ToxPoint: Dissecting Functional RNA Modifications in Responses to Environmental Exposure-Mechanistic Toxicology Research Enters a New Era

Self-attention enabled deep learning of dihydrouridine (D) modification on mRNAs unveiled a distinct sequence signature from tRNAs

Dihydrouridine (D) is a modified pyrimidine nucleotide universally found in viral, prokaryotic, and eukaryotic species. It serves as a metabolic modulator for various pathological conditions, and its elevated levels in tumors are associated with a series of cancers. Precise identification of D sites on RNA is vital for understanding its biological function. A number of computational approaches have been developed for predicting D sites on tRNAs; however, none have considered mRNAs. We present here DPred, the first computational tool for predicting D on mRNAs in yeast from the primary RNA sequences. Built on a local self-attention layer and a convolutional neural network (CNN) layer, the proposed deep learning model outperformed classic machine learning approaches (random forest, support vector machines, etc.) and achieved reasonable accuracy and reliability with areas under the curve of 0.9166 and 0.9027 in jackknife cross-validation and on an independent testing dataset, respectively. Importantly, we showed that distinct sequence signatures are associated with the D sites on mRNAs and tRNAs, implying potentially different formation mechanisms and putative divergent functionality of this modification on the two types of RNA. DPred is available as a user-friendly Web server.

Epigenetic and epitranscriptomic mechanisms of chromium carcinogenesis

Hexavalent chromium [Cr(VI)], a Group I carcinogen classified by the International Agency for Research on Cancer (IARC), represents one of the most common occupational and environmental pollutants. The findings from human epidemiological and laboratory animal studies show that long-term exposure to Cr(VI) causes lung cancer and other cancer. Although Cr(VI) is a well-recognized carcinogen, the mechanism of Cr(VI) carcinogenesis has not been well understood. Due to the fact that Cr(VI) undergoes a series of metabolic reductions once entering cells to generate reactive Cr metabolites and reactive oxygen species (ROS) causing genotoxicity, Cr(VI) is generally considered as a genotoxic carcinogen. However, more and more studies have demonstrated that acute or chronic Cr(VI) exposure also causes epigenetic dysregulations including changing DNA methylation, histone posttranslational modifications and regulatory non-coding RNA (microRNA and long non-coding RNA) expressions. Moreover, emerging evidence shows that Cr(VI) exposure is also capable of altering cellular epitranscriptome. Given the increasingly recognized importance of epigenetic and epitranscriptomic dysregulations in cancer initiation and progression, it is believed that Cr(VI) exposure-caused epigenetic and epitranscriptomic changes could play important roles in Cr(VI) carcinogenesis. The goal of this chapter is to review the epigenetic and epitranscriptomic effects of Cr(VI) exposure and discuss their roles in Cr(VI) carcinogenesis. Better understanding the mechanism of Cr(VI) carcinogenesis may identify new molecular targets for more efficient prevention and treatment of cancer resulting from Cr(VI) exposure.

Chronic Hexavalent Chromium Exposure Upregulates the RNA Methyltransferase METTL3 Expression to Promote Cell Transformation, Cancer Stem Cell-Like Property, and Tumorigenesis

Hexavalent chromium [Cr(VI)] is a common environmental carcinogen causing lung cancer in humans. This study investigates the mechanism of Cr(VI) carcinogenesis focusing on the role of the epitranscriptomic dysregulation. The epitranscriptomic effect of Cr(VI) was determined in Cr(VI)-transformed human bronchial epithelial cells, chromate-exposed mouse and human lungs. The epitranscriptomic effect and its role in Cr(VI)-induced cell transformation, cancer stem cell (CSC)-like property, and tumorigenesis were determined by microarray analysis, soft agar colony formation, suspension spheroid formation, and mouse xenograft tumorigenesis assays. It was found that chronic Cr(VI) exposure causes epitranscriptomic dysregulations as evidenced by the increased levels of total RNA N6-methyladenosine (m6A) modification and the RNA m6A methyltransferase like-3 (METTL3) in Cr(VI)-transformed cells and chromate exposure-caused mouse and human lung tumors. Knockdown of METTL3 expression in Cr(VI)-transformed cells significantly reduces their m6A levels and transformed phenotypes and tumorigenicity in mice. Moreover, knockdown of METTL3 expression in parental nontransformed cells significantly reduces the capability of chronic Cr(VI) exposure to induce cell transformation and CSC-like property. Together, this study reveals that chronic Cr(VI) exposure is capable of altering cellular epitranscriptome by increasing the m6A RNA modification via upregulating the RNA methyltransferase METTL3 expression, which plays an important role in Cr(VI)-induced cell transformation, CSC-like property, and tumorigenesis.

RNA adduction derived from electrophilic species in vitro and in vivo

RNA molecules are essential for cell function by not only serving as genetic materials, but also providing cells with structural support and catalytic functions. Due to nucleophilicity of nucleobases, RNA molecules can react with electrophilic species thus to be "adducted". The electron-deficient agents potentially inducing adduction exist in a variety of natural sources including metabolic products of biomolecules. Although evident and readily detected in human tissue, RNA adduction remains poorly understood for their physiological and pathological function. In this article, we review a collection of exogenous and endogenous molecular species that participate in RNA adduction and elaborates on the chemical nature of their RNA adduction sites. Furthermore, we provide perspectives on the potential of RNA adducts as biomarkers of environmental insults. Finally, we project future investigations that are necessary for understanding the mechanisms of cellular toxicity of RNA adduction.

