Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray analysis reveals differential effects of conjugated linoleic acid isomers in ritonavir-treated 3T3-L1 adipocytes

ABSTRACT: Objective: To quantify changes in adipogenic gene expression in the presence of ritonavir (RTV) or tenofovir (TDF), and determine whether conjugated linoleic acid (CLA) isomers (cis9,trans11 or trans10,cis12) can mitigate detrimental effects of antiretoviral drugs. Methods: Affymetrix Mouse Genome 430 2.0 microarray was used to investigate gene expression in 3T3-L1 adipocytes treated with (1) RTV, TDF or ethanol control, or (2) ritonavir +c9,t11-CLA, ritonavir+t10,c12-CLA or ritonavir+DMSO control. RT-PCR validation of Pparg, Adipoq and Retn was carried out. ELISA and DNA binding ELISA were used to investigate secreted proteins and Pparg binding to its gene response element. Oil Red O staining was used to investigate triglyceride accumulation. Results: No effect was observed for TDF. Expression of 389 genes was altered more than 5-fold in the presence of RTV. Down-regulated genes included Pparg, Adipoq, Retn, Cfd and Cidec. Pparg and Adipoq down-regulation were confirmed by RT-PCR. PPAR-Î³ binding to its gene response element, adiponectin protein secretion and triglyceride accumulation were decreased by RTV. t10,c12-CLA in the presence of RTV decreased the expression of Ppargand Adipoq in microarray and RT-PCR. c9,t11-CLA increased PPAR-Î³ binding to its gene response element. Both isomers increased triglyceride storage in the presence of RTV. Conclusion: Ritonavir altered genes involved in adipocyte differentiation, lipid accumulation and glucose metabolism. Down-regulation of Pparg may be mediated by changes in Cepba and regulatory genes Pparg1c and Nr1h3. 3T3-L1 adipocytes were treated with ritonavir (20Î¼M; n=4), tenofovir (1Î¼M; n=4) or vehicle control (ethanol 0.1%; n=4) for 5 days and in a second experiment with ritonavir (20 ÂµM) +c9,t11-CLA (100Î¼M; n=4), ritonavir (20 ÂµM) +t10,c12-CLA (100Î¼M; n=4) or ritonavir+fatty acid vehicle control (DMSO 0.1%; n=4) for 5 days.

ORGANISM(S): Mus musculus

SUBMITTER: Matthew Arno

PROVIDER: E-GEOD-70854 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:A summary of the work associated to these microarrays is the following: Diet plays a role in the development of the immune system, and polyunsaturated fatty acids can modulate the expression of a variety of genes. Human milk contains conjugated linoleic acid (CLA), a fatty acid that seems to contribute to immune development. Indeed, recent studies carried out in our group in suckling animals have shown that the immune function is enhanced after feeding 80:20 isomer mix of c9,t11 and t10,c12 CLA, respectively. However, little work has been done on the effects of CLA on gene expression, and even less regarding immune system development in early life. With all these concepts in mind, we determined the expression profile of Mesentheric Lymph Nodes (MLN) from animals supplemented with CLA during gestation and suckling through dam’s milk (Group A) or by oral gavage (Group B), supplemented just during suckling (Group C) and control animals (Group D) with the aid of the specific GeneChip ® Rat Genome 230 2.0 (Affymettrix). Bioinformatic analyses were performed using the GeneSpring GX software package v10.0.2 and lead to the identification of 123 genes differentially expressed in all three dietary approaches. Generation of a Biological Association Network (BAN) evidenced several genes, such as connective tissue growth factor (Ctgf), tissue inhibitor of metalloproteinase 1 (Timp1), galanin (Gal), synaptotagmin 1 (Syt1), growth factor receptor bound protein 2 (Grb2) actin gamma 2 (Actg2) and smooth muscle alpha actin (Acta2), as highly interconnected nodes of the resulting network. Gene underexpression was confirmed by Real-Time RT-PCR. We conclude that Ctgf, Timp1, Gal and Syt1, among others, are genes modulated by CLA supplementation that may have a role on lymphoproliferation and mucosal immune responses in early life. The aim of our study was to evaluate, by using whole genome microarrays, the effects of dietary supplementation with an 80:20 isomer mix of c9,t11 and t10,c12 CLA, respectively, on Mesentheric Lymph Nodes gene expression, during gestation and/or suckling. Three experimental approaches were conducted to assess the effects of CLA supplementation on I) pups from dams fed with 1% CLA diet during the two weeks of gestation and throughout the suckling period (Group A). These pups received CLA through the dam’s milk during suckling (Total Period of CLA Supplementation (TPS) 5 wk); II) pups from dams fed with 1% CLA diet during gestation and standard diet during suckling. These pups were CLA-supplemented daily during suckling by oral gavage (TPS 5 wk) (Group B); III) pups from dams fed standard diet during gestation and suckling and receiving CLA by daily oral gavage throughout the suckling period (TPS 3 wk) (Group C). Group D, pups from dams fed standard diet throughout the study, constituted the reference diet group (TPS 0 wk). Triplicate samples were hybridized for each experimental condition (12 samples in total). The samples provided were analyzed using the specific software GeneSpring GX.

