Crizotinib inhibits the metabolism of tramadol by non-competitive suppressing the activities of CYP2D1 and CYP3A2.

Objectives: To investigate the interaction between tramadol and representative tyrosine kinase inhibitors, and to study the inhibition mode of drug-interaction. Methods: Liver microsomal catalyzing assay was developed. Sprague-Dawley rats were administrated tramadol with or without selected tyrosine kinase inhibitors. Samples were prepared and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used for analysis. Besides, liver, kidney, and small intestine were collected and morphology was examined by hematoxyline-eosin (H&E) staining. Meanwhile, liver microsomes were prepared and carbon monoxide differential ultraviolet radiation (UV) spectrophotometric quantification was performed. Results: Among the screened inhibitors, crizotinib takes the highest potency in suppressing the metabolism of tramadol in rat/human liver microsome, following non-competitive inhibitory mechanism. In vivo, when crizotinib was co-administered, the AUC value of tramadol increased compared with the control group. Besides, no obvious pathological changes were observed, including cell morphology, size, arrangement, nuclear morphology with the levels of alanine transaminase (ALT) and aspartate transaminase (AST) increased after multiple administration of crizotinib. Meanwhile, the activities of CYP2D1 and CYP3A2 as well as the total cytochrome P450 abundance were found to be decreased in rat liver of combinational group. Conclusions: Crizotinib can inhibit the metabolism of tramadol. Therefore, this recipe should be vigilant to prevent adverse reactions.

Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation.

The super elongation complex (SEC) containing P-TEFb plays a critical role in regulating transcription elongation. AFF1 and AFF4, members of the AF4/FMR2 family, act as central scaffold proteins of SEC and are associated with various human diseases. However, their precise roles in transcriptional control remain unclear. We here reveal differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites (TSSs). AFF1 mainly binds upstream of the TSSs, while AFF4 is enriched downstream of the TSSs. Notably, disruption of AFF4 results in slow elongation and early termination in a subset of AFF4 bound active genes, whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same gene subset. Additionally, AFF1 knockdown increases AFF4 levels at chromatin, and vice versa. In summary, these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate Pol II transcription.

Young LINE-1 transposon 5' UTRs marked by elongation factor ELL3 function as enhancers to regulate naïve pluripotency in embryonic stem cells.

LINE-1s are the major clade of retrotransposons with autonomous retrotransposition activity. Despite the potential genotoxicity, LINE-1s are highly activated in early embryos. Here we show that a subset of young LINE-1s, L1Md_Ts, are marked by the RNA polymerase II elongation factor ELL3, and function as enhancers in mouse embryonic stem cells. ELL3 depletion dislodges the DNA hydroxymethylase TET1 and the co-repressor SIN3A from L1Md_Ts, but increases the enrichment of the Bromodomain protein BRD4, leading to loss of 5hmC, gain of H3K27ac, and upregulation of the L1Md_T nearby genes. Specifically, ELL3 occupies and represses the L1Md_T-based enhancer located within Akt3, which encodes a key regulator of AKT pathway. ELL3 is required for proper ERK activation and efficient shutdown of naïve pluripotency through inhibiting Akt3 during naïve-primed transition. Our study reveals that the enhancer function of a subset of young LINE-1s controlled by ELL3 in transcription regulation and mouse early embryo development.

Characteristics and provenances of rare earth elements and Nd isotopes in surface sediments of mangrove wetlands in the Jiulong River Estuary, China.

Rare earth elements (REEs) and Nd isotopes are frequently employed to determine provenance, although their characteristics and provenances in the surface sediments of mangrove wetlands are rarely analyzed. In this study, a thorough analysis of the characteristics and provenances of REEs and Nd isotopes in the surface sediments of mangrove wetland in the Jiulong River Estuary was carried out. According to the results, the mean concentration of REEs in the surface sediments was 290.9 mg·kg-1, which was greater than the background value. Unpolluted to moderately polluted for La and Ce, as well as a moderate ecological risk for Lu, were indicated by the geoaccumulation index (Igeo) and potential ecological risk of individual factors ([Formula: see text]), respectively. The surface sediments showed substantial negative Eu anomalies but no significant Ce anomalies. The enrichments in LREE and flat HREE patterns are visible in the chondrite-normalized REE patterns. REEs in the surface sediments might be attributed to both natural sources (granite and magmatic rocks) and anthropogenic activities, including coal combustion, vehicle exhaust, steel smelting, and fertilizer, based on the (La/Yb)N-∑REE and ternary (La/Yb)N-(La/Sm)N-(Gd/Yb)N plots. The three-dimensional ∑LREE/∑HREE-Eu/Eu*-εNd(0) plot, when combined with the Nd isotope, further demonstrated that the REEs in the surface sediments appeared to have come from additional nonlocal potential sources.

