Expression changes in CD45neg subpopulation of YUMM1.7 melanoma pre MAPKi treatment vs. on MAPKi treatment [Y1.7.FPKM.batch3]

Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination with a MEKi typically elicits partial responses. We compared the transcriptomes of patient-derived tumors regressing on MAPKi therapy against MAPKi-induced temporal transcriptomic states in human melanoma cell lines or murine melanoma in immune-competent mice. Despite heterogeneous dynamics of clinical tumor regression, residual tumors displayed highly recurrent transcriptomic alterations and enriched processes, which were also observed in MAPKi-selected cell lines (implying tumor cell-intrinsic reprogramming) or in bulk mouse tumors (and the CD45-negative or -positive fractions,, implying tumor cell-intrinsic or stromal/immune alterations, respectively). Tumor cell-intrinsic reprogramming attenuated MAPK-dependency, while enhancing mesenchymal, angiogenic and IFN-inflammatory features and growth/survival dependence on multi-RTKs and PD-L2. In the immune compartment, PD-L2 upregulation in CD11c+ immunocytes drove the loss of T-cell inflammation and promoted BRAFi resistance. Thus, residual melanoma early on MAPKi therapy already displays potentially exploitable adaptive transcriptomic, epigenomic, immune-regulomic alterations. Sorted CD45- cells from YUMM1.7 melanoma tumors in C57BL/6 mice before treatment, during treatment with MAPKi were sent for transcriptomic analysis by single end 1x50bp HiSeq 3000 RNAseq analysis

针对晚期BRAF V600突变型黑色素瘤（advanced V600BRAF mutant melanoma），采用BRAF抑制剂（BRAF inhibitor, BRAFi）单药或联合MEK抑制剂（MEK inhibitor, MEKi）的治疗方案，通常仅能诱导部分临床缓解。本研究对比了接受MAPK抑制剂（MAPK inhibitor, MAPKi）治疗后发生消退的患者来源肿瘤（patient-derived tumors），与人类黑色素瘤细胞系或免疫健全小鼠（immune-competent mice）体内小鼠黑色素瘤中MAPKi诱导的瞬时转录组状态（transcriptomic states）。尽管临床肿瘤消退的动力学特征存在异质性，但残留肿瘤均表现出高度重复性的转录组改变与富集生物学通路；这类改变同样可在MAPKi筛选获得的细胞系（提示肿瘤细胞内在重编程）或整体小鼠肿瘤（以及CD45阴性、阳性组分，分别对应肿瘤细胞内在改变与基质/免疫细胞改变）中观察到。肿瘤细胞内在重编程会减弱肿瘤细胞对MAPK信号通路的依赖性，同时增强其间充质、血管生成与干扰素（IFN）炎性特征，并使其生长/存活依赖于多受体酪氨酸激酶（multi-RTKs）与PD-L2。在免疫微环境组分中，CD11c+免疫细胞上的PD-L2上调会驱动T细胞炎症反应丧失，并促进BRAFi耐药。综上，在MAPKi治疗早期，残留黑色素瘤即已出现具有潜在可靶向干预价值的适应性转录组、表观基因组（epigenomic）与免疫调控组（immunoregulomic）改变。本研究对C57BL/6小鼠体内YUMM1.7黑色素瘤在治疗前、接受MAPKi治疗期间分选得到的CD45阴性细胞，采用单端1×50bp HiSeq 3000 RNA测序（single end 1x50bp HiSeq 3000 RNAseq）进行了转录组分析。