Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.

The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a ß-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila. Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail.

Establishment of risk quality control charts based on risk management strategies.

BACKGROUND: Risk management strategies have been proposed for applications in clinical laboratories to reduce patient risks; however, effective and visual risk-monitoring tools are currently lacking in medical laboratories. In this study, we constructed a risk quality control (QC) chart based on risk management strategies. METHODS: We calculated the risk levels of QC materials based on Bayes' theorem by combining the total allowable error, QC results, and the maximum number of unacceptable errors in the laboratory. Then, we constructed a risk QC chart by presenting the Z values and corresponding risk levels of QC materials simultaneously. Finally, we evaluated the risk-monitoring capabilities of the risk QC charts by simulating different long-term errors in the laboratory. RESULTS: The risk levels of QC materials increased as the QC results moved further away from the set mean. Larger sigma values led to fewer risks obtained for the same QC results. The constructed risk QC charts intuitively showed specific risk levels and could warn lab staff out-of-control, without the need for QC rules to make judgments. The risk levels of erroneous results differed for items with different sigma performance. CONCLUSIONS: Risk-based QC charts allowed visualization of the QC results and specific risk levels simultaneously, providing more intuitive results than those obtained from traditional QC charts.

Identification of downstream signaling cascades of ACK1 and prognostic classifiers in non-small cell lung cancer.

Activated Cdc42-associated kinase 1 (ACK1) is an oncogene in multiple cancers, but the underlying mechanisms of its oncogenic role remain unclear in non-small cell lung cancer (NSCLC). Herein, we comprehensively investigated the ACK1-regulated cell processes and downstream signaling pathways, as well as its prognostic value in NSCLC. We found that ACK1 gene amplification was associated with mRNA levels in The Cancer Genome Atlas (TCGA) lung cancer cohort. The Oncomine databases showed significantly elevated ACK1 levels in lung cancer. In vitro, an ACK1 inhibitor (dasatinib) increased the sensitivity of NSCLC cell lines to AKT or MEK inhibitors. RNA-sequencing results demonstrated that an ACK1 deficiency in A549 cells affected the MAPK, PI3K/AKT, and Wnt pathways. These results were validated by gene set enrichment analysis (GSEA) of data from 188 lung cancer cell lines. Using Cytoscape, we dissected 14 critical ACK1-regulated genes. The signature with the 14 genes and ACK1 could significantly dichotomize the TCGA lung cohort regarding overall survival. The prognostic accuracy of this signature was confirmed in five independent lung cancer cohorts and was further validated by a prognostic nomogram. Our study unveiled several downstream signaling pathways for ACK1, and the proposed signature may be a promising prognostic predictor for NSCLC.

Combined inhibition of ACK1 and AKT shows potential toward targeted therapy against KRAS-mutant non-small-cell lung cancer.

Non-small-cell lung cancer (NSCLC) with Kirsten RAt Sarcoma 2 viral oncogene homolog (KRAS) mutation has become a clinical challenge in cancer treatment as KRAS-mutant tumors are often resistant to conventional anti-tumor therapies. Activated CDC42-associated kinase 1 (ACK1), an activator of protein kinase B (AKT), is a promising target for KRAS-mutant tumor therapy, but the downstream ACK1 signaling remains poorly understood. The aim of this study was to evaluate the effectiveness of combined ACK1/AKT inhibition on the proliferation, migration, invasion, and apoptosis of KRAS-mutant NSCLC cell lines (NCI-H23, NCI-H358, and A549). The cells were treated with an inhibitor of either ACK1 (dasatinib or sunitinib) or AKT (MK-2206 or GDC-0068), and the optimal concentrations of the two yielding synergistic tumor-killing effects were determined by applying the Chou-Talalay equation for drug combinations. We showed that combined administration of ACK1 and AKT inhibitors at the optimal concentrations effectively suppressed NSCLC cell viability and promoted apoptosis while inducing cell cycle arrest at the G2 phase. Moreover, NSCLC cell migration and invasion were inhibited by combined ACK1/AKT inhibition. These phenomena were associated with the reduced phosphorylation levels of ACK1 and AKT (at Ser473 and Thr308), as well as alterations in caspase-dependent apoptotic signaling. Collectively, our results demonstrate the promising therapeutic potential of combined ACK1/AKT inhibition as a strategy against KRAS-mutant NSCLC. Our findings provide the basis for the clinical translation of biological targeted drugs (ACK1 and AKT inhibitors) and their rational combination in cancer treatment.

Distribution and sources of DDT and its metabolites in porewater and sediment from a typical tropical bay in the South China Sea.

