Identification and validation of key genes associated with non-small-cell lung cancer

Non-small-cell lung cancer (NSCLC) is one of the main causes of death induced by cancer globally. However, the molecular aberrations in NSCLC patients remain unclearly. In the present study, four messenger RNA microarray datasets (GSE18842, GSE40275, GSE43458, and GSE102287) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between NSCLC tissues and adjacent lung tissues were obtained from GEO2R and the overlapping DEGs were identified. Moreover, functional and pathway enrichment were performed by Funrich, while the protein–protein interaction (PPI) network construction were obtained from STRING and hub genes were visualized and identified by Cytoscape software. Furthermore, validation, overall survival (OS) and tumor staging analysis of selected hub genes were performed by GEPIA. A total of 367 DEGs (95 upregulated and 272 downregulated) were obtained through gene integration analysis. The PPI network consisted of 94 nodes and 1036 edges in the upregulated DEGs and 272 nodes and 464 edges in the downregulated DEGs, respectively. The PPI network identified 46 upregulated and 27 downregulated hub genes among the DEGs, and six (such as CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M) of that have not been identified to be associated with NSCLC so far. Moreover, the expression differences of the mentioned hub genes were consistent with that in lung adenocarcinoma and lung squamous cell carcinoma in the TCGA database. Further analysis showed that all the six hub genes were associated with tumor staging except MYH11, while only the upregulated DEG CENPE was associated with the worse OS of patients with NSCLC. In conclusion, the current study showed that CENPE, NCAPH, MYH11, LRRK2, HSD17B6, and A2M might be the key genes contributed to tumorigenesis or tumor progression in NSCLC, further functional study is needed to explore the involved mechanisms.     

Identification of a Highly Conserved Epitope on Avian Influenza Virus Non-Structural Protein 1 Using a Peptide Microarray

Avian influenza virus (AIV) non-structural protein 1 (NS1) is a multifunctional protein. It is present at high levels in infected cells and can be used for AIV detection and diagnosis. In this study, we generated monoclonal antibody (MAb) D7 against AIV NS1 protein by immunization of BALB/c mice with purified recombinant NS1 protein expressed in Escherichia coli. Isotype determination revealed that the MAb was IgG₁/κ-type subclass. To identify the epitope of the MAb D7, the NS1 protein was truncated into a total of 225 15-mer peptides with 14 amino acid overlaps, which were spotted for a peptide microarray. The results revealed that the MAb D7 recognized the consensus DAPF motif. Furthermore, the AIV NS1 protein with the DAPF motif deletion was transiently expressed in 293T cells and failed to react with MAb D7. Subsequently, the DAPF motif was synthesized with an elongated GSGS linker at both the C- and N-termini. The MAb D7 reacted with the synthesized peptide both in enzyme-linked immunosorbent assay (ELISA) and dot-blot assays. From these results, we concluded that DAPF motif is the epitope of MAb D7. To our knowledge, this is the first report of a 4-mer epitope on the NS1 protein of AIV that can be recognized by MAb using a peptide microarray, which is able to simplify epitope identification, and that could serve as the basis for immune responses against avian influenza.     

Association between TNFA Gene Polymorphisms and Helicobacter pylori Infection: A Meta-Analysis

Background

Several host genetic factors are thought to affect susceptibility to Helicobacter pylori infection-related diseases, including tumor necrosis factor (TNF)-α. Previous studies have evaluated the association between TNFA gene polymorphisms and H. pylori infection, but the results were inconclusive. We conducted this meta-analysis to clarify the association between TNFA polymorphisms and H. pylori infection.

Methods

Published literature within PubMed, Embase, and the Cochrane Library were used in our meta-analysis. Data were analyzed with the Stata13.1 software package using pooled odds ratios (ORs) with 95% confidence intervals (CI).

Results

A total of 24 studies were included in our study. The TNFA -308G>A polymorphism was associated with decreasing H. pylori infection (AA vs. AG+GG, OR = 0.64, 95% CI = 0.43–0.97; AA vs. GG, OR = 0.64, 95% CI = 0.43–0.97). A significantly decreased risk was also found for -1031T>C polymorphism (CC vs. CT+TT, OR = 0.61, 95% CI = 0.44–0.84). -863C>A polymorphism was associated with increasing risk of H. pylori infection (AA+AC vs. CC, OR = 1.47, 95% CI = 1.16–1.86; A allele vs. C allele, OR = 1.40, 95% CI = 1.14–1.72). There was no significant association between -857C>T polymorphism and H. pylori infection. When stratified analysis was conducted on H. pylori infection detection methods, -857C>T and -863C>A polymorphisms were associated with H. pylori infection for the non-ELISA subgroup. When stratified for ethnicity or study design, -863C>A significantly increased the risk and -1031T>C decreased the risk for the Asian subgroup and hospital-based subgroup.

