Metabolic Respiration Induces AMPK- and Ire1p-Dependent Activation of the p38-Type HOG MAPK Pathway
ABSTRACT: 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:The evolutionary origin of vertebrate type 2 immunity is a topic of great interest. Several studies have focused on the immune cell components of evolutionary older vertebrates such as fish. However, how fish cytokines function and whether they have similar roles as in mammals is still a matter of speculation. Here, we have used the zebrafish (Danio rerio) to gain insights into il4/13a and il4/13b genes and characterized their role under both homeostatic and inflammatory conditions. We established knockouts for both il4/13a and il4/13b genes and showed that they are needed to suppress inflammation in larvae and in the gill mucosa. As a counterpoint, we examined the gills of il10 defective zebrafish and revealed the importance of il10 in maintaining homeostasis in this mucosal tissue. As in mammals, zebrafish il10 appears to have an anti-inflammatory function.
Project description:The development of autonomic nerve fibres in the tumour microenvironment is a pivotal event that regulates prostate cancer initiation and dissemination, but how nerves emerge in tumours is presently unknown. Here we show that Doublecortine-expressing (DCX+) neural precursors from the central nervous system (CNS) infiltrate prostate tumours and differentiate into neo-neurons that contribute to tumour development. In human primary prostate tumours and transgenic mouse cancer tissues, the density of DCX+ neural progenitors is strongly associated with tumour aggressiveness, invasion and recurrence. We found that DCX+ neural precursors egress from the subventricular zone, a neurogenic area of the CNS, and circulate in the blood to reach the tumour where they initiate neurogenesis. Hence, the DCX+ cells in prostate tumour can differentiate into neurons ex vivo and build up a tumour-associated neural network in vivo. Selective genetic depletion of DCX+ cells in mice significantly inhibits the early phases of prostate cancer development, whereas orthotopic transplantation of DCX+ cells purified from prostate tumour or brain tissues promotes tumour growth and cancer cell dissemination. These results unveil a unique crosstalk between the CNS and the tumour that drives a process of neurogenesis necessary for prostate cancer development, and indicate a novel neural element of the tumour microenvironment as a potential target for cancer treatment.
Project description:Large scale RNA-Seq analysis was performed to investigate the transcriptomic response to osteoarthritis in cartilage and investigate potential subgroups of patients. Data were collected from intact knee cartilage (posterior lateral condyle) from at total of 60 patients with osteoarthritis (OA) following total knee replacement and 10 control non-OA patients following amputation.
Project description:Intestinal tumours from genetically engeenierd mouse modesl (GEMMs), of various gentopyes, were isolated at endpoint and RNA was isolated. In an additional experiment, epithelial tumour organoids were isolated at end point and grown in vitro. These organoids were harvested 72 hours after seeding and RNA was isolated.
Project description:"The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects of the omics data integration problem such as the design of multiomics experiments, integrative transcriptional and regulatory networks, integrative variable selection, data fusion, integration of public domain data, and integrative pathway analysis. To support method development STATegra uses a model biological system, namely the differentiation process of mouse pre-B-cells. The STATegra consortium generated data focused on a critical step in the differentiation of B lymphocytes, which are key components of the adaptive immune system. Transcription factors of the Ikaros family are central to the normal differentiation of B cell progenitors and their expression increases in response to developmental stage-specific signals to terminate the proliferation of B cell progenitors and to initiate their differentiation. In particular, a novel biological system that models the transition from the pre-BI stage to the pre-BII subsequent stage, where B cell progenitors undergo growth arrest and differentiation, was used. The approach involves a pre-B cell line, B3 , and an inducible version of the Ikaros transcription factor, Ikaros-ERt2. Ikaros factors act to down-regulate genes that drive proliferation and to simultaneously up-regulate the expression of genes that promote the differentiation of B cell progenitors. Hence, in the B3 system, before induction of Ikaros, cells proliferate and their gene expression pattern is similar to proliferating B cell progenitors in vivo. Following Ikaros induction, B3 cells undergo gene expression changes that resemble those that occur in vivo during the transition from cycling to resting pre-B cells, followed by a marked reduction in cellular proliferation and by G1 arrest. On this system the consortium has created a high-quality data collection consisting of a replicated time course using seven different omics platforms: RNA-seq, miRNA-seq, ChIP-seq, DNase-seq, Methyl-seq, proteomics and metabolomics, which is used to assess and to validate STATegra methods."
