Bioinformatics analysis and verification of gene targets for renal clear cell carcinoma

BackgroundIt is estimated that there are 338,000 new renal-cell carcinoma releases every year in the world. Renal cell carcinoma (RCC) is a heterogeneous tumor, of which more than 70% is clear cell renal cell carcinoma (ccRCC). It is estimated that about 30% of new renal-cell carcinoma patients have metastases at the time of diagnosis. However, the pathogenesis of renal clear cell carcinoma has not been elucidated. Therefore, it is necessary to further study the pathogenesis of ccRCC.MethodsTwo expression profiling datasets (GSE68417, GSE71963) were downloaded from the GEO database. Differentially expressed genes (DEGs) between ccRCC and normal tissue samples were identified by GEO2R. Functional enrichment analysis was made by the DAVID tool. Protein-protein interaction (PPI) network was constructed. The hub genes were excavated. The clustering analysis of expression level of hub genes was performed by UCSC (University of California Santa Cruz) Xena database. The hub gene on overall survival rate (OS) in patients with ccRCC was performed by Kaplan-Meier Plotter. Finally, we used the ccRCC renal tissue samples to verify the hub genes.Results1182 common DEGs between the two datasets were identified. The results of GO and KEGG analysis revealed that variations in were predominantly enriched in intracellular signaling cascade, oxidation reduction, intrinsic to membrane, integral to membrane, nucleoside binding, purine nucleoside binding, pathways in cancer, focal adhesion, cell adhesion molecules. 10 hub genes ITGAX, CD86, LY86, TLR2, TYROBP, FCGR2A, FCGR2B, PTPRC, ITGB2, ITGAM were identified. FCGR2B and TYROBP were negatively correlated with the overall survival rate in patients with ccRCC (P < 0.05). RT-qPCR analysis showed that the relative expression levels of CD86, FCGR2A, FCGR2B, TYROBP, LY86, and TLR2 were significantly higher in ccRCC samples, compared with the adjacent renal tissue groups.ConclusionsIn summary, bioinformatics technology could be a useful tool to predict the progression of ccRCC. In addition, there are DEGs between ccRCC tumor tissue and normal renal tissue, and these DEGs might be considered as biomarkers for ccRCC.     

UPLC‐MS/MS based diagnostics for epithelial ovarian cancer using fully sialylated C4‐binding protein

Serum levels of fully sialylated C4‐binding protein (FS‐C4BP) are remarkably elevated in patients with epithelial ovarian cancer (EOC) and can be used as a marker to distinguish ovarian clear cell carcinoma from endometrioma. This study aimed to develop a stable, robust and reliable liquid chromatography–hybrid mass spectrometry (UPLC‐MS/MS) based diagnostic method that would generalize FS‐C4BP as a clinical EOC biomarker. Glycopeptides derived from 20 μL of trypsin‐digested serum glycoprotein were analyzed via UPLC equipped with an electrospray ionization time‐of‐flight mass spectrometer. This UPLC‐MS/MS‐based diagnostic method was optimized for FS‐C4BP and validated using sera from 119 patients with EOC and 127 women without cancer. A1958 (C4BP peptide with two fully sialylated biantennary glycans) was selected as a marker of FS‐C4BP because its level in serum was highest among FS‐C4BP family members. Preparation and UPLC‐MS/MS were optimized for A1958, and performance and robustness were significantly improved relative to our previous method. An area under the curve analysis of the FS‐C4BP index receiver operating characteristic curve revealed that the ratio between A1958 and A1813 (C4BP peptide with two partially sialylated biantennary glycans) reached 85%. A combination of the FS‐C4BP index and carbohydrate antigen‐125 levels further enhanced the sensitivity and specificity.     

