Promoter methylation and downregulated expression of the TBX15 gene in ovarian carcinoma

DNA methylation profile of inflammatory breast cancer and its impact on prognosis and outcome

BACKGROUND

Inflammatory breast cancer (IBC) is a rare disease characterized by rapid progression, early metastasis, and a high mortality rate.

METHODS

Genome-wide DNA methylation analysis (EPIC BeadChip platform, Illumina) and somatic gene variants (105 cancer-related genes) were performed in 24 IBCs selected from a cohort of 140 cases.

RESULTS

We identified 46,908 DMPs (differentially methylated positions) (66% hypomethylated); CpG islands were predominantly hypermethylated (39.9%). Unsupervised clustering analysis revealed three clusters of DMPs characterized by an enrichment of specific gene mutations and hormone receptor status. The comparison among DNA methylation findings and external datasets (TCGA-BRCA stages III-IV) resulted in 385 shared DMPs mapped in 333 genes (264 hypermethylated). 151 DMPs were associated with 110 genes previously detected as differentially expressed in IBC (GSE45581), and 68 DMPs were negatively correlated with gene expression. We also identified 4369 DMRs (differentially methylated regions) mapped on known genes (2392 hypomethylated). BCAT1, CXCL12, and TBX15 loci were selected and evaluated by bisulfite pyrosequencing in 31 IBC samples. BCAT1 and TBX15 had higher methylation levels in triple-negative compared to non-triple-negative, while CXCL12 had lower methylation levels in triple-negative than non-triple-negative IBC cases. TBX15 methylation level was associated with obesity.

CONCLUSIONS

Our findings revealed a heterogeneous DNA methylation profile with potentially functional DMPs and DMRs. The DNA methylation data provided valuable insights for prognostic stratification and therapy selection to improve patient outcomes.

An Atlas of Promoter Chromatin Modifications and HiChIP Regulatory Interactions in Human Subcutaneous Adipose-Derived Stem Cells

The genome of human adipose-derived stem cells (ADSCs) from abdominal and gluteofemoral adipose tissue depots are maintained in depot-specific stable epigenetic conformations that influence cell-autonomous gene expression patterns and drive unique depot-specific functions. The traditional approach to explore tissue-specific transcriptional regulation has been to correlate differential gene expression to the nearest-neighbor linear-distance regulatory region defined by associated chromatin features including open chromatin status, histone modifications, and DNA methylation. This has provided important information; nonetheless, the approach is limited because of the known organization of eukaryotic chromatin into a topologically constrained three-dimensional network. This network positions distal regulatory elements in spatial proximity with gene promoters which are not predictable based on linear genomic distance. In this work, we capture long-range chromatin interactions using HiChIP to identify remote genomic regions that influence the differential regulation of depot-specific genes in ADSCs isolated from different adipose depots. By integrating these data with RNA-seq results and histone modifications identified by ChIP-seq, we uncovered distal regulatory elements that influence depot-specific gene expression in ADSCs. Interestingly, a subset of the HiChIP-defined chromatin loops also provide previously unknown connections between waist-to-hip ratio GWAS variants with genes that are known to significantly influence ADSC differentiation and adipocyte function.

The overexpression and clinical significance of TBX15 in human gliomas

T-box transcription factor 15 (TBX15) is upregulated in a variety of tumors and has been reported to promote uncontrolled proliferation of tumor cells and induce tumor cells to avoid apoptosis, thus accelerating the malignant transformation of malignant tumors. However, the prognostic value of TBX15 in glioma and its relationship with immune infiltration remain unknown. In this study, we intended to explore the prognostic value of TBX15 and its link to glioma immune infiltration and examine TBX15 expression in pan-cancer using RNAseq data in TPM format from TCGA and GTEx. TBX15 mRNA and protein expressions in glioma cells and adjacent normal tissue were detected and compared by RT-qPCR and Western blot. The effect of TBX15 on survival was assessed by Kaplan-Meier Method. The correlation between TBX15 upregulation and the clinicopathological characteristics of glioma patients was assessed by using TCGA databases, and the relationship between TBX15 and other genes in glioma was evaluated by using TCGA data. The top 300 genes most significantly associated with TBX15 were selected to establish a PPI network through the STRING database. The relationship between TBX15 mRNA expression and immune cell infiltration was explored by using ssGSEA and the TIMER Database. It was found that TBX15 mRNA expression in glioma tissues was significantly higher than that in the adjacent normal tissues, and this difference was most obvious in high-grade gliomas. TBX15 expression was increased in human gliomas and associated with worse clinicopathological characteristics and poorer survival prognosis in glioma patients. In addition, elevated TBX15 expression was linked to a collection of genes involved in immunosuppression. In conclusion, TBX15 played an important role in immune cell infiltration in glioma and may prove to be a predictor of the prognosis in glioma patients.

