Mechanistic dissection and inhibitor targeting of autophagy in RAS driven cancers

自噬是一种自我降解的过程，细胞可以有序地清除有缺陷的细胞器并进行再循环 大分子作为营养源。自噬是KRAS的致瘤性生长所必需的， 突变型胰腺导管腺癌（PDAC），为自噬的临床评价提供了理论基础。 PDAC抑制剂羟氯喹（HCQ）。令人不安的是，当作为单药治疗或联合治疗时， 在标准治疗下，HCQ对PDAC显示出有限的临床疗效或无临床疗效。我们最近确定， 用关键KRAS效应子途径的抑制剂治疗PDAC，RAF-MEK-ERK促有丝分裂活化 蛋白激酶（MAPK）级联，意外地引起自噬的进一步升高，使PDAC急性 依赖于这一过程，并对自噬抑制过敏。我们确定ERK抑制 损害其他关键过程，然后导致自噬的补偿性上调。我们的发现， 与另一项独立的共同发表的研究基本相同的结论，导致了 评价MEK（曲美替尼、比尼替尼）或ERK（LY 3214996）抑制剂与 HCQ用于转移性KRAS突变型PDAC。虽然早期观察到同情使用这种组合 支持显著的临床影响，我们的初步研究支持我们的前提，我们可以改善这一点 疗法我们提出了三个目标，以进一步推进自噬抑制作为抗RAS治疗方法。 首先，我们将确定ERK MAPK + HCQ组合在KRAS/NRAS/BRAF中是否同样有效。 突变CRC（Aim 1）。HCQ是一种溶酶体抑制剂，因此对自噬没有选择性。我们假设 ULK 1/2丝氨酸/苏氨酸蛋白激酶的抑制剂，饥饿诱导的自噬的关键启动子， 作为更特异的自噬抑制剂。然而，与所有蛋白激酶抑制剂一样， 补偿机制将促进对ULK抑制剂功效的抗性。此外，全面 ULK 1/2底物的测定仍有待完成。我们将以实际行动， ULK抑制对磷酸化蛋白质组和激酶组的补偿作用，以严格评估ULK抑制剂 作为自噬抑制剂（Aim 2）。我们的Aim 3研究是基于我们应用一种2,500个基因的药物 基因组CRISPR/Cas9基因功能丧失筛选以鉴定调节CQ抗肿瘤活性的基因。 所鉴定的增强或降低CQ生长抑制活性的命中物代表候选组合 或CQ抗性的生物标志物。我们已经确定了DNA损伤反应的介质， 细胞周期调节因子作为两大类抗性促进基因。我们将机械地剖析这些 关系，并确定如何抑制这些途径的成员影响自噬通量。在 总之，我们的研究将增强我们对癌症中自噬调节的理解，并有助于 开发靶向自噬的新型组合疗法，用于治疗KRAS突变型癌症。

Autophagy is a self-degradation process whereby cells can orderly clear defective organelles and recycle macromolecules as a nutrient source. Autophagy is elevated and essential for the tumorigenic growth of KRAS- mutant pancreatic ductal adenocarcinoma (PDAC), providing the rationale for clinical evaluation of the autophagy inhibitor hydroxychloroquine (HCQ) for PDAC. Disappointingly, when used as monotherapy or in combination with standard of care, HCQ has shown limited to no clinical efficacy for PDAC. We recently determined that the treatment of PDAC with inhibitors of the key KRAS effector pathway, the RAF-MEK-ERK mitogenic activated protein kinase (MAPK) cascade, unexpectedly caused further elevation of autophagy, rendering PDAC acutely dependent on this process, and hypersensitive to autophagy inhibition. We determined that ERK inhibition impaired other critical processes that then led to compensatory upregulation of autophagy. Our findings, together with essentially identical conclusions by another independent co-published study, have led to the initiation of clinical trials evaluating either MEK (trametinib, binimetinib) or ERK (LY3214996) inhibitor in combination with HCQ for metastatic KRAS-mutant PDAC. While early observations from compassionate use of this combination support a significant clinical impact, our preliminary studies support our premise that we can improve upon this therapy. We propose three aims to further advance autophagy inhibition as an anti-RAS therapeutic approach. First, we will determine if the ERK MAPK + HCQ combination will be similarly effective in KRAS/NRAS/BRAF- mutant CRC (Aim 1). HCQ is a lysosome inhibitor and consequently not selective for autophagy. We hypothesize that inhibitors of the ULK1/2 serine/threonine protein kinases, key initiators of starvation-induced autophagy, will act as more specific autophagy inhibitors. However, as with all protein kinase inhibitors, inhibitor-induced compensatory mechanisms will promote resistance to ULK inhibitor efficacy. Additionally, a comprehensive determination of ULK1/2 substrates remains to be completed. Thus, we will determine the direct and compensatory effects of ULK inhibition on the phosphoproteome and kinome to critically evaluate ULK inhibitors as autophagy inhibitors (Aim 2). Our Aim 3 studies are based on our application of a 2,500-gene druggable genome CRISPR/Cas9 genetic-loss-of-function screen to identify genes that modulate CQ anti-tumor activity. The identified hits that either enhance or reduce CQ growth inhibition activity represent candidate combinations or biomarkers for CQ resistance, respectively. We have identified mediators of the DNA damage response and cell cycle regulators as two major classes of resistance-promoting genes. We will mechanistically dissect these relationships and determine how inhibition of members of these pathways influences autophagic flux. In summary, our studies will enhance our understanding of autophagy regulation in cancer and aid in the development of novel combination therapies to target autophagy for the treatment of KRAS-mutant cancers.