Mediator subunits: gene expression pattern, a novel transcript identification and nuclear localization in human endothelial progenitor cells

DNA hypermethylation of MED1 and MED23 as early diagnostic biomarkers for unsolved issues in atrial fibrillation

BACKGROUND

Atrial fibrillation (AF) is the most common cardiac arrhythmia worldwide. Much effort was spent to identify biomarkers useful to stratify AF patients. Mediator complex (MED) is an ancestral regulator of transcriptional mechanisms. Here, we investigated the role of methyl DNA-MED regulatory networks in AF patients.

METHODS

We analyzed the methylome of circulating CD4+T lymphocytes isolated from patients at the time of first AF diagnosis vs. healthy subjects for identifying epigenetic dysregulation of MED-related genes.

RESULTS

We identified 10 differentially methylated regions (DMRs) which were hypermethylated and annotated to 10 genes encoding for MED complex subunits in CD4+T lymphocytes of AF patients vs. healthy subjects (HS). Network-oriented analysis prioritized 6 subunits including MED1, MED13, MED15, MED17, MED23 and MED30, which enriched significantly lipid metabolism pathways and cardiopathy onset. ROC curve analysis showed that elevated methylation levels of MED1 and MED23 discriminated AF patients with an area under the curve (AUC) of 92.7 % (p < 0.001) and an AUC = 100 % (p < 0.001), respectively. Methylation levels of MED23 correlated with the presence of mitral valve disease (p < 0.05) and NT-proBNP (p < 0.05); moreover, MED23 had a not inferior diagnostic value than circulating levels of NT-proBNP (AUC = 0.923, p < 0.001).

CONCLUSIONS

For the first time, we showed that DNA methylation changes are associated with regulation of MED complex subunits in early diagnosis of AF patients. Clinically, MED1 and MED23 hypermethylation showed a diagnostic value not inferior to circulating levels of NT-proBNP suggesting early diagnostic biomarker pathogenic molecular routes underlying disease onset.

Immune complexome analysis of a rich variety of serum immune complexes identifies disease-characteristic immune complex antigens in systemic sclerosis

Systemic sclerosis (SSc) is an autoimmune disease characterized by vascular endothelial dysfunction and skin fibrosis. Recently, the presence and pathogenic role of immune complexes (ICs) of SSc patients were reported. However, the identities of antigens in these ICs are unknown. Therefore, we examined ICs in the serum of SSc patients to elucidate SSc pathogenesis. In this study, IC concentrations in serum samples from SSc and systemic lupus erythematosus (SLE) patients were measured by C1q enzyme-linked immunosorbent assays; immune complex analysis was used for comprehensive identification and comparison of antigens incorporated into ICs (IC-antigens). The expression patterns of SSc-specific IC-antigens in skin sections were investigated by immunohistochemistry. Compared with SLE patients who developed disease because of IC deposition, SSc patients had a greater number of IC-antigens and a smaller difference in IC concentrations, suggesting that SSc pathogenesis is affected by the proteins present in ICs. In contrast, the IC concentration and number of IC-antigens did not significantly differ according to the clinical phenotype of SSc. We identified 478 IC-antigens in SSc patients, including multiple RNAP II-associated proteins that were targeted by antibodies previously associated with SSc pathogenesis. The most frequently detected RNAP II-associated protein, RNA polymerase II transcription subunit 30 (MED30), was strongly expressed at lesion sites and reportedly regulates endothelial differentiation. Therefore, increased expression of MED30 in lesions may have an antigenic effect, and MED30 function may be impaired or inhibited by IC formation. RNAP II-associated proteins may SSc pathogenesis through mechanisms such as the MED30 pathway.

Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models

Positive Regulatory Domain (PRDM) gene family members commonly express two main molecular variants, the PR-plus isoform usually acting as tumor suppressor and the PR-minus one functioning as oncogene. Accordingly, PRDM2/RIZ encodes for RIZ1 (PR-plus) and RIZ2 (PR-minus). In human cancers, genetic or epigenetic modifications induce RIZ1 silencing with an expression level imbalance in favor of RIZ2 that could be relevant for tumorigenesis. Additionally, in estrogen target cells and tissues, estradiol increases RIZ2 expression level with concurrent increase of cell proliferation and survival. Several attempts to study RIZ2 function in HeLa or MCF-7 cells by its over-expression were unsuccessful. Thus, we over-expressed RIZ2 in HEK-293 cells, which are both RIZ1 and RIZ2 positive but unresponsive to estrogens. The forced RIZ2 expression increased cell viability and growth, prompted the G2-to-M phase transition and organoids formation. Accordingly, microarray analysis revealed that RIZ2 regulates several genes involved in mitosis. Consistently, RIZ silencing in both estrogen-responsive MCF-7 and -unresponsive MDA-MB-231 cells induced a reduction of cell proliferation and an increase of apoptosis rate. Our findings add novel insights on the putative RIZ2 tumor-promoting functions, although additional attempts are warranted to depict the underlying molecular mechanism.

Increasing evidence of pathogenic role of the Mediator (MED) complex in the development of cardiovascular diseases

Cardiovascular diseases (CVDs) are the first cause of death in the World. Mediator (MED) is an evolutionarily conserved protein complex, which mediates distinct protein-protein interactions. Pathogenic events in MED subunit have been associated with human diseases. Novel increasing evidence showed that missense mutations in MED13L gene are associated with transposition of great arteries while MED12, MED13, MED15, and MED30, have been correlated with heart development. Moreover, MED23 and MED25 have been associated with heart malformations in humans. Relevantly, MED1, MED13, MED14, MED15, MED23, MED25, and CDK8, were found modify glucose and/or lipid metabolism. Indeed, MED1, MED15, MED25, and CDK8 interact in the PPAR- and SREBP-mediated signaling pathways. MED1, MED14 and MED23 are involved in adipocyte differentiation, whereas MED23 mediates smooth muscle cell differentiation. MED12, MED19, MED23, and MED30 regulate endothelial differentiation by alternative splicing mechanism. Thus, MEDs have a central role in early pathogenic events involved in CVDs representing novel targets for clinical prevention and therapeutic approaches.

Splicing regulators in endothelial cell differentiation

AIMS

Alternative splicing represents a key mechanism of gene regulation. Despite its role in regulating cell pluripotency and differentiation being well known, the underlining mechanisms are still poorly studied. Here, we investigated the possible involvement of splicing regulators during the different steps of endothelial cell differentiation through expression studies on human circulating progenitors.

METHODS

Total RNAs were extracted from all cells and reverse-transcribed. Semiquantitative and real-time RT-PCR was performed using selective oligonucleotides. Differences between group means were considered significant at P value less than 0.05 and more significant at P value less than 0.01. Protein extracts were incubated with an antibody directed against MED23. Immunoprecipitation of supernatants and pellets was probed with both anti-Muscleblind-like splicing regulator (MBNL)1 and anti-MBNL2 antibodies.

RESULTS

Several clinical trials demonstrated the safety and efficacy of progenitor cells in regenerative therapy of the cardiovascular system. Particularly, we analyzed the expression of genes belonging to muscleblind family members and MED complex subunits, which are known to be involved during differentiation in other models. This study shows that MED23, MBNL1 and MBNL2 were all expressed at high levels only in differentiated cells. Moreover, immunoprecipitation assays indicated that MED23 is able to bind MBNLs in endothelial cells.

CONCLUSION

Our data suggest that MED23, MBNL1 and MBNL2 could regulate alternative splicing events activated during differentiation through a common mechanism. Hence, these observations corroborate previous evidence that splicing regulators may have an essential role in the basic apparatus required for cell pluripotency and reprogramming, allowing identification of novel biomarkers to use for early diagnosis in cardiovascular diseases.

Transcriptome Profiling in Human Diseases: New Advances and Perspectives

In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements) and TCGA (The Cancer Genome Atlas), to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.

Epigenetic-related therapeutic challenges in cardiovascular disease

Progress in human genetic and genomic research has led to the identification of genetic variants associated with specific cardiovascular diseases (CVDs), but the pathogenic mechanisms remain unclear. Recent studies have analyzed the involvement of epigenetic mechanisms such as DNA methylation and histone modifications in the development and progression of CVD. Preliminary work has investigated the correlations between DNA methylation, histone modifications, and RNA-based mechanisms with CVDs including atherosclerosis, heart failure (HF), myocardial infarction (MI), and cardiac hypertrophy. Remarkably, both in utero programming and postnatal hypercholesterolemia may affect the epigenetic signature in the human cardiovascular system, thereby providing novel early epigenetic-related pharmacological insights. Interestingly, some dietary compounds, including polyphenols, cocoa, and folic acid, can modulate DNA methylation status, whereas statins may promote epigenetic-based control in CVD prevention through histone modifications. We review recent findings on the epigenetic control of cardiovascular system and new challenges for therapeutic strategies in CVDs.

RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells

Mediator (MED) complex is a multiprotein playing a key role in the eukaryotic transcription. Alteration of MED function may have enormous pathophysiological consequences and several MED genes have been implicated in human diseases. Here, we have combined computational and experimental approaches to identify and characterize, new transcripts generated by alternative splicing (AS) for all MED genes, through the analysis of our recently published RNA-Sequencing datasets of endothelial progenitor cells (EPCs). This combined strategy allowed us to identify novel transcripts for MED4, MED9, MED11, MED14, MED27 and CDK8 most of them generated by AS. All the newly identified transcripts, except MED11, are predicted to encode novel protein isoforms. The identification of novel MED variants could lead to the finding of other MED complexes with different functions depending on their subunit composition. Finally, the expression profile of all MED genes, together with an extensive gene expression analysis, may be useful to better classify the diverse subsets of cell populations that contribute to neovascularization.

The roles of mediator complex in cardiovascular diseases

Despite recent treatment advances, an increase in cardiovascular diseases (CVD) mortality is expected for the next years. Mediator (MED) complex plays key roles in eukaryotic gene transcription. Currently, while numerous studies have correlated MED alterations with several diseases, like cancer or neurological disorders, fewer studies have investigated MED role in CVD initiation and progression. The first finding of MED involvement in these pathologies was the correlation of missense mutations in MED13L gene with transposition of the great arteries. Nowadays, also MED13 and MED15 have been associated with human congenital heart diseases and others could be added, like MED12 that is involved in early mouse development and heart formation. Interestingly, a missense mutation in MED30 gene causes a progressive cardiomyopathy in homozygous mice suggesting a potential role for this subunit also in human CVDs. Moreover, several subunits like MED1, MED13, MED14, MED15, MED23, MED25 and CDK8 exert important roles in glucose and lipid metabolism. Although these evidences derive from in vitro and animal model studies, they indicate that their deregulation may have a significant role in human CVD-related metabolic disorders. Finally, alternative transcripts of MED12, MED19 and MED30 are differently expressed in circulating endothelial progenitor cells thus suggesting they can play a role in the field of regenerative medicine. Overall, further functional studies exploring MED role in human CVD are warranted. The results could allow identifying novel biomarkers to use in combination with imaging techniques for early diagnosis; otherwise, they could be useful to develop targets for novel therapeutic approaches.

Gene expression profile of the whole Mediator complex in human osteosarcoma and normal osteoblasts

Mediator complex (MED) is an essential multi-subunit component of the transcription apparatus and plays a key role in the transcription regulation of many genes involved in several diseases, including cancer. Recently, numerous MED subunits have been implicated in cancer development and metastasis, and specific alterations in their coding genes have been found to correlate with some malignancies. It is conceivable that a specific MED alteration pattern can characterize each cancer type. However, to date, no study has reported the complete picture of MED subunits in a specific tumor. Thus, the aim of this study was to investigate for the first time the gene expression profile of the whole MED complex in human osteosarcoma (OS). To this purpose, we have examined all the MED subunit genes in three OS cell lines compared to normal osteoblasts by real-time RT-PCR. Interestingly, our findings indicate that the expression of most of the MED genes is altered in OS. Moreover, a very high overexpression of MED20 and MED31 can be observed in all the analyzed OS cells, thus suggesting for the first time a potential role of these subunits in human malignancies. Overall, this study may open the way to other functional studies exploring the role of the whole complex in cancer development and progression. These findings may lead to the identification of novel biomarkers, which can be used also in combination with imaging techniques for early detection, and/or to develop novel targets for innovative therapeutic approaches.