Dichlorodiphenyltrichloroethane (DDT) is well known for its harmful effects and has been banned around the world. However, DDT is still frequently detected in natural environments, particularly in aquaculture and harbor sediments. In this study, 15 surface sediment samples were collected from a typical tropical bay (Zhanjiang Bay) in the South China Sea, and the levels of DDT and its metabolites in sediment and porewater samples were investigated. The results showed that concentrations of DDXs (i.e., DDT and its metabolites) in bulk sediments were 1.58-51.0 ng g-1 (mean, 11.5 ng g-1). DDTs (DDT and its primary metabolites, dichlorodiphenyldichloroethane (DDD) and dichlorodiphenyldichloroethylene (DDE)) were the most prominent, accounting for 73.2%-98.3% (86.1% ± 12.8%) of the DDXs. Additionally, high-order metabolites (i.e., 1-chloro-2,2-bis(4'-chlorophenyl)ethylene (p,p'-DDMU), 2,2-bis(p-chlorophenyl)ethylene (p,p'-DDNU), 2,2-bis(p-chlorophenyl)ethanol (p,p'-DDOH), 2,2-bis(p-chlorophenyl)methane (p,p'-DDM), and 4,4'-dichlorobenzophenone (p,p'-DBP)) were also detected in most of the sediment and porewater samples, with DDMU and DBP being predominant. The DDTs concentration differed among the sampling sites, with relatively high DDTs concentrations in the samples from the aquaculture zone and an area near the shipping channel and the Haibin shipyard. The DDD/DDE ratios indicated a reductive dichlorination of DDT to DDD under anaerobic conditions at most of the sampling sites of Zhanjiang Bay. The possible DDT degradation pathway in the surface sediments of Zhanjiang Bay was p,p'-DDT/p,p'-DDD(p,p'-DDE)/p,p'-DDMU/p,p'-DDNU/ … /p,p'-DBP. The DDXs in the sediments of Zhanjiang Bay were mainly introduced via mixed sources of industrial DDT and dicofol, including fresh input and historical residue. The concentrations of DDXs in porewater samples varied from 66.3 to 250 ng L-1, exhibiting a distribution similar to that in the accompanying sediments. However, the content of high-order metabolites was relatively lower in porewater than in sediment, indicating that high-order degradation mainly occurs in particles. Overall, this study helps in understanding the distribution, source, and degradation of DDT in a typical tropical bay.

Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis.

ASPP (apoptosis-stimulating proteins of p53) proteins bind PP-1c (protein phosphatase 1) and regulate p53 impacting cancer cell growth and apoptosis. Here we determine the crystal structure of the oncogenic ASPP protein, iASPP, bound to PP-1c. The structure reveals a 1:1 complex that relies on interactions of the iASPP SILK and RVxF motifs with PP-1c, plus interactions of the PP-1c PxxPxR motif with the iASPP SH3 domain. Small-angle X-ray scattering analyses suggest that the crystal structure undergoes slow interconversion with more extended conformations in solution. We show that iASPP, and the tumor suppressor ASPP2, enhance the catalytic activity of PP-1c against the small-molecule substrate, pNPP as well as p53. The combined results suggest that PxxPxR binding to iASPP SH3 domain is critical for complex formation, and that the modular ASPP-PP-1c interface provides dynamic flexibility that enables functional binding and dephosphorylation of p53 and other diverse protein substrates.

[Distribution Characteristics and Ecological Risk Assessment of Organochlorine Pesticides in Sediments of Zhanjiang Bay].

Sixteen surface sediment samples were collected from the estuary of the Suixi river to the mouth of Zhanjiang Bay and then analyzed for organochlorine pesticides (OCPs) by GC-MS to investigate their distribution and ecological risk. The results showed that the concentrations of OCPs in the sediments ranged from nd to 189.52 ng·g-1 (mean 32.17 ng·g-1), including HCHs (mean 5.81 ng·g-1) and DDTs (mean 26.90 ng·g-1). The distribution characteristics showed that the highest OCPs concentrations were found in the estuary and the main shipping lane areas, and the concentration in the nearshore area was higher than that offshore. Source analysis indicated that the HCHs mainly originated from agricultural applications, while no industrial input was observed. Some "hot-spots" areas occurred in harbors and shipping channels, likely as a result of the presence of paint flakes. Additionally, the concentrations of DDTs were found to be higher than the limits of Chinese Marine sediment quality criteria, and p,p'-DDT was the main type of DDT, presenting inevitable adverse biological effects and high ecological risk. Compared with other bays in China, the concentrations of OCPs in this study were in the upper-median pollution level, especially in harbors and boat maintenance facility areas. High OCPs inputs may occur, and thereby represent a certain ecological risk in Zhanjiang Bay.

