Genomics of Host Defense Against Infectious Disease Humans are - - PowerPoint PPT Presentation

Genomics of Host Defense Against Infectious Disease

Humans are genetically diverse. Genes influence disease susceptibility, immune responses and responses to vaccines and therapy. Evidence for the heritability of human immune response variation Identification of genes responsible for immune response variation Prior to genome-wide association studies Use of genome-wide association studies Evolutionary biology of human host-pathogen interaction. Personalized medicine infectious disease (not discussed) Today’s Lecture:

Heritability of Human Immune Response Variation

Gregersen and Behrens (2006) Nat Rev Genetics 7: 917

Relative Risk of Autoimmune Diseases Among Siblings

Genetic Variability of Human Vaccine Response Identical Twin Study

Variations in Antibody Response Genetic Contribution to Variation

Identical Non-Identical

Tan, et al. (2001) Vaccine 19: 2434–2439

Do you think genetics plays a greater role in: > your risk of dying of cancer OR > your risk of dying of an infection?

What about Risk of Death by Infection?

Adoptee’s Relative Risk of Death by Same Cause as Biological Parent (Genetics) Adoptee’s Relative Risk of Death by Same Cause as Adoptive Parent (Environment) All Causes 1.71 Infections 5.81 Cardio- and Cerebrovascular 4.52 Cancer 1.19 All Causes ~1.0 Infections ~1.0 Cardio- and Cerebrovascular 3.02 Cancer 5.16

Strong Genetic Contribution to the Relative Risk of Death by Infection

Sørensen, et al. (1988) New Engl J Med 318:727

Identification of genes responsible for immune response variation

Manolio, et al. (2008) J Clin Invest 118: 1590

Genetic and Environmental Contributions to Monogenic and Complex Disorders

Major Genetic Determinant Minor Genetic Determinants Environmental Determinants

Mendelian and non-Mendelian diseases

• Geneticists have been very successful in discovering the

variations due to Mendelian disorders. These are characterized by in that they follow the Mendelian rules of inheritance.

• The study of particular families using linkage studies has been

successful for the Mendelian diseases.

• However, the more common complex (i.e. non-Mendelian)

disorders have been much more difficult to investigate, even when there are clear genetic components of the disease. Genes contributing to complex traits may be identified by association studies.

Simple Sequence Repeats (SSR): Stretches of 1-6 nucleotides repeated in tandem. Slippage of DNA polymerase generates variation in repeat number Microsatellite: Short tandem repeats that vary in number among individuals

Common Markers used in Molecular Genetics Common Markers used in Molecular Genetics

Single nucleotide polymorphism (SNP): Single base pair differences present in at least 1% of the population

Candidate Gene Trial and error Genome Wide Genotyping No prior assumptions Gene-Marker Relationship

Poland, et al. (2007) Clin Pharm Therap 82: 653

Interplay between Innate and Acquired Immune Responses to Measles

Examples of Genes Affecting Infectious Disease Susceptibility and Resistance

TLR Polymorphisms Genes Associated with HIV Susceptibility and Progression HLA and Viral Disease Susceptibility

LPS, Lipopolysaccharide LTA, Lipoteichoic Acid, LTA PG, Peptidoglycan, PG TLRs, Toll Like Receptors NLRs, Nucleotide Binding Oligomerization Like Receptors MyD88, Myeloid Differentiation Antigen 88, MyD88

Toll Like Receptor Signaling

Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542

Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542

Mutations Affecting Innate Immunity

TLR Polymorphisms and Disease

Misch and Hawn (2008) Clinical Science 114: 347-360

Genetic Influences on HIV Susceptibility and Progression

Telenti and U. M. Zanger Annu. Rev. Pharmacol. Toxicol. 2008. 48:227-256

HLA Associations with Viral Infections

Martin and Carrington (2005) Current Opinion in Immunology 17: 510516

A, B & C, Class I, Cytotoxic T cells D, Class II, Helper T cells

Mapping Genetic Traits By Genome-Wide Association

Requires:

• Large numbers of genetic markers to cover genome
• Methods to extensively genotype large numbers of people

Genetic Linkage and Association

Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542

How many SNPs?

Nickerson and Kruglyak, Nature Genetics, 2001

~ 10 million common SNPs (> 1- 5% MAF) - 1/300 bp

Common Genotyping Strategies

Bochud, P-Y., et al. (2007) Lancet Infect Dis 7: 531-542

Golden Gate Genotyping (Ilumina, Inc.) Golden Gate Genotyping (Ilumina, Inc.)