Synthesis and antiproliferative evaluation of oxime,methyloxime, and amide‐containing quinazolinones

Certain oxime, methyloxime, and amide‐containing quinazolinone derivatives were synthesized and evaluated in vitro for their antiproliferative activities against a panel of human cancer cell lines including nasopharyngeal carcinoma (NPC‐TW01), lung carcinoma (NCI‐H226), and leukemia (Jurkat). Quinazolinone 2 was inactive against all three cell lines tested, while quinazolinone 4 was weakly active against both Jurkat and H226 cancer cells with IC₅₀ values of 6.55 and 12.27 μM, respectively, indicating that the oxime derivative 4 is more favorable than its ketone precursor 2 . Our results have also indicated that quinazolinone 8g and its biphenyl counterpart 8f exhibited more potent antiproliferative activities than the positive control methotrexate against all three cancer cell lines tested. Among these quinazolinone derivatives, 8g was the most active against NPC‐TW01 with an IC₅₀ value of 4.78 μM. Further study on NPC‐TW01 cell cycle distribution indicated that the compound 8g induced cell arrest at the G1/G0 phase in a time‐ and concentration‐dependent manner. Moreover, a characteristic hypo‐diploid DNA content peak (sub‐G1) was found to increase from 1 to 4% in NPC‐TW01 cells treated with 8g for 72 hr. These results indicate that 8g can induce cells arrest in the G1/G0 phase and cause cell death. Further structural optimization of 8g and detailed study of its antiproliferative mechanism are going on.     

C(4)取代紫杉醇类似物的定量构效关系研究

用量子化学B3LYP／6-31G方法计算了23个C（4）取代紫杉醇类似物的结构,用遗传算法（GFA）对能量、电性、拓扑及热力学等类型的278个结构描述符进行筛选,并回归建立其抑制人体结肠癌细胞HCT-116活性的定量构效关系（QSAR）．QSAR方程含分子体积Vm、分子分支度指数CHI-O、分子中带正电荷原子的溶剂可积面积与其所带电荷之积的加和值Jurs-PPSA-3以及分子表面积S4个结构描述符．方程的拟合相关系数的平方R^0及交叉验证系数Q^2分别为0．956和0．913,所得QSAR具有可信的预报能力．由优化后的几何构型知,C（4）取代基、C（13）侧链和2-OBz三基团共同形成疏水腔,C（4）取代基的改变影响C（13）侧链的电子结构．C（13）连接的18号O原子的负电荷越大、3’位连接的NHBz基团的极性越小活性越高;C（4）取代基若为吸电子基对活性不利;适当增大分子体积、表面积和疏水性,保持一定的分支度对活性有利．     

Proteomic approach for purification of seminal plasma proteins involved in tumor proliferation

Human seminal plasma contains a large array of proteins required for the normal physiology and metabolism of spermatozoa. These are mainly secreted from prostate epithelium, testes, and seminal vesicles. Fortunately, many of these are found to be present at elevated concentration in seminal plasma and act as a biomarker of different carcinomas as their levels are also enhanced in serum and are found to be involved in tumor progression and metastasis apart from fertility. The proteins which were overexpressed in the seminal plasma of prostate carcinoma patients were identified by 2-DE and MALDI-TOF/MS. We have designed a strategy to purify these four proteins prostate specific antigen (PSA), prostatic acid phosphatase (PAP), Zinc alpha2-glycoprotein (ZAG), and progastricsin (PG), together in homogeneity by using simple chromatographic techniques. Acidic and basic fractions of human seminal plasma were separated by ion exchange chromatography and further purified by gel permeation chromatography. Our results form a new and valuable resource for those attempting structure-based drug designing for prostate and other cancers where the amount of proteins is required in plenty and in native form.     

Identification of human hepatocellular carcinoma-related proteins by proteomic approaches

Hepatocellular carcinoma (HCC) is the most common malignant liver tumor. Analysis of human serum from HCC patients using two-dimensional gel electrophoresis (2DE) combined with nano-high-performance liquid chromatography electrospray ionization tandem mass spectrometry (nano-HPLC–ESI-MS/MS) identified fourteen different proteins differentially expressed between HCC patients and the control group. Twelve proteins were up-regulated and two down-regulated. By using nano-HPLC–MS/MS system to analyze proteome in human serum, 317 proteins were identified, twenty-nine of which to high confidence levels (protein matched at last two unique peptide sequences). Of these twenty-nine proteins, six were present only in HCC patients and may serve as biomarkers for HCC. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Diffusion-weighted magnetic resonance imaging in differentiation of postobstructive consolidation from central lung carcinoma

Purpose

To prospectively evaluate diffusion-weighted (DW) magnetic resonance (MR) imaging for differentiation of postobstructive consolidation from centrally located lung carcinomas by using apparent diffusion coefficients (ADCs).

