Biallelic variants in YRDC cause a developmental disorder with progeroid features

Abstract

The highly conserved YrdC domain-containing protein (YRDC) interacts with the well-described KEOPS complex, regulating specific tRNA modifications to ensure accurate protein synthesis. Previous studies have linked the KEOPS complex to a role in promoting telomere maintenance and controlling genome integrity. Here, we report on a newborn with a severe neonatal progeroid phenotype including generalized loss of subcutaneous fat, microcephaly, growth retardation, wrinkled skin, renal failure, and premature death at the age of 12 days. By trio whole-exome sequencing, we identified a novel homozygous missense mutation, c.662T > C, in YRDC affecting an evolutionary highly conserved amino acid (p.Ile221Thr). Functional characterization of patient-derived dermal fibroblasts revealed that this mutation impairs YRDC function and consequently results in reduced t6A modifications of tRNAs. Furthermore, we established and performed a novel and highly sensitive 3-D Q-FISH analysis based on single-telomere detection to investigate the impact of YRDC on telomere maintenance. This analysis revealed significant telomere shortening in YRDC-mutant cells. Moreover, single-cell RNA sequencing analysis of YRDC-mutant fibroblasts revealed significant transcriptome-wide changes in gene expression, specifically enriched for genes associated with processes involved in DNA repair. We next examined the DNA damage response of patient’s dermal fibroblasts and detected an increased susceptibility to genotoxic agents and a global DNA double-strand break repair defect. Thus, our data suggest that YRDC may affect the maintenance of genomic stability. Together, our findings indicate that biallelic variants in YRDC result in a developmental disorder with progeroid features and might be linked to increased genomic instability and telomere shortening.

A novel single-cell RNA-sequencing approach and its applicability connecting genotype to phenotype in ageing disease

“…In order to validate the scRNA-seq approach and to shed light on the transcriptional signatures, we used the unique patient cohort, all representing premature ageing phenotypes. These samples have been previously described from gene panels and whole exome sequencing, reporting causative mutations 16 , 17 . To evaluate transcriptional heterogeneity, we searched for genes expressed selectively in each of the samples that were described previously on cellular hallmarks of ageing driving physiological and pathological ageing processes, such as genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, mitochondrial dysfunction, deregulated nutrient sensing, stem cell exhaustion, cellular senescence and altered intercellular communication 22 , 23 .…”

“…Here we report a novel high-throughput single-cell RNA-seq approach with full coverage of transcripts using the SMART-Seq technology, demonstrating the molecular characterization of mutational and transcriptional heterogeneity in dermal fibroblasts derived from six patients with different segmental progeria syndromes. In addition to the causative mutations previously identified in these patients 16 , 17 , we performed regulon analysis to identify interactions of genetic alterations that can be held responsible for the phenotypic heterogeneity.…”

A novel single-cell RNA-sequencing platform and its applicability connecting genotype to phenotype in ageing-disease

“…In the frame of the clinical and molecular work in our recently established Center for Progeroid Disorders, we had previously used NGS-based approaches to determine the molecular diagnosis of progeria patients in early stages of a disease [16][17][18][19] . Although the identification of primary causative genes and pathogenic variants is essential for understanding the patient-specific pathogenesis, systematic biological screens are necessary to elucidate variant and transcriptional heterogeneity.…”

“…[homozygous], p.Ile221Thr 19 ), GOE486 (AHCTF1, c.6329C>G [de novo], p.Ser2110Cys For dimensionality reduction and data visualisation we performed the t-SNE algorithm (as implemented in CogentDS). To evaluate transcriptional events regarding samples in both scRNA-seq methods, we analysed cell groups based on their sample association (Figure 4a) and performed, in parallel, unsupervised graph-based clustering of cells based on their gene expressions (Figure 4c).…”

“…Here we report a single-cell full-length RNA-seq approach that uses the SMART-Seq technology in the single-cell platforms, demonstrating the molecular characterization of mutational and transcriptional heterogeneity in dermal fibroblasts derived from six patients with different segmental progeria syndromes. In addition to the causative mutations previously identified in these patients [16][17][18][19] , we performed regulon analysis to identify interactions of genetic alterations that can be held responsible for the phenotypic heterogeneity.…”