Rat Models

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As an initial effort to characterize these lines, these models are being behaviorally phenotyped at SIDB and the Center for Development and Repair in Bangalore. Rat models are phenotyped according to a rigorous pipeline that assesses behaviours relevant to autism spectrum disorder, such as social and motor skills, and learning and sensory processing. Different cohorts of rats are run through different subsets of tasks to overcome potential order effects on behaviours and to limit the number of tasks each animal is put through. 

Resulting data will be available pre-publication via downloadable behavioral datasheets (see links to available datasheets above).  

The SIDB behavioral pipeline includes the following tasks:

• Auditory and visual fear conditioning (Pavlovian fear conditioning)
• Water maze (spatial learning and memory and reversal learning)
• Object recognition task (non-spatial recognition memory)
• Object location recognition task (spatial recognition memory)
• Active place avoidance (allocentric spatial learning and memory, cognitive control, cognitive flexibility)
• Prey-capture task (complex learning, involving various cognitive processes and sensorimotor learning

• Paired play paradigm (developmental social behavior)
• Tube co-occupancy test (adult social behavior)
• Social habituation paradigm (social learning and memory)

• Pup righting (neurodevelopmental reflex)
• Tail flick (pain response)
• Rota rod (motor coordination)
• Wood chew (anxiety marker)
• Marble interaction task (novel object interaction)

In addition, prior to pipeline phenotyping, some rats are characterized using the following experimental set-ups/methods:   

Eco-ethological housing system that permits rats to express a wide-range of innate behaviors that can be recorded and analyzed without disturbing animals. 

The following schematic of the Habitat is an experimental set up devised by Peter Kind and colleagues at SIDB to study rat social, cognitive and motor behaviors in the lab. These complex behaviors include rat social hierarchies, fear and isolation, communication, play, memory, motor coordination, reaction to novelty and circadian rhythms.   

Mimicking rat burrows

(Image courtesy of Peter Kind/Edinburgh University)

 Automated, machine-learning-based method developed by Sandeep Robert Datta and colleagues to characterize behavior in rodents (mice and rats) (Wiltschko AB et al, 2015). More information about this tool can be found here. 

Peter: Between the SIDB Edinburgh site and the Bangalore site, we have somewhere between 15 and 20 different rat models, all to monogenic forms of autism spectrum disorder, typically the high-confidence genes on the SFARI Gene list.

We started with the fragile X and the SynGAP rats because Fmr1 and Syngap are two genes we were particularly interested in. We moved to the rat model primarily because of the complex social behaviors that rats have that mice do not. Rats evolved to live in large groups of up to 150 individuals, and they have numerous cooperative behaviors, such as hunting and playing. Mice are much more loner animals and have evolved far fewer social interactions.

But I would never say one model is better than another model. In fact, I’m a firm believer that we need more models, not fewer. We’ve learned a huge amount from flies, from fish[…]. It really comes down to the hypothesis you’re testing and the experiments you need to do to test that hypothesis. Different models are better than others to address particular questions. We thought the complex social repertoire of behaviors in the rat would be a particular advantage for studying autism.

There is also a lot of autism data coming out of mice1, and we thought that cross-species validation would be very important to understand any translatability across mammalian species2. I know people look at rats and just see big mice, but there’s actually about 12 million years of evolution between them. To put that into perspective, there’s six million years of evolution between a chimpanzee and a human. So rats and mice are very distinct species, but offer many of the same advantages in terms of large litter size and shortened developmental periods. Rat neurons are also much more robust in culture than mouse neurons, and that’s turned into a huge advantage for many of our colleagues. Also, from a lab-specific point of view, we are very interested in using longitudinal functional magnetic resonance imaging, and because of the rat’s bigger brain, we can get much more resolution using rats.

Peter: When we set up the pipeline, we wanted our tasks to be as unbiased and as comprehensive as possible. In that context, it’s important to remember that the behavioral repertoire of a rat is very distinct from the behavioral repertoire of a human. So, we don’t ask if our rats look like a human with the corresponding condition, something often referred to as ‘face validity.’ Instead, we ask how a given mutation affects the natural behaviors of a rat, including a lot of spontaneous behaviors that rely on a wide range of brain areas.

To keep the pipeline standardized and to make sure that we can reproduce behaviors across sites, we also set it up at two different locations, running many of the tasks in both Bangalore, India, and here in Edinburgh, Scotland. All of the people across those sites are trained to do the behavioral assays using identical, and very detailed, protocols that take into account not just what the tasks are but how the tasks are run and the context in which they are run. For example, tasks are run for every rat model in the exact same order and at the same point in the animal’s light-dark cycle. Everybody running the tasks and the Principal Investigators involved also meet once a week to make sure things remain standardized. And at those sessions, the discussions can get very lively and everyone contributes to how the data should be analyzed and interpreted. With all of this, we’re trying to build what we loosely call an ‘ethogram’ for each animal model.

 Peter: When people think of treatments, they typically think of therapeutic testing in animal models. Pharmaceutical companies have used rats for decades because they are particularly well suited, as the metabolism of the rat is closer than mice’s to that of a human. However, there is also still much to be learned from fundamental science that has important implications for neurodevelopmental conditions. For example, Adrian Bird’s work on Rett Syndrome showed that if you re-express the gene even late in an animal’s life, the animal recovers amazing function6. That challenged the whole idea that there are critical periods during development when treatments would be more effective. But we have no idea how generalizable this is. So a focal point for SIDB is to determine whether the monogenic forms of autism are issues of neural development or neural maintenance. I’d like to see the field start classifying, gene by gene, which conditions have a critical period for intervention — those that are truly neural developmental — and which are associated with neural maintenance and able to be corrected even later in life. That stratification has huge implications for treatment strategies in humans.

In terms of testing pharmaceuticals, we also need to remember that it’s not just about bringing things into clinical trials. Every time you give a drug, that’s a valid fundamental experiment on cellular biochemistry and physiology as well as the circuits involved.

Loren: I can just add one other perspective on this. People are starting to think about therapies that might live at a circuit level, as opposed to a pharmacological level. These animal models have real power to help us figure out the systems and to know how they respond.

 Loren: The question for me is: What are the things that SFARI can do that nobody else is going to do? Their amazing human genetic work, in terms of putting together the Simons Simplex Collection, Simons Searchlight and SPARK cohorts, has really been fairly unique. And the addition of all of these animal models, doing all the work of creating them and making them easily available, is a huge service to the field. It allows you to ask questions about whether there are common phenotypes and common underlying mechanisms.

I’d also like to see them continue the support for fundamental biology that helps everybody in the community. And I’d like them to think hard about other long-term initiatives, like they did with the Circuit Dynamics request for applications. Things that we could really push and that allow people to try out some slightly crazy things that could move the needle and really change things. For example, our lab is thinking about whether we can teach animals to amplify patterns of brain activity — you know, neurofeedback. And if so, can we then translate that to disease models where we’re using in-built learning mechanisms to push the circuits to a state that’s back toward the standard behavior.

Peter: SFARI has always appreciated the importance of fundamental biology and exploratory science and that you often don’t know where the next big discovery is going to come from. We can learn amazing things about fundamental and autism biology. I think SFARI has done an incredible job at casting that wide net. The SFARI meetings are definitely amazing, bringing everyone together and fostering collaborative work.

SFARI could also play a big part in guiding clinical trials. If a scientific standard was set by SFARI, the premier foundation for autism research, it would change how we think about translating something through to a clinical trial.