The evolution of gene expression impacting human disease

1. The evolution of gene expression impacting human disease Hunter Fraser

2. Evolution of pathogenicity • How does this transition occur?

3. Evolution of pathogenicity • How does this transition occur? • Huge implications for surveillance and control of both emerging and established pathogens

4. Evolution of pathogenicity • How does this transition occur? • Huge implications for surveillance and control of both emerging and established pathogens • Previously implicated mechanisms focus on gain of entire genes • Horizontal transfer • Gene duplication

5. Saccharomycescerevisiae Pros: • Amazing model organism • Gives us wine, beer, and bread

6. Saccharomycescerevisiae Pros: • Amazing model organism • Gives us wine, beer, and bread Cons: • Occasionally evolves pathogenicity

7. Sources of evolutionary adaptations

8. Sources of evolutionary adaptations Protein sequence evolution

9. Sources of evolutionary adaptations Protein sequence evolution Gene expression evolution

10. Two types of gene expression change • These can act in cisortrans x cis: e.g. promoter, enhancer

11. Two types of gene expression change • These can act in cisortrans trans: e.g. transcription factor x x x x x cis: e.g. promoter, enhancer

12. Two types of gene expression change • These can act in cisortrans trans: e.g. transcription factor x x x x x cis: e.g. promoter, enhancer

13. Examples of cis-regulatory adaptations Kingsley Lab Carroll Lab

14. Single gene/trait approach Transgenic lines Identify phenotype Signature of selection QTL mapping Test fitness effects Colosimo et al. 2005 Barrett & Hoekstra 2011

15. Single gene/trait approach Transgenic lines Identify phenotype • Only works for major-effect genes • Candidate genes must be known a priori Signature of selection QTL mapping Test fitness effects Colosimo et al. 2005 Barrett & Hoekstra 2011

16. Single gene/trait approach Yeast pathogenicity • Only works for major-effect genes • Candidate genes must be known a priori • May not involve any major-effect genes • No known candidate genes

17. Our approach: discovery of selection on gene sets If selection on a trait is ongoing, multiple mutations may push the expression of many genes in the same direction

18. Our approach: discovery of selection on gene sets If selection on a trait is ongoing, multiple mutations may push the expression of many genes in the same direction • Proteincomplex Metabolic pathway

19. Our approach: discovery of selection on gene sets

20. Our approach: discovery of selection on gene sets No selection Single trans mutation

21. Our approach: discovery of selection on gene sets No selection Single trans mutation Multiple cis mutations

22. Our approach: discovery of selection on gene sets Selection! Multiple reinforcingcis mutations Single trans mutation Multiple cis mutations

23. Our approach: discovery of selection on gene sets Same expression levels Multiple reinforcingcis mutations Single trans mutation Multiple cis mutations

24. Our approach: discovery of selection on gene sets • Step 1: Identify all genes with • cis-regulatory divergence • Step 2: Find gene sets with biased • directionality of cis effects

25. Step 1: cis-regulatory divergence • Allele-specific expression in hybrids can only be caused by cis-acting changes • Can be quantified by either RNA sequencing or allele-specific microarrays x

26. Step 1: cis-regulatory divergence • Allele-specific expression in hybrids can only be caused by cis-acting changes • Can be quantified by either RNA sequencing or allele-specific microarrays 3:3

27. Step 1: cis-regulatory divergence • Allele-specific expression in hybrids can only be caused by cis-acting changes • Can be quantified by either RNA sequencing or allele-specific microarrays x 3:3 5:1

28. S • Y Lab strain Pathogenic • Lab strain: “S” (S288c) • Pathogenic strain: “Y” (YJM789) • Genomes differ by >350 kb of sequence (~3%)

29. S • Y Lab strain Pathogenic

30. S • Y

31. S • Y x • Allele-specific expression = red:green ratio

32. S • Y x • Allele-specific expression = red:green ratio • Step 1: Identify all genes with • cis-regulatory divergence • Step 2: Find gene sets with biased • directionality of cis effects

33. S • Y x • Allele-specific expression = red:green ratio Allele-specific microarray RNA-seq • Step 1: Identify all genes with • cis-regulatory divergence • Step 2: Find gene sets with biased • directionality of cis effects

34. S • Y x • Allele-specific expression = red:green ratio Allele-specific microarray RNA-seq • Step 1: Identify all genes with • cis-regulatory divergence • Step 2: Find gene sets with biased • directionality of cis effects Gene ontology Protein complexes

35. Test for positive selection • Test ~300 gene sets for biased allelic expression • One protein complex significantly biased • All 10 subunits with bias had higher expression from lab strain alleles (p = 4.3x10-5) • Confirmed 8/10 by pyrosequencing • S • Y

36. 13/17 genes in complex involved in endocytosis

37. Complex is involved in endocytosis Toret and Drubin, 2007

38. Which lineage changed? - + or - + - + - + S (lab) Y (pathogenic) S (lab) Y (pathogenic)

39. Another test of positive selection • Beneficial mutations “sweep” through the population due to positive selection • Genetic variants nearby are also swept Strain 1 Strain 1 2 2 3 3 4 4 5 5

40. Which lineage changed? - + or - + - + - + lab pathogenic lab pathogenic

41. No sweep Recent sweep

42. No sweep Recent sweep

43. No sweep Recent sweep No sweep Recent sweep

44. Which lineage changed? • Sweeps occurred in Y lineage, so must have been down-regulating • First example of gene expression adaptation acting on a protein complex! - + - + - + - + S (lab) Y (pathogenic) S (lab) Y (pathogenic)

45. Can we increase pathogenicity by down-regulating these genes?

46. Can we increase pathogenicity by down-regulating these genes? • Roughly recreate down-regulation by deleting one copy of a gene from a diploid • Called “reciprocal hemizygous” (RH) strains • RH pair:

47. Fitness in vitro • No fitness advantage of down-regulation in the lab Fitter than wt Less fit than wt Reciprocal hemizygous strains

48. Fitness in vivo • Most relevant environment for evolution of pathogenicity is in vivo 24 RH strains + wt hybrid n = 25 barcoded strains x 3 for 5-day timepoint x 3 for 14-day timepoint

49. Fitness in vivo • Most relevant environment for evolution of pathogenicity is in vivo 24 RH strains + wt hybrid x 3 for 5-day timepoint x 3 for 14-day timepoint

50. Fitness in vivo • Most relevant environment for evolution of pathogenicity is in vivo • Change in abundance reflects relative fitness 24 RH strains + wt hybrid x 3 for 5-day timepoint x 3 for 14-day timepoint