Potential regulatory role of epigenetic RNA methylation in cardiovascular diseases

The role and mechanism of epigenetics in anticancer drug-induced cardiotoxicity

Cardiovascular disease is the main factor contributing to the global burden of diseases, and the cardiotoxicity caused by anticancer drugs is an essential component that cannot be ignored. With the development of anticancer drugs, the survival period of cancer patients is prolonged; however, the cardiotoxicity caused by anticancer drugs is becoming increasingly prominent. Currently, cardiovascular disease has emerged as the second leading cause of mortality among long-term cancer survivors. Anticancer drug-induced cardiotoxicity has become a frontier and hot topic. The discovery of epigenetics has given the possibility of environmental changes in gene expression, protein synthesis, and traits. It has been found that epigenetics plays a pivotal role in promoting cardiovascular diseases, such as heart failure, coronary heart disease, and hypertension. In recent years, increasing studies have underscored the crucial roles played by epigenetics in anticancer drug-induced cardiotoxicity. Here, we provide a comprehensive overview of the role and mechanisms of epigenetics in anticancer drug-induced cardiotoxicity.

Mutuality of epigenetic and nanoparticles: two sides of a coin

Nowadays nanoparticles (NPs) due to their multidimensional applications in enormous different fields, has become an exciting research topic. In particular, they could attract a noticeable interest as drug deliver with increased bioavailability, therapeutic efficacy and drug specificity. Epigenetic can be considered as a complex network of molecular mechanism which are engaged in gene expression and have a vital role in regulation of environmental effects on ethology of different disorders like neurological disorders, cancers and cardiovascular diseases. For many of them epigenetic therapy was proposed although its application accompanied with limitations, due to drug toxicity. In this review we evaluate two aspects to epigenetic in the field of NPs: firstly, the role of epigenetic in regulation of nanotoxicity and secondly application of NPs as potential carriers for epidrugs.

A review on the role of RNA methylation in aging-related diseases

Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.

N6-methyladenosine (M6A) in fetal offspring modifies mitochondrial gene expression following gestational nano-TiO2 inhalation exposure

N6-methyladenosine (m6A) is the most prominent epitranscriptomic modification to RNA in eukaryotes, but it's role in adaptive changes within the gestational environment are poorly understood. We propose that gestational exposure to nano titanium dioxide (TiO2) contributes to cardiac m6A methylation in fetal offspring and influences mitochondrial gene expression. 10-week-old pregnant female FVB/NJ wild-type mice underwent 6 nonconsecutive days of whole-body inhalation exposure beginning on gestational day (GD) 5. Mice were exposed to filtered room air or nano-TiO2 with a target aerosol mass concentration of 12 mg/m3. At GD 15 mice were humanely killed and cardiac RNA and mitochondrial proteins extracted. Immunoprecipitation with m6A antibodies was performed followed by sequencing of immunoprecipitant (m6A) and input (mRNA) on the Illumina NextSeq 2000. Protein extraction, preparation, and LC-MS/MS were used for mitochondrial protein quantification. There were no differences in maternal or fetal pup weights, number of pups, or pup heart weights between exposure and control groups. Transcriptomic sequencing revealed 3648 differentially expressed mRNA in nano-TiO2 exposed mice (Padj ≤ 0.05). Transcripts involved in mitochondrial bioenergetics were significantly downregulated (83 of 85 genes). 921 transcripts revealed significant m6A methylation sites (Padj ≤ 0.10). 311 of the 921 mRNA were identified to have both 1) significantly altered expression and 2) differentially methylated sites. Mitochondrial proteomics revealed decreased expression of ATP Synthase subunits in the exposed group (P ≤ 0.05). The lack of m6A modifications to mitochondrial transcripts suggests a mechanism for decreased transcript stability and reduced protein expression due to gestational nano-TiO2 inhalation exposure.

Insulin-like growth factor binding protein 2: a core biomarker of left ventricular dysfunction in dilated cardiomyopathy

BACKGROUND

RNA modifications, especially N6-methyladenosine, N1-methyladenosine and 5-methylcytosine, play an important role in the progression of cardiovascular disease. However, its regulatory function in dilated cardiomyopathy (DCM) remains to be undefined.

