Modelling and inference reveal nonlinear length-dependent suppression of somatic instability for small disease associated alleles in myotonic dystrophy type 1 and Huntington disease

Abstract

More than 20 human genetic diseases are associated with inheriting an unstable expanded DNA simple sequence tandem repeat, for example, CTG (cytosinethymine-guanine) repeats in myotonic dystrophy type 1 (DM1) and CAG (cytosine-adenine-guanine) repeats in Huntington disease (HD). These sequences mutate by changing the number of repeats not just between generations, but also during the lifetime of affected individuals. Levels of somatic instability contribute to disease onset and progression but as changes are tissue-specific, age-and repeat length-dependent, interpretation of the level of somatic instability in an individual is confounded by these considerations. Mathematical models, fitted to CTG repeat length distributions derived from blood DNA, from a large cohort of DM1-affected or at risk individuals, have recently been used to quantify inherited repeat lengths and mutation rates. Taking into account age, the estimated mutation rates are lower than predicted among individuals with small alleles (inherited repeat lengths less than 100 CTGs), suggesting that these rates may be suppressed at the lower end of the disease-causing range. In this study, we propose that a length-specific effect operates within this range and tested this hypothesis using a model comparison approach. To calibrate the extended model, we used data derived from blood DNA from DM1 individuals and, for the first time, buccal DNA from HD individuals. In a novel application of this extended model, we identified individuals whose effective repeat length, with regards to somatic instability, is less than their actual repeat length. A plausible explanation for this distinction is that the expanded repeat tract is compromised by interruptions or other unusual features. We quantified effective length for a large cohort of DM1 individuals and showed that effective length better predicts age of onset than inherited repeat length, thus improving the genotype-phenotype correlation. Under the extended model, we removed some of the bias in mutation rates making them less length-dependent. Consequently, rates adjusted in this way will be better suited as quantitative traits to investigate cis-or trans-acting modifiers of somatic mosaicism, disease onset and progression.

Age-, tissue- and length-dependent bidirectional somatic CAG•CTG repeat instability in an allelic series of R6/2 Huntington disease mice

“…Similarly, in R6/2 mice inheriting the large alleles (N500 repeats), it seems likely that the high levels of variance observed within tissues with two populations of cells diverging in average repeat length are generated by frequent expansions and contractions in both cell populations, but with the relative balance between expansions and contractions subtly reversed. Mathematical modeling of repeat length variation also revealed evidence for a non-linear allele length-dependent increase in the contraction frequency over a similar range of allele lengths Higham and Monckton, 2013) and is entirely consistent with the repeat dynamics observed here in R6/2 mice. Interestingly, data from intergenerational transmissions and direct sperm analyses in DM1 also reveal both a decreasing expansion rate and increasing contraction frequency with increasing allele length (Ashizawa et al, 1994;Fig.…”

“…In HD mouse models deficient for either Msh2 or Msh3 mismatch repair genes, somatic mosaicism is completely suppressed with neither expansions nor contractions accumulating (Manley et al, 1999;Wheeler et al, 2003;Dragileva et al, 2009). Similarly, individual-specific expansion and contraction frequencies are highly correlated with each other in HD and DM1 patients Higham and Monckton, 2013). These observations argue for one major mutational pathway in which expansions and contractions are alternative outcomes of the same underlying process (Gomes-Pereira et al, 2004b).…”

“…It is thus possible that a similar effect may serve to limit the overall degree of expansion observed in human HD patients. In addition, recent modeling of somatic mosaicism in DM1 and HD patients (with alleles in the range 39 to 48 repeats) revealed that, despite a clear net bias toward expansion, the high levels of variance observed in the distributions could only be explained by a mutational pathway in which the frequency of contractions was also relatively high Higham and Monckton, 2013). The high levels of variance observed here in R6/2 mice inheriting smaller alleles (b400 repeats) suggests that despite the clear net bias toward expansions, frequent small contractions also contribute toward variability.…”

MSH3 Promotes Dynamic Behavior of Trinucleotide Repeat Tracts In Vivo

“…This is consistent with the behavior of CAG repeats at both the HD and androgen receptor loci in humans (Zhang et al 1994;Leeflang et al 1995). Recent work modeling human DM1 expansion data also has demonstrated that these expansions are likely to occur through small incremental steps Morales et al 2012;Higham and Monckton 2013). In induced pluripotent stem cells (iPSCs) from HD and DM1 patients, Du et al (2013) observed that (CAG) $46 and (CTG) $57 tracts were stable after 12 and 16 passages, respectively.…”

“…Studies of TNR tract length changes have largely relied on end point experiments and therefore do not address the dynamic behavior of the tracts, i.e., the rate at which tracts continue to expand. Modeling of human data has predicted that threshold-length TNR tracts will continue to increase in length in increments smaller than the repeat itself Morales et al 2012;Higham and Monckton 2013), although this has never been demonstrated directly. Single-sperm typing studies in humans demonstrated small expansion and contraction events (one-two repeats) in TNR sequences in Kennedy's disease, HD, and DM1 patients (Zhang et al 1994;Leeflang et al 1995Leeflang et al , 1999Martorell et al 2004), particularly in alleles near the pathogenic threshold (Zhang et al 1994;Leeflang et al 1995;Castel et al 2010).…”