A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA.

Cell behaviors are dictated by epigenetic and transcriptional programs. Little is known about how extracellular stimuli modulate these programs to reshape gene expression and control cell behavioral responses. Here, we interrogated the epigenetic and transcriptional response of endothelial cells to VEGFA treatment and found rapid chromatin changes that mediate broad transcriptomic alterations. VEGFA-responsive genes were associated with active promoters, but changes in promoter histone marks were not tightly linked to gene expression changes. VEGFA altered transcription factor occupancy and the distal epigenetic landscape, which profoundly contributed to VEGFA-dependent changes in gene expression. Integration of gene expression, dynamic enhancer, and transcription factor occupancy changes induced by VEGFA yielded a VEGFA-regulated transcriptional regulatory network, which revealed that the small MAF transcription factors are master regulators of the VEGFA transcriptional program and angiogenesis. Collectively these results revealed that extracellular stimuli rapidly reconfigure the chromatin landscape to coordinately regulate biological responses.

Identification of Serum Biomarkers for Systemic Lupus Erythematosus Using a Library of Phage Displayed Random Peptides and Deep Sequencing.

Systemic lupus erythematosus (SLE) is one of the most serious autoimmune diseases, characterized by highly diverse clinical manifestations. A biomarker is still needed for accurate diagnostics. SLE serum autoantibodies were discovered and validated using serum samples from independent sample cohorts encompassing 306 participants divided into three groups, i.e. healthy, SLE patients, and other autoimmune-related diseases. To discover biomarkers for SLE, a phage displayed random peptide library (Ph.D. 12) and deep sequencing were applied to screen specific autoantibodies in a total of 100 serum samples from 50 SLE patients and 50 healthy controls. A statistical analysis protocol was set up for the identification of peptides as potential biomarkers. For validation, 10 peptides were analyzed using enzyme-linked immunosorbent assays (ELISA). As a result, four peptides (SLE2018Val001, SLE2018Val002, SLE2018Val006, and SLE2018Val008) were discovered with high diagnostic power to differentiate SLE patients from healthy controls. Among them, two peptides, i.e. SLE2018Val001 and SLE2018Val002, were confirmed between SLE with other autoimmune patients. The procedure we established could be easily adopted for the identification of autoantibodies as biomarkers for many other diseases.

Molecular simulation of SARS-CoV-2 spike protein binding to pangolin ACE2 or human ACE2 natural variants reveals altered susceptibility to infection.

We constructed complex models of SARS-CoV-2 spike protein binding to pangolin or human ACE2, the receptor for virus transmission, and estimated the binding free energy changes using molecular dynamics simulation. SARS-CoV-2 can bind to both pangolin and human ACE2, but has a significantly lower binding affinity for pangolin ACE2 due to the increased binding free energy (9.5 kcal mol-1). Human ACE2 is among the most polymorphous genes, for which we identified 317 missense single-nucleotide variations (SNVs) from the dbSNP database. Three SNVs, E329G (rs143936283), M82I (rs267606406) and K26R (rs4646116), had a significant reduction in binding free energy, which indicated higher binding affinity than wild-type ACE2 and greater susceptibility to SARS-CoV-2 infection for people with them. Three other SNVs, D355N (rs961360700), E37K (rs146676783) and I21T (rs1244687367), had a significant increase in binding free energy, which indicated lower binding affinity and reduced susceptibility to SARS-CoV-2 infection.

Cell Lysate Microarray for Mapping the Network of Genetic Regulators for Histone Marks.

Proteins, as the major executer for cell progresses and functions, its abundance and the level of post-translational modifications, are tightly monitored by regulators. Genetic perturbation could help us to understand the relationships between genes and protein functions. Herein, to explore the impact of the genome-wide interruption on certain protein, we developed a cell lysate microarray on kilo-conditions (CLICK) with 4837 knockout (YKO) and 322 temperature-sensitive (ts) mutant strains of yeast (Saccharomyces cerevisiae). Taking histone marks as examples, a general workflow was established for the global identification of upstream regulators. Through a single CLICK array test, we obtained a series of regulators for H3K4me3, which covers most of the known regulators in S. cerevisiae We also noted that several group of proteins are involved in negatively regulation of H3K4me3. Further, we discovered that Cab4p and Cab5p, two key enzymes of CoA biosynthesis, play central roles in histone acylation. Because of its general applicability, CLICK array could be easily adopted to rapid and global identification of upstream protein/enzyme(s) that regulate/modify the level of a protein or the posttranslational modification of a non-histone protein.

Ropivacaine inhibits proliferation, invasion, migration and promotes apoptosis of papillary thyroid cancer cells via regulating ITGA2 expression.

The present study aimed to investigate the roles of Ropivacaine in papillary thyroid cancer (PTC) and identify the possible mechanisms. The expression of integrin alpha-2 (ITGA2) in TC cell lines was tested using Western blotting and RT-qPCR. Subsequently, the level of ITGA2 in human PTC cell line (TPC-1) was measured following intervention with a series of concentrations of Ropivacaine. Then, cell counting kit-8 (CCK-8) assay and colony formation assay were executed for detecting proliferation of cells after transfection with ITGA2 pcDNA3.1. The expression of proliferation-related protein was determined by Western blotting. Additionally, the abilities of TPC-1 cell invasion and migration were examined using Transwell assay and scratch wound healing assay. Apoptosis of TPC-1 cells was analyzed using TUNEL assay and the expressions of apoptosis-related proteins were tested via West blotting. The results suggested that ITGA2 was highly expressed in TC cell lines, especially in TPC-1 cells. Ropivacaine decreased the expression of ITGA2 in a dose-dependent manner. Moreover, after treatment with Ropivacaine, cell proliferation was inhibited accompanied by changes of proliferation-related protein expressions, which was reversed following co-transfection with ITGA2 pcDNA3.1. Furthermore, Ropivacaine concentration-dependently suppressed invasion and migration of TPC-1 cells, whereas these inhibitory effects were attenuated after ITGA2 overexpression. Furthermore, apoptosis was promoted, coupled with a decrease of Bcl-2 expression and increases of Bax, cleaved caspase-3 and cleaved caspase-9 expression, in Ropivacaine-treated TPC-1 cells, which was restored following ITGA2 overexpression. These findings demonstrated that Ropivacaine could suppress proliferation, invasion, migration, and accelerate apoptosis of PTC cells via regulating ITGA2 expression.

Rapid Production of Virus Protein Microarray Using Protein Microarray Fabrication through Gene Synthesis (PAGES).

The high genetic variability of RNA viruses is a significant factor limiting the discovery of effective biomarkers, the development of vaccines, and characterizations of the immune response during infection. Protein microarrays have been shown to be a powerful method in biomarker discovery and the identification of novel protein-protein interaction networks, suggesting that this technique could also be very useful in studies of infectious RNA viruses. However, to date, the amount of genetic material required to produce protein arrays, as well as the time- and labor-intensive procedures typically needed, have limited their more widespread application. Here, we introduce a method, protein microarray fabrication through gene synthesis (PAGES), for the rapid and efficient construction of protein microarrays particularly for RNA viruses. Using dengue virus as an example, we first identify consensus sequences from 3,604 different strains and then fabricate complete proteomic microarrays that are unique for each consensus sequence. To demonstrate their applicability, we show that these microarrays can differentiate sera from patients infected by dengue virus, related pathogens, or from uninfected patients. We anticipate that the microarray and expression library constructed in this study will find immediate use in further studies of dengue virus and that, more generally, PAGES will become a widely applied method in the clinical characterization of RNA viruses.

Identification of Serum Biomarkers for Gastric Cancer Diagnosis Using a Human Proteome Microarray.

We aimed to globally discover serum biomarkers for diagnosis of gastric cancer (GC). GC serum autoantibodies were discovered and validated using serum samples from independent patient cohorts encompassing 1,401 participants divided into three groups, i.e. healthy, GC patients, and GC-related disease group. To discover biomarkers for GC, the human proteome microarray was first applied to screen specific autoantibodies in a total of 87 serum samples from GC patients and healthy controls. Potential biomarkers were identified via a statistical analysis protocol. Targeted protein microarrays with only the potential biomarkers were constructed and used to validate the candidate biomarkers using 914 samples. To provide further validation, the abundance of autoantibodies specific to the biomarker candidates was analyzed using enzyme-linked immunosorbent assays. Receiver operating characteristic curves were generated to evaluate the diagnostic accuracy of the serum biomarkers. Finally, the efficacy of prognosis efficacy of the final four biomarkers was evaluated by analyzing the clinical records. The final panel of biomarkers consisting of COPS2, CTSF, NT5E, and TERF1 provides high diagnostic power, with 95% sensitivity and 92% specificity to differentiate GC patients from healthy individuals. Prognosis analysis showed that the panel could also serve as independent predictors of the overall GC patient survival. The panel of four serum biomarkers (COPS2, CTSF, NT5E, and TERF1) could serve as a noninvasive diagnostic index for GC, and the combination of them could potentially be used as a predictor of the overall GC survival rate.

Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic.

Arsenic is highly effective for treating acute promyelocytic leukemia (APL) and has shown significant promise against many other tumors. However, although its mechanistic effects in APL are established, its broader anticancer mode of action is not understood. In this study, using a human proteome microarray, we identified 360 proteins that specifically bind arsenic. Among the most highly enriched proteins in this set are those in the glycolysis pathway, including the rate-limiting enzyme in glycolysis, hexokinase-1. Detailed biochemical and metabolomics analyses of the highly homologous hexokinase-2 (HK2), which is overexpressed in many cancers, revealed significant inhibition by arsenic. Furthermore, overexpression of HK2 rescued cells from arsenic-induced apoptosis. Our results thus strongly implicate glycolysis, and HK2 in particular, as a key target of arsenic. Moreover, the arsenic-binding proteins identified in this work are expected to serve as a valuable resource for the development of synergistic antitumor therapeutic strategies.

Bilevel Optimization-Based Time-Optimal Path Planning for AUVs.

Using the bilevel optimization (BIO) scheme, this paper presents a time-optimal path planner for autonomous underwater vehicles (AUVs) operating in grid-based environments with ocean currents. In this scheme, the upper optimization problem is defined as finding a free-collision channel from a starting point to a destination, which consists of connected grids, and the lower optimization problem is defined as finding an energy-optimal path in the channel generated by the upper level algorithm. The proposed scheme is integrated with ant colony algorithm as the upper level and quantum-behaved particle swarm optimization as the lower level and tested to find an energy-optimal path for AUV navigating through an ocean environment in the presence of obstacles. This arrangement prevents discrete state transitions that constrain a vehicle's motion to a small set of headings and improves efficiency by the usage of evolutionary algorithms. Simulation results show that the proposed BIO scheme has higher computation efficiency with a slightly lower fitness value than sliding wavefront expansion scheme, which is a grid-based path planner with continuous motion directions.

Catalyst-free synthesis of novel dimeric ß-carboline derivatives via an unexpected [2 + 2 + 2] annulation.

We report here an unexpected catalyst-free [2 + 2 + 2] annulation reaction which allows access to novel complex dimeric ß-carboline derivatives in a single step. Various substituted ynones could react with dihydro-ß-carboline imines to deliver interesting [2 + 2 + 2] annulation products in moderate to good yields. Alkynoates can also be tolerated in this system.

A polysaccharide from pumpkin induces apoptosis of HepG2 cells by activation of mitochondrial pathway.

Purified white polysaccharide (PPW) is a homogenous polysaccharide isolated from pumpkin, with an average molecular weight of 34 kDa. In this study, we aimed at examining the anti-proliferative activity of PPW against hepatocellular carcinoma (HCC) HepG2 cells and the underlying mechanisms. We found that PPW-induced inhibition of cell proliferation in HepG2 cells was associated with the induction of apoptosis. Exposure of HepG2 cells to PPW (100, 200, and 400 µg/mL) resulted in a loss of mitochondrial membrane potential (Δψm) and the release of cytochrome c from the mitochondria to the cytosol. Also, Western blot analysis revealed dose-dependent increase of pro-apoptotic Bax protein and decrease of anti-apoptotic Bcl-2 protein in PPW-treated cells. Besides, caspase-9 and caspase-3 activities were also enhanced in HepG2 cells followed by PPW treatment. Additionally, the cleavage of poly (ADP-ribose) polymerase (PARP) was observed in PPW-treated HepG2 cells, which altogether account for apoptotic cell death. These results suggested that PPW-induced apoptosis involved a caspase-3-mediated mitochondrial pathway and may have potential as a cancer chemopreventive and therapeutic agent for the prevention and treatment of HCC.

Enhancing the Magnetic Anisotropy of Linear Cr(II) Chain Compounds Using Heavy Metal Substitutions.

Magnetic properties of the series of three linear, trimetallic chain compounds Cr2Cr(dpa)4Cl2, 1, Mo2Cr(dpa)4Cl2, 2, and W2Cr(dpa)4Cl2, 3 (dpa = 2,2'-dipyridylamido), have been studied using variable-temperature dc and ac magnetometry and high-frequency EPR spectroscopy. All three compounds possess an S = 2 electronic ground state arising from the terminal Cr(2+) ion, which exhibits slow magnetic relaxation under an applied magnetic field, as evidenced by ac magnetic susceptibility and magnetization measurements. The slow relaxation stems from the existence of an easy-axis magnetic anisotropy, which is bolstered by the axial symmetry of the compounds and has been quantified through rigorous high-frequency EPR measurements. The magnitude of D in these compounds increases when heavier ions are substituted into the trimetallic chain; thus D = -1.640, -2.187, and -3.617 cm(-1) for Cr2Cr(dpa)4Cl2, Mo2Cr(dpa)4Cl2, and W2Cr(dpa)4Cl2, respectively. Additionally, the D value measured for W2Cr(dpa)4Cl2 is the largest yet reported for a high-spin Cr(2+) system. While earlier studies have demonstrated that ligands containing heavy atoms can enhance magnetic anisotropy, this is the first report of this phenomenon using heavy metal atoms as "ligands".

Cavitron Ultrasonic Surgical Aspirator in Laparoscopic Nerve-Sparing Radical Hysterectomy: A Pilot Study.

OBJECTIVE: Pelvic autonomic nerve preservation during radical hysterectomy for cervical cancer has become a priority in recent years. This pilot study was undertaken to evaluate laparoscopic nerve-sparing radical hysterectomy (L-NSRH) using the Cavitron Ultrasonic Surgical Aspirator (CUSA) in women with cervical cancer. METHODS: Patients with stage IB1 or IIA1 cervical cancer underwent L-NSRH with pelvic lymphadenectomy. The patients were randomly assigned to receive L-NSRH using a CUSA (CUSA group; n = 24) or using other techniques (non-CUSA group; n = 21). Recovery of bladder function (indwelling catheter time and time to spontaneous voiding) blood loss, duration of hospital stay, lymph node harvesting, and postoperative complications were compared between the 2 groups. Patients were followed for up to 3 years to determine the maintenance of effect. RESULTS: All patients underwent L-NSRH successfully. Intraoperative blood loss was significantly less in the CUSA than in the non-CUSA group (P = 0.005). Length of hospital stay (P = 0.006) and indwelling catheter time (P = 0.008) were both significantly reduced in the CUSA group compared with that in the non-CUSA group. The spontaneous voiding rate 10 days postoperatively was 95.8% with CUSA and 85.7% with non-CUSA techniques. Two patients developed postoperative complications in the CUSA group as did 3 patients in the non-CUSA group. These were cases of lymphocyst formation or urinary tract infection. CONCLUSIONS: Laparoscopic nerve-sparing radical hysterectomy using CUSA was safe and feasible in patients with cervical cancer. Our results provide initial evidence that L-NSRH using CUSA preserves pelvic autonomic nerve function.

Polygala tenuifolia polysaccharide PTP induced apoptosis in ovarian cancer cells via a mitochondrial pathway.

