomic characteristics of brain tumors and could therefore be used as a minimally invasive liquid biopsy. For their newly reported studies, the scientists wanted to establish whether they could effectively characterize the immunological phenotypes of brain metastases through the analysis of cerebrospinal fluid.
The team collected samples from 48 consenting patients with brain metastasis, who were being treated at the Vall d’Hebron University Hospital (HUVH), as well as the Hospital Clínic in Barcelona. The researchers assessed the immune cells present in the brain metastases, and in parallel performed immune cell profiling of the patients’ cerebrospinal fluid, to identify and compare the immune cell types present in the CSF and in the metastatic lesions. Directed by Holger Heyn, PhD, Head of CNAG-CRG’s Single Cell Genomics Team, the investigators carried out single cell transcriptome sequencing of around 6000 cells, using scRNA-seq technology.
By analysing the cerebrospinal fluid, the researchers were able to identify the T-cells that recognized the tumor, and those that were active in treatment. “Single cell transcriptome sequencing provides the highest resolution for the detection and monitoring of several different diseases,” Heyn stated.
“Each immune T-cell has a unique sequence that recognizes a particular tumor antigen,” Seoane further noted. “When their tracing and targeting commence, these cells are activated and begin to proliferate. Through this study, we have been able to characterize the individual sequences of immune cells and, in this way, identify which immune cells are fighting the tumor and discern how they evolve over time.”
The authors concluded, “Consistently, identical T cell receptor clonotypes are detected in brain lesions and CSF, confirming cell exchange between these compartments.” They said that their finding that the CSF can recapitulate the immune landscape of the brain lesion points to potential use of the CSF to provide “critical information” about the brain TME in a relatively noninvasive manner, and avoiding intracranial surgery. They further suggested that future studies are warranted to more completely characterize in detail each of the immune cell types present in the CSF and compare them to the tumor lesions. “Together, our results show that the CSF immune cell profile can facilitate the characterization of the immune TME in brain metastatic lesions and longitudinally monitor the evolution of the cancer immune response,” they stated.
Seoane added, “By establishing similarities between the two, we have identified a novel and minimally invasive method that can allow us to predict response to immunotherapy in these patients. This pioneering approach could more precisely guide clinical decision making in treating these patients with immune-based therapeutic strategies.” “The identification of clonal T-cells in both metastasis and liquid biopsy is of particular interest,” Heyn further stated. We have shown that the sequencing of T-cell receptors provides a cellular barcode that can be assessed outside of the tumor. Importantly, this approach opens up new avenues for the detection of systemic disease.”