The endogenous zinc finger transcription factor, ZNF24, modulates the angiogenic potential of human microvascular endothelial cells

Potential diagnostic markers and biological mechanism for osteoarthritis with obesity based on bioinformatics analysis

Numerous observational studies have shown that obesity (OB) is a significant risk factor in the occurrence and progression of osteoarthritis (OA), but the underlying molecular mechanism between them remains unclear. The study aimed to identify the key genes and pathogeneses for OA with OB. We obtained two OA and two OB datasets from the gene expression omnibus (GEO) database. First, the identification of differentially expressed genes (DEGs), weighted gene co-expression network analysis (WGCNA), and machine learning algorithms were used to identify key genes for diagnosing OA with OB, and then the nomogram and receiver operating characteristic (ROC) curve were conducted to assess the diagnostic value of key genes. Second, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to explore the pathogenesis of OA with OB. Third, CIBERSORT was created to investigate immunocyte dysregulation in OA and OB. In this study, two genes (SOD2, ZNF24) were finally identified as key genes for OA with OB. These two key genes had high diagnostic values via nomogram and ROC curve calculation. Additionally, functional analysis emphasized that oxidative stress and inflammation response were shared pathogenesis of OB and AD. Finally, in OA and OB, immune infiltration analysis showed that SOD2 closely correlated to M2 macrophages, regulatory T cells, and CD8 T cells, and ZNF24 correlated to regulatory T cells. Overall, our findings might be new biomarkers or potential therapeutic targets for OA and OB comorbidity.

Tumor-suppressive zinc finger protein 24 (ZNF24) sensitizes colorectal cancer cells to 5-fluorouracil by inhibiting the Wnt pathway and activating the p53 signaling

Carcinogenesis and colorectal cancer (CRC) development are associated with dysregulation of various pathways, including Wnt and p53. 5-fluorouracil (5-FU) is a common chemotherapeutic agent for CRC treatment, but its efficacy is restricted by drug resistance. Doxycycline is an orally active tetracycline antibiotic known for its antimicrobial and anticancer cell proliferation activities. This study intends to delineate the potential role of bioinformatically predicted ZNF24 in the 5-FU resistance of CRC cells. The expression of ZNF24 was measured in clinically collected CRC tissues and cells. Afterward, ectopic ZNF24 expression was induced by DOX to evaluate the viability, colony-forming ability and sphere-forming ability of CRC cells. It was found that ZNF24 was validated to be poorly expressed in CRC tissues, and ectopic expression of ZNF24 was revealed to restrict the malignant phenotypes of CRC cells. In addition, restored ZNF24 attenuated 5-FU resistance of CRC cells by inhibiting the Wnt pathway and activating p53 signaling. Furthermore, an inhibitor of Wnt production 2 (IWP-2) treatment was an alternative to ZNF24 up-regulation in sensitizing CRC cells to 5-FU treatment. In conclusion, our results indicate that ZNF24 inhibits 5-FU resistance of CRC cells by suppressing the Wnt pathway and activating p53 signaling, which offers a potential strategy for managing chemoresistance in CRC.

DNA methylation signatures on vascular differentiation genes are aberrant in vessels of human cerebral arteriovenous malformation nidus

Arteriovenous malformation (AVM) is a tangle of arteries and veins, rupture of which can result in catastrophic hemorrhage in vulnerable sites such as the brain. Cerebral AVM is associated with a high mortality rate in humans. The causative factor or the stimulus at the artery-venous junction and the molecular basis of the development and progression of cerebral AVM remain unknown. While it is known that aberrant hemodynamic forces in the artery-vein junction contribute to the development of AVMs, the mechanistic pathways are unclear. Given that various environmental stimuli modulate epigenetic modifications on the chromatin of cells, we speculated that misregulated DNA methylome could lead to cerebral AVM development. To identify the aberrant epigenetic signatures, we used AVM nidus tissues and analyzed the global DNA methylome using the Infinium DNA methylome array. We observed significant alterations of DNA methylation in the genes associated with the vascular developmental pathway. Further, we validated the DNA hypermethylation by DNA bisulfite sequencing analysis of selected genes from human cerebral AVM nidus. Taken together, we provide the first experimental evidence for aberrant epigenetic signatures on the genes of vascular development pathway, in human cerebral AVM nidus.