METHODS

In the study, key RNA modification regulators (RMRs) were screened by three machine learning models. Subsequently, a risk prediction model for DCM was developed and validated based on these important genes, and the diagnostic efficiency of these genes was assessed. Meanwhile, the relevance of these genes to clinical traits was explored. In both animal models and human subjects, the gene with the strongest connection was confirmed. The expression patterns of important genes were investigated using single-cell analysis.

RESULTS

A total of 4 key RMRs were identified. The risk prediction models were constructed basing on these genes which showed a good accuracy and sensitivity in both the training and test set. Correlation analysis showed that insulin-like growth factor binding protein 2 (IGFBP2) had the highest correlation with left ventricular ejection fraction (LVEF) (R = -0.49, P = 0.00039). Further validation expression level of IGFBP2 indicated that this gene was significantly upregulated in DCM animal models and patients, and correlation analysis validation showed a significant negative correlation between IGFBP2 and LVEF (R = -0.87; P = 6*10-5). Single-cell analysis revealed that this gene was mainly expressed in endothelial cells.

CONCLUSION

In conclusion, IGFBP2 is an important biomarker of left ventricular dysfunction in DCM. Future clinical applications could possibly use it as a possible therapeutic target.

Biological roles of RNA m7G modification and its implications in cancer

M7G modification, known as one of the common post-transcriptional modifications of RNA, is present in many different types of RNAs. With the accurate identification of m7G modifications within RNAs, their functional roles in the regulation of gene expression and different physiological functions have been revealed. In addition, there is growing evidence that m7G modifications are crucial in the emergence of cancer. Here, we review the most recent findings regarding the detection techniques, distribution, biological functions and Regulators of m7G. We also summarize the connections between m7G modifications and cancer development, drug resistance, and tumor microenvironment as well as we discuss the research's future directions and trends.

ALKBH5 inhibitors as a potential treatment strategy in heart failure-inferences from gene expression profiling

Heart Failure (HF) is a complex clinical syndrome in which the heart is unable to provide enough blood flow to meet metabolic needs and lacks efficient venous return. HF is a major risk factor for morbidity and mortality with cardiovascular diseases globally. Despite enormous research, the molecular markers relevant to disease prognosis and management remain not well understood. Here, we analyzed the whole transcriptomes of 18 failing hearts and 15 non-failing hearts (predominantly of Caucasian origin), by applying the standard in silico tools. The analyses revealed novel gene-markers including ALKBH5 of mRNA demethylation and KMT2E of histone modification processes, significantly over-expressed in the HF compared with the non-failing hearts (FDR < 0.05). To validate the over-expression of ALKBH5, we determined the global m6A level in hypoxic H9c2 cells using a dot blot assay. The global m6A level was found markedly lower in the hypoxic H9c2 cells than in the control cells. Additionally, the expression of ALKBH5 in the H9c2 cells was quantified by the qPCR and found to be 1.18 times higher at 12 h (p < 0.05), and 1.67 times higher at 24 h of hypoxia (p < 0.01) compared with the control cells, indicating a likely role of ALKBH5 in the failing cardiac cells. Furthermore, we identified several compounds through the virtual screening of 11,272 drug-like molecules of the ZINC15 database to inhibit the ALKBH5 in a molecular docking process. Collectively, the study revealed novel markers potentially involved in the pathophysiology of HF and suggested plausible therapeutic molecules for the management of the disease.

Identification of m7G regulator-mediated RNA methylation modification patterns and related immune microenvironment regulation characteristics in heart failure

BACKGROUND

N⁷-methylguanosine (m⁷G) modification has been reported to regulate RNA expression in multiple pathophysiological processes. However, little is known about its role and association with immune microenvironment in heart failure (HF).

RESULTS

One hundred twenty-four HF patients and 135 nonfailing donors (NFDs) from six microarray datasets in the gene expression omnibus (GEO) database were included to evaluate the expression profiles of m⁷G regulators. Results revealed that 14 m⁷G regulators were differentially expressed in heart tissues from HF patients and NFDs. Furthermore, a five-gene m⁷G regulator diagnostic signature, NUDT16, NUDT4, CYFIP1, LARP1, and DCP2, which can easily distinguish HF patients and NFDs, was established by cross-combination of three machine learning methods, including best subset regression, regularization techniques, and random forest algorithm. The diagnostic value of five-gene m⁷G regulator signature was further validated in human samples through quantitative reverse-transcription polymerase chain reaction (qRT-PCR). In addition, consensus clustering algorithms were used to categorize HF patients into distinct molecular subtypes. We identified two distinct m⁷G subtypes of HF with unique m⁷G modification pattern, functional enrichment, and immune characteristics. Additionally, two gene subgroups based on m⁷G subtype-related genes were further discovered. Single-sample gene-set enrichment analysis (ssGSEA) was utilized to assess the alterations of immune microenvironment. Finally, utilizing protein-protein interaction network and weighted gene co-expression network analysis (WGCNA), we identified UQCRC1, NDUFB6, and NDUFA13 as m⁷G methylation-associated hub genes with significant clinical relevance to cardiac functions.

