Activity-dependent Regulation of Histone Lysine Demethylase KDM1A by a Putative Thiol/Disulfide Switch

Exploring the potential of histone demethylase inhibition in multi-therapeutic approaches for cancer treatment

Histone demethylases play a critical role in gene transcription regulation and have been implicated in cancer. Numerous reports have highlighted the overexpression of histone demethylases, such as LSD1 and JmjC, in various malignant tumor tissues, identifying them as effective therapeutic targets for cancer treatment. Despite many histone demethylase inhibitors entering clinical trials, their clinical efficacy has been limited. Therefore, combination therapies based on histone demethylase inhibitors, along with other modulators like dual-acting inhibitors, have gained significant attention and made notable progress in recent years. In this review, we provide an overview of recent advances in drug discovery targeting histone demethylases, focusing specifically on drug combination therapy and histone demethylases-targeting dual inhibitors. We discuss the rational design, pharmacodynamics, pharmacokinetics, and clinical status of these approaches. Additionally, we summarize the co-crystal structures of LSD1 inhibitors and their target proteins as well as describe the corresponding binding interactions. Finally, we also provided the challenges and future directions for utilizing histone demethylases in cancer therapy, such as PROTACs and molecular glue etc.

KDM1A inhibition increases UVA toxicity and enhances photodynamic therapy efficacy

BACKGROUND

Lysine-specific histone demethylase 1 (KDM1A/LSD1) regulates multiple cellular functions, including cellular proliferation, differentiation, and DNA repair. KDM1A is overexpressed in squamous cell carcinoma of the skin and inhibition of KDM1A can suppress cutaneous carcinogenesis. Despite the role of KDM1A in skin and DNA repair, the effect of KDM1A inhibition on cellular ultraviolet (UV) response has not been studied.

METHODS

The ability of KDM1A inhibitor bizine to modify cell death after UVA and UVB exposure was tested in normal human keratinocytes and melanocytes, HaCaT, and FaDu cell lines. KDM1A was also downregulated using shRNA and inhibited by phenelzine in HaCaT and FaDu cells to confirm the role of KDM1A in UVA response. In addition, cellular reactive oxygen species (ROS) changes were assessed by a lipid-soluble fluorescent indicator of lipid oxidation, and ROS-related gene regulation using qPCR. During photodynamic therapy (PDT) studies HaCaT and FaDu cells were treated with aminolaevulinic acid (5-ALA) or HPPH (2-[1-hexyloxyethyl]-2-devinyl pyropheophorbide-a) sodium and irradiated with 0-8 J/cm2 red LED light.

RESULTS

KDM1A inhibition sensitized cells to UVA radiation-induced cell death but not to UVB. KDM1A inhibition increased ROS generation as detected by increased lipid peroxidation and the upregulation of ROS-responsive genes. The effectiveness of both ALA and HPPH PDT significantly improved in vitro in HaCaT and FaDu cells after KDM1A inhibition.

CONCLUSION

KDM1A is a regulator of cellular UV response and KDM1A inhibition can improve PDT efficacy.

Salinomycin suppresses T24 cells by regulating KDM1A and the unfolded protein response pathway

