Targeting regenerative reprogramming in colorectal cancer

摘要 定义不佳的适应度特征使一部分癌细胞能够在治疗中存活，最终导致 难治性肿瘤测序工具的广泛使用使人们认识到， 肿瘤通常缺乏耐药的遗传机制，而是选择一种再生程序， 通过激活发育、炎症、间充质和干细胞特征。重要的是这些 再生状态在上皮来源的各种癌症中是保守的，并且是潜在可逆的。我们 初步数据表明，结肠直肠癌（CRC）中的治疗耐药性是由预先存在的细胞通过一种 YAP驱动的再生程序，与CRC的共有分子亚型4惊人相似， 在难治性肿瘤中经常观察到的风险表型。 我们的中心假设是，预先存在的人口驱动再生重编程和肿瘤逃逸 通过表观遗传适应来治疗。首先，我们建议将 使用条形码谱系追踪和单细胞技术检测预先存在的（抗性前）状态。使用患者来源的 为了分离抗性的创始克隆，我们将研究预先存在的与 通过全外显子组（WES）和RNA测序（RNA-seq）积极获得适应性特征。使用临床前 KRAS抑制抗性模型（KRASi），我们将定义遗传和非遗传驱动因素的作用， 肿瘤逃逸为了开发废除再生重编程的方法，我们将进行一项重点研究。 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 靶向筛选的最高命中的化合物与标准疗法组合。我们相信我们的 创新的工具将使我们有最大的机会开发具有即时临床效果的治疗方法。 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 斯隆凯特琳（MSK）在卢卡斯·道博士和一个咨询委员会的指导下。候选人将 在研究和职业发展活动中投入至少9个人月的专业努力 在这里概述。与他的导师和咨询委员会，候选人设计了一个5年计划，旨在 扩展他在癌症研究方面的知识和专业知识，包括单细胞技术，计算 生物学、基因工程和功能筛选。职业生涯计划的目标是推出一个独立的 作为实验室研究者的职业生涯专注于治疗耐药性和CRC反应的生物标志物。

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.