Source apportionment and transfer characteristics of Pb in a soil-rice-human system, Jiulong River Basin, southeast China.

The source apportionment and transfer of Pb in a paddy soil-rice-human system within the Jiulong River Basin in southeast China was investigated by analyzing (1) the chemical fractionation of Pb in paddy soils using a modified BCR four-step sequential extraction procedure, and (2) the bioaccessibility of Pb in both paddy soils and rice grains using a Simple Bioaccessibility Extraction Test method. In addition, a qualitative Pb isotopic model was used in combination with IsoSource software to quantify the contribution of potential Pb sources. The results show the enrichment of Pb in agro-ecosystems in the Jiulong River Basin. Contaminant Pb in paddy soils was mainly present in the reducible (42.9%) and the residual fractions (27.1%). The average bioaccessibility of Pb in rice grains was significantly higher than that in paddy soil, with values of 77.85% and 37.44%, respectively. Lead in paddy soils was primarily derived from agricultural (35.3%), natural (25.5%), industrial (24.5%) and coal combustion sources (14.7%), while Pb in rice grains was primarily derived from coal combustion (54.1%), agricultural (35.1%), industrial (6.0%) and natural sources (4.8%). The bioaccessible Pb was mainly derived from anthropogenic sources [agricultural (42.3% for soil and 25.3% for grain) and coal combustion sources (25.3% for soil and 59.3% for grain)]. Lead isotopic ratios are an effective tracer of Pb transfer from potential sources to rice plants and within the rice plants. Rice plants absorb Pb from the soil and the atmosphere through the roots and leaves, respectively. Most of the Pb was accumulated in roots. The integrated use of chemical fractionation, bioaccessibility and Pb isotopic data provides an effective method to study the source apportionment and transfer characteristics of Pb in paddy soil-rice-human systems.

The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release.

Release of promoter-proximally paused RNA Pol II into elongation is a tightly regulated and rate-limiting step in metazoan gene transcription. However, the biophysical mechanism underlying pause release remains unclear. Here, we demonstrate that the pausing and elongation regulator SPT5 undergoes phase transition during transcriptional pause release. SPT5 per se is prone to form clusters. The disordered domain in SPT5 is required for pause release and gene activation. During early elongation, the super elongation complex (SEC) induces SPT5 transition into elongation droplets. Depletion of SEC increases SPT5 pausing clusters. Furthermore, disease-associated SEC mutations impair phase properties of elongation droplets and transcription. Our study suggests that SEC-mediated SPT5 phase transition might be essential for pause release and early elongation and that aberrant phase properties could contribute to transcription abnormality in diseases.

QSER1 preserves the suppressive status of the pro-apoptotic genes to prevent apoptosis.

Activation of the pro-apoptotic genes by the p53 family is a critical step in induction of apoptosis. However, the molecular signaling underlying their suppression remains largely unknown. Here, we report a general role of QSER1 in preventing apoptosis. QSER1 is widely up-regulated in multiple cancers, and its up-regulation correlates with poor clinic outcomes. QSER1 knockdown significantly promotes apoptosis in both p53 wild type and mutant cancer cells. Interestingly, we show that QSER1 and p53 occupy distinct cis-regulatory regions in a common subset of the pro-apoptotic genes, and function antagonistically to maintain their proper expression. Furthermore, we identify a key regulatory DNA element named QSER1 binding site in PUMA (QBP). Deletion of QBP de-represses PUMA and induces apoptosis. Mechanistically, QSER1 functions together with SIN3A to suppress PUMA in a p53-dependent and -independent manner, suggesting that QSER1 inhibition might be a potential therapeutic strategy to induce apoptosis in cancers.

Phase Separation Properties in Transcriptional Organization.