Sulforaphane Targets the TBX15/KIF2C Pathway to Repress Glycolysis and Cell Proliferation in Gastric Carcinoma Cells

The effects of sulforaphane on glycolysis and proliferation of SGC7901 and BGC823 gastric carcinoma cell lines were analyzed, and the potential mediating role of the TBX15/KIF2C axis was explored. SGC7901 and BGC823 cells stably over- or underexpressing TBX15 were exposed to sulforaphane, and cell viability was assessed together with the expression of TBX15, KIF2C, and proteins involved in glycolysis, glucose uptake, and lactate production. Overexpressing TBX15 in SGC7901 and BGC823 cells significantly reduced glucose uptake, lactate production, cell viability, expression of KIF2C, and pyruvate kinase M2-mediated (PKM2) glycolysis. These effects were recapitulated by treatment with sulforaphane. The anti-tumor effects of sulforaphane were antagonized by down-regulation of TBX15, up-regulation of KIF2C or addition of a PKM2 agonist. Sulforaphane can reduce cell proliferation and PKM2-mediated glycolysis in gastric carcinoma cells, apparently by activating the TBX15/KIF2C pathway.

Transcriptome profiling of lncRNA and co-expression network in the vaginal epithelial tissue of women with lubrication disorders

Background

Vaginal lubrication is a crucial physiological response that occurs at the beginning of sexual arousal. However, research on lubrication disorders (LD) is still in its infancy, and the role of long non-coding RNAs (lncRNAs) in LD remains unclear. This study aimed to explore the function of lncRNAs in the pathogenesis of vaginal LD.

Methods

The expression profiles of LD and normal control (NC) lncRNAs were examined using next-generation sequencing (NGS), and eight selected differentially expressed lncRNAs were verified by quantitative real-time PCR. We conducted GO annotation and KEGG pathway enrichment analyses to determine the principal functions of significantly deregulated genes. LncRNA-mRNA co-expression and protein-protein interaction (PPI) networks were constructed and the lncRNA transcription factors (TFs) were predicted.

Results

From the results, we identified 181,631 lncRNAs and 145,224 mRNAs in vaginal epithelial tissue. Subsequently, our preliminary judgment revealed a total of 499 up-regulated and 337 down-regulated lncRNAs in LD. The top three enriched GO items of the dysregulated lncRNAs included the following significant terms: “contractile fiber part,” “actin filament-based process,” and “contractile fiber”. The most enriched pathways were “cell-extracellular matrix interactions,” “muscle contraction,” “cell-cell communication,” and “cGMP-PKG signaling pathway”. Our results also showed that the lncRNA-mRNA co-expression network was a powerful platform for predicting lncRNA functions. We determined the three hub genes, ADCY5, CXCL12, and NMU, using PPI network construction and analysis. A total of 231 TFs were predicted with RHOXF1, SNAI2, ZNF354C and TBX15 were suspected to be involved in the mechanism of LD.

Conclusion

In this study, we constructed the lncRNA-mRNA co-expression network, predicted the lncRNA TFs, and comprehensively analyzed lncRNA expression profiles in LD, providing a basis for future studies on LD clinical biomarkers and therapeutic targets. Further research is also needed to fully determine lncRNA’s role in LD development.

TBX15/miR-152/KIF2C pathway regulates breast cancer doxorubicin resistance via promoting PKM2 ubiquitination

Background

Chemoresistance is a critical risk problem for breast cancer treatment. However, mechanisms by which chemoresistance arises remains to be elucidated. The expression of T-box transcription factor 15 (TBX-15) was found downregulated in some cancer tissues. However, role and mechanism of TBX15 in breast cancer chemoresistance is unknown. Here we aimed to identify the effects and mechanisms of TBX15 in doxorubicin resistance in breast cancer.

Methods

As measures of Drug sensitivity analysis, MTT and IC50 assays were used in DOX-resistant breast cancer cells. ECAR and OCR assays were used to analyze the glycolysis level, while Immunoblotting and Immunofluorescence assays were used to analyze the autophagy levels in vitro. By using online prediction software, luciferase reporter assays, co-Immunoprecipitation, Western blotting analysis and experimental animals models, we further elucidated the mechanisms.

Results

We found TBX15 expression levels were decreased in Doxorubicin (DOX)-resistant breast cancer cells. Overexpression of TBX15 reversed the DOX resistance by inducing microRNA-152 (miR-152) expression. We found that KIF2C levels were highly expressed in DOX-resistant breast cancer tissues and cells, and KIF2C was a potential target of miR-152. TBX15 and miR-152 overexpression suppressed autophagy and glycolysis in breast cancer cells, while KIF2C overexpression reversed the process. Overexpression of KIF2C increased DOX resistance in cancer cells. Furthermore, KIF2C directly binds with PKM2 for inducing the DOX resistance. KIF2C can prevent the ubiquitination of PKM2 and increase its protein stability. In addition, we further identified that Domain-2 of KIF2C played a major role in the binding with PKM2 and preventing PKM2 ubiquitination, which enhanced DOX resistance by promoting autophagy and glycolysis.

Conclusions

Our data identify a new mechanism by which TBX15 abolishes DOX chemoresistance in breast cancer, and suggest that TBX15/miR-152/KIF2C axis is a novel signaling pathway for mediating DOX resistance in breast cancer through regulating PKM2 ubiquitination and decreasing PKM2 stability. This finding suggests new therapeutic target and/or novel strategy development for cancer treatment to overcome drug resistance in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-021-02235-w.

TBX15 rs98422, DNM3 rs1011731, RAD51B rs8017304, and rs2588809 Gene Polymorphisms and Associations With Pituitary Adenoma

BACKGROUND

Pituitary adenoma (PA) is a benign tumor of parenchymal cells in the adenohypophysis, and it's development is strongly associated with genetic factors.This study aim was to find whether TBX15 rs98422, DNM3 rs1011731, RAD51B rs8017304, and rs2588809 single nucleotide polymorphisms can be associated with pituitary adenoma. While the TBX15 gene belongs to the T-box family of genes and is a transcription factor involved in many developmental processes, the DNM3 encodes a protein that is a member of the dynamin family with mechanochemical properties involved in actin-membrane processes, predominantly in membrane budding, and the RAD51B gene plays a significant role in homologous recombination in DNA repair for genome stability.

MATERIALS AND METHODS

The study enrolled 113 patients with pituitary adenoma and 283 healthy control subjects. DNA samples were extracted and purified from peripheral blood leukocytes. Genotyping was carried out using real-time polymerase chain reaction. The results were assessed using binomial logistic regression.

RESULTS

Our study revealed that RAD51B rs2588809 TT genotype could be associated with PA development in the co-dominant (OR=6.833; 95% CI=2.557-18.262; p<0.001) and recessive (OR=7.066; 95% CI=2.667-18.722; p<0.001) models. The same results were observed in females but not in males and PA without recurrence, while in PA with recurrence, no statistically significant results were obtained.

CONCLUSION

RAD51B rs2588809 TT genotype may increase the odds of PA development in women; it may also be associated with non-recurrent PA development.

DNA methylation association with stage progression of head and neck squamous cell carcinoma

Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide, which accounts for approximately 6% of all cases and is responsible for an estimated 2% of all cancer deaths. Despite progress in the treatment of squamous cell carcinomas, survival rates remain low. It is a fact that epigenetic modifications have numerous associations with biological processes and complex diseases such as cancer. Hence, a more systematic approach is needed to provide potential screening targets and have an effective therapy method. This study developed a workflow to analyze HM450 methylation arrays with mRNA expression profiles that identified novel signatures of epigenetic regulators for tumor progression. We identified differentially expressed genes and differentially methylated regions and the correlation between associated genes to identify epigenetic modifications underlying regulation roles. We have taken the differentiation direction of expressions into account during the integration of gene expression and DNA methylation modification to detect epigenetic regulators of core genes of tumor-stage progression. Enrichment analysis of selected key genes provides better insight into their functionality. Thus, we have investigated gene copy number alteration and mutations to filter differentially expressed genes, including some members of the fibroblast growth factor family and cyclin-dependent kinase inhibitor family with other potential known regulators. Our analysis has revealed the list of 61 commercial methylation probes positively correlated with 31 differentially expressed genes, which can be associated with HNSC metastasis stages. Most of these genes have already reported potential epigenetic regulators, and their role in cancer progression was studied. We suggest these selected probes of DNA methylation as potential targets of the epigenetic regulators in revealed genes that have displayed significant genetic and epigenetic modification behavior during cancer stage progression and tumor metastasis.

