[Predicting tumor drug sensitivity with multi-omics data].

The prediction of tumor drug sensitivity plays an important role in clinically guiding patients' medication. In this paper, a multi-omics data-based cancer drug sensitivity prediction model was constructed by Stacking ensemble learning method. The data including gene expression, mutation, copy number variation and drug sensitivity value (IC50) of 198 drugs were downloaded from the GDSC database. Multiple feature selection methods were applied for dimensionality reduction. Six primary learners and one secondary learner were integrated into modeling by Stacking method. The model was validated with 5-fold cross-validation. In the prediction results, 36.4% of drug models' AUCs were greater than 0.9, 49.0% of drug models' AUCs were between 0.8-0.9, and the lowest drug model's AUC was 0.682. The multi-omics model for drug sensitivity prediction based on Stacking method is better than the known single-omics or multi-omics model in terms of accuracy and stability. The model based on multi-omics data is better than the single-omics data in predicting drug sensitivity. Function annotation and enrichment analysis of feature genes revealed the potential resistance mechanism of tumors to sorafenib, providing the model interpretability from a biological perspective, and demonstrated the model's potential applicability in clinical medication guidance.

Rare and misincorporated DNA N6-methyladenine is a hallmark of cytotoxic stresses for selectively stimulating the stemness and proliferation of glioblastoma cells.

The entity of DNA N6-methyladenine (6mA) in mammals remains elusive and subsequently its roles in diseases are poorly understood. Here we exploited a bacterial DNA contamination-free and ultrasensitive UHPLC-MS/MS assay to reassess DNA 6mA in human glioblastomas and unveiled that DNA 6mA (~0.08 ppm) is extremely rare. By the use of two independent heavy stable isotope-labeling strategies, we further prove that the observed 6mA is solely generated by DNA polymerase-mediated misinocorporation. In vitro experiments point toward that the generation of misincorporated DNA 6mA is associated with the cellular stresses-caused release of RNA N6-methyladenine (m6A) nucleoside, which is profoundly inhibited by hypoxia milieu. Consistently, compared with normal brain tissues, DNA 6mA decreases in hypoxic human gliomas. Our data also strongly support that rare DNA 6mA rather than relatively abundant DNA 5-methylcytosine and 5-hydroxymethylcytosine is a hallmark of poor prognosis of IDH1/2 mutation-absent glioblastoma patients, reflecting the incidence of cytotoxic stresses and subsequent release of m6A nucleoside. The released m6A nucleoside may selectively preserve a subset of the glioblastoma cells and stimulate their stemness and proliferation. Noteworthily, demethylation-inhibiting IDH1 mutation increases the DNA 6mA content in human gliomas, but the depletion of the demethylase candidate ALKBH1 fails to do so, together suggesting the presence of other unknown 6mA demethylase for erasing misincorporated DNA 6mA. This is the first report on the identification of the misincorporated 6mA together with its origin and roles in diseases.

Metabolomics analysis reveals potential mechanisms of phenolic accumulation in lettuce (Lactuca sativa L.) induced by low nitrogen supply.

The roles of nitrogen availability in determining the phenolic accumulation of vegetables have been widely studied, but the underlying mechanism involved remains unknown. Thus, primary and secondary metabolites profiling of lettuce leaves were performed using non-targeted metabolomics analysis. The results showed that carbon metabolism, amino acid metabolism, and phenolic biosynthesis metabolism in lettuce were significantly affected by low nitrogen supply (LN). The phenolic content was significantly increased in LN-treated lettuce, indicating that the activated phenolic biosynthesis was triggered by the LN treatment. The reduced citrate cycle and enhanced glucose and sucrose content suggested there is a relative excess of carbon resources in LN-treated lettuce. In addition, the decreased nitrogen-rich amino acids (glutamine and aspartate acid) and the maintained phenylalanine content indicated the redirection of nitrogen resources to phenylalanine biosynthesis. Meanwhile, no significant changes of chlorophyll content were observed in LN-treated lettuce leaves. The LN-treated lettuce showed lower glutamine synthetase activity but higher glutamate synthase activity compared to control. These findings together suggest that LN treatment may increase the phenolic accumulation in lettuce by effectively redirecting more carbon and nitrogen resources to the phenolic biosynthesis pathway.