CONCLUSIONS

Our study discovered for the first time that m⁷G RNA modification and immune microenvironment are closely correlated in HF development. A five-gene m⁷G regulator diagnostic signature for HF (NUDT16, NUDT4, CYFIP1, LARP1, and DCP2) and three m⁷G methylation-associated hub genes (UQCRC1, NDUFB6, and NDUFA13) were identified, providing new insights into the underlying mechanisms and effective treatments of HF.

Epigenetic Regulation of Macrophage Polarization in Cardiovascular Diseases

Cardiovascular diseases (CVDs) are the leading cause of hospitalization and death worldwide, especially in developing countries. The increased prevalence rate and mortality due to CVDs, despite the development of several approaches for prevention and treatment, are alarming trends in global health. Chronic inflammation and macrophage infiltration are key regulators of the initiation and progression of CVDs. Recent data suggest that epigenetic modifications, such as DNA methylation, posttranslational histone modifications, and RNA modifications, regulate cell development, DNA damage repair, apoptosis, immunity, calcium signaling, and aging in cardiomyocytes; and are involved in macrophage polarization and contribute significantly to cardiac disease development. Cardiac macrophages not only trigger damaging inflammatory responses during atherosclerotic plaque formation, myocardial injury, and heart failure but are also involved in tissue repair, remodeling, and regeneration. In this review, we summarize the key epigenetic modifications that influence macrophage polarization and contribute to the pathophysiology of CVDs, and highlight their potential for the development of advanced epigenetic therapies.

ALKBH1-mediated m1 A demethylation of METTL3 mRNA promotes the metastasis of colorectal cancer by downregulating SMAD7 expression

Colorectal cancer (CRC) is one of the most common malignancies, and the main cause of death from CRC is tumor metastasis. m¹ A RNA modification plays critical role in many biological processes. However, the role of m¹ A modification in CRC remains unclear. Here, we find that the m¹ A demethylase alkB homolog 1, histone H2A dioxygenase (ALKBH1) is overexpressed in CRC and is associated with metastasis and poor prognosis. Upregulation of ALKBH1 expression promotes CRC metastasis in vitro and in vivo. Mechanistically, knockdown of ALKBH1 results in a decrease in methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit (METTL3) expression, probably due to m¹ A modification of METTL3 mRNA, followed by m⁶ A demethylation of SMAD family member 7 (SMAD7) mRNA. In addition, downregulation of SMAD7 establishes an aggressive phenotype. More importantly, the cell migration and invasion defects caused by ALKBH1 depletion or METTL3 depletion are significantly reversed by SMAD7 silencing. Considering these results collectively, we propose that ALKBH1 promotes CRC metastasis by destabilizing SMAD7 through METTL3.

Identification of m7G Methylation-Related miRNA Signature Associated with Survival and Immune Microenvironment Regulation in Uterine Corpus Endometrial Carcinoma

Background. N7-methylguanosine (m7G) has been implicated in the development of cancer. The role of m7G-related miRNAs in the survival prediction of UCEC patients has not been investigated. Current research was the first to construct an m7G-related miRNA model to accurately predict the survival of patients with uterine corpus endometrial carcinoma (UCEC) and to explore immune cell infiltration and immune activity in the tumor microenvironment. Methods. RNA-seq data and clinical information of UCEC patients were derived from The Cancer Genome Atlas (TCGA) database. Using the TargetScan online database, we predicted miRNAs linked to the m7G-related genes and identified miRNAs which were significantly associated with the survival in UCEC patients and constructed a risk scoring model. The TCGA-UCEC cases were scored according to the risk model, and the high- and low-risk groups were divided by the median risk value. Gene enrichment analysis and immune cell infiltration and immune function analysis were performed using “clusterProfiler” and “GSVA” packages in R. Results. The survival prediction model consisted of 9 miRNAs, namely, hsa-miR-1301, hsa-miR-940, hsa-miR-592, hsa-miR-3170, hsa-miR-876, hsa-miR-215, hsa-miR-934, hsa-miR-3920, and hsa-miR-216b. Survival of UCEC patients in the high-risk group was worse than that in the low-risk group ( $p<0.001$ ). The receiver operating characteristic (ROC) curve showed that the model had good predictive performance, and the area under the curve was 0.800, 0.690, and 0.705 for 1-, 3-, and 5-year survival predictions, respectively. There were differences in the degree of immune cell infiltration and immune activity between the low-risk and high-risk groups. The expression levels of the identified differentially expressed genes correlated with the susceptibility to multiple anticancer drugs. Conclusions. The survival prediction model constructed based on 9 m7G-related miRNAs had good predictive performance.

