Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Paul Cullen

PROVIDER: E-GEOD-61783 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:The goal of the RNA-sequencing experiment was to identify differentially expressed genes, ontologies, and pathways based on cell cycle traverse rate (CCTR) in pre-treatment malignant samples from patients with primary operable invasive triple-negative breast cancer (TNBC). TNBC patients belonged to the well-characterized Nottingham Primary Breast Carcinoma series, the database of which was prospectively maintained for another study, although its design accommodates the present retrospective analysis. Most TNBCs exhibited high Nottingham grade and about half of patients exhibited positive lymph nodes. All patients received chemotherapy with cyclophosphamide-methotrexate-5-fluoruracil after surgery (radical mastectomy or breast-conserving surgery). Stained slides used for quantitation of Ki67 index (KI) and mitotic index (MI) were independently scored by two pathologists blinded to clinical annotation, and the scores were averaged. Cell cycle traverse rate (CCTR) was defined as the ratio of the percentage of mitotic cells to the percentage of Ki67-positive cells in full-face formalin-fixed paraffin-embedded sections from primary tumors. To estimate percentages of mitotic cells for each sample, the average mitotic counts for each mitotic score category were first determined, followed by a conversion into percentage after accounting for sample cellularity. Separate slides from formalin-fixed paraffin-embedded malignant samples were used for RNA-sequencing based on the availability of sufficient tissue for analysis. Only tissue from pre-marked tumor areas in these slides were used for RNA-sequencing. RNA was extracted from deparaffinized tissue and first- and second-strand synthesis were performed using commercial kits. Pair-read sequencing was performed using the Illumina HiSeq2500 instrument. The Human Genome Assembly GRCh38.P10 was used as the reference genome for mapping sequence reads. Transcript expression was quantified using Salmon. Differentially expressed genes, ontologies, and pathways were determined based on mean CCTR as well as the optimal CCTR to predict breast cancer-specific survival.

Project description:Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with exercise adaptation in Arabian horses. Methods: Whole transcriptome profiling of blood was performed for untrained horses and horses from which samples were collected during at 3 different periods of training procedure (T1-during intense training period - March, T2- before starts - May and T3 -after flat racing season - October). The muscle transcriptome sequencing was performed for 37 blood samples using Illumina HiScan SQ in 75 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes in blood tissue were detected by DESeq2. The RNA-seq results were validated using by qPCR. Results: The increase of the number of DEGs between subsequent training periods has been observed and the highest amount of DEGs was detected between untrained horses (T0) and horses at the end of the racing season (T3) â 440. The comparison of transcriptome of T2 vs T3 and T0 vs T3 showed a significant advantage of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in T3 period compared T2 and T0; respectively). Our results showed that the largest number of identified genes encoded transcription factors, nucleic acid binding proteins and G-protein modulators, which mainly were transcriptional activated at the last training phase (T3) . Moreover, in the T3 period the identified DEGs represented genes coded for cytoskeletal proteins including actin cytoskeletal proteins and kinases. The most abundant exercise-upregulated genes were involved in pathways important in regulating the cell cycle (PI3K-Akt signaling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis as well as immunity processes (Jak-STAT signaling pathway). We also observed exercise induced expression of genes related in regulation of actin cytoskeleton, gluconeogenesis (FoxO signaling pathway; Insulin signaling pathway), glycerophospholipid metabolism and calcium signaling. Conclusions: TOur results allow to identify changes in genes expression profile following training schedule in Arabian horses. Based on comparison analysis of blood transcriptomes, several exercise-regulated pathways and genes most affected by exercise were detected. We pinpointed overrepresented molecular pathways and genes essential for exercise adaptive response via maintaining of body homeostasis. The observed transcriptional activation of such gene as LPGAT1, AGPAT5, PIK3CG, GPD2, FOXN2, FOXO3, ACVR1B and ACVR2A can be a base for further research in order to identify genes potentially associated with race performance in Arabian horses. Such markers will be essential to choice the training type, and could result in differences in racing performance specific to various breeds. The blood transcriptome sequencing was performed for 37 samples collected form Arabian horses using Illumina HiScan SQ in75 single-end cycles and in 3-4 technical repetitions.repetitions.

Dataset Information

Metabolic Respiration Induces AMPK- and Ire1p-Dependent Activation of the p38-Type HOG MAPK Pathway

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets