Editing Personalized Medicine

=Personalized Medicine=

==Lecture Objectives==
*Define/describe personalized medicine and how it could be and is used, including 
**Direct to Consumer (DTC) testing
*Describe factors contributing to drug responses
*List examples of how genetic polymorphisms effect drug metabolism
*Describe some of the genetic differences in the cytochrome P450 genes and the resulting effects on drug metabolism

==“Personalized Medicine”==
*Personalized medicine is "customized healthcare tailored to individual patients in whatever ways possible".
*From a genetic and pracitcal perspective, personalized medicine is screening to identify genetic predisposing risk factors in order to reduce the risk by changing:
**diet
**behavior
**life style
**environmental exposures
**medications
*Already happening and expected to increase.


*As an example of the need for personalized medicine, compare the clinical cases of Dr. Jim Fixx and Sir Winston Churchill.
**Fixx: Marathon runner, Health guru, 5’8” 150 lbs, Abstinence, Died at age 52
**Churchill: Prime minister, Couch potato, 5’8” 270 lbs, Smoker, drinker, eater, Died at age 90
*Both died of heart attacks!

==Assessing Risk==
*Risk assessment is important in many diseases, including breast cancer.
**Recall that we have previously discussed the role brca1 and brca2 play.
**High risk calls for pre-emptive treatment in many cases / diseases.
**Low risk calls for avoiding iatrogenic morbidity.

*Effective risk assessment can save society much spending

*But what if cancer does occur?

===HER2 as a personalized medicine risk factor===
*HER2 is known to be expressed in excess in 20-30% of breast cancers (and also in many other cancers).
*HER2 is know to be associated with more aggressive tumors.
*HER2 status (positive or negative) affects treatment and outcomes.
*Therefore, HER2 status is an example of a piece of personal disease information (specific to the pt) that can be leveraged to augment outcomes.
**That is, HER2 status is personalized medicine.


*Tx for HER2+ breast CA:
**Monoclonal Ab against HER2 (Trastuzumab = Herceptin)
**Hormone treatment unlikely to be effective.


*HER2 overexpression is accomplished by '''gene amplification'''.
*HER2 is karyotypically observed as:
**'''double minutes''' (small, accessory chromosomes)
**'''HSRs''' (homogenously staining regions)


*Other examples of personalized medicine surrounding tumor-expression variation include EGFR and BCR-ABL.
*Each of these has a diagnostic and drug that are used to determine the status and to treat a particular status.
*EGFR variable expression in colorectal cancer:
**EGFR IHC test
**Erbitux
**c-kit expression in gastrointestinal stromal tumors:
**c-kit IHC test
**Gleevec

==Direct To Consumer (DTC) Testing==
*Direct to consumer genetic testing refers to genetic tests that are marketed directly to consumers (e.g. via the Internet,  television, print or advertisements.).
**May also be called other things such as at-home genetic testing, etc.
*DTC raises multiple issues, including the concern that DTC testing does not necessarily involve a physician.
*Groups taking issue are the American College of Medical Genetics and the College of American Pathologists.

===ACMG's Stance on DTC Testing===
*American College of Medical Genetics (ACMG) Policy statement on DTC testing (2008). 
**“…it is critical for the public to realize that genetic testing is only one part of a complex process which has the potential for both positive and negative impact on health and well being.”
*Suggestion of minimum requirements for DTC:
**A knowledgeable '''professional should be involved in the process of ordering and interpreting''' a genetic test
**The consumer should be fully informed regarding '''what the test can and cannot say''' about his or her health
**The '''scientific evidence on which a test is based''' should be clearly stated
**The clinical testing laboratory must be '''accredited by CLIA, the State and / or other''' applicable accrediting agencies
**'''Privacy concerns''' must be addressed 

===Some DTC Testing Questions===
*What is the disorder for which the test is being used?
*What is the test?
*What evidence links the test to the disorder?
*How is the disorder usually diagnosed?
*What are the implications of a positive test result vs. a negative test result on medical management? Personal decision-making?
*Risks to other family members?
*Who is going to help explain the results to all the family members who need to know?