Materials and Methods

An institutional review board approved this study; informed consent was obtained from patients. Forty-nine consecutive patients (3 women, 46 men; mean age, 63.6 years; age range, 42–85 years) with lung carcinoma underwent DW MR imaging. Forty patients had central and nine patients had peripheral lung carcinomas. ADC of each lung carcinoma was calculated from DW MR images obtained with two different b values (0, 1000 s/mm²).In the final study group including 27 patients with central lung carcinoma accompanying distal lung consolidation (mean age, 67.2 years; 3 women, 24 men), ADCs of lung carcinomas were statistically compared among cytologic/histologic types and accompanying postobstructive consolidations. Unpaired t test was used for measurable variables with normal distribution, and Kruskal–Wallis variance analysis and Mann–Whitney U tests were used for the measurable variables without normal distribution.

Results

There was no significant difference between mean ADC values of all types of carcinomas (P=.302) and also between mean ADC values of central (1.91 ± 0.7×10⁻³ mm²/s) and peripheral carcinomas (1.58 ± 0. 6×10⁻³ mm²/s) (P=.224). The mean ADC value for the masses of central lung carcinoma with postobstructive consolidations was 1.83 ± 0.75×10⁻³ mm²/s, and for consolidation was 2.50 ± 0.76×10⁻³ mm²/s. ADC of central carcinoma masses was significantly lower than that of postobstructive consolidations (P=.003).

Conclusions

ADC values of central lung carcinoma masses appear to be lower than accompanying postobstructive consolidations. ADC values could be considered useful as a differentiating parameter among central lung carcinomas and accompanying postobstructive consolidations.     

淮安市食管鳞癌患者血清~1 H NMR波谱初步研究

测试了30例正常人血清和60例淮安市食管鳞癌患者血清的氢核磁共振波谱.观察到正常人血清的共振峰主要集中在化学位移δH(ppm)1.00 ～5.00,构建了正常人血清的~1H NMR指纹图谱.同时将食管鳞癌患者血清1H NMR与正常人血清~1H NMR进行比较,发现食管鳞癌患者与正常人血清样品在δ_H 1.0 ～1.2 和δ_H 3.0 ～3.8(如δH 3.25、3.23、3.36、3.41、3.43)存在一定的差异波峰,即食管鳞癌的可能特征峰.表明借助于1H NMR特征峰有助于食管鳞癌的早期诊断.     

Screen anticancer drug in vitro using resonance light scattering technique

An in vitro screening model using resonance light scattering (RLS) technique with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) reagent as the reactive probe to target cancer cell was firstly developed. In this model, MTT was reduced by viable cancer cells to produce a purple formazan. Cell viability was proportional to the number of formazan induced strong light scattering signal. The inhibition rate of anticancer drug was found to vary inversely with the H₂₂-MTT system RLS intensity. So it was intuitive to see the sequence of the tumor suppressive activity of six anticancer drugs without data processing by RLS/MTT screening spectra. Compared with the traditional MTT method, this method has high sensitivity, low detection limit and quite intuitive screening results which were identical to those obtained from the MTT colorimetric assay.     

HBx介导的促肝癌作用

乙型肝炎病毒（Hepatitis B virus,HBV）感染是诱发原发性肝癌的主要原因之一.HBV存在4个相互重叠的开放读码框：S,C,P和X区.其中X基因表达的蛋白HBx被认为是诱导肝癌发生的一种多功能致癌蛋白,它可以作用于众多信号通路及细胞因子从而诱发肝癌.本文根据最新的研究,选择其中p53和NF-κB两条信号通路及HBx与表观遗传修饰的相关性进行了探讨,目的在于部分揭示HBV感染诱发肝癌的发病机理.