An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus [Ribo-seq, RNA-seq]. An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus [Ribo-seq, RNA-seq]

Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis, however its effects on cancer progression remain poorly understood. To address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed novel regression-based methods to analyze ribosome profiling and alternative polyadenylation data, and identified HNRNPC as a translational controller of a specific mRNA regulon. Mechanistically, HNRNPC, in concert with PABPC4, binds near to poly(A) signals, thereby governing the alternative polyadenylation of a set of mRNAs. We found that HNRNPC and PABPC4 are downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3’ UTR lengthening and subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. We also found that a small molecule, previously shown to induce a distal-to-proximal poly(A) site switching, counteracts the HNRNPC-PABPC4 driven deregulation of alternative polyadenylation and decreases the metastatic lung colonization by breast cancer cells in vivo. Overall design: Comparison of translation efficiencies in highly and poorly metastatic breast cancer cell lines

癌细胞通常会劫持转录后调控机制，以实现驱动肿瘤转移的基因网络的病理性表达。翻译调控（translational control）是肿瘤发生过程中的核心调控枢纽，但其对癌症进展的影响仍有待深入解析。为解决这一科学问题，我们采用核糖体谱（ribosome profiling）技术，对比了低转移与高转移乳腺癌细胞及患者来源的异种移植瘤（patient-derived xenografts）的全基因组翻译效率。我们开发了全新的基于回归分析的方法，用于分析核糖体谱与可变多聚腺苷酸化（alternative polyadenylation）数据，并鉴定出异质性核核糖核蛋白C（HNRNPC）作为特定mRNA调控子（mRNA regulon）的翻译调控因子。机制研究表明，HNRNPC与聚腺苷酸结合蛋白C4（PABPC4）协同结合于多聚腺苷酸化信号（poly(A) signals）附近，从而调控一组mRNA的可变多聚腺苷酸化过程。我们发现，在高转移癌细胞中HNRNPC与PABPC4均表达下调，这导致结合HNRNPC的mRNA发生3'非翻译区（3' untranslated region, 3'UTR）延长，进而引发翻译抑制。我们证实，调控HNRNPC的表达可影响异种移植小鼠模型（xenograft mouse models）中乳腺癌细胞的转移能力。我们还发现，一种此前被证实可诱导远端至近端多聚腺苷酸化位点切换（distal-to-proximal poly(A) site switching）的小分子化合物，能够抵消HNRNPC-PABPC4介导的可变多聚腺苷酸化失调，并在体内（in vivo）降低乳腺癌细胞的肺转移定植能力。实验设计：对比高转移与低转移乳腺癌细胞系的翻译效率。