The Genome Scan in IBD

Transcription

1 SESSION III WORKSHOPS HOT TOPICS FROM BED TO BENCH TO POLICY The Genome Scan in IBD Charlie Lees, PhD FRCP(Ed) Aleixo Muise, MD PhD FRCPC

2 The Genome Scan in IBD Objectives: To identify patients who should be considered for a genome scan; and To identify patients who should NOT be considered for a genome scan.

3 Case Jim is a 21- year- old Caucasian man with severe small bowel and colonic Crohn s disease with significant perianal disease. He is being treated with infliximab. Jim developed typical IBD around 13 years of age that has become more difficult to treat. He has a strong maternal history of IBD and other autoimmune diseases. He presents to the ER with a five- day history of fever and worsening colijs. He develops liver dysfuncjon and pancytopenia.

4 Points for Discussion: Canada has one of the highest rates of IBD in the world. In 2019 (hypothe<cal) all Canadians with IBD will have free access to next genera<on sequencing (NGS) to: 1) Determine the best treatment op<ons based on mul<ple drug op<ons 2) Determine the cause of disease (in a small percentage of pa<ents) Are we ready? How can the genome scan help achieve the goals of precision medicine? How do we use NGS? What are the differences between GWAS and WES? Can we use NGS now to berer diagnose and treat IBD pajents? What is pharmacogenejcs? Are there clues in the history that suggest a genejc form (monogenic) of IBD? If so why do we care? Can we change treatment? Who should have stem cell transplant? What do we need to think about when considering things like stem cell or bone marrow transplant?

5 References Adams DR, Eng CM. Next-Generation Sequencing to Diagnose Suspected Genetic Disorders. N Engl J Med. 2018;379(14): Uhlig HH, Schwerd T, Koletzko S, et al. The diagnostic approach to monogenic very early onset inflammatory bowel disease. Gastroenterology. 2014;147(5): Uhlig HH, Muise AM. Clinical Genomics in Inflammatory Bowel Disease. Trend in Genetics (9):

6 Precision Medicine the goal!!

7 What are Genetics? What do we do with it?

8 Types of Genetic Mutations

9 Autosomal Dominant GI Disease Colon Cancer Gastric Cancer PancreaJc Cancer Wilson Disease

10 CASE: AUTOSMAL DOMINANT DISEASE History Patient Phenotype - Ancestry Dad Croation / Mom - Scottish - age of onset birth (born June 2016) Congenital Sodium Losing Diarrhea/enteropathy Query bowel transplant?? MCM-016 (father) poor DNA QC MCM-015 (mother) Total variants n = 155,464 Read Depth and Genotype score n = 75,379 Rare Variants (maf < 0.01) n = 5,933 Rare Damaging Coding Variants n = 657 Shared in proband and mom n= 354 GUCY2C MCM-014 (patient) Homozygous recessive n = 1 Compound Heterozygous n = 70 De novo n = genes n = 17 mostly in dad alone (likely false positives) NOD2 pathway n = 5 Jostins GWAS n = 26 Known Pathogenic n = 2 not relevant to phenotype

11 GUCY2/NHE3 AND IBD GUCY2 activating mutations Encodes - guanylate cyclase C (GC-C) Activating mutation (GoF) Diarrhea IBS-like CSD 6/36 developed IBD (Finkerstrand, 2012; Muller, 2015) NHE3 2/9 developed IBD developed IBD Others with early pathological evidence of bowel inflammation? Why??

