PURPOSE The development of leptomeningeal melanoma metastases (LMM) is a rare and devastating complication of the late-stage disease, for which no effective treatments exist. Here, we performed a multi-omics analysis of the cerebrospinal fluid (CSF) from patients with LMM to determine how the leptomeningeal microenvironment shapes the biology and therapeutic responses of melanoma cells. EXPERIMENTAL DESIGN A total of 45 serial CSF samples were collected from 16 patients, 8 of these with confirmed LMM. Of those with LMM, 7 had poor survival (<4 months) and one was an extraordinary responder (still alive with survival >35 months). CSF samples were analyzed by mass spectrometry and incubated with melanoma cells that were subjected to RNA sequencing (RNA-seq) analysis. Functional assays were performed to validate the pathways identified. RESULTS Mass spectrometry analyses showed the CSF of most patients with LMM to be enriched for pathways involved in innate immunity, protease-mediated damage, and IGF-related signaling. All of these were anticorrelated in the extraordinary responder. RNA-seq analysis showed CSF to induce PI3K/AKT, integrin, B-cell activation, S-phase entry, TNFR2, TGFβ, and oxidative stress responses in the melanoma cells. ELISA assays confirmed that TGFβ expression increased in the CSF of patients progressing with LMM. CSF from poorly responding patients conferred tolerance to BRAF inhibitor therapy in apoptosis assays. CONCLUSIONS These analyses identified proteomic/transcriptional signatures in the CSF of patients who succumbed to LMM. We further showed that the CSF from patients with LMM has the potential to modulate BRAF inhibitor responses and may contribute to drug resistance.See related commentary by Glitza Oliva and Tawbi, p. 2083.

中文翻译：

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对软脑膜黑色素瘤转移患者的脑脊液进行蛋白质组学分析，确定与疾病进展和治疗耐药相关的特征。


目的 软脑膜黑色素瘤转移（LMM）是晚期疾病的一种罕见且具有破坏性的并发症，目前尚无有效的治疗方法。在这里，我们对 LMM 患者的脑脊液 (CSF) 进行了多组学分析，以确定软脑膜微环境如何影响黑色素瘤细胞的生物学和治疗反应。实验设计 从 16 名患者中收集了总共 45 个系列 CSF 样本，其中 8 名患者患有确诊的 LMM。在患有 LMM 的患者中，7 人的生存率很差（<4 个月），而 1 人的反应非常出色（仍然存活，生存率 >35 个月）。通过质谱分析脑脊液样本，并与黑色素瘤细胞一起孵育，进行 RNA 测序 (RNA-seq) 分析。进行功能测定以验证所识别的途径。结果 质谱分析显示，大多数 LMM 患者的脑脊液富含涉及先天免疫、蛋白酶介导的损伤和 IGF 相关信号传导的通路。所有这些在杰出反应者中都是反相关的。 RNA-seq 分析显示，CSF 可诱导黑色素瘤细胞中的 PI3K/AKT、整合素、B 细胞激活、S 期进入、TNFR2、TGFβ 和氧化应激反应。 ELISA 测定证实，LMM 进展患者的 CSF 中 TGFβ 表达增加。在细胞凋亡检测中，反应不佳的患者的脑脊液赋予了对 BRAF 抑制剂治疗的耐受性。结论 这些分析确定了死于 LMM 的患者脑脊液中的蛋白质组/转录特征。我们进一步表明，LMM 患者的 CSF 有可能调节 BRAF 抑制剂反应，并可能导致耐药性。参见 Glitza Oliva 和 Tawbi 的相关评论，第 14 页。 2083.