Predicting sensitivity and resistance in RET-driven cancers

Selpercatinib（LOXO-292）是一种高活性选择性RET抑制剂，正在进行注册研究。 RET依赖性癌症的LIBRETTO-001 1/2期试验（美国FDA于2020年批准RET 融合阳性肺癌/甲状腺癌和RET突变型甲状腺癌）。不幸的是， 没有特征，仍然是一种负担。本提案预计并解决了这一未满足的需求， 和功能表征的内在和获得性基因组和非基因组抗性的机制， RET依赖性癌症中的选择性RET抑制。为了实现这一目标，我们将利用独特的临床， 计算和翻译资源。目标1将确定内在的决定因素 RET依赖性癌症中对RET抑制的抗性。selpercatinib应答者的治疗前活检 而无应答者将进行靶向/全外显子组测序。计算分析将探索 克隆性、等位基因失衡和共突变特征相对于selpercatinib应答的作用， 无进展生存期。目的2建立选择性RET获得性耐药的机制 抑制作用配对的治疗前和进展后肿瘤活检和纵向无细胞（cf）DNA 将对来自LIBRET 0 -001患者的所有患者（基线、治疗中、进展时/进展后）进行分析。利用配对 样本将允许识别紧急基因组和非基因组（包括组织学/EMT） 转化）抗性机制。此外，血浆分析将允许动态评估 selpercatinib耐药性，其捕获了连续基因组进化的结果。目标3将在功能上 表征对选择性RET抑制的抗性。独特而丰富的患者衍生模型库， 未治疗和RET抑制剂耐药的RET依赖性癌症将通过正在进行的前瞻性 从LIBRETTO-001和商业用途收集和模型开发。在这些模型中， （继发性RET突变）和脱靶（MET/PI 3 K/KRAS/MDM 2激活）耐药机制将被研究。 在细胞/肿瘤活力、受体酪氨酸激酶活化和下游功能方面进行功能表征， 信令依赖性。新的治疗策略，特别是RET酪氨酸激酶抑制剂类型转换 将在体外和体内探索靶向耐药（中靶耐药）和组合疗法（脱靶耐药）。 最佳联合治疗将用于同情使用项目，以确认其 有效性，并为患者提供量身定制的挽救生命的治疗。此外，目标患者 耐药性将按照方案（Drilon PI）使用下一代RET抑制剂TPX-0046进行治疗。这 考虑到约400名患者已接受治疗， 随着selpercatinib在世界各地的试验和潜在的批准和快速采用这种药物， 多个监管机构。这些当前和未来的患者迫切需要重新建立 选择性RET抑制治疗进展后的持久疾病控制。

Selpercatinib (LOXO-292) is a highly active selective RET inhibitor explored on an ongoing registrational program (LIBRETTO-001 phase 1/2 trial) in RET-dependent cancers (US FDA approval in 2020 for RET fusion-positive lung/thyroid cancer and RET-mutant thyroid cancer). Unfortunately, resistance is uncharacterized and remains a liability. This proposal anticipates and addresses this unmet need by identifying and functionally characterizing mechanisms of intrinsic and acquired genomic and non-genomic resistance to selective RET inhibition in RET-dependent cancers. To accomplish this, we will leverage unique clinical, computational, and translational resources at our disposal. Aim 1 will identify determinants of intrinsic resistance to RET inhibition in RET-dependent cancers. Pre-treatment biopsies of selpercatinib responders and non-responders will undergo targeted/whole exome sequencing. Computational analysis will explore the role of clonality, allelic imbalance, and co-mutational signatures relative to selpercatinib response and progression-free survival. Aim 2 will establish the mechanisms of acquired resistance to selective RET inhibition. Paired pre-treatment and post-progression tumor biopsies and longitudinal cell-free (cf)DNA (baseline, on-treatment, at/post- progression) from LIBRETTO-001 patients will be profiled. Utilizing paired samples will allow for the identification of emergent genomic and non-genomic (including histologic/EMT transformation) resistance mechanisms. In addition, plasma profiling will allow for a dynamic assessment of selpercatinib resistance that captures the consequences of serial genomic evolution. Aim 3 will functionally characterize resistance to selective RET inhibition. A unique and rich library of patient-derived models of treatment-naïve and RET inhibitor resistant RET-dependent cancers will be augmented by ongoing prospective collection and model development from LIBRETTO-001 and commercial use. In these models, on-target (secondary RET mutations) and off-target (MET/PI3K/KRAS/MDM2 activation) resistance mechanisms will be functionally characterized in terms of cell/tumor viability, receptor tyrosine kinase activation, and downstream signaling dependencies. Novel therapeutic strategies, specifically RET tyrosine kinase inhibitor type switching (on-target resistance) and combinatorial therapies (off-target resistance), will be explored in vitro and in vivo. Optimal combination therapies will then be employed in compassionate use programs to confirm their effectiveness and provide tailored, life-saving treatment to patients. In addition, patients with on-target resistance will be treated on-protocol (Drilon PI) with the next-generation RET inhibitor, TPX-0046. This proposal has both immediate and long-term relevance considering that about 400 patients have been treated with selpercatinib around the world on trial and the potential approval and rapid adoption of this drug by multiple regulatory agencies. These current and future patients are in dire need of strategies to re-establish durable disease control after progression on selective RET inhibition.