===Pt example===
*Patient evaluated by our cytogenetics laboratory
*Found to have deletion associated with Wolf Hirschorn syndrome.
*Clinical features not all typical.
*Family thought that patient may be a mosaic.
*Family sent buccal swab to DTC company for testing.
*Results came back with a number of increased and decreased estimates related to a variety of diseases.
*The company did not identify the deletion found by the cytogenetics lab, so, the family decided that this was evidence for  mosaicism.

==Pharmacogenetics==
*Pharmacogenetics is the study of how genetics affects drug effects.
*Pharmacogenomics: Application of genomic information or methods to pharmacogenetic problems
*The promise / hope is that the knowledge of a patient's DNA sequence could be used to optimize drug efficacy and reduce adverse effects.

===Drug Response===
*Response rate of most drugs is 25-75%.
*Thus, use of drugs in “non-responders” increases occurrence of side effects and health care costs.
*About 15% of prescribed drugs have severe adverse effects.
*Some side effects can be so severe that individuals can be hospitalized, even when the drugs are prescribed and administered according to established protocols.


*As specific examples (drug, disease, efficacious population):
*ACE inhibitors, HTN, 10-30%.
*Beta blockers, heart failure, 15-25%
*Anti-depressants, depression, 20-50%
*Statins, cholesterol, 30-70%
*Beta-2-agonists, asthma drugs, 40-70%

===Adverse Reactions===
*Over 2 million people are hospitalized each year for adverse reactions to prescription drugs, most of which are avoidable.
*More than 100,000 people die from adverse reactions (~sixth leading cause of death).

===Pharmacogenetic Questions===
*Why at a recommended prescribed dose, is a drug:
**Efficacious in most
**Not efficacious in others
**Harmful in a few
**Fatal in 0.32%


*Goal: get the right drug and dosage for each patient based on genetic metabolic profile


*By way of pharmacogenomic-driven trials, the daily dose for many medications has been "personalized" based on broad descriptors.
**Descriptor examples are sex, race, age, etc.

===Drug Response Factors===
*Drug metabolism ('''pharmacokinetics''')
*Drug target reactivity ('''pharmacodynamics''')
*Environmental conditions
*Acquired problems (pathological processes)
*General health, race, age, and gender
*Genetic / genomic factors
*Combinations of factors


===Pharmacokinetics and Pharmacodynamics===
*'''Pharmacokinetics explores what the body does to the drug'''
*'''Pharmacodynamics explores what a drug does to the body'''


*Alteration(s) of drug target reactivity (dynamics) and / or drug metabolism (kinetics) often have a genetic origin.
*These genetic changes that cause pharmacodynamic (target) and pharmacokinetic (metabolism) changes can change the '''drug responsiveness'''.
*Mutation may impact:
**Distribution
**Biotransformation (converting drug)
**Metabolism
**Excretion
**et cetera

===Drug Conversion===
*Drug conversion is the metabolic change of a prodrug to an active drug once inside the body.
**Synonyms for drug conversion include "transformation" and "biotransformation".
*Active drugs do NOT need to be converted / transformed (anywhere in the body) to be active at the target site.
*Prodrugs REQUIRE metabolic conversion or biotransformation to be active at the target.
*Complete '''biotransformation typically requires several different enzymes.'''
*Some drugs are converted in the liver.


*Variation in drug conversion efficiency from person to person can lead to differing effective doses.
*When drug conversion is excessive, less of a drug need be given for desired effect.
**Upon deficiency, much of the prodrug is lost to excretion before it can be converted and act at the target site.
*When drug conversion is deficient, more of a drug need be given for desired effect.
**Upon deficiency, most of the prodrug is converted and active at the target site and little is lost to excretion.