Zinc Finger Protein 24 is a Prognostic Factor in Ovarian Serous Carcinoma

OBJECTIVE

As a member of the zinc finger protein family, zinc finger protein 24 (ZNF24) contains a Cys2His2 zinc finger domain and acts as a transcription factor. ZNF24 has been reported to be downregulated in gastric cancer and breast cancer. However, little is known about its expression and function in ovarian serous carcinoma (OSC).

PATIENTS AND METHODS

We collected 117 OSC patients during 2011 to 2017 and retrospectively retrieved their clinicopathologic characteristics as well as their survival data. Protein level was analyzed by immunohistochemistry, mRNA level was evaluated by RT-qPCR assay, and transcriptional data was obtained from TCGA data sets. The correlations between ZNF24 expression and patients' features were assessed using χ2 test. Univariate and multivariate analyses were used to identify the prognosis predicative potential of ZNF24 in OSC. The function of ZNF24 in the epithelial ovarian cancer cells was also verified by in vitro cellular experiments.

RESULTS

Among the 117 cases, ZNF24 was downregulated in 52 OSC samples (44.6%) and significantly correlated with tumor stages. According to univariate and multivariate analyses, ZNF24 can act as an independent prognostic indicator for the overall survival of OSC patients, whose lower expression was associated with poorer clinical outcomes. Ectopic overexpression and knockdown assays indicated that ZNF24 can negatively regulate the OSC cell viability.

CONCLUSIONS

OSC patients with low level of ZNF24 have worse overall survival compared with those possess high-ZNF24 expression. Downregulated ZNF24 may be involved in the proliferation of OSC, and ZNF24 expression can serve as an independent survival predictor.

miR-940 is a new biomarker with tumor diagnostic and prognostic value

miR-940 is a microRNA located on chromosome 16p13.3, which has varying degrees of expression imbalance in many diseases. It binds to the 3′ untranslated region (UTR) and affects the transcription or post-transcriptional regulation of target protein-coding genes. For a diversity of cellular processes, including cell proliferation, migration, invasion, apoptosis, epithelial-to-mesenchymal transition (EMT), cell cycle, and osteogenic differentiation, miR-940 can affect them not only by regulating protein-coding genes but also long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in pathways. Intriguingly, miR-940 participates in four pathways that affect cancer development, including the Wnt/β-catenin pathway, mitogen-activated protein kinase (MAPK) pathway, PD-1 pathway, and phosphatidylinositol 3-kinase (PI3K)-Akt pathway. Importantly, the expression of miR-940 is intimately correlated with the diagnosis and prognosis of tumor patients, as well as to the efficacy of tumor chemotherapy drugs. In conclusion, our main purpose is to outline the expression of miR-940 in various diseases and the molecular biological and cytological functions of target genes in order to reveal its potential diagnostic and prognostic value as well as its predictive value of drug efficacy.

Cigarette smoke modulates binding of the transcription factor MZF1 to the VEGF promoter and regulates VEGF expression in dependence of genetic variation SNP 405

BACKGROUND

Vascular endothelial growth factor (VEGF) affects carcinogenesis of the upper aerodigestive tract. Cigarette smoke (CSE) influences VEGF-gene regulation. The single nucleotide polymorphism +405 G/C (SNP +405 G/C) and the transcriptional factor (TF) myeloid zinc finger 1 (MZF1) are endogenic regulators of the VEGFpromoter as the polymorphism 405 potentially affects binding of the transcription factor MZF1. Therefore, this in vitro study analysed cancer cells of the upper aerodigestive tract after CSE incubation concerning MZF1-binding specificity and VEGF expression in dependency of VEGF polymorphism +405 G/C compared to wild type (wt).

