miR-1246 promotes osteosarcoma cell migration via NamiRNA-enhancer network dependent on Argonaute 2.

High metastatic propensity of osteosarcoma leads to its therapeutic failure and poor prognosis. Although nuclear activation miRNAs (NamiRNAs) are reported to activate gene transcription via targeting enhancer and further promote tumor metastasis, it remains uncertain whether NamiRNAs regulate osteosarcoma metastasis and their exact mechanism. Here, we found that extracellular vesicles of the malignant osteosarcoma cells (143B) remarkably increased the migratory abilities of MNNG cells representing the benign osteosarcoma cells by two folds, which attributed to their high miR-1246 levels. Specially, miR-1246 located in nucleus could activate the migration gene expression (such as MMP1) to accelerate MNNG cell migration through elevating the enhancer activities via increasing H3K27ac enrichment. Instead, MMP1 expression was dramatically inhibited after Argonaute 2 (AGO2) knockdown. Notably, in vitro assays demonstrated that AGO2 recognized the hybrids of miR-1246 and its enhancer DNA via PAZ domains to prevent their degradation from RNase H and these protective roles of AGO2 may favor the gene activation by miR-1246 in vivo. Collectively, our findings suggest that miR-1246 could facilitate osteosarcoma metastasis through interacting with enhancer to activate gene expression dependent on AGO2, highlighting the nuclear AGO2 as a guardian for NamiRNA-targeted gene activation and the potential of miR-1246 for osteosarcoma metastasis therapy.

Anthropocene microplastic stratigraphy of Xiamen Bay, China: A history of plastic production and waste management.

Microplastics (MPs) are considered one of the significant stratigraphic markers of the onset of the Anthropocene Epoch; however, the interconnections between historic plastic production, waste management as well as social-economic and timing of MP accumulation are not well understood. Here, stratigraphic data of MPs from a sediment core from Xiamen Bay, China, was used to reconstruct the history of plastic pollution. Generalized Additive Modeling indicates a complex temporal evolution of MP accumulation. The oldest MPs deposited in 1952 was 30,332 ± 31,457 items/kg•dw, coincide with the infancy of the plastic industry and onset of the Anthropocene. The Cultural Revolution (1966-1976) curtailed these initial increases. Subsequent rapid growth in MPs during the late 1970s was peaked at 189,241 ± 29,495 items/kg•dw in 1988 and was followed by a drastic decline in the late 1980s to a low value in 1996 (16,626 ± 26,371 items/kg•dw), coinciding with proliferation of MP sources, coupled with evolution of plastic production, consumption, and regulation. Increasing MPs over the past decades implies that previous mitigation measures have been compromised by the escalated influx of MPs from increasing plastics production, legacy MPs remaining in circulation and insufficient waste management for a growing population. The present methodology and results represent a conceptual advance in understanding how changes in policy and economics over time correlate to changes in MP records in Anthropocene strata, which may help make decisions on plastic pollution mitigation strategies worldwide.

An epigenetic perspective on tumorigenesis: Loss of cell identity, enhancer switching, and NamiRNA network.

Various tumorigenic theories have been proposed in the past century, which contribute to the prevention and treatment of cancer clinically. However, the underlying mechanisms of the initiation of cancer, drug resistance, neoplasm relapse, and metastasis are still challenging to be panoramically addressed. Based on the abundant evidence provided by others and us, we postulate that Tumor Initiated by Loss of Cell Identity (LOCI), which is an inevitable initiating event of tumorigenesis. As a result, normal cells are transformed into the cancerous cell. In this process, epigenetic regulatory program, especially NamiRNA (Nuclear activating miRNA)-enhancer-gene activation network, is vital for the cell identity. The disorganization of NamiRNA-enhancer-gene activation network is a causal predisposition to the cell identity loss, and the altered cell identity is stabilized by genetic variations of the NamiRNA-enhancer-gene activation network. Furthermore, the additional genetic or epigenetic abnormities confer those cells to carcinogenic characteristics, such as growth advantage over normal cells, and finally yield cancer. In this review, we literally explain our tumor imitation hypothesis based on the corresponding evidence, which will not only help to refresh our understanding of tumorigenesis but also bring benefits to developing "cell identity reversing" based therapies.

