Role of the Epigenetic Modifier JMJD6 in Tumor Development and Regulation of Immune Response

Biochemical investigations using mass spectrometry to monitor JMJD6-catalysed hydroxylation of multi-lysine containing bromodomain-derived substrates

Jumonji-C domain-containing protein 6 (JMJD6) is a human 2-oxoglutarate (2OG)/Fe(ii)-dependent oxygenase catalysing post-translational C5 hydroxylation of multiple lysine residues, including in the bromodomain-containing proteins BRD2, BRD3 and BRD4. The role(s) of JMJD6-catalysed substrate hydroxylation are unclear. JMJD6 is important in development and JMJD6 catalysis may promote cancer. We report solid-phase extraction coupled to mass spectrometry assays monitoring JMJD6-catalysed hydroxylation of BRD2-4 derived oligopeptides containing multiple lysyl residues. The assays enabled determination of apparent steady-state kinetic parameters for 2OG, Fe(ii), l-ascorbate, O2 and BRD substrates. The JMJD6 K app m for O2 was comparable to that reported for the structurally related 2OG oxygenase factor inhibiting hypoxia-inducible factor-α (FIH), suggesting potential for limitation of JMJD6 activity by O2 availability in cells, as proposed for FIH and some other 2OG oxygenases. The new assays will help development of small-molecule JMJD6 inhibitors for functional assignment studies and as potential cancer therapeutics.

JMJD6 K375 acetylation restrains lung cancer progression by enhancing METTL14/m6A/SLC3A2 axis mediated cell ferroptosis

BACKGROUND

The Jumonji domain-containing protein 6 (JMJD6), a histone arginine demethylase, is known to have a multifaceted and significant role on cancer progression. However, the specific function and mechanism of JMJD6 in non-small cell lung cancer (NSCLC) have yet to be fully elucidated.

METHODS

The elevated expression of JMJD6 in lung cancer tissues was confirmed through a combination of bioinformatics and immunohistochemical analysis. Utilizing lung cancer cell lines H460, H157, A549, and H1299, we further investigated the impact of JMJD6 on various cellular processes such as ferroptosis, proliferation, migration, and invasion both in vivo and in vitro. The acetylation of JMJD6 was characterized using immunoprecipitation, co-immunoprecipitation, GST pull down, and immunofluorescence techniques. The regulatory role of JMJD6 acetylation in ferroptosis was assessed by measuring levels of ROS, MDA, and JC-1. WB, qRT-PCR, ChIP and MeRIP techniques were employed to investigate the relationship between the JMJD6 acetylation/METTL14/m6A/SLC3A2 axis.

RESULTS

This study revealed elevated levels of JMJD6 in tumor tissue, with high expression correlating strongly with advanced clinical stage in lung cancer patients, and identified JMJD6 as a significantly poor prognostic factor for lung cancer. Functional experiments verified that ectopic overexpression of JMJD6 enhanced the proliferation and migratory capacities of lung cancer cells, while JMJD6 knockdown showed opposite effects. We further find that JMJD6 functions as a negative modulator in regulating ferroptosis process. Mechanistically, JMJD6 affects METTL14 expression in an arginine demethylase dependent manner, and mediates m6A modification of SLC3A2 to regulate its expression level, thereby affecting the sensitivity of lung cancer cells to ferroptosis. Besides, our findings indicate that acetyltransferase p300/CBP associated factor (PCAF) interacts with and acetylates JMJD6 at lysine 375. Acetylation weakens the activity of JMJD6 demethylase, thereby enhancing METTL14 expression and affecting its mediated m6A modification to regulate SLC3A2. Acetylation at lysine 375 also augment the modulation of ferroptosis in lung cancer cells by JMJD6, consequently impeding the lung cancer progression.

CONCLUSION

Taken together, we elucidated the JMJD6 acetylation/METTL14/m6A/SLC3A2 axis as a key mediator of lung cancer progression, indicating that JMJD6 may serve as a potentially prognostic biomarker and therapeutic target for NSCLC.

CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays

Determining the genomic localization of chromatin features is an essential aspect of investigating gene expression control, and ChIP-Seq has long been the gold standard technique for interrogating chromatin landscapes. Recently, the development of alternative methods, such as CUT&Tag, have provided researchers with alternative strategies that eliminate the need for chromatin purification, and allow for in situ investigation of histone modifications and chromatin bound factors. Mindful of technical differences, we set out to investigate whether distinct chromatin modifications were equally compatible with these different chromatin interrogation techniques. We found that ChIP-Seq and CUT&Tag performed similarly for modifications known to reside at gene regulatory regions, such as promoters and enhancers, but major differences were observed when we assessed enrichment over heterochromatin-associated loci. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 at a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons. IAPEz-int elements for example, exhibited underrepresentation in mouse ChIP-Seq datasets but strong enrichment using CUT&Tag. Additionally, we identified several euchromatin-associated proteins that co-purify with repetitive loci and are similarly depleted when applying ChIP-based methods. This study reveals that our current knowledge of chromatin states across the heterochromatin portions of the mammalian genome is extensively incomplete, largely due to limitations of ChIP-Seq. We also demonstrate that newer in situ chromatin fragmentation-based techniques, such as CUT&Tag and CUT&RUN, are more suitable for studying chromatin modifications over repetitive elements and retrotransposons.

Bibliometric and visualization analysis in the field of epigenetics and glioma (2009-2024)

Introduction

Glioma represents the most prevalent primary malignant tumor in the central nervous system, a deeper understanding of the underlying molecular mechanisms driving glioma is imperative for guiding future treatment strategies. Emerging evidence has implicated a close relationship between glioma development and epigenetic regulation. However, there remains a significant lack of comprehensive summaries in this domain. This study aims to analyze epigenetic publications pertaining to gliomas from 2009 to 2024 using bibliometric methods, consolidate the extant research, and delineate future prospects for investigation in this critical area.

Methods

For the purpose of this study, publications spanning the years 2009 to 2024 were extracted from the esteemed Web of Science Core Collection (WoSCC) database. Utilizing advanced visualization tools such as CiteSpace and VOSviewer, comprehensive data pertaining to various aspects including countries, authors, author co-citations, countries/regions, institutions, journals, cited literature, and keywords were systematically visualized and analyzed.

Results

A thorough analysis was conducted on a comprehensive dataset consisting of 858 publications, which unveiled a discernible trend of steady annual growth in research output within this specific field. The nations of the United States, China, and Germany emerged as the foremost contributors to this research domain. It is noteworthy that von Deimling A and the Helmholtz Association were distinguished as prominent authors and institutions, respectively, in this corpus of literature. A rigorous keyword search and subsequent co-occurrence analysis were executed, ultimately leading to the identification of seven distinct clusters: "epigenetic regulation", "DNA repair", "DNA methylation", "brain tumors", "diffuse midline glioma (DMG)", "U-87 MG" and "epigenomics". Furthermore, an intricate cluster analysis revealed that the primary foci of research within this field were centered around the exploration of glioma pathogenesis and the development of corresponding treatment strategies.

Conclusion

This article underscores the prevailing trends and hotspots in glioma epigenetics, offering invaluable insights that can guide future research endeavors. The investigation of epigenetic mechanisms primarily centers on DNA modification, non-coding RNAs (ncRNAs), and histone modification. Furthermore, the pursuit of overcoming temozolomide (TMZ) resistance and the exploration of diverse emerging therapeutic strategies have emerged as pivotal avenues for future research within the field of glioma epigenetics.

