HBV integrations reshaping genomic structures promote hepatocellular carcinoma.

OBJECTIVE: Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), mostly characterised by HBV integrations, is prevalent worldwide. Previous HBV studies mainly focused on a few hotspot integrations. However, the oncogenic role of the other HBV integrations remains unclear. This study aimed to elucidate HBV integration-induced tumourigenesis further. DESIGN: Here, we illuminated the genomic structures encompassing HBV integrations in 124 HCCs across ages using whole genome sequencing and Nanopore long reads. We classified a repertoire of integration patterns featured by complex genomic rearrangement. We also conducted a clustered regularly interspaced short palindromic repeat (CRISPR)-based gain-of-function genetic screen in mouse hepatocytes. We individually activated each candidate gene in the mouse model to uncover HBV integration-mediated oncogenic aberration that elicits tumourigenesis in mice. RESULTS: These HBV-mediated rearrangements are significantly enriched in a bridge-fusion-bridge pattern and interchromosomal translocations, and frequently led to a wide range of aberrations including driver copy number variations in chr 4q, 5p (TERT), 6q, 8p, 16q, 9p (CDKN2A/B), 17p (TP53) and 13q (RB1), and particularly, ultra-early amplifications in chr8q. Integrated HBV frequently contains complex structures correlated with the translocation distance. Paired breakpoints within each integration event usually exhibit different microhomology, likely mediated by different DNA repair mechanisms. HBV-mediated rearrangements significantly correlated with young age, higher HBV DNA level and TP53 mutations but were less prevalent in the patients subjected to prior antiviral therapies. Finally, we recapitulated the TONSL and TMEM65 amplification in chr8q led by HBV integration using CRISPR/Cas9 editing and demonstrated their tumourigenic potentials. CONCLUSION: HBV integrations extensively reshape genomic structures and promote hepatocarcinogenesis (graphical abstract), which may occur early in a patient's life.

Whose Oxygen Atom Is Transferred to the Products? A Case Study of Peracetic Acid Activation via Complexed MnII for Organic Contaminant Degradation.

Identifying reactive species in advanced oxidation process (AOP) is an essential and intriguing topic that is also challenging and requires continuous efforts. In this study, we exploited a novel AOP technology involving peracetic acid (PAA) activation mediated by a MnII-nitrilotriacetic acid (NTA) complex, which outperformed iron- and cobalt-based PAA activation processes for rapidly degrading phenolic and aniline contaminants from water. The proposed MnII/NTA/PAA system exhibited non-radical oxidation features and could stoichiometrically oxidize sulfoxide probes to the corresponding sulfone products. More importantly, we traced the origin of O atoms from the sulfone products by 18O isotope-tracing experiments and found that PAA was the only oxygen-donor, which is different from the oxidation process mediated by high-valence manganese-oxo intermediates. According to the results of theoretical calculations, we proposed that NTA could tune the coordination circumstance of the MnII center to elongate the O-O bond of the complexed PAA. Additionally, the NTA-MnII-PAA* molecular cluster presented a lower energy gap than the MnII-PAA complex, indicating that the MnII-peroxy complex was more reactive in the presence of NTA. Thus, the NTA-MnII-PAA* complex exhibited a stronger oxidation potential than PAA, which could rapidly oxidize organic contaminants from water. Further, we generalized our findings to the CoII/PAA oxidation process and highlighted that the CoII-PAA* complex might be the overlooked reactive cobalt species. The significance of this work lies in discovering that sometimes the metal-peroxy complex could directly oxidize the contaminants without the further generation of high-valence metal-oxo intermediates and/or radical species through interspecies oxygen and/or electron transfer.

Calculation, elasticity and regional differences of agricultural greenhouse gas shadow prices.