Allele-Specific Ligation…. Primer Hybridization to Amplified Genomic DNA Allows Amplification with One of Two Universal Fluorescent Primer Pairs Gene-Specific Tags Direct Hybridization To Gene-Specific Spots On Microarray Beads

International HapMap project

Feb 2001 - 1.42 million (1/1900 bp) Nov 2003 - 2.0 million (1/1500 bp) Feb 2004 - 3.3 million (1/900 bp) Mar 2005 - 5.0 million (validated - 1/600 bp)

• Provide a collection of millions of SNPs spanning the

genome, and serving as genetic markers.

• Study correlations in the inheritance of SNPs

(linkage disequilibrium, LD)

• Characterize haplotype blocks
• Provide a guide for whole genome association studies

Haplotypes and Tag SNPs

In theroy, 6 SNPs would distinguish 26 = 64 different haplotypes, if each is inherited independently of the others. However in this example, just 4 haplotypes comprise 90% of the observed chromosomes. This indicates the presence of linkage disequilibrium. The SNPs fall into 2 groups (SNPs 1, 2 & 3 and SNPs 4, 5 & 6) such that by knowing nucleotide of any one of the SNPs (known as a Tag SNP) one can predict the sequences of the other SNPs in the group. The use of Tag SNPs and linkage disequilibrium reduces the number of SNPs required for genome-wide association mapping studies.

Linkage equilibrium: Loci Aa and Bb are in equilibrium if their transmission probabilities πA and πB are independent Linkage disequilibrium: Loci linked in transmission, i.e. that are inherited together. πAB πA πB = r 2 = (πAB - πA πB ) πA πB πa πb

Linkage Disequilibrium Linkage Disequilibrium

Haplotype Blocks

Recombination Hotspots are Widespread and Account for LD Structure

Recombination Hot Spots SNPs

Ancestral DNA Non-ancestral DNA

Loss of Linkage (Linkage Disequilibrium) Around a Mutation

Low LD High LD

Distance kB R2

LD Usually does not Extend Beyond 100 kB

Genome-Wide Scan for Allele Frequency Differences Between 2 Control Groups

P values SNP allele frequencies Test Statistics

Wellcome Trust Case Control Consortium (2007) Nature 447: 661

Genome-Wide Scan for Allele Frequency Differences By Geographic Region

Wellcome Trust Case Control Consortium (2007) Nature 447: 661

Illustrates Stratification

Example of Chromosome Region with Strong Evidence of Geographic Association

Wellcome Trust Case Control Consortium (2007) Nature 447: 661

Geographic Bias may Still be Interesting

Genome-Wide Scan for Allele Frequency Differences Associated with Seven Diseases

Wellcome Trust Case Control Consortium (2007) Nature 447: 661

Examples of Chromosome Regions with Strong Evidence of Disease Association

Note effect of recombination on SNP association

Wellcome Trust Case Control Consortium (2007) Nature 447: 661

Genome Regions with Strongest Disease Associations

Odds Ratio

Wellcome Trust Case Control Consortium (2007) Nature 447: 661

GW Association: Admixure

Hafler and Dejager (2005) Nat Rev Immunol 5: 83

Genome-Wide SNP Associations with Gene Expression Variation

Genes frequently display variations in expression levels among individuals Much of the variation is linked to statistically significant associations with SNPs Most associated SNPs are linked to the differentially expressed gene itself (cis-effects) Modest differences in gene expression (20%) can be associated with individual SNP alleles. R2 values for single allele effects on gene expression range from 0.2 to 0.6. Variations in gene expression also results from sequence copy number variation as assessed by comparative genomic hybridization.

Stranger et al., (2005) Plos Genetics 1: e78 Stranger et al. (2007); Science 315: 848 . Cheung et al. (2005); Nature 437: 1365 .

SNP Mapping of Gene Expression Variation

Genome Annotation

Gene models Sequence elements ChIP on Chip (Histone Acetyl., etc)

Haplotype Block Expression

Evolutionary Genomics

Epidemic Disease in New World Following European Contact

Mortality from infectious disease (e.g. smallpox, measles, influenza, etc.) contributing to declines of 80-95% among indigenous peoples. The concept of innate susceptibility is controversial due to complex interplay among genetic, epidemiologic, and socio-environmental factors and difficulties estimating pre-contact population sizes. Academic jealousies, politics and turf wars add to the fun. Innate susceptibility implies rapid evolution between the time of common ancestry and renewed contact (10- 20,000 years).

Brazilian Shaman, 1578.

Noble David Cook. Born to Die. Cambridge University Press, 1998, page 119.

Recent Acceleration of Human Adaptive Evolution

High Linkage Disequilibrium Around Selected Alleles Age Distribution of Ascertained Selected Alleles

Wang E. T. et.al. PNAS 2006;103:135-140 Hawks J. et.al. PNAS 2007;104: 2053-2058

Lethal Response to 1918 Flu

Loo and Gale (2007) Nature 445: 267

In such cases, strong selection against immune responses