PDF(Pubmed)
Abstract：
Neurofibromatosis Type 1 (NF1) is caused by loss of function variants in the NF1 gene. Most patients with NF1 develop skin lesions called cutaneous neurofibromas (cNFs). Currently the only approved therapeutic for NF1 is selumetinib, a mitogen -activated protein kinase (MEK) inhibitor. The purpose of this study was to analyze the transcriptome of cNF tumors before and on selumetinib treatment to understand both tumor composition and response. We obtained biopsy sets of tumors both pre- and on- selumetinib treatment from the same individuals and were able to collect sets from four separate individuals. We sequenced mRNA from 5844 nuclei and identified 30,442 genes in the untreated group and sequenced 5701 nuclei and identified 30,127 genes in the selumetinib treated group. We identified and quantified distinct populations of cells (Schwann cells, fibroblasts, pericytes, myeloid cells, melanocytes, keratinocytes, and two populations of endothelial cells). While we anticipated that cell proportions might change with treatment, we did not identify any one cell population that changed significantly, likely due to an inherent level of variability between tumors. We also evaluated differential gene expression based on drug treatment in each cell type. Ingenuity pathway analysis (IPA) was also used to identify pathways that differ on treatment. As anticipated, we identified a significant decrease in ERK/MAPK signaling in cells including Schwann cells but most specifically in myeloid cells. Interestingly, there is a significant decrease in opioid signaling in myeloid and endothelial cells; this downward trend is also observed in Schwann cells and fibroblasts. Cell communication was assessed by RNA velocity, Scriabin, and CellChat analyses which indicated that Schwann cells and fibroblasts have dramatically altered cell states defined by specific gene expression signatures following treatment (RNA velocity). There are dramatic changes in receptor-ligand pairs following treatment (Scriabin), and robust intercellular signaling between virtually all cell types associated with extracellular matrix (ECM) pathways (Collagen, Laminin, Fibronectin, and Nectin) is downregulated after treatment. These response specific gene signatures and interaction pathways could provide clues for understanding treatment outcomes or inform future therapies.
摘要：
1型神经纤维瘤病（NF1）是由NF1基因中功能变体的丧失引起的。大多数NF1患者会出现皮肤损伤，称为皮肤神经纤维瘤（cNFs）。目前，NF1唯一批准的治疗方法是司美替尼，丝裂原活化蛋白激酶（MEK）抑制剂。这项研究的目的是分析cNF肿瘤在司美替尼治疗之前和之后的转录组，以了解肿瘤的组成和反应。我们从同一个体获得了司鲁美替尼治疗前和经司美替尼治疗的肿瘤活检组，并能够从四个单独的个体收集组。我们对5844个细胞核的mRNA进行了测序，并在未处理组中鉴定了30,442个基因，对5701个细胞核进行了测序，并在司美替尼处理组中鉴定了30,127个基因。我们鉴定并定量了不同的细胞群(雪旺氏细胞，成纤维细胞,周细胞,骨髓细胞，黑素细胞,角质形成细胞，和两个内皮细胞群）。虽然我们预计细胞比例可能会随着治疗而改变，我们没有发现任何一个细胞群体发生显著变化，可能是由于肿瘤之间固有的变异性。我们还基于每种细胞类型的药物治疗评估了差异基因表达。还使用独创性途径分析(IPA)来鉴定在治疗上不同的途径。如预期,我们发现,在包括施万细胞在内的细胞中,ERK/MAPK信号显著降低,但在骨髓细胞中最为特异.有趣的是,在髓样细胞和内皮细胞中,阿片样物质信号显著减少;在施万细胞和成纤维细胞中也观察到这种下降趋势.通过RNA速度评估细胞通讯，斯克里亚宾,和CellChat分析表明施万细胞和成纤维细胞在处理后具有由特定基因表达特征定义的显著改变的细胞状态(RNA速度)。治疗后受体-配体对发生了巨大变化（Scriabin），以及与细胞外基质（ECM）途径相关的几乎所有细胞类型之间的强大细胞间信号（胶原蛋白，层粘连蛋白,纤连蛋白,和Nectin）在治疗后下调。这些反应特异性基因特征和相互作用途径可以为理解治疗结果或为未来的治疗提供线索。