Global warming is one of the major threats to human survival and social development. Agriculture, as an important source of greenhouse gas (GHG) emissions, cannot be ignored. China is the world's largest carbon emitter, and if it does not actively participate, other countries in the world will not be able to achieve the 1.5 degree temperature control target. Hence, the issue of China's agricultural emissions reduction is worthy of attention. As part of this study a framework for estimating agricultural GHG emissions was constructed. A directional distance function was then used to estimate the cost of emission reduction from the perspective of economic output. Furthermore, through the economic elasticity of shadow prices, agricultural economic development and emission reduction were included in the same framework to study the regional gap of agricultural emission reduction models. Finally, reducing agricultural emission reduction costs was discussed from the perspective of economy, technology, and policy. We found that (1) Agricultural emission reduction costs have phased characteristics and regional differences, and differentiated emission reduction cost improvement measures can help with efficient emission reduction. (2) The emission reduction cost in developed regions is more likely to be affected by technological progress and the strength of environmental governance by government. The emission reduction cost in regions dominated by planting is affected by the industrial structure and energy consumption structure. The emission reduction cost in underdeveloped regions is affected by the economic level. (3) We must give full play to the leading role of benchmarking regions in reducing emissions.

The phosphorylation of the Smad2/3 linker region by nemo-like kinase regulates TGF-ß signaling.

Smad2 and Smad3 (Smad2/3) are structurally similar proteins that primarily mediate the transforming growth factor-ß (TGF-ß) signaling responsible for driving cell proliferation, differentiation, and migration. The dynamics of the Smad2/3 phosphorylation provide the key mechanism for regulating the TGF-ß signaling pathway, but the details surrounding this phosphorylation remain unclear. Here, using in vitro kinase assay coupled with mass spectrometry, we identified for the first time that nemo-like kinase (NLK) regulates TGF-ß signaling via modulation of Smad2/3 phosphorylation in the linker region. TGF-ß-mediated transcriptional and cellular responses are suppressed by NLK overexpression, whereas NLK depletion exerts opposite effects. Specifically, we discovered that NLK associates with Smad3 and phosphorylates the designated serine residues located in the linker region of Smad2 and Smad3, which inhibits phosphorylation at the C terminus, thereby decreasing the duration of TGF-ß signaling. Overall, this work demonstrates that phosphorylation on the linker region of Smad2/3 by NLK counteracts the canonical phosphorylation in response to TGF-ß signals, thus providing new insight into the mechanisms governing TGF-ß signaling transduction.

Catalytic ozonation of iohexol with α-Fe0.9Mn0.1OOH in water: Efficiency, degradation mechanism and toxicity evaluation.

Iohexol, a widely used iodinated X-ray contrast media, is difficult to completely degrade with the traditional water treatment process. Catalytic ozonation with synthesized α-Fe0.9Mn0.1OOH as the catalyst can significantly promote the degradation of iohexol relative to that with ozonation alone. Hydroxyl radicals play a predominant role during the degradation of iohexol. The effect of various factors, including catalyst dose, ozone dose, iohexol concentration and water matrix factors, on the catalytic performance were investigated. The presence of α-Fe0.9Mn0.1OOH in the catalytic system can significantly promote the removal of iohexol and mineralization of the dissolved organic carbon in real water samples. The intermediate products were determined by high-resolution liquid chromatography, and the reaction site was predicted by frontier electron density (FED) calculations. The degradation mechanism of iohexol followed the processes of H-abstraction, amide hydrolysis, amide oxidation, and ·OH substitution. Higher exposure concentrations of iohexol had a negative effect on the survival and hatching rates in the development of zebrafish embryos. The autonomic movement process and heartbeat rate of the zebrafish larvae showed significant differences as the exposure concentration of iohexol increased. The catalytic ozonation process with α-Fe0.9Mn0.1OOH can decrease the toxicity of iohexol containing water.

Global changes in chromatin accessibility and transcription following ATRX inactivation in human cancer cells.

α-Tthalassemia mental retardation X-linked (ATRX) is a chromatin remodeler frequently mutated in many cancers. Despite the binding pattern of ATRX in heterochromatin, ATRX-mediated epigenomic changes in cancer cells have not been profiled, especially for the heterochromatin regions. Here, we profiled genome-wide maps of chromatin accessibility in ATRX-intact and ATRX-null human cancer cells. We found extensive changes in chromatin accessibility in both repetitive DNA regions and non-repetitive regulatory regions following ATRX loss. These changes are highly correlated with changes in transcription, which lead to alterations in cancer-related signalling pathways, such as upregulation of the TGF-ß pathway and downregulation of the cadherin family of proteins. These findings indicate that ATRX deficiency induces epigenomic changes and promotes tumorigenesis through both genome instability and shifts in transcription.

P53-R273H mutation enhances colorectal cancer stemness through regulating specific lncRNAs.

