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Use of GWAS and exome sequencing to identify genes relevant to drug-induced liver injury Ann K. Daly Institute of Cellular Medicine Newcastle University.

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Presentation on theme: "Use of GWAS and exome sequencing to identify genes relevant to drug-induced liver injury Ann K. Daly Institute of Cellular Medicine Newcastle University."— Presentation transcript:

1 Use of GWAS and exome sequencing to identify genes relevant to drug-induced liver injury Ann K. Daly Institute of Cellular Medicine Newcastle University

2 Idiosyncratic adverse drug reations  Serious health problem which is expensive for society Common cause of death Loss of new drugs late in development or soon after licensing  Typical incidence 1 in 10,000 to 100,000 patients exposed  Local drug concentration may contribute but concentration- independent effects important Contribution from immune system in many but not all cases  Examples Drug-induced liver injury Hypersensitivity reactions and skin rash Cardiotoxicity Muscle toxicity

3 Drug-induced toxicities associated with 28 drugs withdrawn from the US market 1976 to 2005 Wilke et al. Nature Reviews Drug Discovery 2007; 6, Range of drugs give rise to idiosyncratic DILI but due to value of drugs and rarity of problem are still used widely

4 Drug-induced liver injury (DILI)  Rare but serious idiosyncratic toxicity  Several phenotypes Cholestatic  Effects on bile secretion Hepatocellular  Inflammatory disease  Aims Develop strategies to prevent DILI reactions by genotyping patients prior to treatment Develop screening approaches for use during drug development

5  Aim: Find genes predisposing to DILI  Drugs Anti-TB medication or Flucloxacillin or Amoxicillin-clavulanate  Multicentre collaboration involving Newcastle, Liverpool, Nottingham and London  UK-wide recruitment of cases Retrospective and prospective UK-wide study on drug-induced liver injury

6 Worldwide study on DILI genetics-Ann Daly and Guru Aithal-co-chairs study Genotyping methods Confirmed cases of flucloxacillin DILI were genotyped for HLA-B*57:01 by genotyping for rs in HCP5. The assay involved amplification of a 250bp fragment by PCR followed by digestion with BstNI and resolution of restriction digest patterns on an 10% polyacrylamide gel. Positive cases were confirmed by direct genotyping using SSP-PCR for HLA-B*57:01 using an AllSet+™ Gold SSP B17 High Res Kit (Invitrogen). Results Recruitment and Adjudication A total of 1333 cases have been recruited to date. As summarised in Table 1, 856 (64%) have passed adjudication. Table 1. Case adjudication results The ethnicity of cases is summarized in Table 2 which shows that the vast majority of study participants are of white European ethnicity. Table 2. Case ethnicity Samples for genome-wide association study From the 856 samples that have passed adjudication, 747 have been selected for inclusion in a genome-wide association study (GWAS) on the basis of the number of cases available for particular drugs. The GWAS is being performed in collaboration with the US DILIN network and will include ethnically-matched controls from selected worldwide control sets including the POPRES cohort used in previous studies. Rare coding variants will also be genotyped (exome chip). The drugs represented among the iDILIC cases are shown in Figure 2. Fig 2: Number of cases relating to particular drugs included in the genome-wide association study. The other drugs category comprises imatinib, coumarin anticoagulants, methotrexate, sulphasalazine, ticlopidine, montelukast, enalapril, cyproterone, cyclophosphamide, ebrotidine, fenofibrate, sevoflurane, dronedarone, gabapentin, phenytoin, lamotrigine, interferon and retinoids. The anti-TB drug category includes various combinations of isoniazid, rifampicin, pyrazinamide and ethambutol.