Microplastics in a pelagic dolphinfish (Coryphaena hippurus) from the Eastern Pacific Ocean and the implications for fish health.

Microplastic pollution in fish is a growing concern worldwide due to its implication for human health. Microplastic contaminations and impacts were investigated in 15 wild-caught commercially important dolphinfish (Coryphaena hippurus L.) from the Eastern Pacific Ocean waters. 1741 suspected particles were extracted from gills, esophagus, stomachs, intestinal tracts, and muscle of C. hippurus. Only 139 of them were identified as microplastics by microscopic inspections and micro-Raman spectroscopic analysis. 10, 34, 51, 35, and 9 out of these 139 microplastic particles were extracted from the gill, esophagus, stomach, intestinal tract, and muscle respectively. Overall, microplastics were detected in 15 out of 15 fish (100%), with ~9.3 pieces per individual on average. The prevalence and high incidence of occurrence of microplastics in the C. hippurus suggest that this pelagic species are at high risk of exposure to microplastic pollutions. The chemical composition of microplastics was made of polyester (PES, 46.8%), polyethylene terephthalate (PET, 38.1%), polypropylene (PP, 7.9%), polystyrene (PS, 5.0%), polyethylene-polypropylene copolymer (PE-PP, 1.4%), and polyethylene (PE, 0.7%). 36.7% and 13.7% of microplastics in the fish were 1-2.5 mm and 2.5-5 mm, respectively. Microplastics of 0.1-0.5 mm and 0.5-1 mm roughly shared equally the remaining 50%. Molecular docking results implied that interaction of the four dominant microplastic polymers (PES, PET, PP, and PS) with cytochrome P450 17A1 would lead to impairment of the reproductive function of C. hippurus. The findings provide insights on the harms from microplastic exposure, along with quantitative information of occurrence, abundance, and distribution of microplastics in the fish tissues, which will ultimately improve understanding of bioavailability and hazards of microplastics to the organisms and beyond to human via food chain transfer.

UHRF1 regulates alternative splicing by interacting with splicing factors and U snRNAs in a H3R2me involved manner.

The well-established functions of UHRF1 converge to DNA biological processes, as exemplified by DNA methylation maintenance and DNA damage repair during cell cycles. However, the potential effect of UHRF1 on RNA metabolism is largely unexplored. Here, we revealed that UHRF1 serves as a novel alternative RNA splicing regulator. The protein interactome of UHRF1 identified various splicing factors. Among them, SF3B3 could interact with UHRF1 directly and participate in UHRF1-regulated alternative splicing events. Furthermore, we interrogated the RNA interactome of UHRF1, and surprisingly, we identified U snRNAs, the canonical spliceosome components, in the purified UHRF1 complex. Unexpectedly, we found H3R2 methylation status determines the binding preference of U snRNAs, especially U2 snRNAs. The involvement of U snRNAs in UHRF1-containing complex and their binding preference to specific chromatin configuration imply a finely orchestrated mechanism at play. Our results provided the resources and pinpointed the molecular basis of UHRF1-mediated alternative RNA splicing, which will help us better our understanding of the physiological and pathological roles of UHRF1 in disease development.

Reactivation of tumour suppressor in breast cancer by enhancer switching through NamiRNA network.

