CISBIC Sub-project 1: Stephen Muggleton, Brendan Wren, Victor Lesk CISBIC, Imperial College London. Modeling genotype-phenotype relations in Campylobacter

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? 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 N O Basic sugars UDP-  -D-GlcNAc PglB Cj1126 C 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 Statistical analysis 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 Cj present Genes Cj 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 functions Genetic 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) Cj1432 Cj1434 Cj1438 Cj1440 Cj1442 Cj1432 Cj1434 Cj1438 Cj1440 Cj1442 Cj1432 Cj1434 Cj1438 Cj1440 Cj1442 ? ? ? WTCj1433-Cj1432- Glycan mutant observations Hypothesized transferase- encoding genes

Integrating multi-strain genetic data with machine learning of gene functions Knowledgebase (KEGG, BioCyc) Cj1438 Cj1442 Cj1432 Cj1434 ? ? ? WTCj1433-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