Hedgehog pathway negatively regulated depleted uranium-induced nephrotoxicity.

Depleted uranium (DU) retains the radiological toxicities, which accumulates preferentially in the kidneys. Hedgehog (Hh) pathway plays a critical role in tissue injury. However, the role of Hh in DU-induced nephrotoxicity was still unclear. This study was carried out to investigate the effect of Gli2, which was an important transcription effector of Hh signaling, on DU induced nephrotoxicity. To clarify it, CK19 positive tubular epithelial cells specific Gli2 conditional knockout (KO) mice model was exposed to DU, and then histopathological damage and Hh signaling pathway activation was analyzed. Moreover, HEK-293 T cells were exposed to DU with Gant61 or Gli2 overexpression, and cytotoxicity of DU as analyzed. Results showed that DU caused nephrotoxicity accompanied by activation of Hh signaling pathway. Meanwhile, genetic KO of Gli2 reduced DU-induced nephrotoxicity by normalizing biochemical indicators and reducing Hh pathway activation. Pharmacologic inhibition of Gli1/2 by Gant61 reduced DU induced cytotoxicity by inhibiting apoptosis, ROS formation and Hh pathway activation. However, overexpression of Gli2 aggravated DU-induced cytotoxicity by increasing the levels of apoptosis and ROS formation. Taken together, these results revealed that Hh signaling negatively regulated DU-inducted nephrotoxicity, and that inhibition of Gli2 might serve as a promising nephroprotective target for DU-induced kidney injury.

First Report of Phytopythium helicoides Causing Stalk Rot on Corn in China.

Corn (Zea mays L.) is one of the most important grain crops in the world, especially in China. Besides, corn stalks are often used in production of bio-fuels (Xue et al., 2017). Recently, the production and quality of corn have been severely influenced by corn stalk rot in China caused by Fusarium spp. (Yu et al., 2017). At the end of June of 2019, a field survey of corn was carried out in Tai'an City, western Shandong Province, China. During the survey, the average day time temperature ranged between 22-28°C with intermittent rainfall, the relative humidity was 50-70%. In this survey, the symptomatic corn plants showed signs of necrosis and rotting on stalks and root collars. Five fields were surveyed and symptomatic corn plants were observed in three fields. The incidence rate of disease was about 5%, and the disease was more of a problem in low-lying areas. A total of twenty-eight symptomatic corn plants (7-12 per field), hybrid Denghai-618, at the 3-4 leaf stage were collected and tested for the presence of pathogens. The diseased tissues were excised, surface-sterilized with 75% ethanol for 30 seconds, rinsed for 3 to 5 times with sterile distilled water, and plated on potato dextrose agar (PDA). All plates were incubated at 28°C for 48 hours, emerging colonies were sub-cultured onto PDA plates. Forty-two isolates were obtained, and twenty-seven isolates were identified as Fusarium spp. The remaining fifteen isolates had similar morphology, with colonies that were white and cottony in texture after incubation at 28°C for three days on PDA. The suitable temperature range for growth of hyphae was between 15°C to 40°C, and sporangia were ellipsoidal, papillate, and 23 - 34×21 - 31 µm in diameter. Oogonia (smooth, 22 - 30 µm in diameter) were present in the cultures after 28 days at 28°C. The isolates were identified using both morphological characteristics and DNA sequencing. Identity of the oomycete was confirmed using the BLAST algorithm available through the GenBank with the DNA sequences of rDNA internal transcribed spacer region (ITS), cytochrome c oxidase Ⅰ (coxⅠ) gene and cytochrome c oxidase Ⅱ (coxⅡ) gene, which were amplified using the primers ITS1/ITS4 (White et al. 1990), FM35/FM59 and FM66/FM58 (Martin 2000), respectively. The fifteen isolates selected for sequence analysis had identical gene sequences, and hence, only sequences for isolate RMSD1 were submitted to GenBank (ITS - MW440691, coxI - MW450815 and cox II - MW450816). The ITS, coxI and coxII sequences of the isolate RMSD1 showed 97% identity (751/774 bp), 99% identity (1087/1098 bp) and 99% identity (548/554 bp) with Phytopythium helicoides Accession nos: HQ643382, FR774199, and AB108014, respectively. The pathogenicity of RMSD1 was tested on the corn hybrid Denghai-618. Three-leaf-stage corn plants (N = 15) were inoculated with mycelial agar disks (3 to 4 mm in diameter) colonized with RMSD1 placed on their root-collars. Sterile PDA disks (3 to 4 mm in diameter) served as the negative control (N = 9). Inoculated plants were placed in the growth chamber at 28°C, 60% relative humidity, 16 h / 8 h light regime cycle. Ten days post-inoculation, the inoculated plants showed necrosis, with symptoms of stem rot similar to those observed in the field. The inoculation experiments were repeated twice with the same results, fulfilling Koch's postulates. The root-collars and stems of negative control remained asymptomatic, and P. helicoides was not isolated. Previously, P. helicoides has been reported as a pathogen of strawberry (Zhan et al. 2020) and kiwi fruits (Wang et al. 2015) from China, but not from corn. To our knowledge, it is the first report of P. helicoides causing corn stalk rot in China. In the future, P. helicoides can be considered as a potential candidate causing stem and collar-rot of corn in China, but not the only one. There are other microbes that can produce similar symptoms on corn, and control methods for pathogenic oomycetes differ from those for fungi.

Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages.

Circular RNAs (circRNAs) are a novel class of regulatory RNAs. Here, we present a comprehensive investigation of circRNA expression profiles across 11 tissues and four developmental stages in rats, along with cross-species analyses in humans and mice. Although the expression of circRNAs is positively correlated with that of cognate mRNAs, highly expressed genes tend to splice a larger fraction of circular transcripts. Moreover, circRNAs exhibit higher tissue specificity than cognate mRNAs. Intriguingly, while we observed a monotonic increase of circRNA abundance with age in the rat brain, we further discovered a dynamic, age-dependent pattern of circRNA expression in the testes that is characterized by a dramatic increase with advancing stages of sexual maturity and a decrease with aging. The age-sensitive testicular circRNAs are highly associated with spermatogenesis, independent of cognate mRNA expression. The tissue/age implications of circRNAs suggest that they present unique physiological functions rather than simply occurring as occasional by-products of gene transcription.

Quantifying circular RNA expression from RNA-seq data using model-based framework.

MOTIVATION: Circular RNAs (circRNAs) are a class of non-coding RNAs that are widely expressed in various cell lines and tissues of many organisms. Although the exact function of many circRNAs is largely unknown, the cell type-and tissue-specific circRNA expression has implicated their crucial functions in many biological processes. Hence, the quantification of circRNA expression from high-throughput RNA-seq data is becoming important to ascertain. Although many model-based methods have been developed to quantify linear RNA expression from RNA-seq data, these methods are not applicable to circRNA quantification. RESULTS: Here, we proposed a novel strategy that transforms circular transcripts to pseudo-linear transcripts and estimates the expression values of both circular and linear transcripts using an existing model-based algorithm, Sailfish. The new strategy can accurately estimate transcript expression of both linear and circular transcripts from RNA-seq data. Several factors, such as gene length, amount of expression and the ratio of circular to linear transcripts, had impacts on quantification performance of circular transcripts. In comparison to count-based tools, the new computational framework had superior performance in estimating the amount of circRNA expression from both simulated and real ribosomal RNA-depleted (rRNA-depleted) RNA-seq datasets. On the other hand, the consideration of circular transcripts in expression quantification from rRNA-depleted RNA-seq data showed substantial increased accuracy of linear transcript expression. Our proposed strategy was implemented in a program named Sailfish-cir. AVAILABILITY AND IMPLEMENTATION: Sailfish-cir is freely available at https://github.com/zerodel/Sailfish-cir . CONTACT: tongz@medicine.nevada.edu or wanjun.gu@gmail.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The role of RNA structure at 5' untranslated region in microRNA-mediated gene regulation.

