CRISPR-Cas9 screening of salmon cells ‘in the lab’ could replace the use of live fish in challenge testing
Farmed Atlantic salmon is one of the world’s most popular marine-based foods.
The majority of salmon product that reaches our dinner plates has been raised from eggs in salmon farms (aquaculture) located all around the world.
For Norway this represents a particularly important industry, with more than half of global production coming from our fjords and ocean areas.
Keeping farmed fish healthy and disease-free is a major challenge for aquaculture industry.
With large numbers of fish living in close quarters, contagious infections can rapidly spread and have devastating effects. Improving disease resistance would be of enormous benefit to the health and well-being of farmed fish.
Challenge testing – a suboptimal approach to fighting fish disease in aquaculture
The most common current practice for reducing disease threats in aquaculture involves an approach called ‘challenge testing’.
In this approach, large numbers of fish are exposed to an infectious agent (e.g. virus) for a number of days, after which biological samples are obtained from survivors and non-survivors.
Analyzing the genetics of these samples can then identify the key genetic differences between resistant (survivor) and sensitive (non-survivor) fish.
These genetic differences can then be used to guide targeted breeding of more resistant offspring and/or reveal new knowledge about the biology underlying disease resistance, thereby creating opportunities for therapies (e.g. vaccines).
Whilst challenge testing has helped to improve disease resistance in aquaculture, several problems make it an unsuitable long-term solution:
- The repeated mass infection of thousands of fish, many of which are killed or suffer from the resulting disease, has substantial animal welfare issues
- The tests are expensive and, since there can be many variables, sometimes inconclusive
- Success is entirely dependent upon the existence of resistant fish within the test population; if all fish are sensitive to the disease then the test achieves nothing. Since fish have been intensively bred over many generations for characteristics such as growth, sometimes there is not enough genetic variation among the tested fish to make some of them resistant (i.e., the ‘rare’ parts of fish DNA that promote resistance are missing from the population) and a challenge test will be unhelpful.
CRISPR-Cas9 screening of salmon cells ‘in the lab’ could replace the use of live fish in challenge testing
So what if there was another way to identifying the genes that promote resistance to different diseases, without harming fish in the process?
The PETRI-fish project running at the Norwegian University of Life Sciences (NMBU) aims to answer this question, and thereby develop a more sustainable approach for identifying genes associated with disease resistance.
Instead of using live fish, the project will use salmon cells grown in petri dishes in the lab to represent fish, and a powerful genetic tool called CRISPR-Cas9 screening, whichuses a type of molecular scissors to make changes to DNA inside many thousands of salmon cells (micro-fish) such that each cell receives a different change, or ‘edit’.
These genetically edited salmon cells represent an ideal substitute for the mass infection of live salmon used in traditional challenge testing (Fig 1). The cells – not salmon – can be treated en mass with e.g., a virus.
Those that survive infection are collected and the researchers can determine which specific gene edits enabled them to survive a viral attack. This gives new insights into the biology underlying disease resistance; information that can be used to breed more resistant fish.
A range of benefits compared to lab-based screening
Applying cell culture and CRISPR-Cas9 screening to aquaculture offers a range of benefits compared to current strategies to improve disease resistance, namely:
- It will help reduce the use of live fish in experimental testing
- It does not rely on pre-existing variation in resistant fish
- Once the tools are in place, it is cheaper and easier to implement cell-based experiments compared to live fish
- It can more precisely identify potential targets for genome editing for fish breeding. Regulations for genome editing in farmed animals are currently very strict, but conversations are ongoing as to how this can be performed in an ethical and responsible manner.
Broad long-term applications
The PETRI-fish project will initially focus on viral infection of salmon, but once the key tools are developed, the screening approach could be adapted and applied to a range of fish species and different diseases.
Furthermore, CRISPR-Cas9 screening would be a powerful tool to answer a range of important biological questions in farmed fish species, identifying genes that regulate cell growth, fertility, diet and nutrition etc.