In‐frame deletion of SMC5 related with the phenotype of primordial dwarfism, chromosomal instability and insulin resistance

Abstract

Background SMC5/6 complex plays a vital role in maintaining genome stability, yet the relationship with human diseases has not been described. Methods SMC5 variation was identified through whole‐exome sequencing (WES) and verified by Sanger sequencing. Immunoprecipitation, cytogenetic analysis, fluorescence activated cell sorting (FACS) and electron microscopy were used to elucidate the cellular consequences of patient's cells. smc5 knockout (KO) zebrafish and Smc5 K371del knock‐in mouse models were generated by CRISPR‐Cas9. RNA‐seq, quantitative real‐time PCR (qPCR), western blot, microquantitative computed tomography (microCT) and histology were used to explore phenotypic characteristics and potential mechanisms of the animal models. The effects of Smc5 knockdown on mitotic clonal expansion (MCE) during adipogenesis were investigated through Oil Red O staining, proliferation and apoptosis assays in vitro. Results We identified a homozygous in‐frame deletion of Arg372 in SMC5 , one of the core subunits of the SMC5/6 complex, from an adult patient with microcephalic primordial dwarfism, chromosomal instability and insulin resistance. SMC5 mutation disrupted its interaction with its interacting protein NSMCE2, leading to defects in DNA repair and chromosomal instability in patient fibroblasts. Smc5 KO zebrafish showed microcephaly, short length and disturbed glucose metabolism. Smc5 depletion triggers a p53‐related apoptosis, as concomitant deletion of the p53 rescued growth defects phenotype in zebrafish. An smc5 K371del knock‐in mouse model exhibited high mortality, severe growth restriction and fat loss. In 3T3‐L1 cells, the knockdown of smc5 results in impaired MCE, a crucial step in adipogenesis. This finding implies that defective cell survival and differentiation is an important mechanism linking growth disorders and metabolic homeostasis imbalance.

The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress

“…Biallelic missense mutations in NSMCE3 cause lung disease-immunodeficiency-chromosomal breakage syndrome (LICS) due to reduced complex stability 31 . Heterozygous frameshift mutations affecting NSMCE2 or SMC5 result in primordial dwarfism and insulin resistance 30,33 . Altogether these human syndromes demonstrate that compromise of a single SMC5/6 subunit can substantially impact function of the complex.…”

“…Germline defects in SMC5/6 subunits associated with human diseases provide insight into how compromise of a single SMC5/6 subunit disrupts genome stability. For example, SMC5/6-destabilizing mutations in NSMCE3 cause lung disease-immunodeficiency-chromosomal breakage syndrome (LICS)(van der Crabben et al 2016), and NSMCE2 or SMC5 mutations result in primordial dwarfism and insulin resistance(Payne et al 2014; Zhu et al 2023). In this study, we find that deleterious mutations in SMC5/6 subunits correlate with high tumor mutational burdens in human cancers.…”

“…While condensin and cohesin act in chromosome folding and segregation, the function of SMC5/6 in genome maintenance is less well defined. Experimental suppression of SMC5/6 as well as human syndromes caused by germline defects in SMC5/6 result in replication and repair defects and chromosomal aberrations [29][30][31][32][33] . Despite these data indicating an important role for the complex in genome integrity, SMC5/6 deficiency in human cancer is poorly understood.…”

“…Experimental suppression of SMC5/6 as well as germline defects in SMC5/6 in human syndromes result in replication and repair defects and chromosomal aberrations(Payne et al 2014; van der Crabben et al 2016; Venegas et al 2020; Grange et al 2022; Zhu et al 2023). Despite these data indicating an important role for the complex in genome integrity, SMC5/6 deficiency in human cancer is poorly understood.…”

SMC5 Plays Independent Roles in Congenital Heart Disease and Neurodevelopmental Disability

“…This patient was reported to die at age 33 from a sudden cardiovascular event [ 50 ]. Recent work on NSMCE2 and SMC5 demonstrates that the p.Arg372del variant in SMC5 can destabilize the interaction of SMC5 and NSCME2 [ 51 ], indicating that SMC5 variants can potentially play a role in heart disease by disrupting its interaction with NSMCE2 . Additional work has described patients with variants in SMC5 and a variety of non-cyanotic cardiac defects, including persistent ductus arteriosus, atrial septal defect, or supravalvular pulmonic stenosis [ 22 ].…”