Chromatin regulators with tumor suppressor properties and their alterations in human cancers

Development and validation of a chromatin regulator signature for predicting prognosis hepatocellular carcinoma patient

BACKGROUND

Hepatocellular carcinoma (HCC) is a malignancy with a bleak prognosis. Although emerging research increasingly supports the involvement of chromatin regulators (CRs) in cancer development, CRs in HCC patients have not received proportionate attention. This study aimed to investigate the role and prognostic significance of CRs in HCC patients, providing new insights for clinical diagnosis and treatment strategies.

METHODS

We analyzed 424 samples in The Cancer Genome Atlas-Liver hepatocellular carcinoma (TCGA-LIHC) data to identify key CR genes associated with HCC prognosis by differential expression and univariate Cox regression analyses. LASSO-multivariate Cox regression method was used for construction of a prognostic signature and development of a CR-related prognosis model. The prognosis capacity of the model was evaluated via Kaplan-Meier method. Relationship between the model and tumor microenvironment (TME) was evaluated. Additionally, clinical variables and the model were incorporated to create a nomogram. The role of the prognostic gene MRG-binding protein (MRGBP) in HCC was elucidated by immunohistochemistry and semiquantitative analysis.

RESULTS

A risk score model, comprising B-lymphoma Mo-MLV insertion region 1 (BMI1), chromobox 2 (CBX2), and MRGBP, was constructed. The area under the curve (AUC) of the CR-based signature is 0.698 (P<0.05), exhibiting robust predictive power. Functional and pathway analyses illuminated the biological relevance of these genes. Immune microenvironment analysis suggested potential implications for immunotherapy. Drug sensitivity analysis identified agents for targeted treatment. Clinical samples show that MRGBP is highly expressed in HCC tissues.

CONCLUSIONS

This CR-based signature shows promise as a valuable prognostic tool for HCC patients. It demonstrates predictive capabilities, independence from other clinical factors, and potential clinical applicability. In addition, we need more experiments to validate our findings. These findings offer insights into HCC prognosis and treatment, with implications for personalized medicine and improved patient outcomes.

Role of the Circadian Gas-Responsive Hemeprotein NPAS2 in Physiology and Pathology

Neuronal PAS domain protein 2 (NPAS2) is a hemeprotein comprising a basic helix-loop-helix domain (bHLH) and two heme-binding sites, the PAS-A and PAS-B domains. This protein acts as a pyridine nucleotide-dependent and gas-responsive CO-dependent transcription factor and is encoded by a gene whose expression fluctuates with circadian rhythmicity. NPAS2 is a core cog of the molecular clockwork and plays a regulatory role on metabolic pathways, is important for the function of the central nervous system in mammals, and is involved in carcinogenesis as well as in normal biological functions and processes, such as cardiovascular function and wound healing. We reviewed the scientific literature addressing the various facets of NPAS2 and framing this gene/protein in several and very different research and clinical fields.

Tumor subtypes and signature model construction based on chromatin regulators for better prediction of prognosis in uveal melanoma

Background: Uveal Melanoma (UM) is the most prevalent primary intraocular malignancy in adults. This study assessed the importance of chromatin regulators (CRs) in UM and developed a model to predict UM prognosis. Methods: Gene expression data and clinical information for UM were obtained from public databases. Samples were typed according to the gene expression of CRs associated with UM prognosis. The prognostic key genes were further screened by the protein interaction network, and the risk model was to predict UM prognosis using the least absolute shrinkage and selection operator (LASSO) regression analysis and performed a test of the risk mode. In addition, we performed gene set variation analysis, tumor microenvironment, and tumor immune analysis between subtypes and risk groups to explore the mechanisms influencing the development of UM. Results: We constructed a signature model consisting of three CRs (RUVBL1, SIRT3, and SMARCD3), which was shown to be accurate, and valid for predicting prognostic outcomes in UM. Higher immune cell infiltration in poor prognostic subtypes and risk groups. The Tumor immune analysis and Tumor Immune Dysfunction and Exclusion (TIDE) score provided a basis for clinical immunotherapy in UM. Conclusion: The risk model has prognostic value for UM survival and provides new insights into the treatment of UM.