One purified polysaccharide protein tyrosine phosphatase (PTP) was isolated from the roots of Polygala tenuifolia. The aim of the present study is to investigate the antitumor effect of PTP on human ovarian cancer OVCAR-3 cells and explore the molecular mechanism of the action involved. The results of MTT assay and apoptosis detection assay showed that PTP inhibited cellular proliferation of OVCAR-3 cells and induced apoptotic cellular death via arresting cell circle at the G0/G1 phase. Reverse transcription-polymerase chain reaction (RT-PCR) and Western blot analysis identified that bcl-2 gradually decreased at both transcription and protein levels after PTP treatment for 48 h in OVCAR-3 cells, while those of bax, cytochrome c, caspase-3, and caspase-9 increased. In addition, the low expression of NF-κB in PTP-treated OVCAR-3 cells would trigger the extrinsic pathway of programmed cell death signaling in tumor cells. These results together suggest that PTP may induce apoptosis of OVCAR-3 cells through a mitochondrial pathway.

Polygala tenuifolia polysaccharide (PTP) inhibits cell proliferation by repressing Bmi-1 expression and downregulating telomerase activity.

In our previous study, we isolated a homogeneous polysaccharide (PTP) with antitumor activity from the roots of Polygala tenuifolia. In view of the close correlation between Bmi-1 expression and progression of ovarian cancer, we intend to elucidate the mechanism of its activity by determining the Bmi-1 expression and the telomerase activity in human ovarian carcinoma OVCAR-3 cells following treatment with PTP at three concentrations of 0.5, 1, and 2 mg/mL for 48 h. MTT and colony-forming assays revealed that PTP had a significant inhibitory effect on the cell growth and colony formation of OVCAR-3 cells. Furthermore, Western blot and real-time PCR analysis showed that PTP inhibited Bmi-1 both in protein and transcript levels. Besides, the telomerase activity in OVCAR-3 cells was also downregulated after PTP treatment for 48 h. Taken together, the inhibitory effect of PTP on the cell growth was at least in part mediated via the downregulation of Bmi-1 expression and the telomerase activity in OVCAR-3 cells, and PTP might be a new candidate for chemotherapeutic agent against human ovarian cancer.

The distribution pattern of DNA and protoxin in Bacillus thuringiensis as revealed by laser confocal microscopy analysis.

It was reported that the parasporal crystal from Bacillus thuringiensis contained DNA fragments. To investigate the distribution of protoxin and DNA in B. thuringiensis cells at different growth stages, a cry1Ac-gfp fusion gene was constructed and expressed in an acrystalliferous B. thuringiensis strain, in which the localization of DNA and protoxin were indicated by DNA-specific dye and green fluorescent protein, respectively. When the recombinant cells were at the vegetative growth stage, the Cry1Ac-GFP fusion protein was not expressed and the DNA fluorescent signal was evenly distributed throughout the cell. At the initial stage of sporulation, the Cry1Ac-GFP fusion protein was expressed and accumulated as inclusion body, while two condensed DNA signals existed at each pole of the cell. With the extension of culture time, it seemed that the DNA fluorescence from the region of spore development gradually became faint or vanishing, while the DNA signal was still present in the other pole or the remaining area of the mother cell. Interestingly and unexpectedly, there was no DNA fluorescence signal in the region of the growing and mature inclusion body of Cry1Ac-GFP in B. thuringiensis cell, which might indicate that the DNA embodied in the inclusion body was not accessible to the DNA-specific dye. This was the first investigation devoted exclusively to the in vivo distribution of protoxin and DNA in B. thuringiensis at different growth stages. These data shed light on deeply understanding the process of sporulation and parasporal crystal formation as well as further exploring the interaction of DNA and protoxin in B. thuringiensis.

Pi-pi Stacking Mediated Cooperative Mechanism for Human Cytochrome P450 3A4.