7 Genome-wide association study (GWAS) on flucloxacillin DILI  51 UK cases (DILIGEN study) and population control group (n=282)  Illumina IM chip  No previous genetic studies on this form of DILI  GWAS design allowed for an open study

8 Manhattan plot for flucloxacillin GWAS MHC region Strongest signal with SNP in HCP5 gene which tags HLA-B*57:01 Daly et al., Nature Genetics 2009; 41:

9 Flucloxacillin DILI and B*57:01  Association with HLA B*57:01 similar to that for abacavir hypersensitivity  83% of 150 cases now studied are B*57:01- positive No indication that other forms of DILI show this particular association  Sensitivity of B*57:01 genotyping lower as predictor of flucloxacillin DILI than abacavir hypersensitivity Other genetic and non-genetic risk factors may contribute

10 HLA genes-common thread in serious adverse drug reactions  HLA class I genes expressed on most cells Proteins present antigens (particularly peptides) to CD8- positive cytotoxic T cells A, B and C genes  HLA class II genes expressed on antigen presenting cells Proteins present antigens to T cells- mainly CD4-positive T helper cells DR, DQ, DP genes

11 Amoxicillin-clavulanate-induced liver injury  Important cause of DILI worldwide  Several small independent candidate gene studies showed role for HLA class II DRB1*15:01 allele in susceptibility  GWAS involving international collaboration performed to identify additional risk factors

12 Amoxicillin-clavulanate DILI GWAS MHC zoom-in, conditioned on the top SNP from class II (rs ) rs (A*02:01) MHC zoom-in rs rs (DRB1*15:01) 201 cases- UK DILIGEN (n=77), US DILIN (n=56), Spanish DILI (n=49), EUDRAGENE (n=19); 532 matched controls MHC region (Lucena et al., Gastroenterology 2011)

13 HLA typing and amoxicillin- clavulanate DILI  Detailed HLA typing performed on 177 cases and 219 controls  DRB1*15:01 and A*02:01 alleles associated independently with risk of DILI (OR approx. 2.5 for each)  Additional risk also seen from individual A*02:01 and DRB1*15:01 alleles (not on same haplotype) If positive for both  OR= 9.47 ( ), p=2.56 x Evidence for genetic interaction (p=0.0015)

14 HLA associations with DILI Daly, Annual Review of Pharmacology & Toxicology 2012; 52:21-35

15 Flucloxacillin Abacavir Clavulanic acid Lumiracoxib Lapatanib Ximelagatran DRB1*07:01-DQA1*02:01 DRB1*15:01 B*57:01 Chemical structures and HLA toxicity associations

16 HLA and related gene associations with DILI-underlying mechanism  Specific HLA protein interacts with drug or metabolite inappropriately  Triggers T-cell response  Local cellular damage

17 Abacavir-B*57:01 interaction From Illing et al., Nature 2012

18 Norcross et al., 2012; AIDS 26: F21-F29 Effect of different drugs on peptide binding in B*57:01-positive cell line No apparent direct effect by flucloxacillin unlike abacavir Different mechanism for antigen presentation to abacavir?

19  Very recent findings suggest possible direct effect of flucloxacillin in some B*57:01-positive healthy volunteers o No covalent adduct  Need to incubate with flucloxacillin for 24 to 48 hours to see cell proliferation o Covalent adduct formed o Hapten mechanism likely CD8-positive T cell clones from B*57:01- positive flucloxacillin DILI cases: response to various penicillins Monshi et al., Hepatology 2013 Wuillemin et al., J Immunol, 2013

20 Is metabolism of flucloxacillin relevant to DILI reactions?  Flucloxacillin is a PXR ligand so may induce its own metabolism? Induction will also affect bile acid synthesis and transporter levels  Our attempts to demonstrate that CYP3A4 or other CYPs can generate 5'-hydroxymethyl metabolite unsuccessful Human liver microsomes with 1 mM flucloxacillin Overlay of 5'-hydroxymethylflucloxacillin standard

21 Studies on pooled DILI cases  DILI due to any prescribed drug  Cases from UK (Diligen), Spain (Spanish DILI) and US (DILIN)  Total number of cases =783

22 All drug DILI GWAS results 783 cases, 3,001 population controls After correcting for known HLA risk alleles for flucloxacillin- and amoxicillin-clavulanate-DILI, no deviation from expected p-value distribution No SNPs in HLA region approaching genome-wide significance for "other drugs" All Without Fluclox/amoxicilli n-clavulanate All with HLA taken out Urban et al, 2013 Pharmacogenetics and Genomics

