Understanding Drug Resistance of Melanoma Brain Metastasis with Single-Cell Omics

Brain metastases, as its name indicated, means that cancer spread from the original site to the brain. All kinds of cancers are likely to spread to the brain and form one or more tumors in the brain, be it lung, breast, colon, or kidney. However, statistics in the United States show that only lung and breast cancers are the most frequent primary sites associated with brain metastases and approximately 10 percent of advanced melanoma patients would also develop brain metastases. Though the prognosis for melanoma brain metastasis (MBM) patients has been substantially improved due to advances in neuroimaging, improved disease management, as well as the development of immunotherapies, the understanding of the underlying biology behind MBM is relatively rudimentary and the treatment options for MBM remain limited, especially when it comes to the discovery of novel therapeutics.

To reveal evidence of melanoma brain metastases immune evasion, researchers from Columbia University have recently conducted single-cell RNA sequencing to analyze hundreds of thousands of cells combined with spatial single-cell transcriptomics and single-cell T cell receptor sequencing (scTCR-seq). Different from most single-cell genetic analyses using fresh brain samples, cells in this study are obtained from frozen brain samples of 22 treatment-naive MBMs and 10 extracranial melanoma metastases (ECMs). Researchers make these off-the-shelf samples in their tissue bank adapted to the research process, solving the problem of the short supply of fresh samples.

Extensive heterogeneity in cancer cells has a negative impact on treatment efficacy and survival of patients. Traditional molecular methods for biomarker discovery of cancer cells often fail to capture the heterogeneity of cell populations. Recent advances in single cell-based profiling approach allowed the detection of molecular changes in individual cancer cells. Therefore, single cell omics analysis is leading to build a complete landscape of cell types within tumor cells and facilitate the study of molecular heterogeneity in cancer cell populations. With continuous technological improvements, single-cell omics is becoming increasingly prevalent and contribute to the discovery of new and rare cell types, and to the deciphering of disease pathogenesis and outcome.

The application of single-cell omics for melanoma in the study has enabled researchers to find out the reason for melanoma spreading to the brain and resisting current treatments. By analyzing and comparing the brain and extracranial samples, researchers noticed obvious differences in chromosomal stability, one of the several ways that MBM may evade attack by the immune system, between two types of samples. Compared to melanoma cells in other parts of the body, brain metastatic tumor cells are more unstable in gaining and losing large chromosomal fragments. The chromosomal instability featured in brain metastatic tumor cells could activate signaling pathways that enable them more likely to spread and to better suppress the immune response, which is believed to be the major troublemaker of drug resistance of melanoma brain metastases.

Understanding drug resistance of melanoma brain metastasis with single-cell omics provides insights into improving the prognosis of MBM patients. For instance, some experimental drugs that can reduce chromosomal instability have been developed and will be tested in humans in the near future. In some aspects, the findings in this study would be an encouragement for melanoma brain metastasis patients to be enrolled in clinical trials for new treatment investigation.

Besides chromosomal instability, this study also described more abundant intra-tumoral B cell to plasma cell differentiation in lymphoid aggregates and a larger proportion of monocyte-derived macrophages and dysfunctional TOX+CD8+ T cells with different expression of immune checkpoints in melanoma brain metastases. That's to say, brain metastasis is likely to change macrophages and T cells in the tumor microenvironment, and consequently, it promotes cancer growth in the brain and adopts a neuronal-like state inside the brain.

To sum up, Columbia University researchers making use of single-cell genetic analyses of frozen brain samples have not only revealed how MBM evade immunotherapies and resist ready-for-use drugs but also provided a more comprehensive understanding of MBM biology, which might be a supportive resource for further drug discovery and therapeutic exploration.