Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase.

Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2 tetramers as part of the replication-dependent chromatin assembly process. Loss of CAF-1 leads to a delay in chromatin maturation, albeit with minimal impact on steady-state chromatin structure. However, the mechanisms by which CAF-1 mediates the deposition of (H3-H4)2 tetramers and the phenotypic consequences of CAF-1-associated assembly defects are not well understood. We used nascent chromatin occupancy profiling to track the spatiotemporal kinetics of chromatin maturation in both wild-type (WT) and CAF-1 mutant yeast cells. Our results show that loss of CAF-1 leads to a heterogeneous rate of nucleosome assembly, with some nucleosomes maturing at near WT kinetics and others showing significantly slower maturation kinetics. The slow-to-mature nucleosomes are enriched in intergenic and poorly transcribed regions, suggesting that transcription-dependent assembly mechanisms can reset the slow-to-mature nucleosomes following replication. Nucleosomes with slow maturation kinetics are also associated with poly(dA:dT) sequences, which implies that CAF-1 deposits histones in a manner that counteracts resistance from the inflexible DNA sequence, promoting the formation of histone octamers as well as ordered nucleosome arrays. In addition, we show that the delay in chromatin maturation is accompanied by a transient and S-phase-specific loss of gene silencing and transcriptional regulation, revealing that the DNA replication program can directly shape the chromatin landscape and modulate gene expression through the process of chromatin maturation.

Macrophage-organoid co-culture model for identifying treatment strategies against macrophage-related gemcitabine resistance.

BACKGROUND: Gemcitabine resistance (GR) is a significant clinical challenge in pancreatic adenocarcinoma (PAAD) treatment. Macrophages in the tumor immune-microenvironment are closely related to GR. Uncovering the macrophage-induced GR mechanism could help devise a novel strategy to improve gemcitabine treatment outcomes in PAAD. Therefore, preclinical models accurately replicating patient tumor properties are essential for cancer research and drug development. Patient-derived organoids (PDOs) represent a promising in vitro model for investigating tumor targets, accelerating drug development, and enabling personalized treatment strategies to improve patient outcomes. METHODS: To investigate the effects of macrophage stimulation on GR, co-cultures were set up using PDOs from three PAAD patients with macrophages. To identify signaling factors between macrophages and pancreatic cancer cells (PCCs), a 97-target cytokine array and the TCGA-GTEx database were utilized. The analysis revealed CCL5 and AREG as potential candidates. The role of CCL5 in inducing GR was further investigated using clinical data and tumor sections obtained from 48 PAAD patients over three years, inhibitors, and short hairpin RNA (shRNA). Furthermore, single-cell sequencing data from the GEO database were analyzed to explore the crosstalk between PCCs and macrophages. To overcome GR, inhibitors targeting the macrophage-CCL5-Sp1-AREG feedback loop were evaluated in cell lines, PDOs, and orthotopic mouse models of pancreatic carcinoma. RESULTS: The macrophage-CCL5-Sp1-AREG feedback loop between macrophages and PCCs is responsible for GR. Macrophage-derived CCL5 activates the CCR5/AKT/Sp1/CD44 axis to confer stemness and chemoresistance to PCCs. PCC-derived AREG promotes CCL5 secretion in macrophages through the Hippo-YAP pathway. By targeting the feedback loop, mithramycin improves the outcome of gemcitabine treatment in PAAD. The results from the PDO model were corroborated with cell lines, mouse models, and clinical data. CONCLUSIONS: Our study highlights that the PDO model is a superior choice for preclinical research and precision medicine. The macrophage-CCL5-Sp1-AREG feedback loop confers stemness to PCCs to facilitate gemcitabine resistance by activating the CCR5/AKT/SP1/CD44 pathway. The combination of gemcitabine and mithramycin shows potential as a therapeutic strategy for treating PAAD in cell lines, PDOs, and mouse models.

Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase.

Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2 tetramers as part of the replication-dependent chromatin assembly process. Loss of CAF-1 leads to a delay in chromatin maturation, albeit with minimal impact on steady-state chromatin structure. However, the mechanisms by which CAF-1 mediates the deposition of (H3-H4)2 tetramers and the phenotypic consequences of CAF-1-associated assembly defects are not well understood. We used nascent chromatin occupancy profiling to track the spatiotemporal kinetics of chromatin maturation in both wild-type (WT) and CAF-1 mutant yeast cells. Our results show that loss of CAF-1 leads to a heterogeneous rate of nucleosome assembly, with some nucleosomes maturing at near WT kinetics and others exhibiting significantly slower maturation kinetics. The slow-to-mature nucleosomes are enriched in intergenic and poorly transcribed regions, suggesting that transcription-dependent assembly mechanisms can reset the slow-to-mature nucleosomes following replication. Nucleosomes with slow maturation kinetics are also associated with poly(dA:dT) sequences, which implies that CAF-1 deposits histones in a manner that counteracts resistance from the inflexible DNA sequence, promoting the formation of histone octamers as well as ordered nucleosome arrays. In addition, we demonstrate that the delay in chromatin maturation is accompanied by a transient and S-phase specific loss of gene silencing and transcriptional regulation, revealing that the DNA replication program can directly shape the chromatin landscape and modulate gene expression through the process of chromatin maturation.

Decreased Expression of Programmed Death Ligand-L1 by Seven in Absentia Homolog 2 in Cholangiocarcinoma Enhances T-Cell-Mediated Antitumor Activity.

N6-methyladenosine (m6A) has been reported as an important mechanism of post-transcriptional regulation. Programmed death ligand 1 (PD-L1) is a primary immune inhibitory molecule expressed on tumor cells that promotes immune evasion. In addition, seven in absentia homolog 2 (Siah2), a RING E3 ubiquitin ligase, has been involved in tumorigenesis and cancer progression. However, the role of m6A-METTL14-Siah2-PD-L1 axis in immunotherapy remains to be elucidated. In this study, we showed that METTL14, a component of the m6A methyltransferase complex, induced Siah2 expression in cholangiocarcinoma (CCA). METTL14 was shown to enrich m6A modifications in the 3'UTR region of the Siah2 mRNA, thereby promoting its degradation in an YTHDF2-dependent manner. Furthermore, co-immunoprecipitation experiments demonstrated that Siah2 interacted with PD-L1 by promoting its K63-linked ubiquitination. We also observed that in vitro and in vivo Siah2 knockdown inhibited T cells expansion and cytotoxicity by sustaining tumor cell PD-L1 expression. The METTL14-Siah2-PD-L1-regulating axis was further confirmed in human CCA specimens. Analysis of specimens from patients receiving anti-PD1 immunotherapy suggested that tumors with low Siah2 levels were more sensitive to anti-PD1 immunotherapy. Taken together, our results evidenced a new regulatory mechanism of Siah2 by METTL14-induced mRNA epigenetic modification and the potential role of Siah2 in cancer immunotherapy.

Corrigendum: Decreased expression of programmed death ligand-L1 by seven in absentia homolog 2 in cholangiocarcinoma enhances T-cell-mediated antitumor activity.

[This corrects the article DOI: 10.3389/fimmu.2022.845193.].

A review on phytoremediation of mercury contaminated soils.

