Identification of Plasma Lipid Biomarkers for Prostate Cancer by Lipidomics and Bioinformatics

Background

Lipids have critical functions in cellular energy storage, structure and signaling. Many individual lipid molecules have been associated with the evolution of prostate cancer; however, none of them has been approved to be used as a biomarker. The aim of this study is to identify lipid molecules from hundreds plasma apparent lipid species as biomarkers for diagnosis of prostate cancer.

Methodology/Principal Findings

Using lipidomics, lipid profiling of 390 individual apparent lipid species was performed on 141 plasma samples from 105 patients with prostate cancer and 36 male controls. High throughput data generated from lipidomics were analyzed using bioinformatic and statistical methods. From 390 apparent lipid species, 35 species were demonstrated to have potential in differentiation of prostate cancer. Within the 35 species, 12 were identified as individual plasma lipid biomarkers for diagnosis of prostate cancer with a sensitivity above 80%, specificity above 50% and accuracy above 80%. Using top 15 of 35 potential biomarkers together increased predictive power dramatically in diagnosis of prostate cancer with a sensitivity of 93.6%, specificity of 90.1% and accuracy of 97.3%. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) demonstrated that patient and control populations were visually separated by identified lipid biomarkers. RandomForest and 10-fold cross validation analyses demonstrated that the identified lipid biomarkers were able to predict unknown populations accurately, and this was not influenced by patient''s age and race. Three out of 13 lipid classes, phosphatidylethanolamine (PE), ether-linked phosphatidylethanolamine (ePE) and ether-linked phosphatidylcholine (ePC) could be considered as biomarkers in diagnosis of prostate cancer.

Conclusions/Significance

Using lipidomics and bioinformatic and statistical methods, we have identified a few out of hundreds plasma apparent lipid molecular species as biomarkers for diagnosis of prostate cancer with a high sensitivity, specificity and accuracy.     

Tubular anomalous bones found in both thighs of a long-tailed macaque (Macaca fascicularis)

Tubular anomalous bones were found in both thighs of a 6-year-old male long-tailed macaque (Macaca fascicularis) bred in captivity. The bones had jagged ends and protruded from the skin. Radiographs showed that they developed in the femurs at the middle and elongated. They were removed with surgery under anesthesia. Histological analysis revealed that these bones had the same histological structure as the femur, though they were composed of primary and secondary osteon regions. This finding indicated that the new bones developed from the old bone piece(s), acquired a tubular shape, and elongated. It is suggested that the anomalous bones were produced not by the congenital deformity but by regeneration from fragments of the fractured femur that were embedded in the bone marrow; these acquired a tubular pattern and elongated.     

Overlapping functions of different dynamin isoforms in clathrin-dependent and -independent endocytosis in pancreatic beta cells

Previously, we identified a clathrin-dependent slow endocytosis and a clathrin-independent fast endocytosis in pancreatic β cells, both triggered by elevated cytoplasmic Ca²⁺ concentration. In the current study, we attempted to explore the roles of different dynamin isoforms in these endocytotic processes. We first confirmed the existence of both neuron-specific dynamin 1 and ubiquitous dynamin 2 in INS-1 cells using both quantitative RT-PCR and Western blot experiments. By specifically knocking down the endogenous level of either dynamin isoform from INS-1 cells, we showed that dynamin 1 and dynamin 2 simultaneously participate in the clathrin-independent and -dependent membrane retrieval in pancreatic β cells. Transferrin internalization was also inhibited in cells with knock down of both dynamin 1 and dynamin 2. Based on these results, we argue that different dynamin isoforms play overlapping roles in different types of endocytosis.     

Yeast expression and NMR analysis of the extracellular domain of muscle nicotinic acetylcholine receptor alpha subunit.

