Somatic mutations and progressive monosomy modify SAMD9-related phenotypes in humans
Federica Buonocore, … , Annette Grüters, John C. Achermann
Federica Buonocore, … , Annette Grüters, John C. Achermann
Published March 27, 2017
Citation Information: J Clin Invest. 2017;127(5):1700-1713. https://doi.org/10.1172/JCI91913.
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Research Article Endocrinology Genetics

Somatic mutations and progressive monosomy modify SAMD9-related phenotypes in humans

Abstract

It is well established that somatic genomic changes can influence phenotypes in cancer, but the role of adaptive changes in developmental disorders is less well understood. Here we have used next-generation sequencing approaches to identify de novo heterozygous mutations in sterile α motif domain–containing protein 9 (SAMD9, located on chromosome 7q21.2) in 8 children with a multisystem disorder termed MIRAGE syndrome that is characterized by intrauterine growth restriction (IUGR) with gonadal, adrenal, and bone marrow failure, predisposition to infections, and high mortality. These mutations result in gain of function of the growth repressor product SAMD9. Progressive loss of mutated SAMD9 through the development of monosomy 7 (–7), deletions of 7q (7q–), and secondary somatic loss-of-function (nonsense and frameshift) mutations in SAMD9 rescued the growth-restricting effects of mutant SAMD9 proteins in bone marrow and was associated with increased length of survival. However, 2 patients with –7 and 7q– developed myelodysplastic syndrome, most likely due to haploinsufficiency of related 7q21.2 genes. Taken together, these findings provide strong evidence that progressive somatic changes can occur in specific tissues and can subsequently modify disease phenotype and influence survival. Such tissue-specific adaptability may be a more common mechanism modifying the expression of human genetic conditions than is currently recognized.

Authors

Federica Buonocore, Peter Kühnen, Jenifer P. Suntharalingham, Ignacio Del Valle, Martin Digweed, Harald Stachelscheid, Noushafarin Khajavi, Mohammed Didi, Angela F. Brady, Oliver Blankenstein, Annie M. Procter, Paul Dimitri, Jerry K.H. Wales, Paolo Ghirri, Dieter Knöbl, Brigitte Strahm, Miriam Erlacher, Marcin W. Wlodarski, Wei Chen, George K. Kokai, Glenn Anderson, Deborah Morrogh, Dale A. Moulding, Shane A. McKee, Charlotte M. Niemeyer, Annette Grüters, John C. Achermann

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Figure 2

SAMD9 is expressed in key tissues and represses cell growth.

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SAMD9 is expressed in key tissues and represses cell growth. (A) Immunoh...
(A) Immunohistochemistry showing SAMD9 expression in human fetal adrenal gland at 9 weeks postconception (red) with NR5A1 (also known as steroidogenic factor 1) shown in green and DAPI-stained nuclei in blue. C, capsule; DZ, definitive zone; FZ, fetal zone. Scale bar: 100 μm. (B) SAMD9 expression in different human fetal and adult tissues showing high expression in fetal adrenal as well as in tissues affected in the clinical phenotype. Tissues especially relevant to the phenotype are highlighted (*). Data are shown as relative expression compared with GAPDH. Representative data are shown as mean ± SEM for a single study performed with triplicate technical replicates. Similar patterns were seen in independent studies using both GAPDH and ACTB as housekeeping genes. (C) Growth of HEK293 cells was reduced following stable transfection of WT SAMD9 (mean ± SD; mock vs. WT, P < 0.001) and reduced further by the gain-of-function mutations found in patients (WT vs. samples, P < 0.0001, black bars). Data represent mean ± SD for the absolute cell number in 3 independent studies, each performed in triplicate (n = 9; 2-tailed t tests). (D) BrdU assays showing significantly reduced growth of patient fibroblasts (patients 4, 6, and 8) compared with fibroblasts from 3 independent controls. Data represent mean ± SD cell proliferation for 3 independent studies, each with 6 technical replicates (unless specified, n = 18; 1-way ANOVA with Tukey’s multiple comparison test, controls vs. patients, P < 0.001). (E) qRT-PCR analysis of fibroblast samples from 3 patients with a SAMD9 gene mutation revealed a significant reduction of gene expression compared with SAMD9 expression in fibroblasts derived from 3 healthy control individuals. Data represent mean ± SEM relative expression for 4 independent studies, each with 2 replicates (Mann-Whitney test, controls vs. patients, P < 0.05).