The Epigenetics of Chronic Kidney Disease

Chronic kidney disease (CKD) affects 20 million people in the United States and an estimated 8 to 16 percent of the world’s population. It is known that anomalous DNA methylation, aberrant histone alterations, and changes to microRNA expression all contribute to its pathogenesis. These epigenetic factors are crucial to the development and proper functioning of the kidneys. The manner and extent to which these factors modulate inflammation, fibrosis, and the transition of mesenchymal to epithelial cells is still being elucidated. The result of these explorations should provide more viable approaches to identifying and treating CKD (Beckerman, 2014).

Epigenetic modifications are essential for normal cell development and function. They regulate gene expression by switching genes on or off, thus determining which proteins are transcribed. Disruptions in epigenetic alterations have been associated with contributing to certain disease states, from breast cancer, to Alzheimer’s, diabetes, and more.

Wing et. al lists three reasons CKD is amenable to epigenetic analysis: “(1) a heritability that could not be fully explained by strict genetic inheritance patterns; (2) evidence of the influence of environmental exposure; and (3) an increase in prevalence with aging.” There is also, as the paper later notes, the fact that while genome-wide association studies have uncovered previously “unsuspected pathways,” they have failed to provide anything but very modest correlations between the identified gene variants, even when aggregated, and CKD. Tissue damage leads to inflammatory and repair responses which, when repeated over time, lead to fibrosis. Under a histologist’s microscope renal fibrosis is an enlargement of the extracellular matrix. To a physician it is the overgrowth of this matrix (mostly collagen) or the loss of functional parenchyma areas relative to connective tissue.

Methylation is the most widely known form of epigenetic modification. While there have been several investigations into the relationship between global methylation and CKD, no significant differences have been found. However, it must be noted that all of the studies conducted thus far have had fewer than 100 participants which means they, as Cañadas-Garre et. al remind us, “lack [the] power to detect significant differences in global DNA methylation.” This begs the question of why they were funded in the first place, but that is a less interesting topic than some specific methylation changes.

A paper prepared by Ko et. al provides a more nuanced perspective: “a core set of genes that are known to be related to kidney fibrosis, including genes encoding collagens, show cytosine methylation changes correlating with downstream transcript levels.” Sustained RASAL1 hypermethylation is behind the sustained fibroblast activation that leads to fibrogenesis. This process begins with methyltransferase Dnmt1, which is overactivated by prolonged exposure to the profibrotic growth factor TGF-β1 (Bechtel, 2017).

Because, among many other functions, histone deacetylase inhibitors (HDAC-i’s) in part regulate immune response, it is of little wonder that they also contribute to fibrosis. The expression of Connective Tissue Growth Factor (CTGF) can be influenced by HDAC inhibitors (Komorowsky, 2009). As well, different HDAC-i’s have different effects, which holds the not too remote promise of tailoring treatment by using a variety of HDAC-i combinations according to the patient’s needs (Van Beden, 2013).

One of the first investigations into diabetic kidney diseases reported an increase in HDAC-2 isoform as the result of transforming growth factor (TGF-1) activation, the complications of diabetes, and reactive oxidative stress. This may have accelerated the accumulation of extracellular matrix (ECM) and epithelial-to-mesenchymal transition (EMT) contributing to diabetic-induced renal fibrosis. (Noh, 2009).

HDA-5 is part of the body’s regenerative response to acute kidney injury and has also shown promise as a therapeutic intervention in both CKD and acute kidney injury. The literature on HDAC-i’s and renal diseases is already sizeable, interested readers are advised to peruse Brilli’s review.

More than one article calls diabetes the most common “cause” of CKD around the world. However, given its numerous comorbidities, like hypertension and atherosclerosis, it could be argued that this title should go to metabolic syndrome (Reidy, 2014). Since the 1970s, some researchers have chosen to see diabetes as a form of accelerated aging and it has been known for decades that diabetes greatly increases collagen glycation (Monickaraj, 2012; Dyer, 1993). CKD’s inflammation, telomere shortening, accumulation of senescent cells, end product glycation, and mitochondrial dysfunction suggest a SENS approach, among many other polygenic disorders that become more likely to develop with time, could prove fruitful (De Grey, 2007). These factors are associated with the aging process and are largely regulated by epigenetic mechanisms. They also serve as diagnostic tools. For example, P16, a critical gene in the cell cycle process and a common biomarker in gerontological research, can be used as a metric for gauging a donor organ’s viability (McGuiness et al., 2016).

