Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases

Abstract

There is a critical need to improve our understanding of the pathogenesis of melanoma brain metastases (MBM). Thus, we performed RNA sequencing on 88 resected MBMs and 42 patient-matched extracranial metastases; tumors with suffi cient tissue also underwent wholeexome sequencing, T-cell receptor sequencing, and IHC. MBMs demonstrated heterogeneity of immune infi ltrates that correlated with prior radiation and post-craniotomy survival. Comparison with patientmatched extracranial metastases identifi ed signifi cant immunosuppression and enrichment of oxidative phosphorylation (OXPHOS) in MBMs. Gene-expression analysis of intracranial and subcutaneous xenografts, and a spontaneous MBM model, confi rmed increased OXPHOS gene expression in MBMs, which was also detected by direct metabolite profi ling and [U-13 C]-glucose tracing in vivo. IACS-010759, an OXPHOS inhibitor currently in early-phase clinical trials, improved survival of mice bearing MAPK inhibitor-resistant intracranial melanoma xenografts and inhibited MBM formation in the spontaneous MBM model. The results provide new insights into the pathogenesis and therapeutic resistance of MBMs. SIGNIFICANCE: Improving our understanding of the pathogenesis of MBMs will facilitate the rational development and prioritization of new therapeutic strategies. This study reports the most comprehensive molecular profi ling of patient-matched MBMs and extracranial metastases to date. The data provide new insights into MBM biology and therapeutic resistance.

Multi-site clonality analyses uncovers pervasive subclonal heterogeneity and branching evolution across melanoma metastases

“…5). The brain metastases in particular had relatively fewer immune cells compared to lung and other extracranial metastases, which might corroborate studies suggesting the brain represents a relatively 'immuno-privileged' organ 33,35 . Inflammatory macrometastases in the brain were however high for activated M2 macrophages (including significant up-regulation of the macrophage marker CD163 in brain vs lung metastases, log-fold change 5.5, FDR-adjusted p-value < 0.004) which have been described as having anti-inflammatory or tumour supporting activities, including in malignant brain tumours (although it is important to recognise that it may be difficult to distinguish between microglia and macrophages, both of monocyte lineage, using these methods) 36 .…”

Oxidative phosphorylation as a potential therapeutic target for cancer therapy

“…Moreover, KRAS‐induced lung cancer induced in mice can be attenuated in its progression by genetically inhibiting OXPHOS, namely by deleting AIFM1 from the cancer cells, thereby reducing the biogenesis of respiratory chain complexes . Resistance to chemotherapy appears to be generally coupled to an increase in OXPHOS, explaining why OXPHOS inhibition overcomes resistance to docetaxel in prostate cancer, cytarabine in acute myeloid leukemia (AML), 5‐fluorouracil in colorectal and MYC/PGC‐1‐α driven pancreatic cancer, to EGFRi in EGFR‐driven lung adenocarcinoma and MAPKi in melanoma . Accordingly, multiple strategies that reduce OXPHOS (see below) such as inhibition of mitochondrial DNA replication, protein synthesis, biogenesis of respiratory chain complexes, electron transfer, mitochondrial protease ClpP (which interacts with respiratory chain proteins), or mitochondrial fatty acid transport and α‐oxidation all can be used to enhance the antineoplastic effects of cytarabine against AML .…”

“…16 Resistance to chemotherapy appears to be generally coupled to an increase in OXPHOS, explaining why OXPHOS inhibition overcomes resistance to docetaxel in prostate cancer, cytarabine in acute myeloid leukemia (AML), 5-fluorouracil in colorectal and MYC/PGC-1-α driven pancreatic cancer, to EGFRi in EGFR-driven lung adenocarcinoma and MAPKi in melanoma. [17][18][19][20] Accordingly, multiple strategies that reduce OXPHOS (see below) such as inhibition of mitochondrial DNA replication, protein synthesis, biogenesis of respiratory chain complexes, electron transfer, mitochondrial protease ClpP (which interacts with respiratory chain proteins), or mitochondrial fatty acid transport and α-oxidation all can be used to enhance the antineoplastic effects of cytarabine against AML. 18,19 These findings indicate that therapy-resistant cancer cells acquire new metabolic dependencies that render them vulnerable to OXPHOS inhibition.…”

LEF1 supports metastatic brain colonization by regulating glutathione metabolism and increasing ROS resistance in breast cancer

“…Interestingly, circulating tumor cells (CTCs) reduce production of ROS to survive by switching towards a glycolytic metabolism and decreasing their aerobic respiration rate (oxidative phosphorylation) . In contrast, a recent molecular profiling study of malignant melanoma specimens derived from in vivo models and from a patient cohort with matched extracranial and brain metastasis revealed the importance of oxidative phosphorylation in brain metastases . This indicates that during colonization of the brain, CTCs have to re‐activate oxidative phosphorylation despite the associated increase in ROS production.…”

“…38 In contrast, a recent molecular profiling study of malignant melanoma specimens derived from in vivo models and from a patient cohort with matched extracranial and brain metastasis revealed the importance of oxidative phosphorylation in brain metastases. 39 This indicates that during colonization of the brain, CTCs have to re-activate oxidative phosphorylation despite the associated increase in ROS production. Moreover, metastatic cancer cells are exposed to additional extrinsic oxidative stress from the resident brain parenchymal cells.…”