Transcription is of great importance to stress response, fate control, and development, involving the functional cooperation of a large number of transcription factors and cofactors. Transcription machineries assemble rapidly to respond to the physiological and functional needs of cells. Recently, phase-separated biomolecular condensates have emerged as a universal biophysical basis for the spatiotemporal coordination of various cellular activities, including transcription. Here, we summarize and discuss recent advances in understanding of how phase separation contributes to RNA polymerase II (Pol II)-mediated transcriptional regulation, with a focus on the physical properties and dynamics of transcriptional condensates.

ZFP281-BRCA2 prevents R-loop accumulation during DNA replication.

R-loops are prevalent in mammalian genomes and involved in many fundamental cellular processes. Depletion of BRCA2 leads to aberrant R-loop accumulation, contributing to genome instability. Here, we show that ZFP281 cooperates with BRCA2 in preventing R-loop accumulation to facilitate DNA replication in embryonic stem cells. ZFP281 depletion reduces PCNA levels on chromatin and impairs DNA replication. Mechanistically, we demonstrate that ZFP281 can interact with BRCA2, and that BRCA2 is enriched at G/C-rich promoters and requires both ZFP281 and PRC2 for its proper recruitment to the bivalent chromatin at the genome-wide scale. Furthermore, depletion of ZFP281 or BRCA2 leads to accumulation of R-loops over the bivalent regions, and compromises activation of the developmental genes by retinoic acid during stem cell differentiation. In summary, our results reveal that ZFP281 recruits BRCA2 to the bivalent chromatin regions to ensure proper progression of DNA replication through preventing persistent R-loops.

Epigenetic reorganization during early embryonic lineage specification.

BACKGROUND: Dynamic chromatin reorganization occurs during two waves of cell lineage specification process, blastocyst formation and gastrulation, to generate distinct cell types. Epigenetic defects have been associated with severe developmental defects and diseases. How epigenetic remodeling coordinates the two lineage specification waves is becoming uncovered, benefiting from the development and application of new technologies including low-input or single-cell epigenome analysis approached in the past few years. OBJECTIVE: In this review, we aim to highlight the most recent findings on epigenetic remodeling in cell lineage specification during blastocyst formation and gastrulation. METHODS: First, we introduce how DNA methylation dynamically changes in blastocyst formation and gastrulation and its function in transcriptional regulation lineage-specific genes. Then, we discuss widespread remodeling of histone modification at promoters and enhancers in orchestrating the trajectory of cell lineage specification. Finally, we review dynamics of chromatin accessibility and 3D structure regulating developmental gene expression and associating with specific transcription factor binding events at stage specific manner. We also highlight the key questions that remain to be answered to fully understand chromatin regulation and reorganization in lineage specification. CONCLUSION: Here, we summarize the recent advances and discoveries on epigenetic reorganization and its roles in blastocyst formation and gastrulation, and how it cooperates with the lineage specification, painting from global sequencing data from mouse in vivo tissues.

Thermosensitive hydrogel-functionalized gold nanorod/mesoporous MnO2 nanoparticles for tumor cell-triggered drug delivery.

MnO2 owns distinct redox, imaging, and degradable properties corresponding to the tumor microenvironment. However, the onefold structure and non-modifiable property cause many obstacles to anticancer applications. In this report, we first prepared a typical core-shell gold nanorod (GNR)/manganese dioxide (MnO2) nanoparticles (GNR/MnO2 NPs). Interestingly, the MnO2 had a mesoporous channel and modifiable hydroxyl group (OH). Here, the unique 'OH' groups were modified and further grafted with poly(N-isopropylacrylamide-co-acrylic acid) (PNA). As a dual-sensitive hydrogel, it was selected as the thermal/pH-sensitive component in the hybrid nanoparticles (GNR/MnO2/PNA NPs). The anticancer drug doxorubicin hydrochloride (DOX) was selected and loaded into the hybrid nanoparticles (GNR/MnO2/PNA-DOX NPs). The GNR/MnO2/PNA NPs achieved satisfying drug-loading efficiency and glutathione (GSH)/pH/thermal-responsive drug-controlled release. As a side benefit, the GNR/MnO2/PNA NPs showed potential as excellent near-infrared (NIR)-excited nanoplatforms for photothermal therapy (PTT). Delightedly, the studies demonstrated that the GNR/MnO2/PNA-DOX NPs showed a noticeable killing effect on tumor cells, whether it is tumor cell-triggered drug release or photothermal effect. Besides, it not only could enhance mitochondrial damage but also could inhibit the migration and invasion of tumor cells. Quite the reverse, it had little negative impact on normal cells. The feature can prevent anticancer drugs and nanoparticles from killing normal cells. Consequently, GNR/MnO2/PNA NPs have potential applications in drug delivery and synergistic therapy due to these advantageous features.