Human Cytochrome P450 3A4 (CYP3A4) is an important member of the cytochrome P450 superfamily with responsibility for metabolizing ~50% of clinical drugs. Experimental evidence showed that CYP3A4 can adopt multiple substrates in its active site to form a cooperative binding model, accelerating substrate metabolism efficiency. In the current study, we constructed both normal and cooperative binding models of human CYP3A4 with antifungal drug ketoconazoles (KLN). Molecular dynamics simulation and free energy calculation were then carried out to study the cooperative binding mechanism. Our simulation showed that the second KLN in the cooperative binding model had a positive impact on the first one binding in the active site by two significant pi-pi stacking interactions. The first one was formed by Phe215, functioning to position the first KLN in a favorable orientation in the active site for further metabolism reactions. The second one was contributed by Phe304. This pi-pi stacking was enhanced in the cooperative binding model by the parallel conformation between the aromatic rings in Phe304 and the dioxolan moiety of the first KLN. These findings can provide an atomic insight into the cooperative binding in CYP3A4, revealing a novel pi-pi stacking mechanism for drug-drug interactions.

Construction and characterization of the interdomain chimeras using Cry11Aa and Cry11Ba from Bacillus thuringiensis and identification of a possible novel toxic chimera.

Three structural domains of mosquitocidal Cry11Aa and Cry11Ba from Bacillus thuringiensis were exchanged to produce interdomain chimeras [BAA (11Ba/11Aa/11Aa), ABA (11Aa/11Ba/11Aa), AAB (11Aa/11Aa/11Ba), ABB (11Aa/11Ba/11Ba), BAB (11Ba/11Aa/11Ba), BBA (11Ba/11Ba/11Aa]. Chimeras BAB, BAA, BBA, and AAB formed inclusion bodies in the crystal-negative B. thuringiensis host and produced expected protein bands on SDS-PAGE gel. However, no inclusion body or target protein could be found for chimeras ABA and ABB. In bioassays using the fourth-instar larvae of Culex quinquefasciatus and Aedes aegypti, AAB had ~50 % lethal concentrations of 4.8 and 2.2 µg ml(-1), respectively; however, the rest of chimeras were not toxic. This study thus helps to understand the domain-function relationships of the Cry11Aa and Cry11Ba toxins. The toxic chimera, AAB, might be a candidate for mosquito control as its amino acid sequence is different from the two parental toxins.

Targeted regulation of miR-154-5p/Cullin2 pathway by hsa_circ_TRIM22 in promoting human papillomavirus 16 positive cervical cancer progression.

Background. Tripartite motif-containing 22 (TRIM22) is characterized by a canonical RING domain with ubiquitin E3 ligase activity and is closely associated with tumorigenesis. As a product of TRIM22 transcription, whether hsa_circ_TRIM22 has a function of regulating tumorigenesis is unclear. Thus, we aimed to explore the role and mechanism of hsa_circ_TRIM22 in human papillomavirus (HPV) 16 positive cervical cancer (CC). Methods. We collected HPV16-positive cervical tissues including chronic cervicitis, high-grade squamous intraepithelial lesions (HSIL), low-grade squamous intraepithelial lesions (LSIL), and CC, and along with CC cell lines to detect the hsa_circ_TRIM22 level using real-time fluorescence quantitative polymerase chain reaction (RT-qPCR). Hsa_circ_TRIM22 was silenced using specific short hairpin ribonucleic acid (shRNA) in CC cell lines and functional assays were performed thereafter. Mechanistically, the targeting and regulatory relationship between hsa_circ_TRIM22 and miR-154-5p were confirmed using the luciferase report assay and rescue experiments. Results. We found hsa_circ_TRIM22 expression level was significantly higher in CC cells and tissues. Further, hsa_circ_TRIM22 knockdown inhibited migration, proliferation, invasiveness, enhanced apoptosis, and slowed the cell cycle. Mechanistically, hsa_circ_TRIM22 could bind miR-154-5p and prevent miR-154-5p from reducing the levels of Cullin2 (CUL2). Notably, the application of miR-154-5p inhibitor significantly rescued hsa_circ_TRIM22-mediated tumorigenesis. Conclusions. Our observations suggest hsa_circ_TRIM22 is upregulated in HPV16-positive CC and promotes CC progression by regulating the miR-154-5p/CUL2 axis, thereby serving as a promising candidate for diagnosis and treatments of CC.