During adipocyte differentiation, significant alternative splicing changes occur in association with the adipogenic process. However, little is known about roles played by splicing factors in this process. We observed that mice deficient for the splicing factor SRSF10 exhibit severely impaired development of subcutaneous white adipose tissue as a result of defects in adipogenic differentiation. To identify splicing events responsible for this, RNA-seq analysis was performed using embryonic fibroblast cells. Several SRSF10-affected splicing events that are implicated in adipogenesis have been identified. Skipping of lipin1 exon 7 is controlled by SRSF10-regulated cis-element located in the constitutive exon 8. The activity of this element depends on the binding of SRSF10 and correlates with the relative abundance of lipin1a mRNA. A series of experiments demonstrated that SRSF10 controls the production of lipin1a and thus promotes adipocyte differentiation. Indeed, lipin1a expression could rescue SRSF10-mediated adipogenic defects. Taken together, our results identify SRSF10 as an essential regulator for adipocyte differentiation and also provide new insights into splicing control by SRSF10 in lipin1 pre-mRNA splicing. Overall design: RNA-seq for wide type (WT) and SRSF10-deficient (KO) mouse MEF cells
SRSF10 regulates alternative splicing and is required for adipocyte differentiation.
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Genetic susceptibility underlies the pathogenesis of cancer. Through genome-wide association studies, we and others have previously identified a novel susceptibility gene, TNFRSF19, which encodes an orphan member of the TNF receptor superfamily, to be associated with nasopharyngeal carcinoma (NPC) and lung cancer risk. Here, we show that TNFRSF19 is highly expressed in NPC and is required for cell proliferation and NPC development. However, unlike most of TNF receptors, TNFRSF19 is not involved in NF-B activation or associated with TRAF proteins. By affinity purification, we identified TGF receptor type-I (TRI) as a specific binding partner for TNFRSF19. TNFRSF19 binds to the kinase domain of TRI in the cytoplasm and thereby blocks the Smad2/3 association with TRI and subsequent signal transduction. Ectopic expression of TNFRSF19 in normal epithelial cells confers resistance to the cell cycle block induced by TGF, whereas knockout of TNFRSF19 in NPC cells unleashes a potent TGF response characterized by upregulation of Smad2/3 phosphorylation and TGF target gene transcription. Furthermore, elevated TNFRSF19 expression correlates with reduced TGF activity and poor prognosis in NPC patients. Our data reveal that gain-of-function of TNFRSF19 in NPC represents a mechanism by which tumor cells evade the growth-inhibitory action of TGF.
TNFRSF19 Inhibits TGFβ Signaling through Interaction with TGFβ Receptor Type I to Promote Tumorigenesis.
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The goals of this study aim to reveal functional and phenotypic diversity of leukemia-associated macrophages in response to the microenvironmental cues in mouse T cell acute lymphoblastic leukemia Overall design: Compare Transcriptomes of macrophages in T cell acute leukemia which are suggested as leukemia-associated macrophages (LAMs) with homeostasis
Organ-specific microenvironment modifies diverse functional and phenotypic characteristics of leukemia-associated macrophages in mouse T cell acute lymphoblastic leukemia.
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We used microarray to monitor the differentially expresed genes during Jurkat T cell activaiton.
IκB Kinase ε Is an NFATc1 Kinase that Inhibits T Cell Immune Response.
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To identify RA-regulated genes in mSSCs, we treated mSSCs with vehicle, RA and RA plus CHX. To characterize the induced spermatogenic cells by transcriptome profiling, we cultured mSSCs on pup Sertolic cells supplemented with RA. Induced differentiating spermatogonia and induced spermatocytes were collected after a 3-day- and 6-day-induction, respectively. Overall design: We carried out RNA-seq analysis of samples after different treatment and samples from different in vitro induction stages.Two biological replicates were included for each sample.
Retinoic Acid Is Sufficient for the In Vitro Induction of Mouse Spermatocytes.
