A Cancer Gene-Drug Connectivity Map for DrBioRight

https://openworks.mdanderson.org/sumexp22/1064/thumbnail.jp

Group SCAD Regression Analysis for Microarray Time Course Gene Expression Data

Since many important biological systems or processes are dynamic systems, it is important to study the gene expression patterns over time in a genomic scale in order to capture the dynamic behavior of gene expression. Microarray technologies have made it possible to measure the gene expression levels of essentially all the genes during a given biological process. In order to determine the transcriptional factors involved in gene regulation during a given biological process, we propose to develop a functional response model with varying coefficients in order to model the transcriptional effects on gene expression levels and to develop a group smoothly clipped absolute deviation (SCAD) regression procedure for selecting the transcriptional factors with varying coefficients that are involved in gene regulation during a biological process. Simulation studies indicated that such a procedure is quite effective in selecting the relevant variables with time-varying coefficients and in estimating the coefficients. Application to the yeast cell cycle microarray time course gene expression data set identified 19 of the 21 known transcriptional factors related to the cell cycle process. In addition, we have identified another 52 TFs that also have periodic transcriptional effects on gene expression during the cell cycle process. Compared to simple linear regression analysis at each time point, our procedure identified more known cell cycle related transcriptional factors. The proposed group SCAD regression procedure is very effective for identifying variables with time-varying coefficients, in particular, for identifying the transcriptional factors that are related to gene expression over time. By identifying the transcriptional factors that are related to gene expression variations over time, the procedure can potentially provide more insight into the gene regulatory networks

Effect of vitamin B 12 and n-3 polyunsaturated fatty acids on plasma homocysteine, ferritin, C-reaction protein, and other cardiovascular risk factors: a randomized controlled trial

Objectives: Vitamin B 12 and n-3 polyunsaturated fatty acids (PUFA) decrease blood homocysteine (Hcy) concentrations. However, the combined effect of these nutrients on Hcy and ferritin, and C-reactive protein is limited and inconclusive. The objective was to examine the synergistic effect of vitamin B 12 in combination of n-3 PUFA on plasma Hcy, ferritin, and other biochemical markers. Methods: In a randomized controlled trial, thirty eligible subjects were randomly divided into three groups, and assigned to receive 1000 μg of vitamin B 12 , 2 g fish oil, or 1000 μg vitamin B 12 and 2 g fish oil, respectively, for 8 weeks. Plasma phospholipids (PL) fatty acids and biochemical markers were determined. This study was registered under ClinicalTrials.gov Identifier: NCT01762072. Results: Plasma PL 20:5n-3, 22:6n-3 and n-3 PUFA was increased after 4 and 8 week supplementation of fish oil, and vitamin B 12 +fish oil. Plasma concentrations of triacylglycerol, uric acid, C-reactive protein, and ferritin were significantly decreased after 4 and 8 week supplementation of fish oil, and vitamin B 12 +fish oil. In all groups, significant changes in plasma Hcy were observed during the study period. Vitamin B 12 , fish oil, and vitamin B 12 +fish oil supplementation lowered plasma Hcy concentrations by 22%, 19%, and 39%, respectively. Conclusions: The combination of vitamin B 12 and fish oil has a synergistic effect on lowering plasma concentrations of Hcy

Differential Expressed Genes Identified Between African American and European American Keloid Fibroblasts

Keloids are benign fibroproliferative tumors due to dysregulation of collagen remodeling and abnormal wound healing. Although worldwide, there is a higher incidence of keloid disease (KD) in skin of color, little is known about this predisposition. In this study, we used one tissue micro array slide comprised of six AA and 6 EA punch biopsies of primary untreated keloid tissue from the head and neck area was created, following the NanoString® DSP Technology Access Program protocol. The GeoMx Human Whole Transcriptome Atlas Assay was performed, using morphology marker FAP. Polygonal region of interests selection strategy for Fibroblast Activation Protein (FAP) positive cells was conducted. Univariate analysis was performed, using linear regression models to identify differentially expressed genes (DEG) at a false discovery rate (FDR) of 0.05. Ingenuity pathway analysis (IPA) software was used to determine DEG pathway enrichment. 1,450 DEG were identified (p-va