While at this point the exact relationships between telomere shortening, senescence, and inflammation are not known, what is clear is they are irrevocably intertwined — all can be partially controlled through sensible lifestyle changes. Novel therapeutics such as the telomerase activators being developed by Sierra Sciences and BioViva are likely, as Blasco et. al’s research indicates, to ameliorate the numerous vicious cycles that drive the aging process and the pathologies that spring from it (Kordinas 2016; Willis, 2011; Harley, 2014).

The gene Klotho (KL), when suppressed, produces a number of premature aging phenotypes. It is named after the Moirai, one of the Fates – not a goddess as Kuro-o calls her in his otherwise excellent paper — in Greek mythology who spun the thread of life which her sisters, Lachesis and Atropos, would respectively draw out and cut. KL hypermethylation has been associated with the pathogenesis of both acute and chronic kidney disease. Problems with Klotho FGF23, a gene which when suppressed creates phenotypes similar to those of klotho deficient animals, result in “phosphatopathies.” This disorder in mineral metabolism results in phosphate retention which in turns produces “complex aging-like phenotypes.” Kur-o observes that “phosphate retention associated with Klotho deficiency is universally observed in patients with CKD, suggesting that CKD may be viewed as a state of accelerated aging.” In animal models, reduced levels of circulating klotho and KL in renal tissues, as well as a likely causal relationship between low KL and vascular calcification in the kidney (Hu, 2011), also suggest their role in CKD (Chen, 2013).

Research with microRNAs (mRNAs) into the subclasses of CKD have been conducted since the early 2000s. Antifibrotic mRNAs began being evaluated for applications to cardiac diseases some time ago (Thum, 2008), and it looks as though they have uses for other organs. Several studies with Dicer1 knockout mice have confirmed the role of mRNA biogenesis in glomerulosclerosis and fibrosis. In rats miR-29b overexpression inhibits transforming growth factor beta 1 (TGF-β) upregulation of collagens I and III (Chung, 2013). The Smad7 gene is also implicated in regulating TGF-β. It suppresses renal fibrosis by downregulating expression of two other mRNAs, which in turn revives miR-29b (Saal, 2009). These efforts may be enhanced with increasingly tissue or cell specific mRNA modulators, which can be achieved through the conjugation of antibodies, peptides, or, though not mentioned in Lorenzen et. al, the use of nanoparticle delivery systems (Triofini, 2015; Lorenzen, 2011; Gao. 2014).

It’s usually worth investing in a couple ounces of prevention. Shortcoming of serum creatinine (SCr) is often used to gauge renal function, but its levels can be influenced by a patient’s gender, muscle mass, age, and level of physical activity. Even when these are taken into account, however, around 50% of kidney function can be lost before a red flag is raised by SCr assays (Cañadas-Garre, 2018). Urinary albumin is another marker of kidney damage. Although it can be an early sign of glomerulonephritis, it is not a surefire way of telling if someone has CKD. Diagnosing diabetic CKD can also be tricky, as albuminuria may progress or regress. GFR may decline even without albuminuria, and diabetics in the throes of kidney failure may not display the histopathological signs of classical diabetic nephropathy (Hadden, 2018).

While it is extremely unlikely that a single golden biomarker for CKD will ever be found, there is no doubt that uncovering more will help with diagnostics and prognostics. It is clear that new indicators are desperately needed and, as we have seen, they are likely to come from the burgeoning study of renal epigenetics.

Works Cited and Suggested Reading – page 2

Beckerman, Pazit, Yi-An Ko, and Katalin Susztak. “Epigenetics: a new way to look at kidney diseases.” Nephrology Dialysis Transplantation 29.10 (2014): 1821-1827.

Bechtel, Wibke, et al. “Methylation determines fibroblast activation and fibrogenesis in the kidney.” Nature medicine 16.5 (2010): 544.

Blasco, Maria A. “Telomeres and human disease: ageing, cancer and beyond.” Nature Reviews Genetics 6.8 (2005): 611.

Brilli, Lauren L., et al. “HDAC inhibitors in kidney development and disease.” Pediatric nephrology 28.10 (2013): 1909-1921.