===Drug Metabolism===
*Most drugs are metabolized in the liver.
**Recall that the goal of ''metabolism'' is to get rid of the drug.
**The goal at the liver is usually to ''make them more water soluble for subsequent elimination through the kidneys''.
**In a similar manner, the liver can metabolize lipophilic drugs to an hydrophilic form so that they can be excreted.
***'''Lipophilic drugs that reach the kidney are often reabsorbed (retained).'''


*'''Variation in drug responses usually due to genetic variation in drug metabolism enzymes.'''
*Almost all of the major enzymes involved in drug metabolism display clinically significant genetic polymorphisms / variants.


===Drug target mutations (pharmacodynamics)===
*Recall that drug ''dynamics'' describe the drug's activity at the target site.
**Pharmacodynamics encompasses a activity at many levels: expression, modification, ..., metabolism, signaling, etc.
*Mutations can increase or decrease the target affinity for the drug.
*Mutations can increase or decrease the density of target sites.
**Density can be affected at many levels: transcription, processing, translation, post-translational processing, transport, reuptake, and or degradation.
*Mutations can affect the response to activation of the target by the drug.
**For example, the drug may bind to the target in the same way but the cell may respond differently (perhaps a metabolic change).

===Hypothetical Scenario===
*After a surgery, your surgeon prescribes codeine to treat your post-surgical pain.
*Two hours post initiation of treatment, you are still experiencing excruciating pain!
*Why isn’t codeine working the way anticipated / desired?
*To be an effective analgesic, '''codeine must be converted to morphine.'''

===CYP2D6 and Drug Metabolism===
*Recall that drug metabolism is called '''pharmacokinetics'''.


*CYP2D6 is '''predominantly expressed in the liver'''.
*CYP2D6 is a drug metabolizing machine!
*Metabolizes 20-25% of commonly prescribed drugs.
*It metabolizes at least 28 major drugs.
*Major, mentionalable drugs include: '''codeine''', oxycodone, amphetamines, lidocaine, haloperidol, risperidone, fluoxetine, and carvediolol.
*Major classes include: beta blockers, anti-depressants, antipsychotics, anti-cancer agents, and '''opioids'''.
*'''CYP2D6 catalyzes conversion of codeine to morphine.'''
**That means that 10% of the population (who have deficient CYP2D6 codeine->morphine conversion) have no pain relief from codeine.

====CYP2D6 Variation====
*Variation in CYP2D6 activity can lead to serious drug reactions.
*CYP2D6 is highly polymorphic: SNPs (of all sorts), copy number polymorphisms, etc.
*There are over 100 alleles.
*These alleles are found in different frequencies the many different ethnic populations.
*We classify alleles as "functional", "dysfunctional", and "non-functional".
**Functional: *1, *2, *35
**Dysfunctional: *9, *10, *17, *29, *37, *41
**Non-functional: *3-8, *11-16, *18-20, *36, *38, *40, *42


*CYP2D6 can be divided into subpopulations (sub-allelic populations, sub-"functional/dysfunctional/non-functiona") of "metabolizers" based on the functional activity of the resulting protein: "poor", "extensive", "ultrarapid".
*'''The normal CYP2D6 response is rapid conversion of codeine to morphine.'''
**That is, the "normal allele" would be considered an '''extensive metabolizer (EM)'''.
**For extensive metaboliziers, pain relief with codeine is effective.
**Extensive metabolizers are much less likely to develop toxicity with standard dose of codeine.

====CYP2D6 Inadequate Expression Alleles====
*Alleles that lead to "inadequate expression" are '''poor metabolizers'''.
*Poor metabolizers demonstrate decreased codeine->morphine conversion.
**Poor metabolizers, therefore, have poor pain relief from codeine.
*Poor metabolizers '''can develop adverse effects''' from codeine.
**Nausea, as an example.
 **Adverse effects may be due to increased codein consumption.
*24 alleles have '''no activity''' and are therefore considered to be poor metabolizers.
*6 alleles have decreased activity.
*'''5-10% of caucasians are homozygous for low / no-activity alleles.'''

