BACH1, the master regulator of oxidative stress, has a dual effect on CFTR expression

Abstract

The cystic fibrosis transmembrane conductance regulator (CFTR) gene lies within a TAD in which multiple cis-regulatory elements (CREs) and transcription factors (TFs) regulate its cell-specific expression. The CREs are recruited to the gene promoter by a looping mechanism that depends upon both architectural proteins and specific TFs. An siRNA screen to identify TFs coordinating CFTR expression in airway epithelial cells suggested an activating role for BTB Domain and CNC Homolog 1 (BACH1). BACH1 is a ubiquitous master regulator of the cellular response to oxidative stress. Here we show that BACH1 may have a dual effect on CFTR expression by direct occupancy of CREs at physiological oxygen (~8%), while indirectly modulating expression under conditions of oxidative stress. Hence BACH1, can activate or repress the same gene, to fine tune expression in response to environmental cues such as cell stress. Furthermore, our 4C-seq data suggest that BACH1 can also directly regulate CFTR gene expression by modulating locus architecture through occupancy at known enhancers and structural elements, and depletion of BACH1 alters the higher order chromatin structure.

Cellular heterogeneity in the 16HBE14o− airway epithelial line impacts biological readouts

“…CFTR expression is controlled by distal and intronic cis ‐regulatory elements (CREs) and adopts cell‐type specific 3D conformations, which are required for normal CRE‐promoter interactions. We showed previously that deletion of CREs or depletion of activating transcription factors (TFs) disrupts these higher order chromatin interactions and alters CFTR expression levels (Kerschner et al, 2021 ; NandyMazumdar et al, 2020 , 2021 ; Paranjapye et al, 2021 , 2022 ; Yang et al, 2016 ; Yin et al, 2022 ). Hence, we next investigated whether the CFTR locus adopts different chromatin conformations and 3D interactions in the CFTR high and CFTR low clonal cells.…”

“…This line has the advantage over some others that it is amenable to genome editing and the derivation of single cell clones (Kerschner et al, 2022 ; NandyMazumdar et al, 2020 ; Paranjapye et al, 2022 ; Santos et al, 2023 ; Valley et al, 2019 ). We identified and characterized two strong airway‐selective enhancers at −35 kb and −44 kb upstream of the CFTR promoter (Kerschner et al, 2022 ; NandyMazumdar et al, 2020 ; NandyMazumdar et al, 2021 ; Paranjapye et al, 2022 ; Zhang et al, 2012 , 2013 , 2015 ). These enhancers, and many of the transcription factors and mechanisms driving their activity, are conserved in other airway cells including the lung carcinoma cell line Calu3, primary human bronchial epithelial cells, iPSC‐derived airway epithelial cells (Kerschner et al, 2021 ; Mutolo et al, 2018 ; NandyMazumdar et al, 2020 , 2021 ; Paranjapye et al, 2022 ) and adult and fetal human tissues (Bergougnoux et al, 2014 ).…”

“…We identified and characterized two strong airway‐selective enhancers at −35 kb and −44 kb upstream of the CFTR promoter (Kerschner et al, 2022 ; NandyMazumdar et al, 2020 ; NandyMazumdar et al, 2021 ; Paranjapye et al, 2022 ; Zhang et al, 2012 , 2013 , 2015 ). These enhancers, and many of the transcription factors and mechanisms driving their activity, are conserved in other airway cells including the lung carcinoma cell line Calu3, primary human bronchial epithelial cells, iPSC‐derived airway epithelial cells (Kerschner et al, 2021 ; Mutolo et al, 2018 ; NandyMazumdar et al, 2020 , 2021 ; Paranjapye et al, 2022 ) and adult and fetal human tissues (Bergougnoux et al, 2014 ). DNA sequence analysis of 16HBE14o − cells indicates that at least one copy of the pSV40 (ori‐) plasmid has integrated into intron 6 of the CFTR locus, and it has been suggested that this results in mono‐allelic expression of CFTR in these cells (Valley et al, 2019 ).…”

Gene Network Analyses Identify Co-regulated Transcription Factors and BACH1 as a Key Driver in Rheumatoid Arthritis Fibroblast-like Synoviocytes

“…Pathway analyses of the identified DEGs increased the representation of genes implicated in “intrinsic apoptotic signaling pathways in response to endoplasmic reticulum (ER) stress”, “response to ER stress” and “response to EIF2AK1” (Figure 5C, and Supplementary Table S14). BACH1 is implicated in oxidative stress [62], and oxidative stress may have a role in ER stress.…”

CFTR and Gastrointestinal Cancers: An Update

“…In airway cells under normoxic conditions, BACH1 occupies a distal -44kb antioxidant response element (ARE) located in a CRE and CFTR expression is repressed, while under hypoxic conditions, NRF2 displaces BACH1 from the ARE, permitting the activation of CFTR. Of added interest, BACH1 has shown that it can independently and indirectly activate CFTR by a mechanism that is not clearly understood [ 62 ].…”