2'-O-methylation at internal sites on mRNA promotes mRNA stability.

2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.

MLL4 Is Required to Maintain Broad H3K4me3 Peaks and Super-Enhancers at Tumor Suppressor Genes.

Super-enhancers are large clusters of enhancers that activate gene expression. Broad trimethyl histone H3 lysine 4 (H3K4me3) often defines active tumor suppressor genes. However, how these epigenomic signatures are regulated for tumor suppression is little understood. Here we show that brain-specific knockout of the H3K4 methyltransferase MLL4 (a COMPASS-like enzyme, also known as KMT2D) in mice spontaneously induces medulloblastoma. Mll4 loss upregulates oncogenic Ras and Notch pathways while downregulating neuronal gene expression programs. MLL4 enhances DNMT3A-catalyzed DNA methylation and SIRT1/BCL6-mediated H4K16 deacetylation, which antagonize expression of Ras activators and Notch pathway components, respectively. Notably, Mll4 loss downregulates tumor suppressor genes (e.g., Dnmt3a and Bcl6) by diminishing broad H3K4me3 and super-enhancers and also causes widespread impairment of these epigenomic signatures during medulloblastoma genesis. These findings suggest an anti-tumor role for super-enhancers and provide a unique tumor-suppressive mechanism in which MLL4 is necessary to maintain broad H3K4me3 and super-enhancers at tumor suppressor genes.

Low RNA stability signifies increased post-transcriptional regulation of cell identity genes.

Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.

Effects of Inorganic Salts on the Phase Separation of Partially Miscible Solutes.

Partially miscible solutions with a lower critical solution temperature have promising applications in the field of physical chemistry. To better guide the utilization of these solutions in practice, we conduct an in-depth study about the phase separation behavior of the solution added with inorganic salts. The addition of the inorganic salts into the solution is found to consequently reduce the phase separation temperature. The variation of concentrations of inorganic salts does not notably affect the mass fraction of the separation. Moreover, the addition of inorganic salts in the solutions at lower mass fractions improves the separation mass fraction, while the addition of inorganic salts decreases the separation mass fraction at the mass fractions above 30%. It sheds light on selecting the proper mass fractions and inorganic salt concentrations. Furthermore, we explore the phase separation behavior of mixed solutions under different inorganic salt additions by means of a high-speed camera. The phase separation behavior under different inorganic salt systems shows a similar trend. However, calcium ions and Fe3+ ions in the solutions can greatly decrease the rate of droplet coalescence and result in an increase in phase separation. For better regulating the solutions with a lower critical solution temperature through inorganic salts, sodium chloride or potassium chloride is recommended with an appropriate concentration.

A wireless fluorescent flexible force sensor based on aggregation-induced emission doped liquid crystal elastomers.

Flexible strain sensors have drawn a lot of interest in various applications including human mobility tracking, rehabilitation/personalized health monitoring, and human-machine interaction, but suffer from interference of electromagnetic (EM). To overcome the EM interference, flexible force sensors without sensitive electronic elements have been developed, with drawbacks of bulky modules that hinders their applications in remote measurement with power-free environment. Therefore, it is highly desirable to fabricate a compact wireless flexible force sensor but it is still a challenge. Here, we demonstrate a fluorescent flexible force sensor based on aggregation-induced emission (AIE) doped liquid crystal elastomer (LCE) experimentally. The proposed force sensor film can be used to measure force through the variation of fluorescent intensity induced by the extension or contraction of LCE film, which leads to reduce or increase of the aggregation degree of AIE molecules within. This compact wireless force sensor features lightweight, low-cost, high flexibility, passivity and anti-EM interference, which also enables the naked eye observation. The proposed sensor provides inspiration and a platform for a new concept of non-contact detection, showing application potential in human-friendly interactive electronics and remote-control integration platform.

CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells.

Despite being a member of the chromodomain helicase DNA-binding protein family, little is known about the exact role of CHD6 in chromatin remodeling or cancer disease. Here we show that CHD6 binds to chromatin to promote broad nucleosome eviction for transcriptional activation of many cancer pathways. By integrating multiple patient cohorts for bioinformatics analysis of over a thousand prostate cancer datasets, we found CHD6 expression elevated in prostate cancer and associated with poor prognosis. Further comprehensive experiments demonstrated that CHD6 regulates oncogenicity of prostate cancer cells and tumor development in a murine xenograft model. ChIP-Seq for CHD6, along with MNase-Seq and RNA-Seq, revealed that CHD6 binds on chromatin to evict nucleosomes from promoters and gene bodies for transcriptional activation of oncogenic pathways. These results demonstrated a key function of CHD6 in evicting nucleosomes from chromatin for transcriptional activation of prostate cancer pathways.