In recent years, salinomycin has been shown to exert an anticancer effect in a variety of tumors; however, its function and mechanism in bladder cancer (BC) remain unclear. This study examined the effect of salinomycin on bladder cancer and analyzed its regulatory mechanism. T24 cells were treated with different concentrations of salinomycin to detect subsequent changes in cell proliferation, apoptosis, oxidative stress, H3K4 methylation, and related gene expression by the CCK8 assay, Edu staining, Tunel staining, ELISA, RT-qPCR, and western blotting, respectively. A KDM1A overexpression plasmid, catalytically inactive KDM1A overexpression plasmid, or short hairpin RNA (shRNA) plasmid was transfected into T24 cells to evaluate their effects. A xenograft tumor model was used to further confirm the anti-tumor effect of salinomycin. Our results showed that salinomycin significantly inhibited cell proliferation, promoted apoptosis, increased MDA levels, decreased SOD levels, induced H3K4 histone methylation, and suppressed KDM1A expression. Furthermore, the sh-KDM1A plasmid had effects similar to those of salinomycin and also activated the unfolded protein response pathway. The KDM1A overexpression plasmid had effects opposite to those of the sh-KDM1A plasmid, and the catalytically inactive KDM1A overexpression plasmid had no effect. Meanwhile, KDM1A overexpression reversed the effects of salinomycin on T24 cells. Finally, in vivo experiments confirmed the above results. In the salinomycin treatment group, tumor growth and KDM1A expression were suppressed and cell apoptosis and UPR were induced, while treatment with the KDM1A overexpression plasmid produced the opposite effects. Collectively, our study revealed that salinomycin suppressed T24 cell proliferation and promoted oxidative stress and apoptosis by regulating KDM1A and the UPR pathway.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10616-022-00546-y.

Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1

A machine learning approach has been applied to virtual screening for lysine specific demethylase 1 (LSD1) inhibitors. LSD1 is an important anti-cancer target. Machine learning models to predict activity were constructed using Morgan molecular fingerprints. The dataset, consisting of 931 molecules with LSD1 inhibition activity, was obtained from the ChEMBL database. An evaluation of several candidate algorithms on the main dataset revealed that the support vector regressor gave the best model, with a coefficient of determination (R2) of 0.703. Virtual screening, using this model, identified five predicted potent inhibitors from the ZINC database comprising more than 300,000 molecules. The virtual screening recovered a known inhibitor, RN1, as well as four compounds where activity against LSD1 had not previously been suggested. Thus, we performed a machine-learning-enabled virtual screening of LSD1 inhibitors using only the structural information of the molecules.

Physiological interrelationships between NADPH oxidases and chromatin remodelling

The epigenetic landscape describes the chromatin structure of the eukaryotic genome and is therefore the major determinant of gene transcription and hence cellular phenotype. The molecular processes which act to shape the epigenetic landscape through cellular differentiation are thus central to cellular determination and specification. In addition, cellular adaptation to (patho)-physiological stress requires dynamic and reversible chromatin remodelling. It is becoming clear that redox-dependent molecular mechanisms are important determinants of this epigenetic regulation. NADPH oxidases generate reactive oxygen species (ROS) to activate redox-dependent signalling pathways in response to extracellular and intracellular environmental cues. This mini review aims to summarise the current knowledge of the role of NADPH oxidases in redox-dependent chromatin remodelling, and how epigenetic changes might feedback and impact upon the transcriptional expression of these ROS-producing enzymes themselves. The potential physiological significance of this relationship in the control of cellular differentiation and homeostasis by Nox4, specifically, is discussed.

A mechanism of inheritance of acquired traits in animals

Observational and experimental evidence for the inheritance of acquired traits in animals is slowly, but steadily accumulating. The onset and transmission of acquired traits implies the acquisition and transmission from parents to progeny of new information, which is different from the genetic information contained in DNA. The new non-genetic information most commonly is passed on from parents to the offspring via gamete(s), but how it is precisely transmitted to the successive generations is still unknown. Based on adequate empirical evidence presented herein, a hypothesis is proposed of the inheritance of acquired traits in animals and the flow of the relevant parental information to the offspring.

Cytoprotective effects of antioxidant supplementation on mesenchymal stem cell therapy

Mesenchymal stem cells (MSCs) are earmarked as perfect candidates for cell therapy and tissue engineering due to their capacity to differentiate into different cell types. However, their potential for application in regenerative medicine declines when the levels of the reactive oxygen and nitrogen species (RONS) increase from the physiological levels, a phenomenon which is at least inevitable in ex vivo cultures and air-exposed damaged tissues. Increased levels of RONS can alter the patterns of osteogenic and adipogenic differentiation and inhibit proliferation, as well. Besides, oxidative stress enhances senescence and cell death, thus lowering the success rates of the MSC engraftment. Hence, in this review, we have selected some representatives of antioxidants and newly emerged nano antioxidants in three main categories, including chemical compounds, biometabolites, and protein precursors/proteins, which are proved to be effective in the treatment of MSCs. We will focus on how antioxidants can be applied to optimize the clinical usage of the MSCs and their associated signaling pathways. We have also reviewed several paralleled properties of some antioxidants and nano antioxidants which can be simultaneously used in real-time imaging, scaffolding techniques, and other applications in addition to their primary antioxidative function.