The alpha subunit of the nicotinic acetylcholine receptor (AChR) from Torpedo electric organ and mammalian muscle contains high affinity binding sites for alpha-bungarotoxin and for autoimmune antibodies in sera of patients with myasthenia gravis. To obtain sufficient materials for structural studies of the receptor-ligand complexes, we have expressed part of the mouse muscle alpha subunit as a soluble, secretory protein using the yeast Pichia pastoris. By testing a series of truncated fragments of the receptor protein, we show that alpha211, the entire amino-terminal extracellular domain of AChR alpha subunit (amino acids 1-211), is the minimal segment that could fold properly in yeast. The alpha211 protein was secreted into the culture medium at a concentration of >3 mg/liter. It migrated as a 31-kDa polypeptide with N-linked glycosylation on SDS-polyacrylamide gel. The protein was purified to homogeneity by isoelectric focusing electrophoresis (pI 5.8), and it appeared as a 4.5 S monomer on sucrose gradient at concentrations up to 1 mm ( approximately 30 mg/ml). The receptor domain bound monoclonal antibody mAb35, a conformation-specific antibody against the main immunogenic region of the AChR. In addition, it formed a high affinity complex with alpha-bungarotoxin (k(D) 0.2 nm) but showed relatively low affinity to the small cholinergic ligand acetylcholine. Circular dichroism spectroscopy of alpha211 revealed a composition of secondary structure corresponding to a folded protein. Furthermore, the receptor fragment was efficiently (15)N-labeled in P. pastoris, and proton cross-peaks were well dispersed in nuclear Overhauser effect and heteronuclear single quantum coherence spectra as measured by NMR spectroscopy. We conclude that the soluble AChR protein is useful for high resolution structural studies.     

Proteomic Analysis of Shoot Tips from Two Alfalfa Cultivars with Different Florescence

Plant Molecular Biology Reporter - Flowering is an indispensable biological process for the complete life cycle of angiosperms, crucial to the regeneration of plants and the continuation of...     

Palmitoylated proteins: purification and identification

This proteomic protocol purifies and identifies palmitoylated proteins (i.e., S-acylated proteins) from complex protein extracts. The method relies on an acyl-biotinyl exchange chemistry in which biotin moieties are substituted for the thioester-linked protein acyl-modifications through a sequence of three in vitro chemical steps: (i) blockade of free thiols with N-ethylmaleimide; (ii) cleavage of the Cys-palmitoyl thioester linkages with hydroxylamine; and (iii) labeling of thiols, newly exposed by the hydroxylamine, with biotin-HPDP (Biotin-HPDP-N-[6-(Biotinamido)hexyl]-3'-(2'-pyridyldithio)propionamide. The biotinylated proteins are then affinity-purified using streptavidin-agarose and identified by multi-dimensional protein identification technology (MuDPIT), a high-throughput, tandem mass spectrometry (MS/MS)-based proteomic technology. MuDPIT also affords a semi-quantitative analysis that may be used to assess the gross changes induced to the global palmitoylation profile by mutation or drugs. Typically, 2-3 weeks are required for this analysis.     

人类成肌发育候选基因ASB12 RNAi稳定细胞系的构建与鉴定

目的:利用siRNA表达载体构建抑制人类成肌发育候选基因ASB12表达的pSUPER RNAi载体(pSU-PER-ASB12),筛选构建C2C12-pSUPER-ASB12稳定表达细胞系。方法:化学合成一对编码短发夹RNA序列的、靶向成肌发育候选基因ASB12的寡核苷酸链60个碱基,退火,克隆到经BglⅡ、XhoⅠ双酶切的pSUPER质粒上,构建重组RNAi质粒(pSUPER-ASB12)。通过酶切鉴定及测序分析检测构建效果。将正确构建的质粒转染小鼠骨骼肌细胞C2C12,通过G418筛选,免疫荧光检测,RT-PCR分析,建立稳定表达pSUPER-ASB12的细胞系C2C12-pSUPER-ASB12。结果:pSUPER-ASB12载体经酶切鉴定及测序分析,结果表明60个碱基成功插入到预计位点,并且序列完全一致。C2C12-pSUPER-ASB12稳定表达细胞系可表达绿色荧光蛋白,RT-PCR检测结果显示C2C12-pSUPER-ASB12细胞中ASB12表达量明显降低。结论:靶向ASB12的pSUPER RNAi载体和C2C12-pSUPER-ASB12稳定表达细胞系构建成功,为进一步从分子水平探讨ASB12在成肌发育中的功能奠定了基础。