A Randomized Trial of Hypnosedation Versus General Anesthesia for Women with Breast Cancer Undergoing Surgery

Reshonda Smith and Karen Cleckler-Hughes pictured.https://openworks.mdanderson.org/aprn-week-23/1003/thumbnail.jp

Targeting immunosuppressive classical monocytes prevents immunotherapy resistance

View full abstracthttps://openworks.mdanderson.org/leading-edge/1053/thumbnail.jp

Effects of egg and vitamin A supplementation on hemoglobin, retinol status and physical growth levels of primary and middle school students in

Lack of protein and vitamin A influences the growth of student in impoverished mountain areas. The aim of the study was to assess the effects of egg and vitamin A supplementation on hemoglobin, serum retinol and anthropometric indices of 10-18 years old students of a low socioeconomic status. A total number of 288 students from four boarding schools were randomly selected by using cluster sampling method in Chongqing, and they were assigned into supplement group and control group non-randomly. Students in supplement group received a single 200,000 international units vitamin A and 1 egg/day (including weekends) for 6 months. The control group did not receive any supplementation. We measured hemoglobin, serum retinol and height and weight at baseline and after supplementation. The supplementation increased the mean hemoglobin concentration by 7.13 g/L compared with 1.38 g/L in control group (p<0.001), the mean serum retinol concentration by 0.31 μmol/L compared with 0.09 μmol/L in the control group (p=0.005), the mean height-for-age z score by 0.05 compared with 0.03 in the control group (p=0.319), the mean weight-for-age z score by 0.05 compared with -0.12 in the control group (p<0.001). Our results revealed that egg and vitamin A supplementation is an effective, convenient, and practical method to improve the levels of hemoglobin, serum retinol and prevent the deterioration of growth in terms of weight for primary and middle school students from outlying poverty-stricken areas. Our intervention did not have a beneficial effect on linear growth

Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration

View full abstracthttps://openworks.mdanderson.org/leading-edge/1055/thumbnail.jp

Phosphate concentration and arbuscular mycorrhizal colonisation influence the growth, yield and expression of twelve PHT1 family phosphate transporters in foxtail millet (Setaria italica)

Phosphorus (P) is an essential element which plays several key roles in all living organisms. Setaria italica (foxtail millet) is a model species for panacoid grasses including several millet species widely grown in arid regions of Asia and Africa, and for the bioenergy crop switchgrass. The growth responses of S. italica to different levels of inorganic phosphate (Pi) and to colonisation with the arbuscular mycorrhizal fungus Funneliformis mosseae (syn. Glomus mosseae) were studied. Phosphate is taken up from the environment by the PHT1 family of plant phosphate transporters, which have been well characterized in several plant species. Bioinformatic analysis identified 12 members of the PHT1 gene family (SiPHT1;1-1;12) in S. italica, and RT and qPCR analysis showed that most of these transporters displayed specific expression patterns with respect to tissue, phosphate status and arbuscular mycorrhizal colonisation. SiPHT1;2 was found to be expressed in all tissues and in all growth conditions tested. In contrast, expression of SiPHT1;4 was induced in roots after 15 days growth in hydroponic medium of low Pi concentration. Expression of SiPHT1;8 and SiPHT1;9 in roots was selectively induced by colonisation with F. mosseae. SiPHT1;3 and SiPHT1;4 were found to be predominantly expressed in leaf and root tissues respectively. Several other transporters were expressed in shoots and leaves during growth in low Pi concentrations. This study will form the basis for the further characterization of these transporters, with the long term goal of improving the phosphate use efficiency of foxtail millet