====CYP2D6 Overexpression Alleles====
*'''Overexpression of CYP2D6 leads to increased conversion of codeine to morphine--called ''ultrametabolizing'''''.
*Ultrametabolism results in excessive morphine at a given dose.
*Extra morphine can result in advers events.
**Impaired respiration
**Sedation
*Alleles 1, 2, 4 and others have '''copy number polymorphisms that cause their overexpression'''.
**For example, variant 2 can have 1-13 copies.
**Recall that "normal" is to have ''two functional copies''.
*'''30% of East Africans have hyperactive CYP2D6.'''
**These pts should be given less codeine!

====Personalizing Doses====
*It ''is'' possible to test for variations in the gene for the CYP2D6 enzyme.
*However, genetic testing is not yet routinely done.
*In the future, it should be possible to determine what genetic variations exist in CYP2D6 gene before prescribing a pain reliever.

===Thiopurine Methyltransferase and Drug Metabolism===
*Recall that metabolism of a drug (pharmacokinetics) has to down with activating and excreting a drug.


*Thiopurine methytransferase is also called TPMT.
*'''TPMT breaks down a class of chemotherapeutic compounds called thiopurines.'''
*TMPT (and the pt's specific variant) influences the outcome of chemotherapy for leukemia in children.
*Thiopurines can reach toxic levels if the drug is eliminated too slowly.
*The dose must be adjusted according to an individual's TPMT “speed”.
**Adjusting appropriately to the pt's TPMT variation '''has dramatically improved the survival rate of affected children.'''
*The label for thiopurines even suggests “Recommendation to use pharmacogenetic testing to guide dosing”.
*TPMT*3A is the primary allele responsible for the '''trimodal distribution''' of thipurine methyltransferase activity: normal, poor, and subpoor metabolizing activities.

====TPMT: Normal metabolizers====
*"Normal" TPMT pts.
*These pts metabolize thiopurines normally.
*90% of the population is homozygous for wild type allele.
*In "normal" pts, '''thiopurine toxicity is low, but relapse is high.'''

====TPMT: Poor metabolizers====
*Poor metabolizers
*These pts metabolize thiopurines slowly.
*Thiopurine toxicity is high in poor metabolizers.
*Children are at risk of dying of the toxicicity of thiopurine.

====TPMT: Supboor metabolizers====
*Subpoor metabolizers
*These pts metabolize thiopurines via TPMT very slowly.
*Thiopurine toxicity is highest in these pts.
*0.3% are '''homozygous for low activity variants'''
*Mostly '''TPMT*3A allele homozygotes'''
*These subpoor metabolizers (with TPMT*3A) are at '''high risk of myelosuppression'''.
*These pts should be '''treated with 1/10 to 1/15 the standard dose'''.

===Personalized Medicine Over Multiple Genes===
*The preceding examples involve pharmacogenetic variations as a result of variation in a single gene.
*However, there are examples of '''multiple genes that affect both the pharmacokinetics and pharmacodynamics''' of a drug.


*“With 30 million prescriptions written annually for warfarin in the United States and nearly 43,000 reported annually as being seen in emergency rooms for adverse side effects, the potential for genetic testing to minimize pain and suffering is tremendous,” said Joe Leigh Simpson, MD, FACMG, President of the American College of Medical Genetics.

====Warfarin====
*One of the most widely prescribed oral anticoagulants.
*Warfarin has a narrow therapeutic window (that is, the serum active metabolite level must fall within a tight window).
*Warfarin has wide inter-individual variability.
*These two factors make dosing warfarin very difficult, thus the many ER visits for adverse effects.
*If the dose is too low (under-anticoagulation), thromboembolic stroke may occur.
*If the dose is too high (over-anticoagulation), bleeding complications can result, including intracranial bleeding.


*Warfarin began as a rat poison!