Project description:Cis-9, trans-11-conjugated linoleic acid (c9, t11-CLA), a functional fatty acid, is one of the research hotspots in the fields of functional dairy products development because of its multiple beneficial effects in humans and animals. In milk, most c9, t11-CLA is de novo synthesized from trans-11-octadecenoic acid (TVA) and it is confirmed that genes such as stearoyl-coA desaturase 1 (SCD1) play a key role in the synthesis. However, few studies have been reported to deeply elucidate the SCD1-dependent molecular mechanism of cis9, trans11-CLA synthesis and its relationship with the pathways of energy metabolism and lipid metabolism. Therefore, in the present study, MAC-T cells were divided into three groups: CAY group (SCD1-inhibited MAC-T cell model with the addition of CAY, TVA), TVA group (only TVA), and Control group (without CAY, TVA). The relative mRNA expression of SCD1 was measured using real-time PCR, while TVA accumulation and c9, t11 -CLA synthesis were analyzed using gas chromatography (GC). The SCD1-related proteins were firstly screened in MAC-T cells by Tandem Mass Tag (TMT)-based quantitative proteomics analysis, then their functions were annotated by bioinformatic analysis, and finally their relationships with SCD1 were evaluated by parallel reaction monitoring (PRM) analysis and small RNA interference. The results showed that the deficiency of SCD1 led by CAY10566 blocked the synthesis of c9, t11-CLA in MAC-T cells. Sixty-one SCD1-associated proteins were screened and found to be mainly involved in the pathways of energy metabolism and lipid metabolism, such as glycolytic pathway, pentose phosphate pathway, fatty acid elongation pathway, and unsaturated fatty acid biosynthesis. Among these genes, 17 proteins were validated under the PRM analysis. PGAM1 (phosphoglycerate mutase 1), TPI1 (triosephosphate isomerase 1), LDHB (lactate dehydrogenase B), and ALDOA (aldolase, fructose-bisphosphate A) were verified to have a negative relationships with SCD1. This study furthered our understanding of the molecular mechanisms of c9, t11-CLA synthesis in the mammary glands of dairy cows.

Project description:Primary afferent collateral sprouting (PACS) is a process whereby non-injured primary afferent neurons respond to some stimulus by extending new branches from existing axons. In the model used here (spared dermatome), the intact sensory neurons respond to the denervation of adjacent areas of skin by sprouting new axon branches into that adjacent denervated territory. Neurons of both the central and peripheral nervous systems undergo this process, which contributes to both adaptive and maladaptive plasticity. Investigations of gene expression changes associated with PACS can provide a better understanding of the molecular mechanisms controlling this process. Consequently, it can be used to develop treatment for spinal cord injury to promote functional recovery. In this study, we sought to identify gene expression changes in PACS using 20 Affymetrix Rat Genome 230 2.0 microarrays. The experiments were designed to discover global gene expression changes in non-injured DRG neurons undergoing PACS. T11 DRG neurons remained intact and undergo PACS after the cutaneous nerves of the adjacent segments (T9, T10, T12, and T13) were injured and regeneration of those injured nerves prevented by ligation. Thus, the T9, T10, T12, and T13 dermatomes were denervated, but the T11 dermatome remained intact. Axons of the T11dermatome (and thus housed in the T11 dorsal root ganglion (DRG)), extended new branches to innervate the T9, T10, T12, and T13 dermatomes. N.B.: This is NOT a spared root experiment. ALL spinal roots were non-injured. Peripheral nerves were used. A total of 20 Affymetrix Rat Genome 230 2.0 microarrays were analyzed: six naÃ¯ve controls, seven replicates at day 7 post-surgery (presumed to represent an â??initiation phaseâ??), and seven replicates at day 14 post-surgery (presumed to represent a â??maintenance phaseâ??). DRGs were NOT pooled onto microarrays. Each animal had its own microarray with T11 DRG sample which underwent 2-round amplification. After quality control analysis, one of the naÃ¯ve control microarrays was removed from further analysis.

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Microarray analysis reveals differential effects of conjugated linoleic acid isomers in ritonavir-treated 3T3-L1 adipocytes

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