Targeting regenerative reprogramming in colorectal cancer

摘要 定义不明确的健康特征使一部分癌细胞能够在治疗中存活下来，最终导致 治疗--难治性肿瘤。测序工具的广泛使用使人们认识到耐火材料 肿瘤通常缺乏耐药的遗传机制，而是选择以再生为特征的程序 通过激活发育、炎症、间充质和干细胞功能。重要的是，这些 再生状态在不同的上皮性癌症中是保守的，并且有可能是可逆的。我们的 初步数据表明，结直肠癌(CRC)的治疗抵抗是由预先存在的细胞通过一种 YAP驱动的再生计划，与公认的CRC分子亚型4惊人地相似，是一种糟糕的 风险表型常见于治疗难治性肿瘤。 我们的中心假设是，预先存在的种群驱动再生重新编程和肿瘤逃逸 通过表观遗传适应，可以在治疗上有针对性。首先，我们建议将 使用条形码谱系跟踪和单细胞技术的预先存在(预先抵抗)状态。使用患者派生的 有机化合物(PDO)为了分离抗性的创建克隆，我们将研究先前存在的与 通过全外显子组(WES)和RNA测序(RNA-seq)主动获得适应度特征。使用临床前 对KRAS抑制的抗性模型(Krasi)，我们将定义遗传和非遗传驱动因素在 肿瘤逃逸。为了开发废除再生性重新编程的方法，我们将执行一个有重点的 靶向50个染色质调节子的shRNA筛选。为了加快临床翻译，我们将测试现成的 针对屏幕上最热门的化合物，与标准疗法相结合。我们相信我们的 创新的工具将最大限度地扩大我们开发可立即产生临床影响的治疗方法的机会。 在获奖期间，候选人将在威尔·康奈尔医学(WCM)和纪念馆进行研究 斯隆·凯特林(MSK)，在卢卡斯·道博士和一个咨询委员会的指导下。候选人将会 将至少9个人月的专业精力投入到研究和职业发展活动 概述如下。在他的导师和咨询委员会的帮助下，这位候选人设计了一个旨在 扩展他在癌症研究方面的知识和专长，包括单细胞技术，计算 生物学、基因工程和功能筛选。职业生涯规划的目标是推出一家独立的 作为一名实验室调查员，职业生涯侧重于结直肠癌的治疗耐药性和反应的生物标记物。

ABSTRACT Poorly defined fitness features enable a subset of cancer cells to survive therapy, ultimately giving rise to treatment-refractory tumors. The expanded use of sequencing tools have led to the recognition that refractory tumors often lack a genetic mechanism of resistance, and instead co-opt a regenerative program characterized by activation of developmental, inflammatory, mesenchymal and stem cell features. Importantly, these regenerative states are conserved across diverse cancers of epithelial origin, and are potentially reversible. Our preliminary data indicate that therapy resistance in colorectal cancer (CRC) is fueled by preexisting cells via a YAP-driven regenerative program that is strikingly similar to the consensus molecular subtype 4 of CRC, a poor risk phenotype often observed in treatment-refractory tumors. Our central hypothesis is that a preexisting population drives regenerative reprogramming and tumor escape through epigenetic adaptations that can be targeted therapeutically. First we propose characterizing the preexisting (pre-resistant) state using barcode lineage tracing and single-cell technologies. Using patient-derived organoids (PDOs) to isolate the founding clones of resistance, we will study the contribution of preexisting versus actively gained fitness features through whole-exome (WES) and RNA sequencing (RNA-seq). Using pre-clinical models of resistance to KRAS-inhibition (KRASi), we will define the role of genetic and non-genetic drivers of tumor escape. To develop approaches that abrogate regenerative reprogramming, we will perform a focused shRNA screen targeting 50 chromatin regulators. To expedite clinical translation, we will test readily available compounds targeting the top hits of the screen, in combination with standard therapies. We believe that our innovative tools will maximize our opportunity to develop treatment approaches with immediate clinical impact. During the award period, the candidate will conduct research at Weill Cornell Medicine (WCM) and Memorial Sloan Kettering (MSK) under the mentorship of Dr. Lukas Dow and an advisory committee. The candidate will commit at least 9 person-months of his professional effort to the research and career development activities outlined here. With his mentor and advisory committee, the candidate has designed a 5-year plan aimed at expanding his knowledge and expertise in cancer research, including single cell technologies, computational biology, genetic engineering, and functional screens. The goal of the career plan is to launch an independent career as a laboratory investigator focused on therapy resistance and biomarkers of response in CRC.