Cañadas-Garre, M., et al. “Genomic approaches in the search for molecular biomarkers in chronic kidney disease.” Journal of translational medicine 16.1 (2018): 292.

Chen, Jing, et al. “Elevated Klotho promoter methylation is associated with severity of chronic kidney disease.” PloS one8.11 (2013): e79856.

Chung AC, Dong Y, Yang W, Zhong X, Li R, Lan HY. “Smad7 suppresses renal fibrosis via altering expression of TGF-beta/Smad3-regulated microRNAs.” Mol Ther. 2013;21:388–98

De Grey, Aubrey, and Michael Rae. Ending aging: The rejuvenation breakthroughs that could reverse human aging in our lifetime. St. Martin’s Press, 2007.

Hadden, Mitchell, and Andrew Advani. “Histone Deacetylase Inhibitors and Diabetic Kidney Disease.” International journal of molecular sciences 19.9 (2018): 2630.

Harley, Calvin B., et al. “A natural product telomerase activator as part of a health maintenance program.” Rejuvenation research 14.1 (2011): 45-56.

Hu, Ming Chang, et al. “Klotho deficiency causes vascular calcification in chronic kidney disease.” Journal of the American Society of Nephrology 22.1 (2011): 124-136.

Ko, Yi-An, et al. “Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development.” Genome biology 14.10 (2013): R108.

Ko, Yi-An, and Katalin Susztak. “Epigenomics: the science of no-longer-junk DNA. Why study it in chronic kidney disease?.” Seminars in nephrology. Vol. 33. No. 4. WB Saunders, 2013.

Komorowsky, Claudiu, Matthias Ocker, and Margarete Goppelt‐Struebe. “Differential regulation of connective tissue growth factor in renal cells by histone deacetylase inhibitors.” Journal of cellular and molecular medicine 13.8b (2009): 2353-2364.

Kuro-o, Makoto. “Klotho and the aging process.” The Korean journal of internal medicine 26.2 (2011): 113.

Kordinas, Vasileios, Anastasios Ioannidis, and Stylianos Chatzipanagiotou. “The telomere/telomerase system in chronic inflammatory diseases. Cause or effect?.” Genes 7.9 (2016): 60.

Lorenzen, Johan M., Hermann Haller, and Thomas Thum. “MicroRNAs as mediators and therapeutic targets in chronic kidney disease.” Nature Reviews Nephrology 7.5 (2011): 286.

McGuinness, Dagmara, et al. “Identification of molecular markers of delayed graft function based on the regulation of biological ageing.” PloS one 11.1 (2016): e0146378.

Monickaraj, Finny, et al. “Accelerated aging as evidenced by increased telomere shortening and mitochondrial DNA depletion in patients with type 2 diabetes.” Molecular and cellular biochemistry 365.1-2 (2012): 343-350.

Noh, Hyunjin, et al. “Histone deacetylase-2 is a key regulator of diabetes-and transforming growth factor-β1-induced renal injury.” American Journal of Physiology-Renal Physiology297.3 (2009): F729-F739.

Reidy, Kimberly, et al. “Molecular mechanisms of diabetic kidney disease.” The Journal of clinical investigation 124.6 (2014): 2333-2340.

Saal, Samuel, and Scott J. Harvey. “MicroRNAs and the kidney: coming of age.” Current opinion in nephrology and hypertension 18.4 (2009): 317-323.

Thum, Thomas, et al. “MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts.” Nature 456.7224 (2008): 980.

Trionfini, Piera, Ariela Benigni, and Giuseppe Remuzzi. “MicroRNAs in kidney physiology and disease.” Nature Reviews Nephrology 11.1 (2015): 23.

Van Beneden, Katrien, et al. “HDAC inhibitors in experimental liver and kidney fibrosis.” Fibrogenesis & tissue repair 6.1 (2013): 1.

Wills, Lauren P., and Rick G. Schnellmann. “Telomeres and telomerase in renal health.” Journal of the American Society of Nephrology 22.1 (2011): 39-41.

Wing, Maria R., et al. “Epigenetics of progression of chronic kidney disease: fact or fantasy?.” Seminars in nephrology. Vol. 33. No. 4. WB Saunders, 2013.