Monday, April 2, 2012

Paper trail day trip: Genomic systems neuroscience

Theoretically, each animal's taste repertoire is determined by the food it eats. For herbivores, the important tastes are sweet and bitter, which lets animals distinguish between calories and poison. For carnivores, they are umami and sour, which help identify whether meat is fresh. Flies, for whatever reason, detect carbonation in water. As omnivores, humans combine the taste repertoires of herbivores and carnivores. A recent paper in PNAS looked at the relationship between feeding behaviour and taste receptors by sequencing the genes for taste receptors in a variety of species.

They started by sequencing the Tas1r2 gene (sweet receptor) from twelve species in the order Carnivora. Of these species, seven had pseudogenized versions of Tas1r2, via a wide variety of ORF-disrupting mechanisms including false start codons, frame-shifts, and premature stop-codons. (Genomic papers' figures are quite staid, which is why this is a day trip.)

The Tas1r2 gene for seven animals has been disrupted. *s denote points where the ORF has been ruined. (Below) The coding sequence of two of these mutations.

After establishing that the sweet receptor had been pseudogenized, they performed an evolutionary analysis that showed that many species had lost the sweet receptor individually, rather than via a shared ancestor (the genomic analysis here was a bit beyond my ken). To verify that these genes were indeed non-functional, they selected two species to perform a taste preference task for sweet. The asian otter, which has a pseudogenized Tas1r2 had no preference; while the spectacled bear, which had an intact Tas1r2, preferred sweet tastes. (I would pay five francs to see these videos. I bet they were adorable.)

Asian otters, which have a pseudogenized Tas1r2, have no sweet preference. Spectacled bears, which have an intact Tas1r2, prefer sweet tastes.

Dolphins and sea lions swallow their food whole, and have sparse taste receptors on their "lingual epithelium" (tongue). Jiang et al sequenced the umami and bitter receptors of these two species, and found that the sea lion lacks both sweet and umami receptors, while the dolphin seems to lack sweet, umami, and bitter receptors.

Genomic Neuroscience

I love how this paper was able to directly connect genes to behaviour. As the cost of sequencing has plummeted - a whole genome now costs ~$1,000, or will soon - I've been trying to think of systems neuroscience experiments (viz. electrodes in the brain) that can leverage genomic information. In particular, I am interested in using genomics to understand individual differences, whereas neuroscience until now has utilized genetics and mutant models to study disease.

The two key parts to a genomic analysis (to me as an outsider) are having genes with diverse alleles, and having a readout that you can correlate with the genes. On the genetic front, neuroscience is lucky to rely on receptors, which can tolerate small mutations and still function. For example, the Serotonin transporter has more than dozen variants in humans.

On the readout front, neuroscience is suboptimal. Since the influence of a single gene can be small, to be able to detect the influence, one wants to measure many traits from many animals. In contrast, in neuroscience, one thoroughly characterizes a small number of cells in a small number of animals. For example, I record from the olfactory bulb, and determine the odorant receptive field of ~50 cells in one animal; for a set of experiments, I might record 5-10 animals. This is time intensive, and not specific to any particular gene of interest. To get a data set large enough to correlate with genes, I would need to record from fifty animals - a year's work - with no sure outcome. Simple forward genomics will not work for systems neuroscience.

Ultimately, I think the best genomics-of-individual-differences experiments would work similarly to the disease paradigm: you perform a behavioural screen on a large number of mice, sequence them all, and identify the alleles of interest. Then you record from selected brain areas of the interesting mice.

Given this framework, I tried to think of an interesting experiment. The first set of genes I considered were the chemosensory receptors, whether for olfaction or taste. But correlating receptor mutations with function is really a biophysics question.

So this is my best idea: there are a large number of signaling molecules involved in feeding behaviour, including leptin, insulin, cannabinoids, AgRP, etc. Most studies have concentrated on knocking these genes (the fuck) out. However, feeding behaviour is quite complex. Individuals can vary not only in outcome (weight), but in how they feed (sporadically or continuously) or how body state effects their behaviour. So I propose devising a set of simple behavioural experiments to tease out differences in feeding behaviour. Body weight is the simplest. You could quantify how quickly satiety sets in during feeding; or how quickly satiety fades. Then for all the subjects, you sequence the genes of interest (or the whole genome if it's cheaper), and hope to find a strong correlation between some alleles and feeding behaviour. Then you take mice with specific alleles, and record from their hypothalamus during feeding to see if their brain is acting different.

In the end, I'm not entirely satisfied with this experiment. It's a fishing expedition, although I guess most genomic experiments are so. Perhaps the key is fishing in a well-stocked lake. In any case, genomics is getting ever cheaper, and there are great rewards (i.e. prestige) for whoever can figure out how to combine genomics with more sophisticated assays like in vivo physiology. They can even coin a term like geneuromics, or neurosomics.


References


Jiang P, Josue J, Li X, Glaser D, Li W, Brand JG, Margolskee RF, Reed DR, & Beauchamp GK (2012). Major taste loss in carnivorous mammals. Proceedings of the National Academy of Sciences of the United States of America, 109 (13), 4956-61 PMID: 22411809

2 comments:

  1. This is, unfortunately, very hard to do properly. Look up studies on, say, dopamine receptors and you get tons of hits (google drd4 or something). It's hard to correlate SNPs with behavior. Maybe something that's less of an everywhere chemical than dopamine would work, but I'm somewhat dubious. It seems like the cross species comparisons might be a uniquely suitable approach...

    (sorry this is rambling and confusingly written, I'm really tired ;)

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    1. Yeah, correlating SNPs with behaviour is probably the hardest part of the idea. Fortunately, leptin and Agrp seem to be feeding specific neurotransmitters (cannabinoids and NPY less so).

      What would a cross-species comparison look like? Sensory receptor level biophysics/cell biology?

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