Transcriptomic analysis of SEL1L and HRD1 knockout cell lines reveals multifaceted roles of SEL1L beyond the ER quality control

The endoplasmic reticulum (ER) orchestrates major cellular processes, including protein synthesis, folding, assembly and degradation, to maintain cellular proteostasis. Central to these processes are highly stringent quality control machineries like the ER-associated protein degradation (ERAD). Key players in ERAD include HRD1 and SEL1L, which target misfolded proteins for ubiquitination and facilitate their retro-translocation to the cytosol. Bi-allelic loss-of-function of HRD1 and SEL1L is considered lethal, with hypomorphic variants linked to human diseases, including neurodevelopmental disorders. Despite their well-known roles, a comprehensive transcriptomic characterization of their bi-allelic loss has been lacking. In this study, we employed CRISPR/Cas9 to generate bi-allelic HRD1-KO and SEL1L-KO HEK293 cell models. Through differential gene expression analysis and co-expression network construction, we identified hub genes and novel regulatory networks. HRD1-KO cells displayed enrichment solely in ER-related processes, suggesting its specific role in ER protein quality control. Conversely, SEL1L-KO cells exhibited a broader impact, affecting mitochondrial function, ERAD-ribosomal quality control interactions, ER-Golgi transport, and Wnt signaling pathway. These results highlight the distinct roles of HRD1 and SEL1L in ERAD. By unraveling their whole transcriptome impact, our study sheds light on their potential involvement in diverse cellular processes, potentially enhancing our understanding of their cellular processes and disease mechanisms.