The genetic galaxy: stars, planets and asteroids Sverine Vermeire - - PowerPoint PPT Presentation

The genetic galaxy: stars, planets and asteroids

Séverine Vermeire MD, PhD Department of Gastroenterology and Catholic University of Leuven Belgium

Concering the universe… where IBD genetics really started

1997 Oxford - 1999 Canberra - 2001 Paris - 2003 Orlando – 2004 Rome – 2006 Amsterdam

International IBD Genetics Consortium

The stars

The stars

NOD2/CARD15

Arg702Trp SNP8 Gly908Arg SNP12 Leu1007fsinsC 3020insC SNP13

CARD 2

220 127

NBD

273 577

LRR

1020 744 1040

CARD 1

1 124 28

Protein/protein interactions Protein Oligomerisation PAMP recognition

NOD2/CARD15 (16q12)

Caspase Recruitment Domain Family member 15

Blau syndrome

NOD2 pointed out the concept of impaired innate immunity in Crohn’s disease

NOD2 mutation prevalance

20 40 60 80 100 % controls CD

effect size one mutation RR 2.5

NOD2/CARD15 associated with stricturing ileal Crohn’s

Lala S et al; Gastroenterology 2003; 125: 47-57 Ogura et al; Gut 2003; 52: 1591-1597

Wehkamp J Gut 2004; 53: 1658-64 Kobayashi et al Science 2005;307:731-734

Defensins in the gut are impaired in patients carrying NOD2 mutations

 99 loci IBD

Genome-wide Association Scan

The planets

The planets of “autophagy”: IRGM and ATG16L1

Autophagy and IBD

Mycobacteria Salmonella Shigella Listeria Toxoplasma Herpes simplex …

• ATG16L1 (sensor for invading pathogens)
• IRGM (Immunity-related GTPase family M protein; regulates

autophagy induction in response to intracellular pathogens)

• ULK1 (kinase required for induction of autophagy; regulated by

mTOR)

• MTMR3 (PI3P fosfatase; regulates initiation of autophagy;

unknown whether positive or negative)

• LRRK2 (kinase, GTPase; relation with autophagy; unknown

whether positive or negative)

The planets of “autophagy”: IRGM and ATG16L1

Cadwell K et al Nature 2008

CD patients homozygous for the disease risk allele of ATG16L1 display Paneth cell abnormalities

Wild type ATG16L1 Risk Allele

Sirolimus as therapy for Crohn’s?

Massey DC et al Gut. 2008;57:1294-6

before After 16 weeks

The “ER stress” planets (XBP1, ORMDL3 )

McGuckin M A et al. Am J Physiol Gastrointest Liver Physiol 2010;298:G820-G832

neurodegenerative diseases developmental disorders Cancer Diabetes cystic fibrosis IBD

Increased AIEC in ER-stressed Paneth cells (GRP78 scoring) from ATG16L1 patients

ER stress (+) ER stress (−) CD N (%) Controls N (%) CD N (%) Controls N (%) Total number 8 4 13 4 AIEC fimH 8 (100) 0 (0) 1 (7.7) 0 (0) AIEC eaeA 8 (100) 0 (0) 1 (7.7) 0 (0) Listeria monocytogenes 2 (25) 0 (0) 1 (7.7) 0 (0) MAP 1 (12.5) 0 (0) 0 (0) 0 (0) Salmonella spp. 2 (25) 0 (0) 0 (0) 0 (0) Deuring JJ et al Gut 2013 August DNA and biopsies from 78 CD and 12 controls

Microbial sensing, autophagy and ER stress pathways in CD

0.0 5.0 10.0 15.0 20.0 25.0 30.0 1 2 3 4 5 6 7 8 9 10 11 12 Percentage of individuals Number of risk alleles

Healthy controls CD patients UC patients

Hoefkens E & Nys K et al Autophagy 2013 in press

The (LPS-induced) cytokine response is increasingly induced in carriers of higher # of risk alleles in susceptibility SNPs