Dynamic regulation of epigenetic demethylation by oxygen availability and cellular redox

The chromatin structure of the mammalian genome must facilitate both precisely-controlled DNA replication together with tightly-regulated gene transcription. This necessarily involves complex mechanisms and processes which remain poorly understood. It has long been recognised that the epigenetic landscape becomes established during embryonic development and acts to specify and determine cell fate. In addition, the chromatin structure is highly dynamic and allows for both cellular reprogramming and homeostatic modulation of cell function. In this respect, the functions of epigenetic "erasers", which act to remove covalently-linked epigenetic modifications from DNA and histones are critical. The enzymatic activities of the TET and JmjC protein families have been identified as demethylases which act to remove methyl groups from DNA and histones, respectively. Further, they are characterised as members of the Fe(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. This provides the intriguing possibility that their enzymatic activities may be modulated by cellular metabolism, oxygen availability and redox-based mechanisms, all of which are likely to display dynamic cell- and tissue-specific patterns of flux. Here we discuss the current evidence for such [O₂]- and redox-dependent regulation of the TET and Jmjc demethylases and the potential physiological and pathophysiological functional consequences of such regulation.

Drug Design Concepts for LSD1-Selective Inhibitors

Lysine-specific demethylase 1 (LSD1) is one of the flavin-dependent oxidases and is involved in many cellular processes by controlling the methylation of histone H3. Recently, it has been reported that LSD1 is associated with several diseases such as cancer, metabolic disorders, and psychiatric diseases. Thus, LSD1 is an attractive molecular target for the treatment of these diseases, and its inhibitors are predicted as therapeutic agents. Although a variety of LSD1 inhibitors have been reported to date, many of them show insufficient activities and selectivity toward LSD1. Meanwhile, we identified several LSD1-selective inhibitors using target-guided synthesis strategies based on our original ideas. Our LSD1 inhibitors show not only potent LSD1-selective inhibitory activities, but also unique bioactivities both in vitro and in vivo. This account highlights our drug design concepts for and identification of LSD1-selective inhibitors.

ROLE OF THIOLS IN OXIDATIVE STRESS

A well-regulated redox state is essential for normal physiological function and cellular metabolism. In most eukaryotic cells, protein cysteine thiols are most sensitive to fluctuations in the cellular redox state. Under normal physiological conditions, the cytosol has a highly reducing environment, which is due to high levels of reduced glutathione and complex system of redox enzymes that maintain glutathione in the reduced state. The reducing environment of the cytosol maintains most protein thiols in the reduced state; although some non-exposed cysteine could be present as disulfides. Upon physiological increase in cellular oxidants, such as due to growth factors, cytokines and thiol-disulfide exchange reactions, specific proteins could act as redox switches that regulate the conformation and activity of different proteins. This reversible post translational modification enables redox-sensitive dynamic changes in cell signaling and function. Physiological oxidative stress could lead to the formation of sulfenic acids, which are usually intermediate states of thiol oxidation that are converted to higher order oxidation states, intramolecular disulfides or mixed disulfides with glutathione. Such glutathiolation reactions have been found to regulate the function of several proteins involved in intracellular metabolism, signal transduction and cell structure. Excessive oxidative stress results in indiscriminate and irreversible oxidation of protein thiols, depletion of glutathione and cell death. Further elucidation of the relationship between changes in cell redox and thiol reactivity could provide a better understanding of how redox changes regulate cell function and how disruption of these relationships lead to tissue injury and dysfunction and the development of chronic diseases such as cancer and cardiovascular disease.