Reproducible cancer biomarker discovery in SELDI-TOF MS using different pre-processing algorithms

Background

There has been much interest in differentiating diseased and normal samples using biomarkers derived from mass spectrometry (MS) studies. However, biomarker identification for specific diseases has been hindered by irreproducibility. Specifically, a peak profile extracted from a dataset for biomarker identification depends on a data pre-processing algorithm. Until now, no widely accepted agreement has been reached.

Results

In this paper, we investigated the consistency of biomarker identification using differentially expressed (DE) peaks from peak profiles produced by three widely used average spectrum-dependent pre-processing algorithms based on SELDI-TOF MS data for prostate and breast cancers. Our results revealed two important factors that affect the consistency of DE peak identification using different algorithms. One factor is that some DE peaks selected from one peak profile were not detected as peaks in other profiles, and the second factor is that the statistical power of identifying DE peaks in large peak profiles with many peaks may be low due to the large scale of the tests and small number of samples. Furthermore, we demonstrated that the DE peak detection power in large profiles could be improved by the stratified false discovery rate (FDR) control approach and that the reproducibility of DE peak detection could thereby be increased.

Conclusions

Comparing and evaluating pre-processing algorithms in terms of reproducibility can elucidate the relationship among different algorithms and also help in selecting a pre-processing algorithm. The DE peaks selected from small peak profiles with few peaks for a dataset tend to be reproducibly detected in large peak profiles, which suggests that a suitable pre-processing algorithm should be able to produce peaks sufficient for identifying useful and reproducible biomarkers.     

Human amniotic epithelial cells maintain mouse spermatogonial stem cells in an undifferentiated state due to high leukemia inhibitor factor (LIF) expression

Spermatogonial stem cells (SSCs), like other stem cells, have unique properties: prolonged proliferation, self-renewal, generation of differentiated progeny, and maintenance of developmental potential. Long-term cultivation of normal SSCs into stable cell lines, and maintaining SSCs in an undifferentiated state capable of self-renewal, is a major challenge. Here, we compare the effect of leukemia inhibitory factor (LIF) expression on mouse SSCs isolated from testicular tissue cultured under different conditions. We found that human amniotic epithelial cells (hAECs) with high LIF expression (LIF(high)) feeder cells allowed mouse SSCs to maintain a high level of AP activity when cultured long term. Expression of some important stem cell markers was higher in mouse SSCs cultured on hAECs (LIF(high)) compared to those cultured on hAECs (LIF(low)). Taken together, these results suggest that LIF expression could be a crucial component for feeder cells to maintain mouse SSCs in an undifferentiated, proliferative state capable of self-renewal.     

miR-223 regulates migration and invasion by targeting Artemin in human esophageal carcinoma

Background

Artemin (ARTN) is a neurotrophic factor belonging to the glial cell-derived neurotrophic factor family of ligands. To develop potential therapy targeting ARTN, we studied the roles of miR-223 in the migration and invasion of human esophageal carcinoma.

Methods

ARTN expression levels were detected in esophageal carcinoma cell lines KYSE-150, KYSE-510, EC-9706, TE13, esophageal cancer tissues and paired non-cancerous tissues by Western blot. Artemin siRNA expression vectors were constructed to knockdown of artemin expression mitigated migration and invasiveness in KYSE150 cells. Monolayer wound healing assay and Transwell invasion assay were applied to observe cancer cell migration and invasion. The relative levels of expression were quantified by real-time quantitative PCR.

Results

ARTN expression levels were higher in esophageal carcinoma tissue than in the adjacent tissue and was differentially expressed in various esophageal carcinoma cell lines. ARTN mRNA contains a binding site for miR-223 in the 3'UTR. Co-transfection of a mir-223 expression vector with pMIR-ARTN led to the reduced activity of luciferase in a dual-luciferase reporter gene assay, suggesting that ARTN is a target gene of miR-223. Overexpression of miR-223 decreased expression of ARTN in KYSE150 cells while silencing miR-223 increased expression of ARTN in EC9706 cells. Furthermore, overexpression of miR-223 in KYSE150 cells decreased cell migration and invasion. Silencing of miR-223 in EC9706 cells increased cell migration and invasiveness.

Conclusions

These results reveal that ARTN, a known tumor metastasis-related gene, is a direct target of miR-223 and that miR-223 may have a tumor suppressor function in esophageal carcinoma and could be used in anticancer therapies.     