23 Diclofenac-induced liver injury Rare toxicity associated with diclofenac use Serious hepatotoxicity 11 per 100,000 patients Believed to be due to metabolic idiosyncracy ?Specific reactive metabolite which binds covalently to proteins

24 LumiracoxibDiclofenac HLA-DRB1*15:01 No significant HLA class II association DILI and related NSAIDs Both drugs metabolized by broadly similar pathways

25 Candidate gene studies on genetic susceptibility to diclofenac-related DILI UGT2B7*2 and ABCC2 C-24T previously identified as significant risk factors in small (n=24) candidate gene study Daly et al. Gastroenterology 2007; 132: Majority of these cases plus additional cases from UK/US included in "all drug" GWAS

26 GWAS on diclofenac DILI cases (n=30) GWAS QQADME gene QQ Urban et al, 2013 Pharmacogenetics and Genomics

27 GWAS hits on diclofenac DILI cases and data on ADME genes as candidates PPAR-gamma association did not replicate in 26 additional cases ADME associations in agreement with our earlier UGT2B7 finding but PXR an interesting additional candidate

28 Exome sequencing and exome chip studies on DILI  Exome sequencing performed on 125 amoxicillin-clavulanate DILI cases 66 from UK and 59 from Spain All from previous GWAS  Exome chip studies 112 further amoxicillin-clavulanate DILI cases from iDILIC study and 93 from US DILIN network for replication of exome sequencing 73 UK flucloxacillin DILI cases

29 Controls for exome sequencing/exome chip studies  Exome sequencing 353 NIMH (white US) plus 102 from Spain (EGA)  Exome chip 3900 controls from several cohorts  Combined studies 4300 controls from European sequencing project (EVS)

30 Amoxicillin-clavulanate: best results for sequencing plus exome chip with combined data also shown SGSM3: Small G Protein Signaling Modulator 3 CHRBP SEQ_MAF_ A SEQ_MAF_ USEQ_P SEQ_O R EC_MAF_ AEC_MAF_UEC_P EC_O RGENEFUNCTPPHEN EVS_MA FPOR E E-020.2ZNF304missense_variantbenign E E E SGSM3splice_region_variant possibly_damagin g E E E-041.8LAMB1missense_variantprobably_damaging E E E-041.7MTHFSmissense_variantbenign E E E-022.3C14orf101missense_variantbenign E E E-031.4PCDH15missense_variantNA E E E-031.3NA E E-02NA E-02NAWDR75missense_variantpossibly_damaging E E-02NA E PSTPIP1missense_variantpossibly_damaging E E E-041.5ERAP1missense_variantbenign E E-01NA E-03NAC6orf170missense_variantbenign E E E-051.6ERAP1synonymous_variantNA E E-02NA E MGAmissense_variantbenign E E-03NA E-036.4MFHAS1missense_variantpossibly_damaging E E E-031.9XRCC4missense_variantpossibly_damaging E E E-030.7PROM2missense_variantbenign E E-02NA E-029.6ALMS1missense_variantpossibly_damaging E E E-020.5MYO19upstream_gene_variantNA E E E-03NASLC9A3R1downstream_gene_variantNA E E-01NA E-039.6ADAMTS18missense_variantbenign E-049.6

31 SNPCHRBPMAF_AMAF_UPORGENEFUNCTIONPOLYPHEN exm-IND E-061.6NA exm E CACNB2missense_variantbenign exm E-06NAMAPK12downstream_gene_variantNA exm E-060.6NA exm E CD72missense_variantbenign exm E-055.1SLITRK6missense_variantpossibly_damaging exm E-050.6PLEKmissense_variantbenign exm E ADCY3missense_variantpossibly_damaging exm E TMCC3missense_variantprobably_damaging exm E-051.9PTPRKintron_variantNA exm E-051.8SLCO2B1missense_variantbenign exm E-050.6TKTintron_variantNA exm-IND E-051.5NA exm E D21S2091 Eupstream_gene_variantNA exm E-042.3DNMBPmissense_variantbenign exm E-04NARP1L1missense_variantprobably_damaging exm E-04NAMALT1missense_variantprobably_damaging Amoxicillin-clavulanate-exome chip only CACNB2 not well covered in exome sequencing

