The Impact of Epigenomics on Understanding Kidney Diseases

Histone modifications

Histone modifications are vital in various biological processes,⁷ impacting gene expression and chromatin structure in conditions like AKI and CKD. Histone acetyltransferases (HATs) add acetyl groups, while histone deacetylases (HDACs) remove them, influencing transcription and DNA repair. Key modifications include H3K4me3 and AcH3 for activation, and H3K27me3 and H4K20me3 for repression. The reversible nature of acetylation opens potential therapeutic options. Wang et al.⁷ highlighted the role of histone acetylation in AKI pathogenesis, suggesting that targeting histone modifications may offer new therapies. Li et al.⁸ studied EZH2 in sepsis-induced AKI using lipopolysaccharide (LPS)-injected mice, finding that silencing EZH2 protects renal function by activating the Wnt/β-catenin pathway while reducing apoptosis and inflammation, marking it as a potential therapeutic target. Guo et al.⁹ noted that AKI leads to rapid kidney function decline and emphasized the impact of post-translational modifications (PTMs) in CKD, advocating for new preventive strategies [Figure 2].

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Figure 2:

Role and mechanism of EZH2 inhibition in AKI. nhibition of EZH2 plays a protective role in acute kidney injury (AKI) by preserving the expression of key proteins such as RKIP (Raf kinase inhibitor protein), E-cadherin, TIMP-2 (metalloproteinase-2), TIMP-3 (metalloproteinase-3). Additionally, it represses the activation of various fibrosis and inflammatory signaling pathways, including NF-κB (nuclear factor-κB), ERK1/2 (extracellular signal-regulated kinase 1/2), p38, and ALK5/Smad2/3. EZH: Methyltransferases enhancer of zeste homolog, NF-kB: Nuclear factor kappa-light-chain-enhancer of activated B cells, EPK: Eukaryotic protein kinase, ZO: Zonula occludens, TIMP: Tissue inhibitor of metalloproteinase, ALK: Anaplastic lymphoma kinase, ROS: Reactive oxygen species, NOX: NADPH oxidase, Smad2: SMAD family member 2.

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The bromodomain and extra-terminal (BET) protein family (BRD2, BRD3, BRD4, BRDT) regulates gene transcription by binding to acetylated lysines. It is associated with diseases such as tumors and CKD. Selective BET protein inhibitors show promise for treatment. A novel modification, histone lysine β-hydroxybutyrylation (Kubb), impacts transcription during carbohydrate restriction and is linked to metabolic and kidney issues. Increased histone acetylation may offer protection against AKI, which is also associated with changes in DNA methylation, although the precise mechanisms remain unclear. β-Hydroxybutyrate (BHB), an energy source during starvation, provides anti-inflammatory benefits. It has been examined for its epigenetic roles in diseases, particularly in kidney disease, where acetylation is essential, but specific protective treatments are lacking.

Histon methylation

Researchers have found that H3K9 trimethylation (H3K9me3) increases significantly in kidney fibrosis after UUO, indicating an altered epigenetic landscape. In UUO mice and fibrotic kidneys of patients with CKD, elevated EZH2 and H3K27me3 levels were observed. In DN, treatment with anti-CCL2 antibodies reversed histone methylation linked to glomerulosclerosis, revealing CCL2’s role in inflammation and epigenetic regulation. Clinical studies highlight the reno-protective effects of advanced glycation end-products (AGE), histone modification inhibitors, and incretin-related medications. Hypoxia-inducible prolyl hydroxylase inhibitors and NF-E2-related factor 2 activators may enhance GFRs in DKD patients. Silencing EZH2 protects renal function by alleviating Sox9 repression, activating the Wnt/β-catenin pathway, and reducing apoptosis and inflammation.

Research indicates that targeting EZH2 may have therapeutic potential in sepsis-induced AKI. Studies on arginine methyltransferases, elevated in various kidney injury models (AKI, obstructive nephropathy, DN, lupus nephritis), suggest that inhibiting these enzymes could mitigate kidney damage. Zhang et al.¹⁴ found that the mitochondrial protein SIRT3 is crucial for regulating mitochondrial function; reduced SIRT3 is linked to increased mitochondrial acetylation in renal fibrosis. Sirt3 knockout mice showed heightened susceptibility to fibrosis, while activating SIRT3 with honokiol reduced acetylation and prevented fibrosis. Post-UUO, 26.76% of hyper-acetylated kidney proteins were mitochondrial, affecting energy metabolism, particularly PDHE1α, which is regulated by SIRT3. Additionally, DOT1L enhances renal fibrosis management by inhibiting key pathways and boosting protective factors like PTEN, Klotho, and Smad7, while reducing ROS production through the PI3K/Akt pathway [Figure 3].

