Immunogenetic Disease Associations

M. Sue Leffell, PhD Professor of Medicine Director, JHU Immunogenetics Immunogenetic Disease Associations HLA: Auto-immune Disorders HLA: Infectious Diseases HLA: Adverse Drug Reactions KIR: Auto-immunity, Infect. Dis, CA Other MHC and immune function genes 1

Basis for HLA Disease Associations Linkage disequilibrium Monogenic disorders closely linked to MHC; disease allele associated with 1 or a few HLA alleles Molecular mimicry Cross reactions with viruses or bacteria evoke autoimmune response MHC Function Primary involvement of MHC molecules in disease pathogenesis Interaction with other predisposing genes Multi-genic process confers susceptibility Associations Due to Linked Genes Congentital Adrenal Hyperplasia Caused by deficiency of 21-hydroxylase CYP212A2 encodes 21-hydroxylase Presence of pseudogene, CYP21AP, can result in conversion of CYP212A2 with deleterious sequence Associated with B8, B47, B14, B21 Idiopathic Hemochromatosis HFE, class I like gene, telomeric to HLA-A HFE= human hemachromatosis protein (High Fe) Associated with HLA-A locus alleles, particularly A3 2

Molecular Mimicry Due to shared sequences between MHC and/or disease susceptibility peptides and certain viruses TCR plasticity permits binding of multiple peptides activation of T cells to crossreactive, self-antigens Viruses Implicated by Molecular Mimicry Virus Autoimmune Disease RNA Viruses Coxsackievirus Type 1 Diabetes Rubella virus Type 1 Diabetes HTLV-1 a HTLV-associated myelopathy DNA Viruses EBV (HHV-4) b Multiple Sclerosis Rheumatoid Arthritis SLE a HTLV= human T cell leukemia virus type 1 b HHV = human herpes virus Adapted from: Munz C. Nat Rev Immunol. 2009;9:246 3

Viruses Triggers for Auto-immunity? Possible mechanisms: 1. Molecular Mimicry 2. Adjuvant effect Viral infections activate TLRs proinflammatory response bystander auto-reactive damage A. Molecular mimicry activates auto-reactive T cells B. Adjuvant Effect a) TLR activation tissue damage b) Bystander activation; may also occur via super-ags c) Tissue damage exposes self Ags d) Epitope spreading auto-reactivity Munz C. Nat Rev Immunol. 2009;9:246 4

Emerging Concept of HLA Disease Associations - For certain HLA associated disorders, pathogenesis appears to involve: Aberrant antigen processing and/or posttranslational modification of peptides Altered peptides binding with high affinity to associated HLA alleles Amplification of auto-aggressive immune response through products of other immune genes, e.g., cytokines Examples: ankylosing spondylitits, rheumatoid arthritis, celiac disease Understanding of the Contribution of HLA Associations Early studies, based on HLA serology identified many significant HLA disease associations, most being autoimmune disorders Binding of potential disease provoking peptides elucidated by crystalline structure analyses of MHC and TCR More recent genetic technologies have identified many more non-hla loci Microarray transcriptional analyses Genome-wide association studies (GWAS) 5

HLA Serotype Associations with Autoimmune Disease Disease HLA Ag RR &:% Ankylosing spondylitis B27 87.4 0.3 Acute anterior uveitits B27 10.0 <0.5 Goodpasture s syndrome DR2 15.9 ~1 Multiple sclerosis DR2 4.8 10 Graves disease DR3 3.7 4-5 S. lupus erythematosus DR3 5.8 10-20 Myasthenia gravis DR3 2.5 ~1 IDDM DR3,4 3.2 ~1 Rheumatoid arthritis DR4 4.2 3 Pemphigus vulgaris DR4 14.4 ~1 Hashimoto s thyroiditis DR5 3.2 4-5 HLA & Autoimmunity Lessons Learned from Type 1 Diabetes Approx. 5% of people suffer from 1of >80 autoimmune disorders Type 1 Diabetes Mellitus (T1DM) is one of the most common HLA association 1 st noted with HLA-B8; later DR3, DR4 strongest with highest risk haplotypes: DRB1*03-DQA1*05:01-DQB1*02:01 DRB1*04:01-DQA1*03:01-DQB1*03:02 6

Pathogenesis of T1DM Multi-step process destruction of insulin producing β cells in pancreatic islets Viral infection/ damage to pancreatic β cells activation of innate inflammatory response APC phagocytose/process β cell proteins MHC cl II presentation to Th1 cells Activation of CD8+CTL target β cells Activation of B cells Auto-Abs Auto-antigens: Proinsulin, glutamic acid decarboxylase (GAD 65), islet-specific glucose-6- phosphatase related protein (ICRP) Mechanisms in Induction or Prevention of T1D Lehuen A, et al. Nat Rev Immunol. 2010; 10:501 7

