Synthetic Viability project in Cambridge

Josep Forment at his microscope

Thanks to a very generous grant from the Masonic Samaritan Fund, the A-T Society is currently funding a year-long project looking at the potential of synthetic viability as the basis for developing treatments for A-T. The project is being carried out by Dr Josep Forment under the supervision of Professor Steve Jackson of the Gurdon Institute in Cambridge.

Synthetic viability

A-T is one of a family of genetic diseases caused by inherited defects in the detection, signalling and/or repair of DNA damage, also known as ‘DNA-damage response diseases’ (DDR diseases).  A-T is caused by the loss of or mutations in the DNA-damage signalling protein ATM. Other DDR diseases include hereditary breast and ovarian cancers caused by defects on the proteins BRCA1 or BRCA2 and Bloom’s syndrome, which leads to cancer predisposition and developmental disorders.

Recent work has highlighted a new potential therapeutic approach for DDR diseases, and also for other inherited human diseases, based on the concept known as synthetic viability. In simple terms, problems caused by loss of one protein can be alleviated by the loss/inhibition of another protein. Such relationships can be explained if the first gene is needed to remove a toxic product created by the second, or if it controls the activity of the second gene, which becomes overly active and toxic in its absence.

Diagram explaining synthetic viability

Work by Professor Jackson and others has established that the effects of nearly every DDR gene mutant can be largely (and in some cases almost totally) alleviated by mutating another gene. It has also recently been demonstrated that in mouse models the DDR protein BRCA1 can be fully suppressed by inactivation of a particular component. This approach may well lead to the suppression of tumour formation in people with BRCA1 mutations.

Research project

This one-year project proposes to screen for genes whose mutation/loss suppresses cellular defects caused by loss of ATM. ATM-deficient cells will be subjected to a procedure which induces DNA mutations. They will then be grown in conditions in which cells deficient in ATM will not survive. Any cells which do survive will then be analysed to identify what other mutations they have and whether these have contributed to the survival of the cell. Once identified, such synthetic-suppression targets will be explored at a functional level and also exploited as potential targets whose therapeutic inhibition may alleviate ataxia telangiectasia.

Progress to date

The project began in April this year. In order to carry out their study, the team have had to find a way to create mutations in the entire genome. That is, they need to obtain cell populations where every single gene of the genome is mutated at least once in a cell, so that they can see whether the suppression of each gene makes a difference to the survival of cells with no ATM.

Furthermore, they have to create a cell-line with only one copy of each gene (the technical name for this is ‘haploid’) so that when they create a mutation in a given gene they can be sure that gene isn’t expressed. Normal cells have two copies of each gene and if you create a mutation in just one of the pair, the other may still work and you will see no effect.

They have now, in late November, successfully created this cell-line and created all the different mutations using two different techniques. Their next step will be to look at the effects of some differing DNA-damaging agents on their cell populations. These agents would kill normal ATM-deficient cells. Any of the mutated cells that survive this treatment will be isolated and further tested to see if there is a mutation which is protecting these cells. DNA sequencing will be used to identify these mutations.

The work on the ATM protein will be carried out in parallel to similar work on the BRCA1 protein. This work, however, is not funded by the A-T Society.