Smarcd1 is a “Goldilocks” metastasis modifier gene [rnaseq_spheroids]. Smarcd1 is a “Goldilocks” metastasis modifier gene [rnaseq_spheroids]

Breast cancer is the most highly diagnosed cancer worldwide, making up around 12% of all diagnosed cancers in 2020. Mortality caused by breast cancer is largely due to metastasis to distant essential organs, and a lack of metastasis-targeted therapies perpetuates incredibly poor outcomes for late-stage patients. Here we have identified a new class of “Goldilocks” genes for metastasis-targeted therapeutic development, through our focus on meiotic genetics and inherited transcriptional network regulation. Building on previous work identifying the CCR4-NOT RNA deadenylase complex in metastasis, we further demonstrate that RNA binding proteins NANOS1, PUM2, and CPSF4 also regulate metastatic potential. Using cell lines, 3D culture, mouse models, and clinical data, we have identified Smarcd1 mRNA, a key target of all three factors, for which high and low expression is associated with positive clinical outcome, but medium expression significantly reduces probability of survival. Applying the theory of “essential genes” from evolution, we have identified an additional 50 genes that span several cellular processes and must be maintained within a discrete window of expression for metastasis to occur. In the case of Smarcd1, small perturbations in expression level significantly reduced metastasis in laboratory mouse models and altered splicing programs of particular relevance to the ER+HER2 enriched patient subtype. Identification of subtype-specific “Golidlocks” metastasis modifier genes creates a new class of genes and catalogue of potential novel targets that when therapeutically “nudged” in either direction may significantly improve late-stage patient outcomes. Overall design: To investigate the affect of Smarcd1 depletion on mammary tumor transcription shRNA knockdown or overexpression cells were generated and RNA sequencing performed from control and experimental cells grown in 3D as tumor spheroids

乳腺癌是全球确诊率最高的癌症，2020年约占所有确诊癌症病例的12%。乳腺癌患者的死亡主要源于肿瘤向远端重要器官发生转移，而缺乏针对转移的靶向治疗方案，使得晚期患者的预后始终极差。本研究聚焦减数分裂遗传学与遗传转录网络调控，鉴定出一类可用于转移靶向治疗开发的新型"Goldilocks"基因。在既往鉴定出转移相关CCR4-NOT RNA脱腺苷化复合物的工作基础上，我们进一步证实RNA结合蛋白NANOS1、PUM2与CPSF4同样可调控肿瘤转移潜能。我们借助细胞系、三维培养体系、小鼠模型及临床数据，鉴定出同时受上述三种因子调控的关键靶标Smarcd1 mRNA：该基因的高表达与低表达均与良好的临床预后相关，而中等表达水平则会显著降低患者的生存概率。基于进化生物学中的"必需基因"理论，我们又筛选得到另外50个参与多种细胞过程的基因，这些基因的表达量必须维持在特定区间内，才能促进肿瘤转移发生。以Smarcd1基因为例，其表达水平的微小扰动即可显著降低实验室小鼠模型中的肿瘤转移灶形成，并改变与ER阳性HER2富集型乳腺癌患者亚型密切相关的剪接程序。鉴定亚型特异性的"Goldilocks"转移修饰基因，可构建一类新型基因家族及潜在新型治疗靶点目录，通过在任一方向对这些靶点进行治疗性"微调"，即可显著改善晚期患者的预后。实验设计：为探究Smarcd1缺失对乳腺肿瘤转录组的调控作用，我们构建了经shRNA敲低或过表达的细胞系，并对以三维肿瘤球状体形式培养的对照组与实验组细胞开展RNA测序。