Recent studies have suggested that the secondary structure of the 5' untranslated region (5' UTR) of messenger RNA (mRNA) is important for microRNA (miRNA)-mediated gene regulation in humans. mRNAs that are targeted by miRNA tend to have a higher degree of local secondary structure in their 5' UTR; however, the general role of the 5' UTR in miRNA-mediated gene regulation remains unknown. We systematically surveyed the secondary structure of 5' UTRs in both plant and animal species and found a universal trend of increased mRNA stability near the 5' cap in mRNAs that are regulated by miRNA in animals, but not in plants. Intra-genome comparison showed that gene expression level, GC content of the 5' UTR, number of miRNA target sites, and 5' UTR length may influence mRNA structure near the 5' cap. Our results suggest that the 5' UTR secondary structure performs multiple functions in regulating post-transcriptional processes. Although the local structure immediately upstream of the start codon is involved in translation initiation, RNA structure near the 5' cap site, rather than the structure of the full-length 5' UTR sequences, plays an important role in miRNA-mediated gene regulation.

miRNA in plasma exosome is stable under different storage conditions.

Exosomes are small membrane-bound vesicles secreted by most cell types. Exosomes contain various functional proteins, mRNAs and microRNAs (miRNAs) that could be used for diagnostic and therapeutic purposes. How we should store the samples before RNA isolation and whether those long term stored samples could be used for circulating RNA investigation because of RNase is unknown. The aim of the study was to determine the stability of circulating miRNA in exosomes and plasma. Exosomes were isolated from plasma samples by using ExoQuick Precipitation methods. RNA was extracted from exosomes and the corresponding plasma samples with a Qiagen miRNeasy Mini kit. The concentration of RNA was measured by a Qubit® RNA HS Assay Kit, and quantitative PCR was used for individual miRNA expression level detection. Results showed that exosomal miRNA showed extra stability under different storage conditions and no significant influence on plasma miRNA, except for short term storage at 4 °C. It is thus indicated that exosome miRNAs can be good biomarkers based on their stability under various storage conditions.

Application of bundled process control in the prevention of pressure injury in patients with head and neck cancer.

This study aimed to explore the application effects of cluster process control and routine nursing on the prevention of pressure injury (PI) in patients undergoing head and neck cancer surgery and to provide a basis for reducing the occurrence of PI, thereby promoting the safety of the patients. This was a retrospective study. Patients with head and neck cancers who underwent surgical treatment in the Department of Otolaryngology at the Second Affiliated Hospital of Fujian Medical University from July 2022 to June 2023 were selected as the research participants. Participants were classified into experimental and control groups using a convenience sampling method. In the experimental group, cluster process control was implemented, while routine nursing management was applied in the control group. The incidence of PI (p = 0.028) and healing time (p = 0.035) in the experimental group were lower than those in the control group. The process management ability of nurses in the experimental group was significantly improved, with the results for the Braden scale (p = 0.023), effective decompression (p = 0.002), floating heel (p = 0.002), nutrition monitoring (p = 0.005), and patient satisfaction in the experimental group being higher than those in the control group (p = 0.007). This study effectively demonstrated the effect of cluster process control in reducing the incidence of PI in patients undergoing head and neck cancer surgery, thereby determining that cluster process control is suitable for clinical application.

Selection on synonymous sites for increased accessibility around miRNA binding sites in plants.

Synonymous codons are widely selected for various biological mechanisms in both prokaryotes and eukaryotes. Recent evidence suggests that microRNA (miRNA) function may affect synonymous codon choices near miRNA target sites. To better understand this, we perform genome-wide analysis on synonymous codon usage around miRNA target sites in four plant genomes. We observed a general trend of increased site accessibility around miRNA target sites in plants. Guanine-cytosine (GC)-poor codons are preferred in the flank region of miRNA target sites. Within-genome analyses show significant variation among miRNA targets in species. GC content of the target gene can partly explain the variation of site accessibility among miRNA targets. miRNA targets in GC-rich genes show stronger selection signals than those in GC-poor genes. Gene's codon usage bias and the conservation level of miRNA and its target also have some effects on site accessibility, but the expression level of miRNA or its target and the mechanism of miRNA activity do not contribute to site accessibility differences among miRNA targets. We suggest that synonymous codons near miRNA targets are selected for efficient miRNA binding and proper miRNA function. Our results present a new dimension of natural selection on synonymous codons near miRNA target sites in plants, which will have important implications of coding sequence evolution.

