Classification and selection of biomarkers in genomic data using LASSO

High-throughput gene expression technologies such as microarrays have been utilized in a variety of scientific applications. Most of the work has been done on assessing univariate associations between gene expression profiles with clinical outcome (variable selection) or on developing classification procedures with gene expression data (supervised learning). We consider a hybrid variable selection/classification approach that is based on linear combinations of the gene expression profiles that maximize an accuracy measure summarized using the receiver operating characteristic curve. Under a specific probability model, this leads to the consideration of linear discriminant functions. We incorporate an automated variable selection approach using LASSO. An equivalence between LASSO estimation with support vector machines allows for model fitting using standard software. We apply the proposed method to simulated data as well as data from a recently published prostate cancer study.     

Biotinylated GHK peptide incorporated collagenous matrix: A novel biomaterial for dermal wound healing in rats

Matrikines are small peptide fragments of extracellular matrix proteins that display potent tissue repair activities. Difficulties in achieving sustained delivery of bioactive concentration of matrikines in the affected area limits their therapeutic use. The present study evaluates the effects biotinylated matrikine peptide (bio-glycyl-histidyl-lysine) incorporated collagen membrane for dermal wound healing processes in rats. Biotinylated peptide incorporated collagen matrix (PIC) showed better healing when compared to wounds treated with collagen matrix [CF (collagen film)] and without collagen [CR (control)]. Binding studies indicate that biotinylated GHK (Bio-GHK) binds effectively to the collagen matrix and red blood cell (RBC) membrane when compared with t-butyloxycarbonyl substituted GHK (Boc-GHK). Wound contraction, increased cell proliferation, and high expression of antioxidant enzymes in PIC treated group indicate enhanced wound healing activity when compared to CF and CR groups. Interestingly Bio-GHK incorporated collagen increases the copper concentration by ninefold at the wound site indicating the wound healing property of Bio-GHK can also be linked with both copper localization and matrikine activities. These results demonstrate the possibility of using Bio-GHK incorporated collagen film as a therapeutic agent in the wound healing process.     

Comparative mapping of X chromosomes in vole species of the genus Microtus

Comparative mapping of X-linked genes has progressed rapidly since Ohno's prediction that genes on the X chromosome should be conserved as a syntenic group in all mammals. Although several conserved blocks of homology between human and mouse have been discovered, rearrangements within the X chromosome have also been characterized. More recently, some exceptions to Ohno's law have been reported. We have used fluorescence in situ hybridization (FISH) to map five genes, Gla, G6pd, Hprt, Pgk1 and Xist, to two of the largest conserved segments of X material in five members of the genus Microtus (grey vole) and show that vole X chromosomes demonstrate greater homology to human than to mouse. Cytogenetic analysis indicates a relatively high frequency of rearrangement during vole evolution, although certain blocks of homology appear to be highly conserved in all species studied to date. On this basis we were able to predict the probable location of the rat X inactivation centre (Xic) based solely on high-resolution G-banding. Our prediction was then confirmed by mapping the rat Xist gene by FISH. The possible significance of conserving long-range chromosome structure in the vicinity of the Xic is discussed with respect to the mechanism of X inactivation.     

Modified milk fat reduces plasma triacylglycerol concentrations in normolipidemic men compared with regular milk fat and nonhydrogenated margarine

BACKGROUND: A modified milk fat with reduced cholesterol was developed by fractionation technology. OBJECTIVE: The effect of this modified milk fat on the lipoprotein profile of 21 normolipidemic men was compared with that of regular milk fat and nonhydrogenated margarine. DESIGN: A crossover design was used for the administration of the 3 experimental diets, which provided 13240 kJ as 16% protein, 51% carbohydrates, 33-34% lipids, and 21 g fiber/d. The ratio of polyunsaturated to saturated fat was 1.3:1 for the margarine diet and 0.3:1 for the milk-fat diets. The cholesterol content of the modified milk-fat and margarine diets was similar (248 and 254 mg/d, respectively), but was significantly higher (428 mg/d) for the regular milk-fat diet. RESULTS: Modified and regular milk fats did not change plasma total and LDL cholesterol significantly, but margarine did (P < 0.01). Furthermore, modified milk fat maintained initial HDL(2)-cholesterol concentrations, but margarine reduced this variable significantly (P < 0.05). These results can be explained by the lower ratio of polyunsaturated to saturated fat in the modified and regular milk-fat diets than in the margarine diet. Men who ingested modified milk fat had significantly (P < 0.05) lower total and VLDL-triacylglycerol and VLDL-cholesterol concentrations than did those who ingested either regular milk fat or margarine. This may have been, in part, because of the lower intestinal fat absorption with modified milk fat than with regular milk fat and margarine arising from changes in the melting properties of milk fat with fractionation. CONCLUSION: A reduction in plasma triacylglycerol concentrations after the consumption of modified milk fat may prevent the onset of hypertriacylglycerolemia.     

Alpha-methylacyl-CoA racemase protein expression is associated with the degree of differentiation in breast cancer using quantitative image analysis.

Alpha-methylacyl-CoA racemase (AMACR) is an enzyme involved in the metabolism of fatty acids and is an important tissue biomarker in the prostate to distinguish normal glands from prostate cancer. Here, for the first time, we evaluated the expression of AMACR protein in normal breast, ductal carcinoma in situ, and invasive carcinomas. By immunofluorescence and immunohistochemistry, AMACR was seen in cytoplasmic granules consistent with a mitochondrial and peroxisomal localization. AMACR expression was determined by immunohistochemistry on 160 invasive carcinomas with long follow-up, using a high-density tissue microarray, and evaluated by two methods: standard pathology review and quantitative image analysis. AMACR was overexpressed in 42 of 160 (26%) invasive carcinomas, and it was associated with a decrease in tumor differentiation, a feature of aggressive breast cancer. Quantitative analysis allowed for better discrimination and more accurate evaluation of low-intensity staining. In conclusion, AMACR protein is expressed in normal breast and its expression seems to increase in invasive carcinomas. We observed stronger AMACR protein expression in high-grade carcinomas when compared with low-grade ones. Quantitative image analysis is a novel way to accurately and reproducibly evaluate immunohistochemistry in breast tissue samples using high-density tissue microarrays.     

Conjugating doxorubicin to polymannose: a new strategy for target specific delivery to lung cancer cells

Abstract

As mannose receptors are known to be over-expressed in cancer cells, we synthesized polymannose-doxorubicin (PM-DOX) conjugates with the objective of targeting the drug to cancer cells. DOX was conjugated to oxidized PM through Schiff’s linkages to obtain PM-DOX conjugates. In order to examine the superior targeting efficacy of PM-DOX conjugate, sodium alginate (SA) was conjugated to DOX by similar chemistry and compared with PM-DOX conjugate. The cytotoxicity of the conjugates was investigated in A549 cell lines using MTT Assay and the cell uptake and retention studies, were performed using flow cytometry and cell imaging. In vitro drug release studies with both PM-DOX and SA-DOX conjugates showed an initial burst release of DOX up to 37–39% at 1?h, followed by a steady release up to 58–62% at 24?h in human plasma while negligible release was observed in phosphate buffered saline. The conjugates exhibited negligible hemolytic potential to human erythrocytes compared to free DOX. The PM-DOX conjugate showed better cytotoxic potential against A549 cells at lower concentration (equivalent to 0.27?μg/mL of DOX) at 72?h compared to free DOX and SA-DOX conjugate. Further, PM-DOX conjugate showed enhanced uptake by the cells in comparison with SA-DOX conjugate thereby confirming the target specificity of PM to the cancer cells.