Evaluation of the Epigenetic Demethylation of NRF2, a Master Transcription Factor for Antioxidant Enzymes, in Colorectal Cancer

Targeting epigenetic and post-translational modifications of NRF2: key regulatory factors in disease treatment

Nuclear factor erythroid 2-related factor 2 (NRF2) is a key transcription factor involved in regulating cellular antioxidant defense and detoxification mechanisms. It mitigates oxidative stress and xenobiotic-induced damage by inducing the expression of cytoprotective enzymes, including HO-1 and NQO1. NRF2 also modulates inflammatory responses by inhibiting pro-inflammatory genes and mediates cell death pathways, including apoptosis and ferroptosis. Targeting NRF2 offers potential therapeutic avenues for treating various diseases. NRF2 is regulated through two principal mechanisms: post-translational modifications (PTMs) and epigenetic alterations. PTMs, including phosphorylation, ubiquitination, and acetylation, play a pivotal role in modulating NRF2's stability, activity, and subcellular localization, thereby precisely controlling its function in the antioxidant response. For instance, ubiquitination can lead to NRF2 degradation and reduced antioxidant activity, while deubiquitination enhances its stability and function. Epigenetic modifications, such as DNA methylation, histone modifications, and interactions with non-coding RNAs (e.g., MALAT1, PVT1, MIR4435-2HG, and TUG1), are essential for regulating NRF2 expression by modulating chromatin architecture and gene accessibility. This paper systematically summarizes the molecular mechanisms by which PTMs and epigenetic alterations regulate NRF2, and elucidates its critical role in cellular defense and disease. By analyzing the impact of PTMs, such as phosphorylation, ubiquitination, and acetylation, as well as DNA methylation, histone modifications, and non-coding RNA interactions on NRF2 stability, activity, and expression, the study reveals the complex cellular protection network mediated by NRF2. Furthermore, the paper explores how these regulatory mechanisms affect NRF2's roles in oxidative stress, inflammation, and cell death, identifying novel therapeutic targets and strategies. This provides new insights into the treatment of NRF2-related diseases, such as cancer, neurodegenerative disorders, and metabolic syndrome. This research deepens our understanding of NRF2's role in cellular homeostasis and lays the foundation for the development of NRF2-targeted therapies.

Platelet-Derived circRNAs hsa_circ_0004771 and hsa_circ_0019120 Differentially Expressed in Colorectal Cancer and Polyps

Background

Colorectal cancer (CRC) is the second most common cause of cancer-related deaths worldwide. Early detection is crucial for improving survival rates. Liquid biopsies, specifically analyzing circulating tumor-educated platelets (TEPs), have emerged as a promising tool for early CRC detection and monitoring treatment efficacy. This study investigated the expression levels of two specific circRNAs, hsa_circ_0004771 and hsa_circ_0019120, in the platelets of patients with CRC, advanced polyps, and healthy controls.

Methods

Blood samples were obtained from 25 individuals with CRC, 25 individuals with advanced polyps, and 25 healthy controls. Platelet-derived total RNA was extracted, and expression analysis was conducted using reverse transcription quantitative PCR (RT-qPCR). Differential expression and receiver operating characteristic (ROC) curve analysis were performed using GraphPad Prism.

Results

Both circRNAs were found to be upregulated in platelets from individuals with advanced polyps and CRC compared to healthy individuals. However, the upregulation was statistically significant only for hsa_circ_0004771 in CRC patients (p-value = 0.0036) and for hsa_circ_0019120 in both advanced polyp (p-value = 0.0175) and CRC patients (p-value = 0.0356). The combined analysis of both circRNAs achieved an area under the curve (AUC) of 0.8348 (95% CI: 0.7131 to 0.9565) with a sensitivity of 84% and specificity of 80% (p-value = 0.0002).

Conclusions

This study showed that hsa_circ_0004771 and hsa_circ_0019120 dysregulated in both CRC and polyps and have potential as a novel diagnostic biomarker of CRC.

