Making a definitive genetic cause is important to families as it means that they can find out what is wrong with their child, enabling doctors and scientists to help them understand the risks to their future children and help prevent them losing another child.

(A new research paper, ‘Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease’, has been published in Nature Metabolism.

For a family with one child affected with this type of mitochondrial disease, there is a 25% chance of each further child being affected with the devastating condition. When we know beyond reasonable doubt that we have found the cause, the family can have access to counselling which can give them options to help them have a healthy child in future.

What is exciting about the new Deep Mutational Scanning (DMS) technology used in this research is that it can be applied to many other disease-causing mitochondrial genes to provide help in diagnosing many more families.

This collaborative work was undertaken by teams at the Newcastle NHS Highly Specialised Mitochondrial Laboratory (part of the North East and Yorkshire Genomic Laboratory Hub) – led by Professor Rob Taylor and Dr Charlotte Alston – and Washington University St Louis, who have worked together since 2016 when Professor Dave Pagliarini’s group characterised a protein called NDUFAF8.

Dr Charlotte Alston 

His lab used cutting-edge technologies to show that this protein was a potential cause of mitochondrial disease. Dr Alston, Principal Clinical Scientist, NEY GLH Rare Disease Service Lead (Mitochondrial Disease), subsequently identified the first patients whose mitochondrial disease was caused by mistakes in NDUFAF8 in 2020. This collaboration brings together world leading expertise in understanding protein function with leaders in NHS mitochondrial disease diagnostics.

Patient impact

Sometimes, even when we find alterations in proteins that we know can cause problems, it is not always clear cut, and we don’t know if they’re the answer or not for families waiting for a diagnosis.

If we think of genetic variants as a spelling mistake, each person has hundreds of thousands of spelling mistakes in lots of different proteins – and the vast majority of these don’t cause disease.

Working out which of these spelling mistakes are the cause of a clinical problem is a key role for laboratories in the NHS Genomic Medicine Service (NHS GMS). When we can’t confidently say that a spelling mistake is the cause of a patient’s symptoms, these changes are called ‘variants of uncertain significance’ or VUS for short.

Fast forward to today, this current study targets this problem from another angle. We have used a well-known protein, called NDUFAF6, which we have known for many years can cause a severe form of mitochondrial disease in children when it is faulty. Professor Pagliarini has used a powerful tool called ‘Deep mutational scanning’ (DMS) to create every possible spelling mistake in NDUFAF6, and then looked at each one to see if it causes a problem.

The NHS Mitochondrial team in Newcastle have then tested the DMS predictions using all the known spelling mistakes from every NDUFAF6 patient that has ever been reported and found that the DMS results agreed with each spelling mistake found in the affected patients.

Confirming that the DMS data can accurately predict the consequence of these spelling mistakes is really important – it means that this tool can be used to provide crucial evidence to the laboratory Clinical Scientists who collect all the information on these VUS to decide if they are the cause of a patient’s clinical symptoms, or if it’s just one of those many, many variants that just make us different.

Rob Taylor, Professor of Mitochondrial Pathology at Newcastle University, said of the research, “…there’s some very new fundamental biology in here but excitingly, the paper majors on the development of a deep mutational screening approach to help resolve VUSs, a major problem for genomic labs; I think this is the first time this has been applied in the context of mitochondrial disease.”

* Nature Metabolism – Publishing online monthly from January 2019, Nature Metabolism is interested in the best research from across all fields of metabolism research, incorporating the work of basic scientists and researchers in industry.