METHODS

In human alveolar epithelial-like type-II cells (A549) and oral squamous cell cancer cells (HNSCCUM-02T) SNP +405 G/C- and MZF1-dependent VEGF promoter activity and VEGF expression were analysed by qRT-PCR and Western blot after incubation with 10% CSE. Temporary knock-down of MZF1 was performed using siRNA. MZF1 binding was analysed by Co-Chromatin-Immunoprecipitation (Co-ChiP) (each test n = 3).

RESULTS

We found a stronger MZF1 binding to VEGF polymorphism 405 in A549 cells (P < .05) compared to HNSCCUM-02T cells (P = .02), where MZF1 binding was reduced. MZF1 knock out reduced VEGF promoter activity in HNSCCUM-02T cells, showing the relevance of the factor for transcriptional activation of the VEGF promoter. Finally, we found that CSE increases promoter activity in both cell lines and no significant differences between the two analysed polymorphisms concerning their activating capacity.

CONCLUSION

In summary, both VEGF promoter polymorphisms are similar effective in terms of transcriptional activity, and MZF1 is a transcriptional activator of VEGF promoter. Moreover, cigarette smoke increases MZF1 binding of VEGF-promoter and directly affects VEGF-gene regulation.

Dysregulation of the EphrinB2-EphB4 ratio in pediatric cerebral arteriovenous malformations is associated with endothelial cell dysfunction in vitro and functions as a novel noninvasive biomarker in patients

We investigated (1) EphrinB2 and EphB4 receptor expression in cerebral AVMs, (2) the impact of an altered EphrinB2:EphB4 ratio on brain endothelial cell function and (3) potential translational applications of these data. The following parameters were compared between AVM endothelial cells (AVMECs) and human brain microvascular endothelial cells (HBMVECs): quantified EphrinB2 and EphB4 expression, angiogenic potential, and responses to manipulation of the EphrinB2:EphB4 ratio via pharmacologic stimulation/inhibition. To investigate the clinical relevance of these in vitro data, Ephrin expression was assessed in AVM tissue (by immunohistochemistry) and urine (by ELISA) from pediatric patients with AVM (n = 30), other cerebrovascular disease (n = 14) and control patients (n = 29), and the data were subjected to univariate and multivariate statistical analyses. Compared to HBMVECs, AVMECs demonstrated increased invasion (p = 0.04) and migration (p = 0.08), impaired tube formation (p = 0.06) and increased EphrinB2:EphB4 ratios. Altering the EphrinB2:EphB4 ratio (by increasing EphrinB2 or blocking EphB4) in HBMVECs increased invasion (p = 0.03 and p < 0.05, respectively). EphrinB2 expression was increased in AVM tissue, which correlated with increased urinary EphrinB2 levels in AVM patients. Using the optimal urinary cutoff value (EphrinB2 > 25.7 pg/μg), AVMs were detected with high accuracy (80% vs. controls) and were distinguished from other cerebrovascular disease (75% accuracy). Post-treatment urinary EphrinB2 levels normalized in an index patient. In summary, AVMECs have an EphrinB2:EphB4 ratio that is increased compared to that of normal HBMVECs. Changing this ratio in HBMVECs induces AVMEC-like behavior. EphrinB2 is clinically relevant, and its levels are increased in AVM tissue and patient urine. This work suggests that dysregulation of the EphrinB2:EphB4 signaling cascade and increases in EphrinB2 may play a role in AVM development, with potential utility as a diagnostic and therapeutic target.

Tangled blood vessel growths in the brain, known as arteriovenous malformations (AVMs), can be identified with a urine test, and the test protein may also help in treatment. AVMs often have no symptoms and can go undiagnosed, but when they rupture they can cause deadly brain hemorrhage. Better diagnostic tools and nonsurgical treatments are needed. Katie Fehnel and Edward Smith at Boston Children’s Hospital, USA, and co-workers identified an imbalance in a pair of signal/receptor proteins called ephrins in AVMs. Disturbing the balance of ephrin levels in blood vessel-forming cells disrupted growth, causing disorganized vessel formation with too many sprouts and insufficient junctions. Testing ephrin levels in patients’ urine reliably identified AVMs. These results offer a rapid and noninvasive new diagnostic tool and may help find new treatments for this mostly invisible and potentially fatal condition.