Mechanisms of the synergistic lung tumorigenic effect of arsenic and benzo(a)pyrene combined- exposure

Humans are often exposed to mixtures of environmental pollutants especially environmental chemical carcinogens, representing a significant environmental health issue. However, our understanding on the carcinogenic effects and mechanisms of environmental carcinogen mixture exposures is limited and mostly relies on the findings from studying individual chemical carcinogens. Both arsenic and benzo(a)pyrene (BaP) are among the most common environmental carcinogens causing lung cancer and other types of cancer in humans. Millions of people are exposed to arsenic via consuming arsenic-contaminated drinking water and even more people are exposed to BaP via cigarette smoking and consuming BaP-contaminated food. Thus arsenic and BaP combined-exposure in humans is common. Previous epidemiology studies indicated that arsenic-exposed people who were cigarette smokers had significantly higher lung cancer risk than those who were non-smokers. Since BaP is one of the major carcinogens in cigarette smoke, it has been speculated that arsenic and BaP combined-exposure may play important roles in the increased lung cancer risk observed in arsenic-exposed cigarette smokers. In this review, we summarize important findings and inconsistencies about the co-carcinogenic effects and underlying mechanisms of arsenic and BaP combined-exposure and propose new areas for future studies. A clear understanding on the mechanism of co-carcinogenic effects of arsenic and BaP combined exposure may identify novel targets to more efficiently treat and prevent lung cancer resulting from arsenic and BaP combined-exposure.

The m6A RNA methylation regulates oncogenic signaling pathways driving cell malignant transformation and carcinogenesis

The m⁶A RNA methylation is the most prevalent internal modification in mammalian mRNAs which plays critical biological roles by regulating vital cellular processes. Dysregulations of the m⁶A modification due to aberrant expression of its regulatory proteins are frequently observed in many pathological conditions, particularly in cancer. Normal cells undergo malignant transformation via activation or modulation of different oncogenic signaling pathways through complex mechanisms. Accumulating evidence showing regulation of oncogenic signaling pathways at the epitranscriptomic level has added an extra layer of the complexity. In particular, recent studies demonstrated that, in many types of cancers various oncogenic signaling pathways are modulated by the m⁶A modification in the target mRNAs as well as noncoding RNA transcripts. m⁶A modifications in these RNA molecules control their fate and metabolism by regulating their stability, translation or subcellular localizations. In this review we discussed recent exciting studies on oncogenic signaling pathways that are modulated by the m⁶A RNA modification and/or their regulators in cancer and provided perspectives for further studies. The regulation of oncogenic signaling pathways by the m⁶A modification and its regulators also render them as potential druggable targets for the treatment of cancer.

m6AmPred: Identifying RNA N6, 2'-O-dimethyladenosine (m6Am) sites based on sequence-derived information

N6,2'-O-dimethyladenosine (m⁶A_m) is a reversible modification widely occurred on varied RNA molecules. The biological function of m⁶A_m is yet to be known though recent studies have revealed its influences in cellular mRNA fate. Precise identification of m⁶A_m sites on RNA is vital for the understanding of its biological functions. We present here m6AmPred, the first web server for in silico identification of m⁶A_m sites from the primary sequences of RNA. Built upon the eXtreme Gradient Boosting with Dart algorithm (XgbDart) and EIIP-PseEIIP encoding scheme, m6AmPred achieved promising prediction performance with the AUCs greater than 0.954 when tested by 10-fold cross-validation and independent testing datasets. To critically test and validate the performance of m6AmPred, the experimentally verified m⁶A_m sites from two data sources were cross-validated. The m6AmPred web server is freely accessible at: https://www.xjtlu.edu.cn/biologicalsciences/m6am, and it should make a useful tool for the researchers who are interested in N6,2'-O-dimethyladenosine RNA modification.

PCB126 Exposure Revealed Alterations in m6A RNA Modifications in Transcripts Associated With AHR Activation

Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3' UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3' UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.

m5UPred: A Web Server for the Prediction of RNA 5-Methyluridine Sites from Sequences

As one of the widely occurring RNA modifications, 5-methyluridine (m⁵U) has recently been shown to play critical roles in various biological functions and disease pathogenesis, such as under stress response and during breast cancer development. Precise identification of m⁵U sites on RNA is vital for the understanding of the regulatory mechanisms of RNA life. We present here m5UPred, the first web server for in silico identification of m⁵U sites from the primary sequences of RNA. Built upon the support vector machine (SVM) algorithm and the biochemical encoding scheme, m5UPred achieved reasonable prediction performance with the area under the receiver operating characteristic curve (AUC) greater than 0.954 by 5-fold cross-validation and independent testing datasets. To critically test and validate the performance of our newly proposed predictor, the experimentally validated m⁵U sites were further separated by high-throughput sequencing techniques (miCLIP-Seq and FICC-Seq) and cell types (HEK293 and HAP1). When tested on cross-technique and cross-cell-type validation using independent datasets, m5UPred achieved an average AUC of 0.922 and 0.926 under mature mRNA mode, respectively, showing reasonable accuracy and reliability. The m5UPred web server is freely accessible now and it should make a useful tool for the researchers who are interested in m⁵U RNA modification.