Post on 19-Dec-2015
CISBIC Sub-project 1:
Stephen Muggleton, Brendan Wren, Victor LeskCISBIC, Imperial College London.www.imperial.ac.uk/cisbic
Modeling genotype-Modeling genotype-phenotype relations in phenotype relations in CampylobacterCampylobacter
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 NCTC11168from 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?
Use combination of traditional and systems approaches
1)Mutagenesis
2)Natural strain variation
3)Pathway modelling
PglF Cj1120
PglE Cj1121
PglD Cj1123
PglC Cj1124
PglA Cj1125
PglH Cj1129
PglJ Cj1127
PglI Cj1128
PglK Cj1130
NO
Basic sugars
UDP--D-GlcNAc
PglB Cj1126C L
PseB Cj1293
PseC Cj1294
PseH Cj1313
PseG Cj1312
PseI Cj1317
PseF Cj1311
PseA Cj1316
Strain collection
gDNA
Microarray
Quality Control
GeneSpring GACK analysis
Gene Calling
Bayesian analysis
Phylogenetic analysis
Statisticalanalysis Analysis
Values Ratio
Binary data
Evolution of virulence & pathogenesis
Phylogenomics pipeline
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
Identification of sub-clade/niche specific genes
Identified glyco-specific genes for 1) Flagellin glyco (O)2) Capsule (C)E.g. Phosphoramidate
Genes Cj1321-6 present
Genes Cj1321-6 absent
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)
Mutant data(MAS-NMR)
Glycan Structures(MAS-NMR)
Prolog Database
Machine learning
Background rules
Hypotheses
Examples of hypotheses
C. jejuni glycan synthesis pathway
Integrating multi-strain genetic data with machine learning of gene
functionsGenetic data for 75 serotyped
strains of C. jejuni
“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”.
Working assumption for relating gene function to co-presence
Integrating multi-strain genetic data with machine learning of gene
functions
Knowledgebase(KEGG, BioCyc)
Cj1432Cj1434Cj1438Cj1440Cj1442
Cj1432Cj1434Cj1438Cj1440Cj1442
Cj1432Cj1434Cj1438Cj1440Cj1442?
??
WT Cj1433-Cj1432-
Glycan mutant observations
Hypothesized transferase-encoding genes
Integrating multi-strain genetic data with machine learning of gene
functions
Knowledgebase(KEGG, BioCyc)
Cj1438
Cj1442 Cj1432Cj1434?
??
WT Cj1433-Cj1432-
Glycan mutant observations
Hypothesized transferase-encoding genes
Genetic data for serotyped strains
Learning from strain data (work in progress)
Learning curves with and without strain data
Gene functions provided to learning (%)
Gene functions identified by 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 Tamaddoni-Nezhad