Portal hypertension in hepatitis B-related cirrhosis: Diagnostic accuracy of liver and spleen stiffness by 2-D shear-wave elastography.

AIM: To assess the diagnostic accuracy of liver and spleen stiffness measured by 2-D shear-wave elastography (SWE) in evaluation of clinically significant and severe portal hypertension (CSPH and SPH, respectively). METHODS: Clinical data of 155 hepatitis B-related cirrhosis patients and their liver and spleen stiffness (L-SWE and S-SWE, respectively) were collected. The diagnostic performances of L-SWE, S-SWE, the liver stiffness-spleen diameter to platelet ratio score (LSPS) and portal hypertension risk score were evaluated. RESULTS: One hundred and four patients were eligible for analysis. Clinically significant and severe PH were detected in 84 and 74 patients, respectively. Liver and spleen stiffness were significantly correlated with hepatic venous pressure gradient in overall, CSPH, and SPH groups (rL = 0.607, 0.554, and 0.412; rS = 0.665, 0.566, and 0.467, respectively; all P < 0.05). The area under the receiver operating characteristic curves of L-SWE, S-SWE, LSPS, and PH risk score were 0.72 (95% confidence interval [CI], 0.49-0.95), 0.81 (95% CI, 0.55-0.97), 0.76 (95% CI, 0.51-0.96), and 0.73 (95% CI, 0.55-0.88) for CSPH, and 0.77 (95% CI, 0.51-0.93), 0.85 (95% CI, 0.59-0.96), 0.80 (95% CI, 0.58-0.98), and 0.80 (95% CI, 0.59-0.93) for SPH. The best cut-off of L-SWE for determining CSPH and SPH were 16.1 kPa (sensitivity, 78%; specificity, 72%) and 23.5 kPa (sensitivity, 81%; specificity, 79%). For S-SWE, the best cut-offs were 25.3 kPa (sensitivity, 85%; specificity, 79%) and 33.4 kPa (sensitivity, 74%; specificity, 70%). A cut-off of L-SWE <13.2 kPa or S-SWE <23.2 kPa was able to rule out CSPH, whereas a cut-off of L-SWE >24.9 kPa or S-SWE >34.2 kPa was able to rule in CSPH. CONCLUSIONS: Liver and spleen stiffness measured by 2-D SWE are reliable and promising non-invasive parameters to assess CSPH and SPH.

Savitzky-Golay filter based contrast-enhanced ultrasound quantification in hepatic tumors: Methodology and its correlation with tumor angiogenesis.

BACKGROUND: Savitzky-Golay filter is a digital filter used in data smoothing, we introduced a contrast-enhanced ultrasound (CEUS) quantification software based on the filter (SGCQ). OBJECTIVE: To explore the methodology of analyzing hepatic tumors hemodynamics applying SGCQ software and the correlation between SGCQ parameters and hepatocellular carcinoma (HCC) angiogenesis. METHODS: Nighty-seven right-lobe located hepatic mass cases (15 females and 82 males, mean age 58±10y, mean lesion size: 39.9±11.6 mm) underwent CEUS scan preoperatively and had a final diagnosis of HCC (n = 52) or colorectal cancer metastatic liver tumors (MLT, n = 45) were included. CEUS was carried out using a 1-5 MHz convex probe. The CEUS clips were recorded and analyzed off-line to obtain the parameters. The parameters were analyzed by 3 observers separately to investigate inter-observer variability. Parameters were compared between tumor and adjacent liver and between different tumors. Immunohistochemistry was used to evaluate the microvessel density (MVD) of HCC, and the correlation between the parameters and MVD was analyzed. RESULTS: Intraclass correlation coefficient (ICC) of all parameters were greater than 0.75 except wash-in slope (a3) and time to peak (TTP) of adjacent liver. The parameters of a3, wash-out slope (a2), perfusion time (PT) and area under the curve (AUC) were significantly different between HCC and liver. The a2, a3, AUC, PT and enhanced intensity (EI) were significantly different between MLT and liver. AUC, a2, a3, da1 and dPI were significantly different between HCC and MLT. AUC, a2 and EI correlated with MVD. CONCLUSION: SGCQ software quantification have good consistency among three observers, the parameters of SGCQ can display the hemodynamics of HCC and MLT and the difference between them. AUC and EI can serve as useful biomarkers in tumor angiogenesis evaluation.

Association studies of ERCC1 polymorphisms with lung cancer susceptibility: a systematic review and meta-analysis.