Analysis approaches for the identification and prediction of N6-methyladenosine sites.

The global dynamics in a variety of biological processes can be revealed by mapping transcriptional m6A sites, in particular full-transcriptome m6A. And individual m6A sites have contributed to biological function, which can be evaluated by stoichiometric information obtained from the single nucleotide resolution. Currently, the identification of m6A sites is mainly carried out by experiment and prediction methods, based on high-throughput sequencing and machine learning model respectively. This review summarizes the recent topics and progress made in bioinformatics methods of deciphering the m6A methylation, including the experimental detection of m6A methylation sites, techniques of data analysis, the way of predicting m6A methylation sites, m6A methylation databases, and detection of m6A modification in circRNA. At the end, the essay makes a brief discussion for the development perspective in this area.

N-acetyl-L-cysteine attenuated the toxicity of ZIF-8 on EA.hy926 endothelial cells by wnt/ß-catenin pathway.

As kinds of porous crystalline compounds, zeolitic imidazolate frameworks (ZIFs) have been developed quickly and attracted considerable attention for use in nano drug delivery systems, which raised concerns about cardiovascular disorders. At the present, the cytotoxic mechanism of ZIFs in cardiovascular disorders was still unclear. Our experiment explored the toxicity of ZIF-8, a typical kind of ZIFs, on human EA.hy926 vascular endothelial cells. The cell viability, ROS formation, apoptosis level, inflammatory response level, wound healing ability and atherosclerosis-related indicators of EA.hy926 endothelial cells were analyzed after ZIF-8 treatment. Meanwhile, we evaluated the ability of antioxidant N-Acetyl-L-cysteine (NAC) to attenuate the toxicity of ZIF-8 on EA.hy926 endothelial cells. As results, NAC attenuated ROS formation, cell apoptosis, LDH formation and endothelial dysfunction caused by ZIF-8. As the Wnt/ß-catenin pathway was involved in endothelial cell dysfunction, we also studied the expression level of ß-catenin and LEF1 in ZIF-8 and/or NAC treated EA.hy926 cells. As expected, ZIF-8 increased the protein expressions of ß-catenin and LEF1in the IC50 group, which was significantly inhibited by co-treatment with NAC. Taken together, this study could help improve our understanding about the mechanism of ZIF-8-induced endothelial cells injury and NAC had therapeutic potential in preventing ZIF-8-associated endothelial dysfunction by wnt/ß-catenin pathway.

Extracellular RNA profiles in non-small cell lung cancer plasma.

Background: Non-small cell lung cancer (NSCLC) has a high mortality rate and poor prognosis. The early detection of high-risk patients is essential to improve patient prognosis. Thus, the identification of a non-invasive, non-radiative, convenient, and fast diagnostic approach should be a top priority in NSCLC research. Circulating extracellular RNAs (exRNAs) in the plasma are potential biomarkers for NSCLC. Methods: We used RNA-sequencing (RNA-seq) technology to explore the NSCLC-related RNAs, especially the circular RNAs (circRNAs). The circRNA-targeted micro RNAs (miRNAs) were predicted using 3 circRNA databases [i.e., the Cancer-Specific CircRNA Database (CSCD), circBank, and Circular RNA Interactome]. The circRNA-miRNA-messenger RNA (mRNA) network was constructed using Cytoscape V3.8.0 (Cytoscape Consortium, San Diego, CA, USA). The expression levels of some differentially expressed genes were validated by a quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Results: The results showed that the RNA biotypes of the mitochondrial ribosomal RNAs (mt-rRNAs) and mitochondrial transfer RNAs (mt-tRNAs) were upregulated in the NSCLC plasma. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms of the differentially expressed transcripts of NSCLC included oxidative phosphorylation, proton transmembrane transport, and the response to oxidative stress. Additionally, the qRT-PCR validation indicated that hsa_circ_0000722 had significantly higher expression in the NSCLC plasma than the control plasma, but hsa_circ_0006156 did not differ between the NSCLC plasma and the control plasma. The expression levels of miR-324-5p and miR-326 were higher in the NSCLC plasma than the control plasma. Conclusions: In this study, an exRNA-sequencing strategy was used to identify the expression of NSCLC-specific transcription factors in clinical plasma samples, and hsa_circ_0000722 and hsa-miR-324-5p were identified as potential biomarkers in NSCLC.

