UCSC Immunobrowser

Hyunsung John Kim10/16/2013

UCSC Immunobrowser

• Analyze status of Adaptive Immune System• Tracks T-cells based on sequence signature in

the T-Cell Receptor Beta• Targeted Next Generation Sequencing generates

billions of data points• Can we provide Repertoire-level analysis while

preserving Receptor-level detail• Search the literature for clues on T-cell function

Adaptive Immune System

• Specific– Receptors to bind exclusively to a pathogen

• Diverse– Receptors can be designed to almost any pathogen

• Memory– Predesigned receptors are reused for subsequent

infections• Self/non-self recognition– T-Cells/B-Cells do not attack healthy self cells

Specific and Diverse Receptors

• Each receptor has a unique genome sequence

Memory

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What do B-cells and T-cells do?

http://www.unm.edu/~mpachman/Blood/t_cell_killing_cancer_cell.jpg

http://www.hu.liu.se/ike/forskning/cellbiologi/rosen-anders/rosen/1.264183/Bcell200.jpg

B-cell Helper T cell (TH) Cytotoxic T-cell (TC)

• Mature in Bone Marrow• Binds directly to antigen• Secretes soluble

antibodies• Antibodies aggregate

antigens, mark them for phagocytosis or lysis via the complement system

• Mature in Thymus• CD4+• Binds to peptide-MHC

class II molecules present only on Antigen Presenting Cells (APCs)

• Activates B-cells• Regulates Immune

response

• Mature in Thymus• CD8+• Binds to peptide-MHC

class I molecules present on most nucleated cells

• Destroys infected cells

Sciencephoto.com

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Complementarity Determining Regions (CDR) determine binding specificity

Tertiary:

Secondary:

Primary:

Specific and Diverse Receptors

CDRs

Random Receptor Sequence generated through VDJ Recombination

• ~1015-1020 Distinct TCR sequences

• Diversity generated through:– Combinatorial

Joining (left)– Random

Nucleotide addition

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Clonal Expansion Shapes the Repertoire

http://163.16.28.248/bio/activelearner/43/ch43c3.html

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What is an Immune Repertoire?

• Set of all BCR and TCR sequences in an individual– 1011 B-cells and T-cells

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Immunosequencing Workflow

Data Analysis

Sequence Recombined Regions with HTS

Amplify Recombined Regions

Enrich cells for B/T lymphocytes

Blood Draw

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Assay

Modified from Warran, et al 2009

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High throughput sequencers

454 Titanium• Long reads

– ~600bp reads• Medium throughput

– 106 reads• Preferred for B-cells

Illumina HiSeq• Short reads

– 2x100bp Paired-end reads• High throughput

– 3 x 109 reads• Preferred for T-cells

Junctional Analysis

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VJ gene segment usage

Wang et al, 2010

Boyd et al, 2009

Robins et al, 2009

Weinstein et al, 2009

UCSC Immunobrowser

• Takes in annotated sequence data• Generates Repertoire-level visuals• Persistent filters view subsets of a repertoire• Track clonal expansions over multiple samples– Identify aberrant clonal expansions (Blood cancers)– Track clonal expansions (Immune response)

• Search literature• RESTful urls makes sharing easy• (Dev) http://laozi.soe.ucsc.edu:8000

The Future

• Motif Finding• Group vs group comparisons• The personal sequencer– Regular TCR/IG sequencing• Integration with Medbook-like service

– Detect reoccurence of disease or relapse of autoimmune disease

– Know if you’ve got the flu or a cold

Fin.

• Thanks to:– Max Haeussler– Ngan Nguyen– You, for your time

• Questions?