Types of NF-κB methylation and its biological roles.
The nuclear factor κB (NF-κB) is one of the most pivotal transcription factors in mammalian cells. In many pathologies NF-κB is activated abnormally. This contributes to the development of various disorders such as cancer, acute kidney injury, lung disease, chronic inflammatory diseases, cardiovascular disease, and diabetes. This book chapter focuses on how methylation of NF-κB regulates its target genes differentially. The knowledge from this chapter will provide scientific strategies for innovative therapeutic intervention of NF-κB in a wide range of diseases.
- epigenetic enzymes
- gene regulation
- transcription factor
The nuclear factor κB (NF-κB) is one of the most pivotal transcription factors in mammalian cells. In many pathologies NF-κB is activated abnormally. This contributes to the development of various disorders such as cancer, acute kidney injury, lung disease, chronic inflammatory diseases, cardiovascular disease, and diabetes . NF-κB family is comprised of five family members: p65 (RelA), RelB, c-Rel, p50/p105 (NF-kB1), and p52/p100 (NF-kB2). Among them, the Rel homology domain (RHD) at their N-termini is a commonly share feature ( Figure 1 ). It is necessary for protein dimerization, the inhibition of NF-κB (IκB) interaction, nuclear targeting, and DNA binding . Additionally, a carboxy-terminal transactivation domain (TAD) also exists in the Rel proteins, such as p65 ( Figure 1 ), RelB, and c-Rel. Among the NF-κB dimers, the p65:p50 heterodimer is the prototype.
The activity of NF-κB is frequently regulated by various modifications, namely, post-translational modifications (PTM). Among which, methylation is the newest type of modification that is discovered. The knowledge on NF-κB methylation is still scarce and not popularized among wide range of readers. Thus, in this chapter, we will focus on how methylation of NF-κB regulates its target genes differentially and provide perspectives and future directions in term of the research and application of NF-κB methylation. The knowledge from this chapter will provide scientific strategies for innovative therapeutic intervention of NF-κB in a wide range of diseases.
2. NF-κB signaling pathways
The NF-κB signaling pathways play a very important role in signaling innate and adaptive immune responses and in many cellular processes. NF-κB signaling and subsequent target gene activation can be induced by a variety of factors including cytokines, stress, radiation, and also bacteria and viruses . This signaling can be broken down into two signaling pathways: the canonical and non-canonical branches of the NF-κB pathway ( Figure 2 ). In the canonical pathway, activity is regulated by interactions between IκB proteins and the p65:p50 complex. IκB proteins hold NF-κB proteins in inactive conformations by binding in the cytoplasm and preventing nuclear localization. Extracellular signals including cytokines such as interleukin 1 β (IL-1β) and tumor necrosis factor α (TNFα), stress, free radicals, or radiation cause IκB kinase (IKK) activation. IKK is a complex that consists of the IKKα and IKKβ kinases and a third regulatory subunit known as NEMO/IKKγ [4, 5]. In the canonical pathway, IKKβ phosphorylates the N-terminal serine residues 32 and 36 of IκBα, resulting in its polyubiquitination and subsequent rapid proteasomal degradation . This degradation allows the release of p65:p50 into the cytoplasm. The two-unit NF-κB complex then binds to the protein importin and translocates to the nucleus where it further binds to DNA and promotes increased expression of NF-κB target genes . In the noncanonical pathway, the p100 and RelB proteins form an inactive dimer in the cytoplasm. Upon stimulation by a certain group of stimuli, such as B-cell activation factor (BAF) or CD40 ligand (CD40L), IKKα is subsequently activated through NF-κB-inducing kinase (NIK) mediation, leading to the ubiquitin/proteasomal processing of p100 to p52. Once this processing has occurred, the RelB/p52 complex can translocate to the nucleus and bind to DNA to promote increased expression of NF-κB target genes .
3. The state of post-translational modifications (PTM) of NF-κB
Given the role of NF-ĸB in a wide range of important cellular and physiological processes, the potentially disastrous consequences of dysregulated NF-κB necessitates highly complex and finely regulated mechanisms for controlling NF-κB activity. NF-ĸB signaling can be influenced at multiple levels, many of which converge on various components of the pathway including the IKK complex and the IĸB family of proteins . For instance, the IKK complex remains one of the best-studied central regulators of NF-κB activation, and its phosphorylation of IκBα constitutes an essential event for subsequent signal transduction to both the canonical and non-canonical heterodimeric subunits of NF-κB [8, 9] as described above.
