Patients With Brain Metastases From Renal Cell Carcinoma May Have Distinct Immunosuppressive Tumor Microenvironment

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Researchers have created the largest single-cell atlas of renal cell carcinoma brain metastases, with matched primary and extracranial metastases, which has potentially enabled them to discover key biological mechanisms contributing to an immunosuppressive tumor microenvironment in the brain distinct from that of the kidney or other metastatic sites, according to new findings presented by Hasanov et al at the American Association for Cancer Research (AACR) Annual Meeting 2023 (Abstract 5788).

The study may provide further insights into why renal cell carcinoma can be more difficult to treat when it metastasizes to the brain compared with other sites. The new findings may also point to several unique therapeutic targets that could be explored to improve antitumor immune responses.


“Brain metastases are, by far, the most challenging complication of [renal cell carcinoma]. We’ve seen systemic therapies work in treating primary tumors and other metastatic sites, but they are not as effective for brain metastases. The current standard of care, radiation treatment and surgery, helps to treat the brain metastases but does not prevent new metastases,” explained lead study author Elshad Hasanov, MD, PhD, a medical oncology fellow at The University of Texas MD Anderson Cancer Center.

“We now see it’s not just because of the blood-brain barrier, but it also is [because of] interactions between the tumor and other immune and stromal cell populations—creating an immunosuppressive [tumor] microenvironment in the brain that allows tumors to somehow escape immunotherapy,” he emphasized.

Although many patients with renal cell carcinoma are treated with immune checkpoint inhibitors, nearly 30% of them will develop brain metastases as the disease progresses. As a result of poor treatment responses, patients with renal cell carcinoma brain metastases typically have a poor prognosis, underscoring the need to understand the mechanisms driving the brain as an immune-privileged organ that allows for tumor growth and metastases—even after treatment with immunotherapy.  

Study Methods and Results

In the study, the researchers collected matched samples from primary kidney tumors as well as extracranial and brain metastases from patients who also underwent surgery. These consisted of frozen tissue samples from patients with renal cell carcinoma—including 14 brain metastases, 8 matched primary kidney tumors, and 5 matched extracranial metastases. An additional 57 formalin-fixed paraffin-embedded brain metastasis samples were included in the analysis.

The researchers then performed single-nucleus RNA sequencing on nearly 200,000 cancer cells to characterize the genetic expression within the samples. Using RNA spatial molecular imaging techniques, they mapped interactions between the major cell types they found in the tissues.

After conducting their analysis, the researchers discovered that brain metastases had a strikingly immunosuppressive tumor microenvironment compared with primary tumors and extracranial metastases.

Brain metastases had greater infiltration of neuronal and glial cells, driving inflammatory responses that appeared to suppress antitumor activity by binding with immune cells via known immunosuppressive ligand-receptor interactions. The researchers also found that brain metastases had fewer proliferating T cells, memory B cells, dendritic cells, and monocytes; and macrophages in the brain had more highly expressed immune-suppressing M2 gene signatures, which promote cell proliferation and repair.

Additionally, the brain metastases had higher VEGFR and FGFR4 growth-promoting protein activity, higher levels of immune checkpoint proteins, and an enrichment of various targets and pathways—including MYC genes—all of which may allow the cancer cells to thrive in the tumor microenvironment. Interestingly, the presence of naive/memory T cells in the brain was associated with favorable overall survival after surgery, making this a potential prognostic marker.


The researchers plan to use their new findings to pursue further preclinical and clinical trials testing various combination therapies with lenvatinib against VEGFR and FGFR4 as well as other identified targets in combination with immune checkpoint inhibitors such as pembrolizumab for patients with renal cell carcinoma brain metastases.

“There are communication highways between neuronal cells and other cell populations that do not exist in the kidney and other metastatic sites, but they are very dominant in the brain. It’s a whole other world with different tumor- and host organ–driven players and communications,” Dr. Hasanov stressed. “The beauty of single-nucleus sequencing and spatial transcriptomics is that it allows us to look deeper and create snapshots of these cells and their location so we can better understand their biological value at the protein and RNA level. This helps us to identify potential therapeutic targets and to work toward designing therapies that can improve patient outcomes,” he concluded.

Disclosure: The research in this study was supported by the Kidney Cancer Association Young Investigator Award 2021, the International Kidney Cancer Coalition Cecile and Ken Youner Scholarship Award 2021, the Society for Immunotherapy of Cancer–NanoString Technologies Single-Cell Biology Award 2022, and the Cancer Prevention and Research Institute of Texas. Dr. Hasanov has received additional research funding to his institution from the Conquer Cancer Foundation, the Kidney Cancer Association, the International Kidney Cancer Coalition, and the Society for Immunotherapy of Cancer. For full disclosures of the study authors, visit

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