Long-read Transcriptomics of Arrested Human Embryos Implicates Splicing Failure, Retrotransposon Derepression and FAS-associated Stress Signalling

Abstract

Preimplantation developmental arrest remains a major cause of embryo loss during in vitro culture, including in embryos for which morphology alone does not explain developmental failure. Because short-read RNA sequencing has limited ability to resolve transcript isoforms, intron retention, and repetitive-element-derived transcripts, we applied Oxford Nanopore long-read sequencing to 16 post-ICSI samples from seven patients, including four 0PN oocytes and 12 developmentally arrested embryos. The arrested samples showed marked heterogeneity in mitochondrial transcript fraction and mitochondrial variant profiles. In addition, arrested embryos displayed a recurrent long-read signature characterized by increased chimeric alignments, elevated intron retention, impaired developmental isoform switching, and enhanced LINE-1-associated signal. The most disorganized embryos also showed reduced expression of subcortical maternal complex components, particularly NLRP7, together with weaker BRCA1-related transcript output and a FAS-associated stress/apoptosis profile. These findings support a model in which a subset of arrested human embryos undergo coordinated failure of RNA processing, repeat control, and maternal genome-stability-associated programs. Long-read transcriptomics may provide a useful framework for studying embryo arrest at the level of transcript structure and repetitive-element activity, features that are not readily captured by gene-level short-read approaches.