An inactivating mutation in the histone deacetylase SIRT6 causes human perinatal lethality

Abstract

It has been well established that histone and DNA modifications are critical to maintaining the equilibrium between pluripotency and differentiation during early embryogenesis. Mutations in key regulators of DNA methylation have shown that the balance between gene regulation and function is critical during neural development in early years of life. However, there have been no identified cases linking epigenetic regulators to aberrant human development and fetal demise. Here, we demonstrate that a homozygous inactivating mutation in the histone deacetylase SIRT6 results in severe congenital anomalies and perinatal lethality in four affected fetuses. In vitro, the amino acid change at Asp63 to a histidine results in virtually complete loss of H3K9 deacetylase and demyristoylase functions. Functionally, SIRT6 D63H mouse embryonic stem cells (mESCs) fail to repress pluripotent gene expression, direct targets of SIRT6, and exhibit an even more severe phenotype than Sirt6-deficient ESCs when differentiated into embryoid bodies (EBs). When terminally differentiated toward cardiomyocyte lineage, D63H mutant mESCs maintain expression of pluripotent genes and fail to form functional cardiomyocyte foci. Last, human induced pluripotent stem cells (iPSCs) derived from D63H homozygous fetuses fail to differentiate into EBs, functional cardiomyocytes, and neural progenitor cells due to a failure to repress pluripotent genes. Altogether, our study described a germline mutation in SIRT6 as a cause for fetal demise, defining SIRT6 as a key factor in human development and identifying the first mutation in a chromatin factor behind a human syndrome of perinatal lethality.

Mechanism of activation for the sirtuin 6 protein deacylase

“…Previous studies have identified loss-of-function mutations of a neighboring aspartate to either tyrosine or histidine (D63Y/H). SIRT6 D63Y was selected for in naturally occurring human tumors, and D63H was identified as a driving mutation in four consecutive late fetal losses of a consanguineous couple (11,36). These studies and our analysis suggest that SIRT6 catalysis is particularly sensitive to mutation of the NAD ϩ -binding loop.…”

Sirtuins in Metabolic and Epigenetic Regulation of Stem Cells

“…Deletion of SIRT6 in cynomolgus monkey leads to hyperacetylation of histone, activating the long noncoding RNA H19 and resulting in prenatal developmental retardation and neonatal death [60]. A homozygous SIRT6 inactive mutation in human also leads to hyperacetylation of H3K9 and H3K56, dramatically elevating pluripotent genes and causing severe congenital anomalies and perinatal lethality [61].…”

SIRT6 is a DNA Double-Strand Break Sensor

“…The only mutant that showed no effect on binding was D63Y, where the amino acid did not impair the charge as strongly as the D63H. Interestingly, mutations in D63 were previously reported to provoke the loss of SIRT6 function in cancer, and have been recently shown to be lethal in humans (Ferrer et al, 2018) .…”