Uncovering Epigenetic and Transcriptional Drivers of Neuroendocrine Plasticity at Single-Cell Level in Patients with Small Cell Lung Cancer Transformation

项目摘要/摘要 研究：在肺腺癌(LUAD)中，神经内分泌(NE)转化为小细胞肺癌 小细胞肺癌与肿瘤转移和靶向治疗耐药有关。这种谱系可塑性通常会导致 LUAD和SCLC混杂在同一肿瘤中。我们证明了激光显微解剖LUAD和SCLC 肿瘤内成分共享主干突变，证实NE转化。SCLC本身被归类为 经典、变异和非东北亚型。临床前研究表明，变异和非NE亚型 转移和化疗耐药风险增加。人们对什么基因调控机制知之甚少 推动SCLC转型和SCLC子类型切换。单细胞RNA和ATAC测序(scRNA-seq， 在LUAD/SCLC联合组织学样本中的SnATAC-seq)提供了一个理想的平台来表征 NE可塑性的瘤内异质性。作为对照参考，我们在一个序列中完成了scRNA-seq Novo SCLC(Chan等人)BioRxiv，癌症细胞正在审查中)。我们在最初的队列中进行了scRNA-seq 结合LUAD/SCLC，发现转化的小细胞肺癌(T-SCLC)瘤内亚型多样性显著增加。 SCLC)。我们在T-SCLC中发现Notch抑制，并在随后的SCLC亚型多样化中重新激活。 我们观察到SOX2和ELF3在预转化的LUAD和经典的LUAD中过表达，PHOX2B和ELF3在 T-SCLC与从头开始的SCLC。我们假设在RB1和TP53缺失的情况下，关键转录因子(SOX2， PHOX2B、ELF3)、表观遗传调节因子和Notch信号的调制都有助于NE的转化 和亚型多样化。我们将在合并的LUAD/SCLC样本中利用scRNA-seq和snatac-seq 组织学：1)鉴定亚克隆群体的分子标记；2)重建调控网络；3) 在临床前的体外和体内模型中验证NE可塑性的转录和表观遗传驱动因素，包括 Osimertinib治疗后发生NE转化的EGFR LUAD患者来源的异种移植物。 候选人：陈祖泽博士，医学博士，MSKCC肿瘤学研究员。他的目标是成为一名 独立的终身制医生兼科学家研究转移和治疗中的谱系可塑性 癌症中的抗药性。他的导师查尔斯·鲁丁博士和达娜·佩尔博士是肺癌和 分别进行单细胞测序。陈博士建议进行为期五年的指导培训，以获得湿润 实验室和高级计算技能。他的湿法实验室培训将包括1)单细胞库准备和2) 用于功能验证的临床前模型的基因操作。他的计算培训将包括1) SnATAC-SEQ分析和2)高级机器学习。他的顾问委员会查尔斯·索耶斯博士， 海伦娜·余、罗南·夏尔盖和克里斯蒂娜·莱斯利将指导他的训练和研究。 环境：MSKCC是一家以患者护理、创新研究和青少年培训而闻名的癌症中心 寻求独立内科医生-科学家职业生涯的教师。MSKCC支持单细胞研究计划 这推进了单细胞测序，这将支持这一研究和职业发展的提议。

PROJECT SUMMARY/ABSTRACT Research: In lung adenocarcinoma (LUAD), neuroendocrine (NE) transformation to small cell lung cancer (SCLC) is associated with metastasis and resistance to targeted therapies. This lineage plasticity often leads to LUAD and SCLC admixed in the same tumor. We demonstrated that laser-microdissected LUAD and SCLC intratumoral components share truncal mutations, confirming NE transformation. SCLC itself is classified as classical, variant, and non-NE subtypes. Preclinical studies demonstrate that variant and non-NE subtypes have increased risk for metastasis and chemoresistance. It is poorly understood what gene regulatory mechanism drives SCLC transformation and SCLC subtype switching. Single-cell RNA and ATAC sequencing (scRNA-seq, snATAC-seq) in samples of combined LUAD/SCLC histology present an ideal platform to characterize the intratumoral heterogeneity of NE plasticity. As a control reference, we completed scRNA-seq in a cohort of de novo SCLC (Chan, et al. bioRxiv, under review at Cancer Cell). We performed scRNA-seq in an initial cohort of combined LUAD/SCLC and found significantly increased intratumoral subtype diversity in transformed SCLC (T- SCLC). We found Notch suppression in T-SCLC and reactivation with subsequent SCLC subtype diversification. We observed overexpressed SOX2 and ELF3 in pre-transformed vs classical LUAD, and PHOX2B and ELF3 in T-SCLC vs de novo SCLC. We hypothesize that under RB1 and TP53 loss, key transcription factors (SOX2, PHOX2B, ELF3), epigenetic regulators, and modulation of Notch signaling all contribute to NE transformation and subtype diversification. We will leverage scRNA-seq and snATAC-seq in samples of combined LUAD/SCLC histology to 1) identify molecular markers of subclonal populations, 2) reconstruct the regulatory network, and 3) validate transcriptomic and epigenetic drivers of NE plasticity in preclinical in vitro and in vivo models, including an EGFR+ LUAD patient-derived xenograft undergoing NE transformation after osimertinib treatment. Candidate: Dr. Joseph Chan, MD, PhD is a Medical Oncology Fellow at MSKCC. He aims to become an independent, tenure-track physician-scientist investigating lineage plasticity in metastasis and treatment resistance in cancer. His mentors Drs. Charles Rudin and Dana Pe’er are leading experts in lung cancer and single-cell sequencing, respectively. Dr. Chan proposes a five-year period of mentored training to acquire wet lab and advanced computational skills. His wet lab training will include 1) single-cell library preparation and 2) genetic manipulation of preclinical models for functional validation. His computational training will include 1) snATAC-seq analysis and 2) advanced machine learning. His advisory committee—Drs. Charles Sawyers, Helena Yu, Ronan Chaligné, and Christina Leslie—will guide his training and research. Environment: MSKCC is a cancer center renowned for patient care, innovative research, and training for junior faculty seeking careers as independent physician-scientists. MSKCC houses the Single Cell Research Initiative that advances single-cell sequencing, which will support this proposal for research and career development.