Single-cell multi-omics sequencing and its application in tumor heterogeneity.

In recent years, the emergence and development of single-cell sequencing technologies have provided unprecedented opportunities to analyze deoxyribonucleic acid, ribonucleic acid and proteins at single-cell resolution. The advancements and reduced costs of high-throughput technologies allow for parallel sequencing of multiple molecular layers from a single cell, providing a comprehensive insight into the biological state and behavioral mechanisms of cells through the integration of genomics, transcriptomics, epigenomics and proteomics information. Researchers are actively working to further improve the cost-effectiveness, stability and high-throughput capabilities of single-cell multi-omics sequencing technologies and exploring their potential in precision medicine through clinical diagnostics. This review aims to survey the cutting-edge advancements in single-cell multi-omics sequencing, summarizing the representative technologies and their applications in profiling complex diseases, with a particular focus on tumors.

Nigirpexin E, a new azaphilone derivative with anti-tobacco mosaic virus activity from soil-derived fungus Trichoderma afroharzianum LTR-2.

A new compound classified as one new azaphilone derivative, nigirpexin E (1), was obtained from the soil-derived fungus Trichoderma afroharzianum LTR-2, together with seven known compounds (2-8). The structures of 1-8 were determined by their HRESIMS, optical rotation, and NMR spectroscopic data. The absolute configuration of nigirpexin E (1) was determined on the basis of comparisons of experimental and theoretically calculated ECD spectra. Compound 3 was firstly isolated from Trichoderma. Bioactivities of the isolated compounds were assayed their anti-tobacco mosaic virus (anti-TMV) activities. The results showed that compound 1 exhibited significant inactivation effect against TMV with an inhibition rate of 67.25% (0.5 mg ml-1), which was higher than that of positive control ribavirin (56.74%). This is the first report of the anti-TMV activity of azaphilone derivatives.

Tumor-derived exosomal HOTAIRM1 regulates SPON2 in CAFs to promote progression of lung adenocarcinoma.

OBJECTIVE: SPON2 is one of the extracellular matrix proteins, which is closely related to the progression of a variety of tumors including non-small cell lung cancer (NSCLC), but its upstream regulation mechanism remains unclear. Our research aims to find the specific regulatory pathway of SPON2 by exploring the potential crosstalk between tumor cells and cancer-associated fibroblasts (CAFs) in tumor microenvironment (TME) of NSCLC. METHODS: We analyzed T1 lung adenocarcinoma samples from TCGA and screened extracellular matrix proteins that indicate poor prognosis. Expression level of SPON2 was verified by qPCR in clinical samples. The exosomes of NSCLC cell supernatant were extracted and identified by nanoparticle tracking analysis (NTA) and transmission electron microscope, western blots. The exosomes and CAFs were co-cultured, and cell migration and Matrigel invasion assay were used to evaluate the effect of CAFs on the migration and invasion of NSCLC cells. The interaction between LncRNA and miRNA was verified by Targetscan prediction, luciferase reporter assay, and RNA binding protein immunoprecipitation (RIP). RESULTS: We found that the expression of SPON2 was up-regulated in clinical T1a stage NSCLC patients. The expression of lnc HOTAIRM1 (HOTAIRM1) in exosomes secreted by NSCLC tissues increased. After exosomal HOTAIRM1 entered CAFs, HOTAIRM1 can adsorb miR-328-5p to up-regulate the expression of SPON2 in CAFs. Up-regulation of SPON2 in CAFs could promote the migration and invasion of NSCLC cells. CONCLUSION: Tumor-derived exosomal HOTAIRM1 can transfer into CAFs and competitively adsorb miR-328-5p, and regulate the SPON2 expression of CAFs cells, ultimately promote the progression of NSCLC. The discovery of this regulatory pathway can provide a new potential therapeutic target for the diagnosis and treatment of NSCLC.