Are South African Wild Foods the Answer to Rising Rates of Cardiovascular Disease?

The rising burden of cardiovascular disease in South Africa gives impetus to managerial changes, particularly to the available foods in the market. Since there are many economically disadvantaged groups in urban societies who are at the forefront of the CVD burden, initiatives to make healthier foods available should focus on affordability in conjunction with improved phytochemical diversity to incentivize change. The modern obesogenic diet is deficient in phytochemicals that are protective against the metabolic products of sugar metabolism, i.e., inflammation, reactive oxygen species and mitochondrial fatigue, whereas traditional southern African food species have high phytochemical diversity and are also higher in soluble dietary fibres that modulate the release of sugars from starches, nurture the microbiome and produce digestive artefacts that are prophylactic against cardiovascular disease. The examples of indigenous southern African food species with high horticultural potential that can be harvested sustainably to feed a large market of consumers include: Aloe marlothii, Acanthosicyos horridus, Adansonia digitata, Aloe ferox, Amaranthus hybridus, Annesorhiza nuda, Aponogeton distachyos, Bulbine frutescens, Carpobrotus edulis, Citrullus lanatus, Dioscorea bulbifera, Dovyalis caffra, Eleusine coracana, Lagenaria siceraria, Mentha longifolia, Momordica balsamina, Pelargonium crispum, Pelargonium sidoides, Pennisetum glaucum, Plectranthus esculentus, Schinziophyton rautanenii, Sclerocarya birrea, Solenostemon rotundifolius, Talinum caffrum, Tylosema esculentum, Vigna unguiculata and Vigna subterranea. The current review explains the importance of phytochemical diversity in the human diet, it gives a lucid explanation of phytochemical groups and links the phytochemical profiles of these indigenous southern African foods to their protective effects against cardiovascular disease.

Nanoparticles in the diagnosis and treatment of vascular aging and related diseases

Aging-induced alternations of vasculature structures, phenotypes, and functions are key in the occurrence and development of vascular aging-related diseases. Multiple molecular and cellular events, such as oxidative stress, mitochondrial dysfunction, vascular inflammation, cellular senescence, and epigenetic alterations are highly associated with vascular aging physiopathology. Advances in nanoparticles and nanotechnology, which can realize sensitive diagnostic modalities, efficient medical treatment, and better prognosis as well as less adverse effects on non-target tissues, provide an amazing window in the field of vascular aging and related diseases. Throughout this review, we presented current knowledge on classification of nanoparticles and the relationship between vascular aging and related diseases. Importantly, we comprehensively summarized the potential of nanoparticles-based diagnostic and therapeutic techniques in vascular aging and related diseases, including cardiovascular diseases, cerebrovascular diseases, as well as chronic kidney diseases, and discussed the advantages and limitations of their clinical applications.

The Role of RNA Modification in HIV-1 Infection

RNA plays an important role in biology, and more than 170 RNA modifications have been identified so far. Post-transcriptional modification of RNA in cells plays a crucial role in the regulation of its stability, transport, processing, and gene expression. So far, the research on RNA modification and the exact role of its enzymes is becoming more and more comprehensive. Human immunodeficiency virus 1 (HIV-1) is an RNA virus and the causative agent of acquired immunodeficiency syndrome (AIDS), which is one of the most devastating viral pandemics in history. More and more studies have shown that HIV has RNA modifications and regulation of its gene expression during infection and replication. This review focuses on several RNA modifications and their regulatory roles as well as the roles that different RNA modifications play during HIV-1 infection, in order to find new approaches for the development of anti-HIV-1 therapeutics.