ORMDL3

…and the asteroids

Overlapping genes

Alopecia Behcet’s Asthma

IBD

Atopic Dermatitis Rheumatoid arthritis Type II Diabetes Leprosy

Ankylosing Spondylitis

Lupus Erythematosus Multiple Sclerosis

Psoriasis

Coeliac disease vitiligo Type II diabetes

PTGER4, STAT3, IL2RA, IL17R, FCGR2A PRDM1 FCGR2A REL IL2/IL21 PTPN22 TNFRSF14 CCR6 IRF5 IL2RA C11Orf30 NOD2 LRRK2 TNFSF15 IL2RA PTPN22 CCR6 ZMIZ1 PTPN2 IL18RAP ORMDL3 PTPN22 IL10 IL27 TYK2 BACH2 FCGR2A ILR2A PRDM1/ATG5 IL10 PTPN22 FCGR2A IRF5 IL23R ERAP2 IL23R IL12B CDKAL1 PTPN22 IL23R, IL10 ORMDL3 SMAD3 5q31 (IBD5) DENND1B PRDX5 IL2RA IL2/IL21 CDKAL1 GCKR CAPN10 THADA HNF4A (MODY) ZMIZ1 ICOSLG PTPN2 REL IL18RAP KIF21B VAMP3 YDJC BACH2 TNFRSF14 TAGAP IL2/IL21 ZFP36L1

Crohn’s disease Ulcerative colitis

the Immunochip project

• 12 IMISs

– IBD, coeliac disease, T1D, AS, MS, PSC, RA, psoriasis,…

• 196.524 variants
• 38.565 IBD cases
• 37.747 controls

186 fine-mapping regions: ~130,000 SNPs Deep replication: ~50,000 SNPs Other replication: ~6000 SNPs HLA region: ~8000 SNPs Nature 2012 491:119-124

iChip increased the number of IBD loci to 163

25/30 risk allele has same direction of effect in UC (p < 10-3) 18/23 risk allele has same direction of effect in CD (p < 0.01) Nature 2012 491:119-124

The genetic architecture of CD vs. UC

IBD vs. control odds ratio

>1.5 1.3 1.4 1.2 1.1 0.67 1.0 >1.5 IL23R NOD2 PTPN22

CD vs. UC odds ratio

30 CD specific loci 23 UC specific loci 110 IBD loci MHC

Jostins L et al, Nature 2012 491:119-124

• 18% in LD with missense mutations
• 40% in LD with variants regulating gene expression
• 69% shared with other IMIDs (x 8,6 as expected by chance)
• Role of Th17 cells: new RORC (master transcription factor) association
• De/ubiquitination: 15 loci involved (p < 0.001)
• NF-kB: REL, RELA, NFKB1
• Degradation of TGFb signaling components:

– SMURF1, FURIN, SMAD7 (implicated in CRC)

• Susceptibility to infectious diseases

Major themes of interest highlighted by iChip

Host-microbe interactions shape genetic architecture

• f IBD

IBD loci

Immune-mediated diseases

82 82 53 82

Primary immune deficiencies

6/7 leprosy loci also IBD loci

NOD2 IL23R TNFSF15 RIPK2 LRRK2 C13ORF31

IL12B STAT1 IRF8 TYK2 STAT3 IFNGR2

6/8 MSMD* genes within IBD loci

MSMD

*MSMD, Mendelian susceptibility to mycobacterial disease

Nicholas T. Ventham , Nicholas A. Kennedy , Elaine R. Nimmo , Jack Satsangi. Gastroenterology 2013; 145: 293-308

Yet another universe: epigenetics

Back to earth…

How do we use these fantastic findings in our patients?

Examples where genotyping enters the clinic

Gene Drug EMA advice TPMT Thiopurines None EGFR Gefitinib in NSCLC Mandatory KRAS Cetuximab, Panitumumab in CRC Mandatory SLCO1B1 Statin induced myopathy None HLA B*5701 Abacavir in HIV Mandatory CYP2D6 Tamoxifen – Breast cancer None CYP2C19 Clopidogrel None

Genetic predisposition to anti-TNF induced skin lesions?