Identification of Chromatin Regulatory Factors Related to Immunity and Treatment of Alzheimer's Disease

Alzheimer's disease is one of the common neurodegenerative diseases in the elderly, which mainly manifests as progressively severe cognitive impairment, which seriously affects the quality of life of patients. Chromatin regulators have been shown to be associated with a variety of biological processes, and we mainly explore the relationship between chromatin regulators and Alzheimer's disease. Eight hundred seventy chromatin regulators were collected from previous studies, and data related to Alzheimer's disease patients were downloaded from the GEO database. Finally, we screened chromatin regulators related to Alzheimer's disease immunity, established prediction models, and screened related drugs and miRNAs. We screened 160 differentially expressed CRs, constructed an interaction network, obtained 10 hub genes, successfully constructed a prediction model based on immune-related 5 CRs, and obtained 520 related drugs and 3 related miRNA, which provided an idea for the treatment of Alzheimer's disease. Our study identified 5 chromatin regulators related to Alzheimer's disease, which are expected to be new targets for Alzheimer's disease immunotherapy.

Identification of Parkinson's disease-associated chromatin regulators

Parkinson's disease (PD) is a common neurological disorder that causes quiescent tremors, motor delays, depression, and sleep disturbances. Existing treatments can only improve symptoms, not stop progression or cure the disease, but effective treatments can significantly improve patients' quality of life. There is growing evidence that chromatin regulatory proteins (CRs) are involved in a variety of biological processes, including inflammation, apoptosis, autophagy, and proliferation. But the relationship of chromatin regulators in Parkinson's disease has not been studied. Therefore, we aim to investigate the role of CRs in the pathogenesis of Parkinson's disease. We collected 870 chromatin regulatory factors from previous studies and downloaded data on patients with PD from the GEO database. 64 differentially expressed genes were screened, the interaction network was constructed and the key genes with the top 20 scores were calculated. Then we discussed its correlation with the immune function of PD. Finally, we screened potential drugs and miRNAs. Five genes related to the immune function of PD, BANF1, PCGF5, WDR5, RYBP and BRD2, were obtained by using the absolute value of correlation greater than 0.4. And the disease prediction model showed good predictive efficiency. We also screened 10 related drugs and 12 related miRNAs, which provided a reference for the treatment of PD. BANF1, PCGF5, WDR5, RYBP and BRD2 are related to the immune process of Parkinson's disease and can predict the occurrence of Parkinson's disease, which is expected to become a new target for the diagnosis and treatment of Parkinson's disease.

Chromatin Regulator-Related Gene Signature for Predicting Prognosis and Immunotherapy Efficacy in Breast Cancer

BACKGROUND

Many studies have found that chromatin regulators (CRs) are correlated with tumorigenesis and disease prognosis. Here, we attempted to build a new CR-related gene model to predict breast cancer (BC) survival status.

METHODS

First, the CR-related differentially expressed genes (DEGs) were screened in normal and tumor breast tissues, and the potential mechanism of CR-related DEGs was determined by function analysis. Based on the prognostic DEGs, the Cox regression model was applied to build a signature for BC. Then, survival and receiver operating characteristic (ROC) curves were performed to validate the signature's efficacy and identify its independent prognostic value. The CIBERSORT and tumor immune dysfunction and exclusion (TIDE) algorithms were used to assess the immune cells infiltration and immunotherapy efficacy for this signature, respectively. Additionally, a novel nomogram was also built for clinical decisions.