32 Flucloxacillin – Exome chip USP8: ubiquitin specific protease 8 Chromosome 6 includes processed pseudogene with strong homology so finding may due to LD with B*57:01 CASP5-caspase 5 Replication studies on this looking positive SNPCHRBPPORF-AF-UA1GENEFUNCTION (PPH) exm E ANANA (NA) exm E GUSP8missense (probably-damaging) exm-rs E ANANA (NA) exm E CRNPEPL1coding-synonymous (unknown) exm-rs E GNANA (NA) exm-rs E GNANA (NA) exm E CANO10missense (benign) exm E AWDR38missense (benign) exm E AEFTUD2,HIGDmissense (possibly-damaging) exm E CDNAH3missense (probably-damaging) exm ADNAH3missense (probably-damaging) exm AIGSF10missense (benign) exm GIGSF10missense (benign) exm ACCDC116missense (probably-damaging) exm ACCDC116missense (benign) exm ACCDC116missense (benign) exm ACASP5missense (possibly-damaging)

33 Sequencing and exome chip studies on DILI: progress so far and where next?  Studies show little evidence that rare coding variants are consistently contributing to risk of DILI due to amoxicillin-clavulanate and flucloxacillin Findings fairly similar to those for other complex diseases  Moving towards whole genome sequencing is challenging but may be valuable  Further GWAS involving new sample collection with improved power may identify novel associations

34 Successfully adjudicated new cases in iDILIC to date  Cases mainly from Europe  GWAS-exome chip in progress on 747 of these cases  Agreed collaboration with DILIN may improve power Number of cases

35 Summary  Genomics has increased understanding of individual risk for idiosyncratic drug-induced liver injury  HLA associations Strong association for flucloxacillin toxicity with HLA-B*57:01  Underlying mechanism could involve inappropriate T cell response  Probably does not involve metabolism HLA genotype not predictor of DILI with all hepatotoxic drugs  Increasing evidence that genetically-determined metabolism to reactive intermediate is an important step in some idiosyncratic DILI reactions Diclofenac  Attempts to identify additional risk factors by exome sequencing largely unsuccessful to date  Larger sample collections for individual drugs and genome sequencing may provide more complete understanding and better application to drug development process

36 Acknowledgements Newcastle Chris Day Pete Donaldson Julian Leathart Julia Patch Ruth Wake Pallav Bhatnagar Heather Cordell Tom Chamberlain Sally Coulthard Guru Aithal (Nottingham) Munir Pirmohamed (Liverpool) Kevin Park (Liverpool) Dean Naisbitt (Liverpool) Yufeng Shen (Columbia) Aris Floratos (Columbia) Mark Daly (Harvard) Jackie Goldstein (Harvard) Matt Nelson (GSK) Paul Watkins (North Carolina) Tom Urban (Duke) Maribel Lucena (Malaga) Raul Andrade (Malaga) Mariam Molokhia (London) Supported by the UK Department of Health Pharmacogenetics Initiative and International Serious Adverse Events Consortium



39 Cumulative incidence of ALT elevations in lapatinib-plus-letrozole treatment group for HLA- DQA1*02:01 carrier and noncarrier subsets, compared with letrozole-only treatment group Spraggs C F et al. JCO 2011;29:

40 Human diclofenac toxicity: possible relationship to metabolism Biliary excretion MRP2 Covalent adducts Diclofenac 4'-OH-diclofenac Diclofenac acylglucuronide CYP2C9 UGT2B7 Liver injury Other oxidative metabolites Various CYPs

41 Abacavir hypersensitivity-success story for pharmacogenomic screening  Abacavir is a reverse-transcriptase inhibitor AIDS treatment  Approx. 5% of patients develop hypersensitivity reactions which resolve on discontinuation Rechallenge results in more severe reaction  Up to 100% of proven hypersensitivity cases have one or two HLA B*57:01 alleles Not all patients with this genotype will show detectable reaction

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