BACKGROUND: TP53 is one of the most frequently mutated genes among all cancer types, and TP53 mutants occur more than 60% in colorectal cancer (CRC). Among all mutants, there are three hot spots, including p53-R175H, p53-R248W and p53-R273H. Emerging evidence attributes cancer carcinogenesis to cancer stem cells (CSCs). Long noncoding RNAs (lncRNAs) play crucial roles in maintaining the stemness of CSCs. However, it is unknown if mutant p53-regulated lncRNAs are implicated in the maintenance of CSC stemness. METHODS: RNA-sequencing (RNA-seq) and ChIP-sequencing (ChIP-seq) were used to trace the lncRNA network regulated by p53-R273H in HCT116 endogenous p53 point mutant spheroid cells generated by the somatic cell knock-in method. RT-qPCR was used to detect lncRNA expression patterns, verifying the bioinformatics analysis. Transwell, spheroid formation, fluorescence activated cell sorter (FACS), xenograft nude mouse model, tumor frequency assessed by extreme limiting dilution analysis (ELDA), Western blot assays and chemoresistance analysis were performed to elucidate the functions and possible mechanism of lnc273-31 and lnc273-34 in cancer stem cells. RESULTS: p53-R273H exhibited more characteristics of CSC than p53-R175H and p53-R248W. RNA-seq profiling identified 37 up regulated and 4 down regulated differentially expressed lncRNAs regulated by p53-R273H. Combined with ChIP-seq profiling, we further verified two lncRNAs, named as lnc273-31 and lnc273-34, were essential in the maintenance of CSC stemness. Further investigation illustrated that lnc273-31 or lnc273-34 depletion dramatically diminished colorectal cancer migration, invasion, cancer stem cell self-renewal and chemoresistance in vitro. Moreover, the absence of lnc273-31 or lnc273-34 dramatically delayed cancer initiation and tumorigenic cell frequency in vivo. Also, lnc273-31 and lnc273-34 have an impact on epithelial-to mesenchymal transition (EMT). Finally, lnc273-31 and lnc273-34 were significantly highly expressed in CRC tissues with p53-R273H mutation compared to those with wildtype p53. CONCLUSIONS: The present study unveiled a high-confidence set of lncRNAs regulated by p53-R273H specific in colorectal CSCs. Furthermore, we demonstrated that two of them, lnc273-31 and lnc273-34, were required for colorectal CSC self-renewal, tumor propagation and chemoresistance. Also, the expression of these two lncRNAs augmented in colorectal cancer patient samples with p53-R273H mutation. These two lncRNAs may serve as promising predictors for patients with p53-R273H mutation and are vital for chemotherapy.

Pollution characteristics, sources and lung cancer risk of atmospheric polycyclic aromatic hydrocarbons in a new urban district of Nanjing, China.

This paper focused on the pollution characteristics, sources and lung cancer risk of atmospheric polycyclic aromatic hydrocarbons (PAHs) in a new urban district of Nanjing, China. Gaseous and aerosol PM2.5 (particulate matter with aerodynamic diameter smaller than 2.5µm) samples were collected in spring of 2015. Sixteen PAHs were extracted and analyzed after sampling. Firstly, arithmetic mean concentrations of PAHs and BaPeq (benzo[a]pyrene equivalent) were calculated. The mean concentrations of PAHs were 29.26±14.13, 18.14±5.37 and 48.47±16.03ng/m3 in gas phase, particle phase and both phases, respectively. The mean concentrations of BaPeq were 0.87±0.51, 2.71±2.17 and 4.06±2.31ng/m3 in gas phase, particle phase and both phases, respectively. Secondly, diagnostic ratios and principal component analysis were adopted to identify the sources of PAHs and the outcomes were the same: traffic exhaust was the predominant source followed by fuel combustion and industrial process. Finally, incremental lung cancer risk (ILCR) induced by whole year inhalation exposure to PAHs for population groups of different age and gender were estimated based on a Monte Carlo simulation. ILCR values caused by particle phase PAHs were greater than those caused by gas phase PAHs. ILCR values for adults were greater than those for other age groups. ILCR values caused by total (gas+particle) PAHs for diverse groups were all greater than the significant level (l0-6), indicating high potential lung cancer risk. Sensitivity analysis results showed that cancer slope factor for BaP inhalation exposure and BaPeq concentration had greater impact than body weight and inhalation rate on the ILCR.