RESULTS

We identified 98 CR-related DEGs in breast tissues and constructed a novel 6 CR-related gene signature (ARID5A, ASCL1, IKZF3, KDM4B, PRDM11, and TFF1) to predict the outcome of BC patients. The prognostic value of this CR-related gene signature was validated with outstanding predictive performance. The TIDE analysis revealed that the high-risk group patients had a better response to immune checkpoint blockade (ICB) therapy.

CONCLUSION

A new CR-related gene signature was built, and this signature could provide the independent predictive capability of prognosis and immunotherapy efficacy for BC patients.

Development and validation of a chromatin regulator prognostic signature in colon adenocarcinoma

Aberrant expression of chromatin regulators (CRs) could lead to the development of various diseases including cancer. However, the biological function and prognosis role of CRs in colon adenocarcinoma (COAD) remains unclear. We performed the clustering analyses for expression profiling of COAD downloaded from The Cancer Genome Atlas. We developed a chromatin regulator prognostic model, which was validated in an independent cohort data. Time-intendent receiver operating characteristics curve was used to evaluate predict ability of model. Univariate and multivariate cox regression were used to assess independence of risk score. Nomogram was established to assess individual risk. Gene ontology, and Kyoto Encyclopedia of genes and genomes, gene set variation analysis and gene set enrichment analysis were performed to explore the function of CRs. Immune infiltration and drug sensitivity were also performed to assess effect of CRs on treatment in COAD. COAD can be separated into two subtypes with different clinical characteristics and prognosis. The C2 had elevated immune infiltration levels and low tumor purity. Using 12 chromatin regulators, we developed and validated a prognostic model that can predict the overall survival of COAD patients. We built a risk score that can be an independent prognosis predictor of COAD. The nomogram score system achieved the best predict ability and were also confirmed by decision curve analysis. There were significantly different function and pathway enrichment, immune infiltration levels, and tumor mutation burden between high-risk and low-risk group. The external validation data also indicated that high-risk group had higher stable disease/progressive disease response rate and poorer prognosis than low-risk group. Besides, the signature genes included in the model could cause chemotherapy sensitivity to some small molecular compounds. Our integrative analyses for chromatin regulators could provide new insights for the risk management and individualized treatment in COAD.

Human p21-activated kinase 5 (PAK5) expression and potential mechanisms in relevant cancers: Basic and clinical perspectives for molecular cancer therapeutics

An oncogenic role, p21-activated kinase 5 (PAK5), has proven as a significant mediator for many cellular progression, which is expressed highly in human organs such as lung, liver, kidney, blood vessels endothelial cells and inflammatory cells. PAK5 was primitively detected in the cerebrum and accelerated the filopodia formation in neurocytes. It can reverse the effect of Rho and adjust its activity to mediate maintenance and development of nerve axon by binding with Cdc42-GTP. Moreover, PAK5 has been suggested to mediate protean, multitudinous and inscrutable functions in cancer. Currently, many researches indicated that PAK5 was dysregulated in ovarian cancer, cervical cancer, melanoma, osteosarcoma, renal carcinoma, breast cancer, gastric cancer and so on, which was involved in cell proliferation, apoptosis, migration and invasion. This review focuses the latest knowledge on the structure, expression, signalling pathway of PAK5, emphasizing its function in cancer.

Histone Deacetylase 3 Inhibitor Suppresses Hepatitis C Virus Replication by Regulating Apo-A1 and LEAP-1 Expression

Histone deacetylase (HDAC) inhibitors show clinical promise for the treatment of cancers, including hepatocellular carcinoma (HCC). In this study, we investigated the effect of HDAC inhibitor treatment on hepatitis C virus (HCV) replication in Huh7 human liver cells and in a mouse model of HCV infection. Viral replication was markedly suppressed by the HDAC3 inhibitor at concentrations below 1 mmol/L, with no cellular toxicity. This was accompanied by upregulation of liver-expressed antimicrobial peptide 1(LEAP-1) and downregulation of apolipoprotein-A1 (Apo-A1), as determined by microarray and quantitative RT-PCR analyses. Moreover, HDAC3 was found to modulate the binding of CCAAT-enhancer-binding protein α (C/EBPα), hypoxia-inducible factor 1α (HIF1α), and signal transducer and activator of transcription 3 (STAT3) to the LEAP-1 promoter. HDAC3 inhibitor treatment also blocked HCV replication in a mouse model of HCV infection. These results indicate that epigenetic therapy with HDAC3 inhibitor may be a potential treatment for diseases associated with HCV infection such as HCC.