T1D Genetic Susceptibility HLA contributes 50% of genetic basis, but multiple, other genes are involved. Genetic susceptibility is evident: Incidence: Gen Population 0.4% Sibling risk 6.05 Twin Concordance: MZ 27%, DZ 3.8% HLA haplotypes: 90-95% have 1 or both of high risk HLA haplotypes <0.1% have protective haplotype: DR*15:01-DQA1*01:02-DQB1*06:02 Susceptibility to Auto-Immunity DQ$ Alleles:T1DM Susceptibility associated with residue 57 in DQ$ (human) and I-A g7 $ (NOD mice). Susceptibility with Val, Ser, Ala. Resistance with Asp. $57 Asp forms salt bridge with "79 Arg, stabilizes peptide groove. Altered class II groove permits binding of peptides associated with T1D 8

Asp 57: Salt bridge with 76 Effects of DR/DQ on T1DM Susceptibility Effect DRB1 DQB1 DQBp57 04:05 02:01 Ala Susceptible 04:02 03:02 Ala 04:01 06:04 Val 03:01 05:02 Ser 07 03:03 Asp Protective 11 03:01 Asp 04:03 06:02 Asp 04:06 06:02 Asp 9

Peptide Binding: I-A g7 $, DQ2, DQ8 Peptide motif includes GAD 65 peptide (253-265). Key residue at P9 negatively charged. Crystal structure of I-A g7 $ chain revealed positively charged pocket at P9 ( Corper, et al., 99) Crystal structure of HLA-DQ8:insulin peptide also revealed + P9 pocket (Lee, et al., 01) Resistant alleles have negative or neutrally charged pockets. A) Insulin peptide in cleft of DQB1*0302 (Lee, et al., 01) B) P9 pocket of I-Ag 7 showing + charge (Corper, et al., 99) C) P9 pocket of I-Ad showing charge 10

DQB1*06:02 and Narcolepsy DQA1*01:02-DQB1*06:02 confers strong susceptibility to narcolepsy. 90-100% of patients have DQB1*06:02 allele DQB1*06:01, which differs by 9 residues, is protective. Difference is in P4 pocket of binding cleft Defective hypocretin neurotransmission narcolepsy Proposed mechanism is DQB1*06:02 restricted auto-immune attack on hypocretin secreting neurons In addition to HLA, there are multiple factors and genetic loci that may confer disease susceptibility - 11

Application of Proteomics Microarray transcriptional profiling is a powerful tool for: Investigation causes and mechanisms of diseases Diagnosis Assess disease activity Response to treatment SLE Signature. Hierarchical clustering of gene expression in blood leukocytes from healthy children, SLE patients, and juvenile arthritis patients HLA-B27 and Ankylosing Spondylitis HLA- B27 contributes 25% of the genetic risk for AS. Additional risk conferred by 14 other loci identified so far by GWAS. Hypotheses: Presentation of arthritogenic peptide Mis-folding of B27 heavy chains with accumulation in ER 12

Reveille JD. Nat Rev Rheumatol. 2012; 8: 296-304 HLA-B27 Mis-folding and AS B27 molecules have a unique Cys67 residue in the α1 domain of the heavy chain Self-association homodimerization or mis-folding retention in the ER Proinflammatory unfolded protein response could then result 13

Aberrant Antigen Processing in AS ERAP1 a also confers risk for AS ERAP1 acts as molecular ruler for trimming peptides to optimal class I length of 9 residues ERAP1 loss of function alleles only confer increased risk when present in association with HLA-B27 Expression of ERAP1 is higher in dendritic cells of patients with AS a endoplasmic reticulum aminopeptidase 1 Similar Genetic Facors Involved in AS, Psoriasis, PsA, IBD AS, psoriasis and IBD often coexist in the same patients and their families Majority of disease susceptibility is from MHC region For psoriasis and PsA, most of remaining susceptibility from cytokine genes For IBD, genes regulating autophagy and IL-17, IL-23 pathways confer susceptibility PsA = psoriatic arthritis IBD = inflammatory bowel disease 14

Innate immunity, antigen presentation and the T H 17 pathway are all implicated in conferring susceptibility to AS, psoriasis/psa and IBD Reveille JD. Nat Rev Rheumatol. 2012; 8: 296-304 Reveille JD. Nat Rev Rheumatol. 2012; 8: 296-304 15

Genetics of Rheumatoid Arthritis RA is chronic, world-wide disorder affecting 0.5-1% of population Clinical subsets of anti-citrullinated protein (ACPA) Ab + and Ab- patients Certain HLA alleles account for 30-50% of genetic susceptibility Rheumatoid arthritis - Shared Epitope Associated with HLA- DRB1*0401, 0404, 0405, 0408 alleles. Shared sequence, QKRAA, in 3 rd hypervariable region. Same sequence found in DRB1*0101 among Ashkenazi Jews with RA. Sequence shared with EBV capsid protein and E. coli J40 HSP. 16

DRB1*04:01 DRB1*04:04 DRB1*04:08 DRB1*04:05 70 71* 72 73 74 Q K R A A Q R R A A Q R R A A Disease Association: Yes Yes Yes DRB1*04:02 DRB1*04:03 DRB1*04:07 DRB1*01:01 D E R A A Q R R A E Q R R A A No No Yes EBV, E.coli E Q R R A A _ * 71 = K or R Proposed Pathogenesis of RA PAD14 (peptidyl arginine deaminase) is 2 nd genetic risk factor for RA PAD14 converts arg citrulline SE-DR alleles bind arthritogenic, citrullinated peptides Other immune genes that contribute to genetic risk: CTLA3 TRAF STAT4 CD40 17

