Rakoczy, M. | Search bioRxiv

bioRxiv2025

APOBEC3A deaminase catalyzes site-specific editing of transfer RNAs

APOBEC3A is a cytidine deaminase that plays a crucial role in innate immunity; however, it can also drive oncogenesis when dysregulated. While its DNA editing activity is well-studied, the impact of APOBEC3A on RNA has only recently gained attention. Previous studies revealed that APOBEC3A deaminates mRNA stem-loop structures, however, its activity on other RNA classes remains unexplored. Given its likely evolutionary origin from tRNA adenosine deaminases and the prevalence of stem-loop structures in tRNA, we investigated APOBEC3As activity on tRNAs. We found that in vitro APOBEC3A efficiently deaminates a large spectrum of tRNA isoacceptors, primarily at anticodon positions. To assess whether the editing sites identified in vitro can be detected in tumor tissues, we analyzed data from The Cancer Genome Atlas. We identified six editing sites present in numerous patient samples. Our results point to a possible impact of APOBEC3A on tRNA decoding capacity, with potential relevance to mistranslation and cancer development.

molecular biology↗

bioRxiv2024

Identification of neurodevelopmental organization of the cell populations of juvenile Huntington's disease using dorso-ventral HD organoids and HD mouse embryos

Huntingtons disease (HD), especially juvenile-onset HD (JOHD), involves early neurodevelopmental pathogenesis alongside the gradual breakdown of the corticostriatal neural axis. To better understand this mechanism, we created fused dorsal-ventral forebrain organoids from induced pluripotent stem cells (iPSCs) from JOHD to mimic early corticostriatal interactions in the disease. We observed characteristic growth phenotypes in HD organoids and found that these phenotypes were influenced by paracrine signals from opposite regions (dorsal-ventral and ventral-dorsal). These phenotypes were only partially rescued by conditioning with medium in HD compared to control organoids. We also investigated humanized HD embryonic mouse forebrains at E13.5 to validate the phenotypes. Using single-cell RNA sequencing (scRNAseq) and immunofluorescence of the internal structure of HD organoids, we observed early neurodevelopmental signs, including stalling during the phase of increased progenitor cell growth, delayed neuron maturation, and disrupted patterning between pallial and subpallial regions. A consistent feature across in vitro and in vivo models was an abnormal expansion of transthyretin (TTR)-positive cells resembling choroid plexus (ChP), along with ectopic expression of neuronal factors in ChP and a reduction in populations expressing intermediate progenitor and interneuron markers. In mosaic organoids that combined healthy and JOHD tissues, the healthy environment helped reduce ChP overgrowth and restore normal progenitor and neuronal development. This suggests that some developmental defects caused by mutant HTT are reversible and influenced by non-cell-autonomous factors. Overall, these findings point to early ChP-related abnormalities as a key aspect of JOHD neurodevelopmental disturbance and propose the ChP-CSF environment as an important area for future mechanistic studies and potential therapies.

developmental biology↗