Reduction of T-Box 15 gene expression in tumor tissue is a prognostic biomarker for patients with hepatocellular carcinoma

Genome-wide analysis is widely applied to detect molecular alterations during oncogenesis and tumor progression. We analyzed DNA methylation profiles of hepatocellular carcinoma (HCC), and investigated the clinical role of most heypermethylated of tumor, encodes T-box 15 (TBX15), which was originally involved in mesodermal differentiation. We conducted a genome-wide analysis of DNA methylation of tumor and non-tumor tissue of 15 patients with HCC, and revealed TBX15 was the most hypermethylated gene of tumor (Beta-value in tumor tissue = 0.52 compared with non-tumor tissue). Another validation set, which comprised 58 HCC with radical resection, was analyzed to investigate the relationships between tumor phenotype and TBX15 mRNA expression. TBX15 mRNA levels in tumor tissues were significantly lower compared with those of nontumor tissues (p < 0.0001). When we assigned a cutoff value = 0.5-fold, the overall survival 5-year survival rates of the low-expression group (n = 17) were significantly shorter compared with those of the high-expression group (n = 41) (43.3% vs. 86.2%, p = 0.001). Multivariate analysis identified low TBX15 expression as an independent prognostic factor for overall and disease-free survival. Therefore, genome-wide DNA methylation profiling indicates that hypermethylation and reduced expression of TBX15 in tumor tissue represents a potential biomarker for predicting poor survival of patients with HCC.

TERT promoter methylation and protein expression as predictive biomarkers for recurrence risk in patients with serous borderline ovarian tumours

Epithelial ovarian neoplasms can be divided into three distinct clinicopathological groups: benign, malignant and borderline tumours. Borderline tumours are less aggressive than epithelial carcinomas, with an indolent clinical course and delayed recurrence. However, a subset of these cases can progress to malignancy and relapse, and death from recurrent disease can occasionally occur. Telomerase activation is a critical element in cellular immortalisation and cancer. The enzyme telomerase comprises a catalytic subunit (TERT) expressed in various types of cancers and regulated by promoter methylation mainly in epithelial tumours. The aim of this study was to investigate the promoter methylation status and the expression of TERT in 50 serous borderline tumours (SBTs) and their correlation with clinicopathological features and outcome. TERT methylation was analysed by bisulfite pyrosequencing and TERT expression by immunohistochemistry. Methylation of TERT promoter was only observed in four SBTs. A good correlation with immunostochemistry was found: nuclear positivity for TERT expression was observed in the methylated cases, whereas no expression was detected in unmethylated tumours. One of these patients had a recurrence after 7 years and another patient died from the disease. SBTs with hypomethylated tumours and absence of TERT expression showed a good clinical behaviour. Our study highlights the low presence of TERT methylation in SBTs, confirming that these tumours have a different biology than serous carcinomas. Furthermore, the concordance between TERT promoter methylation and TERT expression and their association with clinical outcomes leads to consider TERT alteration as a potential predictive biomarker for recurrence risk identifying patients who should undergo a careful and prolonged follow-up.

Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives

Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.

A Hybrid Ensemble Approach for Identifying Robust Differentially Methylated Loci in Pan-Cancers

DNA methylation is a widely investigated epigenetic mark that plays a vital role in tumorigenesis. Advancements in high-throughput assays, such as the Infinium 450K platform, provide genome-scale DNA methylation landscapes in single-CpG locus resolution, and the identification of differentially methylated loci has become an insightful approach to deepen our understanding of cancers. However, the situation with extremely unbalanced numbers of samples and loci (approximately 1:1,000) makes it rather difficult to explore differential methylation between the sick and the normal. In this article, a hybrid approach based on ensemble feature selection for identifying differentially methylated loci (HyDML) was proposed by incorporating instance perturbation and multiple function models. Experiments on data from The Cancer Genome Atlas showed that HyDML not only achieved effective DML identification, but also outperformed the single-feature selection approach in terms of classification performance and the robustness of feature selection. The intensive analysis of the DML indicated that different types of cancers have mutual patterns, and the stable DML sharing in pan-cancers is of the great potential to be biomarkers, which may strengthen the confidence of domain experts to implement biological validations.

Involvement of epigenetic modification of TERT promoter in response to all-trans retinoic acid in ovarian cancer cell lines

BACKGROUND

All-trans retinoic acid (ATRA) is currently being used to treat hematological malignancies, given the ability to inhibit cell proliferation. This effect seems to be related to epigenetic changes of the TERT (Telomerase Reverse Transcriptase) promoter. When hypomethylated, ATRA-inducible TERT repressors can bind the promoter, repressing transcription of TERT, the rate-limiting component of telomerase. Ovarian carcinomas are heterogeneous tumors characterized by several aberrantly methylated genes among which is TERT. We recently found a hypomethylation of TERT promoter in about one third of serous carcinoma, the most lethal histotype. Our aim was to investigate the potential role of ATRA as an anticancer drug in a sub-group of ovarian carcinoma where the TERT promoter was hypomethylated.

