The Epigenetics of Acute and Chronic Kidney Disease
The Epigenetics of Acute and Chronic Kidney Disease
Several lines of evidence also support the role of histone PTM variations in CKD. Key events related to CKD such as dyregulated expression of fibrotic, cell cycle, and inflammatory genes have recently been associated with changes in histone PTMs, particularly in cell culture models treated with HG and TGF-β. These studies showed TGF-β-induced enrichment of active epigenetic marks H3K9/14Ac, H3K4me1, and H3K4me3, and decreased levels of repressive marks such as H3K9me3 at profibrotic gene promoters. Furthermore, TGF-β upregulated the H3K4-methyltransferase SET7, which enhanced H3K4me1 at TGF-β-induced genes, and SET7 knockdown inhibited TGF-β-induced fibrotic gene expression, implicating SET7 as a key player in DN. Interestingly, HG also triggered similar epigenetic events, which were inhibited by a TGF-β−neutralizing antibody, implicating TGF-β in HG-induced effects. Furthermore, TGF-β also promoted p300 recruitment, with concomitant increase in H3K9/14Ac and chromatin relaxation at fibrotic gene promoters and Smad2/3 acetylation/activation, leading to increased fibrosis. Thus, TGF-β uses both epigenetic histone PTMs and nonepigenetic mechanisms to regulate the expression of genes relevant to DN pathogenesis.
Endoplasmic reticulum stress has a key role in DN by regulating inflammatory and apoptotic pathways, and one report examined the role of epigenetic mechanisms. Endoplasmic reticulum stress–related genes including Xbp1 were upregulated in the kidneys from diabetic db/db mice. Endoplasmic reticulum stress increased SET7 levels through XBP-1, which led to increased H3K4me1 at the Ccl2 promoter and its upregulation. These events were blocked by treatment of db/db mice with the endoplasmic reticulum-stress inhibitor betaine. Furthermore, SET7 siRNAs also blocked Ccl2 expression. In another study, myocardin-related transcription factor A was induced by HG in tubular epithelial cells, which in turn promoted recruitment of HAT p300 and WD repeat-containing protein 5, a key component of the active H3K4 methyltransferase complex, at the collagen 1 promoter and increased H3K18/K27Ac, as well as H3K4me3, to upregulate its expression. In myocardin-related transcription factor A knockout mice, fibrotic gene expression and DN development were attenuated, further implicating myocardin-related transcription factor A in fibrosis. Promoter HKAc–mediated chromatin relaxation was also demonstrated in TGF-β−induced sustained upregulation of miR-192, a key profibrotic microRNA in mesangial cells. This study demonstrated a novel interplay between Smads and Ets-1 transcription factors, HATs and HKAc, as well as Akt kinase activation, in miR-192 expression. The mediatory role of H3KAc was also demonstrated in HG-induced downregulation of miR-29 via HDAC4-induced de-acetylation of miR-29 promoter in podocytes, leading to upregulation of miR-29 targets including HDAC4 and fibrotic genes. Thus, there is substantial evidence to demonstrate the pivotal role of both histone and nonhistone lysine-Ac in regulating genes associated with DN pathogenesis (Figure 4). Results from diabetic mice models also revealed similar changes in H3K9Ac at fibrotic and inflammatory gene promoters. One study found increased expression of HDAC-2, -4, and -5 in kidneys of type 1 diabetic rats and biopsies from diabetic patients. In vitro experiments showed that HDAC4 was upregulated by HG, TGF-β, and advanced glycation end products, and that HDAC4–STAT1 signaling promotes podocyte injury. Furthermore, HDAC4 knockdown using intrarenal delivery of lentivruses ameliorated renal injury in diabetic rats.
(Enlarge Image)
Figure 4.