Conclusion

Results of our meta-analysis demonstrate that TNFA -308G>A and -1031 T>C polymorphisms may be protective factors against H. pylori infection, and -863C>A may be a risk factor, especially in Asian populations. Further studies with larger sample sizes are required to validate these results.     

Inhibition of polypeptide N-acetyl-α-galactosaminyltransferases is an underlying mechanism of dietary polyphenols preventing colorectal tumorigenesis

Ellagitannin-derived ellagic acid (EA) and colonic metabolite urolithins are functional dietary ingredients for cancer prevention, but the underlying mechanism need elucidation. Mucin-type O-glycosylation, initiated by polypeptide N-acetyl-α-galactosaminyltransferases (ppGalNAc-Ts), fine-tunes multiple biological processes and is closely associated with cancer progression. Herein, we aim to explore how specific tannin-based polyphenols affect tumor behavior of colorectal cancer cells (CRC) by modulating O-glycosylation. Utilizing HPLC-based enzyme assay, we find urolithin D (UroD), EA and gallic acid (GA) potently inhibit ppGalNAc-Ts. In particular, UroD inhibits ppGalNAc-T2 through a peptide/protein-competitive manner with nanomolar affinity. Computational simulations combined with site-directed mutagenesis further support the inhibitors’ mode of action. Moreover, lectin analysis and metabolic labelling reveal that UroD can reduce cell O-glycans but not N-glycans. Transwell experiments prove that UroD inhibits migration and invasion of CRC cells. Our work proves that specific tannin-based polyphenols can potently inhibit ppGalNAc-Ts activity to reduce cell O-glycosylation and lead to lowering the migration and invasion of CRC cells, suggesting that disturbance of mucin-type O-glycosylation is an important mechanism for the function of dietary polyphenols.     

Radially Oriented Single‐Crystal Primary Nanosheets Enable Ultrahigh Rate and Cycling Properties of LiNi0.8Co0.1Mn0.1O2 Cathode Material for Lithium‐Ion Batteries

Ni‐rich Li[Ni_xCo_yMn_1?x?y]O₂ (x ≥ 0.8) layered oxides are the most promising cathode materials for lithium‐ion batteries due to their high reversible capacity of over 200 mAh g^?1. Unfortunately, the anisotropic properties associated with the α‐NaFeO₂ structured crystal grains result in poor rate capability and insufficient cycle life. To address these issues, a micrometer‐sized Ni‐rich LiNi_0.8Co_0.1Mn_0.1O₂ secondary cathode material consisting of radially aligned single‐crystal primary particles is proposed and synthesized. Concomitant with this unique crystallographic texture, all the exposed surfaces are active {010} facets, and 3D Li⁺ ion diffusion channels penetrate straightforwardly from surface to center, remarkably improving the Li⁺ diffusion coefficient. Moreover, coordinated charge–discharge volume change upon cycling is achieved by the consistent crystal orientation, significantly alleviating the volume‐change‐induced intergrain stress. Accordingly, this material delivers superior reversible capacity (203.4 mAh g^?1 at 3.0–4.3 V) and rate capability (152.7 mAh g^?1 at a current density of 1000 mA g^?1). Further, this structure demonstrates excellent cycling stability without any degradation after 300 cycles. The anisotropic morphology modulation provides a simple, efficient, and scalable way to boost the performance and applicability of Ni‐rich layered oxide cathode materials.     

Quantitative assessment of optical clearing methods in various intact mouse organs

Various tissue optical clearing techniques have sprung up for large volume imaging. However, there are few methods showed clearing and imaging data on different organs while most of them were focused on mouse brain, and as a result, it is difficult to select the suitable method for organs in practical applications due to lack of quantitative evaluation and comprehensive comparison. Therefore, it is necessary to evaluate and compare the performances of clearing methods for different organs. In this paper, several typical optical clearing methods were applied, including 3DISCO, uDISCO, SeeDB, FRUIT, CUBIC, ScaleS and PACT to clear intact brain, heart, kidney, liver, spleen, stomach, lung, small intestine, skin and muscle. The clearing efficiency, sample deformation, fluorescence preservation and imaging depth of these methods were quantitatively evaluated. Finally, based on the systemic evaluation of various parameters described above, the appropriate clearing method for specific organ including kidney or intestine was screened out. This paper will provide important references for selection of appropriate clearing methods in related researches.      