Construction and Validation of a m7G-Related Gene-Based Prognostic Model for Gastric Cancer

Background

Gastric cancer (GC) is one of the most common malignant tumors of the digestive system. Chinese cases of GC account for about 40% of the global rate, with approximately 1.66 million people succumbing to the disease each year. Despite the progress made in the treatment of GC, most patients are diagnosed at an advanced stage due to the lack of obvious clinical symptoms in the early stages of GC, and their prognosis is still very poor. The m7G modification is one of the most common forms of base modification in post-transcriptional regulation, and it is widely distributed in the 5′ cap region of tRNA, rRNA, and eukaryotic mRNA.

Methods

RNA sequencing data of GC were downloaded from The Cancer Genome Atlas. The differentially expressed m7G-related genes in normal and tumour tissues were determined, and the expression and prognostic value of m7G-related genes were systematically analysed. We then built models using the selected m7G-related genes with the help of machine learning methods.The model was then validated for prognostic value by combining the receiver operating characteristic curve (ROC) and forest plots. The model was then validated on an external dataset. Finally, quantitative real-time PCR (qPCR) was performed to detect gene expression levels in clinical gastric cancer and paraneoplastic tissue.

Results

The model is able to determine the prognosis of GC samples quantitatively and accurately. The ROC analysis of model has an AUC of 0.761 and 0.714 for the 3-year overall survival (OS) in the training and validation sets, respectively. We determined a correlation between risk scores and immune cell infiltration and concluded that immune cell infiltration affects the prognosis of GC patients. NUDT10, METTL1, NUDT4, GEMIN5, EIF4E1B, and DCPS were identified as prognostic hub genes and potential therapeutic agents were identified based on these genes.

Conclusion

The m7G-related gene-based prognostic model showed good prognostic discrimination. Understanding how m7G modification affect the infiltration of the tumor microenvironment (TME) cells will enable us to better understand the TME’s anti-tumor immune response, and hopefully guide more effective immunotherapy methods.

Regulation and roles of RNA modifications in aging-related diseases

With the aging of the global population, accumulating interest is focused on manipulating the fundamental aging-related signaling pathways to delay the physiological aging process and eventually slow or prevent the appearance or severity of multiple aging-related diseases. Recently, emerging evidence has shown that RNA modifications, which were historically considered infrastructural features of cellular RNAs, are dynamically regulated across most of the RNA species in cells and thereby critically involved in major biological processes, including cellular senescence and aging. In this review, we summarize the current knowledge about RNA modifications and provide a catalog of RNA modifications on different RNA species, including mRNAs, miRNAs, lncRNA, tRNAs, and rRNAs. Most importantly, we focus on the regulation and roles of these RNA modifications in aging-related diseases, including neurodegenerative diseases, cardiovascular diseases, cataracts, osteoporosis, and fertility decline. This would be an important step toward a better understanding of fundamental aging mechanisms and thereby facilitating the development of novel diagnostics and therapeutics for aging-related diseases.

N1-Methyladenosine (m1A) Regulation Associated With the Pathogenesis of Abdominal Aortic Aneurysm Through YTHDF3 Modulating Macrophage Polarization

Objectives

This study aimed to identify key AAA-related m1A RNA methylation regulators and their association with immune infiltration in AAA. Furthermore, we aimed to explore the mechanism that m1A regulators modulate the functions of certain immune cells as well as the downstream target genes, participating in the progression of AAA.

Methods

Based on the gene expression profiles of the GSE47472 and GSE98278 datasets, differential expression analysis focusing on m1A regulators was performed on the combined dataset to identify differentially expressed m1A regulatory genes (DEMRGs). Additionally, CIBERSORT tool was utilized in the analysis of the immune infiltration landscape and its correlation with DEMRGs. Moreover, we validated the expression levels of DEMRGs in human AAA tissues by real-time quantitative PCR (RT-qPCR). Immunofluorescence (IF) staining was also applied in the validation of cellular localization of YTHDF3 in AAA tissues. Furthermore, we established LPS/IFN-γ induced M1 macrophages and ythdf3 knockdown macrophages in vitro, to explore the relationship between YTHDF3 and macrophage polarization. At last, RNA immunoprecipitation-sequencing (RIP-Seq) combined with PPI network analysis was used to predict the target genes of YTHDF3 in AAA progression.