Fibrotic and inflammatory gene regulation by histone modifications in CKD. In diabetic nephropathy and other CKDs, signal transduction events triggered by pathological factors such as high glucose (HG) and downstream effectors including TGF-β induce the expression and activation of key transcription factors such as SMAD, NF-κB, XBP1, and MRTF-A, as well as histone-modifying enzymes such as SET7 in glomerular and tubular cells. These signaling events also lead to recruitment of HMTs (such as SET7), HATs (such as P300), and chromatin proteins such as WDR5 at profibrotic and proinflammatory gene promoters, leading to increases in permissive histone modifications (H3KAc and H3K4me) and chromatin relaxation. This enhances chromatin access to transcription factors and RNA polymerase II (Pol II), which increases the expression of profibrotic and proinflammatory genes implicated in renal dysfunction. Renal hypoxia also promotes tubular fibrosis in CKD. Hypoxia-inducible factor-1 (HIF-1) co-operates with histone-modifying enzymes (JMJD) to regulate target genes. Persistence of such changes in epigenetic modifications (Figures 2 and 3) could be the underlying mechanisms involved in transcription memory (in AKI) or 'metabolic memory' (in diabetic nephropathy) associated with a sustained increased risk for CKD and ESRD; JMJD-JMJD1A; and JMJD2B. AKI, acute kidney injury; CKD, chronic kidney disease; ESRD, end-stage renal disease; HMT, histone methyltransferase; H3KAc, Histone H3 lysine acetylation; MRTF-A, myocardin-related transcription factor A; TGF-β, transforming growth factor-β.
The in vivo role of HKme in DN has been reported in a few studies. Kidneys from diabetic rats and mice showed increased H3K4me2 and RNA polymerase II, but decreased H3K27me3 levels, at fibrotic genes. However, the corresponding histone-modifying enzymes showed different expression patterns in rats versus mice kidneys, suggesting species-specific differences (possibly related to severity of DN). Another in vivo study examined multiple histone PTMs in glomeruli from diabetic db/db mice and control db/+ mice to obtain a comprehensive picture of histone code alterations and cross talk among histone PTMs during DN. Results showed alteration in some of the histone PTMs examined, including H3K9/14Ac, at genes encoding PAI-1 and RAGE in db/db mice relative to db/+, which could facilitate open chromatin states, as indicated by enhanced enrichment of RNA polymerase II, and increased gene expression. Several HATs, including Tip60, and H3K4-MTs, including SET7, were also upregulated in db/db mice.
Notably, the protective effects of HDAC inhibitors have been demonstrated in animal models of DN, further supporting the role of HKAc and epigenetic mechanisms in renal dysfunction. However, nonhistone acetylation mediated by HATs cannot be ignored. This was highlighted in a recent study demonstrating a critical role for STAT3 acetylation in DN. It was found that diabetes increases NF-κB and STAT3 acetylation via downregulation of Sirt1 in podocytes to promote pathologic gene expression, and this effect can be mimicked by Sirt1 deletion in db/db mice. Thus, a complex network of epigenetic factors and transcription factors regulate pathologic gene expression in CKD. Cell necrosis and apoptosis in later stages of CKD might significantly affect epigenetic profiles. Further understanding of these mechanisms and determination of time course of changes during CKD are needed, which will be of utmost importance when designing epigenetic therapies.
Chronic hypoxia in renal tubular interstitial compartments can lead to increased fibrosis in CKD, and other kidney disorders. Gene expression under hypoxic conditions is controlled by a master regulatory transcription factor, hypoxia-inducible factor-1 (HIF-1), which binds to the promoter of target genes to induce their expression. Under normoxic conditions, HIF-1 degradation is promoted by prolyl hydroxylase, but under hypoxic conditions prolyl hydroxylase activity is lost, leading to stabilization of HIF-1. Interestingly several epigenetic changes were reported to be associated with hypoxia. Moreover, HIF-1 was shown to induce the expression of several epigenetic regulators such as histone demethylases in mammalian cells. HIF-1 can assist in promoting dynamic changes in chromatin conformation. The epigenetic modifying properties of HIF-1 could be exploited for better approaches to curb chronic hypoxia–induced tubulointerstitial fibrosis in various kidney disorders.
