Pharmacogenomics (GAT3)

what is gene therapy?

using new technology to deliver tailor made genetic material into a patient’s cells to treat disease

what are the 2 types of gene therapies?

• gene therapy → where DNA is inserted artificially into a cell to treat a genetic disease

• gene editing → using human gene editing technology CRISPR-Cas9

describe gene therapy as a type of treatment

• uses non-infectious viral carrier

• delivers a functioning copy of a single gene to cells

• doesn’t alter the patient’s genome/chromosomal DNA

• exists as free-floating DNA in the nucleus where it can transcribed into mRNA

• alters protein production in cells that do not produce a protein when they should, or produce an altered version of the protein that doesn’t function properly

describe gene editing as a type of treatment

• making targeted and deliberate changes to specific regions in the genome

• insert, delete, replace or alter a DNA sequence

• can be carried completely outside the body in the lab (in vitro), within cells to be re-introduced into a living organism (ex vivo), or in the organism itself (in vivo)

give an example of a treatment which uses gene therapy

zolgensma for spinal muscular atrophy

• rare condition caused by variants in SMN1 gene

• SNM protein is required for nerve cells to function → affects motor neurones in spinal cord :. loss of function in muscles used for movement and loss of ability to breathe and swallow

• zolgensma (= onasemnogene abeparvovec) delivers a virus-packaged working copy of the SNM1 gene into patient cells doesn’t alter

• one single dose

what are oncogenes and tumour suppressor genes?

• oncogenes → tells cells when to grow

• tumour suppressor genes → tells cells when to die

how are cancers stratified in order to guide treatment?

stratified based on specific genetic cause

• tumour site agnostic

• mutational signatures → some cancers have mutational signatures e.g. can distinguish lung cancer signatures from smokers vs non-smokers

describe the treatment of non-small-cell lung cancer

• before it was treated as a single disease :. everyone given same chemotherapy

• started to subtype it based on the cells that the tumour grew in, now we stratify it according to different driver mutations

• treatment agents are targeted to the driver mutation

describe the treatment of cystic fibrosis

• CF caused by mutations affecting the CFTR gene

• CFTR proteins acts as an epithelial chloride channel :. decreased membrane conductance and stability

• historically treatment was prophylactic and symptomatic e.g. nebulised antibiotics and mucolytics

• new targeted treatments target the specific molecular defects caused by mutations affecting = personalised and precision medicine

how can we predict drug resistance?

• sequencing genome of infective organism can identify resistance strains and guide treatment options e.g. with TB and COVID-19

• serial sampling of tumour cells to identify new mutations associated with resistance or non-response to treatment → may identify an initial driver mutation then cancer evolves and metastasises :. new driver mutation evolves :. initial targeted treatment won’t work :. now do serial sampling

why is there variation in drug response between individuals?

• co-morbidities

• demographic

• environment

• drug-food interactions

• drug-drug interactions

• renal and hepatic function

• genomic variation

why is genomic variation unique in affecting a patient’s response to drugs?

unlike other factors, a person’s genes do not change during their lifetime

how can we use pharmacogenomics to optimise medicines?

gene variants in an individual can be used to predict likelihood that a drug will be effective, or cause an ADR

describe the significance of the CYP2D6 gene and treatment with codeine

• ¼ of drugs metabolised by CYP2D6 which is encoded by CYP2D6 gene → wide variation in expression of this gene because of variants

• codeine is a prodrug :. needs to be metabolised by CYP2D6 into active form = morphine

• 8% of UK population lack CYP2D6 enzyme due to gene variants = poor metaboliser :. no pain relief from codeine

• 2% have extra copies of the gene :. produce excessive amounts of the enzyme = ultrarapid metaboliser :. rapidly metabolised :. big peak :. side effects

give examples of where pharmacogenomics is already currently used in routine practice

• abacavir

  • = antiretroviral treating HIV

  • variation in HLA allele HLA-B*57:01 pre-disposes patients to severe hypersensitivity reactions causing multiple organ failure

  • introduction of routine testing in all HIV clinics since 2006 → have to do this test before prescribing abacavir

• fluoropyrimidines

  • chemotherapy drugs used to treat solid organ tumours

  • e.g. capecitabine, tegafur

  • metabolised by dihydropyridimine dehydrogenase (DPD) enzyme → some patients have reduced level of DPD associated with variants in the DPYD gene :. increased risk of toxicity

  • all patient have to be screened for DPYD variants prior to commencing therapy

give examples of where genomic testing is recommended but not routine practice

• clopidogrel

  • pro-drug requiring activation by CYP2C19 enzymes → variants of CYP2C19 gene results total non-function, poor or extensive metabolisers

  • CYP2C19*2 allele = loss of function allele → carriers of this have increased risk of CV events and mortality when on clopidogrel for secondary prevention

  • prasugrel and ticagrelor are not affected by CYP2C19 variation

  • testing for CYP2C19 variants are strongly recommended

• antidepressants

  • most undergo metabolism by CYP2C19 and CYP2D6

  • genetic testing can guide dosing

what are the main considerations for implementing pharmacogenomic testing?

• funding → cost effective and need high quality evidence of drug-gene association and a demonstrable benefit on clinical outcomes

• clinical service design → who to test? when? how?

• clinical decision support → front line clinicians need actionable therapeutic recommendations, may be embedded into EPS

• lab considerations → technology? which genes and variants to test?

what is the goal of personalised medicine?

reduce trial and error of prescribing

• pharmacogenomics can predict how we respond to meds

what is the impact of the NHS genomic medicine service?