Genetic and clinical predictors of CD4 lymphocyte recovery during suppressive antiretroviral therapy: Whole exome sequencing and antiretroviral therapy response phenotypes

Increase of peripheral blood CD4 lymphocyte counts is a key goal of combined antiretroviral therapy (cART); most, but not all, recipients respond adequately and promptly. A small number of studies have examined specific genetic factors associated with the extent of CD4 recovery. We report a genome-wide examination of factors that predict CD4 recovery in HIV-infected women. We identified women in in a cohort study who were on cART with viral load below 400 copies, and drew racially and ethnically matched samples of those with good CD4 response over 2 years or poor response. We analyzed the exomes of those women employing next generation sequencing for genes associated with CD4 recovery after controlling for non-genetic factors identified through forward stepwise selection as important. We studied 48 women with good CD4 recovery and 42 with poor CD4 recovery during virologically-suppressive cART. Stepwise logistic regression selected only age as a statistically significant (p<0.05) non-genetic predictor of response type (each additional year of age reduced the odds of good recovery by 11% (OR = 0.89, CI = 0.84–0.96, p = 0.0009). After adjustment for age and genomic estimates of race and ethnicity, 41 genes harbored variations associated with CD4 recovery group (p≤0.001); 5 of these have been previously reported to be associated with HIV infection, 4 genes would likely influence CD4 homeostasis, and 13 genes either had known functions or were members of product families that had functions for which interactions with HIV or effects on lymphocyte homeostasis were biologically plausible. Greater age was the strongest acquired factor that predicted poor CD4 cell recovery. Sequence variations spanning 41 genes were independently predictive of CD4 recovery. Many of these genes have functions that impact the cell cycle, apoptosis, lymphocyte migration, or have known interactions with HIV. These findings may help inform new hypotheses related to responses to HIV therapy and CD4 lymphocyte homeostasis.

Role of the zinc finger and SCAN domain-containing transcription factors in cancer

Transcription factors are key determinants of gene expression that recognize and bind to short DNA sequence motifs, thereby regulating many biological processes including differentiation, development, and metabolism. Transcription factors are increasingly recognized for their roles in cancer progression. Here, we describe a subfamily of zinc finger transcription factors named zinc finger and SCAN domain containing (ZSCAN) transcription factors. In this review, we summarize the identified members of the ZSCAN family of transcription factors and their roles in cancer progression. Due to the complex regulation mechanisms, ZSCAN transcription factors may show promotive or prohibitive efforts in angiogenesis, cell apoptosis, cell differentiation, cell migration and invasion, cell proliferation, stem cell properties, and chemotherapy sensitivity. The upstream regulation mechanisms of their varied expression levels may include gene mutation, DNA methylation, alternative splicing, and miRNA regulation. What's more, to clarify their diverse functions, we summarize the modulation mechanisms of their activity in downstream genes transcription, including protein-protein interactions mediated by their SCAN box, recruitment of co-regulating molecules and post-translational modifications. A better understanding of the widespread regulatory mode of these transcription factors will provide further insight into the mechanism of transcriptional regulation and suggest novel therapeutic strategies against tumor progression.

DeepHistone: a deep learning approach to predicting histone modifications

MOTIVATION

Quantitative detection of histone modifications has emerged in the recent years as a major means for understanding such biological processes as chromosome packaging, transcriptional activation, and DNA damage. However, high-throughput experimental techniques such as ChIP-seq are usually expensive and time-consuming, prohibiting the establishment of a histone modification landscape for hundreds of cell types across dozens of histone markers. These disadvantages have been appealing for computational methods to complement experimental approaches towards large-scale analysis of histone modifications.