Analysis of Prospective Genetic Indicators for Prenatal Exposure to Arsenic in Newborn Cord Blood of Using Machine Learning

Using a machine learning methods, we aim to find biological effect biomarkers of prenatal arsenic exposure in newborn cord blood. From the Gene Expression Omnibus (GEO) database, two datasets (GSE48354 and GSE7967) pertaining to cord blood sequencing while exposed to arsenic were retrieved and merged for additional study. Using the "limma" package in the R, differentially expressed genes (DEGs) were eliminated. Machine learning techniques of the LASSO regression algorithm and SVM-RFE algorithm were used to find potential biological effect biomarkers for cord blood sequencing in pregnant women exposed to arsenic. To evaluate the efficacy of biomarkers, a receiver operating characteristic (ROC) curve was used. Furthermore, we investigated the proportion of invading immune cells in each sample using CIBERSORT, and we investigated the relationship between biomarkers and immune cells using the Spearman approach. Using LASSO regression and the SVM-RFE technique, 28 DEGs were discovered, and the main biomarkers of cord blood exposed to arsenic were discovered to be DENND2D, OLIG1, RGS18, CXCL16, DDIT4, FOS, G0S2, GPR183, JMJD6, and SOCS3. According to an immune infiltration analysis and correlation analysis, key biomarkers were substantially associated with the invading immune cells. Ten genes are important biomarkers of cord blood exposed to arsenic connected with infiltrating immune cells, and infiltrating immune cells may play important roles in cord blood exposed to arsenic, according to the study's findings.

Cyclin B2 impairs the p53 signaling in nasopharyngeal carcinoma

BACKGROUND

Cyclin B2 (CCNB2), a member of the cyclin family, is an oncogene in multiple cancers, including nasopharyngeal carcinoma (NPC). However, the epigenetics mechanism for CCNB2 overexpression in NPC remains unclear. This study dissects the regulatory role of CCNB2 in NPC and the molecular mechanism.

METHODS

Differentially methylated genes (DMG) and differentially expressed genes (DEG) were screened out in GSE52068 and GSE13597 databases, respectively, and candidate targets were identified by the Venn diagram. GO annotation and pathway enrichment analyses were performed on selected DMG and DEG, and a PPI network was constructed to pinpoint hub genes. PCR and qMSP were conducted to detect the expression and methylation of CCNB2 in cells. The siRNA targeting CCNB2 was transfected into NPC cells, and the migration, proliferation, cell cycle, epithelial-mesenchymal transition (EMT), tumorigenesis, and metastasis were examined. The upstream factor responsible for CCNB2 overexpression in NPC was explored. The p53 activity in NPC cells was assessed using western blot analysis.

RESULTS

CCNB2 showed hypomethylation and overexpression in NPC. CCNB2 silencing inhibited cell migration, proliferation, cell cycle entry, and EMT. JMJD6 was overexpressed in NPC and upregulated CCNB2 through demethylation. JMJD6 reversed the effects of CCNB2 downregulation, resulting in elevated cellular activity in vitro and tumorigenic and metastatic activities in vivo. CCNB2 blocked the p53 pathway, while the p53 pathway inhibitor reversed the effect of CCNB2 silencing to increase the activity of NPC cells.

CONCLUSIONS

JMJD6 enhanced CCNB2 transcription by demethylating CCNB2, thereby repressing the p53 pathway and promoting NPC progression.

Critical Roles of Protein Arginine Methylation in the Central Nervous System

A remarkable post-transitional modification of both histones and non-histone proteins is arginine methylation. Methylation of arginine residues is crucial for a wide range of cellular process, including signal transduction, DNA repair, gene expression, mRNA splicing, and protein interaction. Arginine methylation is modulated by arginine methyltransferases and demethylases, like protein arginine methyltransferase (PRMTs) and Jumonji C (JmjC) domain containing (JMJD) proteins. Symmetric dimethylarginine and asymmetric dimethylarginine, metabolic products of the PRMTs and JMJD proteins, can be changed by abnormal expression of these proteins. Many pathologies including cancer, inflammation and immune responses have been closely linked to aberrant arginine methylation. Currently, the majority of the literature discusses the substrate specificity and function of arginine methylation in the pathogenesis and prognosis of cancers. Numerous investigations on the roles of arginine methylation in the central nervous system (CNS) have so far been conducted. In this review, we display the biochemistry of arginine methylation and provide an overview of the regulatory mechanism of arginine methyltransferases and demethylases. We also highlight physiological functions of arginine methylation in the CNS and the significance of arginine methylation in a variety of neurological diseases such as brain cancers, neurodegenerative diseases and neurodevelopmental disorders. Furthermore, we summarize PRMT inhibitors and molecular functions of arginine methylation. Finally, we pose important questions that require further research to comprehend the roles of arginine methylation in the CNS and discover more effective targets for the treatment of neurological diseases.