Overexpression of RYBP inhibits proliferation,invasion, and chemoresistance to cisplatin in anaplastic thyroid cancer cells via the EGFR pathway

Ring1 and YY1 binding protein (RYBP), a new member of the polycomb group protein family, has been reported to play an important role in various biological processes. Recently, more and more studies have demonstrated an implication of RYBP in cancer development. However, the specific role of RYBP in anaplastic thyroid cancer (ATC) remains unknown. In this study, we investigated for the first time the expression pattern and biological functions of RYBP in ATC. We showed that RYBP was lowly expressed in ATC tissues and cell lines. We also found that overexpression of RYBP inhibited ATC cell proliferation, invasion, and cisplatin resistance. Furthermore, we observed that upregulation of RYBP decreased the phosphorylation of EGFR and ERK1/2 in ATC cells. Taken together, our data indicated that RYBP might be considered as a promising therapeutic target for the treatment of ATC.     

超声引导下前列腺穿刺联合外周血循环肿瘤细胞检测对前列腺癌预后分析

目的探讨超声引导下前列腺穿刺联合外周血循环肿瘤细胞(CTCs)检测对前列腺癌预后的预测效果。方法选取2011年1月至2017年12月期间于郑州大学第二附属医院收治的83例前列腺癌患者为研究对象,全部患者均根据超声引导下经直肠前列腺穿刺活检术确诊为前列腺癌,检测病理标本中CK34BE12、p63、α-甲酰基辅酶A消旋酶(AMACR)等免疫标志物的表达状况,并采用Cell Search细胞搜索系统检测外周血CTCs的数量,据此分为阳性组(≥5个/7.5 ml)和阴性组(<5个/7.5 ml)。分析穿刺组织中免疫标志物表达状况、外周血CTCs计数与患者临床病理特征、生存状况的相关性。各标志物的阳性例数、Gleason评分>7分的比例、TNM分期等定性资料的比较采用x^2检验或Fisher确切概率法,年龄、血常规、凝血功能、肝功能、PSA水平等定量资料的比较采用t检验。采用Kaplan-Meier法进行生存分析,采用多因素Cox比例风险回归模型分析患者预后的预测因素。结果(1)全部患者中外周血CTCs、穿刺组织中CK34BE12、p63、AMACR的阳性率分别为31.33、3.61、3.61、86.75。CTCs阳性组的AMACR阳性率为100.00,高于CTCs阴性组的80.70,差异有统计学意义(x^2=4.227,P<0.05)。(2)AMACR阳性组患者的血红蛋白(HB)低于AMACR阴性组[(123.66±13.33)g/L比(134.89±20.08)g/L,t=2.420,P=0.018],血小板(PLT)、血清谷丙转氨酶、D-二聚体(DD)、前列腺特异抗原(PSA)水平、Gleason评分>7分的比例均高于AMACR阴性组[(197.23±36.98)×10^9/L比(172.83±33.33)×10^9/L,t=2.062,P=0.042;(38.80±10.03)U/L比(31.46±7.83)U/L,t=2.317,P=0.023;(255.00±38.80)μg/L比(220.81±30.99)μg/L,t=2.785,P=0.007;(26.60±12.23)ng/ml比(17.90±8.88)ng/ml,t=2.263,P=0.026;45.83比9.09,x^2=3.916,P=0.048],差异有统计学意义(P<0.05)。CTCs阳性组患者的HB低于CTCs阴性组[(121.69±15.89)g/L比(132.73±18.85)g/L,t=2.767,P=0.007],血清碱性磷酸酶、DD、PSA水平、Gleason评分>7分、T3~T4期、M1期的比例均高于CTCs阴性组[(105.69±30.56)U/L比(88.89±35.58)U/L,t=2.205,P=0.030;(256.63±35.86)μg/L比(236.98±33.30)μg/L,t=2.368,P=0.020;(30.09±11.89)ng/ml比(23.33±10.99)ng/ml,t=2.533,P=0.013;57.69比33.33,x^2=4.381,P=0.036;30.77比8.77,x^2=4.981,P=0.026;50.00比17.54,x^2=9.390,P=0.002],差异有统计学意义(P<0.05)。(3)全部患者的中位生存时间为58.33个月,1、3、5年的生存率分别为88.95、51.81、30.12。AMACR阳性组、CTCs阳性组患者的中位生存时间为40.93、36.93个月,低于AMACR阴性组、CTCs阴性组的66.66、69.56个月,差异有统计学意义(P<0.05)。多因素Cox比例风险回归模型分析结果表明,Gleason评分>7分、M1期、AMACR阳性、CTCs阳性是患者死亡的独立危险因素(HR=1.883、3.666、2.009、2.923,P<0.05)。结论超声引导下前列腺穿刺联合外周血CTCs检测对前列腺癌患者的预后具有重要的预测价值,临床上可根据穿刺组织中AMACR表达水平和外周血CTCs计数进行预后的综合分析。     