Dysfunction of Tumour Suppressor Genes (TSGs) is a common feature in carcinogenesis. Epigenetic abnormalities including DNA hypermethylation or aberrant histone modifications in promoter regions have been described for interpreting TSG inactivation. However, in many instances, how TSGs are silenced in tumours are largely unknown. Given that miRNA with low expression in tumours is another recognized signature, we hypothesize that low expression of miRNA may reduce the activity of TSG related enhancers and further lead to inactivation of TSG during cancer development. Here, we reported that low expression of miRNA in cancer as a recognized signature leads to loss of function of TSGs in breast cancer. In 157 paired breast cancer and adjacent normal samples, tumour suppressor gene GPER1 and miR-339 are both downregulated in Luminal A/B and Triple Negative Breast Cancer subtypes. Mechanistic investigations revealed that miR-339 upregulates GPER1 expression in breast cancer cells by switching on the GPER1 enhancer, which can be blocked by enhancer deletion through the CRISPR/Cas9 system. Collectively, our findings reveal novel mechanistic insights into TSG dysfunction in cancer development, and provide evidence that reactivation of TSG by enhancer switching may be a promising alternative strategy for clinical breast cancer treatment.

Integrated genomic and transcriptomic analysis suggests KRT18 mutation and MTAP are key genetic alterations related to the prognosis between astrocytoma and glioblastoma.

BACKGROUND: Astrocytoma and glioblastoma (GBM) are the two main subtypes of glioma, with the 2016 World Health Organization Classification of Tumors of the Central Nervous System (CNS WHO) classifying them into different grades. GBM is the most malignant among all CNS tumors with a 5-year survival rate of less than 5%. Although the prognosis of patients with astrocytoma is better than that of GBM in general, patients with anaplastic astrocytoma (AA) and isocitrate dehydrogenase (IDH) wild type have a similar prognosis as GBM and entail a high risk of progression. Exploring the molecular driving force behind the malignant phenotype of astrocytoma and GBM will help explain the diversity of glioma and discover new drug targets. METHODS: We enrolled 12 patients with astrocytoma and 12 patients with GBM and performed whole-exome sequencing (WES) and RNA sequencing analysis on tumor samples from the patients. RESULTS: We found that the somatic mutation of KRT18, which is associated with cell apoptosis and adhesion by interacting with receptor 1-associated protein (TRADD) and pinin, was significantly enriched in astrocytoma, but rare in GBM. Copy number loss of MTAP, which is closely related to a poor prognosis of glioma, was found to be significantly enriched in GBM. In addition, different somatic copy number alteration (SCNA), gene expression, and immune cell infiltration patterns between astrocytoma and GBM were found. CONCLUSIONS: This study revealed the distinct characteristics of astrocytoma and GBM at the DNA and RNA level. Somatic mutation of KRT18 and copy number loss of MTAP, two key genetic alterative genes in astrocytoma and GBM, have the potential to become therapeutic targets in glioma.

Highly efficient anaerobic co-degradation of complex persistent polycyclic aromatic hydrocarbons by a bioelectrochemical system.

Polycyclic aromatic hydrocarbons (PAHs) that undergo long-distance migration and have strong biological toxicity are a great threat to the health of ecosystems. In this study, the biodegradation characteristics and combined effects of mixed PAHs in bioelectrochemical systems (BESs) were studied. The results showed that, compared with a mono-carbon source, low-molecular-weight PAHs (LMW PAHs)-naphthalene (NAP) served as the co-substrate to promote the degradation of phenanthrene (PHE) and pyrene (PYR). The maximum degradation rates of PHE and PYR were 89.20% and 51.40% at 0.2500 mg/L in NAP-PHE and NAP-PYR at the degradation time of 120 h, respectively. Intermediate products were also detected, which indicated that the appending of relatively LMW PAHs had different effects on the metabolism of high-molecular-weight PAHs (HMW PAHs). The microbe species under different substrates (NAP-B, PHE-B, PYR-B, NAP-PHE, NAP-PYR, PHE-PYR) are highly similar, although the structure of the microbial community changed on the anode in the BES. In this study, the degradation regularity of mixed PAHs in BES was studied and provided theoretical guidance for the effective co-degradation of PAHs in the environment.

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks.

