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

• 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
• 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
• 来源: https://reporter.nih.gov/project-details/10540383
• 关键词: ASCL1 gene; ATAC-seq; Ablation; Advisory Committees; Atlases; Automobile Driving; BETA2 protein; Cancer Center; Cancer Histology; Cancer Model; Cell Nucleus; Cells; Chemoresistance; Classification; Clinical; Collaborations; Computing Methodologies; Doctor of Philosophy; Drug Targeting; ELF3 gene; Environment; Epidermal Growth Factor Receptor; Epigenetic Process; Faculty; Funding; Genes; Genetic Transcription; Genomics; Goals; Histologic; Histology; Human; In Vitro; Knock-out; Lasers; Libraries; Lung; Lung Adenocarcinoma; Machine Learning; Malignant Neoplasms; Malignant neoplasm of lung; Medical Oncology; Memorial Sloan-Kettering Cancer Center; Mentors; Modeling; Molecular; Mus; Mutation; Neoplasm Metastasis; Neurosecretory Systems; Non-Small-Cell Lung Carcinoma; Oncogenic; Patient Care; Patients; Phenotype; Physicians; Play; Population; Pre-Clinical Model; Preparation; Process; RB1 gene; RNA; Recurrence; Regulator Genes; Relapse; Research; Research Proposals; Resistance; Resources; Risk; Role; Sampling; Scientist; Signal Transduction; TP53 gene; Therapeutic; Training; Validation; Variant; biomarker identification; cancer cell; cancer subtypes; cancer type; career; career development; cell transformation; cohort; epigenetic regulation; experience; experimental study; genetic manipulation; in vivo; in vivo Model; innovation; laboratory experience; molecular marker; notch protein; novel drug class; overexpression; patient derived xenograft model; pre-clinical; preclinical study; pressure; prevent; programs; research and development; single cell sequencing; single-cell RNA sequencing; skills; small cell lung carcinoma; targeted treatment; tenure track; therapeutic target; therapy resistant; transcription factor; transcriptomics; tumor; tumor heterogeneity; whole genome

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.

项目总结/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抗性相关。这种谱系可塑性往往导致 LUAD和SCLC在同一肿瘤中混合。我们证明了激光显微切割的LUAD和SCLC 肿瘤内组分共享躯干突变，证实NE转化。SCLC本身被归类为 经典型、变异型和非NE亚型。临床前研究表明，变异型和非NE亚型具有 增加转移和耐药性的风险。人们对基因调控机制知之甚少， 驱动SCLC转换和SCLC子类型切换。单细胞RNA和ATAC测序（scRNA-seq， snATAC-seq）提供了一个理想的平台来表征LUAD/SCLC组织学组合的样品中的 NE可塑性的瘤内异质性。作为对照参考，我们在一个队列中完成了scRNA-seq。 novo SCLC（Chan等人，bioRxiv，在Cancer Cell的综述中）。我们在最初的队列中进行了scRNA-seq， 联合LUAD/SCLC，发现转化的SCLC（T-SCLC）中肿瘤内亚型多样性显著增加。 SCLC）。我们在T-SCLC中发现了Notch抑制，并在随后的SCLC亚型多样化中重新激活。 我们观察到在转化前与经典LUAD中SOX 2和ELF 3过表达，在转化后与经典LUAD中PHOX 2B和ELF 3过表达。 T-SCLC与新发SCLC。我们假设在RB 1和TP 53缺失的情况下，关键转录因子（SOX 2， PHOX 2B、ELF 3）、表观遗传调节因子和Notch信号转导的调节都有助于NE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，以1）鉴定亚克隆群体的分子标记物，2）重建调控网络，以及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 在奥希替尼治疗后经历NE转化的EGFR+ LUAD患者来源的异种移植物。 候选人：Joseph Chan博士，医学博士，博士是MSKCC的医学肿瘤学研究员。他的目标是成为一名 独立的，终身的医生，科学家研究转移和治疗中的谱系可塑性 抵抗癌症他的导师Charles Rudin博士和Dana Pe'er博士是肺癌领域的顶尖专家， 单细胞测序。陈博士建议进行为期五年的辅导培训， 实验室和先进的计算技能。他的湿实验室培训将包括1）单细胞库制备和2） 临床前模型的遗传操作，用于功能验证。他的计算训练将包括1） snATAC-seq分析和2）高级机器学习。他的顾问委员会查尔斯·索耶博士， Helena Yu、罗南Chémé和Christina Leslie将指导他的培训和研究。 环境：MSKCC是一个癌症中心，以患者护理，创新研究和初级培训而闻名。 教师寻求职业作为独立的物理学家，科学家。MSKCC拥有单细胞研究计划 这将推动单细胞测序，这将支持这项研究和职业发展的建议。