Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Mamld1 knockdown with siRNA in mouse Leydig tumor cells

ABSTRACT: MAMLD1 (mastermind-like domain containing 1, alias CXorf6) on human chromosome Xq28 is a causative gene for hypospadias, a mild form of 46,XY disorders of sex development. To date, multiple mutations have been identified in patients with various types of hypospadias. In this regard, the mouse homologous gene Mamld1 is transiently expressed in fetal Sertoli and Leydig cells around the critical period for sex development, and transient Mamld1 knockdown using small interfering RNAs (siRNAs) reduces testosterone production in cultured mouse Leydig tumor cells (MLTCs). We performed detailed analyses in Mamld1 knockdown experiments using MLTCs. We used microarrays to display the global gene expression profile change, after knockdown of Mamld1 expression in MLTCs, to find the gene set regulated by Mamld1. To compare changes in gene expression profile in MLTCs, MLTCs were transfected with control siRNA or Mamld1 siRNA, 48h later, total RNA was subjected to Q-PCR to confirm a significantly decreased Mamld1 mRNA, and then these total RNA samples were for microarray analysis. The microarray data was analyzed to explore gene sets/pathways, which were significantly impacted by knockdown of Mamld1. Real-time RT-PCR and microarray analyses showed significantly decreased Cyp17a1 expression (~70%) in both siRNA1- and siRNA2-transfected MLTCs. The siRNAs knockdown did not affect the expressions of Nr5a1 (Sf1), Star, Por, and Insl3. 47 genes including a Notch-related gene Hey1 were significantly up-regulated (fold change >2.0) and 38 genes were significantly down-regulated (fold change <0.5) in both siRNA1- and siRNA2-transfected MLTCs (Table S1 and Table S2). However, Mamld1 knockdown had no discernible effect on the Hes3 expression level (siRNA1: fold change 0.92, P=0.80; siRNA2: fold change 1.43, P=0.35). MLTCs were maintained in RPMI 1640 supplemented with 10% fetal bovine serum, and were transiently transfected with two siRNAs against Mamld1 or with non-targeting control RNA. To compare changes in gene expression profile in MLTCs, 48h later, total RNA was subjected to Q-PCR to confirm a significantly decreased Mamld1 mRNA, and then these total RNA samples were for microarray analysis. Supplementary file: t-test unpaired [i1] Vs [control], [i2] Vs [control], P <= 0.05 FC >=2.0

ORGANISM(S): Mus musculus

SUBMITTER: Michiko Nakamura

PROVIDER: E-GEOD-26913 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:IL-33 is a nuclear cytokine from the IL-1 family that plays important roles in health and disease. Under healthy conditions, IL-33 is constitutively expressed to high levels in the nucleus of producing cells in various human and mouse tissues. The extracellular function of IL-33 cytokine has been well documented, but it remains unclear whether intracellular nuclear IL-33 has additional functions in the nucleus. Here, we used a global proteomic approach based on quantification of 5000 individual proteins by high-resolution mass spectrometry to compare the extracellular and intracellular roles of IL-33 in primary human endothelial cells, a major source of IL-33 protein in human tissues. Large-scale analysis of protein expression was performed either after stimulation of the cells with the IL-33 mature form IL-3395-270 (during 6h or 24h) or after siRNA knockdown of intracellular IL-33 (two experiments, each with a different pool of distinct siRNAs, noted siRNA1 and siRNA2). In each case, proteins were fractionated by 1D SDS-PAGE in 12 gel bands, and label-free quantitative analysis was performed. The present dataset contains the files for the two experiments of knockdown of endogenous nuclear IL-33 expression: - RNA silencing strategy 1. Knockdown of endogenous nuclear IL-33 expression was performed with a pool of four distinct siRNAs (Dharmacon ON-TARGETplus SMARTpool IL-33 siRNAs) that have been specifically modified for efficient silencing of the target gene with reduced off-target effects. Cells transfected with these siRNA duplexes (si1) were compared with those transfected with the provided controls (CTsi1). Three independent biological replicates (noted _A, _B, _C) were prepared and analyzed for each condition, leading to 6 different samples. Each of them was fractionated into 12 gel bands analyzed by nanoLC-MS/MS, leading to 72 raw files. - RNA silencing strategy 2. The second knockdown strategy was based on the use of an independent pool of three siRNAs targeting IL-33, predesigned by another provider using new and critical siRNA design rules (Sigma MISSION Predesigned Il-33 siRNAs based on Rosetta siRNA design algorithm). Cells transfected with these siRNA duplexes (si2) were compared with those transfected with the provided controls (CTsi2). Three independent biological replicates (noted _A, _B, _C) were prepared and analyzed for each condition, leading to 6 different samples. Each of them was fractionated into 12 gel bands analyzed by nanoLC-MS/MS, leading to 72 raw files.

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Mamld1 knockdown with siRNA in mouse Leydig tumor cells

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