SIRT1: a novel regulator in colorectal cancer

The class-III histone deacetylase SIRT1 is the most extensively investigated sirtuin deacetylase. It is resistant to the broad deacetylase inhibitor trichostatin A and depends on oxidized nicotinamide adenine nucleotide (NAD+). SIRT1 plays a crucial role in the tumorigenesis of numerous types of cancers, including colorectal cancer (CRC). Accumulating evidence indicates that SIRT1 is a therapeutic target for CRC; however, the function and underlying mechanism of SIRT1 in CRC still need to be elucidated. Herein, we provide a detailed and updated review to illustrate that SIRT1 regulates many processes that go awry in CRC cells, such as apoptosis, autophagy, proliferation, migration, invasion, metastasis, oxidative stress, resistance to chemo-radio therapy, immune evasion, and metabolic reprogramming. Moreover, we closely link our review to the clinical practice of CRC treatment, summarizing the mechanisms and prospects of SIRT1 inhibitors in CRC therapy. SIRT1 inhibitors as monotherapy in CRC or in combination with chemotherapy, radiotherapy, and immune therapies are comprehensively discussed. From epigenetic regulation to its potential therapeutic effect, we hope to offer novel insights and a comprehensive understanding of SIRT1's role in CRC.

The Cancer Antioxidant Regulation System in Therapeutic Resistance

Antioxidants play a pivotal role in neutralizing reactive oxygen species (ROS), which are known to induce oxidative stress. In the context of cancer development, cancer cells adeptly maintain elevated levels of both ROS and antioxidants through a process termed "redox reprogramming". This balance optimizes the proliferative influence of ROS while simultaneously reducing the potential for ROS to cause damage to the cell. In some cases, the adapted antioxidant machinery can hamper the efficacy of treatments for neoplastic diseases, representing a significant facet of the resistance mechanisms observed in cancer therapy. In this review, we outline the contribution of antioxidant systems to therapeutic resistance. We detail the fundamental constituents of these systems, encompassing the central regulatory mechanisms involving transcription factors (of particular importance is the KEAP1/NRF2 signaling axis), the molecular effectors of antioxidants, and the auxiliary systems responsible for NADPH generation. Furthermore, we present recent clinical trials based on targeted antioxidant systems for the treatment of cancer, assessing the potential as well as challenges of this strategy in cancer therapy. Additionally, we summarize the pressing issues in the field, with the aim of illuminating a path toward the emergence of novel anticancer therapeutic approaches by orchestrating redox signaling.

Advances in Understanding the Role of NRF2 in Liver Pathophysiology and Its Relationship with Hepatic-Specific Cyclooxygenase-2 Expression

Oxidative stress and inflammation play an important role in the pathophysiological changes of liver diseases. Nuclear factor erythroid 2-related factor 2 (NRF2) is a transcription factor that positively regulates the basal and inducible expression of a large battery of cytoprotective genes, thus playing a key role in protecting against oxidative damage. Cyclooxygenase-2 (COX-2) is a key enzyme in prostaglandin biosynthesis. Its expression has always been associated with the induction of inflammation, but we have shown that, in addition to possessing other benefits, the constitutive expression of COX-2 in hepatocytes is beneficial in reducing inflammation and oxidative stress in multiple liver diseases. In this review, we summarized the role of NRF2 as a main agent in the resolution of oxidative stress, the crucial role of NRF2 signaling pathways during the development of chronic liver diseases, and, finally we related its action to that of COX-2, where it appears to operate as its partner in providing a hepatoprotective effect.

NRF2 and STAT3: friends or foes in carcinogenesis?

NRF2 is a transcription factor that plays a pivotal role in carcinogenesis, also through the interaction with several pro-survival pathways. NRF2 controls the transcription of detoxification enzymes and a variety of other molecules impinging in several key biological processes. This perspective will focus on the complex interplay of NRF2 with STAT3, another transcription factor often aberrantly activated in cancer and driving tumorigenesis as well as immune suppression. Both NRF2 and STAT3 can be regulated by ER stress/UPR activation and their cross-talk influences and is influenced by autophagy and cytokines, contributing to shape the microenvironment, and both control the execution of DDR, also by regulating the expression of HSPs. Given the importance of these transcription factors, more investigations aimed at better elucidating the outcome of their networking could help to discover new and more efficacious strategies to fight cancer.