The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility

Classical bovine spongiform encephalopathy is a transmissible prion disease that is fatal to cattle and is a human health risk due to its association with a strain of Creutzfeldt-Jakob disease (vCJD). Mutations to the coding region of the prion gene (PRNP) have been associated with susceptibility to transmissible spongiform encephalopathies in mammals including bovines and humans. Additional loci such as the retinoic acid receptor beta (RARB) and stathmin like 2 (STMN2) have also been associated with disease risk. The objective of this study was to refine previously identified regions associated with BSE susceptibility and to identify positional candidate genes and genetic variation that may be involved with the progression of classical BSE. The samples included 739 samples of either BSE infected animals (522 animals) or non-infected controls (207 animals). These were tested using a custom SNP array designed to narrow previously identified regions of importance in bovine genome. Thirty one single nucleotide polymorphisms were identified at p < 0.05 and a minor allele frequency greater than 5%. The chromosomal regions identified and the positional and functional candidate genes and regulatory elements identified within these regions warrant further research.

Identification of valid reference housekeeping genes for gene expression analysis in tumor neovascularization studies

INTRODUCTION

Real time RT-PCR is a widely used technique to evaluate and confirm gene expression data obtained in different cell systems and experimental conditions. However, there are many conflicting reports about the same gene or sets of gene expression. A common method is to report the interest gene expression relative to an internal control, usually a housekeeping gene (HKG), which should be constant in cells independently of experimental conditions.

MATERIALS AND METHODS

In this study, the expression stability of ten HKGs was considered in parallel in two cell systems (endothelial and osteosarcoma cells): beta actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), TATA box binding protein (TBP), hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Cyclophilin A (PPIA), beta-2-microglobulin (B2M), glucuronidase beta (GUSB), eukaryotic translation elongation factor 1 alpha1 (EEF1A1), transferrin receptor (TFRC), ribosomal protein S18 (RPS18). In order to study the stability of candidate reference genes, data have been also analyzed by several algorithms (geNorm, NormFinder, BestKeeper and delta-Ct method).

RESULTS AND CONCLUSIONS

The overall analysis obtained by the comprehensive ranking showed that RPS18 and PPIA are appropriate internal reference genes for tumor neovascularization studies where it is necessary to analyze both systems at the same time.

Distinct alternative splicing patterns of mediator subunit genes during endothelial progenitor cell differentiation

Mediator (MED) is a fundamental component of the RNA polymerase II-mediated transcription machinery playing a pivotal role in the regulation of eukaryotic mRNA synthesis. Human MED complexes contain at least 30 distinct MED subunits. Our previous study, aimed to analyse MED complex during the pattern of endothelial progenitor cells (EPCs) differentiation, found an alternative transcript of MED30 subunit expressed only in circulating immature progenitor cells. Here, we report two novel transcripts of MED12 and MED19 subunits both generated by alternative splicing and displaying similar expression patterns, thereby indicating their involvement during endothelial cell differentiation.

Different expression of CD146 in human normal and osteosarcoma cell lines

The CD146 cell membrane adhesion molecule is highly expressed on the cell surface of several tumours. The level of its expression has been found to correlate directly with tumour progression and metastatic potential, thus establishing CD146 as an important candidate of tumour growth and metastasis. In order to characterize its expression in human osteosarcoma (OS) cell lines, we have examined the CD146 expression at protein and RNA levels in both normal and tumour osteoblast-like cell lines by several methods. Our results indicate that CD146 protein is expressed at low levels in normal osteoblast cells whereas it is highly expressed in all OS cell lines analysed, (SaOS, MG-63, U-2OS). Moreover, CD146 overexpression was partially reduced in shYY1 cells, where the Yin Yang 1 transcription factor, also found over-expressed in human OS cells, has been silenced.

Maternal-foetal epigenetic interactions in the beginning of cardiovascular damage

Several studies indicate that impaired foetal growth, and in utero exposure to risk factors, especially maternal hypercholesterolaemia, may be relevant for the early onset of cardiovascular damage. The exact molecular mechanisms of such foetal programming are still unclear. Epigenetics may represent one of the possible scientific explanations of the impact of such intrauterine risk factors for the subsequent development of cardiovascular disease (CVD) during adulthood. Translational studies support this hypothesis; however, a direct causality in humans has not been ascertained. This hypothesis could be investigated in primates and in human post-mortem foetal arteries. Importantly, some studies also suggest the transgenerational transmission of epigenetic risk. The recently launched International Human Epigenome Consortium and the NIH Roadmap Epigenomics Mapping Consortium will provide the rationale for a useful clinical scenario for primary prevention and therapy of CVD. Despite the heritable nature of epigenetic modification, the clinically relevant information shows that it could be reversible through therapeutic approaches, including histone deacetylase inhibitors, histone acetyltransferase inhibitors, and commonly used drugs such as statins.

