Comprehensive molecular classification predicted microenvironment profiles and therapy response for HCC.

BACKGROUND AND AIMS: Tumor microenvironment (TME) heterogeneity leads to a discrepancy in survival prognosis and clinical treatment response for patients with HCC. The clinical applications of documented molecular subtypes are constrained by several issues. APPROACH AND RESULTS: We integrated 3 single-cell data sets to describe the TME landscape and identified 6 prognosis-related cell subclusters. Unsupervised clustering of subcluster-specific markers was performed to generate transcriptomic subtypes. The predictive value of these molecular subtypes for prognosis and treatment response was explored in multiple external HCC cohorts and the Xiangya HCC cohort. TME features were estimated using single-cell immune repertoire sequencing, mass cytometry, and multiplex immunofluorescence. The prognosis-related score was constructed based on a machine-learning algorithm. Comprehensive single-cell analysis described TME heterogeneity in HCC. The 5 transcriptomic subtypes possessed different clinical prognoses, stemness characteristics, immune landscapes, and therapeutic responses. Class 1 exhibited an inflamed phenotype with better clinical outcomes, while classes 2 and 4 were characterized by a lack of T-cell infiltration. Classes 5 and 3 indicated an inhibitory tumor immune microenvironment. Analysis of multiple therapeutic cohorts suggested that classes 5 and 3 were sensitive to immune checkpoint blockade and targeted therapy, whereas classes 1 and 2 were more responsive to transcatheter arterial chemoembolization treatment. Class 4 displayed resistance to all conventional HCC therapies. Four potential therapeutic agents and 4 targets were further identified for high prognosis-related score patients with HCC. CONCLUSIONS: Our study generated a clinically valid molecular classification to guide precision medicine in patients with HCC.

Evaporation-Induced Transformations in Volatile Chemical Product-Derived Secondary Organic Aerosols: Browning Effects and Alterations in Oxidative Reactivity.

Volatile chemical products (VCPs) are increasingly recognized as significant sources of volatile organic compounds (VOCs) in urban atmospheres, potentially serving as key precursors for secondary organic aerosol (SOA) formation. This study investigates the formation and physicochemical transformations of VCP-derived SOA, produced through ozonolysis of VOCs evaporated from a representative room deodorant air freshener, focusing on the effects of aerosol evaporation on its molecular composition, light absorption properties, and reactive oxygen species (ROS) generation. Following aerosol evaporation, solutes become concentrated, accelerating reactions within the aerosol matrix that lead to a 42% reduction in peroxide content and noticeable browning of the SOA. This process occurs most effectively at moderate relative humidity (∼40%), reaching a maximum solute concentration before aerosol solidification. Molecular characterization reveals that evaporating VCP-derived SOA produces highly conjugated nitrogen-containing products from interactions between existing or transformed carbonyl compounds and reduced nitrogen species, likely acting as chromophores responsible for the observed brownish coloration. Additionally, the reactivity of VCP-derived SOA was elucidated through heterogeneous oxidation of sulfur dioxide (SO2), which revealed enhanced photosensitized sulfate production upon drying. Direct measurements of ROS, including singlet oxygen (1O2), superoxide (O2•-), and hydroxyl radicals (•OH), showed higher abundances in dried versus undried SOA samples under light exposure. Our findings underscore that drying significantly alters the physicochemical properties of VCP-derived SOA, impacting their roles in atmospheric chemistry and radiative balance.

Assembly and characterization of the complete mitochondrial genome of Ventilago leiocarpa.