The Transcription Factor NRF2 Has Epigenetic Regulatory Functions Modulating HDACs, DNMTs, and miRNA Biogenesis

The epigenetic regulation of gene expression is a complex and tightly regulated process that defines cellular identity and is associated with health and disease processes. Oxidative stress is capable of inducing epigenetic modifications. The transcription factor NRF2 (nuclear factor erythroid-derived 2-like 2) is a master regulator of cellular homeostasis, regulating genes bearing antioxidant response elements (AREs) in their promoters. Here, we report the identification of ARE sequences in the promoter regions of genes encoding several epigenetic regulatory factors, such as histone deacetylases (HDACs), DNA methyltransferases (DNMTs), and proteins involved in microRNA biogenesis. In this research, we study this possibility by integrating bioinformatic, genetic, pharmacological, and molecular approaches. We found ARE sequences in the promoter regions of genes encoding several HDACs, DNMTs, and proteins involved in miRNA biogenesis. We confirmed that NRF2 regulates the production of these genes by studying NRF2-deficient cells and cells treated with dimethyl fumarate (DMF), an inducer of the NRF2 signaling pathway. In addition, we found that NRF2 could be involved in the target RNA-dependent microRNA degradation (TDMD) of miR-155-5p through its interaction with Nfe2l2 mRNA. Our data indicate that NRF2 has an epigenetic regulatory function, complementing its traditional function and expanding the regulatory dimensions that should be considered when developing NRF2-centered therapeutic strategies.

Oxidative imbalance increases the risk for colonic polyp and colorectal cancer development

BACKGROUND

The role of oxidative stress in the pathogenesis of colorectal carcinoma (CRC) has garnered considerable interest recently. Specific oxidative factors have been implicated in the pathogenesis of adenomatous polyps and ultimately adenocarcinoma.

AIM

To evaluate the effect of oxidative imbalance as quantified by specific serological markers in the development of sporadic colon adenocarcinoma.

METHODS

A total of 170 patients that underwent endoscopy of the lower gastrointestinal tract in a tertiary center within 3 years were included in the study. They were allocated in three groups; those with sporadic colon adenocarcinoma (n = 56, 32.9%), those with colonic polyps (n = 33, 19.4%) and healthy controls (n = 81, 47.7%). All patients were evaluated for oxidant activity and antioxidant capacity with serum measurements of specific markers such as vitamins A, 25(OH) D3, E, C, B12, folic acid, glutathione, selenium (Se), zinc (Zn), free iron (Fe²⁺), and malondialdehyde and results were compared between groups.

RESULTS

Serum levels of vitamins C, E, D, Se, Zn, vitamin B12 and total antioxidant capacity were significantly lower in the combined neoplasia/polyp group than in the control group (P = 0.002, P = 0.009, P < 0.001, P < 0.001, P < 0.001, P = 0.020 and P < 0.001, correspondingly). Increased levels of vitamin E (P = 0.004), vitamin D (P < 0.001), Se (P < 0.001) and Zn (P < 0.001) seem to bestow a protective effect on the development of CRC. For vitamin D (P < 0.001) and Zn (P = 0.036), this effect seems to extend to the development of colon polyps as well. On the other hand, elevated serum levels of malondialdehyde are associated with a higher risk of CRC (OR = 2.09 compared to controls, P = 0.004). Regarding colonic polyp development, increased concentrations of vitamin Α and Fe²⁺ are associated with a higher risk, whereas lower levels of malondialdehyde with a lower risk.

CONCLUSION

Increased oxidative stress may play an important role in the pathogenesis and progression of CRC. Antioxidants’ presence may exert a protective effect in the very early stages of colon carcinogenesis.

Design and experimental validation of OPERA_MET-A panel for deep methylation analysis by next generation sequencing

DNA methylation is the most recognized epigenetic mark that leads to a massive distortion in cancer cells. It has been observed that a large number of DNA aberrant methylation events occur simultaneously in a group of genes, thus providing a growth advantage to the cell in promoting cell differentiation and neoplastic transformation. Due to this reason, methylation profiles have been suggested as promising cancer biomarkers. Here, we designed and performed a first step of validation of a novel targeted next generation sequencing (NGS) panel for methylation analysis, which can simultaneously evaluate the methylation levels at CpG sites of multiple cancer-related genes. The OPERA_MET-A methylation panel was designed using the Ion AmpliSeq™ technology to amplify 155 regions with 125-175 bp mean length and covers a total of 1107 CpGs of 18 cancer-related genes. The performance of the panel was assessed by running commercially available fully methylated and unmethylated control human genomic DNA (gDNA) samples and a variable mixture of them. The libraries were run on Ion Torrent platform and the sequencing output was analyzed using the “methylation_analysis” plugin. DNA methylation calls on both Watson (W) and Crick (C) strands and methylated:unmethylated ratio for each CpG site were obtained. Cell lines, fresh frozen and formalin-fixed paraffin-embedded (FFPE) lung cancer tissues were tested. The OPERA_MET-A panel allows to run a minimum of 6 samples/530 chip to reach an observed mean target depth ≥2,500X (W and C strands) and an average number of mapped reads >750,000/sample. The conversion efficiency, determined by spiking-in unmethylated Lambda DNA into each sample before the bisulfite conversion process, was >97% for all samples. The observed percentage of global methylation for all CpGs was >95% and <5% for fully methylated and unmethylated gDNA samples, respectively, and the observed results for the variable mixtures were in agreement with what was expected. Methylation-specific NGS analysis represents a feasible method for a fast and multiplexed screening of cancer patients by a high-throughput approach. Moreover, it offers the opportunity to construct a more robust algorithm for disease prediction in cancer patients having a low quantity of biological material available.

Roles of NRF2 in Fibrotic Diseases: From Mechanisms to Therapeutic Approaches

Fibrosis is a persistent inflammatory response that causes scarring and tissue sclerosis by stimulating myofibroblasts to create significant quantities of extracellular matrix protein deposits in the tissue. Oxidative stress has also been linked to the development of fibrosis in several studies. The nuclear erythroid 2-related factor 2 (NRF2) transcription factor controls the expression of several detoxification and antioxidant genes. By binding to antioxidant response elements, NRF2 is activated by oxidative or electrophilic stress and promotes its target genes, resulting in a protective effect on cells. NRF2 is essential for cell survival under oxidative stress conditions. This review describes Kelch-like epichlorohydrin-associated protein 1 (KEAP1)/NRF2 signaling mechanisms and presents recent research advances regarding NRF2 and its involvement in primary fibrotic lesions such as pulmonary fibrosis, hepatic fibrosis, myocardial fibrosis, and renal fibrosis. The related antioxidant substances and drugs are described, along with the mechanisms by which KEAP1/NRF2 regulation positively affects the therapeutic response. Finally, the therapeutic prospects and potential value of NRF2 in fibrosis are summarized. Further studies on NRF2 may provide novel therapeutic approaches for fibrosis.

Investigation of Decitabine Effects on HDAC3 and HDAC7 mRNA Expression in NALM-6 and HL-60 Cancer Cell Lines

Background

Decitabine is a potent anticancer hypomethylating agent and changes the gene expression through the gene's promoter demethylation and also independently from DNA demethylation. So, the present study was designed to distinguish whether Decitabine, in addition to inhibitory effects on DNA methyltransferase, can change HDAC3 and HDAC7 mRNA expression in NALM-6 and HL-60 cancer cell lines.

Methods

HL-60, NALM-6, and normal cells were cultured, and the Decitabine treatment dose was obtained (1 µM) through the MTT assay. Finally, HDAC3 and HDAC7 mRNA expression were measured by Real-Time PCR in HL-60 and NALM-6 cancerous cells before and after treatment. Furthermore, HDAC3 and HDAC7 mRNA expression in untreated HL-60 and NALM-6 cancerous cells were compared to normal cells.

Results

Our results revealed that the expression of HDAC3 and HDAC7 in HL-60 and NALM-6 cells increases as compared to normal cells. After treatment of HL-60 and NALM-6 cells with Decitabine, HDAC3, and HDAC7 mRNA expression were decreased significantly.

Conclusion

Our data confirmed that the effects of Decitabine are not limited to direct hypomethylation of DNMTs, but it can indirectly affect other epigenetic factors, such as HDACs activity, through converging pathways.

Genetic and epigenetic regulation of the NRF2-KEAP1 pathway in human lung cancer

Electrophilic and oxidative stress is caused when homeostatic mechanisms are disrupted. A major defense mechanism involves the activation of the nuclear factor erythroid 2-related factor 2 (NRF2) transcription factor encoded by the NFE2L2 gene, which can accelerate the detoxification of electrophilic carcinogens and prevent cancer and on the other hand in certain exposure contexts may exacerbate the carcinogenic process. NRF2-target genes activated under these conditions can be used as biomarkers of stress signalling, while activation of NRF2 can also reveal the epigenetic mechanisms that modulate NFE2L2 expression. Epigenetic mechanisms that regulate NFE2L2 and the gene for its adaptor protein KEAP1 include DNA methylation, histone modifications and microRNA. Understanding the activation of the NRF2-KEAP1 signalling pathway in human lung cancer, its epigenetic regulation and its role in oncogenesis is the subject of this review.

The Benefits of Curcuminoid to Expression Nuclear Factor Erythroid 2 Related Factor 2 (NRF2) and Signal to Noise Ratio (SNR) Value in the Noise Exposed Organ of Corti of Rattus Norvegicus

BACKGROUND

Noise-induced hearing loss (NIHL) can cause damage to the cochlea. Curcumin and nuclear factor erythroid 2-related factor 2 (NRF2) are transcription activators that play a crucial role in defence mechanisms against oxidative stress. The aim of this study was to determine the effect of curcuminoid administration on NRF2 expression, in the organ of Corti of cochlea of Rattus norvegicus that were exposed to noise, from the results of the distortion product otoacoustic emission (DPOAE) examination.

METHODS

We divided 36 rats into six groups including Group 1 (control); Group 2 (noise exposure without curcuminoid administration); Group 3 (noise exposure+curcuminoid dose 100 mg/day for four days); Group 4 (noise exposure+curcuminoid dose 200 mg/day for four days); Group 5 (curcuminoid dose of 100 mg/day for 14 days followed by two days of noise exposure); Group 6 (curcuminoid dose 200 mg/day for 14 days followed by two days of noise exposure).

RESULTS

Following noise exposure in rats, there was an effect/correlation between NRF2 expression, the SNR values obtained from DPOAE and curcuminoid administration.

CONCLUSION

There was a correlation between curcuminoid administration, NRF2 expression and DPOAE treatment. Following noise exposure in rats (Rattus norvegicus), SNR values obtained from DPOAE showed improved cochlear function.

NRF2 and the Ambiguous Consequences of Its Activation during Initiation and the Subsequent Stages of Tumourigenesis

NF-E2 p45-related factor 2 (NRF2, encoded in the human by NFE2L2) mediates short-term adaptation to thiol-reactive stressors. In normal cells, activation of NRF2 by a thiol-reactive stressor helps prevent, for a limited period of time, the initiation of cancer by chemical carcinogens through induction of genes encoding drug-metabolising enzymes. However, in many tumour types, NRF2 is permanently upregulated. In such cases, its overexpressed target genes support the promotion and progression of cancer by suppressing oxidative stress, because they constitutively increase the capacity to scavenge reactive oxygen species (ROS), and they support cell proliferation by increasing ribonucleotide synthesis, serine biosynthesis and autophagy. Herein, we describe cancer chemoprevention and the discovery of the essential role played by NRF2 in orchestrating protection against chemical carcinogenesis. We similarly describe the discoveries of somatic mutations in NFE2L2 and the gene encoding the principal NRF2 repressor, Kelch-like ECH-associated protein 1 (KEAP1) along with that encoding a component of the E3 ubiquitin-ligase complex Cullin 3 (CUL3), which result in permanent activation of NRF2, and the recognition that such mutations occur frequently in many types of cancer. Notably, mutations in NFE2L2, KEAP1 and CUL3 that cause persistent upregulation of NRF2 often co-exist with mutations that activate KRAS and the PI3K-PKB/Akt pathway, suggesting NRF2 supports growth of tumours in which KRAS or PKB/Akt are hyperactive. Besides somatic mutations, NRF2 activation in human tumours can occur by other means, such as alternative splicing that results in a NRF2 protein which lacks the KEAP1-binding domain or overexpression of other KEAP1-binding partners that compete with NRF2. Lastly, as NRF2 upregulation is associated with resistance to cancer chemotherapy and radiotherapy, we describe strategies that might be employed to suppress growth and overcome drug resistance in tumours with overactive NRF2.