Transcriptomic analysis of flies with Yki gut tumors
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA954832 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24149824.fastq.gz | Fastqsanger.gz | |||
| SRR24149825.fastq.gz | Fastqsanger.gz | |||
| SRR24149826.fastq.gz | Fastqsanger.gz | |||
| SRR24149827.fastq.gz | Fastqsanger.gz | |||
| SRR24149828.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Flies with Yki gut tumors is a widely used Drosophila model of cancer cachexia. Since cancer cachexia is a multi-organ syndrome, its investigation requires understanding how tumors induce metabolic dysfunction in peripheral organs. To address this, we performed a body-wide single-cell transcriptome analysis of Yki tumor model flies. Methods: snRNA-seq analysis of whole-body flies (without heads) with and without Yki gut tumors. Results: The data provides information of transcriptome alternations related to tumor-induced cachexia, including expression of metabolic genes and tumor-host organ communications. Conclusions: Cachexia phenotypes in Yki tumor model flies originated from metabolic dysregulation in peripheral organs that induced by tumor secreted factors.
2025-02-21 | GSE229526 | GEO
Project description:Purpose: identify global changes in gene expression in thorax tissues caused by the presence of gut tumors generated by yki expression in intestine stem cells. Note that the thorax of adult flies is composed mainly by muscle tissue but fat body is also present. Changes in gene expression do not exclusively reflect the muscle transcriptome Methods: To extract total RNAs for RNA-Seq experiment, we used 8-10 thoraces dissected out from both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-yki-act (yki) flies, making sure the gut of these flies was completely removed. Crosses were kept at 18°C to avoid expression of yki during development. Adult males were collected every 24-48 hours and then shifted to 29°C to induce gut yki-tumors. To assess transcriptional changes during the recovery phase, flies were moved to 18°C after a period of 14 days at 29°C in order to shutdown yki expression in the gut and suppress tumor growth. 6-day time points were analyzed during the recovery phase and included T20R, T26R, T32R and T38R. After assessing RNA quality with Agilent Bioanalyzer, rRNA depletion was performed. Then, sequencing libraries constructed with Illumina TruSeq RNA prep kit were sequenced using. We multiplexed samples in each lane, which yields targeted number of single-end 75 bp reads for each sample, as a fraction of 180 million reads for the whole lane. Sequence reads were mapped back to the Drosophila genome (flybase genome annotation version r6.30) using STAR. With the uniquely mapped reads, we quantified gene expression levels using Cufflinks (FPKM values). Next, differentially expressed genes between experimental and control data were analyzed with DESeq2. Results: Gene list enrichment analysis of the downregulated muscle transcriptome by yki overexpression in intestine stem cells revealed a striking enrichment of multiple metabolic processes impinging on carbohydrate metabolism, amino acid metabolism, and energy metabolism. Interestingly, target genes of Foxo, a transcription factor inhibited by insulin/IGF signaling, are enriched in the upregulated thorax transcriptome of ISCs yki overexpression flies and downregulated during recovery (T20R, T26R, T32R and T38R). In particular, induction of InR and Thor, well-characterized targets of Foxo, are validated with qPCR. Also, the transcription factor REPTOR that is modulated by mTOR signaling and regulates metabolism, was found to be upregulated in thoraces of flies with yki-tumors and downregulated during recovery. Conclusions: Our study discovered that the generation of yki-tumors in the gut drives the upregulation of REPTOR in the thorax of adult flies.
2023-06-01 | GSE189214 | GEO
Project description:To investigate the effect of gut microbiota on host wasting, we established a wasting model in fly by activation of Yki in adult midgut ISCs, in which the host flies present the sysytmeic organ wasting and metabolic abnormalities.
2022-05-30 | GSE204975 | GEO
Project description:To investigate the function of Malpighian tubules on host wasting, we established a fly model of tumor-induced wasting by activation of an oncogene Yki in adult intestinal stem cells (ISCs) for 8 days to cause gut-tumor formation and systemic organ wasting and metabolic abnormalities. We then performed RNA-seq and gene expression analysis in Malpighian tubules from control and yki3SA tumor-bearing flies
2022-05-29 | GSE204866 | GEO
Project description:Purpose: Activation of yki or Ras signaling pathways in ISCs causes overproliferation and ISC reprogramming. To gain insight into yki- and Ras-induced ISC reprogramming and gene expression, we performed a transcriptomic analysis of adult midgut with overexpression of yki-3SA or Ras1A in the ISCs.