KEY MESSAGE: We reported the mitochondrial genome of Ventilago leiocarpa for the first time. Two and one sites lead to the generation of stop and stat codon through editing were verified. Ventilago leiocarpa, a member of the Rhamnaceae family, is frequently utilized in traditional medicine due to the medicinal properties of its roots. In this study, we successfully assembled the mitogenome of V. leiocarpa using both BGI short reads and Nanopore long reads. This mitogenome has a total length of 331,839 bp. The annotated results showed 36 unique protein-coding, 16 tRNA and 3 rRNA genes in this mitogenome. Furthermore, we confirmed the presence of a branched structure through the utilization of long reads mapping, PCR amplification, and Sanger sequencing. Specifically, the ctg1 can form a single circular molecule or combine with ctg4 to form a linear molecule. Likewise, ctg2 can form a single circular molecule or can be connected to ctg4 to form a linear molecule. Subsequently, through a comparative analysis of the mitogenome and cpgenome sequences, we identified ten mitochondrial plastid sequences (MTPTs), including two complete protein-coding genes and five complete tRNA genes. The existence of MTPTs was verified by long reads. Colinear analysis showed that the mitogenomes of Rosales were highly divergent in structure. Finally, we identified 545 RNA editing sites involving 36 protein-coding genes by Deepred-mt. To validate our findings, we conducted PCR amplification and Sanger sequencing, which confirmed the generation of stop codons in atp9-223 and rps10-391, as well as the generation of a start codon in nad4L-2. This project reported the complex structure and RNA editing event of the V. Leiocarpa mitogenome, which will provide valuable information for the study of mitochondrial gene expression.

Aqueous production of secondary organic aerosol from fossil-fuel emissions in winter Beijing haze.

Secondary organic aerosol (SOA) produced by atmospheric oxidation of primary emitted precursors is a major contributor to fine particulate matter (PM2.5) air pollution worldwide. Observations during winter haze pollution episodes in urban China show that most of this SOA originates from fossil-fuel combustion but the chemical mechanisms involved are unclear. Here we report field observations in a Beijing winter haze event that reveal fast aqueous-phase conversion of fossil-fuel primary organic aerosol (POA) to SOA at high relative humidity. Analyses of aerosol mass spectra and elemental ratios indicate that ring-breaking oxidation of POA aromatic species, leading to functionalization as carbonyls and carboxylic acids, may serve as the dominant mechanism for this SOA formation. A POA origin for SOA could explain why SOA has been decreasing over the 2013-2018 period in response to POA emission controls even as emissions of volatile organic compounds (VOCs) have remained flat.

Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data.

Cell fate conversion by overexpressing defined factors is a powerful tool in regenerative medicine. However, identifying key factors for cell fate conversion requires laborious experimental efforts; thus, many of such conversions have not been achieved yet. Nevertheless, cell fate conversions found in many published studies were incomplete as the expression of important gene sets could not be manipulated thoroughly. Therefore, the identification of master transcription factors for complete and efficient conversion is crucial to render this technology more applicable clinically. In the past decade, systematic analyses on various single-cell and bulk OMICs data have uncovered numerous gene regulatory mechanisms, and made it possible to predict master gene regulators during cell fate conversion. By virtue of the sparse structure of master transcription factors and the group structure of their simultaneous regulatory effects on the cell fate conversion process, this study introduces a novel computational method predicting master transcription factors based on group sparse optimization technique integrating data from multi-OMICs levels, which can be applicable to both single-cell and bulk OMICs data with a high tolerance of data sparsity. When it is compared with current prediction methods by cross-referencing published and validated master transcription factors, it possesses superior performance. In short, this method facilitates fast identification of key regulators, give raise to the possibility of higher successful conversion rate and in the hope of reducing experimental cost.

Identification of miR-1-3p, miR-143-3p and miR-145-5p association with bone metastasis of Gleason 3+4 prostate cancer and involvement of LASP1 regulation.

Gleason Score (GS) 3 + 4 prostate cancer (PCa) is heterogeneous in clinical course and molecular features. Risk stratification of indolent and aggressive PCa with GS 3 + 4 is critical, especially those with bone metastasis (BM) potential. Microarray-based microRNA(miRNA) profiling with eight PCa cases with or without BM was used to screen the candidate miRNAs associated with BM. Transwell and MTS assays were used to characterize the function of miRNAs and target gene LASP1. RT-qPCR and immunohistochemistry assays were utilized to illustrate the clinical significance of miRNAs and target gene in a cohort of 309 Chinese PCa cases. In the current study, we identified that miR-1-3p, miR-143-3p and miR-145-5p are associated with BM of GS 3 + 4 PCa. Through functional experiments, we show that miR-1-3p/143-3p/145-5p promotes proliferation and migration of PCa in vitro. LASP1 was predicted as the common target of these three miRNAs which was further confirmed by a luciferase assay. Overexpression of LASP1 was correlated with higher GS, higher pathological stage, and the presence of metastasis by immunohistochemistry. siRNA knockdown of LASP1 significantly suppressed proliferation and migration, whereas overexpression of LASP1 promoted it. Bioinformatics analysis revealed the involvement of Wnt signaling pathway in LASP1 mediated function. LASP1 may activate Wnt signaling by interacting with ß-catenin. In all, we suggest that miR-1-3p/143-3p/145-5p are associated with BM of Gleason 3 + 4 PCa. LASP1 is the common target of these miRNAs and may active Wnt signaling by interacting with ß-catenin.

