A novel layer for the understanding of HGPS disease mechanisms

4.6. A novel layer for the understanding of HGPS disease

mechanisms

In summary, the results obtained in this work establish the epigenetic deregulation of LADs as a previously unrecognized characteristic of the HGPS epigenome and add a novel layer to our understanding of the disease’s molecular pathology. Based on the integration of different epigenomic approaches and gene expression profiling, they indicate that disease-related changes in the LAD architecture, accompanied by alterations in DNA methylation and chromatin accessibility, contribute to the pathological transcriptomic signature observed in patient fibroblasts. Illustrating the crucial role of the nuclear lamina in transcriptional regulation, these findings thus demonstrate that a disease mechanism, which has been observed in cells from other laminopathies before (Perovanovic et al., 2016; Cheedipudi et al., 2019), is also involved in the molecular pathology of HGPS. While requiring additional experimental verification, this mechanistic insight represents an attractive starting point for future studies of the effect that the presence of Progerin exerts on the global LAD structure, and thus, the HGPS transcriptome. If experimentally validated and confirmed in other cell types typically affected in HGPS patients, it will help close a significant gap in our understanding of the molecular foundation underlying the disease.

At the same time, these results raise a number of intriguing mechanistic and translational questions, the answers to which should help to better define the importance of HGPS-related epigenomic alterations in the future. Some of these, including the question of the mechanism behind the disease-specific PMD hypermethylation or the interconnection with previously observed histone modification changes, have already been discussed herein and will accordingly require further experimental efforts. Others, however, constitute more conceptual questions that have not been touched upon hitherto.

One of such questions, for example, is whether some parts of the LAD landscape are more vulnerable to epigenetic deregulation upon Progerin expression than others. Assuming that the accumulation of the mutant protein at the nuclear envelope obeys a somewhat stochastic pattern - an interesting question in and of itself - one would theoretically expect different LAD stretches to become deregulated in different cells. Crucially, the population-scale analyses performed in this work demonstrate that a number of loci are preferentially affected in HGPS fibroblasts and it will be interesting to discover the underlying mechanisms. In conjunction with

4. Discussion 4.6 A novel layer for the understanding of HGPS disease mechanisms

this, the question arises whether the relationship between the cellular quantity of Progerin and the occurrence of LAD alterations is linear and / or whether a certain threshold concentration of the mutant protein precedes the appearance of changes in the LAD structure. In the case of the latter, one would expect a sufficiently large reduction of Progerin levels below this threshold to normalize gene expression patterns in individual cells. Closely related is the question whether the observed changes in the LAD landscape are reversible, i.e., whether a reduction of Progerin levels would restore a normal LAD architecture, thereby allowing a mitigation of the pathological gene expression. While this was not tested after FTI-treatment in this work, it generally appears plausible and could be examined using Progerin knock-down/-out cells or constructs for the inducible expression of the mutant protein.

Regarding the DNA methylation dynamics observed in HGPS cells in the present study, it is surprising to see that they culminate in an epigenetic age acceleration for only a subset of patients. Although the obtained data represent a good starting point for a more thorough characterization of the two subgroups at the level of DNA methylation, a conclusive answer to this question may also involve genetic factors and will therefore require additional studies. These will also be beneficial for finding out whether the observed alterations ultimately result in differences in survival between the two subgroups.

Finally, one of the most fascinating questions with respect to the results obtained in this study is whether the epigenetic deregulation of LADs as identified in HGPS cells could also play a role in healthy aging. Such a possibility is not inconceivable, given that Progerin is expressed in healthy cells and that HGPS-related phenotypic alterations including those in the cardiovascular system resemble the ones observed in aged, unaffected individuals (McClintock et al., 2007; Scaffidi and Misteli, 2006; Olive et al., 2010). The available evidence for an involvement of this mechanism in physiological aging is further discussed in section 4.7.

The process of finding answers to some of the questions raised above will profit substantially from the establishment of single-cell analysis technologies in the near future. As highlighted throughout this work, the heterogeneity of individual cells in the fibroblast samples represented a key limitation of the population-based analyses performed as part of this study. Enabling the deciphering of individual changes in such highly heterogeneous populations, single-cell-based profiling methods therefore have the potential to tremendously advance our understanding of HGPS-specific mechanisms of disease.

As noted before, single-cell Dam ID-seq has already been employed successfully (Kind et al., 2015). In addition, the establishment of single-cell ATAC-seq and single-cell-based DNA