Sex, Specimen part, Cell line, SubjectView Samples
Human myoblast cell line 54-1 is transfected with either a srambled control siRNA or siRNA against UPF1. Two days after transfection, cell were induced to differentiate by changing grow meida to differentiation media. 2 days after induction of differentiation, cells are collected for extraction of RNA. Overall design: Human myoblast cell line 54-1 is transfected with either a srambled control siRNA or siRNA against UPF1. Two days after transfection, cell were induced to differentiate by changing grow meida to differentiation media. 2 days after induction of differentiation, cells are collected for extraction of RNA.
The RNA Surveillance Factor UPF1 Represses Myogenesis via Its E3 Ubiquitin Ligase Activity.
Specimen part, Cell line, Treatment, Subject, TimeView Samples
Pancreatic ß and a cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse ß and a cells sorted from fetal to adult stages. We discovered that ß and a cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the ß lineage and a lineage are synchronous in their maturation states. The heterogeneity of juvenile ß cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult ß cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both ß and a cells. Overall design: The overall goal of this study was to define the roadmaps for pancreatic ß- and a-cell development. Specifically, we performed single-cell RNA-seq at various developmental stages of E17.5, P0, P3, P9, P15, P18 and P60 of ß- and a- cells (except P3), as well as endocrine progenitor cells at P0, which were fluorescence-activated cell sorting (FACS) sorted from Insulin-RFP, Gcg-Cre; Rosa-RFP or Ngn3-GFP mouse strains, respectively. To develop a workflow to decipher the maturation process through bulk-cell transcriptomic analysis, we performed RNA-seq using 3-5 × 10^4 sorted cells at various developmental time points as we have done in the single-cell study. The background strains of our mouse samples are: Ngn3-GFP mice: mixed background of C57BL/6 and C3H Ins1-RFP mice: mixed background of C57BL/6 and C3H Gcg-Cre, Rosa-RFP mice: mixed background of C57BL/6, CBA/J and C3H.
Deciphering Pancreatic Islet β Cell and α Cell Maturation Pathways and Characteristic Features at the Single-Cell Level.
Specimen part, Cell line, SubjectView Samples
Acrylamide is a type-2 alkene monomer with established human neurotoxic effects. While the primary source of human exposure to acrylamide is occupational, other exposure sources include food, drinking water, and smoking. In this study, neurobehavioral assays coupled with transcriptional profiling analysis were conducted to assess both behavioral and gene expression effects induced by acrylamide neurotoxicity in rats when administered during early postnatal life. Acrylamide administration in rat pups induced significant characteristic neurotoxic symptoms including increased heel splay, decrease in grip strength, and decrease in locomotor activity. Transcriptome analysis with the Affymetrix Rat Genome 230 2.0 array indicated that acrylamide treatment caused a significant alteration in the expression of genes involved in muscle contraction, pain regulation, and dopaminergic neuronal pathways. First, in agreement with the observed behavioral effects, expression of the Mylpf gene involved in muscle contraction was downregulated in the spinal cord in response to acrylamide. Second, in sciatic nerves, acrylamide repressed the expression of the opioid receptor gene Oprk1 that is known to play a role in neuropathic pain regulation. Finally, in the cerebellum, acrylamide treatment caused a decrease in the expression of the nuclear receptor gene Nr4a2 that is required for development of dopaminergic neurons. Thus, our work examining the effect of acrylamide at the whole-genome level on a developmental mammalian model has identified novel genes previously not implicated in acrylamide neurotoxicity that can be further developed into biomarkers for assessing the risk of acrylamide exposure.
Neurobehavioral and transcriptional effects of acrylamide in juvenile rats.
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This study aimed to perform transcriptome profiling of Nfic-/- and corresponding control tooth germ at root initiation stage to identify differentially expressed for key regulators of root development. Coordination between the Hertwigâ€™s Epithelial Root Sheath (HERS) and apical papilla (AP) is crucial for proper root development process. The Hedgehog (Hh) signaling pathway and Nfic are both involved in tooth root development. Overall design: mRNA profiling of apical half of tooth germ from 6 pairs of 4-day-old Nfic-/- and littermate Nfic+/- control mice were generated using Illumina Next-Seq 500
An Nfic-hedgehog signaling cascade regulates tooth root development.
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We performed microarray experiments with RNAs from dissected immature anthers (stages 4-7) from wild-type, dyt1 and ams mutant plants, using the Affymetrix ATH1 chip.
Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development.
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