Target sequencing and CRISPR/Cas editing reveal simultaneous loss of UTX and UTY in urothelial bladder cancer

UTX is a histone demethylase gene located on the X chromosome and is a frequently mutated gene in urothelial bladder cancer (UBC). UTY is a paralog of UTX located on the Y chromosome. We performed target capture sequencing on 128 genes in 40 non-metastatic UBC patients. UTX was the most frequently mutated gene (30%, 12/40). Of the genetic alterations identified, 75% were truncating mutations. UTY copy number loss was detected in 8 male patients (22.8%, 8/35). Of the 9 male patients with UTX mutations, 6 also had copy number loss (66.7%). To evaluate the functional roles of UTX and UTY in tumor progression, we designed UTX and UTY single knockout and UTX-UTY double knockout experiments using a CRISPR/Cas9 lentiviral system, and compared the proliferative capacities of two UBC cell lines in vitro. Single UTX or UTY knockout increased cell proliferation as compared to UTX-UTY wild-type cells. UTX-UTY double knockout cells exhibited greater proliferation than single knockout cells. These findings suggest both UTX and UTY function as dose-dependent suppressors of UBC development. While UTX escapes X chromosome inactivation in females, UTY may function as a male homologue of UTX, which could compensate for dosage imbalances.

Oncogenic Epstein-Barr virus recruits Nm23-H1 to regulate chromatin modifiers

In cancer progression, metastasis is a major cause of poor survival of patients and can be targeted for therapeutic interventions. The first discovered metastatic-suppressor Nm23-H1 possesses nucleoside diphosphate kinase, histidine kinase, and DNase activity as a broad-spectrum enzyme. Recent advances in cancer metastasis have opened new ways for the development of therapeutic molecular approaches. In this review, we provide a summary of the current understanding of Nm23/NDPKs in the context of viral oncogenesis. We also focused on Nm23-H1-mediated cellular events with an emphasis on chromatin modifications. How Nm23-H1 modulates the activities of chromatin modifiers through interaction with Epstein-Barr virus-encoded oncogenic antigens and related crosstalks are discussed in the context of other oncogenic viruses. We also described the current understanding of the cellular and viral interactions of Nm23-H1 and their reference to transcription regulation and metastasis. Further, we summarized the recent therapeutic approaches targeting Nm23 and its potential links to pathways that can be exploited by oncogenic viruses.

(-)-Epigallocatechin-3-gallate reverses the expression of various tumor-suppressor genes by inhibiting DNA methyltransferases and histone deacetylases in human cervical cancer cells

There has been increasing evidence that numerous bioactive dietary agents can hamper the process of carcinogenesis by targeting epigenetic alterations including DNA methylation. This therapeutic approach is considered as a significant goal for cancer therapy due to the reversible nature of epigenetic-mediated gene silencing and warrants further attention. One such dietary agent, green tea catechin, (-)-epigallocatechin-3-gallate (EGCG) has been shown to modulate many cancer-related pathways. Thus, the present study was designed to investigate the role of EGCG as an epigenetic modifier in HeLa cells. DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibition assays were conducted, and the transcription levels of DNMT3B and HDAC1 were assessed by enzymatic activity assay and RT-PCR, respectively. Furthermore, we studied the binding interaction of EGCG with DNMT3B and HDAC1 by molecular modeling as well as promoter DNA methylation and expression of retinoic acid receptor-β (RARβ), cadherin 1 (CDH1) and death-associated protein kinase-1 (DAPK1) in EGCG-treated HeLa cells by RT-PCR and MS-PCR. In the present study, time-dependent EGCG-treated HeLa cells were found to have a significant reduction in the enzymatic activity of DNMT and HDAC. However, the expression of DNMT3B was significantly decreased in a time-dependent manner whereas there was no significant change in HDAC1 expression. Molecular modeling data also supported the EGCG-mediated DNMT3B and HDAC1 activity inhibition. Furthermore, time-dependent exposure to EGCG resulted in reactivation of known tumor-suppressor genes (TSGs) in HeLa cells due to marked changes in the methylation of the promoter regions of these genes. Overall, the present study suggests that EGCG may have a significant impact on the development of novel epigenetic-based therapy.