Histone PTMs and CKD
Several lines of evidence also support the role of histone PTM variations in CKD. Key events related to CKD such as dyregulated expression of fibrotic, cell cycle, and inflammatory genes have recently been associated with changes in histone PTMs, particularly in cell culture models treated with HG and TGF-β. These studies showed TGF-β-induced enrichment of active epigenetic marks H3K9/14Ac, H3K4me1, and H3K4me3, and decreased levels of repressive marks such as H3K9me3 at profibrotic gene promoters. Furthermore, TGF-β upregulated the H3K4-methyltransferase SET7, which enhanced H3K4me1 at TGF-β-induced genes, and SET7 knockdown inhibited TGF-β-induced fibrotic gene expression, implicating SET7 as a key player in DN. Interestingly, HG also triggered similar epigenetic events, which were inhibited by a TGF-β−neutralizing antibody, implicating TGF-β in HG-induced effects. Furthermore, TGF-β also promoted p300 recruitment, with concomitant increase in H3K9/14Ac and chromatin relaxation at fibrotic gene promoters and Smad2/3 acetylation/activation, leading to increased fibrosis. Thus, TGF-β uses both epigenetic histone PTMs and nonepigenetic mechanisms to regulate the expression of genes relevant to DN pathogenesis.
Endoplasmic reticulum stress has a key role in DN by regulating inflammatory and apoptotic pathways, and one report examined the role of epigenetic mechanisms. Endoplasmic reticulum stress–related genes including Xbp1 were upregulated in the kidneys from diabetic db/db mice. Endoplasmic reticulum stress increased SET7 levels through XBP-1, which led to increased H3K4me1 at the Ccl2 promoter and its upregulation. These events were blocked by treatment of db/db mice with the endoplasmic reticulum-stress inhibitor betaine. Furthermore, SET7 siRNAs also blocked Ccl2 expression. In another study, myocardin-related transcription factor A was induced by HG in tubular epithelial cells, which in turn promoted recruitment of HAT p300 and WD repeat-containing protein 5, a key component of the active H3K4 methyltransferase complex, at the collagen 1 promoter and increased H3K18/K27Ac, as well as H3K4me3, to upregulate its expression. In myocardin-related transcription factor A knockout mice, fibrotic gene expression and DN development were attenuated, further implicating myocardin-related transcription factor A in fibrosis. Promoter HKAc–mediated chromatin relaxation was also demonstrated in TGF-β−induced sustained upregulation of miR-192, a key profibrotic microRNA in mesangial cells. This study demonstrated a novel interplay between Smads and Ets-1 transcription factors, HATs and HKAc, as well as Akt kinase activation, in miR-192 expression. The mediatory role of H3KAc was also demonstrated in HG-induced downregulation of miR-29 via HDAC4-induced de-acetylation of miR-29 promoter in podocytes, leading to upregulation of miR-29 targets including HDAC4 and fibrotic genes. Thus, there is substantial evidence to demonstrate the pivotal role of both histone and nonhistone lysine-Ac in regulating genes associated with DN pathogenesis (Figure 4). Results from diabetic mice models also revealed similar changes in H3K9Ac at fibrotic and inflammatory gene promoters. One study found increased expression of HDAC-2, -4, and -5 in kidneys of type 1 diabetic rats and biopsies from diabetic patients. In vitro experiments showed that HDAC4 was upregulated by HG, TGF-β, and advanced glycation end products, and that HDAC4–STAT1 signaling promotes podocyte injury. Furthermore, HDAC4 knockdown using intrarenal delivery of lentivruses ameliorated renal injury in diabetic rats.
(Enlarge Image)
Figure 4.