Mercury (Hg) and its compounds are one of the most dangerous environmental pollutants and Hg pollution exists in soils in different degrees over the world. Phytoremediation of Hg-contaminated soils has attracted increasing attention for the advantages of low investment, in-situ remediation, potential economic benefits and so on. Searching for the hyperaccumulator of Hg and its application in practice become a research hotspot. In this context, we review the current literatures that introduce various experimental plant species for accumulating Hg and aided techniques improving the phytoremediation of Hg-contaminated soils. Experimental plant species for accumulating Hg and accumulation or translocation factor of Hg are listed in detail. The translocation factor (TF) is greater than 1.0 for some plant species, however, the bioaccumulation factor (BAF) is greater than 1.0 for Axonopus compressus only. Plant species, soil properties, weather condition, and the bioavailability and heterogeneity of Hg in soils are the main factors affecting the phytoremediation of Hg-contaminated soils. Chemical accelerator kinds and promoting effect of chemical accelerators for accumulating and transferring Hg by various plant species are also discussed. Potassium iodide, compost, ammonium sulphate, ammonium thiosulfate, sodium sulfite, sodium thiosulfate, hydrochloric acid and sulfur fertilizer may be selected to promote the absorption of Hg by plants. The review introduces transgenic gene kinds and promoting effect of transgenic plants for accumulating and transferring Hg in detail. Some transgenic plants can accumulate more Hg than non-transgenic plants. The composition of rhizosphere microorganisms of remediation plants and the effect of rhizosphere microorganisms on the phytoremediation of Hg-contaminated soils are also introduced. Some rhizosphere microorganisms can increase the mobility of Hg in soils and are beneficial for the phytoremediation.

Toxicity assessment of artificially added zinc, selenium, and strontium in water.

The present research was to study the toxicology of artificially added Zn, Se and Sr in water. Specifically, we investigated the mortality and liver toxicity in zebrafish (Danio rerio), caused by different water concentrations of zinc sulfate (ZnSO4), sodium selenite (Na2SeO3), and strontium chloride hexahydrate (6H2O·SrCl2). Adult and embryo-larval zebrafish were used in the experiment. Analysis was performed of mortality, liver area and impermeability, delayed absorption area of the yolk sac, and liver tissue structure. The concentration change of sodium selenite exerted the most significant effect on the mortality of adult zebrafish, followed by that of strontium chloride hexahydrate, and zinc sulfate. Elevated strontium chloride hexahydrate concentration was associated with liver toxicity in zebrafish in the preliminary experiment. However, embryo-larval zebrafish were observed to die when the concentration of Zn2+ or Se4+ increased to a certain extent, without obvious liver toxicity. Our results indicated strontium chloride hexahydrate was hepatotoxic to embryo-larval zebrafish, which was manifested mainly as hepatomegaly and delayed absorption of the yolk sac. In addition, the artificially added strontium chloride hexahydrate destroyed liver tissue structure, resulting in hepatocyte enlargement, cell nucleus enlargement, blurred cytoplasmic boundaries, and formation of a vacuolar liver. These findings suggest the amount of strontium chloride hexahydrate added in soft drinks should be limited to certain levels.

Effects of a foliar spray of selenite or selenate at different growth stages on selenium distribution and quality of blueberries.

BACKGROUND: Foliar spraying of selenium (Se) has increasingly been applied to improve Se concentrations in grain crops, although little information is available about the properties of Se-enriched fruits. In the present study, selenium distribution in blueberry and Se effect on blueberry quality were investigated by foliar spraying selenite or selenate (200 g ha-1 ) on two blueberry cultivars (Bluecrop and Northland) during the young fruit or coloring stage. RESULTS: Selenium concentration in blueberry was mainly affected by cultivar and spray stage relative to the Se source. Northland was 1.3- to 1.5-fold higher than Bluecrop with respect to Se enrichment. Se treatment at the young fruit stage induced a 1.5- to 2.3-fold increase compared to that at the coloring stage with respect to the Se concentration of blueberry. Additionally, selenium was mainly stored in pomace, with an accumulative distribution ratio of 89.3-94.9%. The proportion of organic Se reached up to 77.0% in blueberry. Furthermore, the foliar application of Se significantly increased the anthocyanin concentration and the intact fruit rate of blueberry. CONCLUSION: Se-enriched blueberry can be used as a 'functional food'. Because Se was mainly accumulated in the pomace, the consumption of blueberries as fresh fruit, dried fruit and jam can improve the efficiency of Se supplement. © 2018 Society of Chemical Industry.