Unraveling framework of the ancestral Mediator complex in human diseases

Mediator (MED) is a fundamental component of the RNA polymerase II-mediated transcription machinery. This multiprotein complex plays a pivotal role in the regulation of eukaryotic mRNA synthesis. The yeast Mediator complex consists of 26 different subunits. Recent studies indicate additional pathogenic roles for Mediator, for example during transcription elongation and non-coding RNA production. Mediator subunits have been emerging also to have pathophysiological roles suggesting MED-dependent therapeutic targets involving in several diseases, such as cancer, cardiovascular disease (CVD), metabolic and neurological disorders.

MED29, a component of the mediator complex, possesses both oncogenic and tumor suppressive characteristics in pancreatic cancer

Mediator complex subunit 29 (MED29) is part of a large multiprotein coactivator complex that mediates regulatory signals from gene-specific activators to general transcription machinery in RNA polymerase II mediated transcription. We previously found that MED29 is amplified and overexpressed in pancreatic cancer and that MED29 silencing leads to decreased cell survival in PANC-1 pancreatic cancer cells with high MED29 expression. Here we further demonstrate decreased migration, invasion and colony formation in PANC-1 cells after MED29 silencing. Unexpectedly, lentiviral-based overexpression of MED29 led to decreased proliferation of NIH/3T3 cells as well as MIAPaCa-2 pancreatic cancer cells with low endogenous expression. More importantly, subcutaneous inoculation of the MED29-transduced pancreatic cancer cells into immuno-compromised mice resulted in dramatic tumor suppression. The mock-control mice developed large tumors, whereas the animals with MED29-xenografts showed both decreased tumor incidence and a major reduction in tumor size. Gene expression analysis in the MED29-transduced pancreatic cancer cells revealed differential expression of genes involved in control of cell cycle and cell division. The observed gene expression changes are expected to modulate the cell cycle in a way that leads to reduced cell growth, explaining the in vivo tumor suppressive phenotype. Taken together, these data implicate MED29 as an important regulator of key cellular functions in pancreatic cancer with both oncogenic and tumor suppressive characteristics. Such a dualistic role appears to be more common than previously thought and is likely to depend on the genetic background of the cancer cells and their surrounding environment.

Transferase activity function and system development process are critical in cattle embryo development

Microarray gene expression experiments often consider specific developmental stages, tissue sources, or reproductive technologies. This focus hinders the understanding of the cattle embryo transcriptome. To address this, four microarray experiments encompassing three developmental stages (7, 25, 280 days), two tissue sources (embryonic or extra-embryonic), and two reproductive technologies (artificial insemination or AI and somatic cell nuclear transfer or NT) were combined using two sets of meta-analyses. The first set of meta-analyses uncovered 434 genes differentially expressed between AI and NT (regardless of stage or source) that were not detected by the individual-experiment analyses. The molecular function of transferase activity was enriched among these genes that included ECE2, SLC22A1, and a gene similar to CAMK2D. Gene POLG2 was over-expressed in AI versus NT 7-day embryos and was under-expressed in AI versus NT 25-day embryos. Gene HAND2 was over-expressed in AI versus NT extra-embryonic samples at 280 days yet under-expressed in AI versus NT embryonic samples at 7 days. The second set of meta-analyses uncovered enrichment of system, organ, and anatomical structure development among the genes differentially expressed between 7- and 25-day embryos from either reproductive technology. Genes PRDX1and SLC16A1 were over-expressed in 7- versus 25-day AI embryos and under-expressed in 7- versus 25-day NT embryos. Changes in stage were associated with high number of differentially expressed genes, followed by technology and source. Genes with transferase activity may hold a clue to the differences in efficiency between reproductive technologies.