VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
Personalized medicine
1. Dumontier::BIOL4301:Personalized Medicine
Personalized
Medicine
Michel Dumontier, Ph.D.
Associate Professor of Bioinformatics
Department of Biology, Institute of Biochemistry, School of Computer Science
Carleton University
Ottawa Institute for Systems Biology
Ottawa-Carleton Institute for Biomedical Engineering
Nov 18, 2010
3. Dumontier::BIOL4301:Personalized Medicine
SNPs – a major source of variation
• Single Nucleotide Polymorphisms
(SNPs)
– Single base change in DNA
AAGCCTA
AAGCTTA
– SNPs arise as a consequence of
mistakes during normal DNA replication
– Average frequency 1/1000bp
• Other sources of variation
– Insertions, deletions, translocation,
duplications, repeats
– copy number variation is a major
element
SNP
Deletion
Translocation
Insertion
Most Common
4. Dumontier::BIOL4301:Personalized Medicine
Human Variation
• In human beings, 99.9 percent bases are same.
• Remaining 0.1 percent (~3M bases) makes a
person unique.
– Different attributes / characteristics / traits
• how a person looks,
• diseases he or she develops.
• These variations can be:
– Harmless (change in phenotype)
– Harmful (diabetes, cancer, heart disease, Huntington's
disease, and hemophilia )
– Latent (variations found in coding and regulatory
regions, are not harmful on their own, and the change
in each gene only becomes apparent under certain
conditions e.g. susceptibility to lung cancer)
8. Dumontier::BIOL4301:Personalized Medicine
Personalized Medicine
The ability to offer
• The Right Drug
• To The Right Patient
• For The Right Disease
• At The Right Time
• With The Right Dosage
Genetic and metabolic data
will allow drugs to be
tailored to patient
subgroups
9. Dumontier::BIOL4301:Personalized Medicine
Benefits of Personalized Medicine
• Better matching patients to drugs instead of “trial
and error
• Customized pharmaceuticals may eliminate life-
threatening adverse reactions
• Reduce costs of clinical trials by
– Quickly identifying total failures
– Favourable responses for particular backgrounds
• Improved efficacy of drugs
10. Dumontier::BIOL4301:Personalized Medicine
Personalized Medicine : BiDil
• Combination pill containing two medications for
heart failure, cardiovascular disease, and/or
diabetes.
• Clinical trials did not show overall benefit across
entire population.
• Subgroup of patients showed best overall benefit
– BiDil approved solely for use in African-descent patients.
Controversial!
11. Dumontier::BIOL4301:Personalized Medicine
PGx
• Pharmacokinetics
– What the body does to the drug
– dose, dosage regimen, delivery form
– Drug fate: Absorption, distribution, metabolism, and elimination
of drugs (ADME)
• Pharmacodynamics
– What the drug does to the body
– Biochemical and physiological effects of drugs
– mechanism of drug action
– relationship between drug concentration and effect
• Pharmacokinetics and pharmacodynamics are essential to assess
the drug efficacy.
13. Dumontier::BIOL4301:Personalized Medicine
PGx + genetics/genomics
• Pharmacogenetics
– The effect of genetic variation on drug response.
• Pharmacogenomics
– The application of genomics to the study of human
variability in drug response.
• Pharmacogenetics and pharmacogenomics are
expected to play an important role in the development of
better medicines for populations and targeted therapies
with improved benefit/risk ratios for individuals
14. Dumontier::BIOL4301:Personalized Medicine
Cytochrome P450 Enzymes
In bacteria, fungi, insects, plants, fish, mammals
Catalyze monooxygenation reaction:
RH + 2H+
+O2 + NADPH
ROH + H2O + NADP+
Act on:
– Endogenous substrates (cholesterol,
steroids, fatty acids)
– Exogenous (drugs, food additives,
environmental toxins)
Involved in
– Production of steroids
– Metabolism of fatty acids, prostaglandins,
leukotrienes, retinoids
– Activation or inactivation of therapeutic
agents
– Enzyme activation/inhibition resulting in
drug-drug interactions, adverse events
20. Dumontier::BIOL4301:Personalized Medicine
CYP3A4
• Abundant in liver and intestines
and accounts for nearly 50% of
CYP450 enzymes.