Peroxides on the Surface of Organic Aerosol Particles Using Matrix-Assisted Ionization in Vacuum (MAIV) Mass Spectrometry.

Organic peroxides are key intermediates in the atmosphere but are challenging to detect, especially in the particle phase, due to their instability, which has led to substantial gaps in the understanding of their environmental effects. We demonstrate that matrix-assisted ionization in vacuum (MAIV) mass spectrometry (MS), which does not require an ionization source, enables in situ characterization of peroxides and other products in the surface layers of organic particles. Hydroxyl radical oxidation of glutaric acid particles yields hydroperoxides and organic peroxides, which were detected with signals of the same order of magnitude as the major, more stable products. Product identification is supported by MS/MS analysis, peroxide standards, and offline high-resolution MS. The peroxide signals relative to the stable carbonyl and alcohol products are significantly larger using MAIV compared to those in the offline bulk analysis. This is also the case for analysis using fast, online easy ambient sonic-spray ionization mass spectrometry. These studies demonstrate the advantage of MAIV for the real-time characterization of labile peroxides in the surface layers of solid particles. The presence of peroxides on the surface may be important for surface oxidation processes as well as for the toxicity of inhaled particles.

Size Dependence of Liquid-Liquid Phase Separation by in Situ Study of Flowing Submicron Aerosol Particles.

Liquid-liquid phase separation (LLPS) of atmospheric particles impacts a range of atmospheric processes. Driven by thermodynamics, LLPS occurs in mixed organic-inorganic particles when high inorganic salt concentrations exclude organic compounds, which develop into a separate phase. The effect of particle size on the thermodynamic and kinetic drivers of LLPS, however, remains incompletely understood. Here, the size dependence was studied for the separation relative humidity (SRH) of LLPS. Submicron organic-inorganic aerosol particles of ammonium sulfate mixed with 1,2,6-hexanetriol and polyethylene glycol (PEG) were studied. In a flow configuration, upstream size selection was coupled to a downstream fluorescence aerosol flow tube (F-AFT) at 293 ± 1 K. For both mixed particle types, the SRH values for submicron particle diameters of 260-410 nm agreed with previous measurements reported in the literature for supermicron particles. For smaller particles, the SRH values decreased by approximately 5% RH for diameters of 130-260 nm for PEG-sulfate particles and of 70-190 nm for hexanetriol-sulfate particles. From these observations, the nucleation rate in the hexanetriol-sulfate system was constrained, implying an activation barrier to nucleation of +1.4 to +2.0 × 10-19 J at 70% RH and 293 K. Quantifying the activation barrier is an approach for predicting size-dependent LLPS in the atmosphere.

Distribution, source, risk and phytoremediation of polycyclic aromatic hydrocarbons (PAHs) in typical urban landscape waters recharged by reclaimed water.

