ぱらぱらめくる『high_dimensional_immune_analysis』

• 記事の目次・リストはこちら
• New dimensions in immunology
  • heterogeneity and randomnessとを捉えることが免疫系の理解
  • heterogeneity and randomnessを扱うための実験技術・データ解析技術の登場・進歩
  • 個別細胞解析を許す諸技術(Deep seqence、然り)
  • heterogeneity and randomnessとは、たとえば
    • 体差・個人内差(interindividual and intraindividual diversity)
    • 実験動物とは異なる遺伝的多様性と環境多様性
    • 確率的決定機構であること
• Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium
  • NIH系のHuman Immunology Project Consortium (HIPC) が立ち上がり、以下を目標に
    • Development and implementation of standards for data collection, integration and data exchange
    • Development of state-of-the-art algorithms and tools for the modeling and integration of heterogeneous immunological data
    • Development and implementation of a central database and analysis engine providing easy access to all data generated through HIPC.
  • NIAID Immunology Database and Analysis Portal (ImmPort) systemは既存の免疫系データレポジトリ
  • データ解析手法の方は：
    • Modeling bead-level data for advanced Luminex data analysis
    • Deconvoluting high-bandwidth data to parse out cell-specific effects
    • Creating an immune signatures collection for gene set enrichment analysis ([(ttp://www.broadinstitute.org/gsea/msigdb/collections.jsp#C7:title=リンク]
    • Network modeling of vaccine responses
    • Designing more advanced human leukocyte antigen typing methods13, 14
    • Developing ultrasensitive physical detection technologies to identify T-cell epitopes15.
  • ちなみにImmune Spaceという免疫系データ解析サイトがあり、R,Bioconductor,knitrを使っているそうです。
• Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology
  • discovery-driven quantitative proteomics
  • 何をターゲットにするかでいくつか分類
    • Total proteomes: dynamic composition of total proteomes including protein synthesis and degradation
    • Subcellular proteomes: dynamics of proteomes of organelles and subcellular structures, intracellular trafficking or protein secretion
    • Protein-protein interaction: association of proteins (such as receptors) with protein ligands, co-receptors or adaptor proteins and their assembly into macromolecular 'machines'. Protein-nucleic acid interaction: interaction of proteins with DNA or RNA in a sequence-dependent and context-dependent manner.
    • Post-translational modifications: dynamics of covalent protein modifications such as phosphorylation (P), ubiquitylation (U), acetylation, glycosylation and others.
  • Shotgun proteomicsの４ステップ
    • In step 1, proteins are extracted from tissues, body fluids, cells or subcellular compartments.
    • In step 2, proteins are proteolytically digested.
    • In step 3, peptides are separated by UHPLC.
    • In step 4, peptides are ionized by electrospray (electrospray ionization, ESI), and their masses and fragment masses are acquired in a mass spectrometer.
  • Quantitationについて
  • データ解析(FDR)
    • Identification of peptides: Peptide and fragment masses are searched in an organism-specific sequence database and then scored. Identifications are evaluated with a target-decoy–based FDR threshold.
    • tides are mapped to proteins in an FDR-controlled approach
    • Presentation and integration of data
• Unifying immunology with informatics and multiscale biology
  • 免疫関係でゲノム・エピゲノム・・・Cytome(フローサイトメータ)…フェノームを縦串する
  • 機能と実体とネットワークとの知的マイニング
  • 色々なデータベースをつなぎましょう→ウェブリソース
• Single-cell technologies for monitoring immune systems
  • １細胞解析で免疫系を理解する
  • PFC : highly multiplexed polychromatic flow cytometry
    • multiplexed depth for flow cytometry
    • up to 20 distinct channels of data for a given cell and can routinely process millions of cells per sample in a few minutes
  • Mass cytometry
    • mass spectrometry with single-cell fluidics
  • Imaging flow cytometry
    • The combination of fluorescence flow cytometry with microscopy imaging
  • その他の１細胞解析技術(Microtools)
    • microfluidic systems and simple spatial arrays of nanoliter-scale wells
      • １細胞発現など
      • １細胞⇔１細胞コミュニケーションも俎上に
    • １細胞RNAseq
• The promise and challenge of high-throughput sequencing of the antibody repertoire
  • １細胞シークエンスにより、リンパ球のゲノム配列変化が調べられるようになっている
  • 実験エラーと真の体細胞組換えのバリエーションの区別はまだ課題
• Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells
  • １個のＴ細胞のフェノタイプ評価、その時間変化
  • 利用技術は１題前の、「１細胞解析技術」で