Pharmacogenetics / Pharmacogenomics

Here's an interesting observation I made while preparing for a presentation. This is a plot of the yearly publications where you can find the term "Pharmacogenetics" or "Pharmacogenomics". This is obtained by just searching via SCOPUS using those keywords.

"Pharmacogenetics" had a steady hit rate of about 50-60 before 1995, and publications took off after that on a steady incline. The word "Pharmacogenomics" was first used in 1997, and then really kicked in after 1999. But what really surprised me was that, unlike "Pharmacogenetics", the hit rate has since plateaued off after 4-5 years.

I am not too sure what the reason is, but I suspect there may be a bit of "Pharmacogenomics" fatigue, and the genomics people moving into broader areas of "Genomics", have stopped using the term "Pharmacogenomics". The "Pharmacogenomics" people by contrast, have tended to remain faithful to their cause and the science continues to expand.

Ethanol pharmacokinetics

Ethanol is a small molecule that has a strong affinity for water. It is absorbed efficiently and rapidly after consumption. Regardless of how it is consumed and in what form of spirits, the effect of alcohol on the central nervous system is closely correlated with the circulating concentrations of alcohol in the blood. This allows enforcement authorities to set certain tolerable (legal) limits of blood alcohol concentrations (BAC) as a surrogate limit for alcoholic intoxication (Singapore's legal limit is 0.08%, or 80 milligrams of alcohol per 100 millitres of blood). As the alcohol in the blood equilibrates very rapidly with the alveolar concentrations, breath alcohol concentrations (BrAC) are often used by the traffic police as an alternative to measuring blood alcohol concentrations. In Singapore, the BrAC limit is 35 micrograms of alcohol per 100 millilitres of breath. See Singapore Traffic Police.

It is therefore of some interest to the public to know how much alcohol one can drink without exceeding the BrAC limits.

The peak (maximum) BrAC after consuming alcohol depends on a number of factors:

a] the total amount of alcohol consumed (not the volume of beverage). Obviously the larger the quantum of alcohol, the higher the BAC will be.

b] the rate of absorption of the alcohol. The rate will be faster if the stomach is empty, and if the concentrations are high but not too high. Higher concentrations of spirit (alcohol) will produce a greater concentration gradient to drive the absorption. However, if the concentrations are too high, there may be slower gastric emptying of stomach contents into the small intestines where absorption of the alcohol is faster and more complete. Men theoretically therefore absorb more alcohol then women.

c] the amount of first pass metabolism in the linings of the stomach. There is some controvery about how important this actually is. Women are said to have less alcohol dehydrogenase expressed in the stomach walls and therefore have less first pass metabolism. The less metabolism, the greater the absorption.

d] the 'volume of the body' into which the alcohol is distributed. Pharmacokinetically this is referred to as the volume of distribution. Men have a higher water content in their body compared to women, and since alcohol is distributed primarily into body water, men will weight for weight, develop lower BrACs.

e] the rate of elimination of alcohol. The ADH genetic polymorphims have been discussed elsewhere. If consumed quickly, the rate of elimination will not affect the BrAC much, but if the consumption is protracted over a period of time, long enough for elimination to occur, the rate of elimination may have a significant effect on the BrAC.

Based on the above understanding, it is a reasonable expectation (assuming that the amount of alcohol consumed is exactly the same) that a muscular Chinese man sipping several glasses of wine over the course of a 4-course meal will produce substantially lower BrACs compared to an Indian lady quaffing down a series of stiff drinks on an empty stomach.

Alcohol and the breathalyzer #1

The question is: Given the genetic polymorphism affecting alcohol dehydrogenase (ADH), how much variability is there in the population, and how does this variability affect the amount of alcohol that can be consumed before one exceeds the breathalyzer legal limits?

Today we begin a study at Changi General Hospital to find out.

Keep watching this space. We'll have the results out soon....