A park that had used reclaimed water as the sole water supply for fourteen years, was selected to analyze the distribution, sources and risks of 16 priority polycyclic aromatic hydrocarbons (PAHs) in waters and sediments. The effects of phytoremediation were investigated in waterbodies classified as phytoremediation, transitional and non-phytoremediation areas. Diagnostic ratio (DR) and principal component analysis (PCA) were used to analyze the sources of PAHs, while risk quotient (RQ) was used as risk assessment tool. Results showed that ∑PAH concentrations in sediments ranged from 29.4 to 1245.6 ng‧g-1, with average of 354.3 ng‧g-1, corresponding to a moderate pollution level. The concentration of PAHs in water ranged from 10.6 to 326.3 ng‧L-1, with average of 147.2 ng‧L-1, corresponding to a low pollution level. The ∑PAHs in sediments showed a downward trend from northwest to southeast along with the water flow direction, with average values of 459.5, 362.9 and 246.1 ng‧L-1 in the upstream, midstream and downstream, respectively. In contrast, PAH concentrations in water were consistent with recreational activities in the urban park area. There were 95% of water samples and 72% of sediment samples obtaining the Ant/(Ant + Phe) > 0.1 and Flu/(Flu + Pyr) > 0.5, indicating that coal combustion was the major source of PAHs in both the water and sediment. The RQ∑PAH(NCs) values in water and sediment were all between 1 and 800, while RQ∑PAH(MPCs) reached equal to 0, suggesting that ∑PAHs presented a low ecological risk. Acenaphthene accounted for 28.4% of RQ(NCs), and became the most risk PAH in water column. Aquatic plants effectively removed high-ring PAHs from water and middle-ring PAHs from sediments, reducing the overall risks posed by PAHs.

Anticancer Activity and Mode of Action of Cu(II), Zn(II), and Mn(II) Complexes with 5-Chloro-2-N-(2-quinolylmethylene)aminophenol.

Developing a new generation of anticancer metal-based drugs that can both kill tumor cells and inhibit cell migration is a promising strategy. Herein, we synthesized three Cu(II), Zn(II), and Mn(II) complexes derived from 5-chloro-2-N-(2-quinolylmethylene)aminophenol (C1-C3). Among these complexes, the Cu(II) complex (C1) showed significantly greater cytotoxicity toward lung cancer cell lines than cisplatin. C1 inhibited A549 cell metastasis and suppressed the growth of the A549 tumor in vivo. In addition, we confirmed the anticancer mechanism of C1 by triggering multiple mechanisms, including inducing mitochondrial apoptosis, acting on DNA, blocking cell cycle arrest, inducing cell senescence, and inducing DNA damage.

Partitioning of Organonitrates in the Production of Secondary Organic Aerosols from α-Pinene Photo-Oxidation.

The chemical pathways for the production of secondary organic aerosols (SOA) are influenced by the concentration of nitrogen oxides (NOx), including the production of organonitrates (ON). Herein, a series of experiments conducted in an environmental chamber investigated the production and partitioning of total organonitrates from α-pinene photo-oxidation from <1 to 24 ppb NOx. Gas-phase and particle-phase organonitrates (gON and pON, respectively) were measured by laser-induced fluorescence (LIF). The composition of the particle phase and the particle mass concentration were simultaneously characterized by online aerosol mass spectrometry. The LIF and MS measurements of pON concentrations had a Pearson correlation coefficient of 0.91 from 0.3 to 1.1 µg m-3. For 1-6 ppb NOx, the yield of SOA particle mass concentration increased from 0.02 to 0.044 with NOx concentration. For >6 ppb NOx, the yield steadily dropped, reaching 0.034 at 24 ppb NOx. By comparison, the yield of pON steadily increased from 0.002 to 0.022 across the range of investigated NOx concentrations. The yield of gON likewise increased from 0.005 to 0.148. The gas-to-particle partitioning ratio (pON/(pON + gON)) depended strongly on the NOx concentration, changing from 0.27 to 0.13 as the NOx increased from <1 to 24 ppb. In the atmosphere, there is typically a cross-over point between clean and polluted conditions that strongly affects SOA production, and the results herein quantitatively identify 6 ppb NOx as that point for α-pinene photo-oxidation under these study conditions, including the production and partitioning of organonitrates. The trends in SOA yield and partitioning ratio as a function of NOx occur because of the changes in pON volatility.

Production and Stabilization of Specific Upregulated Long Noncoding RNA HOXD-AS2 in Glioblastomas Are Mediated by TFE3 and miR-661, Respectively.

