Transcript Equinox Pharma Ltd - Imperial College London

CISBIC Sub-project 1:
Modeling genotype-phenotype
relations in Campylobacter
Stephen Muggleton, Brendan Wren, Victor Lesk
CISBIC, Imperial College London.
www.imperial.ac.uk/cisbic
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
C. iejuni NCTC11168
from gene sequence to glycostructure
Kelly J,
2006
Aim. Model variation in pathogen genome sequence of glycosylated surface
structures & understand how this variation affects immune response.
Glycostructure questions
How do we get from sequence
to full glycostructure?
How does glycan diversity
affect disease potential and
niche adaptation?
Basic sugars
UDP--D-GlcNAc
PseB Cj1293
PseC Cj1294
Use combination of traditional
and systems approaches
1)Mutagenesis
2)Natural strain variation
3)Pathway modelling
PglF Cj1120
PglE Cj1121
PseH Cj1313
PglD Cj1123
PseG Cj1312
PglC Cj1124
PseI Cj1317
PglA Cj1125
PseF Cj1311
PglH Cj1129
PseA Cj1316
PglJ Cj1127
PglI Cj1128
PglK Cj1130
C
L
O
PglB Cj1126
N
Phylogenomics pipeline
Phylogenetic analysis
Statistical
analysis
Analysis
Strain collection
gDNA
Evolution of virulence
& pathogenesis
Bayesian analysis
Binary data
GeneSpring
GACK analysis
Ratio
Values
Microarray
Quality Control
Gene Calling
Natural strain variation and phylogenomics
•A livestock and nonlivestock 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
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
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
Machine learning approach
Biochemical
Pathways
(KEGG,
Biocyc)
Glycan
Structures
(MAS-NMR)
Background
rules
Mutant data
(MAS-NMR)
Prolog
Database
Machine
learning
Hypotheses
Examples of hypotheses
C. jejuni glycan
synthesis pathway
Integrating multi-strain genetic data with
machine learning of gene functions
Genetic data for 75 serotyped
strains of C. jejuni
Working assumption for relating
gene function to co-presence
“If the product of Gene1
synthesises a sugar precursor
which is transformed by the
product of Gene2, then Gene1
tends to be present in strains
with the same serotype as
those expressing Gene2”.
Integrating multi-strain genetic data with
machine learning of gene functions
Knowledgebase
(KEGG, BioCyc)
Glycan mutant
observations
WT
Cj1432-
Cj1433-
Hypothesized transferaseencoding genes
?
Cj1432
Cj1434
Cj1438
Cj1440
Cj1442
Cj1432
Cj1434
Cj1438
Cj1440
Cj1442
?
Cj1432
Cj1434
Cj1438
Cj1440
Cj1442
?
Integrating multi-strain genetic data with
machine learning of gene functions
Knowledgebase
(KEGG, BioCyc)
Genetic data for
serotyped strains
Hypothesized transferaseencoding genes
?
Cj1438
Glycan mutant
observations
WT
Cj1432-
Cj1433-
Cj1442
?
Cj1432
Cj1434
?
Learning from strain data (work in progress)
Learning curves with and without strain data
Gene functions
identified by
learning (%)
Gene functions provided to learning (%)
Acknowledgements
PI‘s 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 TamaddoniNezhad