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Although lung adenocarcinomas frequently metastasize to the brain, treatment options for lung adenocarcinoma brain metastases are limited. We discovered novel candidate drivers of progression by using case-control analyses to compare whole-exome sequencing data from a cohort of 73 lung adenocarcinoma brain metastases to a control cohort of 503 primary lung adenocarcinomas. We identified 3 genomic regions with significantly more frequent amplifications in brain metastases compared to the control cohort: MYC (12% vs 6%), YAP1 (7% vs 0.8%) and MMP13 (10% vs 0.6%). We also identified CDKN2A/B as a region deleted at a significantly greater frequency in brain metastases compared to primary lung adenocarcinomas (27% vs 13%, respectively). We confirmed frequent amplifications of MYC and YAP1/MMP13 in an independent validation cohort of 105 lung adenocarcinoma brain metastasis samples using fluorescence in situ hybridization. We further validated that MYC, YAP1 and MMP13 can drive brain metastases in a patient-derived xenograft mouse model. We found a higher incidence of metastases to the brain in mice receiving intracardiac injections of tumor cells expressing the candidate drivers compared to tumor cells expressing LacZ as a control. These results indicate that somatic alterations can drive lung adenocarcinomas to metastasize to the brain. The candidate brain metastasis drivers that we identified may serve as therapeutic targets in patients with lung adenocarcinomas who develop this devastating complication.

Progressive meningiomas that have failed surgery and radiation have a poor prognosis and no standard therapy. While meningiomas are more common in females overall, progressive meningiomas are enriched in males. We performed a comprehensive molecular characterization of 169 meningiomas from 53 patients with progressive/high-grade tumors, including matched primary and recurrent samples. Exome sequencing in an initial cohort (n = 24) detected frequent alterations in genes residing on the X chromosome, with somatic intragenic deletions of the dystrophin-encoding and muscular dystrophy-associated DMD gene as the most common alteration (n = 5, 20.8%), along with alterations of other known X-linked cancer-related genes KDM6A (n =2, 8.3%), DDX3X, RBM10 and STAG2 (n = 1, 4.1% each). DMD inactivation (by genomic deletion or loss of protein expression) was ultimately detected in 17/53 progressive meningioma patients (32%). Importantly, patients with tumors harboring DMD inactivation had a shorter overall survival (OS) than their wild-type counterparts [5.1 years (95% CI 1.3–9.0) vs. median not reached (95% CI 2.9–not reached, p = 0.006)]. Given the known poor prognostic association of TERT alterations in these tumors, we also assessed for these events, and found seven patients with TERT promoter mutations and three with TERT rearrangements in this cohort (n = 10, 18.8%), including a recurrent novel RETREG1–TERT rearrangement that was present in two patients. In a multivariate model, DMD inactivation (p = 0.033, HR = 2.6, 95% CI 1.0–6.6) and TERT alterations (p = 0.005, HR = 3.8, 95% CI 1.5–9.9) were mutually independent in predicting unfavorable outcomes. Thus, DMD alterations identify a subset of progressive/high-grade meningiomas with worse outcomes.

Reversal of immune cell exhaustion through immune checkpoint blockade (ICB) has become a first-line approach for patients with metastatic melanoma due to success in controlling extracranial tumors. However, patients frequently experience discordant responses, with extracranial response and intracranial progression. We hypothesize that ICB exerts selective pressure leading to the clonal evolution of treatment resistant clones that ultimately culminate in disease progression. We collected a cohort of 97 patients, encompassing 312 pre- and post-immunotherapy melanoma tumors, for whole exome sequencing (WES) and included primary, extracranial, or intracranial samples. Each tumor was analyzed for somatic mutations, copy number alterations, neoantigen profile, and patient specific phylogenetic trees were constructed encompassing a tumor’s genetic subclones. Heterogeneity of the tumor microenvironment was evaluated using high multiplicity single-cell immunofluorescent staining (CycIF). Single cell sequencing was performed on fresh tissue from 4 pre-treatment and 14 post-immunotherapy melanoma brain metastases using the Smart-Seq2 protocol. WES of pre- and post-immunotherapy tumors yielded distinct patterns of clonal evolution and immunoediting within brain metastases compared to their extracranial counterparts, including mutations in B2M. In paired pre- and post-immunotherapy samples, CycIF demonstrated decreased in CD8 infiltration and increased CD45RO, FOXP3, and PD-L1 staining suggesting less cytotoxic, terminally differentiated T cells in resistant tumors. Single cell sequencing analysis of 3,974 tumor and immune cells demonstrated patient-specific tumor clustering and gene expression profiles mediating resistance to ICB. In conclusion, we document, for the first time, evidence of ongoing branched evolution during immunotherapy in brain metastases with divergence compared to systemic sites of disease. Next-generation sequencing provides novel insights into clonal evolution mediating discordant responses of intra- and extracranial sites and immunosuppressive features of the intracranial tumor microenvironment. Targeting these mechanisms of resistance provide potential therapeutic avenues for patients with progressive intracranial disease.

Progressive meningiomas that have failed surgery and radiation have poor a prognosis and no standard therapy. While meningiomas are more common in females overall, progressive meningiomas are enriched in males. We performed a comprehensive molecular characterization of 169 meningiomas from progressive/high-grade tumors, including matched primary and recurrent samples. We detected frequent alterations in genes residing on the X-chromosome, with somatic intragenic deletions of the dystrophin-encoding and muscular dystrophy-associated DMD gene as the most common alteration (n= 5, 20.8%), along with alterations of other known X-linked cancer-related genes KDM6A (n= 2, 8.3%), DDX3X, RBM10 and STAG2 (n= 1, 4.1% each). DMD inactivation (by genomic deletion or loss of protein expression) was detected in 17/53 progressive meningioma patients (32%). Importantly, patients with tumors harboring DMD inactivation had a shorter overall survival (OS) than their wild-type counterparts [5.1 years (95% CI 1.3–9.0) vs. median not reached (95% CI 2.9–not reached), p=0.006)]. We also assessed for TERT alterations, which have a known poor prognostic association, and found seven patients with TERT promoter mutations and three with TERT rearrangements in this cohort (n= 10, 18.8%), including a recurrent novel RETREG1-TERT rearrangement that was present in two patients. In a multivariate model, DMD inactivation (p=0.033, HR=2.6, 95% CI 1.0–6.6) and TERT alterations (p= 0.005, HR= 3.8, 95% CI 1.5- 9.9) were mutually independent in predicting unfavorable outcomes. Thus, alterations of the mesodermal gene DMD identify a subset of progressive/high-grade meningiomas with worse outcomes.