Aberrant DNA methylation is a distinguishing feature of cancer. Yet, how methylation affects immune surveillance and tumor metastasis remains ambiguous. We introduce a novel method, Guide Positioning Sequencing (GPS), for precisely detecting whole-genome DNA methylation with cytosine coverage as high as 96% and unbiased coverage of GC-rich and repetitive regions. Systematic comparisons of GPS with whole-genome bisulfite sequencing (WGBS) found that methylation difference between gene body and promoter is an effective predictor of gene expression with a correlation coefficient of 0.67 (GPS) versus 0.33 (WGBS). Moreover, Methylation Boundary Shift (MBS) in promoters or enhancers is capable of modulating expression of genes associated with immunity and tumor metabolism. Furthermore, aberrant DNA methylation results in tissue-specific enhancer switching, which is responsible for altering cell identity during liver cancer development. Altogether, we demonstrate that GPS is a powerful tool with improved accuracy and efficiency over WGBS in simultaneously detecting genome-wide DNA methylation and genomic variation. Using GPS, we show that aberrant DNA methylation is associated with altering cell identity and immune surveillance networks, which may contribute to tumorigenesis and metastasis.

Microplastics in the Northwestern Pacific: Abundance, distribution, and characteristics.

Prevalence of microplastics (MPs) throughout the world's oceans has raised growing concerns due to its detrimental effects on the environment and living organisms. Most recent studies of MPs, however, have focused on the estuaries and coastal regions. There is a lack of study of MPs pollution in the open ocean. In the present study, we conducted field observations to investigate the abundance, spatial distribution, and characteristics (composite, size, color, shape and surface morphology) of MPs at the surface of the Northwestern Pacific Ocean. Samples of MPs were collected at 18 field stations in the Northwestern Pacific Ocean using a surface manta trawl with a mesh size of ~330 µm and width of 1 m from August 25 to September 26, 2017. The MPs were characterized using light microscopy, Micro-Raman spectroscopy, and scanning electron microscopy (SEM). Our field survey results indicate the ubiquity of MPs at all stations with an abundance from 6.4 × 102 items km-2 to 4.2 × 104 items km-2 and an average abundance of 1.0 × 104 items km-2. The Micro-Raman spectroscopic analysis of the MPs samples collected during our field survey indicates that the dominant MPs is polyethylene (57.8%), followed by polypropylene (36.0%) and nylon (3.4%). The individual chemical compositions of MPs from the stations within the latitude range 123-146°E are comparable with each other, with PE being the dominating composition. Similar chemical fingerprints were observed at these field stations, suggesting that the MPs originated from similar sources. In contrast, the major MPs at the field stations adjacent to Japan is polypropylene, which may originate from the nearby land along the coast of Japan. Physical oceanography parameters were also collected at these stations. The spatial distribution of MPs is largely attributed to the combined effects of flow pattern, adjacent ocean circulation eddies, the Kuroshio and Kuroshio Extension system.

An epigenetic perspective on tumorigenesis: Loss of cell identity, enhancer switching, and NamiRNA network.

Various tumorigenic theories have been proposed in the past century, which contribute to the prevention and treatment of cancer clinically. However, the underlying mechanisms of the initiation of cancer, drug resistance, neoplasm relapse, and metastasis are still challenging to be panoramically addressed. Based on the abundant evidence provided by others and us, we postulate that Tumor Initiated by Loss of Cell Identity (LOCI), which is an inevitable initiating event of tumorigenesis. As a result, normal cells are transformed into the cancerous cell. In this process, epigenetic regulatory program, especially NamiRNA (Nuclear activating miRNA)-enhancer-gene activation network, is vital for the cell identity. The disorganization of NamiRNA-enhancer-gene activation network is a causal predisposition to the cell identity loss, and the altered cell identity is stabilized by genetic variations of the NamiRNA-enhancer-gene activation network. Furthermore, the additional genetic or epigenetic abnormities confer those cells to carcinogenic characteristics, such as growth advantage over normal cells, and finally yield cancer. In this review, we literally explain our tumor initiation hypothesis based on the corresponding evidence, which will not only help to refresh our understanding of tumorigenesis but also bring benefits to developing "cell identity reversing" based therapies.

miR-19a-mediated downregulation of RhoB inhibits the dephosphorylation of AKT1 and induces osteosarcoma cell metastasis.

Osteosarcoma is a primary malignancy that develops in bone, along with serious recurrence and metastasis. As an isoform of Rho family GTPases, RhoB could suppress cell proliferation, invasion, and anti-angiogenesis. But it is not clear how RhoB involves in tumor metastasis. Here we found that expression of RhoB was decreased in osteosarcoma primary samples and cell lines. Ectopic expression of RhoB restrains the migration of osteosarcoma cells in vitro and in vivo, and induces osteosarcoma cell apopotsis. Further study showed that overexpression of RhoB could increase the proportion of B55 in PP2A complex and enhance the dephosphorylation of AKT1 by interacting with B55. Moreover, we demonstrated that miR-19a, which exhibits abnormal expression in highly metastatic osteosarcoma cell lines, could inhibit the expression of RhoB and promote the lung metastasis of osteosarcoma cells in vivo. Our results indicate that miR-19a-mediated RhoB is a critical regulator for the dephosphorylation of AKT1 in osteosarcoma cells. It may have a possible strategy on suppressing osteosarcoma metastasis by miR-19a inhibitory oligonucleotides. The miR-19a/RhoB/AKT1 network may help us to better understand the mechanism of osteosarcoma metastasis.

Steering Against Wind: A New Network of NamiRNAs and Enhancers.

MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs with regulatory functions. Traditionally, miRNAs are thought to play a negative regulatory role in the cytoplasm by binding to the 3'UTR of target genes to degrade mRNA or inhibit translation. However, it remains a challenge to interpret the potential function of many miRNAs located in the nucleus. Recently, we reported a new type of miRNAs present in the nucleus, which can activate gene expression by binding to the enhancer, and named them nuclear activating miRNAs (NamiRNAs). The discovery of NamiRNAs showcases a complementary regulatory mechanism of miRNA, demonstrating their differential roles in the nucleus and cytoplasm. Here, we reviewed miRNAs in nucleus to better understand the function of NamiRNAs in their interactions with the enhancers. Accordingly, we propose a NamiRNA-enhancer-target gene activation network model to better understand the crosstalk between NamiRNAs and enhancers in regulating gene transcription. Moreover, we hypothesize that NamiRNAs may be involved in cell identity or cell fate determination during development, although further study is needed to elucidate the underlying mechanisms in detail.

miRNA-Mediated RNAa by Targeting Enhancers.

MicroRNAs (miRNAs) are small noncoding RNAs that act as negative regulators of gene expression in the cytoplasm. Yet, emerging evidence has shown that miRNAs are also distributed in the nucleus, with its function largely undetermined. At the same time, while miRNAs and enhancers show obvious tissue specificity, the interaction between miRNAs and enhancers in gene regulation remains unknown. By screening miRNA databases, we have identified a subset of miRNAs, called nuclear activating miRNAs (NamiRNAs). As enhancer regulators, NamiRNAs are able to activate gene expression at the transcriptional level. In addition, we found that the regulation of enhancers mediated by NamiRNAs depends on the presence of intact enhancers and AGO2 protein. More interesting is that NamiRNAs promote global gene transcription through the binding and activation of their targeted enhancers. Our results demonstrate a novel role for miRNA as an enhancer trigger for transcriptional gene activation. Further study of the function and molecular mechanism for NamiRNAs in tumorigenesis and development is of great significance.

MBD3L2 promotes Tet2 enzymatic activity for mediating 5-methylcytosine oxidation.

Ten-eleven translocation (Tet) proteins are key players involved in the dynamic regulation of cytosine methylation and demethylation. Inactivating mutations of Tet2 are frequently found in human malignancies, highlighting the essential role of Tet2 in cellular transformation. However, the factors that control Tet enzymatic activity remain largely unknown. Here, we found that methyl-CpG-binding domain protein 3 (MBD3) and its homolog MBD3-like 2 (MBD3L2) can specifically modulate the enzymatic activity of Tet2 protein, but not Tet1 and Tet3 proteins, in converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). Moreover, MBD3L2 is more effective than MBD3 in promoting Tet2 enzymatic activity through strengthening the binding affinity between Tet2 and the methylated DNA target. Further analysis revealed pronounced decreases in 5mC levels at MBD3L2 and Tet2 co-occupied genomic regions, most of which are promoter elements associated with either cancer-related genes or genes involved in the regulation of cellular metabolic processes. Our data add new insights into the regulation of Tet2 activity by MBD3 and MBD3L2, and into how that affects Tet2-mediated modulation of its target genes in cancer development. Thus, they have important applications in understanding how dysregulation of Tet2 might contribute to human malignancy.