TESTIN suppresses tumor growth and invasion via manipulating cell cycle progression in endometrial carcinoma

BACKGROUND

The TESTIN gene was demonstrated to be a tumor suppressor in prostate and breast cancer through inhibiting tumor growth and invasion. Herein, we aimed to investigate the detailed functions of TESTIN in the highly sexual hormone (estrogen)-dependent malignancy, endometrial carcinoma.

MATERIAL AND METHODS

TESTIN mRNA and protein expression were measured by qRT-PCR, Western blot and immunohistochemistry. Upregulation of TESTIN was achieved by transfecting the pcDNA3.1-TESTIN plasmids into AN3CA cells. Knockdown of TESTIN was achieved by transfecting the shRNA-TESTIN into Ishikawa cells. MTT assay, colony formation assay, and Transwell assay were used to investigate the effects of TESTIN on cellular proliferation and invasion. The apoptotic status and cell cycle were analyzed using flow cytometry. MMP2 secretion was determined by ELISA assay. The xenograft assay was used to investigate the functions of TESTIN in nude mice.

RESULTS

Compared to the non-malignant adjacent endometrium, 54% of tumor samples presented downregulation of TESTIN (P<0.001). Loss of TESTIN protein was correlated with advanced tumor stage (P=0.047), high grade (P=0.034), and lymphatic vascular space invasion (P=0.036). In vitro, overexpression of TESTIN suppressed cell proliferation, induced dramatic G1 arrest, and inhibited tumor invasion through blocking the secretion of MMP2. Loss of TESTIN accelerated cellular proliferation, promoted cell cycle progression, and enhanced tumor invasion by increasing the secretion of MMP2. Consistently, TESTIN could significantly delay the growth of xenografts in nude mice.

CONCLUSIONS

TESTIN was commonly downregulated in human endometrial carcinoma and was associated with poor prognostic markers. Moreover, TESTIN significantly inhibited tumor growth and invasion via arresting cell cycle in in vitro and in vivo experiments. Therefore, we propose that TESTIN might be a prognostic marker and therapeutic target for endometrial carcinoma.

Phospho-ΔNp63α/microRNA network modulates epigenetic regulatory enzymes in squamous cell carcinomas

The tumor protein (TP) p63/microRNAs functional network may play a key role in supporting the response of squamous cell carcinomas (SCC) to chemotherapy. We show that the cisplatin exposure of SCC-11 cells led to upregulation of miR-297, miR-92b-3p, and miR-485-5p through a phosphorylated ΔNp63α-dependent mechanism that subsequently modulated the expression of the protein targets implicated in DNA methylation (DNMT3A), histone deacetylation (HDAC9), and demethylation (KDM4C). Further studies showed that mimics for miR-297, miR-92b-3p, or miR-485-5p, along with siRNA against and inhibitors of DNMT3A, HDAC9, and KDM4C modulated the expression of DAPK1, SMARCA2, and MDM2 genes assessed by the quantitative PCR, promoter luciferase reporter, and chromatin immunoprecipitation assays. Finally, the above-mentioned treatments affecting epigenetic enzymes also modulated the response of SCC cells to chemotherapeutic drugs, rendering the resistant SCC cells more sensitive to cisplatin exposure, thereby providing the groundwork for novel chemotherapeutic venues in treating patients with SCC.