Decoding brain encoded by genome.

Human brain is the most complicated living organ in nature. How the human genome encodes the structure and function of brain is a fundamental question to understand the essence of mind. Currently, it is still an unsolved scientific problem requiring the further breakthrough of comprehensive technologies. Here, we summarize the recent advances in brain development/function OMICS studies, and discuss the huge challenges and prospects in understanding how brain is encoded by genome.

Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis.

Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset comparisons at population resolution on simulated and real data. Using Kssd, we prioritize references for all 1,019,179 bacteria whole genome sequencing (WGS) runs from NCBI Sequence Read Archive and find misidentification or contamination in 6164 of these. Additionally, we analyze WGS and exome runs of samples from the 1000 Genomes Project.

Suppression of the NTS-CPS1 regulatory axis by AFF1 in lung adenocarcinoma cells.

Upregulation of the neuropeptide neurotensin (NTS) in a subgroup of lung cancers has been linked to poor prognosis. However, the regulatory pathway centered on NTS in lung cancer remains unclear. Here we identified the NTS-specific enhancer in lung adenocarcinoma cells. The AF4/FMR2 (AFF) family protein AFF1 occupies the NTS enhancer and inhibits NTS transcription. Clustering analysis of lung adenocarcinoma gene expression data demonstrated that NTS expression is highly positively correlated with the expression of the oncogenic factor CPS1. Detailed analyses demonstrated that the IL6 pathway antagonizes NTS in regulating CPS1. Thus, our analyses revealed a novel NTS-centered regulatory axis, consisting of AFF1 as a master transcription suppressor and IL6 as an antagonist in lung adenocarcinoma cells.

[Bioaccessibility and Health Risks of the Heavy Metals in Soil-Rice System of Southwest Fujian Province].

The bioaccessibility and health risks of heavy metals in soil-rice system of southwestern Fujian province were studied by combining a simple bioavailability extraction method (SBET) with a health risk assessment model. The results showed that some heavy metals in the agricultural soils and rice of southwestern Fujian province were enriched. The contents of Cd, Zn, Pb, and Cu were greater than the screening value of soil pollution risk for agricultural land (GB 15618-2018) by 32.4%, 15.5%, 14.1%, and 12.7% in the study areas, respectively. The accumulation ability of heavy metals was different and followed the approximately decreasing order of Cd > Zn > Cu > Ni > Hg > As > Cr > Pb. The bioaccessibility of heavy metals in soils and rice were quite different. The bioaccessibility of each heavy metal in rice was greater than the bioaccessibility of the heavy metals in soil, which indicated that the heavy metals in rice were more easily absorbed by the human body. The comprehensive non-carcinogenic risk index (HI) of heavy metals to adults and children was 2.71 and 4.06, respectively, indicating that there were non-carcinogenic risks. The comprehensive carcinogenic risk index (TCR) of heavy metals to adults and children was 1.42×10-3 and 5.28×10-4, respectively, indicating that there was a carcinogenic risk present. The non-carcinogenic risks were mainly due to As, while the carcinogenic risks were mainly contributed by Cd. The non-carcinogenic risk of children was higher than that of adults, while the carcinogenic risk of children was lower than that of adults. This result may be related to physiological characteristics, exposure period, and dietary intake. The dietary intake route may be the main pathway for heavy metals in the soil-rice system of southwest Fujian province to cause health risks. Therefore, more attention should be paid to the risks of dietary exposure in the risk management of heavy metals.

RNF219 interacts with CCR4-NOT in regulating stem cell differentiation.

