New Insights into the Use of Traditional Chinese Medicine for Treating Diabetic Kidney Disease by Regulating DNA Methylation

INTRODUCTION The prevalence of diabetes mellitus (DM) is increasing annually. The International Diabetes Federation reported that the global diabetic population reached 463 million in 2019 and is projected to rise to 700 million by 2045.[1] Diabetic kidney disease (DKD) —a major chronic complication of DM—is the primary cause of end-stage renal disease (ESRD).[2] Consequently, elucidating the pathogenesis of DKD and identifying effective treatments to prevent its progression to ESRD are critical. The etiology of DKD is multifaceted, involving inflammation, oxidative stress, and lipid metabolic disorders, among others. Although DKD exhibits a degree of heritability, this does not fully account for its development in all cases. Enhancing our understanding of DKD’s molecular mechanisms could pave the way for more effective clinical interventions to manage and prevent this complication. Previous studies have demonstrated that DKD can develop even when blood glucose levels are well controlled—a phenomenon known as “metabolic memory”.[2] Research into metabolic memory has increasingly focused on the epigenetic regulation of DNA methylation, histone modification, and noncoding RNA (ncRNA). DNA methylation—the most extensively studied epigenetic mechanism in DKD—plays a critical role in gene expression regulation and chromosomal stability. Investigating epigenetic alterations in DKD is crucial for developing targeted treatments. Traditional Chinese medicine (TCM), characterized by its multicomponent and multitarget approaches, is extensively used to prevent and treat various diseases.[3] Although TCM has proven effective for managing DKD, the underlying mechanisms remain poorly understood. Research into DNA methylation has significant implications for TCM. DNA methylation—a dynamic and reversible process noted for its heritability and variability—is crucial for uncovering the pharmacological mechanisms underlying TCM and significantly enhancing its clinical application. Studies have indicated that TCM can influence methylation across the entire genome.[4] Consequently, this article provides a concise review of TCM’s role in DKD treatment through the modulation of DNA methylation. DNA METHYLATION DNA methylation is a biological process catalyzed by DNA methyltransferases (DNMTs), whereby a methyl group is transferred to the cytosine residue.[5] DNMT1 is crucial for maintaining DNA methylation during replication, whereas DNMT3a and DNMT3b pivotally underpin DNA remethylation during cell differentiation. Unlike DNA sequence mutations, DNA methylation is reversible and heritable. This process can influence gene expression by directly affecting the binding of transcriptional complexes in the promoter region or indirectly through the recognition of 5-methylcytosine. This occurs via methyl-binding proteins, which recruit corepressors to the promoter region. Thus, alterations in DNA methylation can modulate the expression of key genes without altering the DNA sequence, potentially leading to various diseases. DNA methylation is established during organ development and exhibits a tissue-specific distribution that differs from mRNA expression.[6] DKD AND DNA METHYLATION In recent years, numerous studies have investigated[7–9] the relationship between DKD and DNA methylation, revealing associations with the methylation patterns of certain key genes. Recent research[7] identified 694 hypomethylated and 174 hypermethylated CpG sites across the genome that influence conditions such as inflammation, oxidative stress, mitochondrial stress, and lipid metabolism in DKD pathogenesis. These findings suggest that oxidative stress influences DNA methylation and plays a pivotal role in DKD development. Superoxide dismutase 2 (SOD2) —a critical antioxidant—is negatively regulated by DNA methylation, which promotes smooth muscle cell proliferation.[8] Additionally, aberrant methylation of SOD2 can activate hypoxia-inducible factor 1-alpha (HIF-1alpha), inhibit heme oxygenase-1 (HO-1)-mediated mitochondrial dynamics, and curtail excessive reactive oxygen species (ROS) production.[9] Consequently, HIF-1alpha may exert a protective effect against DKD. Due to the stable nature of DNA methylation, tissue-specific methylation patterns are increasingly recognized as cell-specific markers. A recent study[10] identified significant differences in methylation sites within the peripheral blood between individuals with DM and those with DKD. These findings suggest that DNA methylation sites may serve as potential biomarkers for monitoring DKD progression. DNA METHYLATION AND TCM INTERVENTION TCM is widely used in China and other Asian countries but also in Western nations. It has demonstrated numerous benefits for treating complex diseases due to its holistic approach, dynamic nature, individualized treatments, and interaction with environmental factors. However, due to the complexity of its components and the uncertainty surrounding its pharmacological mechanisms, the therapeutic targets of TCM remain poorly defined. Recently, advances in epigenetics have offered fresh insights for TCM research and have attracted significant interest. Epigenetic principles align closely with the core concepts of TCM. Studies in this domain provide a new lens through which to view TCM and elucidate the elusive mechanisms underlying its extensive clinical use. Research has indicated that TCM significantly influences the regulation and modification of DNA methylation.[11] Investigations into how TCM modulates DNA methylation have primarily focused on genome-wide regulation and the correction of abnormal methylation through single compounds and active ingredients. Many historic TCM treatments are widely used to manage DKD. However, epigenetic research on TCM for DKD treatment is still nascent. Recently, our research group conducted an in-depth analysis of DNA methylation profiles and identified 797 genes potentially impacted by the Tangshen formula which is a compound traditional Chinese medicine. Notably, approximately 2.3% of these genes had previously been identified as homologous genes.[12] The multicomponent, multitarget characteristics of TCM make it less likely to induce drug resistance and side effects, showing unique advantages for the treatment of complex diseases. Classical TCM treatments have been linked to altered methylation patterns in disease therapy. Typically, these modifications occur through the regulation of DNMT or related signaling pathways.[13] In DKD research, studies on TCM’s ability to regulate methylation are scarce. Nonetheless, given the overlap of multiple pathways between DKD and other diseases, such research has significant implications for using TCM to modify methylation levels in DKD treatment. Curcumin—the active compound in turmeric—is renowned for its antioxidant properties, and it can inhibit DNA methylation by blocking the catalytic site of DNMT1 and reducing Sp1 expression.[14,15] Angelica sinensis (Danggui) potentially regulates the demethylation of the NFE2-LIKE BZIP transcription factor (Nrf2) promoter.[16] Liu Wei Di Huang Wan is said to nourish Yin and fortify the kidneys by suppressing DNMT1 expression and reducing androgen (AR) methylation.[17] Qian Yang Yu Yin granules have been shown to alleviate renal injury in animal models and inhibit HEK293T cell proliferation by downregulating S-adenosylhomocysteine (SAH), nicotinamide N-methyltransferase (NNMT), and DNA methylation levels.[11] Uremic clearance granules (UCGs) have been used in China for decades to treat chronic renal failure and adjust the methylation level of transforming growth factor beta (TGF-beta), indicating their therapeutic value.[18] In summary, an increasing number of TCM treatments have been shown to exert therapeutic effects by regulating methylation, warranting further investigation into their potential for DKD treatment through methylation changes. PROSPECTS Based on extensive clinical experience, numerous TCM treatments and bioactive substances have beneficial pharmacological effects for managing DKD. Clarifying the mechanisms of these components is crucial for ensuring the safety and effectiveness of clinical applications of TCM. However, the complexity of TCM components and multitarget treatment strategies, and TCM’s holistic approach, contribute to the ambiguity surrounding TCM. Both cellular and animal studies[19] have underscored the significant role of epigenetic factors, particularly DNA methylation, in the development of DKD. Recent advances in epigenetics have been instrumental in elucidating the mechanisms underlying TCM’s therapeutic effects. Methylation and demethylation are dynamic, reversible processes that maintain equilibrium in the body and exhibit heritability and variability. Increasingly, methylation targets have been recognized as crucial for diagnosing DKD. DNA methylation serves as an intermediate factor playing a vital role in TCM’s therapeutic mechanisms. Numerous studies have validated TCM’s ability to modulate diseases by adjusting the body’s multitarget methylation status. However, regarding TCM treatment for DKD, research on related epigenetic mechanisms remains sparse. Additionally, various challenges hinder the further exploration of TCM, as many underlying mechanisms still require elucidation. Thus, TCM treatment for DKD as a holistic, systematic, and multitarget approach has intricate mechanisms. Epigenetic research, particularly on DNA methylation, may offer an opportunity to overcome these challenges. Continued research into DNA methylation is poised to clarify the mechanisms by which TCM can be used to treat DKD. In conclusion, enhancing the quality of TCM research requires more innovative and specific scientific methods along with more systematic experimental designs and practical techniques. Furthermore, future research should aim to further integrate TCM and epigenetics to develop effective treatments for DKD.