MBD3 localizes at promoters, gene bodies and enhancers of active genes

The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. Recent reports describing localization of NuRD provide new insights that question previous models on NuRD action, but are not in complete agreement. Here, we provide location analysis of endogenous MBD3, a component of NuRD complex, in two human breast cancer cell lines (MCF-7 and MDA-MB-231) using two independent genomic techniques: DNA adenine methyltransferase identification (DamID) and ChIP-seq. We observed concordance of the resulting genomic localization, suggesting that these studies are converging on a robust map for NuRD in the cancer cell genome. MBD3 preferentially associated with CpG rich promoters marked by H3K4me3 and showed cell-type specific localization across gene bodies, peaking around the transcription start site. A subset of sites bound by MBD3 was enriched in H3K27ac and was in physical proximity to promoters in three-dimensional space, suggesting function as enhancers. MBD3 enrichment was also noted at promoters modified by H3K27me3. Functional analysis of chromatin indicated that MBD3 regulates nucleosome occupancy near promoters and in gene bodies. These data suggest that MBD3, and by extension the NuRD complex, may have multiple roles in fine tuning expression for both active and silent genes, representing an important step in defining regulatory mechanisms by which NuRD complex controls chromatin structure and modification status.

Chromatin structure is tightly regulated by multiple mechanisms; its dysregulation is associated with developmental abnormalities and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is proposed to regulate chromatin structure by changing the location and/or the chemical properties of the fundamental building block of chromatin, the nucleosome. NuRD has been shown by genetics to be important for normal development, yet the detailed mechanism of how NuRD regulates chromatin structure is still unclear. Here, we study the localization and function of MBD3, a component of NuRD, in two human breast cancer cell lines using two independent genomic technologies. Our data demonstrate that existing models, which associate NuRD with transcriptional repression, are not completely correct. Rather, MBD3 showed cell-type specific localization at active genes. Moreover, we found a previously unidentified localization of MBD3 across gene bodies and identified a regulatory role for MBD3 in nucleosome organization. Our data provide a reliable starting point from which to address mechanisms by which NuRD controls chromatin structure and nuclear biology.

FEZF2, a novel 3p14 tumor suppressor gene, represses oncogene EZH2 and MDM2 expression and is frequently methylated in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus-associated tumor prevalent in southern China and southeast Asia, with the 3p14-p12 locus reported as a critical tumor suppressor gene (TSG) region during its pathogenesis. We identified a novel 3p14.2 TSG, FEZF2 (FEZ family zinc finger 2), for NPC. FEZF2 is readily expressed in normal tissues including upper respiratory epithelium, testis, brain and ovary tissues, as well as in immortalized nasopharyngeal epithelial cell line NP69, but it is completely silenced in NPC cell lines due to CpG methylation of its promoter, although no homozygous deletion of FEZF2 was detected. 5-Aza-2'-deoxycytidine treatment restored FEZF2 expression in NPC cell lines along with its promoter demethylation. FEZF2 was frequently downregulated in NPC tumors, with promoter methylation detected in 75.5% of tumors, but only in 7.1% of normal nasopharyngeal tissues. Restored FEZF2 expression suppressed NPC cell clonogenicity through inducing G2/M cell cycle arrest and apoptosis and also inhibited NPC cell migration and stemness. FEZF2 acted as a histone deacetylase-associated repressor downregulating multiple oncogenes including EZH2 and MDM2, through direct binding to their promoters. Concomitantly, overexpression of EZH2 was frequently detected in NPC tumors. Thus, we have identified FEZF2 as a novel 3p14.2 TSG frequently inactivated by promoter methylation in NPC, which functions as a repressor downregulating multiple oncogene expression.