Identification of the Phosphorus-Solubilizing Bacteria Strain JP233 and Its Effects on Soil Phosphorus Leaching Loss and Crop Growth.

Phosphorus (P) is one of the most limiting nutrients in global agricultural ecosystems, and phosphorus-solubilizing bacteria (PSB) can convert insoluble P into soluble P, thereby improving the absorption and use of soil P by plants. Increasing leaching loss of soil P due to PSB that could lead to water eutrophication is a major concern, although no direct experimental evidence is available to evaluate these effects. In this study, a highly efficient PSB strain, Pseudomonas sp. JP233, was isolated from soil and its P-solubilizing agent was identified by metabolomics and HPLC analyses. The effects of JP233 on P contents in soil leachates were also analyzed by microcosm leaching experiments in the absence and presence of maize. JP233 could solubilize insoluble P into soluble forms, and the molybdate reactive phosphorus (MRP) content reached 258.07 mg/L in NBRIP medium containing 5 g/L Ca3(PO4)2 within 48 h. Metabolomics analysis demonstrated that the organic acid involved in JP233 P solubilization was primarily 2-keto gluconic acid (2KGA). Further, HPLC analysis revealed that 2KGA contents rapidly accumulated to 19.33 mg/mL within 48 h. Microcosm leaching experiments showed that MRP and total phosphorus (TP) contents in soil leaching solutions were not significantly higher after JP233 inoculation. However, inoculation with JP233 into maize plant soils significantly decreased MRP and TP contents in the soil leaching solutions on days 14 (P < 0.01), 21 (P < 0.01), and 28 (P < 0.05). Inoculation with strain JP233 also significantly increased the biomass of maize aerial components and that of whole plants (P < 0.05). Thus, strain JP233 exhibited a significant plant-growth-promoting effect on maize development. In conclusion, the application of PSB into soils does not significantly increase P leachate loss. Rather, the application of PSB can help reduce P leachate loss, while significantly promoting plant absorption and use of soil P.

Five new species of Trichoderma from moist soils in China.

Trichoderma isolates were collected from moist soils near a water source in different areas of China. ITS sequences were submitted to MIST (Multiloci Identification System for Trichoderma) and meets the Trichoderma [ITS76] standard. Combined analyses of phylogenetic analyses of both phylograms (tef1-α and rpb2) and morphological characteristics, revealed five new species of Trichoderma, namely Trichodermahailarense, T.macrofasciculatum, T.nordicum, T.shangrilaense and T.vadicola. Phylogenetic analyses showed T.macrofasciculatum and T.shangrilaense belong to the Polysporum clade, T.hailarense, while T.nordicum and T.vadicola belong to the Viride clade. Each new taxon formed a distinct clade in phylogenetic analysis and have unique sequences of tef1-α and rpb2 that meet the Trichoderma new species standard. The conidiation of T.macrofasciculatum typically appeared in white pustules in concentric rings on PDA or MEA and its conidia had one or few distinctly verrucose. Conidiophores of T.shangrilaense are short and rarely branched, phialides usually curved and irregularly disposed. The aerial mycelium of T.hailarense and T.vadicola formed strands to floccose mat, conidiation tardy and scattered in tufts, conidiophores repeatedly rebranching in dendriform structure. The phialides of T.nordicum lageniform are curved on PDA and its conidia are globose to obovoidal and large.

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks.