12 Autosomal Recessive Autosomal Recessive GI Disease CysJc Fibrosis PancreaJJs Liver Disease VEOIBD Hereditary Hemochromatosis

13 Case : Autosomal Recessive Disease History - Indian Ancestry with consanginuity - age of onset - < 2 months Patient Phenotype secretory diarrhea, pancytopenia, hepatomegaly, HLH Dx IL10RB - disease HPTU-001 (grandfather) (grandmother) Twins (mono vs di zygotic?) Chr21: T/- (Hg19/GRCh37) Homozygous Leu18Trpfs*12 exon 2 of NM ExAC maf = (0 homozygotes) (father) deceased DPLM Lab ID (patient) (mother) (mother) P unborn MSH genetic testing (father)

14 X-linked GI Disease Not many listed? More difficult to find XIAP Maybe most important??

15 CASE X-LINKED DISEASE URUG-007 URUG-006 Maternal Grandpa recurrent skin abscesses mononucleosis ChrX: TAAAG/- V298fsX306 Original TRIO URUG-003 WES URUG-002 WES carrier URUG-008 XIAP carrier (adult - no kids) URUG-009 XIAP carrier (adult - no kids) URUG-001 WES Proband URUG-005 URUG-004 XIAP carrier

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17 X-LINKED X-linked recessive disorder ( > 50 males cases) Granulomatous colitis Perianal disease Non-responsive to conventional therapies including biologics High morbidity and mortality +/- HLH/MAS We do NOT understand the phenotype Onset of disease - months to > 40 years of age May be common? 4% of male Pediatric IBD patients (Zessig, Gut 2014) Sickkids sequencing (WES) lower % - validation stage X-chromosome inactivation female carriers Colitis may be the first or only manifestation Stem cell transplant is curative All images are used with the permission of the patient and family

18 What type of tests should we do?

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20 What Genetic Test to do?

21 Using Next Generation Sequencing to identify Monogenic Intestinal Disease Our Approach with > 1500 IBD

22 What do the test results look like?

23 How to Validate a Mutation GeneJcs Type of MutaJon and MAF Damaging Scores Inheritance PaRern Conserved between Species Animal Studies Biological Plausabiliy

24 WES missed the diagnosis? If the phenotype is obvious, look deeper.

25 Conclusion: Who to Sequence? Some insight into which pajents to sequence SJll will miss pajents with milder phenotypes (??) Crowley and Muise. Gastroenterology Clinics of North America, 2018

26 Goal: to identify novel genes and understand their function to better treat patients with severe intestinal disease (VEOIBD) All images are used with the permission of the patient and family

27 Our Approach to WES in VEOIBD

28 How common is monogenic IBD in a typical Pediatric IBD Centre?

29 Whole Exome Sequencing of >1500 IBD Patients SickKids IBD Cohort Age 0 to 17.9 years of age majority > 12 years Index Case 1069 Full Sibling: Affected 29 Full Sibling: Unaffected 4 Mother: Affected 46 Mother: Unaffected 674 Mother: Unknown 19 Father: Affected 35 Father: Unaffected 531 Father: Unknown 20 Other: Affected 3 Other: Unaffected 1 Total Unique Participants 2431 NEOPICS InternaJonal Cohort Age 0 to 5 years of age majority < 2 years Index Case 475 Full Sibling: Affected 12 Full Sibling: Unaffected 15 Mother: Affected 7 Mother: Unaffected 187 Mother: Unknown 80 Father: Affected 5 Father: Unaffected 179 Father: Unknown 74 Other: Affected 2 Other: Unaffected Total Unique ParJcipants Eileen Crowley and Neil Warner 4

30 SickKids IBD BioBank - Probands Age (years) >10 n= n=% Gender M:F 0.8:1 1.5:1 1.7:1 1.5:1 CD UC/IBD- U Median age diagnosis 11.03yrs IQR ( ) Median age symptom onset 10.65yrs IQR ( )

31 Ethnicity of SickKids IBD BioBank Families Grandparent Ethnicity Parent Ethnicity

32 SickKids IBD BioBank Family Ages 0 to >17 years of age 'Trios' PaVent & Parents who enrolled in WES Study >11 Age (Yrs) Complete Trios = p + both parents Incomplete = p + any relavve(s), but not both parents 32