Results

Eight DEMRGs were identified in our study, including YTHDC1, YTHDF1-3, RRP8, TRMT61A as up-regulated genes and FTO, ALKBH1 as down-regulated genes. The immune infiltration analysis showed these DEMRGs were positively correlated with activated mast cells, plasma cells and M1 macrophages in AAA. RT-qPCR analysis also verified the up-regulated expression levels of YTHDC1, YTHDF1, and YTHDF3 in human AAA tissues. Besides, IF staining result in AAA adventitia indicated the localization of YTHDF3 in macrophages. Moreover, our in-vitro experiments found that the knockdown of ythdf3 in M0 macrophages inhibits macrophage M1 polarization but promotes macrophage M2 polarization. Eventually, 30 key AAA-related target genes of YTHDF3 were predicted, including CD44, mTOR, ITGB1, STAT3, etc.

Conclusion

Our study reveals that m1A regulation is significantly associated with the pathogenesis of human AAA. The m1A “reader,” YTHDF3, may participate in the modulating of macrophage polarization that promotes aortic inflammation, and influence AAA progression by regulating the expression of its target genes.

The role of m6A methylation in osteosarcoma biological processes and its potential clinical value

Osteosarcoma (OS) is the most common primary malignant bone tumor in children and young adults and has a poor prognosis. Recent developments in the field of high-throughput sequencing technology, particularly in methylated RNA immunoprecipitation sequencing (MeRIP-seq), have led to renewed interest in RNA methylation. Among the various RNA modifications, N6-methyladenosine (m6A) modifications are the most common. Emerging evidence suggests that m6A methylation can affect the complexity of cancer progression by regulating biological functions related to cancer. In this review, we will shed light on recent findings regarding the biological function of m6A methylation in OS and discuss future research directions and potential clinical applications of RNA methyltransferases in OS.

Epitranscriptomics of cardiovascular diseases (Review)

RNA modifications have recently become the focus of attention due to their extensive regulatory effects in a vast array of cellular networks and signaling pathways. Just as epigenetics is responsible for the imprinting of environmental conditions on a genetic level, epitranscriptomics follows the same principle at the RNA level, but in a more dynamic and sensitive manner. Nevertheless, its impact in the field of cardiovascular disease (CVD) remains largely unexplored. CVD and its associated pathologies remain the leading cause of death in Western populations due to the limited regenerative capacity of the heart. As such, maintenance of cardiac homeostasis is paramount for its physiological function and its capacity to respond to environmental stimuli. In this context, epitranscriptomic modifications offer a novel and promising therapeutic avenue, based on the fine‑tuning of regulatory cascades, necessary for cardiac function. This review aimed to provide an overview of the most recent findings of key epitranscriptomic modifications in both coding and non‑coding RNAs. Additionally, the methods used for their detection and important associations with genetic variations in the context of CVD were summarized. Current knowledge on cardiac epitranscriptomics, albeit limited still, indicates that the impact of epitranscriptomic editing in the heart, in both physiological and pathological conditions, holds untapped potential for the development of novel targeted therapeutic approaches in a dynamic manner.

Heart Failure in Breast Cancer Survivors: Focus on Early Detection and Novel Biomarkers

PURPOSE OF REVIEW

Breast cancer survival rate has greatly improved in the last two decades due to the emergence of next-generation anti-cancer agents. However, cardiotoxicity remains a significant adverse effect arising from traditional and emerging chemotherapies as well as targeted therapies for breast cancer patients. In this review, we will discuss cardiotoxicities of both traditional and emerging therapies for breast cancer. We will discuss current practices to detect cardiotoxicity of these therapies with the focus on new and emerging biomarkers. We will then focus on 'omics approaches, especially the use of epigenetics to discover novel biomarkers and therapeutics to mitigate cardiotoxicity.

RECENT FINDINGS

Significant cardiotoxicities of conventional chemotherapies remain and new and unpredictable new forms of cardiac and/or vascular toxicity emerge with the surge in novel and targeted therapies. Yet, there is no clear guidance on detection of cardiotoxicity, except for significant left ventricular systolic dysfunction, and even then, there is no uniform definition of what constitutes cardiotoxicity. The gold standard for detection of cardiotoxicity involves a serial echocardiography in conjunction with blood-based biomarkers to detect early subclinical cardiac dysfunction. However, the ability of these tests to detect early disease remains limited and not all forms of toxicity are detectable with these modalities. There is an unprecedented need to discover novel biomarkers that are sensitive and specific for early detection of subclinical cardiotoxicity. In that space, novel echocardiographic techniques, such as strain, are becoming more common-place and new biomarkers, discovered by epigenetic approaches, seem to become promising alternatives or adjuncts to conventional non-specific cardiac biomarkers.

