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

在单细胞水平上揭示小细胞肺癌转化患者神经内分泌可塑性的表观遗传和转录驱动因素

基本信息

批准号：
10540383
负责人：
Joseph Minhow Chan
金额：
$ 27.82万
依托单位：
SLOAN-KETTERING INST CAN RESEARCH
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-12-15 至 2026-11-30
项目状态：
未结题

项目摘要

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.

项目概要/摘要研究：在肺腺癌 (LUAD) 中，神经内分泌 (NE) 转化为小细胞肺癌（SCLC）与转移和对靶向治疗的抵抗有关。这种谱系可塑性通常会导致。我们证明了激光显微切割的 LUAD 和 SCLC 混合在同一肿瘤中。瘤内成分共享躯干突变，证实 NE 转化本身被归类为经典、变异和非 NE 亚型临床前研究表明，变异和非 NE 亚型具有。转移和化疗耐药的风险增加，但人们对基因调控机制知之甚少。驱动 SCLC 转化和 SCLC 亚型转换。单细胞 RNA 和 ATAC 测序（scRNA-seq、 snATAC-seq）在组合 LUAD/SCLC 组织学样本中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，我们在一组 de 中完成了 scRNA-seq。 novo SCLC（Chan 等人，bioRxiv，正在 Cancer Cell 进行审查）我们在初始队列中进行了 scRNA-seq。结合 LUAD/SCLC，发现转化的 SCLC 中瘤内亚型多样性显着增加（T- SCLC）。我们发现 T-SCLC 中存在 Notch 抑制，并随着随后的 SCLC 亚型多样化而重新激活。我们观察到在预转化的 LUAD 中与经典的 LUAD 中过表达 SOX2 和 ELF3，以及在转化中的 PHOX2B 和 ELF3 T-SCLC 与 de novo SCLC 我们追踪了 RB1 和 TP53 丢失情况下的关键转录因子（SOX2、 PHOX2B、ELF3)、表观遗传调节因子和 Notch 信号传导均有助于 NE 转化我们将在 LUAD/SCLC 组合样本中利用 scRNA-seq 和 snATAC-seq。组织学：1) 识别亚克隆群体的分子标记，2) 重建调控网络，3) 在临床前体外和体内模型中验证 NE 可塑性的转录组和表观遗传驱动因素，包括 EGFR+ LUAD 患者来源的异种移植物在奥希替尼治疗后经历 NE 转化。候选人：Joseph Chan 博士，医学博士、哲学博士是 MSKCC 的肿瘤内科研究员，他的目标是成为一名医学博士。独立的终身教授医师科学家研究转移和治疗中的谱系可塑性他的导师 Charles Rudin 和 Dana Pe’er 博士是肺癌和癌症领域的顶尖专家。陈博士分别提出了为期五年的指导培训来获得湿性。他的湿实验室培训将包括 1) 单细胞文库制备和 2) 用于功能验证的临床前模型的基因操作他的计算训练将包括 1) snATAC-seq 分析和 2) 先进的机器学习他的顾问委员会——Charles Sawyers 博士， Helena Yu、Ronan Chaligné 和 Christina Leslie 将指导他的训练和研究。环境：MSKCC 是一家以患者护理、创新研究和初级培训而闻名的癌症中心 MSKCC 拥有单细胞研究计划，致力于成为独立的医师科学家。这推动了单细胞测序的发展，这将支持这项研究和职业发展的提案。