33 1 st Question What is the incidence of the 67 genes known to be associated with monogenic IBD?? The Genome Analysis Toolkit (GATK) was used to idenjfy highly penetrant rare variants of interest. Sanger sequencing verified variant genotypes of interest. A clinical database was reviewed to ascertain phenotypic characterisjcs. FuncJonal/Histological assessment when possible. Uhlig et al Gastroenterology 2014;147:

34 WES - SickKids IBD BioBank 2,431 unique parjcipants 383,027 variants 1,661 monogenic genes HIGH QUALITY, RARE (MAF <0.01), PROTEIN CODING VARIANTS PREDICTED TO BE DELETERIOUS Eileen Crowley and Neil Warner

35 GENE VARIANT 4% with monogenic variants 25 genes 44 pavents PIK3CD NCF4 NCF1 PKIG RTEL1 TRNT1 TTC37 TNFAIP3 TGFBR1 SAP XIAP 18% MASP2 DOCK8 11% ITCH IKBKG HSPA1L HPS6 HPS4 COL7A1 9% HPS1 BTK SLCO2A1 LRBA DKC1 5% FOXP3 7% XIAP DOCK8 COL7A1 FOXP3 DKC1 LRBA SLCO2A1 BTK HPS1 HPS4 HPS6 HSPA1L IKBKG ITCH MASP2 NCF1 NCF4 PIK3CD PKIG RTEL1 SAP TGFBR1 TNFAIP3 TRNT1 TTC37

36 Age Distribution of Monogenic Disease 18 64% 14% EOIBD 22% VEOIBD Median age diagnosis 11.7yrs IQR ( ) n=28 >10yrs n=6 7-10yrs n=10 <6.9yrs

37 Presentation of monogenic disease Phenotypic feature Age at diagnosis (<6.9yrs) OR (95% CI) 5.1 ( ) Gender 1.16 ( ) FHx IBD 1.74 ( ) First degree FHx of IBD FHx of autoimmune disease 2.28 ( ) 2.4 ( ) Any EIM 3.9 ( ) EIM ( ) Surgery 0.9 ( ) Progression to biologic therapy 0.9 ( ) P value <

38 Presentation of monogenic disease PresentaVon Classic symptoms 92.5% 52% EIM at presentajon 1.9% reported consanguinity 54% Family Hx of IBD ClassificaVon 63% Crohn s Disease Treatment Steroid exposure 94% Biologic therapy 36% (16% primary non response) Surgery 9%

39 VEOIBD (< 6 yrs of age) ~20% (based on sequencing of >500 pavents) EOIBD (< 18 years of age ~4%) (based on sequencing of >1000 pavents) COL7A1 FERMT1 CARD9 TNFAIP3 BTK RTEL1 XIAP SLC9A3 POLA1 CD3G ITCH IL10RA HSPA1L TNFAIP3 TRNT1 TTC37 TGFBR1 SEC14L3 RTEL1 PKIG NLRP12 MASP2 LRBA HPS6 [CATEGORY NAME] 16% [CATEGORY NAME] 11% IKBKG IL10RA TRIM22 FOXP3 STXBP2 PTEN CYBB TTC7A WAS MEFV HPS4 HPS1 CR2 BTK ARPC1B SLCO2A PIK3CD IKBKG NCF4 FOXP3 DKC1 COL7A1 NCF1 CYBB [CATEGORY NAME] 7%

40 New Paradigms in IBD Treatment. Can Genetic defects predict treatment response or drug class? Research QuesVons: How to use WES data to understand And bener treat IBD pavents?

41 Pharmacogenetics

42 Drug Toxicity and Effect

43 Ethical Issues Issues with genejcs - sjll many quesjons Consent some people do not want genejc tesjng GeneJc Counselling urgently needed WES - privacy, insurance, discriminajon Who will pay for it? Cannot be research - needs CLIA/SCC approved lab Results: Variant of unknown significance very common for rare diseases (reason why you do the test in the first place) Incidental findings (example BRCA1/2?, colon cancer?, risk for demenja, Alzheimer's?) ValidaJon and FuncJonal studies