The Great Durian Poll outcome

Many thanks to all who participated. We managed a half decent 66 responses... :).

I must say I was somewhat surprised by the results. As a non-durian lover I was expecting to see a much clearer separation of lovers and haters, with perhaps a more distinct bimodality in the distribution, somewhat like the taster/non-taster distribution. Instead we had a kind of log-normal distribution, like the CYP3A4/5 one.

There are a couple of possible reasons for this. One is that there may be a sampling bias, i.e. non-durian lovers aren't that motivated to participate. Secondly, the category axis is an ordinal scale, so even though I tried to space out the responses as 'equally' as I can imagine them to be, there is no certainty that the categories have equal intervals. It could well be that there is a larger separation at the "So-so only....no big deal" category.

In any case, it was an interesting exercise. As has been shown many times before, the lack of a clear 'bi- or poly-modal' distribution does not necessarily exclude any genetic bases for the interindividual differences.

Regardless of the genetic or lack of genetic basis for the interindividual difference, (and assuming the sample represents all of Singapore) there is an interesting lesson for us here...

Firstly, because of the preponderance of durian lovers in the sample, one can say Singaporeans generally love durians...passionately...though they can mostly live without it. Secondly and perhaps more importantly, is to recognize that despite such an overwhelming support for the spikey fruit, there are regulations that protect the interests of the people represented by right tail of the distribution. You don't allow the fruit on airplanes, in cars, shopping centres and restaurents. It is such a common sense thing to do, so we kinda take it for granted. It is actually a very common phenomenon. In a classroom, for example, the (good) teacher's attention is often focused on the poor students, or the bright spark...and not on the majority of the students who (on average) do not have any problems.

We have the same situation in dealing with therapeutic problems. Most dosage regimens are designed for the average patient (central tendency, remember?), and we know (or should know) that the patients who develop problems are those at the tails of the distribution...either inadequate response, or too much response/toxicity. Our mental focus should really be on helping the patients in the tails of distribution achieve an appropriate therapeutic response. Yet physicians often forget this and assume that the recommended (average) dose will meet the needs of all the patients they treat.

The challenge for us is in helping physicians identify which of the patients reside in the tails. This is where pharmacogenetics come in.

There is a nice review, "Pharmacogenetics - Tailoring Treatment for the Outliers" in the New England Journal of Medicine by Woodcock and Lesko that deals with this specific issue. It also reminds us of what Sir William Osler had shared over a hundred years ago: "If it were not for the great variability among individuals, medicine might as well be a science and not an art." Paradoxically, medicine is now at a stage of development where dealing with this variability has become much more of a science.

Alcohol pharmacogenetics in Singapore

The news about the alcohol related death at the National University of Singapore triggered some thinking about the interesting aspects about how alcohol (ethanol) is handled by the Chinese in Singapore.

Ethanol regardless of the form it comes in, is metabolized fairly efficiently in the body by means of an enzyme, alcohol hydrogenase (ADH). Although there are other enzymes that can also do this (e.g. CYP2E1), the most important pathway for alcohol degradation is really ADH. ADH itself is encoded by 7 genes but the major enzyme in the stomach mucosa and liver is the Class 1 enzyme, encoded by the ADH1B gene.

CH₃CH₂OH + NAD⁺ → CH₃CHO + NADH + H⁺

What is important for us to realize is that there is a common genetic polymorphism affecting the ADHB1 gene in Chinese. An 'atypical' ADH was first described in 1968 by Von Wartburg and Schuerch (Ann. N.Y. Acad. Sci. 151: 936-947, 1968). Subsequently Stamatoyannopoulos in 1975 found the atypical variant in 85% of Japanese. The variant is now identified as ADH1B*47 (previously ADH2*2) and exchanges a histidine for arginine in the protein, resulting in an enzyme with very much enhanced activity (100 fold difference in Vmax). A recent study (Alcohol Clin Exp Res. 2004 Jan;28(1):10-4) in Jewish carriers of this variant showed increased rate of elimination of alcohol from the blood (8.09 vs 7.14 g/hr).

