Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia

Hypoxia increases both active and repressive histone methylation levels via decreased activity of histone demethylases. However, how such increases coordinately regulate induction or repression of hypoxia-responsive genes is largely unknown. Here, we profiled active and repressive histone tri-methylations (H3K4me3, H3K9me3, and H3K27me3) and analyzed gene expression profiles in human adipocyte-derived stem cells under hypoxia. We identified differentially expressed genes (DEGs) and differentially methylated genes (DMGs) by hypoxia and clustered the DEGs and DMGs into four major groups. We found that each group of DEGs was predominantly associated with alterations in only one type among the three histone tri-methylations. Moreover, the four groups of DEGs were associated with different TFs and localization patterns of their predominant types of H3K4me3, H3K9me3 and H3K27me3. Our results suggest that the association of altered gene expression with prominent single-type histone tri-methylations characterized by different localization patterns and with different sets of TFs contributes to regulation of particular sets of genes, which can serve as a model for coordinated epigenetic regulation of gene expression under hypoxia.111Ysciescopu

Clioquinol as an inhibitor of JmjC-histone demethylase exhibits common and unique histone methylome and transcriptome between clioquinol and hypoxia

© 2022Clioquinol (CQ) is a hypoxic mimicker to activate hypoxia-inducible factor-1α (HIF-1α) by inhibiting HIF-1α specific asparaginyl hypoxylase (FIH-1). The structural similarity of the Jumonji C (JmjC) domain between FIH-1 and JmjC domain-containing histone lysine demethylases (JmjC-KDMs) led us to investigate whether CQ could inhibit the catalytic activities of JmjC-KDMs. Herein, we showed that CQ inhibits KDM4A/C, KDM5A/B, and KDM6B and affects H3K4me3, H3K9me3, and H3K27me3 marks, respectively. An integrative analysis of the histone methylome and transcriptome data revealed that CQ-mediated JmjC-KDM inhibition altered the transcription of target genes through differential combinations of KDMs and transcription factors. Notably, functional enrichment of target genes showed that CQ and hypoxia commonly affected the response to hypoxia, VEGF signaling, and glycolysis, whereas CQ uniquely altered apoptosis/autophagy and cytoskeleton/extracellular matrix organization. Our results suggest that CQ can be used as a JmjC-KDM inhibitor, HIF-α activator, and an alternative therapeutic agent in hypoxia-based diseases.N

YAP-dependent Wnt5a induction in hypertrophic adipocytes restrains adiposity

Wnt5a, a prototypic non-canonical Wnt, is an inflammatory factor elevated in the sera of obese humans and mice. In the present study, fat-specific knockout of Wnt5a (Wnt5a-FKO) prevented HFD-induced increases in serum Wnt5a levels in male C57BL/6 J mice, which suggested adipocytes are primarily responsible for obesity-induced increases in Wnt5a levels. Mouse subcutaneous white adipose tissues (WATs) more sensitively responded to HFD, in terms of cell size increases and Wnt5a levels than epididymal WATs. Furthermore, adipocyte sizes were positively correlated with Wnt5a levels in vitro and in vivo. In hypertrophic adipocytes, enlarged lipid droplets increased cell stiffness and rearranged the f-actin stress fibers from the cytoplasm to the cortical region. The activities of YAP (Yes-associated protein) and TAZ (transcriptional co-activator with PDZ-binding motif) increased in response to these mechanical changes in hypertrophic adipocytes, and inhibition or knock-down of YAP and TAZ reduced Wnt5a expression. ChIP (chromatin immunoprecipitation) analyses revealed that YAP was recruited by Wnt5a-1 gene promoter and increased Wnt5a expression. These results suggested that YAP responds to mechanical stress in hypertrophic adipocytes to induce the expression Wnt5a. When 8-week-old Wnt5a-FKO mice were fed an HFD for 20 weeks, the fat mass increased, especially in subcutaneous WATs, as compared with that observed in floxed mice, without significant changes in food intake or activity. Furthermore, Wnt5a-FKO mice showed impaired glucose tolerance regardless of diet type. Our findings show that hypertrophy/YAP/Wnt5a signaling constitutes a negative-feedback loop that retrains adipose tissue hypertrophy.Y

Chenodeoxycholic Acid Reduces Hypoxia Inducible Factor-1α Protein and Its Target Genes.

This study evaluated HIF-1α inhibitors under different hypoxic conditions, physiological hypoxia (5% O2) and severe hypoxia (0.1% O2). We found that chenodeoxy cholic acid (CDCA) reduced the amount of HIF-1α protein only under physiological hypoxia but not under severe hypoxia without decreasing its mRNA level. By using a proteasome inhibitor MG132 and a translation inhibitor cyclohexamide, we showed that CDCA reduced HIF-1α protein by decreasing its translation but not by enhancing its degradation. The following findings indicated that farnesoid X receptor (FXR), a CDCA receptor and its target gene, Small heterodimer partner (SHP) are not involved in this effect of CDCA. Distinctly from CDCA, MG132 prevented SHP and an exogenous FXR agonist, GW4064 from reducing HIF-1α protein. Furthermore a FXR antagonist, guggulsterone failed to prevent CDCA from decreasing HIF-1α protein. Furthermore, guggulsterone by itself reduced HIF-1α protein even in the presence of MG132. These findings suggested that CDCA and guggulsterone reduced the translation of HIF-1α in a mechanism which FXR and SHP are not involved. This study reveals novel therapeutic functions of traditional nontoxic drugs, CDCA and guggulsterone, as inhibitors of HIF-1α protein

Effect of CDCA on HIF-1α expression.

