Coeliac disease

Can genotyping help

to diagnose coeliac disease?

Difficult diagnosis

• Asymptomatic patients: relatives

• Moderate histological lesions (Marsh 1-2)

• Positive Ab without histological lesion: not perfectly specific

• Gluten free diet before intestinal biopsy

• Usefulness of HLA genotyping?

Genetic origins

• Ethnic differences in disease incidence/prevalence

• Familial aggregation:– 5–15% first-degree relatives– 30% HLA identical sibs– Monozygotic twins 83–86%– Dizygotic twins 11%

Greco. Gut. 02Sollid. J Exp Med 89

Genes involvement

• Susceptibility loci: chromosomes 2, 5, 6, 9, 15, 19

• Genetic association studies of functional candidate genes:– CTLA4– MYO1XB

• Association with genetic syndromes:– Down syndrome– Turner syndrome – Williams syndrome

MHC Class II

Wolters. Am J Gastroenterol. 08

HLA• Major histocompatibility complex (MHC): 6p21

• MHC class II :– Loci HLA-DQ, HLA-DP and HLA-DR, – Expressed on professional antigen presenting cells

• HLA-DQ2:– Alleles DQA1*0501 and DQB1*0201– DQ2 (DR3 or DR5/7): 90-95% of CD patients vs 15-20% of controls– 3% of HLA-DQ2 positive population will develop a CD– Risk effect: 38-53%

• DQ8: – 5-10% of CD patients vs 20% of controls

Sollid. J Exp Med. 89Petronzelli. Ann Hum Genet. 97

HLA-DQ2 alleles: a gene dosage effect

• Highest risk if:– 2 alleles (DQA1*0501 and DQB1*0201) – In cis or in trans

• Further increased if:– Homozygous for the DQ2.5cis – A second DQB1*02 on the 2nd chromosome

Vader. Proc Natl Acad Sci USA. 03

Sollid. Nat Rev Immunol. 02

HLA DQ2/DQ8 are more frequent in female

• Female: 94% vs 85% in males (P = 1.6 × 10−3)• NPV: 99.1% in female and 90.5% in males• Majority of the DQ2/DQ8 negative cases were

male

• DQ2/DQ8 transmission is more frequent from fathers to daughters (P = 0.02):– 61% of female patients – 42% of male patients

Megiorni. Am J Gastroenterol. 08

HLA: an excellent NPV

Kaukinen. AM J Gastroenterol. 02

HLA genotyping in practice

Kaukinen. AM J Gastroenterol. 02

Kaukinen. AM J Gastroenterol. 02

When diagnosis still remains uncertain

• Borderline small bowel mucosal finding

• Positive serology without villous atrophy

• Gluten-free diet before biopsy

Familial screening

Srivastava. J Gastroenterol Hepatol. 10

first-degree relatives

• 2.8-12% CD prevalence in relatives

• 5.8% to 14% of serology positive relatives

• Higher prevalence in siblings vs parents?

• 59%-85% HLA DQ2/DQ3 DQ2-positive relatives

• 14.3% HLA negative relatives

Srivastava. J Gastroenterol Hepatol. 10Bonamico. JPGN. 06

Cost/effectiveness

Srivastava. J Gastroenterol Hepatol. 10

tTG + Total IgA

POSITIVE :

Intestinal biopsy

NEGATIVE: 2 years later

HLA genotyping

tTG screening

Ab POSITIVE

Ab NEGATIVE

HLA +

Serologic follow-up

HLA -

Clinical follow-up

Bonamico. JPGN. 06

HLA genotyping

• Non specific: only NPV• Long-life information

• Diagnosis remained uncertain: – Borderline intestinal lesions, – Positive serological diagnosis without villous atrophy

• If gluten free diet:– Surveillance for HLA positive cases– Role of:

• Positive EmA?• Increased / IELs?

First coeliac disease GWAS

• 778 patients, 1422 controls, 310 605 SNP

• 4q27 SNP rs13119723:– English, dutch and irish populations: p=2x10-7

– Meta-analysis: p=4.8x10-11

– Replication in UK and scandinavian populations

Van Heel. Nat Genet. 07

First coeliac disease GWAS

– Several genes in high level of linkage disequilibrium:

• KIAA1109: unknown function• Adenosine deaminase domain containing 1

(ADAD1)• Interleukin2 (IL2): T cell activation and proliferation• IL21: B, T and NK cells proliferation and IFN

production

– Also linked to type 1 diabetes and rheumatoid arthritis

Van Heel. Nat Genet. 07

Follow-up of Coeliac GWAS

• Genotyping of 1020 non-HLA SNP

• In Dutch, Irish and UK collections

• Meta-analysis of 2410 cases vs 4828 controls

• 7 new significant regions

Hunt. Nat Genet. 08

Regions of the coeliac GWAS • In 5’ region of regulator of G protein signalling 1 (RGS1):

– Regulation of G protein signalling activity

• 3p21: CCR3 and CCR5

• 3q25–2: IL12A cytokine subunit

• 6q25: TAGAP: a T cell activation GTPase activating protein

• 3q28: Lim domain containing preferred translocation partner in lipoma (LPP): not immune?

• 2q11–12: IL1RL1, IL18R1, IL18RAP and solute carrier SLC9A4

• 12q23: SH2B3

• TNFAIP3

• RELHunt. Nat Genet. 08 Trynka. Gut. 09

Non-HLA genes: a new diagnostic tool?

Romanos. Gastroenterology. 09

3 risk groups

• Low risk: – HLA-DQ2 negative (DQ2.5 and DQ2.2)

• Intermediate risk: – Homozygous for HLA-DQ2.2– Heterozygous for HLA-DQ2.5– Heterozygous for HLA-DQ2.2

• High risk for:– Homozygous for HLA-DQ2.5– Composite heterozygote HLA-DQ2.5/DQ2.2

The tested SNPs

Romanos. Gastroenterology. 09

Non HLA genes increase CD risk

Romanos. Gastroenterology. 09

7.5% of HLA DQ2 positive cases are reclassified if ≥ 13 non HLA allelesSensitivity increases from 46.6 to 49.5%

Specificity decreases from 93.6% to 92.8%

What changes?

Romanos. Gastroenterology. 09

Conclusive remarks

• HLA:– Good NPV, especially in female– Long-life information– Can avoid repeted exams in:

• Asymptomatic DQ2/DQ8 negative cases (screening)• Serology negative patients with atypical symptoms

– Cost/effectiveness?

• Non-HLA genotypes:– Slight increasing of diagnostic effectiveness– Will evoluate with new susceptibility SNPs– Cost as to be evaluated!