METHODS

The potential antiproliferative and cytotoxic effect of ATRA was investigated in seven serous ovarian carcinoma and one teratocarcinoma cell lines and the results were compared to the methylation status of their TERT promoter.

RESULTS

The serous ovarian carcinoma cell line OVCAR3, harboring a hypomethylated TERT promoter, was the best and fastest responder. PA1 and SKOV3, two cell lines with an intermediate methylated promoter, revealed a weaker and delayed response. On the contrary, the other 5 cell lines with a highly methylated promoter did not respond to ATRA, indicative of ATRA-resistant cells.

CONCLUSIONS

Our results demonstrate an inverse correlation between the methylation level of TERT promoter and ATRA efficacy in ovarian carcinoma cell lines. Although these results are preliminary, ATRA treatment could become a new powerful, personalized therapy in serous ovarian carcinoma patients, but only in those with tumors harboring a hypomethylated TERT promoter.

Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data

Human tumors undergo massive changes in DNA methylation. Recent studies showed that site-specific methylation of CpG sites is determined by the DNA sequence context surrounding the CpG site, which alludes to a possible mechanism for site-specific aberrant DNA methylation in cancer through DNA-binding proteins. In this paper, DNA methylation data and RNA-Seq data of breast tumors and normal tissues in the database of The Cancer Genome Atlas (TCGA) were integrated with information of DNA motifs in seven databases to find DNA-binding proteins and their binding motifs that were involved in aberrant DNA methylation in breast cancer. A total of 42,850 differentially methylated regions (DMRs) that include 77,298 CpG sites were detected in breast cancer. One hundred eight DNA motifs were found to be enriched in DMRs, and 109 genes encoding proteins binding to these motifs were determined. Based on these motifs and genes, 63 methylation modulator genes were identified to regulate differentially methylated CpG sites in breast cancer. A network of these 63 modulator genes and 645 transcription factors was constructed, and 20 network modules were determined. A number of pathways and gene sets related to breast cancer were found to be enriched in these network modules. The 63 methylation modulator genes identified may play an important role in aberrant methylation of CpG sites in breast cancer. They may help to understand site-specific dysregulation of DNA methylation and provide epigenetic markers for breast cancer.

Distinct DNA Methylation Profiles in Ovarian Tumors: Opportunities for Novel Biomarkers

Aberrant methylation of multiple promoter CpG islands could be related to the biology of ovarian tumors and its determination could help to improve treatment strategies. DNA methylation profiling was performed using the Methylation Ligation-dependent Macroarray (MLM), an array-based analysis. Promoter regions of 41 genes were analyzed in 102 ovarian tumors and 17 normal ovarian samples. An average of 29% of hypermethylated promoter genes was observed in normal ovarian tissues. This percentage increased slightly in serous, endometrioid, and mucinous carcinomas (32%, 34%, and 45%, respectively), but decreased in germ cell tumors (20%). Ovarian tumors had methylation profiles that were more heterogeneous than other epithelial cancers. Unsupervised hierarchical clustering identified four groups that are very close to the histological subtypes of ovarian tumors. Aberrant methylation of three genes (BRCA1, MGMT, and MLH1), playing important roles in the different DNA repair mechanisms, were dependent on the tumor subtype and represent powerful biomarkers for precision therapy. Furthermore, a promising relationship between hypermethylation of MGMT, OSMR, ESR1, and FOXL2 and overall survival was observed. Our study of DNA methylation profiling indicates that the different histotypes of ovarian cancer should be treated as separate diseases both clinically and in research for the development of targeted therapies.

EGFL7 and RASSF1 promoter hypermethylation in epithelial ovarian cancer

DNA methylation is one of the epigenetic mechanisms associated with gene expression and plays a key role as in activation and deactivation of oncogenes and tumor suppressor genes, respectively. This study employed DNA methylation array to identify methylated genes which are highly correlated with various phenotypes of epithelial ovarian cancer (EOC) in Thai patients and to quantify promoter CpG-island methylation of candidate genes. Tissues from patients with serous and non-serous EOC showed significantly higher promoter methylation of EGFL7 and RASSF1 compared to benign cases. These results indicate the potential of investigating promoter CpG-island methylation of cancer-associated genes as biomarkers of disease progression and even possibly of early detection.