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Figure 3:

Role and mechanism of DOT1L inhibition in renal fibrosis. Inhibition of DOT1L leads to an increase in renal fibrosis by up-regulating endothelin 1 (ET1). In contrast, when DOT1L is inhibited, renal fibrosis can be alleviated. This is achieved by suppressing various fibrosis pathways, including Smad3, epidermal growth factor receptor (EGFR), platelet-derived growth factor receptor (PDGFR), and the nuclear factor-κB (NF-κB) pathway. Additionally, the inhibition of DOT1L enhances the expression of renal protective factors such as PTEN, Klotho, and Smad7. Furthermore, it reduces the generation of reactive oxygen species (ROS) through the PI3K/Akt pathway. KMT: Lysine methyltransferases, KDM: Lysine demethylase, FR: Functional renal failure, IR: Ischemia-reperfusion, UUO: Unilateral ureteral obstruction, SNx: Subtotal nephrectomy, EMT: Epithelial-mesenchymal transition, ECM: Extracellular matrix.

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Phosphorylation

This is crucial for chromatin structure and cellular function. It involved the addition of a phosphoryl group to proteins. Key podocyte proteins include nephrin, podocin, CD2AP, synaptopodin, and ACTN4. Genetic studies underscore phosphorylation as a vital post-translational modification that regulates protein activity. Feng (2020)²⁹ reviews its impact on podocyte proteins and its role in proteinuria and kidney diseases. The link between high glucose and phosphorylation in nephrin and ACTN4 suggests disruptions in the podocyte cytoskeleton in diabetes, warranting further research on how these changes may lead to proteinuria in DN.

Ubiquitin-proteasome system

The ubiquitin-proteasome system (UPS) is essential in fibrotic diseases, influencing renal fibrosis through various signaling pathways, inflammation, and oxidative stress. Renal tubular epithelial cells (RTECs) are crucial for kidney function, and dysfunction can lead to fibrosis. Key cellular quality control processes include UPS, autophagy, and mitochondrial health. RTEC quality control deficiencies can trigger pro-fibrotic effects like senescence and immune cell recruitment. HUWE1, an E3 ligase in the UPS, degrades the epidermal growth factor receptor (EGFR) to help prevent renal fibrosis; however, the specific E2 enzymes involved with HUWE1 have not yet been identified. Research indicates significant down-regulation of UBE2Q2 in fibrotic models, suggesting a collaborative role with HUWE1 in kidney injury that deserves further exploration.

MicroRNAs

MicroRNAs (miRNAs) are short, noncoding RNAs (18-25 nucleotides) that regulate gene expression in eukaryotes. With over 3,000 miRNAs in the human genome, they influence protein levels of target mRNAs without altering gene sequences and can be affected by epigenetic modifications. These miRNAs play a crucial role in diseases such as DN and polycystic kidney disease. Table 3 illustrates the implication of miRNAs in different nephropathies.^30-37 For example, deleting podocyte-specific Dicer in mice leads to significant kidney impairment, and miRNA-192 is associated with DN. Changes in miRNA expression are also observed during kidney allograft rejection. Ongoing research aims to enhance understanding of kidney disease mechanisms and identify potential diagnostic and therapeutic targets.

A study found that microRNA-223 (miR-223) levels were significantly higher in renal biopsies³⁴ of patients with progressive chronic renal failure than those with stable CKD, suggesting miR-223 may worsen renal dysfunction. Neal et al.³⁸ observed that most miRNA levels decreased as CKD advanced, with lower serum levels of miR-125b, miR-145, and miR-155 in stages 3- 5D. Additionally, specific heart miRNAs in serum were inversely related to renal function. Ulbing et al.³⁹ noted reduced miR-223 expression in CKD stages IV and V compared to healthy controls, but this down-regulation ceased post-transplant. Current evidence on the impact of renal function on circulating miRNA levels is limited and inconsistent. Pharmacokinetic studies suggest that kidneys excrete specific miRNAs, with in vivo imaging showing proximal tubular cells filter and reabsorb siRNAs quickly. Neal et al.³⁸ concluded that decreased circulating miRNA levels in CKD patients were not linked to increased urinary excretion.

miRNA levels differ based on kidney and vascular contexts. New strategies for modulating these regulatory molecules have emerged—advanced gene therapy vectors, like adeno-associated viruses and lentiviruses, target diseased tissues with miRNA precursors. Researchers explore chemically modified RNAs and inhibitory sponges to suppress specific miRNAs, aiming to restore normal function. Conjugating miRNAs with nanoparticles increases delivery and bioavailability. The CRISPR/Cas9 system enables selective alteration of miRNA sequences for therapeutic optimization. These techniques offer a promising approach to treating kidney and vascular diseases through miRNA modulation.

