RNA-seq of brown and white mouse adipose tissue at thermoneutrality and high-fat diet
ABSTRACT: Mice were kept at RT, thermoneutrality (humanized condition) and thermoneutrality plus high fat diet. Inter scapular brown adipose tissue and inguinal white adipose tissue were used for RNA seq. Illumina Truseq ribosomal RNA depletion protocol was used.
Project description:Ambient temperature affects energy intake and expenditure to maintain homeostasis in a continuously fluctuating environment. Here, mice with an adipose-specific defect in fatty acid oxidation (Cpt2A-/-) were subjected to varying temperature to determine the role of adipose bioenergetics to environmental adaptation. Cpt2A-/- brown adipose tissue (BAT) failed to induce thermogenic genes such as Ucp1 and Pgc1α in response to adrenergic stimulation, which is exacerbated by increasing temperature. Thermoneutrality induced a mitochondrial DNA stress in Cpt2A-/- BAT that resulted in a loss of classical interscapular BAT, but did not affect body weight gain or glucose tolerance in response to a high-fat diet. In this dataset, we include the expression data obtained from dissected mouse interscapular brown adipose tissue from mice acclimatized to thermoneutrality (30C) with and without beta3adrenergic stimulation with and without the deletion of carnitine palmitoyltransferase 2 (i.e., adipose unable to beta-oxidize long chain fatty acids in mitochondria). WildType and Cpt2A KnockOut mice were treated either with or without beta3adrenergic stimulation, thus four classes. Three biologic replicates were compared per class, thus twelve mice.
Project description:We have reported that cold temperature challenge results in a dramatic decrease in levels of the transcriptional repressor, Rev-erb alpha. Performing Rev-erb alpha ChIP-seq on brown adipose from wildtype animals kept at thermoneutrality or cold-challenged (and using Rev-erb alpha KO brown adipose as a control), we were able to globally determine the genomic regions undergoing Rev-erb alpha-dependent de-repression. Overall design: Examination of Rev-erb alpha binding in brown adipose tissues under thermoneutral and cold-challenged conditions
Project description:Immune protection of the body cavities depends on the swift activation of innate and adaptive immune responses in non-classical secondary lymphoid organs known as fat-associated lymphoid clusters (FALCs). While it is well-established that fibroblastic reticular cells (FRCs) are an integral component of the immune-stimulating infrastructure of lymph nodes and other classical secondary lymphoid organs, it has remained elusive whether and how FRCs in FALCs contribute to peritoneal immunity. Using FRC-specific gene targeting, we found that FALCs are underpinned by an elaborated FRC network and that initiation of peritoneal immunity was governed through FRC activation via MyD88-dependent innate immunological sensing. FRC-specific ablation of Myd88 expression blocked recruitment of inflammatory monocytes into FALCs and subsequent CD4+ T cell-dependent B-cell activation. Moreover, containment of Salmonella infection was compromised in conditionally Myd88-deficient mice indicating that FRCs in FALCs function as initial checkpoint in the orchestration of protective immune responses in the peritoneal cavity.
Project description:Splenic white pulp (WP) structures are underpinned by fibroblastic stromal cells (FSCs) to facilitate splenic compartmentalization and execute efficient immune responses. Although distinct WP FSCs exhibit various molecular traits, the origin and the hierarchical differentiation of different cell subsets are not characterized. Here we showed, the organization of splenic WP and the differentiation of WP FSCs were governed by lymphotoxin beta receptor (LTβR) signaling pathway. Cell fate mapping analysis revealed that different WP fibroblastic stromal cells descend from a common perivascular LTβR-sensitive mesenchymal lymphoid organizer cells (mLTo) at prenatal stage. Moreover, embryonic mLTo cells required LTβR signaling to give rise to different WP stromal cell subsets, while the proliferation of these cells was devoid of LTβR signaling but followed the development of WP during ontogeny. Moreover, cell fate mapping from different time point indicated a consecutive commitment of mLTo cells initiated from the proximal region around the splenic artery. RNAseq and differentiation trajectory analysis of distinct FSCs showed that Ltbr-deficient cells and perivascular reticular cells (PRCs) from adult spleen exhibited a progenitor phenotype and revealed a closer hierarchical lineage with embryonic mLTo cells. Taken together, our results unveil that embryonic mLTo cells residing in the perivascular niches can give rise to different FSC populations in a LTβR-dependent manner during development.