Differential expression of long noncoding RNAs (lncRNA) plays a key role in the development of gliomas. Because gliomas are the most common primary central nervous system tumor and glioblastomas have poor prognosis, it is urgent to develop new diagnostic methods. We have previously reported that lncRNA HOXD-AS2, which is specifically up-regulated in gliomas, can activate cell cycle and promote the development of gliomas. It is expected to be a new marker for molecular diagnosis of gliomas, but little is known about HOXD-AS2. Here, we demonstrate that TFE3 and miR-661 maintain the high expression level of HOXD-AS2 by regulating its production and degradation. We found that TFE3 acted as a transcription factor binding to the HOXD-AS2 promoter region and raised H3K27ac to activate HOXD-AS2. As the cytoplasmic-located lncRNA, HOXD-AS2 could be degraded by miR-661. This process was inhibited in gliomas due to the low expression of miR-661. Our study explains why HOXD-AS2 was specifically up-regulated in gliomas, helps to understand the molecular characteristics of gliomas, and provids insights for the search for specific markers in gliomas.

Humidity Dependence of the Condensational Growth of α-Pinene Secondary Organic Aerosol Particles.

The influence of relative humidity (RH) on the condensational growth of organic aerosol particles remains incompletely understood. Herein, the RH dependence was investigated via a series of experiments for α-pinene ozonolysis in a continuously mixed flow chamber in which recurring cycles of particle growth occurred every 7 to 8 h at a given RH. In 5 h, the mean increase in the particle mode diameter was 15 nm at 0% RH and 110 nm at 75% RH. The corresponding particle growth coefficients, representing a combination of the thermodynamic driving force and the kinetic resistance to mass transfer, increased from 0.35 to 2.3 nm2 s-1. The chemical composition, characterized by O:C and H:C atomic ratios of 0.52 and 1.48, respectively, and determined by mass spectrometry, did not depend on RH. The Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) was applied to reproduce the observed size- and RH-dependent particle growth by optimizing the diffusivities Db within the particles of the condensing molecules. The Db values increased from 5 α-1 × 10-16 at 0% RH to 2 α-1 × 10-12 cm-2 s-1 at 75% RH for mass accommodation coefficients α of 0.1 to 1.0, highlighting the importance of particle-phase properties in modeling the growth of atmospheric aerosol particles.

Synergistic Uptake by Acidic Sulfate Particles of Gaseous Mixtures of Glyoxal and Pinanediol.

The uptake of gaseous organic species by atmospheric particles can be affected by the reactive interactions among multiple co-condensing species, yet the underlying mechanisms remain poorly understand. Here, the uptake of unary and binary mixtures of glyoxal and pinanediol by neutral and acidic sulfate particles is investigated. These species are important products from the oxidation of volatile organic compounds (VOCs) under atmospheric conditions. The uptake to acidic aerosol particles greatly increased for a binary mixture of glyoxal and pinanediol compared to the unary counterparts. The strength of the synergism depended on the particle acidity and water content (i.e., relative humidity). The greater uptake was up to 2.5× to 8× at 10% relative humidity (RH) for glyoxal and pinanediol, respectively. At 50% RH, it was 2× and 1.2× for the two species. Possible mechanisms of acid-catalyzed cross reactions between the species are proposed to explain the synergistic uptake. The proposed mechanisms are applicable to a broader extent across atmospheric species having carbonyl and hydroxyl functionalities. The results thus suggest that synergistic uptake reactions can be expected to significantly influence the gas-particle partitioning of VOC oxidation products under atmospheric conditions and thus greatly affect their atmospheric transport and lifetime.

mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers.

Cancer therapies have experienced rapid progress in recent years, with a number of novel small-molecule kinase inhibitors and monoclonal antibodies now being widely used to treat various types of human cancers. During cancer treatments, mutations can have important effects on drug sensitivity. However, the relationship between tumor genomic profiles and the effectiveness of cancer drugs remains elusive. We introduce Mutation To Cancer Therapy Scan (mTCTScan) web server (http://jjwanglab.org/mTCTScan) that can systematically analyze mutations affecting cancer drug sensitivity based on individual genomic profiles. The platform was developed by leveraging the latest knowledge on mutation-cancer drug sensitivity associations and the results from large-scale chemical screening using human cancer cell lines. Using an evidence-based scoring scheme based on current integrative evidences, mTCTScan is able to prioritize mutations according to their associations with cancer drugs and preclinical compounds. It can also show related drugs/compounds with sensitivity classification by considering the context of the entire genomic profile. In addition, mTCTScan incorporates comprehensive filtering functions and cancer-related annotations to better interpret mutation effects and their association with cancer drugs. This platform will greatly benefit both researchers and clinicians for interrogating mechanisms of mutation-dependent drug response, which will have a significant impact on cancer precision medicine.