• Activity can vary markedly among
members of a population
– Constitutive variability is ~5-fold
but can increase to 400-fold
through induction and inhibition
• Activity affected by other drugs:
– Grapefruit juice is an inhibitor
Felodipine is a calcium channel
blocker (calcium antagonist), a
drug used to control hypertension
(high blood pressure)
5mg tablet
with juice
22. Dumontier::BIOL4301:Personalized Medicine
Quantitative Structure-Activity
Relationship (QSAR)
• find consistent relationship between biological activity
and molecular properties, so that these “rules” can be
used to evaluate the activity of new compounds.
• extract features (hydrophobicity, pK, van der Waals radii,
hydrogen bonding energy, conformation)
• build mathematical relationship f(activity|features)
• automatically assesses the contribution of each feature
• can be used to make predictions on a new molecule
26. Dumontier::BIOL4301:Personalized Medicine
Wilson. PXR, CAR, and drug metabolism. Nat Rev Drug Disc 2002
CYP3A4 mediated Drug-Drug Interaction
PXR: pregnane X receptor; RXR: retinoid X receptor
• Protect against xenobiotics
• Diverse drugs activate through heterodimer complex
• Cause drug-drug interactions
28. Dumontier::BIOL4301:Personalized Medicine
Codeine
Metabolism
Gasche Y et al. Codeine intoxication associated with ultrarapid
CYP2D6 metabolism. NEJM 2004
• 80% codeine normally converted
to glucuronide, eliminated by
kidney.
• 5-10% codeine is metabolized
into morphine by CYP2D6
• inhibition of CYP3A4 or rapid
metabolic variants of CYP2D6
during renal failure would
show toxicity
– 7% of caucasians have a
nonfunctional CYP2D6 variant
– <2% are CYP2D6 ultrarapid
metabolizers which may suffer
from opioid intoxication
31. Dumontier::BIOL4301:Personalized Medicine
Known side effects
Unavoidable Avoidable
Medication
errors
Product quality
defects
Preventable
adverse
events
Injury
or death
Remaining
uncertainties
• Unexpected side effects
• Unstudied uses
• Unstudied populations
Sources of risk from drug products
FDA: Center for Drug Evaluation and Research
2005 - Report to the Nation
32. Dumontier::BIOL4301:Personalized Medicine
LIPITOR:
Known Side Effects
• Lipitor blocks the
production of
cholesterol in the body.
• May reduce risk of
hardening of the
arteries, which can lead
to heart attacks, stroke,
and peripheral vascular
disease
33. Dumontier::BIOL4301:Personalized Medicine
FDA: Center for Drug Evaluation and Research
2005 - Report to the Nation
Drug recalls are surprisingly common
Drug Recalls
191
226 248
352 354
254
215
401
60
53
34
88
72 156 83
88
71
101
248
316
176
72
0
300
600
1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Fiscal year
Number
Prescription Over-the-counter
34. Dumontier::BIOL4301:Personalized Medicine
Many reasons for drug recalls
Reported Drug Quality Defects
Other, 9%
Contamination/
sterility, 3%
Fill problem,
4%
Packaging, 6%
Delivery
system, 10%
Product defect,
14% Formulation/
substitution,
22%
Adverse drug
reports, 18%
Labeling, 14%
Fiscal year 2005
FDA: Center for Drug Evaluation and Research
2005 - Report to the Nation
36. Dumontier::BIOL4301:Personalized Medicine
Vioxx targets prostaglandin
biosynthesis
• Prostaglandins, derivatives of C20
fatty acids, often trigger pain,
fever, and inflammation.
• Aspirin, Ibuprofen,
acetominaphen are non-steroidal
anti-inflammatory drugs
(NSAIDS) that inhibit
prostaglandin H2 synthase
(A.K.A. COX) – no pain.
37. Dumontier::BIOL4301:Personalized Medicine
• 3 isoforms: COX-1, COX-2, COX-3.
