Equinox Pharma Ltd

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CISBIC Sub-project 1
Modeling genotype-phenotype relations in
Campylobacter
Stephen Muggleton, Brendan Wren, Victor
LeskCISBIC, Imperial College London.www.imperial
.ac.uk/cisbic
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Campylobacter jejuni Unanswered questions

• Are all strains equally pathogenic to humans?
• ? Do strains from different sources share common
  features?
• ? Why is C. jejuni a commensal in avians, but
  highly infectious in humans?
• How does C. jejuni in some cases perturb the
  immune system to cause neurological sequelae?
• Answers are likely to lie in glyco-surface
  structures

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C. iejuni NCTC11168from gene sequence to
glycostructure
Aim. Model variation in pathogen genome sequence
of glycosylated surface structures understand
how this variation affects immune response.
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Glycostructure questions

• How do we get from sequence to full
  glycostructure?
• How does glycan diversity affect disease
  potential and niche adaptation?
• Use combination of traditional and systems
  approaches
• Mutagenesis
• Natural strain variation
• Pathway modelling

Basic sugars
UDP-?-D-GlcNAc
PglF Cj1120
PseB Cj1293
PglE Cj1121
PseC Cj1294
PglD Cj1123
PseH Cj1313
PglC Cj1124
PseG Cj1312
PglA Cj1125
PseI Cj1317
PglH Cj1129
PseF Cj1311
PseA Cj1316
PglJ Cj1127
PglI Cj1128
PglK Cj1130
C
L
O
N
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Phylogenomics pipeline
Phylogenetic analysis
Statistical analysis Analysis
Strain collection
gDNA
Evolution of virulence pathogenesis
Bayesian analysis
Binary data
GeneSpring
GACK analysis
Ratio
Values
Microarray
Gene Calling
Quality Control
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Natural strain variation and phylogenomics

• A livestock and non-livestock clade, but most
  clinical isolates fall in the non-livestock clade
• Unknown source of C. jejuni infection
• 10 further sub-clades
• Water/wildlife sub-clade

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Identification of sub-clade/niche specific genes
Genes Cj1321-6 present
Genes Cj1321-6 absent
Identified glyco-specific genes for 1) Flagellin
glyco (O) 2) Capsule (C) E.g. Phosphoramidate
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Importance of Capsule
Side branch sugars more widely conserved than
core sugars? Phosphoramidate present in
86 of strains (232/270)? Link to subproject
3 ? Capsule prevents excessive cytokine
production by dendritic cells ? Presence of
phosphoramidate appears to reduce cytokine
production
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Machine learning approach
Biochemical Pathways (KEGG, Biocyc)
Mutant data (MAS-NMR)
Glycan Structures (MAS-NMR)
Prolog Database
Hypotheses
Background rules
Machine learning
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Examples of hypotheses
C. jejuni glycan synthesis pathway
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Integrating multi-strain genetic data with
machine learning of gene functions
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Integrating multi-strain genetic data with
machine learning of gene functions
Knowledgebase (KEGG, BioCyc)
Hypothesized transferase-encoding genes
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Integrating multi-strain genetic data with
machine learning of gene functions
Knowledgebase (KEGG, BioCyc)
Genetic data for serotyped strains
Hypothesized transferase-encoding genes
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Learning from strain data (work in progress)
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Acknowledgements
PIs and senior staff Anne Dell, Stephen
Muggleton, Jeremy Nicholson, Chris Rawlings,
Mike Sternberg, Brendan Wren Postdocs Richard
Barton, Paul Hitchen, Emily Kay, Victor Lesk,
Alireza Tamaddoni- Nezhad