Overgrowth syndromes can be caused by pathogenic genetic variants in epigenetic writers, such as DNA and histone methyltransferases. However, no overgrowth disorder has previously been ascribed to variants in a gene that acts primarily as an epigenetic reader. Here, we studied a male individual with generalized overgrowth of prenatal onset. Exome sequencing identified a hemizygous frameshift variant in Spindlin 4 (SPIN4), with X-linked inheritance. We found evidence that SPIN4 binds specific histone modifications, promotes canonical WNT signaling, and inhibits cell proliferation in vitro and that the identified frameshift variant had lost all of these functions. Ablation of Spin4 in mice recapitulated the human phenotype with generalized overgrowth, including increased longitudinal bone growth. Growth plate analysis revealed increased cell proliferation in the proliferative zone and an increased number of progenitor chondrocytes in the resting zone. We also found evidence of decreased canonical Wnt signaling in growth plate chondrocytes, providing a potential explanation for the increased number of resting zone chondrocytes.Taken together, our findings provide strong evidence that SPIN4 is an epigenetic reader that negatively regulates mammalian body growth, and that loss of SPIN4 causes an overgrowth syndrome in humans, expanding our knowledge of the epigenetic regulation of human growth.
4like domains, with SPIN1, an epigenetic reader which recognizes histone H3 trimethylated at lysine-4 (8, 9) and H3 asymmetrically dimethylated at arginine-8 (10). SPIN1 has also been shown to stimulate Wnt signaling and promote cell proliferation and cancer progression (11,12).We evaluated a male individual with generalized overgrowth of prenatal onset, which, at the time of clinical presentation, included extreme tall stature, enlarged liver and spleen, and macrocephaly but no developmental delay. Exome sequencing identified a protein-truncating frameshift variant in SPIN4. In mice, ablation of Spin4 resulted in overgrowth of multiple organs and overall body size, recapitulating the human phenotype. We found that wild-type SPIN4 was able to bind specifically modified histone H3, promote canonical WNT signaling, and inhibit cell proliferation in vitro, but that the variant of SPIN4, which lacks two of the three Tudor-like domains, had lost all of these functions. The findings indicate that SPIN4 normally serves as an epigenetic reader which negatively regulates body size in mice and humans, and, therefore, loss of function of Spin4/SPIN4 increases somatic growth.
Results
Proband and the familyThe proband was a 13-year-old boy who was referred for evaluation of an overgrowth syndrome. He was born large for gestational age, with a birth weight of 5.85 kg (+4.3 SDS) and a length of 62 cm (+4.8 SDS). The mother had no history of gestational diabetes. He has been growing remarkably with height tracking between +4.5 and +5 SDS, although his mid-parental height was +1.2 SDS (Figure 1A). His bone age was advanced by one year; 13 years...