Genome-wide mRNA profiling identifies X-box-binding protein 1 (XBP1) as an IRE1 and PUMA repressor

Abstract

Accumulation of misfolded proteins in ER activates the unfolded protein response (UPR), a multifunctional signaling pathway that is important for cell survival. The UPR is regulated by three ER transmembrane sensors, one of which is inositol-requiring protein 1 (IRE1). IRE1 activates a transcription factor, X-box-binding protein 1 (XBP1), by removing a 26-base intron from XBP1 mRNA that generates spliced XBP1 mRNA (XBP1s). To search for XBP1 transcriptional targets, we utilized an XBP1s-inducible human cell line to limit XBP1 expression in a controlled manner. We also verified the identified XBP1-dependent genes with specific silencing of this transcription factor during pharmacological ER stress induction with both an N-linked glycosylation inhibitor (tunicamycin) and a non-competitive inhibitor of the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) (thapsigargin). We then compared those results to the XBP1s-induced cell line without pharmacological ER stress induction. Using next‐generation sequencing followed by bioinformatic analysis of XBP1-binding motifs, we defined an XBP1 regulatory network and identified XBP1 as a repressor of PUMA (a proapoptotic gene) and IRE1 mRNA expression during the UPR. Our results indicate impairing IRE1 activity during ER stress conditions accelerates cell death in ER-stressed cells, whereas elevating XBP1 expression during ER stress using an inducible cell line correlated with a clear prosurvival effect and reduced PUMA protein expression. Although further studies will be required to test the underlying molecular mechanisms involved in the relationship between these genes with XBP1, these studies identify a novel repressive role of XBP1 during the UPR.

RASSF1 is identified by transcriptome coordination analysis as a target of ATF4

“…As shown in Table 1 and Table S3 , this analysis showed a striking association with processes relevant to ER stress response, especially in relation to PERK signaling that represents one of the three major branches of the UPR, along with IRE1 and ATF6 [ 25 , 26 ]. In conformity with these discoveries, coordination analysis showed a tight association between the transcriptomes of RASSF1 and both BBC3 and GADD45A , two pro‐apoptotic genes primarily induced through the PERK‐eIF2α branch of the UPR [ 27 , 28 , 29 , 30 ] while the correlation between the transcriptomes of RASSF1 and RCAN1 was less tight, aligning with the fact that RCAN1 is an ATF6‐dependent, pro‐survival regulator during ER stress [ 31 , 32 , 33 ] (Fig. S1 ).…”

The Role of the Hypoxia-Related Unfolded Protein Response (UPR) in the Tumor Microenvironment

“…IRE1α is also responsible for IRE1-dependent decay (RIDD) that degrades selected mRNAs in order to reduce the ER load [144][145][146][147] as well as IRE1 α splices the mRNA transcript of X-box binding-protein (XBP) transcription factor into its transcriptionally active isoform (XBP1s) [148]. XBP1s promote the ER membrane's biosynthesis and support its folding capacity [9,36,148,149]. The main consequence of PERK activation is the phosphorylation of the alpha subunit of the eukaryotic initiation factor eIF2.…”

Role of endoplasmic reticulum stress and autophagy in the transition from acute kidney injury to chronic kidney disease

“…The XBP1s further reduced PUMA (p53 upregulated modulator of apoptosis) that causes UPR‐related cell death. A study by Gebert et al (2021) demonstrated that during ER stress‐mediated cell death, increased levels of PUMA was observed. In addition, PUMA can also inhibit all prosurvival Bcl‐2 family members and activate the intrinsic pathway of cell death.…”