Addiction: genes and environment

Question 1

How do we know genes matter in addiction differences between individuals, compared to the environmental causation?

Answer 1

e. g. Smokers
- differ in amounts of cigarettes smoked per day
- some can be explained by environment (time, money)

• However: even in controlled environments, there are differences
• > genes play a role

=> genetic studies of addiction
- we need to understand both genetic and environmental factors to understand addiction

Question 2

What is the simple theory of phenotype variation?

Answer 2

Phenotype = genes + environment

Question 3

What is the aim of genetic studies?

Answer 3

Identify genes that contribute to variation in a phenotype

e.g. age of first use

Question 4

What is the method of genetic studies?

Answer 4

Twin studies

- controlled experiments would be unethical

Question 5

What do twin studies indicate on the variation of addiction-related phenotypes?

Answer 5

> Genes account for 50/70% of variation of addiction-related phenotypes
= heritability

> Environmental factors can be considered “errors”, but not always

Question 6

What is the complex theory of phenotype variation?

Answer 6

There are interactions and correlations between genes and environments

• e.g.: no environmental factor -> no gene expression
  (= no expression of predisposition)

Question 7

How did Caspi and Moffitt (2006) show that environmental factors alter the expression of genes (gene-environment interactions)?

Answer 7

> 2 versions of dopamine receptor gene (DRD4 VNTR) in tobacco smokers

> DRD4 short:
- no differences in self-reported craving between before and after exposure to lit cigarette (environmental stimulus)

> DRD4 long:
- higher level of reported craving after exposure vs. before exposure to lit cigarette

Question 8

What is a gene-environment correlation?

Answer 8

Genetic predisposition that influences likelihood of exposure to particular environmental factors

e. g. people with predisposition toward novelty-seeking behaviours
- not directly predisposed toward drug-taking
- BUT may be more likely to seek out drugs as novel experience

Question 9

How can gene-environment relationships influence addictive behaviours in the real world?

Answer 9

Genetic variation is key, but the strength of genetic expression seems to depend on context

e.g.:
> Public health policies
- some US states have more restrictive smoking legislation -> difficult access to substance
- lower heritability of adolescent daily smoking

> Peer influence

• some social environments are more likely to encourage drug-taking -> easy access to substance
• higher heritability of substance abuse in these groups

Question 10

Which studies allow us to know which genes matter?

Answer 10

Gene association studies:

• Candidate gene association studies
• Genome-wide association studies

Question 11

What do candidate gene association studies consist of?

Answer 11

Investigating small number of genes
- based on known information

-> “usual suspects”

Question 12

What do genome-wide association studies consist of?

Answer 12

Investigating genetic variation across the whole genome
- large sample

-> “finding needle in a hay stack”, by making needle bigger so it’s easier to find

Question 13

What characterises candidate gene association studies?

Answer 13

> Hypothesis driven

> Focus on few, selected genes

> Genes chosen from knowledge of phenotype mechanisms

Question 14

Which type of genes are chosen in candidate gene association studies on addiction phenotypes?

Answer 14

• Genes involved in behaviour
  (e. g. dopamine reward pathway)
• Genes involved in drug’s mechanism of action
  (e. g. drug metabolism -> enzymes or receptors involved)

Question 15

How is a candidate gene study carried out?

Answer 15

> Target neurotransmitter gene from controls and cases

> We calculate the number of controls and cases who have the target genetic variant
-> odds ratio

Question 16

What is the procedure to obtain the odds ratio?

Answer 16

1. Create two-way table of outcomes
2. Multiply the diagonals
3. Divide one product by the other

Question 17

How is an odds ratio of 10 considered for a genetic variant?

Answer 17

Odds ratio of 10 for genetic variant is extremely large

Question 18

What are the limitations of candidate gene studies?

Answer 18

> Circular logic

• selecting candidate genes requires prior knowledge
• > difficult to generate new knowledge of genes

> Small samples
- due to costs, genotyping studies have historically used small samples

> Lack of replication studies

• due to costs, replications are rare
• meta-analyses are often negative
• > no association between genetic variants and phenotypes of addiction studied

Question 19

What characterises genome-wide studies?

Answer 19

> Attempt to examine “all” genes in genome
- millions of genetic variants analysed

> No possible hypothesis -> agnostic approach
-> look at the genome and see what pops up

Question 20

What constitutes a Manhattan plot in a genome-wide study?

Answer 20

> The variants with high statistical significance cluster around particular genes
-> identification of genes associated with a trait

> Each dot represents the statistical significance of the case control test for one specific variant

Question 21

How is a genome wide study carried out?

Answer 21

> Genome of controls and cases

> We can look at different variants in different genes at the same time
-> identification of associations of known genes AND unexpected genes

Question 22

What are the limitations of genome-wide studies?

Answer 22

> Require very large samples (1000s)
- even harder to perform replications

> Testing 1000s of variations raises the statistical threshold
- p-value of 5x10^8 required (rather than 0.05)

> Does not cover all variation in human genome

• designed for single nucleotide polymorphisms (SNPs), where one letter of DNA sequence is different between individuals
• for SNPs, that difference is frequent in the population (approx. 5% of people carry that version)

> Not all genetic variants are biologically plausible

• i.e. they’re not all functional
• > if the identified variant has no known function, it’s difficult to understand its role in the addiction phenotype

Question 23

What is the problem of an identified genetic variant that is not functional?

