Shwachman-Diamond syndrome: mutations compensate ribosome maturation defects

Certain mutations that appear spontaneously during an individual's life can counteract the effects of genetic diseases. For Patrick Revy, co-director of the 'Genome Dynamics in the Immune System' laboratory at the Imagine Institute (Inserm, AP-HP, University of Paris), this somatic genetic rescue (SGR) process is more common than we thought. In a study recently published in Nature Communications, his team identified this type of mutation in Shwachman-Diamond syndrome, a genetic disease leading to a deficiency of certain white blood cells, and specified its effects at the molecular level.

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Throughout our lives, our DNA undergoes spontaneous changes called 'somatic mutations'. Specifically, the sequences of letters (A, T, C and G) - or nucleotides - that define our genetic code are changed. Most of the time, these changes have no significant effect on the body. In some cases, they can affect the functioning of our cells or even lead to the development of cancers. On the other hand, sometimes these mutations are beneficial.

In a review of the literature published in 2019 in Nature Reviews Genetics, Patrick Revy, co-director of the 'Genome Dynamics in the Immune System' laboratory at the Institut Imagine (Inserm, AP-HP, Université de Paris), Prof. Caroline Kannengiesser (*) and Prof. Alain Fischer (**), highlighted that some mutations in the genome were not only beneficial to the body but also to the immune system. They have listed and summarized 30 clinical cases in which somatic mutations had been able to partly compensate the harmful effects of hereditary genetic blood diseases [1]. "This was only the tip of the iceberg. Since then, there have been an incredible number of additional examples of somatic genetic rescue involving new genes in new diseases," says Patrick Revy.

A subtle balance between two proteins 

In a new study published in the journal Nature Communications, his team, in collaboration with the bioinformatics and genomics platforms of the Institut Imagine, and with Prof. Alan Warren (Cambridge, Great Britain), have formally identified somatic genetic rescue (SGR) in the context of an inherited pathology known as "Shwachman-Diamond syndrome" and have clarified its molecular mechanism [2].

The syndrome can affect the pancreas, the bones, or the blood system. In the latter case, patients have a deficiency in a family of white blood cells called "neutrophils", which increases the risk of infection. This syndrome is caused by an abnormality in the maturation of ribosomes (the large molecules responsible for protein synthesis). This maturation consists of the association of two protein complexes: the 40S and 60S subunits. This process is regulated by the combined action of two proteins: eIF6 and SBDS. The first prevents any association by blocking the binding site of the two ribosomal subunits. In the same way that it is impossible to dock with a pontoon already occupied by a boat, the 40S subunit cannot dock with the 60S subunit. The second protein removes this blockage by dislodging the eIF6 protein from the binding site. The proper maturation of ribosomes therefore depends on the balance between these two proteins.

Tracking somatic genetic rescue with deep sequencing

In Shwachman-Diamond syndrome, this balance is upset. Both copies of the SBDS gene (chromosome 16) are mutated, resulting in a deficit in the production of the SBDS proteins," explains Patrick Revy. As a result, the relative proportion of SBDS decreases in favour of eIF6, which hinders ribosome maturation. This anomaly leads to an imbalance in the cellular composition of the blood, with a deficit of neutrophils. However, a previous study had shown that, in rare patients, this composition rebalanced spontaneously over time. The patients in question had a deletion (disappearance of a genetic portion) in some of their blood cells on chromosome 20, which carries many genes including the EIF6 gene [3]. Does this mean that the deletion of EIF6 was the cause of this relative return to normal?

The answer is not self-evident. "The smallest deletion identified in this study contained 28 genes in addition to EIF6," warns Patrick Revy. That is as many suspects to exonerate. Under these conditions, it was impossible to demonstrate that the deletion of the EIF6 gene really provided a selective advantage in the context of Shwachman-Diamond syndrome. The authors then hypothesised that if EIF6 deletions could indeed confer a selective advantage in blood cells, then other mutations could also be detected.

To verify this, they obtained blood samples from 40 patients with this syndrome. They then carried out deep sequencing, which enabled them to identify several types of mutations in the EIF6 gene: complete deletions of the gene; 'reciprocal translocations' (i.e. 'jumps' of gene sequences from chromosome 16 to chromosome 20 and inversely); but also point mutations - in this case changes in a single amino acid. We have shown that some of these point mutations in the EIF6 gene alter the interaction between the eIF6 protein and one of the ribosomal subunits," explains the researcher. This compensates for the SBDS protein deficit and rebalances the ribosome maturation process”.

Hematological parameters that return to normal

To prove the benefit of these mutations, the researchers tested Drosophila flies in which they reproduced Shwachman-Diamond syndrome by introducing mutations in the SBDS gene that kept them in the larval stage. However, when the researchers manipulated the genome of these flies to include the point mutations in the EIF6 gene described above, the Drosophila were able to develop normally. This proves that these mutations are indeed compensatory.

"However, in the patients included in our study, the benefits of this mutation are not that obvious. This can probably be explained by the fact that we are analysing them at a given time. To detect a significant effect, for example on blood composition, we would have to follow them over time, the time it takes for the cells that have spontaneously acquired the compensatory mutations to propagate" explains Patrick Revy. In this respect, the researchers reanalysed a blood sample from a Shwachman-Diamond patient studied by a group of Hong Kong researchers [4] who noticed that the patient's haematological parameters had all returned to normal. By re-analysing his genome, Patrick Revy's team found a compensatory somatic mutation in EIF6 in almost all his blood cells. This means that the advantage provided by this mutation was sufficient to be selected: without necessarily curing the patient, it improved his condition. 

[1] P. Revy et al., Nature Reviews Genetics, DOI: 10.1038/s41576-019-0139-x, 2019.

[2] S. Tan et al., Nature Communications,, 2021.

[3] R.Valli et al.,British journal of haematology 184, 974-981; 2019.

[4] A.L. Koh et al., Am. J. Med. Genet., A 182, 2010-2020, 2020.

(*) AP-HP, Département de Génétique de l’Hôpital Bichat, Université Paris Diderot

(**) Institut Imagine, Inserm, Collège de France, Unité d’immunologie, hématologie et rhumatologie pédiatrique, à l’hôpital Necker-Enfants malade AP-HP