Regulation of RNA stability plays a crucial role in gene expression control. Deadenylation is the initial rate-limiting step for the majority of RNA decay events. Here, we show that RING finger protein 219 (RNF219) interacts with the CCR4-NOT deadenylase complex. RNF219-CCR4-NOT exhibits deadenylation activity in vitro. RNA-seq analyses identify some of the 2-cell-specific genes and the neuronal genes significantly downregulated upon RNF219 knockdown, while upregulated after depletion of the CCR4-NOT subunit CNOT10 in mouse embryonic stem (ES) cells. RNF219 depletion leads to impaired neuronal lineage commitment during ES cell differentiation. Our study suggests that RNF219 is a novel interacting partner of CCR4-NOT and required for maintenance of ES cell pluripotency.

Diploid genome architecture revealed by multi-omic data of hybrid mice.

Although mammalian genomes are diploid, previous studies extensively investigated the average chromatin architectures without considering the differences between homologous chromosomes. We generated Hi-C, ChIP-seq, and RNA-seq data sets from CD4 T cells of B6, Cast, and hybrid mice, to investigate the diploid chromatin organization and epigenetic regulation. Our data indicate that inter-chromosomal interaction patterns between homologous chromosomes are similar, and the similarity is highly correlated with their allelic coexpression levels. Reconstruction of the 3D nucleus revealed that distances of the homologous chromosomes to the center of nucleus are almost the same. The inter-chromosomal interactions at centromere ends are significantly weaker than those at telomere ends, suggesting that they are located in different regions within the chromosome territories. The majority of A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments owing to cis effect. About 95% of the trans-effected B6/Cast divergent compartments converge to the same compartment status potentially because of a shared cellular environment. We showed the differentially expressed genes between the two haploids in hybrid were associated with either genetic or epigenetic effects. In summary, our multi-omics data from the hybrid mice provided haploid-specific information on the 3D nuclear architecture and a rich resource for further understanding the epigenetic regulation of haploid-specific gene expression.

ENL initiates multivalent phase separation of the super elongation complex (SEC) in controlling rapid transcriptional activation.

Release of paused RNA polymerase II (Pol II) requires incorporation of the positive transcription elongation factor b (P-TEFb) into the super elongation complex (SEC), thus resulting in rapid yet synchronous transcriptional activation. However, the mechanism underlying dynamic transition of P-TEFb from inactive to active state remains unclear. Here, we found that the SEC components are able to compartmentalize and concentrate P-TEFb via liquid-liquid phase separation from the soluble inactive HEXIM1 containing the P-TEFb complex. Specifically, ENL or its intrinsically disordered region is sufficient to initiate the liquid droplet formation of SEC. AFF4 functions together with ENL in fluidizing SEC droplets. SEC droplets are fast and dynamically formed upon serum exposure and required for rapid transcriptional induction. We also found that the fusion of ENL with MLL can boost SEC phase separation. In summary, our results suggest a critical role of multivalent phase separation of SEC in controlling transcriptional pause release.

Provenance and bioaccessibility of rare earth elements in atmospheric particles in areas impacted by the optoelectronic industry.

Rare earth elements (REEs) are widely used in optoelectronic industries, and they can be emitted into the environment and may induce biological effects. In this study, we investigated the provenance and bioaccessibility of REEs in atmospheric particles (APs) collected from areas impacted by the optoelectronic industry. The geoaccumulation index (Igeo) values showed that Y, Eu, and Tb were much more enriched in the APs from the optoelectronic recycling sites than in those from the optoelectronic producing sites and were not enriched in the APs from the optoelectronic administrative sites and background sites. The characteristic parameters and the distribution patterns of REEs demonstrated that the AP samples from the recycling sites and producing sites showed remarkably positive Eu and Tb anomalies. According to the positive matrix factorization (PMF) model, the optoelectronic industry was quantitatively determined to contribute 82.8% of Y, 86.5% of Eu, and 83.4% of Tb. Furthermore, an in vitro physiologically based extraction test (PBET) was performed to assess the bioaccessibility of REEs in the APs. The results showed that the bioaccessibility of all the REEs in the APs was below 50.0% in the human gastrointestinal tract, with higher values in the gastric phases than in the intestinal phases. In particular, extremely low gastric bioaccessibilities of Tb and Ce and relatively high gastric bioaccessibilities of Y and Eu were observed in the APs from the recycling sites and producing sites, which may due to the chemical composition of the compounds containing REEs that are used in the optoelectronic industry. In conclusion, our results provide additional information about the contribution and influence of the optoelectronic industry on the provenance and bioaccessibility of REEs in APs.