RESULTS

We proposed a deep learning framework to integrate sequence information and chromatin accessibility data for the accurate prediction of modification sites specific to different histone markers. Our method, named DeepHistone, outperformed several baseline methods in a series of comprehensive validation experiments, not only within an epigenome but also across epigenomes. Besides, sequence signatures automatically extracted by our method was consistent with known transcription factor binding sites, thereby giving insights into regulatory signatures of histone modifications. As an application, our method was shown to be able to distinguish functional single nucleotide polymorphisms from their nearby genetic variants, thereby having the potential to be used for exploring functional implications of putative disease-associated genetic variants.

CONCLUSIONS

DeepHistone demonstrated the possibility of using a deep learning framework to integrate DNA sequence and experimental data for predicting epigenomic signals. With the state-of-the-art performance, DeepHistone was expected to shed light on a variety of epigenomic studies. DeepHistone is freely available in https://github.com/QijinYin/DeepHistone .

A Time-lapse, Label-free, Quantitative Phase Imaging Study of Dormant and Active Human Cancer Cells

The acquisition of the angiogenic phenotype is an essential component of the escape from tumor dormancy. Although several classic in vitro assays (e.g., proliferation, migration, and others) and in vivo models have been developed to investigate and characterize angiogenic and non-angiogenic cell phenotypes, these methods are time and labor intensive, and often require expensive reagents and instruments, as well as significant expertise. In a recent study, we used a novel quantitative phase imaging (QPI) technique to conduct time-lapse and labeling-free characterizations of angiogenic and non-angiogenic human osteosarcoma KHOS cells. A panel of cellular parameters, including cell morphology, proliferation, and motility, were quantitatively measured and analyzed using QPI. This novel and quantitative approach provides the opportunity to continuously and non-invasively study relevant cellular processes, behaviors, and characteristics of cancer cells and other cell types in a simple and integrated manner. This report describes our experimental protocol, including cell preparation, QPI acquisition, and data analysis.

Characterization of dormant and active human cancer cells by quantitative phase imaging

The switch of tumor cells from a dormant, non-angiogenic phenotype to an active, angiogenic phenotype is a critical step in early cancer progression. To date, relatively little is known about the cellular behaviors of angiogenic and non-angiogenic tumor cell phenotypes. In this study, holographic imaging cytometry, a quantitative phase imaging (QPI) technique was used to continuously and non-invasively analyze, quantify, and compare a panel of fundamental cellular behaviors of angiogenic and non-angiogenic human osteosarcoma cells (KHOS) in a simple and economical way. Results revealed that angiogenic KHOS cells (KHOS-A) have significantly higher cell motility speeds than their non-angiogenic counterpart (KHOS-N) while no difference in their cell proliferation rates and cell cycle lengths were observed. KHOS-A cells were also found to have significantly smaller cell areas and greater cell optical thicknesses when compared with the non-angiogenic KHOS-N cells. No difference in average cell volumes was observed. These studies demonstrate that the morphology and behavior of angiogenic and non-angiogenic cells can be continuously, efficiently, and non-invasively monitored using a simple, quantitative, and economical system that does not require tedious and time-consuming assays to provide useful information about tumor dormancy. © 2017 International Society for Advancement of Cytometry.

Zinc and metalloproteinases 2 and 9: What is their relation with breast cancer?

Summary Zinc is the catalytic component of proteins that regulate responses to DNA damage, intracellular signaling enzymes, and matrix metalloproteinases, which are important proteins in carcinogenesis. The objective of this review is to bring current information on the participation of zinc and matrix metalloproteinases types 2 and 9 in mechanisms involved in the pathogenesis of breast cancer. We conducted a literature review, in consultation with the PubMed, Lilacs, and Scielo databases. The zinc and cysteine residues are structural elements shared by all members of the family of matrix metalloproteinases, and these proteins appear to be involved in the propagation of various types of neoplasms, including breast cancer. Moreover, transported zinc is likely to be used for the metalation of the catalytic domain of the newly synthesized metalloproteinases before the latter are secreted. Accordingly, increase in zinc concentrations in cellular compartments and the reduction of this trace element in the blood of patients with breast cancer appear to alter the activity of metalloproteinases 2 and 9, contributing to the occurrence of malignancy. Thus, it is necessary to carry out further studies with a view to clarify the role of zinc and metalloproteinases 2 and 9 in the pathogenesis of breast cancer.