In addition to regulation by the IKK complex and the inhibitory IκB proteins, the NF-ĸB/Rel dimeric proteins are themselves subject to intricate regulation via a host of critical post-translational modification (PTM) events [10, 11, 12]. PTMs on p65, the prototypical subunit of NF-κB, include [13, 14], acetylation [15, 16, 17, 18, 19], methylation [20, 21, 22, 23], ubiquitination , nitrosylation , and sumoylation . The consequences of these regulatory modifications are context dependent, and vary based on the nature and abundance of the NF-κB pathway stimulators [11, 22]. Moreover, the sites and/or crosstalk between modifications [16, 27] can yield different outcomes with even the same modifications yielding quite distinct physiological effects [28, 29, 30, 31]. Eventually, these PTMs work to dictate the duration and strength of activation and, accordingly, the degree of transcriptional output [10, 32]. Moreover, some of these modifications serve as important means for crosstalk with other signaling pathways .
Our laboratory is one of the first few groups to discover that p65 can be methylated on lysine residues upon cytokine stimulation . Subsequently, we pioneered the identification of arginine 30 (R30) methylation of p65 . Below, we will thoroughly discuss the impact of these methylation sites on NF-κB-mediated differential gene regulation.
4. Methylation of the p65 subunit of NF-κB
4.1. Lysine methylation of p65
To date, a total of six lysine methylation sites have been reported: K37, 218, 221, 310, 314, and 315 [18, 20]. By using a novel genetic approach, our lab identified that p65 can be methylated by a lysine methylase, the nuclear receptor-binding SET domain-containing protein 1 (NSD1), and demethylated by a lysine demethylase, the F-box and leucine-rich repeat protein 11 (FBXL11) . This reversible lysine methylation of p65 is targeted at K218/K221 sites and affects NF-κB activity. K218/K221 methylation induces over 80% p65-dependent gene expression in mouse embryonic fibroblast cells (MEFs). The observation indicates that PTMs play an important role in fine-tuning the regulation of NF-κB .
In addition to our discovery of the methylation of K218/221, Ea
Besides the methylated lysine residues on p65 discussed above, another SET family member SETD6, was also reported to monomethylate p65 at K310 under basal condition. Levy and colleagues observed that under the unstimulated condition, a proportion of p65 can be monomethylated by SETD6. This methylation event negatively regulates NF-κB target gene expression, including those involved in inflammatory response. The phenotype was proven in various cell lines, such as bone osteosarcoma U2OS, peripheral blood THP-1, and bone marrow-derived macrophages (BMDM), and therefore represents diverse disease models. Interestingly, Levy
An overlook of the biological roles of p65 lysine methylation and their modifying enzymes is shown in Table 1 . It is evident that under various experimental conditions, p65 lysine methylation may affect NF-κB nucleus localization, transcriptional activity, and NF-κB target gene expression.
|Type of methylation||Site modified||Enzymes||Biological function||Reference|
|Monomethylation||K37||SET9||Stabilizes nuclear localization and enhances p65 binding ability|||
|Monomethylation||K218||NSD1/FBXL11||Promotes NF-κB transcriptional activity and maintains p65 phosphorylation on S536||[20, 34]|
|Dimethylation||K221||NSD1/ FBXL11||Promotes NF-κB transcriptional activity and maintains p65 phosphorylation on S536||[20, 34]|
|Monomethylation||K310||SETD6||Decreases NF-κB target gene expression|||
|Monomethylation||K314||SET9||Decreases NF-κB activity and target gene expression|||
|Monomethylation||K315||SET9||Decreases NF-κB activity and target gene expression|||
|Symmetric dimethylation||R30||PRMT5||Enhances NF-κB DNA binding and transcriptional activities, and increases NF-κB target gene expression||[22, 35]|
|Asymmetric dimethylation||R30||PRMT1||Reduces NF-κB DNA binding ability and decreases NF-κB target genes expression||[22, 35]|
4.2. Arginine methylation of p65
Distinct from the methylation of lysine residues, our lab used Mass Spectrometry to discover that p65 can also be symmetrically methylated at arginine 30 residue (R30) [20, 22]. This important modification is carried out by the protein arginine methyltransferase 5 (PRMT5), an enzyme that belongs to the PRMT superfamily, contains 637 amino acids, and catalyzes the formation of symmetrically dimethylated arginine.
We reported that PRMT5 catalyzed p65 dimethylation upon IL-1β treatment. R30 to A mutant (R30A) of p65 decreased NF-κB activity and led to the downregulation of a subgroup of NF-κB inducible genes; among these are cytokine and chemokine genes. Conditional media from cells expressing the R30A mutant of p65 had much less NF-kB-inducing activity than its wild-type cohort. Additionally, through
Further demonstrating the complexity of R30 methylation, Reintjes
4.3. Differential gene regulation by lysine and arginine methylation
As we mentioned earlier, a total of six lysine methylation sites can be methylated by different histone lysine methyltransferases in response to activating signals. Among them, K37, K218, and K221 are located in the RHD domain, while K310, K314, and K315 are in the linker region between RHD and the transactivation domain (TA)  ( Figure 1 ). Using site mutagenesis, we generated the K218/221Q double mutant (DKQ) or the K37Q single mutant of p65. We found that in response to cytokines, such as IL-1β treatment, ~350 genes were rapidly induced within 5 min after treatment, while an additional ~300 genes were significantly upregulated 30 min later. Additionally, 1500 genes were further induced between the time points of 1 and 24 h. We revealed that
To further determine the difference between K and R methylation of p65 on NF-κB regulation, we conducted similar experiments as described above . R30A and DKA (K218/221 K-A) mutants were generated in HEK293 cells. Illumina microarray experiments were carried out to analyze the gene populations affected by these mutations. We found that ~75% of NF-κB target genes were down-regulated by twofold or more by the R30A mutation, while significantly fewer (~48%) genes were downregulated by the DKA mutation. This data suggests that R30 methylation is in charge of most NF-κB target gene expression, while K218/221 methylation controls a much smaller population of the genes. Not surprisingly, Ingenuity Pathway Analysis
Collectively, the evidence described above proves that methylation on different lysine residues or on different types of amino acids (lysine
5. Histone methylases as potential therapeutic targets in cancer
Due to the important role of NF-κB methylation in differential gene regulation, it is logical to recognize the essential roles of the enzymes that catalyze these methylation modifications. These enzymes are frequently histone methylases, and there are quite a few examples. Since the role of histone methylases in cancer has been well reviewed by Albert and Helin , below, we will only focus on PRMT5.
PRMT5 has been increasingly recognized as an important tumor promoter. We and others have observed elevated PRMT5 expression in cancers of the colon, pancreas, ovary, kidney, lung, bladder, liver, breast, prostate, cervix, and skin. This suggests that high levels of this enzyme may promote tumorigenesis, at least in part by facilitating NF-κB-induced gene expression [22, 38]. For instance, by conducting colorectal cancer (CRC) tissue microarray (TMA), we found that PRMT5 is overexpressed in polyps, advanced stages of colorectal cancer, and in the metastatic stage . Similarly, PRMT5 is also overexpressed in various stages of pancreatic cancer, especially in the metastatic stage . We proved that overexpression of PRMT5 promotes CRC HT29 cell and pancreatic cancer PANC1 cell proliferation, anchorage-independent growth, and cell migration ability. Knockdown of PRMT5 by shRNA showed the opposite effect, confirming PRMT5 functions as a tumor promoter in these cancers .
Additionally, overexpression of PRMT5 has been shown to be associated with poor epithelial ovarian cancer prognosis . In a clinical study with 150 ovarian cancer patient samples, the overexpression of PRMT5 is found to be highly correlated with the Federation of Gynecology and Obstetrics (FIGO) advanced stage, which includes poor cell differentiation, high proliferation activity, and lymph node involvement. The overall survival rate of patients with low PRMT5 expression is 90%. In contrast, only 30% of patients with high PRMT5 expression survived. The progression-free survival rate is 50% for patients with low PRMT5 expression, but in those with high PRMT5 expression the rate is only 10% .
Moreover, Kumar and colleagues showed that the expression level of PRMT5 is inversely correlated with oropharyngeal squamous cell carcinoma (OPSCC) patient outcome. For instance, high PRMT5 expression correlated with low overall survival and had over 1.7 times higher death risk than the patient who has low PRMT5 expression . Together, these studies have identified PRMT5 as a promising therapeutic target in cancers.
To date, multiple efforts have been made to develop the small molecule inhibitors of PRMT5. For instance, EPZ015666 was reported [39, 42] to inhibit PRMT5 methyltransferase activity in panels of mantle cell lymphoma (MCL) cell lines (Maver-1, Mino, Granta-519, Jeko-1 and Z-138). It also significantly inhibits tumor growth in Z-138 and Maver-1 MCL xenograft mouse model as compare with vehicle control.
Recently, by adapting the AlphaLISA technique into a sensitive high throughput screening platform, our lab identified PR5-LL-CM01 as a potent PRMT5 small molecule inhibitor. PR5-LL-CM01 showed greater potency than EPZ015666 in both PDAC and CRC model .
These examples highlight the great potential of using histone methylases, such as PRMT5, as novel therapeutic targets in cancer.
Likewise, other histone methylases ( Table 1 ) that methylate NF-κB may also play critical roles in the development and progression of cancer and other hyper NF-κB driven diseases. Therefore, they constitute a group of highly promising future therapeutic targets for these pathological conditions.
6. Conclusion, perspective, and future directions
The implications of methylation of NF-κB are multi-fold and far reaching. Methylation provides a snapshot of the complexity underlying the regulation of this important transcription factor. Even with the studies done to date, researchers have just begun to understand the crosstalk between these different PTMs and their implications in normal cellular function and disease. Two interesting questions remain. First, how does methylation of these residues on the same subunit affect NF-κB function? Second, can we reconcile the effects of other kinds of PTMs coupled with methylation both in normal and diseases states? A deeper understanding of these aspects will shed important light on the overall strategies for the development of new therapeutic approaches to treat the affected diseases.
Cancer is one of the leading causes of morbidity and mortality worldwide. Methylation of NF-κB as described in this review highlights its significance in cancers and other inflammatory diseases. Over the past decade, several transformative discoveries in epigenetics have led to the development of novel therapies that target epigenetic enzymes. However, the inquiries into acetylation and methylation modifications of lysines and arginines have been mainly focused on histone proteins. Important research identifying methylation residues on important non-histone proteins like NF-κB may be crucial to developing therapeutic interventions that target these modifications. For instance, the PRMT5 inhibitor identified in our laboratory has paved the way for future drug development to treat cancers and other disease with hyper PRMT5-driven NF-κB activity [22, 39]. In addition to PRMT5, other histone methylases, such as NSD1, have been reported by us and others as a significant player in cancer development [20, 43, 44, 45]. Although researchers have been trying to develop a small NSD1 inhibitor for cancer treatment, no NSD1 specific inhibitor has yet been reported due to the large size of NSD1 enzyme and the lack of sufficiently sensitive assay development. Future effort on this front and other histone methylases are equally as important in developing new medicines that target PRMT5.
Additionally, as mentioned in the Introduction, the prototypical NF-κB is comprised of a heterodimer of p65 and p50 subunits. Though multiple sites of methylation have been discovered on the p65 subunit of NF-κB, the potential methylation of the p50 subunit is quite understudied. With recent advances in proteomics and prediction software, novel methylation site(s) on p50 could arise in the near future. The study on p50 methylation could provide more a complete picture in terms of NF-κB regulation, and may possibly lead to novel discoveries regarding the methylation-mediated regulation of this subunit as well.
Since NF-κB is an important transcription factor that also plays a fundamental role in normal cells, one must consider important factors such as specificity of inhibiting modification only in cancer cells but not in normal cells. Multi-targeted approaches that simultaneously cripple several signaling pathways in cancer cells would be ideal, and a better understanding of the crosstalk between these pathways will advance the drug development process. In the future, a combination of advanced animal models, Cas9/CRISPR system, and more sophisticated bioinformatics approaches will serve as invaluable tools to study the implications of methylation on NF-κB and its interactions with other critical cellular factors that are important in the disease context. This will help to expedite the development of therapeutic tools to combat these deadly diseases.
We thank Ms. Lisa King from the Department of Pharmacology and Toxicology at Indiana University School of Medicine for her professional help with revising this book chapter. This work is supported by NIH-NIGMS Grant (# 1R01GM120156-01A1 to TL), NIH-NCI Grant (# 1 R03 CA223906-01 to TL), V foundation Kay Yow Cancer Fund (Grant 4486242 to TL), and 100 VOH Grant (# 2987613 to TL).
|BAF||B-cell activation factor|
|BMDM||bone marrow-derived macrophages|
|ChIP-seq||chromatin immunoprecipitation (ChIP) with DNA sequencing|
|CXCL10||C-X-C motif chemokine 10 (also known as IP10)|
|EGR1||early growth response protein|
|FBXL11||F-box and leucine-rich repeat protein 11|
|FIGO||Federation of Gynecology and Obstetrics|
|IL-1β||interleukin 1 β|
|MCL||mantle cell lymphoma|
|MEFs||mouse embryonic fibroblast cells|
|NF-κB||nuclear factor κB|
|NSD1||nuclear receptor-binding SET domain-containing protein 1|
|OPSCC||oropharyngeal squamous cell carcinoma|
|PHF20||plant homeodomain finger protein 20|
|PKC-ζ||Protein kinase C zeta|
|PRMT1||protein arginine methyltransferase 1|
|PRMT5||protein arginine methyltransferase 5|
|RHD||Rel homology domain|
|Set9||Set domain-containing protein 9|
|TNFα||tumor necrosis factor α|