An Integrative Bioinformatics Approach to Study Single Cancer Cell Heterogeneity

描述：我的长期职业目标是成为翻译生物信息学的领先专家，创造、开发和应用计算和统计方法来揭示癌症的前景并确定治愈癌症的策略。人类癌症是高度异质性的。这种异质性是大多数抗癌药物最终失败的主要原因。然而，由于技术的限制，直到最近才在全基因组范围内、在单细胞水平上对细胞间的异质性进行了研究。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和比之前认为的更深刻的复杂性。然而，到目前为止，这些技术仅限于每个细胞一次检测。从同一肿瘤细胞中进行多种综合分析仍然是一个巨大的挑战，特别是来自小肿瘤活检的那些细胞。考虑到单细胞分辨率的随机性，重复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，启动了单个癌细胞测序分析项目，他也是我这项K01提案的共同导师。我的直接职业目标是利用红白血病K562细胞系，在单个癌细胞中鉴定全基因组的异质性。为此，我提出了一个研究项目，即综合生物信息学方法，以分析从同一单个白血病细胞产生的多种类型的基因组数据，这是一个及时而关键的主题。具体地说，我有兴趣研究以下具体目标：(1)建立生物信息学管道来研究单细胞RNA-Seq的异质性；(2)建立生物信息学管道来研究单细胞CpG甲基组；(3)建立生物信息学管道来研究单细胞Exome-Seq；以及(4)整合从相同单细胞产生的RNA-Seq、甲基组和Exome-Seq数据。这些单细胞基因组数据是由Sherman Weissman博士的实验室提供的，来自30个单一的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、甲基组和Exome-Seq生物信息学管道，然后开发和验证一个集成平台来分析这些多种类型的高通量数据。为了完成研究项目，并成功地从初级教师转变为该领域的专家，我和我的导师委员会制定了一份职业计划，该委员会由与大数据科学相关的不同领域的四位世界级专家组成：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和遗传学的共同导师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，以及夏威夷大学马诺阿大学信息和计算机科学系的大数据可视化的联合导师Jason Leigh博士。在这个奖项期间，我将主要与我的四位共同导师一起规划我的职业发展。

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.