[Mechanisms regulating p21 gene expression by retinoic acid-induced gene G protein].

OBJECTIVE: To investigate the mechanisms by which retinoic acid-induced gene G (RIG-G) protein regulates p21 gene expression. METHODS: Western blot was used to detect the effects of RIG-G protein overexpression on p21 protein expression level in leukemia cell line NB4 cells and the phosphorylation of both c-Jun and JNK in U937 cells. The c-Jun expression plasmid and p21 gene promoter-containing reporter plasmid were co-transfected into 293T cells, to explore the regulatory effect of c-Jun protein on p21 gene expression by luciferase reporter assay. RESULTS: Western blot showed that the overexpression of RIG-G protein significantly upregulated p21 protein level in the NB4 cells, and the level of p21 protein largely increased along with the induction of endogenous RIG-G protein during the differentiation of NB4 cells treated by all-trans retinoic acid (ATRA). Moreover, the phosphorylation of both c-Jun and JNK decreased in RIG-G-overexpressing U937 cells while total c-Jun and JNK proteins remained unchanged. After using the JNK inhibitor SP600125 to block JNK phosphorylation, the level of c-Jun phosphorylation was still dramatically reduced in the RIG-G-overexpressing U937T-RIG-G cells, compared with the control U937T-pTRE cells. These results indicated that the inhibitory effect of Rig-G protein on c-Jun phosphorylation could not only be through the JNK pathway, but also via some JNK-independent pathways. Luciferase reporter assay showed that when 0.1, 0.5, 1.0 and 2.0 µg c-Jun-expressing plasmids were respectively transfected into 293T cells, compared with the empty vector-transfected group, the relative luciferase activities were (83.0 ± 1.7)%, (73.7 ± 0.7)%, (68.9 ± 0.9)% and (64.1 ± 0.9)%, indicating that the transcriptional activity of p21 gene could be inhibited by c-Jun protein. CONCLUSIONS: RIG-G protein may suppress the phosphorylation of c-Jun protein through different signal pathways, thereby increasing the expression of p21 gene, arresting the cell cycle and inhibiting the cell growth in U937 cells.

Rig-G negatively regulates SCF-E3 ligase activities by disrupting the assembly of COP9 signalosome complex.

We previously showed that Rig-G, an antiproliferative protein induced by interferon, can sequester CSN5 protein in the cytoplasm. Here, we report that Rig-G can destroy the functions of CSN5-containing COP9 signalosome (CSN), a highly conserved multiprotein complex implicated in protein deneddylation, deubiquitination, and phosphorylation. By damaging integrity and stability of the CSN complex, Rig-G can dramatically reduce the cellular content of CSN complex and inhibit its regulatory roles in assembly and activation of cullin-RING ubiquitin E3 ligases (CRL). Furthermore, Rig-G can cause excessive activation of CRL through inhibition of CSN-mediated deneddylation, largely decreasing protein levels of Cul1 and ßTrCP, two important subunits of SCF (Skp1-Cul1-F-box protein)-E3 ligase. Rig-G can also attenuate the ability of CSN to recruit USP15 and impair CSN-associated deubiquitination. Increased autoubiquitination of ßTrCP and concomitant accumulation of target substrates (such as IκBα) are observed in Rig-G-expressing cells. Taken together, our findings reveal for the first time the negative regulation of Rig-G on SCF-E3 ligase activities through disrupting CSN complex, not only contributing to further investigation on biological functions of Rig-G, but also leading to better understanding of the CSN complex as a potential target in tumor diagnosis and treatment.