MITF-low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease

The MITF-low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa (MITF-low) to study this biological subtype. We performed whole bulk RNA-seq to classify zebrafish MITF-low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF-low subgroups. Furthermore, using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single-cell and low input RNA-seq we characterise these MITF independent cells and show that they pre-exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.

MITF-low黑色素瘤转录特征（MITF-low melanoma transcriptional signature）可用于预测患者的不良预后，但目前对其生物学特征的认知仍较为匮乏。我们采用mitfa低表达（MITF-low）的斑马鱼遗传模型，对该黑色素瘤生物学亚型展开研究。通过全批量RNA测序（whole bulk RNA-seq），我们对主要按生长方向聚类的斑马鱼MITF-low黑色素瘤进行分类，并评估其与患者MITF-low黑色素瘤亚组的相似性。此外，借助抑制MITF活性的遗传学手段，我们在肿瘤消退部位发现了微量残留病灶；结合单细胞RNA测序（single-cell RNA-seq）与低起始量RNA测序（low input RNA-seq），我们对这些MITF非依赖型细胞进行了系统特征分析，并证实其早在原发性肿瘤中便已存在。实验整体设计：我们对斑马鱼原发性黑色素瘤开展批量RNA测序实验，基于其生长方向或初始突变背景比较不同表型；同时还对原发性与消退型黑色素瘤进行了单细胞RNA测序。