A highly potent small-molecule antagonist of exportin-1 selectively eliminates CD44+CD24- enriched breast cancer stem-like cells.

Breast cancer stem-like cells (BCSCs) have been suggested as the underlying cause of tumor recurrence, metastasis and drug resistance in triple-negative breast cancer (TNBC). Here, we report the discovery and biological evaluation of a highly potent small-molecule antagonist of exportin-1, LFS-1107. We ascertained that exportin-1 (also named as CRM1) is a main cellular target of LFS-1107 by nuclear export functional assay, bio-layer interferometry binding assay and C528S mutant cell line. We found that LFS-1107 significantly inhibited TNBC tumor cells at low-range nanomolar concentration and LFS-1107 can selectively eliminate CD44+CD24- enriched BCSCs. We demonstrated that LFS-1107 can induce the nuclear retention of Survivin and consequent strong suppression of STAT3 transactivation abilities and the expression of downstream stemness regulators. Administration of LFS-1107 can strongly inhibit tumor growth in mouse xenograft model and eradicate BCSCs in residual tumor tissues. Moreover, LFS-1107 can significantly ablate the patient-derived tumor organoids (PDTOs) of TNBC as compared to a few approved cancer drugs. Lastly, we revealed that LFS-1107 can enhance the killing effects of chemotherapy drugs and downregulate multidrug resistance related protein targets. These new findings provide preclinical evidence of defining LFS-1107 as a promising therapeutic agent to deplete BCSCs for the treatment of TNBC.

Carbon dots stabilized photoluminescent blue phase liquid crystals.

Blue phase liquid crystals (BPLCs) have significant potential in the field of liquid crystal displays (LCDs) and are proposed as potential next-generation of LCDs candidates. However, BPLCs do not emit light directly and need an extra backlight device. As a result, the blue phase liquid crystal display retains the disadvantages of low brightness and low energy efficiency, which remarkably limit its application. Recently, as a kind of novel fluorescent carbon nanomaterials, carbon dots (CDs) have captured considerable attention because of their excellent optical properties. Here, CDs were directly synthesized by a simple solvothermal method and introduced into BPLCs. By combining the excellent optical properties of CDs with the blue phase liquid crystal system, the photoluminescent blue phase liquid crystals (CDs-BPLCs) with self-photoluminescence are prepared. Meanwhile, the stability of BPLCs can be improved by CDs. Such CDs-BPLCs have enormous potential in the development of novel energy-saving display devices.

Adsorption Behavior of a Ternary Covalent Organic Polymer Anchored with SO3H for Ciprofloxacin.

Owing to the poor treatment efficiency of wastewater containing fluoroquinolones (FQs), effective removal of such pollutants has become a significant issue in waste management. In this study, a ternary covalent organic polymer anchored with SO3H (COP-SO3H) was designed using the Schiff reaction and a multicomponent solvent thermal method. The synthesized COP-SO3H polymer possesses multiple functional binding sites, including amide groups, sulfonic groups, and aromatic frameworks, enabling it to effectively adsorb ciprofloxacin (which belongs to FQs) through mechanisms such as pore-filling effects, electrostatic interactions, hydrogen bonding, π-π electron donor-acceptor (EDA) interactions, and hydrophilic-lipophilic balance. COP-SO3H demonstrated outstanding adsorption performance for ciprofloxacin, exhibiting a high adsorption capacity, broad pH stability, strong resistance to ionic interference, and good regenerability. Moreover, it displayed preferential selectivity toward fluoroquinolone antibiotics. The present study not only investigates the intricate structural and functional design of COP-SO3H materials but also presents potential applications for the efficient adsorption of specific antibiotics.

MIF as a biomarker and therapeutic target for overcoming resistance to proteasome inhibitors in human myeloma.

