An Integrative Bioinformatics Approach to Study Single Cancer Cell Heterogeneity

描述：我的长期职业目标是成为转化生物信息学领域的领先专家，他创建、开发和应用计算和统计方法来揭示癌症的概况并确定治疗癌症的策略。人类癌症具有高度异质性。这种异质性是大多数癌症药物最终失败的主要原因。然而，由于技术的限制，直到最近才在单细胞水平上对细胞间异质性进行全基因组研究。单细胞转录组测序 (RNA-Seq) 和外显子组等新技术揭示了新的见解，其复杂性比之前想象的更加深刻。然而，到目前为止，这些技术仅限于每个细胞进行一次测定。对同一单个肿瘤细胞（特别是来自小肿瘤活检的细胞）进行多次综合检测仍然是一个巨大的挑战。考虑到单细胞分辨率的随机性，重现性和灵敏度是一项艰巨的任务。为了克服这一挑战，我与耶鲁大学的 Sherman Weissman 博士合作启动了单癌细胞测序分析项目，他也是我这项 K01 提案的共同导师。我近期的职业目标是使用红白血病 K562 细胞系识别单个癌细胞之间的全基因组异质性。为此，我提出了一个关于综合生物信息学方法的研究项目，用于分析从相同的单个白血病细胞生成的多种类型的基因组数据，这是一个及时而关键的主题。具体来说，我有兴趣研究以下具体目标：（1）构建生物信息学管道来研究单细胞RNA-Seq的异质性，（2）构建生物信息学管道来研究单细胞的CpG甲基化组，（3）构建生物信息学管道来研究单细胞外显子组测序，以及（4）整合从相同单细胞生成的RNA-Seq、甲基化组和外显子组Seq数据。这些单细胞基因组数据由 Sherman Weissman 博士的实验室提供，来自 30 个单个 K562 红白血病细胞。我将首先并行构建和验证针对单细胞分析优化的 RNA-Seq、甲基化组和外显子组-Seq 生物信息学流程，然后开发和验证一个综合平台来分析这些多种类型的高通量数据。为了完成这个研究项目，并成功地从一名初级教师转变为该领域的专家，我与我的导师委员会制定了职业计划，该导师委员会由四位与大数据科学相关的不同领域的世界级专家组成：达特茅斯学院生物信息学的主要导师 Jason Moore 博士、耶鲁大学单细胞基因组学和遗传学的联合导师 Sherman Weissman 博士、夏威夷大学癌症中心癌症流行病学的联合导师 Herbert Yu 博士和夏威夷大学马诺阿分校信息与计算机科学系大数据可视化联合导师 Jason Leigh 博士。我将主要与我的四位共同导师一起规划我在获奖期间的职业发展。

DESCRIPTION: My long term career goal is to become a leading expert in translational bioinformatics who creates, develops and applies computational and statistical methods to reveal landscapes of cancers and to identify strategies to cure cancers. Human cancers are highly heterogeneous. Such heterogeneity is the major source of the ultimate failure of most cancer agents. However, due to the limit of technologies, the intercellular heterogeneity has not been investigated genome wide, at single-cell level until recently. New technologies such as single-cell transcriptome sequencing (RNA-Seq) and exome have revealed new insights and more profound complexity than was previously thought. However, so far these technologies are limited to one assay per cell. It remains a grand challenge to perform multiple, integrative assays from the same single tumor cell, in particular, from those derived from small tumor biopsies. Given the stochasticity at the single cell resolution, reproducibility and sensitivity ar daunting tasks. To overcome this challenge, I have started the single cancer cell sequencing analysis project, in collaboration with Dr. Sherman Weissman at Yale University, who is also my co-mentor of this K01 proposal. My immediate career goal is to identify genome-wide heterogeneity among single cancer cells, using the erythroleukemia K562 cell line. Towards this, I am proposing a research project on an integrative bioinformatics approach to analyze multiple types of genomics data generated from the same single leukemia cells, a timely and critical topic. Specifically, I am interested in studying the following specific aims: (1) buildinga bioinformatics pipeline to study heterogeneity of single-cell RNA-Seq, (2) building a bioinformatics pipeline to study CpG methylome of single cells, (3) building a bioinformatics pipeline to study single-cell Exome-Seq, and (4) integrate the RNA-Seq, methylome and Exome-Seq data generated from the same single cells. These single cells genomic data are provided by Dr. Sherman Weissman's lab from 30 single K562 erythroleukemia cells. I will first construct and validate in parallel, the RNA-Seq, methylome, and Exome-Seq bioinformatics pipelines optimized for single-cell analysis, and then develop and validate an integrative platform to analyze these multiple types of high-throughput data. To accomplish the research project, and to successfully transit from a junior faculty to an expert of the field, I have developed a career plan with my mentoring committee composed of four world-class experts in different fields relevant to Big Data Science: Primary Mentor Dr. Jason Moore in Bioinformatics from Dartmouth College, Co-mentor Dr. Sherman Weissman in Single-cell Genomics and Genetics from Yale University, Co-mentor Dr. Herbert Yu in Cancer Epidemiology from University of Hawaii Cancer Center and Co-mentor Dr. Jason Leigh in Big Data Visualization from the Information and Computer Science Department of University of Hawaii Manoa. I will primarily work with my four co-mentors for planning the development of my career during this award.