中枢神经系统(CNS)穿透整体治疗显著促进了黑色素瘤脑转移患者的护理。然而，需要改善对这些病变的分子景观和微环境的理解，以优化患者选择和推进治疗方法。评估黑色素瘤脑转移的整体和单细胞基因组特征与临床结局和治疗反应的关联。这项队列研究分析了来自一家位于加利福尼亚州旧金山的美国全国综合癌症网络肿瘤中心的连续94例黑色素瘤脑转移患者的整体DNA测序和单核RNA测序数据，这些患者经过组织病理学确诊为黑色素瘤脑转移，并在2009年1月1日至2022年12月31日期间接受了单一手术切除。 采用临床实验室改进修正法认证的靶向测序分析肿瘤切除标本，重点关注BRAF V600E变异。对于CNS治疗原始患者进行手术切除的冷冻病理标本，采用商业单核RNA测序方法。主要结局为总生存期(OS)。次要结局包括CNS无进展生存期(PFS)，以及减少T细胞和巨噬细胞群体的微环境组成和免疫治疗反应。 为了将分子状态与临床结果进行相关性分析，对94例连续患者(中位年龄64岁[范围24-82岁]；70名男性[74%])进行了Kaplan-Meier生存分析，其中包括目标BRAF变异检测，结果显示BRAF变异型肿瘤的颅内中位PFS较差(BRAF变异型：3.6个月[四分位数范围0.1-30.6个月]；BRAF野生型：11.0个月[四分位数范围0.8-81.5个月]；P<0.001)，并且OS较差(BRAF变异型：9.8个月[四分位数范围2.5-69.4个月]；BRAF野生型：23.2个月[四分位数范围1.1-102.5个月]；P=0.005；log-rank检验)。多变量Cox比例风险回归分析表明，BRAF V600E状态是独立变量，与PFS (风险比[HR]，2.65；95%可信区间，1.54-4.57；P<0.001）和OS (HR，1.96；95% CI，1.08-3.55；P=0.03）显著相关。在接受靶向DNA测序的45位患有切除黑色素瘤脑转移的患者中，分子分类重复了癌症基因组图谱组(NRAS变异型、BRAF变异型、NF1变异型和三重野生型)，脑转移队列中没有亚型富集。在分子水平上，发现BRAF V600E变异损伤具有明显降低的肿瘤突变负荷。此外，初次接受治疗的BRAF V600E变异(n=3)脑转移与BRAF野生型(n=3)脑转移的单核RNA测序结果显示在BRAF野生型肿瘤中免疫细胞群体增加(均值[标准差]，11%[4.1%] vs 3%[1.6%] CD45阳性细胞；P=0.04)。根据BRAF状态对术后免疫治疗反应进行生存分析结果显示，BRAF野生型病变与检查点抑制治疗的反应相关(OS中位数：应用免疫治疗，未定义；不使用免疫治疗，13.0个月[范围1.1-61.7个月]；P=0.001；log-rank检验)，而BRAF变异型病变(OS中位数：应用免疫治疗，9.8个月[范围2.9-39.8个月]；不使用免疫治疗，9.5个月[范围2.5-67.2个月]；P=0.81；log-rank检验)。 这项对切除黑色素瘤脑转移患者的分子分析发现，BRAF V600E变异是与较差临床结果、不同的微环境组成和免疫治疗受益相关的重要转化生物标志物。因此，患有BRAF V600E变异的黑色素瘤脑转移患者可能受益于其他穿透中枢神经系统的全身方案。

Central nervous system (CNS)-penetrant systemic therapies have significantly advanced care for patients with melanoma brain metastases. However, improved understanding of the molecular landscape and microenvironment of these lesions is needed to both optimize patient selection and advance treatment approaches.To evaluate how bulk and single-cell genomic features of melanoma brain metastases are associated with clinical outcome and treatment response.This cohort study analyzed bulk DNA sequencing and single nuclear RNA-sequencing data from resected melanoma brain metastases and included 94 consecutive patients with a histopathologically confirmed diagnosis of melanoma brain metastasis who underwent surgical resection at a single National Comprehensive Cancer Network cancer center in San Francisco, California, from January 1, 2009, to December 31, 2022.A Clinical Laboratory Improvement Amendments-certified targeted sequencing assay was used to analyze tumor resection specimens, with a focus on BRAF V600E alteration. For frozen pathologic specimens from CNS treatment-naive patients undergoing surgical resection, commercial single nuclear RNA sequencing approaches were used.The primary outcome was overall survival (OS). Secondary outcomes included CNS progression-free survival (PFS), microenvironmental composition with decreased T-cell and macrophage populations, and responses to immunotherapy.To correlate molecular status with clinical outcome, Kaplan-Meier survival analysis of 94 consecutive patients (median age, 64 years [range, 24-82 years]; 70 men [74%]) with targeted BRAF alteration testing showed worse median intracranial PFS (BRAF variant: 3.6 months [IQR, 0.1-30.6 months]; BRAF wildtype: 11.0 months [IQR, 0.8-81.5 months]; P < .001) and OS (BRAF variant: 9.8 months [IQR, 2.5-69.4 months]; BRAF wildtype: 23.2 months [IQR, 1.1-102.5 months]; P = .005; log-rank test) in BRAF V600E variant tumors. Multivariable Cox proportional hazards regression analysis revealed that BRAF V600E status was an independent variable significantly associated with both PFS (hazard ratio [HR], 2.65; 95% CI, 1.54-4.57; P < .001) and OS (HR, 1.96; 95% CI, 1.08-3.55; P = .03). For the 45 patients with resected melanoma brain metastases undergoing targeted DNA sequencing, molecular classification recapitulated The Cancer Genome Atlas groups (NRAS variant, BRAF variant, NF1 variant, and triple wildtype) with no subtype enrichment within the brain metastasis cohort. On a molecular level, BRAF V600E variant lesions were found to have a significantly decreased tumor mutation burden. Moreover, single nuclear RNA sequencing of treatment-naive BRAF V600E variant (n = 3) brain metastases compared with BRAF wildtype (n = 3) brain metastases revealed increased immune cell populations in BRAF wildtype tumors (mean [SD], 11% [4.1%] vs 3% [1.6%] CD45-positive cells; P = .04). Survival analysis of postoperative immunotherapy responses by BRAF status revealed that BRAF wildtype lesions were associated with a response to checkpoint inhibition (median OS: with immunotherapy, undefined; without immunotherapy, 13.0 months [range, 1.1-61.7 months]; P = .001; log-rank test) while BRAF variant lesions (median OS: with immunotherapy, 9.8 months [range, 2.9-39.8 months]; without immunotherapy, 9.5 months [range, 2.5-67.2 months]; P = .81; log-rank test) were not.This molecular analysis of patients with resected melanoma brain metastases found that BRAF V600E alteration is an important translational biomarker associated with worse clinical outcomes, differential microenvironmental composition, and benefit from immunotherapy. Patients with BRAF V600E variant melanoma brain metastases may thus benefit from alternative CNS-penetrant systemic regimens.