Multiple myeloma (MM) remains largely incurable despite significant advances in biotherapy and chemotherapy. The development of drug resistance is a major problem in MM management. Macrophage migration inhibitory factor (MIF) expression was significantly higher in purified MM cells from relapsed patients than those with sustained response, and MM patients with high MIF had significantly shorter progression-free survival (PFS) and overall survival (OS). MM cell lines also express high levels of MIF, and knocking out MIF made them more sensitive to proteasome inhibitor (PI)-induced apoptosis not observed with other chemotherapy drugs. Mechanistic studies showed that MIF protects MM cells from PI-induced apoptosis by maintaining mitochondrial function via suppression of superoxide production in response to PIs. Specifically, MIF, in the form of a homotrimer, acts as a chaperone for superoxide dismutase 1 (SOD1) to suppress PI-induced SOD1 misfolding and to maintain SOD1 activity. MIF inhibitor 4-iodo-6-phenylpyrimidine and homotrimer disrupter ebselen, which do not kill MM cells, enhanced PI-induced SOD1 misfolding and loss of function, resulting in significantly more cell death in both cell lines and primary MM cells. More importantly, inhibiting MIF activity in vivo displayed synergistic antitumor activity with PIs and resensitized PI-resistant MM cells to treatment. In support of these findings, gene-profiling data showed a significantly negative correlation between MIF and SOD1 expression and response to PI treatment in patients with MM. This study shows that MIF plays a crucial role in MM sensitivity to PIs and suggests that targeting MIF may be a promising strategy to (re)sensitize MM to the treatment.

A highly sensitive fluorescent sensor for ammonia detection based on aggregation-induced emission luminogen-doped liquid crystals.

As a toxic substance, ammonia can cause serious irritation to the human respiratory system and lungs. Although many detection techniques have been reported, most of them have drawbacks, such as expensive devices and complex and time-consuming fabrication processes. Thus, it is important to develop a simple method for ammonia detection. In this paper, we demonstrate a highly sensitive fluorescent sensor for ammonia detection based on aggregation-induced emission luminogen-doped liquid crystals without the use of polarizers. The homeotropic orientation of the liquid crystals on a modified substrate can be disturbed by ammonia, resulting in the fluorescence intensity change of an aggregation-induced emission luminogen. This aggregation-induced emission luminogen-doped liquid crystal-based fluorescent sensor for ammonia detection exhibited a low detection limit of 5.4 ppm, which is 3 times lower than previously reported liquid crystal-based optical sensors. The detection range is also broad from 0 ppm to 1600 ppm. Meanwhile, this sensor can be applied to detect aqueous ammonia with a low limit of detection of 1.8 ppm. The proposed fluorescent sensor for ammonia detection based on an aggregation-induced emission luminogen-doped liquid crystal is highly sensitive, highly selective, simple, and low cost with wide potential applications in chemical and biological fields. This strategy of designing a liquid crystal fluorescent sensor provides an inspiring stage for other toxic chemical substrates by changing specific decorated molecules.

Polycomb group proteins EZH2 and EED directly regulate androgen receptor in advanced prostate cancer.

Polycomb group proteins are important epigenetic regulators for cell proliferation and differentiation, organ development, as well as initiation and progression of lethal diseases, including cancer. Upregulated Polycomb group proteins, including Enhancer of zeste homolog 2 (EZH2), promote proliferation, migration, invasion and metastasis of cancer cells, as well as self-renewal of cancer stem cells. In our study, we report that EZH2 and embryonic ectoderm development (EED) indicate respective direct interaction with androgen receptor (AR). In the context of AR-positive prostate cancer, EZH2 and EED regulate AR expression levels and AR downstream targets. More importantly, we demonstrate that targeting EZH2 with the small-molecule inhibitor astemizole in cancer significantly represses the EZH2 and AR expression as well as the neoplastic capacities. These results collectively suggest that pharmacologically targeting EZH2 might be a promising strategy for advanced prostate cancer.

Amorphous Mn3 O4 Nanocages with High-Efficiency Charge Transfer for Enhancing Electro-Optic Properties of Liquid Crystals.

