重构系统
•分子功能干预
转基因动物模型
•Knock-out •Knock-in
揭示分子机制
组份-结构-功能
5
In view of protein expression, what can cause the difference in color sensitivity?
Feb 26, 2015 Internet
13
定义：蛋白组与蛋白组学
蛋白质组（Proteome） • 在一个细胞、一个组织、一个个体内，由基因组编 码的所有全部的蛋白质组分。 蛋白质组学（Proteomics）: 研究蛋白质组的科学。 • 蛋白质的种类、数量（2维电泳 2DE, 液相层析 LC, 质谱分析 MS, 蛋白
质免疫共沉淀 IP & Western blotting , 核糖体轮廓分析 Ribosome Profiling）
• 生物信息学（Bioinformatics）
20
Annotation of Proteomics Strategy
*蛋白质组学的研究策略
1. 差减对比组设立 2. 蛋白质表达的轮廓分析
1. Differences between Samples Healthy vs disease Induced vs background Species vs species
Ritchie (2015) Nat Rev Genet •A systems genomics approaches to achieve a more thorough and informative interrogation of genotype-phenotype association, through building a multivariate model associated with given outcomes
Introduction to Proteome & Proteomics
• To study protein molecules, the principles of protein separation and quantification, and the identity analysis of protein characterization have to be developed. • Proteome indicates the entire of proteins completely expressed by a genome or a tissue or a cell type. (the entirety) • Proteomics is to study quantitative change in expression levels of protein, and their application to drug discovery, diagnostics and therapy. (the quantity ) • The right strategy through proteomics would be applied to quantitatively analyze the induced biological changes versus the inherent background expression of a variety of proteins in source samples to identify the difference in protein expression that may cause disease. (comparison via differential protein expression)
2. Overview on Protein ID & Abundance DIGE-or LC-MS Protein Microarray Database Search 3. Multiple Tests for Protein ID MS analysis PMF & P/r Determination of N-& C-terminal AA Molecule Weight, pI 4. Spatial & Temporal Protein Expression Time course of expression Location of expression Tissue- or Organ-specific expression Cell-specific expression 5. Protein Response & Coordination Signaling Pathway Metabolic Pathway 6. Protein Participating in Development Proliferation Differentiation Matter Metabolism
实用蛋白质组学 Proteomics in Practice
Dept of Biochemistry & Molecular Biology NJMU, NJ, CHN Spring 2015
WILEY-VCH Verlag GmbH & Co. KGaA (ISBN 978-527-31941-1)
Ritchie (2015) Nat Rev Genetic, Synder (2012) Cell
-Trait
Phenotypic Outcomes Generated Genetically & Epigenetically by Multi-Omes
Ritchie (2015) Nat Rev Genetic
Phenomenon
生物表象或疾病 Phenomenon or Disease
候选基因-作用方式，等 Candidate Gene-style, etc.
假说 （基因型-候选基因）
Hypothesis-Candidate Gene
求证
Test
给予 或 剥夺候选基因功能 Gain or Loss of Candidate Gene Function 候选基因功能体现/丧失系统的 组份-结构-功能 Component-Structure-Function 分子机制验证于新的生物系统 Mechanism validated in a new bio-system
6
数据主导的生物系统科研思维逻辑
多个组学数据 （Date of Multiomes）
DTTMV or DDTMV
表型组数据 （Date of Phenome）
生物表象或疾病
Trait or Disease
求证
Test
阐明机制
Mechanism
验证
Validation
Biological Systems Multiple-Omics from Multiomes to Phenome
Categorization of Multi-Staged Analysis of Phenotype
Ritchie (2015) Nat Rev Genet
Categorization of Meta-Dimensional Analysis
Ritchie (2015) Nat Rev Genet
3. 多重验证蛋白质ID
4. 蛋白质时-空表达差别分析
5. 蛋白质相互作用
6. 蛋白质细胞综合功能
21
*Technological Strategy (GE-LC-MS-Database) to Proteomics
Gapelo (2010) Proteomics
HPLC-MS
22
*蛋白质组学研究策略的方法程序
• 蛋白质与蛋白质、蛋白质与其它生物大分子的相互 作用（酵母双杂交Y2H, 荧光共振的能量传递FRET, 染色质免疫共沉淀ChIP）
• 蛋白质的生物学功能（pathway, circuitry）
研究策略（i）组级研究proteome-wide investigation(ii) 差减比较（subtractive comparison）
CYP mutant ↑ DNA repair XRCC↓ ↓ ↓ Estrogen → carcinogenic byproduct → DNA damage → cancer cells↑ ← dysregulation of cell cycle ↑ COMT mutant ↑
Complex-Trait Phenotypes Revealed by Multi-Omes
15
Annotation of Subtractive Comparison of Proteome 组级规模的蛋白质轮廓分析与差减比较
组级范围的蛋白质的差别：种类-数量
•主要差异蛋白-疾病关联 •主要差异蛋白形成原因-机制 •次要差异蛋白-疾病关联 •次要差异蛋白形成原因-机制
致病机制-疾病诊断-治疗方案-疾病预后
甲-样品：A-B-C-D-E 乙-样品： B-C-D-E-F-G 蛋白质 蛋白质
16
−)
甲乙两样品间 蛋白质的差别： A+b-c-d+e-F-G
In view of protein expression, what can cause the difference in color sensitivity?
14
组学研究的基本策略
• 组 级 的 轮 廓 研 究 （ Ome-wide Profiling ） Massive-High throughput-Parallel 大规模-高产 出-平行对照（全部、所有）。 • 差 别 - 差 减 比 对 （ differential-subtractive comparison）有比较就有鉴别；差别因子就是 差别表观的动因，动因是事物发生机制的线索 与事物演变的预设轨道（差别、差异）。