MiR-940 Inhibited Cell Growth and Migration in Triple-Negative Breast Cancer

BACKGROUND Breast cancer is the main type of cancer in women, and triple-negative breast cancer (TNBC) is a unique subtype of breast cancer. The expression of miR-940 has been shown to play an important role in various cancers; however, the role of miR-940 in TNBC remains unknown. MATERIAL AND METHODS The expression of miR-940 in TNBC tissues or cells were tested by qRT-PCR; the expression of miR-940 in cells were overexpressed by miR-940 mimics, and suppressed by anti-miR-940. Bioinformatics algorithms from TargetScanHuman were used to predict the target genes of miR-940. The interaction between miR-940 and ZNF24 was confirmed by dual luciferase assays. The protein level was assayed by Western blot. RESULTS TNBC tissues and cells showed lower miR-940 levels. CONCLUSIONS MiR-940 inhibited cellular proliferation and migration in TNBC.

Zinc finger protein 191 inhibits hepatocellular carcinoma metastasis through discs large 1-mediated yes-associated protein inactivation

Interplay between cell polarity module Scribble-Lethal Giant Larvae-Discs Large 1 (DLG1) and Yes-associated protein (YAP) appears critical in tumor metastasis. We identified zinc finger protein 191 (ZNF191) as a metastasis suppressor acting through DLG-YAP crosstalk in hepatocellular carcinoma (HCC). Overexpression of ZNF191 in HCC cells impaired cell motility, while ZNF191 depletion promoted cell migration in vitro and metastasis in vivo through triggering YAP signaling. Chromatin immunoprecipitation-sequencing revealed that ZNF191 specifically bound to the promoter of DLG1, a cell polarity maintainer and a negative regulator of YAP. The binding sequence of ZNF191 at the DLG1 promoter is a seven-repeat of TCAT motif. Double-knockdown experiments inferred that DLG1 was not only the mediator of the function of ZNF191 to suppress migration but also a link between ZNF191 and YAP signaling. Decreased expression of ZNF191 in human metastatic HCC specimens correlated positively with DLG1 levels but inversely with YAP activation. Our findings illustrate a YAP-targeting, antimetastasis function of ZNF191, thereby representing a possible prognostic marker and a potential target for metastasis therapy.

CONCLUSION

ZNF191 directly binds to the DLG1 promoter at a typical TCAT repeating motif and activates the expression of DLG1; through up-regulating DLG1, ZNF191 inhibits cell migration and YAP activation in HCC cells and eventually inhibits metastasis. (Hepatology 2016;64:1148-1162).

Novel endogenous angiogenesis inhibitors and their therapeutic potential

Angiogenesis, the formation of new blood vessels from the pre-existing vasculature is essential for embryonic development and tissue homeostasis. It also plays critical roles in diseases such as cancer and retinopathy. A delicate balance between pro- and anti-angiogenic factors ensures normal physiological homeostasis. Endogenous angiogenesis inhibitors are proteins or protein fragments that are formed in the body and have the ability to limit angiogenesis. Many endogenous angiogenesis inhibitors have been discovered, and the list continues to grow. Endogenous protein/peptide inhibitors are relatively less toxic, better tolerated and have a lower risk of drug resistance, which makes them attractive as drug candidates. In this review, we highlight ten novel endogenous protein angiogenesis inhibitors discovered within the last five years, including ISM1, FKBPL, CHIP, ARHGAP18, MMRN2, SOCS3, TAp73, ZNF24, GPR56 and JWA. Although some of these proteins have been well characterized for other biological functions, we focus on their new and specific roles in angiogenesis inhibition and discuss their potential for therapeutic application.