Translating dosage compensation to trisomy 21

Abstract

Down syndrome (DS) is a common disorder with enormous medical and social costs, caused by trisomy for chromosome 21 (Chr21). We tested the concept that gene imbalance across an extra chromosome can be de facto corrected by manipulating a single gene, XIST. Using genome editing with zinc finger nucleases, we targeted a large, inducible XIST transgene into the Chr21 DYRK1A locus, in DS pluripotent stem cells. XIST RNA coats Chr21 and triggers stable heterochromatin modifications, chromosome-wide transcriptional silencing and DNA methylation to form a “Chr21 Barr Body.” This provides a model to study human chromosome inactivation and creates a system to investigate genomic expression changes and cellular pathologies of trisomy 21, free from genetic and epigenetic noise. Remarkably, deficits in proliferation and neural rosette formation are rapidly reversed upon silencing one Chr21. Successful trisomy silencing in vitro also surmounts the major first step towards potential development of “chromosome therapy”.

Epigenetics, fragile X syndrome and transcriptional therapy

“…Its role is confirmed by the observations that deletion of the XIST gene in Xq13 prevents X-inactivation [Ørstavik et al, 2007], while certain mutations in its promoter cause preferential X-inactivation [Plenge et al, 1997]. Furthermore, recent experiments show that addition of a XIST transgene on chromosome 21 causes the cis inactivation of the entire hosting chromosome and even the formation of a "Barr body" composed by a condensed chromosome 21 [Jiang et al, 2013]. …”

How to correct chromosomal trisomy

“…Since the XIST insert is within the DYRK1A gene whose dosage is critical for neural differentiation [7], the observed improvement may be due to DYRK1A knockout rather than XIST-mediated epigenetic silencing. Cells with XIST inserts on two or even three of the chromosomes 21 rapidly lost XIST expression [3], consistent with monosomy or nullisomy 21 being incompatible with survival.…”

“…Lawrence and colleagues reasoned that dosage compensation by X inactivation could be appropriated to correct trisomy 21 [3] (Figure 1). X inactivation is initiated by XIST, a long noncoding RNA that encases the inactive X chromosome in a silent compartment.…”

“…Harnessing XIST power to silence one chromosome 21 and restore normal gene expression in trisomic cells was possible because XIST RNA spreads in cis even when inserted or attached to an autosome [4][5][6]. After insertion and induction of a large genomic fragment containing XIST in trisomic iPS cells using a ZFN system to target chromosome 21, Jiang et al [3] observed the accumulation of repressive histone modifications together with DNA methylation of CpG islands. While these epigenetic changes appear stable in differentiated cells, maintenance of silencing of individual chromosome 21-linked genes after many cell divisions remains to be demonstrated.…”

“…In contrast, X inactivation is very stable, suggesting that X-specific elements absent on autosomes may have evolved to help stabilize silencing. Interestingly, cells corrected by XIST insertion on chromosome 21 grow better than control trisomic cells and are more efficient in the formation of neural rosettes [3]. Since the XIST insert is within the DYRK1A gene whose dosage is critical for neural differentiation [7], the observed improvement may be due to DYRK1A knockout rather than XIST-mediated epigenetic silencing.…”