Location of Shared Epitope DRβ1 chain, p70-74 P4 pocket has + charge Peptides with + arg at P4 don t bind Peptides with - charged citrulline are bound avidly Bax M, et al. Immunogenetics.2011:63:459 Celiac Disease: Model for Auto-immunity Celiac disease is T cell-mediated enteropathy with strong HLA association DQA1*05, DQB1*02 (encoded cis or trans) DQB1*03:02 (DQ8) Immune response is directed against deaminated cereal gluten peptides modified by transgluaminase 2 Auto-abs to transglutaminase 2 have high disease specificity and sensitivity 18

Pathogenesis of Celiac Disease Post-translational modification (PTM) of gluten peptides mechanism to break T cell tolerance auto-aggressive response PTM gluten peptides bind more avidly to associated HLA alleles Glutamate is anchor residue at P4,P6, P7 for DQB1*02 Glutamate is anchor residue at P1 and P9 for DQB1*03:02 PTM of Peptides leads to Aberrant Antigen Presentation Sollid LM, Jabri B. Cur Opin Immunol. 2011;23:732 19

HLA Associations Infectious Diseases Possible Mechanisms: Disease susceptibility or resistance thru Ag presentation Interaction with KIR NK function Immune pressure for escape variants (see Vaccine handouts) HLA/KIR Impact on HIV infection illustrates all of the above - HLA class I locus is primary genetic factor affecting HIV infection outcomes- Carrington M, Walker BD. Ann Rev Med. 2012;63:131 GWAS data from 974 HIV controllers and 2,648 progressors. Manhattan plot compares SNPS in the two groups. 313 SNPs were statistically significant all of which were within the MHC. 20

Protection: HLA and HIV-AIDS SNP in HCP5 gene in very strong LD with HLA-B*57:01 (Caucasians) 2 SNPs 35 kb upstream from HLA-C (-35C/T) Intronic variant in LD with B*57:03 (African Americans) Susceptibility: B*35;Cw*04 No consistent nor strong association: HLA class II or HLA-A SNP= single nucleotide polymorphism LD= linkage dysequilibrium Bashirova AA, Thomas R, Carrington M. Ann Rev Immunol.2011;29:295 HLA-C and HIV-AIDS Factors implicating HLA-C molecules in HIV control: HLA-C is not down-regulated by HIV-Nef HLA-C alleles regulate NK function -35 C/T SNP - 2 nd most significant factor in HIV control -35 C/T genotype affects HLA-C surface expression and impacts viral load CC high expression and lowest viral load TT low expression and highest viral load 21

Bashira AA, et al. Ann Rev Immunol. 2011; 29:295 High expression C alleles are in LD with -35 CC protective variant, while low expression C alleles are in LD with -35TT susceptibility variant Possible Mechanisms: C expression effective CTL response C expression promotes effective NK education during maturation and ultimately, stronger anti-viral response KIR 3DL1/3DS1 and HLA-Bw4 Synergy Bashira AA, et al. Ann Rev Immunol. 2011; 29:295 Combination of KIR 3DS1 (NK activating receptor) and HLA-Bw4 alleles with isoleucine at P80: Slower AIDS progression Reduced viral load 22

HLA cl I associations - HIV Infection Outcomes Genotype Effect Possible Mechanisms Heterozygote/rare HLA cl I allele advantage Protection Broader CTL response; viral escape from common alleles B*57 Protection Restriction for multiple conserved Gag epitopes; reduced viral fitness escape mutants; interaction with KIR3DL1/3DS1 B*27 Protection Restriction for conserved Gag epitope; interaction with KIR3DL1 B35*-Px Susceptibility Peptide specificity; ILT4 mediated DC dysfunction -35CC; HLA-C Protection CTL or NK function due to high surface level expression of linked HLA-C molecules KIR3DS1+Bw4 80I Protection NK cytotoxicity via binding to KIR3DS1 KIR3DL1*h/y +Bw4 80I Protection NK cytotoxicity due to efficient NK cell education Adapted from: Bashirova AA, Thomas R, Carrington M. Ann Rev Immunol.2011;29:295 KIR/HLA Disease Associations Disease Association Effect Autoimmune/inflammatory Psoriasis 2DS1/HLA-C*06 Susceptibility Rheumatoid vasculitis 2DS2/HLA-C*03 Susceptibility Type 1 Diabetes 2DS2/HLA-C1 group Susceptibility Infectious HIV-1 3DS1/HLA-Bw4 80I Slows progression HCV 2DL3/HLA-C1 homozygosity Resolution of infection CMV reactivation/hsct >1 donor activating KIR risk of reactivation Cancer Malignant melanoma 2DL2/2DL3; HLA-C1 Susceptibility Leukemia 2DL2 Susceptibility Cervical cancer 3DS1/ HLA-C2- &/or Bw4- Susceptibility Adapted from: Bashirova AA, et al. Ann Rev Genomics Hum Genet. 2006;7:277 23