The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer

The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Integrated Metabolomic and Transcriptomic Analysis of Modified Nucleosides for Biomarker Discovery in Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers. The biallelic inactivation of the von Hippel-Lindau tumor suppressor gene (VHL) is the truncal driver mutation of most cases of ccRCC. Cancer cells are metabolically reprogrammed and excrete modified nucleosides in larger amounts due to their increased RNA turnover. Modified nucleosides occur in RNAs and cannot be recycled by salvage pathways. Their potential as biomarkers has been demonstrated for breast or pancreatic cancer. To assess their suitability as biomarkers in ccRCC, we used an established murine ccRCC model, harboring Vhl, Trp53 and Rb1 (VPR) knockouts. Cell culture media of this ccRCC model and primary murine proximal tubular epithelial cells (PECs) were investigated by HPLC coupled to triple-quadrupole mass spectrometry using multiple-reaction monitoring. VPR cell lines were significantly distinguishable from PEC cell lines and excreted higher amounts of modified nucleosides such as pseudouridine, 5-methylcytidine or 2'-O-methylcytidine. The method's reliability was confirmed in serum-starved VPR cells. RNA-sequencing revealed the upregulation of specific enzymes responsible for the formation of those modified nucleosides in the ccRCC model. These enzymes included Nsun2, Nsun5, Pus1, Pus7, Naf1 and Fbl. In this study, we identified potential biomarkers for ccRCC for validation in clinical trials.

Targeting epigenetic regulators to overcome drug resistance in cancers

Drug resistance is mainly responsible for cancer recurrence and poor prognosis. Epigenetic regulation is a heritable change in gene expressions independent of nucleotide sequence changes. As the common epigenetic regulation mechanisms, DNA methylation, histone modification, and non-coding RNA regulation have been well studied. Increasing evidence has shown that aberrant epigenetic regulations contribute to tumor resistance. Therefore, targeting epigenetic regulators represents an effective strategy to reverse drug resistance. In this review, we mainly summarize the roles of epigenetic regulation in tumor resistance. In addition, as the essential factors for epigenetic modifications, histone demethylases mediate the histone or genomic DNA modifications. Herein, we comprehensively describe the functions of the histone demethylase family including the lysine-specific demethylase family, the Jumonji C-domain-containing demethylase family, and the histone arginine demethylase family, and fully discuss their regulatory mechanisms related to cancer drug resistance. In addition, therapeutic strategies, including small-molecule inhibitors and small interfering RNA targeting histone demethylases to overcome drug resistance, are also described.

Comprehensive analysis, immune, and cordycepin regulation for SOX9 expression in pan-cancers and the matched healthy tissues