Project description:Glucocorticoids are critical regulators of energy metabolism and immunity and major drug targets in inflammatory disease. It is also known that the circadian clock regulates both metabolism and immunity. This experiment is part of wider study to understand the coupling between circadian clock components and Glucocorticoid receptor in multiple mouse tissues. Here, RNA-seq analysis was performed in vehicle and dexamethasone (a synthetic Glucocorticoid) treated WT mouse liver and lung tissues at two circadian times, to understand time of the day variation in Glucocorticoid regulated genes. Mice were treated at ZT6 (6 hours after lights on, 1:30pm) or at ZT18 (6 hours after lights off, 1:30am) with dexamethasone (1 mg/kg intraperitoneal) or vehicle (methylcyclodextrin 1mg/kg intraperitoneal) for 2 hours before sacrifice by cervical dislocation. Lung and liver tissue were lysed and total RNA prepared using SV Total RNA Isolation System (Promega). Quality and integrity of total RNA samples were assessed by 2100 Bioanalyzer or a 2200 TapeStation (Agilent Technologies) according to the manufacturer’s instructions. RNA sequencing (RNA-seq) libraries were generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. Then paired-end sequenced (101 + 101 cycles, plus indices) on an Illumina HiSeq2500 instrument.
Project description:Activation of endogenously expressed KRas[G12D] in the pancreas of mice gives rise primarily to early stage PanIN lesions, however such lesions can occasionally progress to end-stage ductal adenocarcinoma (PDAC). Progression of KRas[G12D]- initiated lesions to PDAC is accelerated by modest expression of MYC from the Rosa26 locus. Deletion of 1 copy of endogenous c-Myc or both copies of endogenous Zbtb17 (aka Miz1), slows progression to PDAC and extends healthful survival of Pdx1-Cre;lsl-KRas[G12D];Rosa26-lsl-MYC[DM] (KMC) mice. Tumours were removed from mice with all 4 genotypes and validated by histological examination prior to RNA-SEQ analysis.
Project description:The gain-of-function mutation in the pleckstrin homology domain of AKT1 (AKT1E17K) occurs in lung and breast cancer. By use of human cellular models and of a AKT1E17K transgenic Cre-inducible murine strain (R26-AKT1E17K mice) we have demonstrated that AKT1E17K is a bona-fide oncogene for lung epithelial cells. However, the role of AKT1E17K in breast cancer remains to be determined. Here, we report the generation and the characterization of a MMTV-CRE;R26-AKT1E17K mouse strain that expresses the mutant AKT1E17K allele in the mammary epithelium. We observed that R26AKT1E17K;MMTV-Cre mice presented a variety of proliferative alterations of the mammary epithelium that were classified as adenosis with low-to-high grade dysplasia. In addition, AKT1E17K stimulates the development of mammary tumors with incidence of 43%. Tumors were morphologically classified as ductal adenocarcinoma of medium-high grade though subsequent immunoistochemical characterization suggested they were of basal-like origin, being PR-/HER2-/ERα+ and CK8-/CK10-/CK5+/CK14+. We also observed that tumors expressing mutant AKT1E17K presented activation of the downstream signaling axis GSK3/cyclin D1 in mammary epithelium, in parallel with increased proliferation rate as demonstrated by cell number count and measurement of Ki67. In conclusion, AKT1E17K is a bona fidae oncogene that is able to initiate tumors at high efficiency in murine mammary epithelium in vivo.
Project description:We sequenced mRNA from 32 muscles (n=16 semimembranosus,n=16 longisimus dorsi) of two pig breeds (Puławska and Polish Landrace), which are differing in firmness. The differences between pig groups with respect to shear force of coocked meat were significant and amounted to 64.88 N (P<0.01) in longisimus dorsi and 14.8 N (P<0.05) for semimembranosus. Examination of mRNA levels between pig breeds differing in shear force. Project ID: 217776 founded National Science Centre (NCN), title: Application of targeted next generation sequencing (NGS) in the identification of genetic markers associated with the pork quality