(Personalised / stratified medicine) Precision Medicine (Personalised / stratified medicine) Andrew P Read Emeritus Professor of Human Genetics, University of Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester Galton Institute teachers’ day, Nowgen, 28th June 2017

Agenda The new technology Predicting individual risk Pharmacogenetics Personalised treatment Stratified medicine in cancer

Precision medicine is driven by technology David Cameron’s 100,000 Genomes Project to ‘transform how diseases are diagnosed and treated’ £300 million Barack Obama’s Precision Medicine initiative, $215 million.

Clinical applications Diagnosis Prediction Treatment Traditional medicine: treat according to phenotype Precision medicine: treat according to genotype Head in clouds Head in sand Cartoon by Maya Evans

SNP chips genotype ca. 1 million single nucleotide polymorphisms in a DNA sample Affymetrix SNP 6 Illumina OmniExpress-24

www.ebi.ac.uk/fgpt/gwas/

Predicting individual risk of common complex disease 6 long-term prospective studies on Type 2 diabetes: Before SNPs After SNPs Clinical indicators AUC from clinical indicators Susceptibility loci genotyped AUC using combined clinical and genetic data Reference BMI, plasma glucose level 0.68 PPARG, CAPN10 Lyssenko et al. (2005) Age, sex, BMI 0.82 GCK, IL6 , TCF7L2 Vaxillaire et al. (2008) 0.78 18 established loci 0.80 Lango et al. (2008) 0.66 Van Hoek et al. (2008) Age, sex, family history, medical history, physical examination, blood sample 0.90 0.901 Meigs et al. (2008) Age, sex, BMI, family history, liver enzyme levels, smoking, measures of insulin secretion and action 0.74 16 established loci 0.75 Lyssenko et al. (2008)

Br J Cancer 110: 827; 2014

Pharmacogenetics Pharmacokinetics – genetic variation in what you do to a drug Pharmacodynamics – genetic variation in what a drug does to you

Debrisoquine and Nortryptilene Effects of variable activity of CYP2D6 In 1975 Bob Smith, a laboratory director at St Mary’s Hospital Medical School in London, ingested 32 mg of debrisoquine, as did some of his co-workers. “Within two hours severe orthostatic hypotension [low blood pressure] set in with blood pressure dropping to 70/50 mm Hg. Hypotensive symptoms persisted for up to two days after the dose…”. His colleagues, who had taken a similar dose, had no significant effects. Effects of variable activity of CYP2D6

Phase 1 and Phase 2 metabolism

P450 cytochromes A family of around 60 enzymes that insert a single oxygen atom derived from molecular oxygen into a very wide range of organic compounds. Wide and often overlapping specificities The Roche Amplichip® genotypes a patient’s DNA sample for 30 P450 variants involved in drug metabolism. Activity often varies widely between different individuals because of point mutations and variable copy number of genes

Basis of variable Phase 2 responses Fast & slow acetylation of Isoniazid Glutathione S-transferases

Adverse drug reactions Responsible for about 100,000 deaths a year in the USA Responsible for 6.5% of admissions to two large general hospitals in the UK 2% of those patients died projected annual cost to the NHS was up to £466 million Pirmohamed M et al. (2004) Adverse drug reactions as cause of admission to hospital: prospective analysis of 18 820 patients. Br.Med. J. 329: 15–19. Two types: Type A ADRs (the great majority) are an exaggerated response to a standard dose of a drug, because of variants that make an individual particularly sensitive to that drug. Type B ADRs are unrelated to the normal action of the drug and are the consequence of some quite unexpected interaction. Type B reactions are rare, can be very serious and are hard to predict or understand.

Adverse drug reactions Adverse reaction Reaction type Azathioprine Life-threatening bone marrow suppression from normal dose in people with low activity thiopurine methyltransferase A Fluorouracil Potentially fatal toxicity in people with deficiency of dihydropyrimidine dehydrogenase Irinotecan Severe neutropenia and diarrhea in people homozygous for a low-activity variant of the UGT1A1 gene Succinylcholine Prolonged apnea in people with butyrylcholinesterase deficiency Warfarin Excessive bleeding in people with low-activity CYP2C9 or VKORC1 Abacavir Serious and sometimes fatal hypersensitivity reactions in patients with HLA-B*5701 genotype B Carbamazepine Life-threatening Stevens–Johnson syndrome in East Asians with HLA-B*1502 and Europeans with HLA-A*3101 genotypes

Warfarin A powerful anticoagulant, used for patients at risk of embolism or thrombosis The therapeutic window is narrow, but the effective dose varies up to twentyfold. After insulin, warfarin is the most common prescription drug responsible for emergency hospital admissions. The estimated average cost of a bleeding episode is $16,000.

Low-tech treatment of genetic disease NCG3 Table 14.2

Inborn errors of phenylalanine / tyrosine metabolism Succinyl acetone Lethal toxicity Use nitisinone to inhibit tyrosine aminotransferase

Hi-tech treatment of genetic disease NCG3 Fig 14.9

Stratified medicine in cancer

Multi-level analysis of tumour samples The Cancer Genome Atlas Research Network (2013) Nat Genet 45, 1113-1120

Dysregulated pathways in tumour cells Blue: inactivating mutations Yellow: activating mutations (A) 87% of glioblastoma multiformae tumours have mutations that compromise the pathways through which p53 affects senescence and apoptosis. B) 88% of tumours have changes affecting the pathways by which receptor tyrosine kinases (EGFR, ERBB2, PDGFRA, and MET) act to control cell proliferation and survival.

Overviews of cancer 6 Hallmarks of cancer. Hanahan & Weinberg Cell 100: 57; 2000; 144: 646; 2011 Signalling pathways affected in cancer Vogelstein Science 339: 1664; 2014

Targeting the BCR-ABL oncogene A ‘magic bullet’ against chronic myelogenous leukaemia

Brand name (generic name) Drug targets in cancer Tissue / cancer Brand name (generic name) Protein target Mode of action Breast Many brands (Tamoxifen) Estrogen receptor in ER-positive breast cancers Blocks ER, preventing growth signals Leukocytes / leukaemia Glivec® (Imatinib) BCR-ABL1 fusion protein Inhibits abnormal signalling by fusion protein tyrosine kinase Skin / melanoma Zelboraf® (Verumafenib) BRAF V600E mutant protein Specifically inhibits V600E mutant BRAF, triggers apoptosis Non-small cell lung cancer Xalkori® (Crizotinib) EML4-ALK fusion protein Ovarian (advanced) Lynparza® (Olaparib) PARP1 enzyme Blocks repair of DNA breaks in BRCA1-mutant cancers Lung / various Iressa® (Gefitinib) EGFR mutants Binds cytoplasmic part of EGFR, blocks signalling Tarceva® (Erlotinib) Various advanced cancers Tagrisso® (Osimertinib) EGFR T790M mutant Binds cytoplasmic part of T790M mutant EGFR, blocks signalling Small molecules Monoclonal antibodies

Synthetic lethality: PARP inhibitors

Companion diagnostics See the Pharmgkb database for information on drug interactions and pharmacogenetic effects: https://www.pharmgkb.org FDA lists around 200 drugs where the label includes pharmacogenomic data – but most are advisory, not mandatory. www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics/ucm083378.htm   Treatment determined by phenotype Treatment determined by genotype