BACKGROUND: Excision repair cross-complimentary group 1 (ERCC1) is an essential component of the nucleotide excision repair system that is responsible for repairing damaged DNA. Functional genetic variations in the ERCC1 gene may alter DNA repair capacity and modulate cancer risk. The putative roles of ERCC1 gene polymorphisms in lung cancer susceptibility have been widely investigated. However, the results remain controversial. OBJECTIVES: An updated meta-analysis was conducted to explore whether lung cancer risk could be attributed to the following ERCC1 polymorphisms: rs11615 (T>C), rs3212986 (C>A), rs3212961 (A>C), rs3212948 (G>C), rs2298881 (C>A). METHODS: Several major databases (MEDLINE, EMBASE and Scopus) and the Chinese Biomedical database were searched for eligible studies. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to measure the strength of associations. RESULTS: Sixteen studies with 10,106 cases and 13,238 controls were included in this meta-analysis. Pooled ORs from 11 eligible studies (8,215 cases vs. 11,402 controls) suggested a significant association of ERCC1 rs11615 with increased risk for lung cancer (homozygous: CC versus TT, OR = 1.24, 95% CI: 1.04-1.48, P = 0.02). However, such an association was disproportionately driven by a single study. Removal of that study led to null association. Moreover, initial analyses suggested that ERCC1 rs11615 exerts a more profound effect on the susceptibility of non-smokers to lung cancer than that of smokers. Moreover, no statistically significant association was found between remaining ERCC1 polymorphisms of interest and lung cancer risk, except for rs3212948 variation (heterozygous: CG vs.GG, OR = 0.78, 95% CI: 0.67-0.90, P = 0.001; dominant: CG/CC vs.GG, OR = 0.79, 95% CI: 0.69-0.91, P = 0.001). CONCLUSION: Overall, this meta-analysis suggests that ERCC1 rs3212948 G>C, but not others, is a lung cancer risk-associated polymorphism. Carefully designed studies with large sample size involving different ethnicity, smoking status, and cancer types are needed to validate these findings.

Complete disassociation of adult pancreas into viable single cells through cold trypsin-EDTA digestion.

The in vitro isolation and analysis of pancreatic stem/progenitor cells are necessary for understanding their properties and function; however, the preparation of high-quality single-cell suspensions from adult pancreas is prerequisite. In this study, we applied a cold trypsin-ethylenediaminetetraacetic acid (EDTA) digestion method to disassociate adult mouse pancreata into single cells. The yield of single cells and the viability of the harvested cells were much higher than those obtained via the two commonly used warm digestion methods. Flow cytometric analysis showed that the ratio of ductal or BCRP1-positive cells in cell suspensions prepared through cold digestion was consistent with that found in vivo. Cell culture tests showed that pancreatic epithelial cells prepared by cold digestion maintained proliferative capacity comparable to those derived from warm collagenase digestion. These results indicate that cold trypsin-EDTA digestion can effectively disassociate an adult mouse pancreas into viable single cells with minimal cell loss, and can be used for the isolation and analysis of pancreatic stem/progenitor cells.

Id1 enhances human ovarian cancer endothelial progenitor cell angiogenesis via PI3K/Akt and NF-κB/MMP-2 signaling pathways.

BACKGROUND: Endothelial progenitor cells (EPCs) contribute to tumor angiogenesis and growth. We previously reported that over-expression of an inhibitor of DNA binding/differentiation 1 (Id1) in EPCs can enhance EPC proliferation, migration, and adhesion. In this study, we investigated the role of Id1 in EPC angiogenesis in patients with ovarian cancer and the underlying signaling pathway. METHODS: Circulating EPCs from 22 patients with ovarian cancer and 15 healthy control subjects were cultured. Id1 and matrix metalloproteinase-2 (MMP-2) expression were analyzed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and western blot. EPC angiogenesis was detected by tube formation assays. Double-stranded DNA containing the interference sequences was synthesized according to the structure of a pGCSIL-GFP viral vector and then inserted into a linearized vector. Positive clones were identified as lentiviral vectors that expressed human Id1 short hairpin RNA (shRNA). RESULTS: Id1 and MMP-2 expression were increased in EPCs freshly isolated from ovarian cancer patients compared to those obtained from healthy subjects. shRNA-mediated Id1 down-regulation substantially reduced EPC angiogenesis and MMP-2 expression. Importantly, transfection of EPCs with Id1 in vitro induced phosphorylation of Akt (p-Akt) via phosphoinositide 3-kinase and increased the expression of MMP-2 via NF-κB. Blockage of both pathways by specific inhibitors (LY294002 and PDTC, respectively) abrogated Id1-enhanced EPC angiogenesis. CONCLUSIONS: Id1 can enhance EPC angiogenesis in ovarian cancer, which is mainly mediated by the PI3K/Akt and NF-κB/MMP-2 signaling pathways. Id1 and its downstream effectors are potential targets for treatment of ovarian cancer because of their contribution to angiogenesis.