SRY-box transcription factor 9 (SOX9) (OMIM 608160) is a transcription factor. The expression of SOX9 in pan-cancers and the regulation by small molecules in cancer cell lines are unclear. In the current study, we comprehensively analyzed the expression of SOX9 in normal tissues, tumor tissues and their matched healthy tissues in pan-cancers. The study examined the correlation between immunomodulators and immune cell infiltrations in normal and tumor tissues. Cordycepin (CD), an adenosine analog for SOX9 expression regulation, was also conducted on cancer cells. The results found that SOX9 protein is expressed in a variety of organs, including high expression in 13 organs and no expression in only two organs; in 44 tissues, there was high expression in 31 tissues, medium expression in four tissues, low expression in two tissues, and no expression in the other seven tissues. In pan-cancers with 33 cancer types, SOX9 expression was significantly increased in fifteen cancers, including CESC, COAD, ESCA, GBM, KIRP, LGG, LIHC, LUSC, OV, PAAD, READ, STAD, THYM, UCES, and UCS, but significantly decreased in only two cancers (SKCM and TGCT) compared with the matched healthy tissues. It suggests that SOX9 expression is upregulated in the most cancer types (15/33) as a proto-oncogene. The fact that the decrease of SOX9 expression in SKCM and the increase of SOX9 in the cell lines of melanoma inhibit tumorigenicity in both mouse and human ex vivo models demonstrates that SOX9 could also be a tumor suppressor. Further analyzing the prognostic values for SOX9 expression in cancer individuals revealed that OS is long in ACC and short in LGG, CESC, and THYM, suggesting that high SOX9 expression is positively correlated with the worst OS in LGG, CESC, and THYM, which could be used as a prognostic maker. In addition, CD inhibited both protein and mRNA expressions of SOX9 in a dose-dependent manner in 22RV1, PC3, and H1975 cells, indicating CD's anticancer roles likely via SOX9 inhibition. Moreover, SOX9 might play an important role in tumor genesis and development by participating in immune infiltration. Altogether, SOX9 could be a biomarker for diagnostics and prognostics for pan-cancers and an emerging target for the development of anticancer drugs.

Tumor cell-derived asymmetric dimethylarginine regulates macrophage functions and polarization

BACKGROUND

Asymmetric dimethylarginine (ADMA), which is significantly elevated in the plasma of cancer patients, is formed via intracellular recycling of methylated proteins and serves as a precursor for resynthesis of arginine. However, the cause of ADMA elevation in cancers and its impact on the regulation of tumor immunity is not known.

METHODS

Three mouse breast cell lines (normal breast epithelial HC11, breast cancer EMT6 and triple negative breast cancer 4T1) and their equivalent 3D stem cell culture were used to analyze the secretion of ADMA using ELISA and their responses to ADMA. Bone marrow-derived macrophages and/or RAW264.7 cells were used to determine the impact of increased extracellular ADMA on macrophage-tumor interactions. Gene/protein expression was analyzed through RNAseq, qPCR and flow cytometry. Protein functional analyses were conducted via fluorescent imaging (arginine uptake, tumor phagocytosis) and enzymatic assay (arginase activity). Cell viability was measured via MTS assay and/or direct cell counting using Countess III FL system.

RESULTS

For macrophages, ADMA impaired proliferation and phagocytosis of tumor cells, and even caused death in cultures incubated without arginine. ADMA also led to an unusual macrophage phenotype, with increased expression of arginase, cd163 and cd206 but decreased expression of il10 and dectin-1. In contrast to the severely negative impacts on macrophages, ADMA had relatively minor effects on proliferation and survival of mouse normal epithelial HC11 cells, mouse breast cancer EMT6 and 4T1 cells, but there was increased expression of the mesenchymal markers, vimentin and snail2, and decreased expression of the epithelial marker, mucin-1 in EMT6 cells. When tumor cells were co-cultured ex vivo with tumor antigen in vivo-primed splenocytes, the tumor cells secreted more ADMA and there were alterations in the tumor cell arginine metabolic landscape, including increased expression of genes involved in arginine uptake, metabolism and methylation, and decreased expression of a gene that is responsible for arginine demethylation. Additionally, interferon-gamma, a cytokine involved in immune challenge, increased secretion of ADMA in tumor cells, a process attenuated by an autophagy inhibitor.

CONCLUSION

Our results suggest initial immune attack promotes autophagy in tumor cells, which then secrete ADMA to manipulate macrophage polarization favoring tumor tolerance.