Project description:We investigated the genomic and physiological impact of acute sleep loss in peripheral tissues, by obtaining adipose tissue and skeletal muscle after one night of sleep loss and after one full night of sleep. Processed data (count table) only. Raw data will be submitted to EGA.
Project description:Mice have their lowest (basal) metabolic rate when housed at thermoneutrality, which starts above 29 degrees C. Although they eat less, and thus reduce their energy intake, their energy balance remains positive leading to an increased adiposity, especially when fed a high fat diet. However, almost all metabolic mouse studies are performed at standard room temperatures ranging between 20 and 22 degrees C. Previously, we showed that housing mice at thermoneutrality lead to massive increased adiposity, while metabolic dysfunction of white adipose tissue (WAT) was absent. Here, we studied whether an increased metabolic flux through WAT induces cellular stress and underlies tissue dysfunction leading to tissue inflammation. C57BL/6JOlaHsd wildtype male mice, aged 9 weeks, were fed purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks to acclimatize, followed by 12 weeks a BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into different treatment groups: i) control group, which remained at thermoneutrality for 5 days, ii) 5 days normal housing temperature (22 C degrees) while housed continously in an indirect calorimetry system. At the end of the study, after 2 hours food removal at the start of the light phase, mice were killed immediately by decapitation after taking them out of the indirect calorimetry system. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays. Overall design: C57BL/6JOlaHsd wildtype male mice, aged 9 weeks, were fed purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks to acclimatize, followed by 12 weeks a BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into different treatment groups: i) control group, which remained at thermoneutrality for 5 days, ii) 5 days normal housing temperature (22 C degrees) while housed continously in an indirect calorimetry system. Mice were killed immediately after taking them out of the indirect calorimetry system by decapitation after 2 hours food removal at the start of the light phase. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays.
Project description:In fungal species, differentiation to the filamentous/hyphal cell type is critical for entry into host cells and virulence. Comparative RNA sequencing was used to explore the pathways that regulate differentiation to the filamentous cell type in yeast. This approach uncovered a role for the stress-response MAPK pathway, HOG, during the increased metabolic respiration that induces filamentous growth. In this context, the AMPK Snf1p and ER stress kinase Ire1p regulated the HOG pathway. Cross-modulation between the HOG and filamentous growth (ERK-type) MAPK pathways optimized the differentiation response. The regulatory circuit described here may extend to behaviors in metazoans. Comparison of expression patterns of wild-type and mutant yeast cells grown in salt, tunicamycin or galactose by comparative RNA sequencing analysis.
Project description:Adaptive thermogenesis of brown adipose tissue (BAT) is critical for thermoregulation and contributes to total energy expenditure. However, whether BAT has non-thermogenic functions is largely unknown. Here, we describe that mice with a BAT-specific Liver kinase b1 deletion (Lkb1BKO mice) exhibited impaired mitochondrial respiration and thermogenesis in BAT, but reduced adiposity and liver triglyceride accumulation under high-fat-diet feeding at room temperature. Importantly, these metabolic benefits were also present in Lkb1BKO mice at thermoneutrality, where BAT thermogenesis was not required. Mechanistically, decreased mRNA levels of mtDNA-encoded electron transport chain (ETC) subunits and ETC proteome imbalance led to impaired mitochondrial respiration in BAT of Lkb1BKO mice. Furthermore, reducing mtDNA gene expression directly in BAT by removing mitochondrial transcription factor A (Tfam) in BAT also showed ETC proteome imbalance and the tradeoff between BAT thermogenesis and systemic metabolism at both room temperature and thermoneutrality. Collectively, our data demonstrates that ETC proteome imbalance in BAT regulates systemic metabolism independently of BAT thermogenic capacity.
Project description:Here we used activating (purmorphamine) and blocking (cyclopamine) drugs characterized of the Hedgehog pathway in adipose tissue-derived stem cells and identified mRNAs associated polysomes or free fraction in each condition.
Project description:To measure gene expression, mRNA from seven different tissues was extracted (adipose, muscle, hypothalamus, duodenum, liver, lung and kidney) from frozen tissues using TRIzol (Invitrogen). Messenger RNA from 7~14 animals was pooled equally before sequencing