<p>After starvation for 20hr, HepG2 cells were pretreated with CDCA (100 μM or indicated dose) for 6 hours then exposed to 20%, 5% or 0.1% O₂ for the indicated hours. (A) Western analyses for HIF-1α, 14-3-3γ and β-actin proteins. 14-3-3γ and β-actin proteins were detected as loading controls. (B) Quantitative RT-PCR of HIF-1α mRNA. (C and D) Western analyses of HIF-1α protein. HepG2 cells which were serum starved with medium containing 0.5% FBS for 20 hours prior to stimulation with MG132 (10 μM) and/or CDCA. 6 hours after treatment, the cells were exposed to 20% or 5% O₂ for 4 hours. Ubiquitinated and original HIF-1α proteins are indicated. HDAC1 protein or β-actin protein were examined in order to verify equal loading. (D) 20 μg of MG132 untreated total cell extracts and 5 μg of MG132 treated total cell extracts are loaded, respectively.</p

Effect of CDCA on hypoxic target genes.

<p>(A) Experimental scheme. HepG2 cells were serum starved with medium containing 0.5% FBS for 20 hours prior to CDCA (100 μM or indicated dose) treatment. 6 hours after CDCA treatment, the cells were exposed to 20%, 5% or 0.1% O₂ for the indicated hours. (B) Quantitative RT-PCR analyses of SHP mRNA. The expression level was normalized with the expression level of 18s rRNA. (C) Western analyses for SHP and β-actin. β-actin protein was detected as a loading control. Data shown are representative of three experiments (C) Quantitative RT-PCR analyses of carbonic anhydrase 9 (CA9), phosphoglycerate kinase1 (PGK1), endoplasmic reticulum oxidoreductin 1-like (EROL1), lysyl oxidase (LOX), prolyl 4-hydroxylase, alpha peptide 1 (P4HA1). a, <i>p</i> ≤ 0.1; b, <i>p</i> ≤ 0.05; c, <i>p</i> ≤ 0.01; d, <i>p</i> ≤ 0.001; e, <i>p</i> = 0.197; f, <i>p</i> = 0.724.</p

Effects of SHP or GW4064 on HIF-1α expression.

<p>(A and B) HepG2 cells were transfected with an empty vector or pcDNA3/HA-SHP. 18 hours after transfection, the cells were serum starved with medium containing 0.5% FBS for 20 hours. The cells were treated DMSO or 100 μM of CDCA for 6 hours in the absence or presence of MG132 and then exposed to 20%, 5% or 0.1% O₂ for 4 hours. 30 μg of total cell extracts are loaded for western analyses. (C to E) After starvation for 20hr, HepG2 cells were pretreated with GW4064 (GW) (5 μM or indicated dose) for 6 hours then exposed to 20%, 5% or 0.1% O₂ for the indicated hours. (C and E) qRT-PCR analyses of SHP or HIF-1α respectively. The expression level was normalized with the expression level of 18s rRNA. a, <i>p</i> ≤ 0.1; b, <i>p</i> ≤ 0.05; c, <i>p</i> ≤ 0.01; d, <i>p</i> ≤ 0.001. (D) Western analyses of HIF-1α, SHP and β-actin. (F) Western analyses of HIF-1α and β-actin in HepG2 cells which were treated with indicated doses of GW4064 and MG132 as described above. Ubiquitinated and original HIF-1α proteins are indicated. β-actin protein were examined in order to verify equal loading.</p

Effect of CDCA on de novo synthesis of HIF-1α protein.

<p>(A) Experimental scheme. After serum starvation for 20 hr, HepG2 cells were pretreated with DMSO or CDCA (100μM), 30 min prior to MG132 (10 μM) treatment. (B) Western analyses of HIF-1α and β-actin proteins (three western blots are shown). (C) Experimental scheme. HepG2 cells were pretreated with CHX (10 μg/ml, 3 hr), then the culture media were replaced with fresh media containing MG132 (10 μM) and/or CDCA (100 μM) as indicated. (D) Western analyses of HIF-1α and β-actin proteins (three western blots are shown). Quantification of western analyses. The intensities of HIF-1α and β-actin bands marked with bars were measured using Image J software. The y-axis indicates the relative band intensities of HIF-1α protein to 0 hr. The band intensities of HIF-1α protein were normalized by β-actin protein. The x-axis indicates the hours for MG132 treatments. <i>p</i> values between band intensities of CDCA-treated and untreated samples are shown. a, <i>p</i> ≤ 0.1; b, <i>p</i> ≤ 0.05; c, <i>p</i> ≤ 0.01; d, <i>p</i> ≤ 0.001; e, <i>p</i> = 0.251.</p