Role of sucrose in modulating the low-nitrogen-induced accumulation of phenolic compounds in lettuce (Lactuca sativa L.).

BACKGROUND: Phenolic compounds are phytochemicals present in vegetables which contribute to human health. Although nitrogen deficiency and sucrose (Suc) are linked to phenolic production in vegetables, the relationship between them in the regulation of phenolic biosynthesis remains unknown. This study investigated the potential role of Suc in regulating phenolic biosynthesis of lettuce under low-nitrogen (LN) conditions. RESULTS: Our results showed that LN treatment significantly increased Suc content in lettuce by inducing rapid increases in activities of sucrose synthesis-related enzymes. Exogenous Suc further stimulated LN-induced phenolic accumulation in lettuce by upregulating the expression of genes (PAL, CHS, F3H, DFR, F35H and UFGT) involved in phenolic biosynthesis. The opposite effects were true for exogenous 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) application. No changes were observed in chlorophyll content in LN-treated lettuce, in either the presence or absence of Suc application. Notably, exogenous DCMU resulted in decreases of maximum quantum efficiency of photosystem II (PSII) photochemistry, actual efficiency of PSII and electron transport rate in PSII and increase of quantum yield of non-regulated energy dissipation in PSII in lettuce under LN conditions, whereas these effects were reversed on Suc application. Exogenous Suc also increased glutamine synthetase and glutamate synthase activities in LN-treated lettuce. CONCLUSIONS: These results suggest that Suc is involved in LN-induced phenolic production in lettuce by enhancing photosynthetic and nitrogen assimilation efficiency to increase the supply of carbon resources and precursors for phenolic biosynthesis. © 2020 Society of Chemical Industry.

p57Kip2 is a master regulator of human adipose derived stem cell quiescence and senescence.

Although human adipose derived stem cells (hADSCs) hold great promises for regenerative medicine, their key biological properties remain poorly understood. In particular, proliferation defects resulted from deep quiescence (dormancy) and senescence represent a major hurdle in hADSC production and clinical application. We have developed a model system for mechanistic dissection of hADSC quiescence and senescence. p57Kip2, a major CDK inhibitor, was highly expressed in quiescent and senescent hADSCs but its level quickly declined upon stem cell activation. p57Kip2 overexpression induced quiescence in spite of proliferative signals and its knockdown promoted cell cycle reentry even with induction of quiescence presumably through modulating the CDK2-CyclinE1 complex. Given its key role in quiescence and senescence, p57Kip2 may be exploited for innovative strategies to amplify hADSCs of high quality for clinics.

Enhancement of polyphenolic metabolism as an adaptive response of lettuce (Lactuca sativa) roots to aluminum stress.

Polyphenols, pivotal secondary metabolites, are involved in plant adaption to abiotic stresses. Here, we investigated the role and metabolism profile of polyphenols under aluminum (Al) stress in different lettuce genotypes grown in 0.5 mM CaCl2 solution with AlCl3 (pH = 4.5). The complementary use of high-resolution mass spectrometry and quantitative biochemical approaches allowed the characterization of total and unique phenols, as well as their roles in Al tolerance. By comparing the most tolerant and sensitive genotype, 8 polyphenols, including 4 phenolic acids, 2 flavonoids, 1 xanthone and 1 unknown compound, were identified in the roots of the tolerant genotype. The total phenolic and flavonoid contents significantly increased in the tolerant genotype under Al stress. Seedlings with more phenolic accumulation usually performed greater Al tolerance. Meanwhile, principal enzymes related to phenolic biosynthesis significantly increased in roots of the tolerance genotype after Al treatment, with phenylalanine ammonia lyase (PAL), cinnamate 4-hydroxylase, and 4-coumarate coenzyme A ligase increased by 16, 18 and 30%, respectively. The elevated total phenolics were significantly suppressed by AIP, a highly specific PAL inhibitor. Consequently, the antioxidant capacity was inhibited, leading to lettuce sensitivity to Al stress. These results clearly suggested the enhancement of unique polyphenolic biosynthesis as an adaptive strategy of lettuce to Al stress by protecting plants from oxidative stress.