Improving electro-optic properties is essential for fabricating high-quality liquid crystal displays. Herein, by doping amorphous Mn3 O4 octahedral nanocages (a-Mn3 O4 ONCs) into a nematic liquid crystal (NLC) matrix E7, outstanding electro-optic properties of the blend are successfully obtained. At a doping concentration of 0.03 wt%, the maximum decreases of threshold voltage (Vth ) and saturation voltage (Vsat ) are 34% and 31%, respectively, and the increase of contrast (Con ) is 160%. This remarkable electro-optic activity can be attributed to high-efficiency charge transfer within the a-Mn3 O4 ONCs NLC system, caused by metastable electronic states of a-Mn3 O4 ONCs. To the best of our knowledge, such remarkable decreased electro-optic activity is observed for the first time from doping amorphous semiconductors, which could provide a new pathway to develop excellent energy-saving amorphous materials and improve their potential applications in electro-optical devices.

PGAP-X: extension on pan-genome analysis pipeline.

BACKGROUND: Since PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properly and effectively interpret and visualize the results data is still a challenge. RESULT: To well present bacterial genomic characteristics, a novel cross-platform software was developed, named PGAP-X. Four kinds of data analysis modules were developed and integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile analysis, and genetic variants analysis. The results from these analyses can be directly visualized in PGAP-X. The modules for data visualization in PGAP-X include: comparison of genome structure, gene distribution by conservation, pan-genome profile curve and variation on genic and genomic region. Meanwhile, result data produced by other programs with similar function can be imported to be further analyzed and visualized in PGAP-X. To test the performance of PGAP-X, we comprehensively analyzed 14 Streptococcus pneumonia strains and 14 Chlamydia trachomatis. The results show that, S. pneumonia strains have higher diversity on genome structure and gene contents than C. trachomatis strains. In addition, S. pneumonia strains might have suffered many evolutionary events, such genomic rearrangements, frequent horizontal gene transfer, homologous recombination, and other evolutionary process. CONCLUSION: Briefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com .

Nickel nanoparticle-stabilized room-temperature blue-phase liquid crystals.

Blue-phase liquid crystals (BPLCs) are regarded as a potential candidate for the next generation of optical devices, but they appear in a narrow temperature range, which restricts their applicability. The nanoparticle (NP) stabilization of BPLCs, is usually about either simple-cubic BP (BPII) or body-centered-cubic BP (BPI). Hence, NP-stabilized BPIIs and BPIs possessing wide temperature ranges have been scarcely reported. Here, nickel nanoparticles (Ni NPs) were synthesized and introduced into a BPLC. The concentration-dependent temperature range effects of Ni NPs on the BPLC were investigated. A trace amount of Ni NPs could stabilize the BPLC and increase the temperature ranges of BPII and BPI; this is attributable to the Ni NPs tending to be trapped at the joints of the disclination lines, as a result of the elastic interaction, stabilizing the overall lattice structure of the BPLC. When doped with 0.05 wt% Ni NPs, the mixture shows a wider range with 7.7 °C than the range with 5.9 °C of the BPLC without Ni NPs. Meanwhile, the phase sequence and range of the aforementioned phases are reproducible upon heating and cooling, which shows that the BPLCs doped with Ni NPs are thermodynamically stable.

LRRK2 mediated Rab8a phosphorylation promotes lipid storage.

BACKGROUND: Several mutations in leucine rich repeat kinase 2 (LRRK2) gene have been associated with pathogenesis of Parkinson's disease (PD), a neurodegenerative disorder marked by resting tremors, and rigidity, leading to Postural instability. It has been revealed that mutations that lead to an increase of kinase activity of LRRK2 protein are significantly associated with PD pathogenesis. Recent studies have shown that some Rab GTPases, especially Rab8, serve as substrates of LRRK2 and undergo phosphorylation in its switch II domain upon interaction. Current study was performed in order to find out the effects of the phosphorylation of Rab8 and its mutants on lipid metabolism and lipid droplets growth. METHODS: The phosphorylation status of Rab8a was checked by phos-tag gel. Point mutant construct were generated to investigate the function of Rab8a. 3T3L1 cells were transfected with indicated plasmids and the lipid droplets were stained with Bodipy. Fluorescent microscopy experiments were performed to examine the sizes of lipid droplets. The interactions between Rab8a and Optineurin were determined by immunoprecipitation and western blot. RESULTS: Our assays demonstrated that Rab8a was phosphorylated by mutated LRRK2 that exhibits high kinase activity. Phosphorylation of Rab8a on amino acid residue T72 promoted the formation of large lipid droplets. T72D mutant of Rab8a had higher activity to promote the formation of large lipid droplets compared with wild type Rab8a, with increase in average diameter of lipid droplets from 2.10 µm to 2.46 µm. Moreover, phosphorylation of Rab8a weakened the interaction with its effector Optineurin. CONCLUSIONS: Y1699C mutated LRRK2 was able to phosphorylate Rab8a and phosphorylation of Rab8a on site 72 plays important role in the fusion and enlargement of lipid droplets. Taken together, our study suggests an indirect relationship between enhanced lipid storage capacity and PD pathogenesis.

Effects of freezing conditions on quality changes in blueberries.

BACKGROUND: Freezing preservation is one of the most effective methods used to maintain the flavour and nutritional value of fruit. This research studied the effects of different freezing conditions, -20 °C, -40 °C, -80 °C, and immersion in liquid nitrogen, on quality changes of freeze-thawed blueberries. The water distribution estimates of blueberries were measured based on low-field nuclear magnetic resonance (LF-NMR) analysis. The pectin content, drip loss, and fruit texture were also detected to evaluate quality changes in samples. RESULTS: The freezing curves of blueberry showed super-cooling points at -20 °C and - 40 °C, whereas super-cooling points were not observed at -80 °C or in liquid nitrogen. After freeze-thaw treatment, the relaxation time of the cell wall water (T21 ), cytoplasm water and extracellular space (T22 ), and vacuole water (T23 ) were significantly shortened compared to fresh samples, which suggested a lower liquidity. Although the freezing speed for samples immersed in liquid nitrogen was faster than other treatments, samples treated at -80 °C showed better quality regarding vacuole water holding, drip loss, and original pectin content retention. CONCLUSION: This study contributed to understanding how freezing temperature affects the qualities of blueberries. The super-fast freezing rate might injure fruit, and an appropriate freezing rate could better preserve blueberries. © 2018 Society of Chemical Industry.

Liquid Crystal Elastomer Actuators from Anisotropic Porous Polymer Template.

Controlling self-assembly behaviors of liquid crystals is a fundamental issue for designing them as intelligent actuators. Here, anisotropic porous polyvinylidene fluoride film is utilized as a template to induce homogeneous alignment of liquid crystals. The mechanism of liquid crystal alignment induced by anisotropic porous polyvinylidene fluoride film is illustrated based on the relationship between the alignment behavior of liquid crystals and surface microstructure of anisotropic polyvinylidene fluoride film. Liquid crystal elastomer actuators with fast responsiveness, large strain change, and reversible actuation behaviors are achieved by the photopolymerization of liquid crystal monomer in liquid crystal cells coated with anisotropic porous films.

Gap-Δenergy, a New Metric of the Bond Energy State, Assisting to Predict Molecular Toxicity.

Molecular toxicity is a critical feature of drug development. It is thus very important to develop computational models to evaluate the toxicity of small molecules. The accuracy of toxicity prediction largely depends on the quality of molecular representation; however, current methods for this purpose do not address this issue well. Here, we introduce a new metric, gap-Δenergy, which is designed to quantify the intermolecular bond energy difference with atom distance. We next find significant variations in the gap-Δenergy distribution among different types of molecules. Moreover, we show that this metric is able to distinguish the toxic small molecules. We collected data sets of toxic and exogenous small molecules and presented a novel index, namely, global toxicity, to evaluate the overall toxicity of molecules. Based on molecular descriptors and the proposed gap-Δenergy metric, we further constructed machine learning models that were trained with 7816 small molecules. The XGBoost-based model achieved the best performance with an AUC score of 0.965 and an F1 score of 0.849 on the test set (1954 small molecules), which outperformed the model that did not use gap-Δenergy features, with a sensitivity score increase of 3.2%.

Protocol to analyze immune cells in the tumor microenvironment by transcriptome using machine learning.

Immunotherapy is a promising strategy to treat cancer. Here, we present a protocol for analyzing the transcriptome-based phenotypic alterations and immune cell infiltration in the tumor microenvironment. We describe steps for integrating single-cell RNA sequencing (scRNA-seq) data, comparing phenotypes and origins of mononuclear phagocytes, inferring the differentiation trajectory and infiltration process, and identifying infiltration-associated genes using machine learning. We then detail procedures for exploring the impact of these genes in prognosis through the integrated microarray and bulk RNA-seq data to obtain potential drug targets. For complete details on the use and execution of this protocol, please refer to Liao et al.1.