Fibrotic and inflammatory gene regulation by histone modifications in CKD. In diabetic nephropathy and other CKDs, signal transduction events triggered by pathological factors such as high glucose (HG) and downstream effectors including TGF-β induce the expression and activation of key transcription factors such as SMAD, NF-κB, XBP1, and MRTF-A, as well as histone-modifying enzymes such as SET7 in glomerular and tubular cells. These signaling events also lead to recruitment of HMTs (such as SET7), HATs (such as P300), and chromatin proteins such as WDR5 at profibrotic and proinflammatory gene promoters, leading to increases in permissive histone modifications (H3KAc and H3K4me) and chromatin relaxation. This enhances chromatin access to transcription factors and RNA polymerase II (Pol II), which increases the expression of profibrotic and proinflammatory genes implicated in renal dysfunction. Renal hypoxia also promotes tubular fibrosis in CKD. Hypoxia-inducible factor-1 (HIF-1) co-operates with histone-modifying enzymes (JMJD) to regulate target genes. Persistence of such changes in epigenetic modifications (Figures 2 and 3) could be the underlying mechanisms involved in transcription memory (in AKI) or 'metabolic memory' (in diabetic nephropathy) associated with a sustained increased risk for CKD and ESRD; JMJD-JMJD1A; and JMJD2B. AKI, acute kidney injury; CKD, chronic kidney disease; ESRD, end-stage renal disease; HMT, histone methyltransferase; H3KAc, Histone H3 lysine acetylation; MRTF-A, myocardin-related transcription factor A; TGF-β, transforming growth factor-β.
The in vivo role of HKme in DN has been reported in a few studies. Kidneys from diabetic rats and mice showed increased H3K4me2 and RNA polymerase II, but decreased H3K27me3 levels, at fibrotic genes. However, the corresponding histone-modifying enzymes showed different expression patterns in rats versus mice kidneys, suggesting species-specific differences (possibly related to severity of DN). Another in vivo study examined multiple histone PTMs in glomeruli from diabetic db/db mice and control db/+ mice to obtain a comprehensive picture of histone code alterations and cross talk among histone PTMs during DN. Results showed alteration in some of the histone PTMs examined, including H3K9/14Ac, at genes encoding PAI-1 and RAGE in db/db mice relative to db/+, which could facilitate open chromatin states, as indicated by enhanced enrichment of RNA polymerase II, and increased gene expression. Several HATs, including Tip60, and H3K4-MTs, including SET7, were also upregulated in db/db mice.
Notably, the protective effects of HDAC inhibitors have been demonstrated in animal models of DN, further supporting the role of HKAc and epigenetic mechanisms in renal dysfunction. However, nonhistone acetylation mediated by HATs cannot be ignored. This was highlighted in a recent study demonstrating a critical role for STAT3 acetylation in DN. It was found that diabetes increases NF-κB and STAT3 acetylation via downregulation of Sirt1 in podocytes to promote pathologic gene expression, and this effect can be mimicked by Sirt1 deletion in db/db mice. Thus, a complex network of epigenetic factors and transcription factors regulate pathologic gene expression in CKD. Cell necrosis and apoptosis in later stages of CKD might significantly affect epigenetic profiles. Further understanding of these mechanisms and determination of time course of changes during CKD are needed, which will be of utmost importance when designing epigenetic therapies.
Chronic hypoxia in renal tubular interstitial compartments can lead to increased fibrosis in CKD, and other kidney disorders. Gene expression under hypoxic conditions is controlled by a master regulatory transcription factor, hypoxia-inducible factor-1 (HIF-1), which binds to the promoter of target genes to induce their expression. Under normoxic conditions, HIF-1 degradation is promoted by prolyl hydroxylase, but under hypoxic conditions prolyl hydroxylase activity is lost, leading to stabilization of HIF-1. Interestingly several epigenetic changes were reported to be associated with hypoxia. Moreover, HIF-1 was shown to induce the expression of several epigenetic regulators such as histone demethylases in mammalian cells. HIF-1 can assist in promoting dynamic changes in chromatin conformation. The epigenetic modifying properties of HIF-1 could be exploited for better approaches to curb chronic hypoxia–induced tubulointerstitial fibrosis in various kidney disorders.