Background:
LMNA
, a gene encoding A-type lamin proteins (abbreviated as lamin A), is one of the most frequently mutated genes in dilated cardiomyopathy (DCM). The molecular mechanisms underlying cardiomyocyte dysfunction in
LMNA
-related DCM remain elusive, translating to the lack of disease-specific therapies. Lamin A has been shown to play a critical role in genome organization via interactions with the chromatin at specific regions called lamina-associated domains (LADs). However, little is known about whether DCM-causing
LMNA
mutations rearrange the genome conformation and chromosome accessibility. The overarching goal of this study is to define the role of genome organization in
LMNA
-related DCM.
Methods:
LMNA
-related DCM was modeled
in vitro
using cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs) from DCM patients carrying a frameshift mutation in the
LMNA
gene (c. 348_349insG; p. K117fs) and isogenic controls. We combined genome-wide single cell functional genomic and epigenomic mapping analyses to define the gene regulation and cis-regulatory interactions in isogenic iPSC-CMs.
Results:
Single-cell RNA-seq revealed global gene dysregulation in
LMNA
mutant compared to isogenic control iPSC-CMs. The homeodomain transcription factor
PRRX1
was significantly upregulated in mutant cells. We showed that LAD integrity is disrupted at the
PRRX1
locus in mutant iPSC-CMs. In agreement, DNA fluorescence
in situ
hybridization (FISH) revealed that the
PRRX1
locus loses peripheral association and relocates towards the transcriptionally active nuclear interior in mutant iPSC-CMs. Correspondingly, single-cell assay for transposase accessible chromatin (ATAC)-seq showed increased chromatin co-accessibility at the
PRRX1
locus, providing a plausible explanation for ectopic activation of
PRRX1
in
LMNA
mutant iPSC-CMs.
Conclusion:
Our data suggest that
LMNA
haploinsufficiency disrupts the structure of LADs, leading to ectopic promoter interactions and altered gene expression in
LMNA
-related DCM iPSC-CMs. We identified
PRRX1
as a promising candidate locus linking changes in LAD organization with gene dysregulation in
LMNA
-related DCM.