Alteration of Phenolic Composition in Lettuce (Lactuca sativa L.) by Reducing Nitrogen Supply Enhances its Anti-Proliferative Effects on Colorectal Cancer Cells.

Consumption of vegetables rich in phenolic compounds has become a useful method to reduce the risk of developing several types of cancer. This study investigated the potential relationship between the alteration of phenolic compounds in lettuce induced by reduced nitrogen supply and its anti-proliferative effects on Caco-2 colorectal cancer cells. Our results showed that phenolic extracts from lettuce grown under low nitrogen conditions (LP) exhibited better anti-proliferative effects against Caco-2 cells, in part, by interfering with the cell cycle and inducing apoptosis, compared with those from lettuce supplied with adequate nitrogen. High performance liquid chromatography (HPLC) analysis and correlation analysis indicated that the better anticancer activity of LP may be not only related to the increased phenolic content, but also associated with the increased percentage contribution of quercetin to total phenolics. Taken together, alteration of phenolic composition by reduced nitrogen supply can be an effectively strategy for the development of healthy vegetables as anticancer products.

Investigation of lead bioimmobilization and transformation by Penicillium oxalicum SL2.

Fungi Penicillium oxalicum SL2 was applied for Pb2+ bioremediation in aqueous solution in this study. After 7 days of incubation at different initial concentrations of Pb2+ (0, 100, 500 and 2500 mg L-1), most of Pb2+ were removed (90, 98.3, and 86.2%), the maximum Pb content in mycelium reached about 155.6 mg g-1 dw. Meanwhile, the formation of extracellular secondary minerals and intracellular Pb-complex were observed and identified, the speciation of Pb in mycelium was also detected by X-ray absorption near-edge structure (XANES) spectroscopy, i.e., Pb-oxalate, Pb-citrate, Pb-hydrogen phosphate and Pb-glutathione analogues. In addition, content of glutathione and oxidized glutathione was increased under the exposure of Pb2+, which implied that glutathione might play a key role in Pb immobilization and detoxification in P. oxalicum SL2. This study elucidated partial mechanisms of Pb immobilization and speciation transformation of this strain, providing an alternative biomaterial in the bioremediation of Pb-contaminated wastewater.

Effects of combined application of nitrogen fertilizer and biochar on the nitrification and ammonia oxidizers in an intensive vegetable soil.

Soil amended with single biochar or nitrogen (N) fertilizer has frequently been reported to alter soil nitrification process due to its impact on soil properties. However, little is known about the dynamic response of nitrification and ammonia-oxidizers to the combined application of biochar and N fertilizer in intensive vegetable soil. In this study, an incubation experiment was designed to evaluate the effects of biochar and N fertilizer application on soil nitrification, abundance and community shifts of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Hangzhou greenhouse vegetable soil. Results showed that single application of biochar had no significant effect on soil net nitrification rates and ammonia-oxidizers. Conversely, the application of only N fertilizer and N fertilizer + biochar significantly increased net nitrification rate and the abundance of AOB rather than AOA, and only AOB abundance was significantly correlated with soil net nitrification rate. Moreover, the combined application of N fertilizer and biochar had greater effect on AOB communities than that of the only N fertilizers, and the relative abundance of 156 bp T-RF (Nitrosospira cluster 3c) decreased but 60 bp T-RF (Nitrosospira cluster 3a and cluster 0) increased to become a single predominant group. Phylogenetic analysis indicated that all the AOB sequences were grouped into Nitrosospira cluster, and most of AOA sequences were clustered within group 1.1b. We concluded that soil nitrification was stimulated by the combined application of N fertilizer and biochar via enhancing the abundance and shifting the community composition of AOB rather than AOA in intensive vegetable soil.

Ammonium reduces oxalate accumulation in different spinach (Spinacia oleracea L.) genotypes by inhibiting root uptake of nitrate.