LncRNAs

LncRNAs play a significant role in kidney diseases by influencing gene and protein expression, although their regulatory mechanisms remain unclear. Renal disorders often involve epigenetic modifications such as DNA/RNA methylation and acetylation, which affect gene expression without changing the genetic sequence. The interaction between lncRNAs and these modifications are observed in various kidney diseases, including glomerulonephritis, AKI, CKD, DN, and renal cell carcinoma (RCC). Future research aims to explore the connections between lncRNAs and modification enzymes in renal disorders, potentially leading to new therapeutic strategies using small-molecule drugs or lncRNA mimetics/antagonists. Additionally, lncRNAs, over 200 nucleotides long, are essential for organismal complexity and regulating genomic enzyme activity.

Non-coding RNAs (lncRNAs) are associated with organ fibrosis and aging, particularly in CKD, where fibrosis complicates progression. Their roles, along with miRNAs in renal fibrosis, remain unclear. Additionally, lncRNAs are crucial in AKI, affecting epigenetics and autophagy in RCC, which is increasing globally, about 1/3 of patients present with metastases. Biomarkers like lncRNAs may help predict disease progression, with significant molecules including MALAT1, RCAT1, and others. A study aimed at developing new biomarkers for kidney renal clear cell carcinoma (KIRC) identified 42 differentially expressed m7G-lncRNAs and noted survival differences for PTCSC3 and RP11-321G12, highlighting PTCSC3 as a prognostic factor. SLE is an autoimmune disease marked by renal involvement and lupus nephritis (LN). Non-coding RNA (lncRNA) and circular RNA (circRNA) play key roles in LN pathogenesis by binding to miRNAs, influencing cell proliferation, inflammation, and oxidative stress. These RNAs may be biomarkers for LN diagnosis and therapeutic targets.

Non-coding RNAs (lncRNAs) play crucial roles in physiological processes, including cell cycle regulation, apoptosis, and metabolism. Recent research highlights their involvement in type 2 diabetes and DN, particularly in hepatic glucose production and insulin resistance. Notably, the lncRNA CYP4B1-PS1-001 is downregulated in early DN. CYP4B1-PS1-001 overexpression may inhibit the proliferation and fibrosis of mouse mesangial cells (MMCs) and regulate NCL’s ubiquitination, impacting MMC proliferation. Abnormal lncRNA expression in diabetes has been linked to kidney damage, suggesting lncRNAs as potential therapeutic targets. A study found that specific signaling pathways connect diabetic retinopathy, peripheral neuropathy, and nephropathy, with lncRNA microarray analysis revealing mis-expressed lncRNAs in renal tissues from diabetic models. Overexpression of downregulated ENSMUST00000147869 in mesangial cells reversed proliferation and fibrosis, indicating its potential as a biomarker and therapeutic target for DN.⁴⁰ Understanding lncRNAs’ interactions with miRNAs and mRNAs is essential for addressing renal diseases.

Future perspectives

Kidney diseases represent a significant global health challenge, with their underlying mechanisms not fully understood. This review connects epigenetic dysregulation to kidney disease, highlighting how DNA methylation, histone modifications, and miRNA expression influence kidney function, inflammation, and disease progression. Although insights have been gained, our grasp of epigenetic factors remains limited. Identifying methylation and histone changes in patients vs. healthy individuals is vital for developing targeted therapies. Advances in high-throughput technologies allow quantitative epigenetic analyses, but quality sample requirements hinder the use of preserved specimens. Targeting reversible DNA modifications may lead to new treatments. Future research should examine how renal epigenome changes interact with genetic mutations and enhance epigenomic testing for precision medicine. As knowledge expands, potential biomarkers for early diagnosis and treatment monitoring of kidney disorders may emerge, steering renal therapy toward personalized medicine based on individual profiles.