Answer 23

If the genetic variant has no known function, it’s difficult to understand its role in the addiction phenotype

Question 24

What are the 4 identified genes associated to alcohol addiction?

Answer 24

> Alcohol metabolism

• ALDH2
• ADH1B

> Receptors related to behavioural side of alcohol use

• GABRA2
• DRD2 (ANKK1)

Question 25

What is the ALDH2 gene associated to?

Answer 25

Alcohol metabolism:
- Decreased capacity to metabolise acetaldehyde to acetate

• Cause high concentrations of acetaldehyde and ‘alcohol flush reaction’
• Decreases alcohol use and the risk of alcohol dependence

Question 26

What is the ADH1B gene associated to?

Answer 26

Alcohol metabolism:
- Increased rate of conversion of ethanol to acetaldehyde

• Causes slightly higher concentrations of acetaldehyde
• Similar deterrent effects on alcohol use and dependence risk

Question 27

What is the GABRA2 gene associated to?

Answer 27

Receptor related to behavioural side of alcohol use:
- Repeatedly associated with alcoholism (non-replications exist)

• Also associated with impulsivity and alcohol-related endophenotypes

Question 28

What is the DRD2 (ANKK1) gene associated to?

Answer 28

Receptor related to behavioural side of alcohol use:
- recognised as risk factor for alcoholism

• presence of considerable across-study heterogeneity

Question 29

What are the 3 identified genes associated to nicotine addiction (tobacco use)?

Answer 29

• CHRNA5/A3/B4
• CHRNB3-CHRNA6
• CYP450

Question 30

What is common about the identified genes associated to nicotine addiction?

Answer 30

• No associations to behavioural phenotypes of nicotine addiction
• All are associated with nicotine’s mechanisms of action

Question 31

What are the limitations of overall gene studies on addiction?

Answer 31

> Lack of replication
- no consistent biologically plausible results found

> Identified genes have small effects
- gene variations account for small amount of phenotype variations

Question 32

What is the consternation in the scientific community regarding gene association studies on addiction?

Answer 32

Even though twin studies show heritability explains 50-70% of phenotype variations between people,
gene variations explain small amount of phenotype variations

Question 33

What does the case of the missing heritability represent in the scientific community?

Answer 33

Different theories on why we’re not finding the genes of interest

• search of rare variants of small effect that are hard to identify by genetic means
• > need to improve methods

Question 34

What can be done against the lack of identification of the rare variants of small effect on addiction phenotypes?

Answer 34

Redefining addiction with:

1. New characterisations of addiction phenotypes
2. New ways to look at the genome

Question 35

How can we redefine addiction through the addiction phenotypes?

Answer 35

> Clinical definitions. (DSM-5) not optimised for research
-> new research definitions more heritable -> so it’s easier to find genes

> Administering drugs in controlled settings and recording effects
-> individual experiences that predict the capacity to develop drug dependency

> Use of endophenotypes
- traits more biologically related to addiction (e.g. brain waves)

> Use biomarkers
- focus on consequences of drug use

> Neuroimaging
- brain activation of users vs. non-users

Question 36

What is the problem of using neuroimaging techniques to investigate addiction phenotypes?

Answer 36

• Brain scans are very expensive

- Lots of data = great statistical complexity

Question 37

How can we redefine addiction through the investigation of genotypes?

Answer 37

> Use “next-generation” sequencing to find the rare variants (<1% frequency)
(since candidate gene and genome wide association studies are focused on particular types of common variants)

> Use different statistical analyses and laboratory work (rather than candidate genome and wide genome studies)
to identify copy number variants

> Use risk scores

> Use epigenetics

Question 38

Why do we need to use different statistical analyses and lab work to identify copy number variants, rather than candidate genome and wide genome association studies?

Answer 38

Copy-number variants:

> Genes are duplicated or deleted during cell division

> Can result in under or over expression of genes

> Even if there’s no functional variant altering gene expression, we still end up with a change in expression
- can’t be seen by genome wide association study because there’s no functional variant

Question 39

What is the benefit of using risk scores when investigating the genome?

Answer 39

> Genome-wide association tests have stringent thresholds
-> arguably missing small effect size variants still contributing to phenotype variation

> Risk scores aggregate information for 1000s variants

Question 40

What is the limit of using risk scores when investigating the genome?

Answer 40

May not reveal individual gene mechanisms

Question 41

What is the benefit of using epigenetic when investigating the genome?

Answer 41

> Drugs alter gene expression
- methyl groups added to DNA, turning expression on/ooff

> Even in identical twins, epigenetics cause phenotype variation

Question 42

What could explain why epigenetics cause phenotype variation even in identical twins?

Answer 42

Possibly because identical twins share same DNA, they might have different patterns of methylation

• > may have different levels of gene expression which can contribute to individual differences
• > may be impacted by drug use

Question 43

What is the benefit of using pharmacogenomics?

Answer 43

Patients vary genetically -> respond differently to treatment

-> DNA profiling could make treatment more efficient
(good responders, non responders, negative side effects)

Question 44

Why is genetic research in addiction important?

Answer 44

> Genetic studies give us an understanding of underlying mechanisms of addiction
-> better treatment

> Understanding genetic factors improves understanding of environmental factors, and their interaction

Question 45

What does research show about addiction phenotypes?

Answer 45

Addiction phenotypes are complex combinations of genetic and environmental factors

-> genetic or environmental factors in isolation are not sufficient to develop addiction phenotypes