• before, testing availability and techniques were varied across different organisations and locations

• GMS provide equitable access to lab-based testing for all eligible patients

• testing provided through 7 regional lab hubs

• published eligibility criteria for testing under national genomic test directory

• centralised annual review process for commissioning new tests

describe the governance and funding for the national genomic test directory

• funding decisions are made at end of evaluation and impact assessment process on a yearly basis

• genomics clinical reference group (CRG) will prioritise tests and make recommendations to the genomics programme board who confirm the correct process has been followed and confirm their support for the CRG’s recommendations

• approval to utilise the test directory updates budget will be acquired through annual specialised commissioning planning processes

• fast-track processes for NHSE/I urgent policy statements and NICE technology appraisals that require genomic testing for patients to be eligible for treatment

what are the 4 pharmacogenomic tests listed in the genomic test directory?

• DPYD variant detection → for patients planned to receive fluoropyrimidine treatment

• TPMT/NUDT15 targeted mutation testing → for patients with acute lymphoblastic leukaemia and proposed treatment with purine analogue drugs e.g. 6-mercaptopurine

• MT-RNR1 targeted mutation testing → aminoglycoside exposure related hearing loss

• CYP2C19 genotyping → to determine appropriate dose of amvacamten for obstructive hypertrophic cardiomyopathy in line with NICE technology appraisal

what are key drivers for pharmacogenomic testing implementation in the NHS?

• MHRA medicine licensing requirements → new medicinal products are being licensed with pharmacogenomic-guided dosing as part of their marketing authoristion

• NICE assessments → technology appraisals, HealthTech

give examples of NICE technology appraisals for medicines requiring pharmacogenomic-guided prescribing

• mavacamten for symptomatic obstructive hypertrophic cardiomyopathy → CYP2C19

• lecanemab for mild cognitive impairment or mild dementia caused by alzheimer’s disease → patients homozygous for APOE E3 have a higher risk or ARIA = collection of side effects causing changes in brain scan

give an example of NICE HealthTech guidance which recommends the use of pharmacogenomic testing

• genedriev MT-RNR1 point of care kit for detecting geentic variant to guide antibiotic use and prevent hearing loss in babies

• CYP2C19 genotype point of care test kit to guide clopidogrel use after stroke → testing is recommended but not routinely used due to logistical challenges

what are the challenges associated with rolling out CYP2C19 testing for clopidogrel?

• formulary issues → ticagrelor is not licensed for stroke :. if clopidogrel is found unsuitable for patient, you would have to use ticagrelor off license

• turnaround time → patients may move across care settings before results are available

describe the type of pharmacogenomic testing used in the NHS

• at present, all routine testing is reactive single gene testing → not cost effective because every time a patient needs a new drug that requires pharmacogenomic testing, HCP has to request a new test and restart the process

• future = panel of pharmacogenes in one test → CYP2C19, CYP2D6, SLCO1B1 and HLA-B are responsible for majority of drug-gene interactions

describe the clinical significance of genetic sequencing

• provides complete sequence of ATCG nucleotides

• requires post-sequencing analysis and interpretation

• expensive and time consuming

• can find anything (not just what you are looking for)

• for pharmacogenomics, it is only used for research (not clinically)

describe the clinical significance of small variant detection (SNP genotyping)

• focuses on specific bases in the genome known to vary qith confirmed clinical significance

• can only find what you are looking for

• most commercial tests only look for most common known variants in white european populations

• unable to detect some types of variants e.g. copy number variants → for some genes where we know copy number variants are likely e.g. CYP2D6, we do SNP genotyping following by some kind of sequencing as a secondary test

• binary result →either variant you are looking for is there or it isn’t

• fast and cheap

• false negatives

what system aims to simplify reporting of CYP pharmacogenomic results?

star (*) allele nomenclature system

describe the star allele system for the CYP2C19 gene

total of 39 star known alelles in the CYP2C19 gene- these are the most common found:

• *1 = normal function

• *2 = no function

• *3 = no function

• *17 = increased function

describe diplotype in terms of the star nomenclature system

• individual has 2 copies of each gene - one from each parent

• pharmacogenomic results are reported as diplotype (i.e. genotype) to represent combination of variants on each allele copy

• combination of each allele will determine what kind of metaboliser you are

• *1/*1 = normal metaboliser

• *2/*2 = poor metaboliser

• *17/*17 = ultrarapid metaboliser

• *1/*2 = intermediate metaboliser

what is the wild type allele?

• *1 allele

• also known as reference allele

• indicates normal activity

• BUT *1 allele is often reported when no variants interrogated by a genotyping test are detected → most pharmacogenomic tests only look for specific variants :. false negative potential

• essential to know which variants are interrogated by a particular test to know the significance of a *1 allele result

what is the significance of ethnicity in CYP2C19 phenotypes?

• often quotes that ¼ of patients will have subtherapeutic response as they are intermediate/poor metabolisers

• this number is higher in certain populations e.g. central/south asian, oceanic groups

what is the impact of pharmacogenomic testings on equalities?

varied impact

• can reduce inequalities by understanding which medications is likely to work for different populations

• can increase inequalities as some less common loss-of-function alleles are more prevalent in certain ethnic groups :. not part of alleles looked for in tests :. false negative potential is higher

what is CERSI and CPIC?

guidelines for pharmacogenomic testing