*Warfarin stops the formation of active clotting factors by '''inhibition of vitamin K epoxide reductase complex subunit 1 (VKORC1).'''
**VKORC1 reduces vitamin K epoxide so that it can be used as a cofactor in the '''activation of clotting factors 2, 7, 9, 10, and proteins C, S, and Z.'''
*Warfarin is found as S-warfarin and R-warfarin in the body.
**S-warfarin is the active form.
*'''S-Warfarin is metabolized by CYP2C9'''.
*Warfarin activity is determined partially by genetic factors.

====CYP2C9 and Warfarin Metabolism (Pharmacokinetics)====
*CYP2C9 metabolizes warfarin.
**CYP2C9*1 is the wildtype allele with "normal" activity.
*Variant '''alleles *2 and *3 have decreased activity''' than the wildtype allele.
*Variation of CYP2C9 exists primarily in Caucasian patients.
**Variation is rare in African American and most Asian patients.
*Recall that this is a metabolic issue and therefore is considered '''pharmacokinetics'''.


*CYP2C9 variants *2 and *3 have lower activity.
**Lower activity means that warfarin is not metabolized as quickly for pts with the *2 and *3 variatns
**Therefore, '''*2 and *3 CYP2C9 variants require less warfarin to achieve the same anticoagulant effect.'''
**Therefore, *2 and *3 CYP2C9 variant pts have an ''increased risk for overdose and subsequent hemorrhage''.

====VKORC1 and Warfarin Target Activity (Pharmacodynamics)====
*Warfarin dose variability is not entirely explained by CYP2C9's metabolic activity.
*VKORC1 (warfarin's target) also provides variability that affects dose response.
**This is a '''pharmacodynamic effect'''.


*Recall that warfarin inhibits VKORC1 so that it cannot recycle (reduce) vitamin K for use as a cofactor in coagulation factor (2, 7, 9, 10, C, S, Z) activation.
*VKORC1 has two main haplotypes: A and B.
*Haplotype A has elevated sensitivity to warfarin; that is '''haplotype A binds warfarin very well'''.
**Therefore ''haplotype A requires a lower dose of warfarin to achieve anticoagulant effect''.
**'''Asian Americans''' are often of haplotype A and therefore extra sensitive to warfarin.
*Haplotype B has decreases sensitivity to warfarin; that is '''haplotype B binds warfarin poorly'''.
**Therefore ''haplotype B requires a higher dose of warfarin to achieve anticoagulant effect''.
**'''African Americans''' are often haplotype B and therefore insensitive to warfarin.

====Warfarin Dosing====
*Recall that CYP2C9 variation produces pharmacokinetic variation that affects warfarin dose response.
*Recall that VKORC1 variation produces pharmacodynamic variation that affects warfarin dose response.
*'''These two variation factors account for only 30-45% of the warfarin dose response differences.'''
*Lower initial doses should be used for:
**CYP2C9 *2 and *3 pts
**VKORC1 haplotype A pts

==Genetic Testing==
*Roche pharmaceuticals has been awarded the license from FDA to detect genetic variations in the activity of cytochrome P450 enzymes 
CYP2D6 and CYP2C19.
**Recall that CYP2D6 is the enzyme that converts codeine to morphine.
*About 25% of all drugs are substrates of either CYP2D6 and CYP2C19.

==Ethical Issues==
#Not giving a nonresponder a certain drug which works in others, patient may feel discriminated against (direct to consumer 
marketing)
#Falsely accusing patient of being noncompliant or having drug-seeking behavior due to increased clearance.
#Nonresponder status influencing risk calculation made by insurance companies (agreeing to cover expensive, toxic or ineffective drug)
#“Do you want to be contacted if your genotype is found at a later time to be associated with a condition you weren’t originally tested for?”
##Referrals
##Privacy
##Who contacts the patients?

==Therapeutic Lessons from Pharmacogenetics==
*All drug effects vary from person to person and drug effects are influenced by genes
*Most drug responses are multifactorial
*The frequency of variation of drug effects, whether multifactorial or genetic, varies considerably in ethnically defined populations.