High-dose rapamycin induces apoptosis in human cancer cells by dissociating mTOR complex 1 and suppressing phosphorylation of 4E-BP1

mTOR, the mammalian target of rapamycin, has been widely implicated in signals that promote cell cycle progression and survival in cancer cells. Rapamycin, which inhibits mTOR with high specificity, has consequently attracted much attention as an anticancer therapeutic. Rapamycin suppresses phosphorylation of S6 kinase at nanomolar concentrations; however, at higher micro-molar doses, rapamycin induces apoptosis in several human cancer cell lines. While much is known about the effect of low-dose rapamycin treatment, the mechanistic basis for the apoptotic effects of high-dose rapamycin treatment is not understood. We report here that the apoptotic effects of high-dose rapamycin treatment correlate with suppressing phosphorylation of the mTOR complex 1 substrate, eukaryotic initiation factor 4E (eIF4E) binding protein-1 (4E-BP1). Consistent with this observation, ablation of eIF4E also resulted in apoptorsis in MDA-MB 231 breast cancer cells. We also provide evidence that the differential dose effects of rapamycin are correlated with partial and complete dissociation of Raptor from mTORC1 at low and high doses, respectively. In contrast with MDA-MB-231 cells, MCF-7 breast cancer cells survived rapamycin-induced suppression of 4E-BP1 phosphorylation. We show that survival correlated with a hyperphosphorylation of Akt at S473 at high rapamycin doses, the suppression of which conferred rapamycin sensitivity. This study reveals that the apoptotic effect of rapamycin requires doses that completely dissociate Raptor from mTORC1 and suppress that phosphorylation of 4E-BP1 and inhibit eIF4E.Key words: rapamycin, mTOR, 4E-BP1, eIF4E, Akt, apoptosis     

Growth factor stimulated cell proliferation is accompanied by an elevated labile intracellular pool of zinc in 3T3 cells

Growth factors such as platelet-derived growth factor (PDGF), epidermal growth factor (EGF), and insulin-like growth factor-I (IGF-I) are required for quiescent 3T3 cells to proliferate, but zinc deprivation impairs IGF-I-induced DNA synthesis. We recently showed that labile intracellular pool of zinc is involved in cell proliferation. Our objective was to determine whether the labile intracellular pool of zinc plays a role in growth factor (PDGF, EGF, and IGF-I)-stimulated proliferation of 3T3 cells. Quiescent 3T3 cells were cultured in DMEM with or without growth factors. Labile intracellular pool of zinc, DNA synthesis, and cell proliferation were assessed using fluorescence microscopy, 3H-thymidine incorporation, and total cell number counts, respectively. After 24 h, growth factors stimulated DNA synthesis (24%) but not cell proliferation. After 48 h, growth factors stimulated both DNA synthesis (37%) and cell proliferation (89%). In response to growth factor stimulation, the labile intracellular pool of zinc was also elevated after 24 or 48 h of treatment. In summary, growth factor (PDGF, EGF, and IGF-I)-stimulated increase in DNA synthesis and cell proliferation were accompanied by an elevated labile intracellular pool of zinc in 3T3 cells. Since elevation of the labile intracellular pool of zinc occurred along with increased DNA synthesis, but cell proliferation remained unchanged, the elevation of the labile intracellular pool of zinc likely occurred during the S phase to provide the zinc needed to support DNA synthesis and ultimately cell proliferation.