• COX-1 constitutively expressed
• COX-2 only expressed in response to inflammation
• Drugs were designed to fit into COX-2 active site
channel, but not COX-1 (20% smaller channel)
• Vioxx & Celebrex lack non-specific side effects of
NSAIDS, but Vioxx caused cardiac side effects & was
withdrawn in 2004
38. Dumontier::BIOL4301:Personalized Medicine
in silico Drug Discovery
• Need 3D structure
• Scan a virtual library of small molecules and “dock” them
to a site of interest on a protein structure
• Predict binding energy
• Filters thousands of compounds relatively quickly
• Top hits can be used for more rigorous
computational/experimental characterization and
optimization
42. Dumontier::BIOL4301:Personalized Medicine
"When you're studying human genetics, you're studying the information that
goes into the making of man and how that information flows from one
generation to the next. To be able to do that well, you have to know the
population structure. We can basically take the list that includes everyone in the
country or 2,000 people with schizophrenia. We can know within minutes
exactly how everyone is related to everyone else, which is key for being
able to study the genetics of anything in a sensible manner."
deCODE
Genetics in
Reykjavik,
Iceland.
Country-wide genotyping and family tree
reconstruction
43. Dumontier::BIOL4301:Personalized Medicine
deCODE Genetics
For example, deCODE has used the Icelandic family tree to look at people who
are taking statins. Approximately 10,000 people in Iceland take statins, but
about 2,000 of those don't respond. The list of patients who don't respond can
be run through the genealogy database. "I can tell you that they are related to
each other, and we can get families that have a structure that allows us to map
a gene that indicates a lack of response to statins."
45. Dumontier::BIOL4301:Personalized Medicine
Things to Consider
• Does my doctor know enough about
genomic medicine to be advising me?
– Are there genetic counselors available?
• Will the test only be for this condition?
– What if I am susceptible to another disease?
• Who will know about this?
– Doctors… insurance companies?
• How exactly will the results be kept secure
and in confidence?
46. Dumontier::BIOL4301:Personalized Medicine
How much will this cost?
• More drugs may succeed in clinical trials due to
positive outcome for smaller subset
– Will pharma attempt to recoup costs with a pricier drug?
• Will public health cover the costs of genetic
testing?
– Reduce overall health cost due to fewer ADRs
– Should we determine clinically validated genes or
should we sequence the genome?
• How will insurance premiums be affected?
47. Dumontier::BIOL4301:Personalized Medicine
There is still lots to figure out…
• Science still early. Limited data in public domain.
• Many variations not clinically significant
• Expensive to test for genotype (currently)
• Ethical issues in testing individual genotype
• Unclear how to deliver information to the
practitioner
Excess amounts can lead to bone marrow toxicity, reducing the normal amounts of white and red blood cells
6-MP ribonucleotide inhibits purine nucleotide synthesis and metabolism. This alters the synthesis and function of RNA and DNA.
congestive heart failure—the progressive weakening of the heart muscle to the point where it can no longer pump blood efficiently
Most drug-metabolizing enzymes exhibit clinically relevant genetic polymorphisms.
Essentially all of the major human enzymes responsible for modification of functional groups [classified as phase I reactions (left)] or conjugation with endogenous substituents [classified as phase II reactions (right)] exhibit common polymorphisms at the genomic level;
Those enzyme polymorphisms that have already been associated with changes in drug effects are separated from the corresponding pie charts.
The percentage of phase I and phase II metabolism of drugs that each enzyme contributes is estimated by the relative size of each section of the corresponding chart. ADH, alcohol dehydrogenase; ALDH, aldehyde dehydrogenase; CYP, cytochrome P450; DPD, dihydropyrimidine dehydrogenase; NQO1, NADPH:quinone oxidoreductase or DT diaphorase; COMT, catechol O-methyltransferase; GST, glutathione S-transferase; HMT, histamine methyltransferase; NAT, N-acetyltransferase; STs, sulfotransferases; TPMT, thiopurine methyltransferase; UGTs, uridine 5&apos;-triphosphate glucuronosyltransferases.
Figure 4. Pharmacogenetics of Nortriptyline. Mean plasma concentrations of nortriptyline after a single 25-mg oral dose are shown in subjects with 0, 1, 2, 3, or 13 functional CYP2D6 genes.
In addition, some subjects with ultrarapid metabolism have been shown to have multiple copies of the CYP2D6 gene. 18 Such
subjects can have an inadequate therapeutic response to standard doses of the drugs metabolized by CYP2D6. Although the occurrence of multiple
copies of the CYP2D6 gene is relatively infrequent among northern Europeans, in East African populations, the allele frequency can be as high as 29
percent. 22 The effect of the number of copies of the CYP2D6 gene — ranging from 0 to 13 — on the pharmacokinetics of the antidepressant drug nortriptyline is shown in Figure 4. 23 There could hardly be a more striking illustration of how genetics influences the metabolism of a drug.
Approximately 5 to 10 percent of white subjects were found to have a relative deficiency in their ability to oxidize the antihypertensive drug debrisoquin. They also had an impaired ability to metabolize the antiarrhythmic and oxytocic drug sparteine. Subjects with poor metabolism of these
two drugs had lower urinary concentrations of metabolites and higher plasma concentrations of the parent drug than did subjects with extensive metabolism
A plot of the ratio of urinary debrisoquin to 4-hydroxydebrisoquin — a so-called metabolic ratio — is shown in Figure 3. The higher the metabolic ratio, the less metabolite was excreted. Therefore, subjects with poor metabolism are shown, counterintuitively, at the far right of the graph, with a few subjects at the far left of the frequency distribution who are now classified as having ultrarapid metabolism. As described subsequently, suchsubjects may have multiple copies of the gene for CYP2D6. Therefore, debrisoquin and sparteine represented “probe drugs” — compounds that could be used to classify subjects as having either poor metabolism or extensive metabolism. That strategy, the administration of a probe compound metabolized by a genetically polymorphic enzyme, became a standard technique used in many pharmacogenetic studies.
Drugミdrug interactions. The molecular basis of a drug-drug interaction. The orphan nuclear receptor PXR is a transcription factor that regulates the expression of the CYP3A gene (yellow) in the liver and intestine. It functions as a heterodimer with the nuclear receptor RXR. Drug A binds to PXR and induces expression of the CYP3A enzyme (pink), accelerating the metabolism of drug B, which is a substrate for CYP3A. CYP, cytochrome P450; OH, hydroxyl group; PXR, pregnane X receptor; RXR, retinoid X receptor.
Figure 1. The Incidence-Rate Ratio for Sudden Death from Cardiac Causes According to the Current Use of the Study Antibiotic Medications and CYP3A Inhibitors.
The bars indicate 95 percent confidence intervals. The reference group for the incidence-rate ratio associated with the concurrent use of erythromycin and CYP3A inhibitors and with the use of CYP3A inhibitors alone is the patients who used none of these medications; that for the incidence-rate ratio associated with the use of erythromycin and use of amoxicillin, regardless of the use of CYP3A inhibitors, is the patients who used neither of these antibiotic medications.
Life-threatening opioid intoxication developed in a patient after he was given small doses of codeine for the treatment of a cough associated with bilateral pneumonia. Codeine is bioactivated by CYP2D6 into morphine, which then undergoes further glucuronidation. CYP2D6 genotyping showed that the patient had three or more functional alleles, a finding consistent with ultrarapid metabolism of codeine. We attribute the toxicity to this genotype, in combination with inhibition of CYP3A4 activity by other medications and a transient reduction in renal function.
Figure 1. Metabolic Pathways of Codeine Biotransformation.
The conversion of codeine into norcodeine by CYP3A4 and into codeine-6-glucuronide by glucuronidation usually represents 80 percent of codeine clearance, and conversion of codeine into morphine by CYP2D6 represents only 10 percent of codeine clearance (blue arrows). Morphine is further metabolized into morphine-6-glucuronide and into morphine-3-glucuronide. Morphine and morphine-6-glucuronide have opioid activity (green arrows). Glucuronides are eliminated by the kidney and are thus susceptible to accumulation in cases of acute renal failure. The patient (red arrows) had ultrarapid CYP2D6 metabolism, inhibition of CYP3A4 as a result of treatment with clarithromycin and voriconazole, and glucuronide accumulation due to acute renal failure. Red arrows with dotted lines indicate low levels of drug conversion or elimination, green arrows with dotted lines indicate low levels of brain penetration, and thick arrows indicate high levels.