BACKGROUND: Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis. RESULTS: A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. A novel computational technique is introduced to decompose such networks, whereby the notion of domain "networking versatility" is derived and measured. The most and least "versatile" domains (termed "core domains" and "peripheral domains" respectively) are examined both computationally via sequence conservation measures and experimentally using selected domains. Our study suggests that such a versatility measure extracted from the bigram networks correlates with the adaptivity of domains during evolution, where the network core domains are highly adaptive, significantly contrasting the network peripheral domains. CONCLUSIONS: Domain recombination has played a major part in the evolution of eukaryotes attributing to genome complexity. From a system point of view, as the results of selection and constant refinement, networks of domain linkage are structured in a hierarchical modular fashion. Domains with high degree of networking versatility appear to be evolutionary adaptive, potentially through functional innovations. Domain bigram networks are informative as a model of biological functions. The networking versatility indices extracted from such networks for individual domains reflect the strength of evolutionary selection that the domains have experienced.

Tumor-associated macrophages secret exosomal miR-155 and miR-196a-5p to promote metastasis of non-small-cell lung cancer.

BACKGROUND: Understanding the molecular basis underlying metastasis of non-small cell lung cancer (NSCLC) may provide a new therapeutic modality for the treatment of NSCLC. However, the mechanisms by which tumor-associated macrophages (TAMs) affect NSCLC metastasis remain undefined. In this study, we aimed to discover a novel regulatory pathway involved in NSCLC metastasis. METHODS: Cell Counting Kit-8 (CCK-8), Transwell, western blot assays were used to assess cell viability, migration, invasion and epithelial-mesenchymal transition (EMT). Exosomes from macrophages medium were characterized, and in vitro cell coculture was further conducted to investigate M2 derived exosomes mediated crosstalk between TAMs and tumor cells. Besides, miRNA microarray was used to analyze miRNA expression profiles of M0 and M2 derived exosomes. Luciferase reporter assay was used to verify the potential binding between miRNA and mRNA. Moreover, 6-week-old male BALB/c nude mice were performed to establish transplantation tumor model using tail vein injection. Hematoxylin & eosin staining was used to detect the metastasis of tumor tissues. RESULTS: We found that M2 TAMs were the main TAMs in metastatic tissues of NSCLC patients and exosomes derived from M2 TAMs were able to promote cell viability, cell migration, cell invasion and EMT in NSCLC. We demonstrated that miR-155 and miR-196a-5p were abundant in M2 TAMs and exosomes secreted by M2 TAMs. Functional experiments demonstrated that the deletion of miR-155 and miR-196a-5p in M2 TAMs significantly prevented NSCLC metastasis in vitro and in vivo. To clarify the mechanism governing miR-155 and miR-196a-5p from M2 TAMs, we carried out bioinformatics analysis to predict potential target genes. Mechanistically, miR-155 and miR-196a-5p directly bound to the 3'-UTR of Ras association domain family member 4 (RASSF4), and negatively regulating RASSF4 expression. At last, rescue assays demonstrated that miR-155 and miR-196a-5p exerted its performance by RASSF4. CONCLUSIONS: Overall, we revealed a new regulatory pathway that was M2 TAMs secreted exosomal miR-155 and miR-196a-5p to promote NSCLC metastasis. This dynamic and reciprocal cross-talk between NSCLC and macrophages innovatively provided a potential opportunity for diagnosis and treatment of NSCLC.

Global analysis of in vivo EGR1-binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencing.

Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by phorbol ester. But the molecule mechanism of EGR1 in this process has not been widely investigated. The identification of direct EGR1 target genes in a global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cells using chromatin immunoprecipitation and massively parallel sequencing. Over 14 000 highly confident in vivo EGR1 binding sites were identified in phorbol 12-myristate 13-acetate-treated K562 cells. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. Molecular functional classification of 6138 putative EGR1 target genes showed that the transcription factor class (695 of 6138; 11%) is the largest significantly enriched one. The results showed that a high coverage of the genome and a high positive rate achieve were achieved. This whole genome study on the EGR1 targets may provide a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation.