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Single cell transcriptomics of hepatostellate organoids derived from DKC1 A353V mutant and DKC1 A353V corrected iPSCs

ABSTRACT: We model liver phenotypes associated with telomere dysfunction using DC patient-derived iPS cells and isogenic controls with CRISPR/Cas9-mediated homology-directed repair correction of the disease-causing DKC1 mutation. Differentiation of these cells into hepatocyte-like cells or hepatic stellate cells indicates that the parenchymal hepatocytes are primarily affected by telomere dysfunction. We develop an admixed hepatostellate organoid culture model which further reveals that mutant hepatocytes exert dominant effects on hepatic stellate cells regardless of stellate cell genotype. Hepatostellate organoids containing DKC1-mutant hepatocytes exhibit hyperplasia in both the hepatocyte compartment and, remarkably, in stellate cells. Moreover, mutant hepatocytes can induce hallmarks of stellate cell activation independently of stellate cell genotype. Interestingly, mutant hepatostellate organoids also contain off-target PLVAP+ endothelial cells reminiscent of scar-associated endothelium observed in non-DC cirrhosis patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE188987 | GEO | 2022/02/28

REPOSITORIES: GEO

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Project description:Mutations in genes encoding components of the telomerase holoenzyme complex result in a spectrum of rare genetic disorders known as telomere diseases, including dyskeratosis congenita (DC). A consistent finding in DC due to pathogenic mutations in DKC1, which encodes dyskerin, is decreased steady-state levels of the non-coding RNA component of telomerase (TERC) and thus impaired telomere maintenance. Dyskerin binds hundreds of other small nucleolar RNAs (snoRNAs). However, the mechanisms by which DKC1 mutations cause variable impacts on these snoRNAs are poorly understood, which is a barrier to understanding disease mechanisms in DC beyond impaired telomere maintenance. Here, using somatic and induced pluripotent stem cells (iPSCs) from DC patients with DKC1 mutations and CRISPR-Cas9-engineered iPSCs, we show that mutations in the N-terminal extension domain (NTE) of dyskerin dysregulate the biogenesis of a subset of snoRNAs, with the most prominent effect on scaRNA13 (small Cajal body-specific RNA 13). In patient iPSCs carrying the del37L dyskerin NTE-domain mutation but not in those with C-terminal mutations, nascent scaRNA13 transcripts showed a discrete population of 3´-extended forms, as seen in the setting of DC-causing mutations in the PARN (polyA-specific ribonuclease) gene. By deep sequencing of RNA 3´ ends, we found that aberrant scaRNA13 transcripts were composed of genomically-encoded extensions and post-transcriptionally oligoadenylated species, mediated by the noncanonical polymerase PAPD5, which counters PARN. NTE domain mutations generated using CRISPR-Cas9 engineering of the endogenous DKC1 recapitulated the scaRNA13 3´-end processing defects seen in del37L patient cells. Conversely, repair of the DKC1 del37L mutation and genetic or pharmacological manipulation of PAPD5 rescued scaRNA13 end processing defects and steady-state levels. Analysis of the human telomerase cryo-EM structure showed that the dyskerin NTE interacts with 3´ end of bound RNA, suggesting that mutations in this domain impair 3´ end protection of nascent scaRNA13 in addition to canonical functions in snoRNA stabilization. Our results provide mechanistic insights into the interplay of dyskerin and the PARN/PAPD5 axis in the biogenesis and accumulation of snoRNAs beyond TERC, which has important implications for our broader understanding of ncRNA dysregulation in human diseases.

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Single cell transcriptomics of hepatostellate organoids derived from DKC1 A353V mutant and DKC1 A353V corrected iPSCs

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