POTASSIUM ALLEVIATES THE INHIBITORY ACTION OF AMMONIUM UPON THE PHOTOSYNTHETIC RECOVERY OF NOSTOC FLAGELLIFORME (CYANOPHYCEAE) DURING REHYDRATION1

Effects of ammonium on the photosynthetic recovery of Nostoc flagelliforme Berk. et M. A. Curtis were assayed when being rehydrated in low‐K⁺ or high‐K⁺ medium. Its photosynthetic recovery was K⁺ limited after 3 years of dry storage. The potassium absorption of N. flagelliforme reached the maximum after 3 h rehydration in low‐K⁺ medium but at 5 min in high‐K⁺ medium. The K⁺ content of N. flagelliforme rehydrated in high‐K⁺ medium was much higher than that in low‐K⁺ medium. The maximal PSII quantum yield (F_v/F_m) value of N. flagelliforme decreased significantly when samples were rehydrated in low‐K⁺ medium treated with 5 mM NH₄Cl. However, the treatment of 20 mM NH₄Cl had little effect on its F_v/F_m value in high‐K⁺ medium. The relative F_v/F_m 24 h EC₅₀ (concentration at which 50% inhibition occurred) value of NH₄⁺ in high‐K⁺ medium (64.35 mM) was much higher than that in low‐K⁺ medium (22.17 mM). This finding indicated that high K⁺ could alleviate the inhibitory action of NH₄⁺ upon the photosynthetic recovery of N. flagelliforme during rehydration. In the presence of 10 mM tetraethylammonium chloride (TEACl), the relative F_v/F_m 24 h EC₅₀ value of NH₄⁺ was increased to 46.34 and 70.78 mM, respectively, in low‐K⁺ and high‐K⁺ media. This observation suggested that NH₄⁺ entered into N. flagelliforme cells via the K⁺ channel. Furthermore, NH₄⁺ could decrease K⁺ absorption in high‐K⁺ medium.     

Modulation of Ca Activity in Cardiomyocytes through Caveolae-Gαq Interactions

Cardiomyocytes have a complex Ca²⁺ behavior and changes in this behavior may underlie certain disease states. Intracellular Ca²⁺ activity can be regulated by the phospholipase Cβ–Gα_q pathway localized on the plasma membrane. The plasma membranes of cardiomycoytes are rich in caveolae domains organized by caveolin proteins. Caveolae may indirectly affect cell signals by entrapping and localizing specific proteins. Recently, we found that caveolin may specifically interact with activated Gα_q, which could affect Ca²⁺ signals. Here, using fluorescence imaging and correlation techniques we show that Gα_q-Gβγ subunits localize to caveolae in adult ventricular canine cardiomyoctyes. Carbachol stimulation releases Gβγ subunits from caveolae with a concurrent stabilization of activated Gα_q by caveolin-3 (Cav3). These cells show oscillating Ca²⁺ waves that are not seen in neonatal cells that do not contain Cav3. Microinjection of a peptide that disrupts Cav3-Gα_q association, but not a control peptide, extinguishes the waves. Furthermore, these waves are unchanged with rynaodine treatment, but not seen with treatment of a phospholipase C inhibitor, implying that Cav3-Gα_q is responsible for this Ca²⁺ activity. Taken together, these studies show that caveolae play a direct and active role in regulating basal Ca²⁺ activity in cardiomyocytes.     

两个对浓核病毒(镇江株)具感性差异的家蚕品种的血液和围食膜蛋白的比较

家蚕品种间对浓核病毒(镇江株)具有不同的感染性,为了进一步探明家蚕对浓核病毒(镇江株)感性差异的分子机制,本文运用蛋白质电泳和质谱技术比较分析了两个对家蚕浓核病毒(镇江株)感性和抗性的近等基因系家蚕品种JS和NIL的血液和围食膜组织蛋白.结果表明:这两个家蚕品种的血液和围食膜组织蛋白组成差异很小.在血液组织蛋白中发现5个差异蛋白点,其中家蚕品种JS血液中有两个差异蛋白,可能分别为酪蛋白激酶和新型组织蛋白;在NIL血液组织中发现3个差异蛋白点,其中两个可能分别为线粒体延伸因子和类丝氨酸蛋白酶,另外1个的含量极显著高于JS,为血淋巴蛋白.在围食膜蛋白中共发现4个差异蛋白点,其中JS围食膜中有1个差异蛋白可能为新型组织蛋白;其余3个蛋白点在含量上相互间存在显著差异.本研究根据组织差异蛋白的功能初步推测家蚕对浓核病毒(镇江株)感性差异与血液蛋白差异无显著相关,与围食膜蛋白差异可能有关.     