This genetic variant is particularly common in South East and East Asia and is an important genetic 'protector' against alcoholism because it is thought to result in more unpleasant outcomes because of higher levels of aldehyde production . The frequency among Taiwanese Han Chinese is about 75% (Hepatology. 1997 Jan;25(1):112-7 ).

A recent report was able to show this global distribution of ALD1B*47 variant (Am J Hum Genet. 2007 Oct;81(4):842-6. Epub 2007 Aug 24). Note the interesting cluster in West Asia. Also the absence of this variant in the Indian subcontinent. More about this later, and its implications for us in Singapore.

Global contour plot of the ADH1B*47His allele frequency

Pharmacogenetics (PGt) vs Pharmacogenomics (PGx)

Pharmacogenetics isn't really a new science. The term was first coined by Friedrich Vogel back in 1959 when not many people were really interested. It was really only in relatively recent time, after genetic/genomic technologies became widely available that it had a renaisance. Now it's become somewhat of a hip and much hyped up science.

Newbies often get confused by the two terms 'pharmacogenetics' and 'pharmacogenomics', often abbreviated to PGt and PGx. The two terms have overlapping characteristics and PGt is often seen nowadays as being a subset of PGx. In fact the two terms have often been used interchangeably by various publications. But for those of us working in this areas, the distinctions can be quite distinct. For us, PGt is often a study of the variations in a targeted gene, or group of functionally related genes. PGx, on the other hand is a much broader investigation of genetic variations at the level of the genome.

Here are some definitions of these terms as given by the FDA and the NCBI.

FDA Guidance for Industry (2008) E15...
PGt: The study of variations in DNA sequence as related to drug response
PGx: The study of variations of DNA and RNA characteristics as related to drug response

NCBI Factsheet
PGt: The study of inherited differences (variation) in drug metabolism and response.
PGx: The general study of all of the many different genes that determine drug behavior.

Rat poison and the F1 driver - the warfarin story

The anticoagulant warfarin actually started life as rat poison. Chemically, it is derived from a natural plant product, coumarin. The way it acts is by inhibiting the enzyme Vitamin K epoxide reductase, and in so doing reduce formation of various Vit K dependent clotting factors.

So what's the deal about F1 drivers?

Well... like F1 drivers, the physician using warfarin needs to keep his eye on the road. Too little warfarin, and there is inadequate therapeutic anticoagulation; too much warfarin and the patient may suffer a catastrophic bleed. Fortunately, he has a way to do this. The Prothrombin Time and other derived measures such as the International Normalized Ratio (INR) provide a heads up to the physician about how much anticoagulation has been provided for the patient. By keeping his eye on the INR, the physician can adjust the dose of warfarin to provide just the right range on anticoagulation the patient needs. This is important, because the warfarin requirements for every patient differ, and the warfarin dose needs to be 'individualized'.

More recently, various other biomarkers enable the physician to make educated guesses about the dosage requirement for the patient. These are genetic markers related to the rate of metabolic degradation of warfarin through cytochrome P450 2C9 (not many such problems in our Chinese population) and the genetically reduced sensitivity of the Vitamin K epoxide reductase C1 subunit (VKORC1). However, using these genetic biomarkers only provide an improved starting dose. Once the race car engine starts, the F1 driver will still have to manage the therapeutic process through keeping a close eye on the INR.

There have been many discussions about the genotyping of patients prior to dosing with warfarin. I have no doubt to its usefulness in helping us to understand the patient a lot better. But becasue there is already a good efficacy marker (the INR) for us to titrate the patients dosing against, the improved starting point may only be of theoretical benefit. I think most of the benefit will come in situations when you need to deliver very fast anticoagulation. Where time is not on an essence, genotyping would likely not be a cost effective option.