RNA m1A Methyltransferase TRMT6 Predicts Poorer Prognosis and Promotes Malignant Behavior in Glioma

Background: Glioma is the most prevalent central nervous system tumor in humans, and its prognosis remains unsatisfactory due to a lack of effective therapeutic targets. The ectopic expression of N1-methyladenosine (m1A) regulators is a key participant in tumorigenesis and progression. However, the m1A regulator expression status, prognostic value, and relationship with tumor clinical features in glioma remain unclear. Methods: Public datasets were used to analyze the mRNA and protein expression levels of m1A regulators. Kaplan-Meier and Cox regression analyses were performed to confirm the prognostic value of m1A regulators in glioma. Cellular experiments were conducted to verify the effect of TRMT6 on cell function. A comprehensive bioinformatics analysis was conducted to identify the potential molecular mechanisms regulated by TEMT6 in glioma. Results: We found that the dysregulation of m1A regulators was closely associated with tumorigenesis and progression in glioma. Furthermore, TRMT6 might be a powerful and independent biomarker for prognosis in glioma. Our study showed that inhibition of TRMT6 suppressed the proliferation, migration, and invasion of glioma cells. Mechanistically, TRMT6 may be involved in glioma progression by regulating cell cycle, PI3K-AKT, TGF-beta, MTORC1, NOTCH, and MYC pathways. Conclusions: Variation in m1A regulators was closely associated with malignant progression in glioma. Silencing TRMT6 suppressed the cell proliferation, migration, and invasion in glioma. m1A regulators, especially TRMT6, might play an essential role in the malignant progression of glioma.

BERT-m7G: A Transformer Architecture Based on BERT and Stacking Ensemble to Identify RNA N7-Methylguanosine Sites from Sequence Information

As one of the most prevalent posttranscriptional modifications of RNA, N7-methylguanosine (m7G) plays an essential role in the regulation of gene expression. Accurate identification of m7G sites in the transcriptome is invaluable for better revealing their potential functional mechanisms. Although high-throughput experimental methods can locate m7G sites precisely, they are overpriced and time-consuming. Hence, it is imperative to design an efficient computational method that can accurately identify the m7G sites. In this study, we propose a novel method via incorporating BERT-based multilingual model in bioinformatics to represent the information of RNA sequences. Firstly, we treat RNA sequences as natural sentences and then employ bidirectional encoder representations from transformers (BERT) model to transform them into fixed-length numerical matrices. Secondly, a feature selection scheme based on the elastic net method is constructed to eliminate redundant features and retain important features. Finally, the selected feature subset is input into a stacking ensemble classifier to predict m7G sites, and the hyperparameters of the classifier are tuned with tree-structured Parzen estimator (TPE) approach. By 10-fold cross-validation, the performance of BERT-m7G is measured with an ACC of 95.48% and an MCC of 0.9100. The experimental results indicate that the proposed method significantly outperforms state-of-the-art prediction methods in the identification of m7G modifications.

The Role of Epigenetics in Congenital Heart Disease

Congenital heart disease (CHD) is the most common birth defect among newborns worldwide and contributes to significant infant morbidity and mortality. Owing to major advances in medical and surgical management, as well as improved prenatal diagnosis, the outcomes for these children with CHD have improved tremendously so much so that there are now more adults living with CHD than children. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. For this reason, the complex process of cardiogenesis, which is governed by multiple interlinked and dose-dependent pathways, is a well investigated process. In addition to the sequence of the genome, the contribution of epigenetics to cardiogenesis is increasingly recognized. Significant progress has been made dissecting the epigenome of the heart and identified associations with cardiovascular diseases. The role of epigenetic regulation in cardiac development/cardiogenesis, using tissue and animal models, has been well reviewed. Here, we curate the current literature based on studies in humans, which have revealed associated and/or causative epigenetic factors implicated in CHD. We sought to summarize the current knowledge on the functional role of epigenetics in cardiogenesis as well as in distinct CHDs, with an aim to provide scientists and clinicians an overview of the abnormal cardiogenic pathways affected by epigenetic mechanisms, for a better understanding of their impact on the developing fetal heart, particularly for readers interested in CHD research.