The effects of myostatin on adipogenic differentiation of human bone marrow-derived mesenchymal stem cells are mediated through cross-communication between Smad3 and Wnt/beta-catenin signaling pathways

The effects of myostatin on adipogenic differentiation are poorly understood, and the underlying mechanisms are unknown. We determined the effects of human recombinant myostatin protein on adipogenesis of bone marrow-derived human mesenchymal stem cells (hMSCs) and adipose tissue-derived preadipocytes. For both progenitor cell types, differentiation in the presence of myostatin caused a dose-dependent reduction of lipid accumulation and diminished incorporation of exogenous fatty acid into cellular lipids. Myostatin significantly down-regulated the expression of adipocyte markers PPARgamma, C/EBPalpha, leptin, and aP2, but not C/EBPbeta. Overexpression of PPARgamma, but not C/EBPbeta, blocked the inhibitory effects of myostatin on adipogenesis. Myostatin induced phosphorylation of Smad3 in hMSCs; knockdown of Smad3 by RNAi or inhibition of its upstream kinase by an Alk5 inhibitor blocked the inhibitory effect of myostatin on adipogenesis in hMSCs, implying an important role of Smad3 activation in this event. Furthermore, myostatin enhanced nuclear translocation of beta-catenin and formation of the Smad3-beta-catenin-TCF4 complex, together with the altered expression of a number of Wnt/beta-catenin pathway genes in hMSCs. The inhibitory effects of myostatin on adipogenesis were blocked by RNAi silencing of beta-catenin and diminished by overexpression of dominant-negative TCF4. The conclusion is that myostatin inhibited adipogenesis in human bone marrow-derived mesenchymal stem cells and preadipocytes. These effects were mediated, in part, by activation of Smad3 and cross-communication of the TGFbeta/Smad signal to Wnt/beta-catenin/TCF4 pathway, leading to down-regulation of PPARgamma.     

Chronic hypoxia stress-induced differential modulation of heat-shock protein 70 and presynaptic proteins

Chronic hypoxia exposure can cause neurobehavioral dysfunction, but the underlying cellular and molecular mechanisms remain unclear. Here, we found that adult Lymnaea stagnalis snails maintained in low O(2) (approximately 5%) for 4 days developed slowed reactions to light stimuli, and reduced righting movement. Semiquantitative immunoblotting analyses showed that hypoxia exposure induced increased expression of heat-shock protein (HSP)70 in ganglion preparations, and suppressed expression of the presynaptic proteins syntaxin I, synaptic vesicle protein 2 (SV2) and synaptotagmin I. Detailed time course analyses showed that an early moderate increase developed within 6 h, preceding a substantial up-regulation of HSP70 after 4 days; an early reduction of syntaxin I in the first 24 h; a delayed reduction of synaptotagmin I after 4 days; and a biphasic change in SV2. Using a double-stranded RNA interference approach, we demonstrated that preventing the hypoxia inducible HSP70 enhanced down-regulation of syntaxin and synaptotagmin, and aggravated motor and sensory suppression. Co-immunoprecipitation analysis revealed an interaction between HSP70 and syntaxin. We have thus provided the first evidence that early induction of HSP70 by chronic hypoxia is critical for maintaining expression levels of presynaptic proteins. These findings implicate a new molecular mechanism underlying chronic hypoxia-induced neurobehavioral adaptation and impairment.     

低氧预适应对小鼠海马组织HIF-1与EPO低氧应答元件结合活性的影响

目的：观察低氧预适应对小鼠海马组织HIF-1与EPO的低氧应答元件（HRE）结合活性的变化,探讨这种变化与低氧预适应形成的关系。方法：小鼠低氧0次（H0）,1次（H1）,4次（H4）后取海马组织,应用凝胶迁移改变试验（EMSA）,染色体免疫共沉淀（ChIP）试验和荧光定量PCR（real—time PCR）技术,检测小鼠海马组织内HIF-1与EPO的低氧应答元件结合能力的变化。结果：EMSA体外结合实验及ChIP体内结合实验发现。H0、H1和H4组结合活力依次增强。结论：HIF-1与EPO的低氧应答元件结合增强可能参与预适应的形成。     

真光层深度的遥感反演及其在富营养化评价中的应用

真光层深度直接影响水体中浮游植物的分布和初级生产力以及水体生态环境,是水生态研究的一个重要参数.利用2006年10月24日～11月2日太湖水下实测光谱数据和光合有效辐射(PAR)数据,通过数据的处理和分析,尝试建立真光层深度与水面以下遥感反射率的关系模型,并利用真光层深度与透明度的关系,建立水体富营养化真光层深度评价模型.研究结果表明:真光层深度与归一化遥感反射率具有很好的相关性;选用特定波段的归一化反射率作为变量,建立两者的关系模型能较好的反演真光层深度,所建立的模型算法中,指数模型拟合方程的综合效果好于其他模型,波段比值算法反演精度要好于单波段算法;利用利用真光层深度进行富营养化评价具有一定的应用价值,利用该模型对太湖水体进行富营养化评价,得出太湖西部湖区大部分已富营养化,东部湖区处于中营养化和轻度富营养化状态.