Excessive accumulation of oxalate negatively affects nutritional value of many vegetables, such as spinach (Spinacia oleracea L.). Mixed solution of ammonium and nitrate could effectively reduce oxalate accumulation, while the mechanism involved remains unknown. High (Heizhenzhu) and low (Weilv) oxalate-accumulated spinach genotypes were used in this study to investigate the association of oxalate accumulation and root uptake of nitrogen. Exposure of increasing nitrate or mixed-nitrogen (nitrate:ammonium = 1:1) significantly increased leaf total and soluble oxalate contents. In contrast, increasing ammonium did not result in elevation of leaf oxalate. Correlation analysis confirmed that leaf oxalate accumulation was positively associated with root uptake of nitrate but not ammonium. Moreover, addition of ammonium significantly reduced nitrate uptake rate, and subsequently decreased leaf oxalate accumulation. The results suggest that oxalate synthesis in spinach leaves is associated with its root uptake of nitrate, and ammonium is able to reduce oxalate accumulation by inhibiting uptake of nitrate.

Comparative effects of 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) on ammonia-oxidizing bacteria and archaea in a vegetable soil.

Nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) have been used extensively to improve nitrogen fertilizer utilization in farmland. However, their comparative effects on ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in agricultural soils are still unclear. Here, we compared the impacts of these two inhibitors on soil nitrification, AOA and AOB abundance as well as their community structure in a vegetable soil by using real-time PCR and terminal restriction fragment length polymorphism (T-RFLP). Our results showed that urea application significantly increased the net nitrification rates, but were significantly inhibited by both NIs, and the inhibitory effect of DMPP was significantly greater than that of DCD. AOB growth was more greatly inhibited by DMPP than by DCD, and the net nitrification rate was significantly related to AOB abundance, but not to AOA abundance. Application of urea and NIs to soil did not change the diversity of the AOA community, with the T-RFs remaining in proportions that were similar to control soils, while the community structure of AOB exhibited obvious shifts within all different treatments compared to the control. Phylogenetic analysis showed that all AOA sequences fell within group 1.1a and group 1.1b, and the AOB community consisted of Nitrosospira cluster 3, cluster 0, and unidentified species. These results suggest that DMPP exhibited a stronger inhibitory effect on nitrification than DCD by inhibiting AOB rather than AOA.

Deriving sorption indices for the prediction of potential phosphorus loss from calcareous soils.

The aim of this study was to develop techniques to evaluate soil phosphorus (P) sorption capacity (PSC) and determine critical soil P levels to predict P loss potential for calcareous soils. Seventy-five soils mostly from Northern China were analyzed for soil P using four extraction methods (water, Pw; carbonate, POls; ammonium oxalate, Pox; and Mehlich 3, PM3) as well as PSC derived from single-point (PSC150) and multipoint sorption (S t) isotherms. Strong correlation was found between PSC150 and S t (r (2)=0.89, p<0.001). The sum of αCaM3 and ßMgM3 as an index of PSC (PSC(CaM3 + MgM3)) was most closely related to the maximum amount of P sorbed (S max) as given by the sum of S t and soil initial P setting α=0.039 and ß=0.462 (r (2)=0.80, p<0.001). The degree of P saturation (DPS) was thereafter calculated from PSC(CaM3 + MgM3) (DPS(CaM3 + MgM3)), to which Olsen P (POls) was significantly correlated (r (2)=0.82, p<0.001). In a split-line regression from Pw against DPS(CaM3 + MgM3) (r (2)=0.87, p<0.05), a change point was identified at 28.1% DPS(CaM3 + MgM3), which was equivalent to 49.2 mg kg(-1) POls and corresponded to a Pw concentration of 8.8 mg kg(-1). After the change point, a sharp increase in Pw was observed. Our results reveal a new approach to approximating DPS from CaM3 and MgM3 for calcareous soils without the need to generate a S max. We conclude that in the absence of an environmental soil test criteria for P, the DPS(CaM3 + MgM3) and POls could be used to predict P loss potential from calcareous soils.