Gene SNP ID Odds ratio [95% CI]

IL23R rs114657791 0.53 [0.28-1.02] IL12B* rs3181225 0.57 [0.38-0.85] COG6* rs7993214 1.54 [1.06-2.23] IL12RB2 rs12131065 1.45 [1.02-2.07]

Cleynen I & Vermeire S. Nat Rev Gastroenterol Hepatol 2012

Genetic panel to predict colectomy in ASUC

McGovern Gastroenterol Suppl 2004;126: A68

1 2.59 3.21 1 2 3 4 5 6 no or 1 at risk genotype 2 or more at risk genotypes 3 or more at risk genotypes RR for colectomy

HLA DRB*103 MDR1 C3435T MEKK1 Asp643Asn

Explaining or predicting the subphenotypes of IBD

Disease severity Disease location & behaviour Extra-intestinal disease manifestations

CD disease location

(conditional on disease behavior and age at diagnosis)

MHC

NOD2

N=19.881

CD disease behaviour

(conditional on disease location and age at diagnosis)

N=19.881

CD UC CD location UC extent

10 20 30 40 50 60 70 80 90

30,500,000 31,000,000 31,500,000 32,000,000 32,500,000 33,000,000 33,500,000

• log10 P value

Class I Class II Class III

D’ r2

HLA-A DQA 2 DRA DRB5 BTNL 2 C6orf48 HSPA1B HLA-C HLA-B

rs9276427 rs9268969 rs6930777 rs3117577

CD 1.90e-17

0.87[0.84-0.90]

5.99e-02

1.03 [0.99-1.07]

6.37e-01

1.01 [0.96-1.07]

3.96e-07

0.86 [0.81-0.91]

UC 1.59e-03

0.95 [0.91-0.98]

5.52e-85

0.68 [0.65-0.70]

3.55e-17

1.26 [1.19-1.33]

6.98e-03

0.95 [0.69-1.00]

CD location 2.25e-01

0.97 [0.91-1.02]

3.86e-07

1.16 [1.10-1.23]

4.02e-22

0.66 [0.61-0.72]

4.11e-03

0.87 [0.78-0.96]

UC extent 1.06e-01

1.05 [0.99-1.10]

1.07e-07

0.84 [0.79-0.90]

6.30e-01

1.02 [0.94-1.11]

2.27e-16

1.46 [1.33-1.59]

• Collaborative efforts since 1997 have made IBD genetics a

successful project:

– GWAS, their meta-analyses & iChip : 163 associated IBD regions

• NOD2 and HLA confer the major genetic effect on disease

phenotype in CD and UC

– But different HLA signals for susceptibility and phenotype

• Genetic findings support the hypothesis that UC, colonic

CD and ileal CD could be considered as part of a continuous spectrum

Conclusions

Leuven IBD Group (www.ibd-kuleuven.com)

Medical staff Gastroenterology

– Paul Rutgeerts – Gert Van Assche – Séverine Vermeire – Marc Ferrante Pathology – Gert De Hertogh Abdominal Surgery – Andre D’Hoore – Albert Wolthuis – Anthony De Buck van Overstraete Paediatric Gastroenterology – Ilse Hoffman Abdominal Imaging – Dirk Van Beckevoort

IBD Laboratory

– Karolien Claes – Sophie Organe – Willem-Jan Wollants – Ingrid Arijs – Isabelle Cleynen – Christine Breynaert – Kathleen Machiels – Jan Van Der Goten – Filip Baert – Zhe Li (CHINA) – Triana Lobaton (SPAIN) – Alessia Settesoldi (ITALY) – Kostas Papamichael (GREECE)

IBD Clinical Trials

– Maja Noman, MD – Karen Rans – Isolde Aerden – Sofie Coenen – Karoline Van Den Broeck – Leen Van Der Biest – Jolien Lefrere – Tine Hermans – Vera Ballet (Databankmanager)

Lab for Pharmaceutical Biology

• Ann Gils
• Niels Vande Casteele
• Griet Compernolle
• Lize Bollen
• Thomas Vanstappen