Real time analysis of lead-containing atmospheric particles in Guangzhou during wintertime using single particle aerosol mass spectrometry.

The toxic effects of lead on human health and the environment have long been a focus of research. To explore sources of lead in Guangzhou, China, we investigated atmospheric lead-containing particles (LCPs) during wintertime using a single particle aerosol mass spectrometer (SPAMS). Based on mass spectral features, LCPs were classified into eight major particle types, including Pb-Cl and Pb-Cl-Li (coal combustion and waste incineration), Pb-Cl-EC and Pb-Cl-OC (diesel trucks and coal combustion), Pb-Cl-Fe (iron and steel industry), Pb-Cl-AlSi (dust), Pb-Sec (secondary formation), and Pb-Cl-Zn (industrial process); these sources (in parentheses) were identified by comparing atmospheric LCP mass spectra with authentic Pb emission source mass spectra. Sampling periods with LCP number fractions (NFs) more than three times the average LCP NF (APF = 4.35%) and below the APF were defined as high LCP NF periods (HLFPs: H1, H3, and H5) and low LCP NF APF periods (LLFPs: L2 and L4), respectively. Diurnal patterns and high Pb-Sec content during LLFPs indicate that photochemical activity and heterogeneous reactions may have controlled Pb-Sec particle formation. The inverse Pb-Cl and Pb-Sec particle diurnal trends during LLFPs suggest the replacement of Cl by sulfate and nitrate. On average over the five periods, ~ 76% of the LCPs likely arose from coal combustion and/or waste incineration, which were dominant sources during all five periods, followed by diesel trucks during LLFPs and iron- and steel-related sources during HLFPs; HLFP LCPs arose mainly from primary emissions. These results can be used to more efficiently control Pb emission sources and prevent harm to human and environmental health from Pb toxicity.

Absence of NUCKS augments paracrine effects of mesenchymal stem cells-mediated cardiac protection.

Bone marrow-derived mesenchymal stem cells (BM-MSCs) contribute to myocardial repair after myocardial infarction (MI) by secreting a panel of growth factors and cytokines. This study was to investigate the potential mechanisms of the nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS) in regulation of the profiles of BM-MSCs secretion and compare the therapeutic efficacy of NUCKS-/-- and wide type-BM-MSCs (WT-BM-MSCs) on MI. The secretion profiles between NUCKS-/-- and WT-BM-MSCs under hypoxia (1%O2) were analyzed. Gene function analysis showed that compared with WT-BM-MSCs-conditioned medium (CdM), some genes over-presented in NUCKS-/--BM-MSCs-CdM were closely associated with inflammatory response, regulation of cell proliferation, death, migration and secretion. Notably, VEGFa in NUCKS-/--BM-MSCs-CdM was higher than that of WT-BM-MSCs-CdM. WT-BM-MSCs and NUCKS-/--BM-MSCs were transplanted into the peri-infarct region in mice of MI. At 4 weeks after cell transplantation, NUCKS-/-- or WT-BM-MSCs group significantly improved heart function and vessels density and reduced infarction size and apoptosis of cardiomyocytes. Furthermore, NUCKS-/--BM-MSCs provided better cardioprotective effects than WT-BM-MSCs against MI. Our study demonstrates that depletion of NUCKS enhances the therapeutic efficacy of BM-MSCs for MI via regulating the secretion.

MicroRNA-141 enhances anoikis resistance in metastatic progression of ovarian cancer through targeting KLF12/Sp1/survivin axis.

BACKGROUND: Cancer metastasis is determined by the formation of the metastatic niche and the ability of cancer cells to adapt to microenvironmental stresses. Anoikis resistance is a fundamental feature of metastatic cancer cell survival during metastatic cancer progression. However, the mechanisms underlying anoikis resistance in ovarian cancer are still unclear. METHODS: Expressions of miRNA-141 and its downstream targets were evaluated by qPCR, Western blotting, Immunohistochemical (IHC) and in situ hybridization (ISH) assays. The luciferase assays were used to prove KLF12 as the downstream target of miR-141. The cDNA microarray and apoptotic protein arrays were used to identify the targets of miR-141 and KLF12. The competition of KLF12 and Sp1 on survivin promoter was examined by ChIP assay. IHC analysis on ovarian cancer tissue array was used to evaluate the expressions of KLF12 and miR-141 and to show the clinical relevance. The functional studies were performed by in vitro and in vivo tumorigenic assays. RESULTS: Enforced expression of miR-141 promotes, while knockdown of miR-141 expression inhibits, cell proliferation, anchorage-independent capacity, anoikis resistance, tumor growth and peritoneal metastases of ovarian cancer cells. Bioinformatics and functional analysis identified that Kruppel-related zinc finger protein AP-2rep (KLF12) is directly targeted by miR-141. Consistent with this finding, knockdown of KLF12 phenocopied the effects of miR-141 overexpression in ovarian cancer cells. In contrast, restoration of KLF12 in miR-141-expressing cells significantly attenuated anoikis resistance in ovarian cancer cells via interfering with Sp1-mediated survivin transcription, which inhibits the intrinsic apoptotic pathway and is crucial for ovarian cancer cell survival, anoikis resistance and peritoneal metastases. Immunohistochemical (IHC) and in situ hybridization (ISH) assays confirmed that miRNA-141 expression is inversely correlated with KLF12 expression and significantly associated with advanced ovarian cancers accompanied with distal metastases, underscoring the clinical relevance of our findings. CONCLUSIONS: Our data identify a novel signaling axis of miR-141/KLF12/Sp1/survivin in enhancing anoikis resistance and likely serves as a potential therapeutic target for metastatic ovarian cancer.

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.

Transcription factors (TFs) play an important role in gene regulation. The interconnections among TFs, chromatin interactions, epigenetic marks and cis-regulatory elements form a complex gene transcription apparatus. Our previous work, ChIP-Array, combined TF binding and transcriptome data to construct gene regulatory networks (GRNs). Here we present an enhanced version, ChIP-Array 2, to integrate additional types of omics data including long-range chromatin interaction, open chromatin region and histone modification data to dissect more comprehensive GRNs involving diverse regulatory components. Moreover, we substantially extended our motif database for human, mouse, rat, fruit fly, worm, yeast and Arabidopsis, and curated large amount of omics data for users to select as input or backend support. With ChIP-Array 2, we compiled a library containing regulatory networks of 18 TFs/chromatin modifiers in mouse embryonic stem cell (mESC). The web server and the mESC library are publicly free and accessible athttp://jjwanglab.org/chip-array.

Glycosaminoglycans' Ability to Promote Wound Healing: From Native Living Macromolecules to Artificial Biomaterials.

Glycosaminoglycans (GAGs) are important for the occurrence of signaling molecules and maintenance of microenvironment within the extracellular matrix (ECM) in living tissues. GAGs and GAG-based biomaterial approaches have been widely explored to promote in situ tissue regeneration and repair by regulating the wound microenvironment, accelerating re-epithelialization, and controlling ECM remodeling. However, most approaches remain unacceptable for clinical applications. To improve insights into material design and clinical translational applications, this review highlights the innate roles and bioactive mechanisms of native GAGs during in situ wound healing and presents common GAG-based biomaterials and the adaptability of application scenarios in facilitating wound healing. Furthermore, challenges before the widespread commercialization of GAG-based biomaterials are shared, to ensure that future designed and constructed GAG-based artificial biomaterials are more likely to recapitulate the unique and tissue-specific profile of native GAG expression in human tissues. This review provides a more explicit and clear selection guide for researchers designing biomimetic materials, which will resemble or exceed their natural counterparts in certain functions, thereby suiting for specific environments or therapeutic goals.