2018-04-27 | GSE113728 | GEO
Project description:Purpose: localized aberrant cell proliferation induced by activation of Yki in ISCs impairs muscle functions. To gain insight into the cross talk between intestine and muscle, we performed a transcriptomic analysis of thoracic muscles in ISC overproliferation flies. Methods: To extract total RNAs for RNA-Seq experiment, we used 10 thoraces dissected out from both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Yki-act (Yki) flies incubated for 8 days at 29°C. After assessing RNA quality with Agilent Bioanalyzer, mRNAs were enriched by poly-A pull-down. Then, sequencing libraries constructed with Illumina TruSeq RNA prep kit were sequenced using Illumina HiSeq2000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). We multiplexed samples in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. Sequence reads were mapped back to the Drosophila genome (flybase genome annotation version r5.51) using Tophat. With the uniquely mapped reads, we quantified gene expression levels using Cufflinks (FPKM values). Next, we performed data normalization on the read counts and applied a negative binomial statistical framework using the Bioconductor package DESeq to quantify differential expression between experimental and control data. Results: Gene list enrichment analysis of the downregulated muscle transcriptome by ISCs Yki overexpressioin revealed a striking enrichment of multiple metabolic processes impinging on carbohydrate metabolism, amino acid metabolism, metabolism of vitamins and cofactors, and metabolism of xenobiotics by cytochrome P450. Interestingly, target genes of Foxo, a transcription factor inhibited by insulin/IGF signaling, are enriched in the upregulated muscle transcriptome of ISCs Yki overepxression flies. In particular, induction of InR and Thor, well-characterized targets of Foxo, are validated with qPCR. Conclusions: Our study represents ISCs overproliferation induced by Yki overepxression remotedly regulates muscle function and gene expression probally via modulation of insulin signaling in muscle. Our results show that RNA-seq offers a comprehensive evaluation of signaling network and biological process in organ communication. Thoraces mRNA profiles of both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Yki-act (Yki) flies incubated for 8 days at 29°C were generated by deep sequencing, in replicate, using Illumina HiSeq2000.
2015-02-01 | E-GEOD-65325 | biostudies-arrayexpress
Project description:The experiment was undertaken to characterize Yki-driven intestinal stem cell tumor proteome from Drosophila adult midguts, and to identify changes in the ISC tumor proteome in flies fed on TONDU peptide, using LC MS/MS approach. esgts>UAS-yki3SA flies on day 1, day 7 of tumor induction; TONDU-peptide fed flies on day 7; and esgts>UAS-yki3SA UAS-vgTONDU on day 7 were used for proteome analysis. Briefly, gut lysate from 20 female flies was obtained in extraction buffer (6M GnHCl in 50mM Tris-Cl pH 7.4, 65 mM DTT) with 50 mM sodium acetate and protease inhibitors (1X protease inhibitor cocktail with 0.2 mM PMSF). 5 microgram of the protein samples were reduced with 5 mM TCEP, further alkylated with 50 mM iodoacetamide, and digested with Trypsin (1:50, Trypsin/lysate ratio) for 16 hours at 37 degree Celsius. Digests were cleaned using a C18 silica cartridge to remove the salt and dried using a speed vac. The dried pellet was resuspended in 5% acetonitrile, 0.1% formic acid (Buffer A). The experiment was performed using an EASY-nLC 1000 system (Thermo Fisher Scientific) coupled to a Thermo Fisher-Orbitrap Fusion mass spectrometer equipped with a nanoelectrospray ion source. 1.0 microgram of the peptide mixture was resolved using a 25 cm Thermo Easy-spray PepMap C18 column. The peptides were loaded with Buffer A and eluted with a 0 to 40% gradient of Buffer B (95% acetonitrile, 0.1% formic acid) at a flow rate of 300 nl/min for 60 min. MS data was acquired using a data-dependent top20 method dynamically choosing the most abundant precursor ions from the survey scan.
2020-01-25 | MSV000084841 | MassIVE
Project description:Time course of transcriptomic changes of thoraces comparing wild type and flies with gut yki-tumors during a tumor induction phase and tumor shutdown phase to analyze the recovery of peripheral tissue.
| PRJNA781988 | ENA
Project description:Purpose: localized aberrant cell proliferation induced by activation of Yki in ISCs impairs muscle functions. To gain insight into the cross talk between intestine and muscle, we performed a transcriptomic analysis of thoracic muscles in ISC overproliferation flies. Methods: To extract total RNAs for RNA-Seq experiment, we used 10 thoraces dissected out from both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Yki-act (Yki) flies incubated for 8 days at 29°C. After assessing RNA quality with Agilent Bioanalyzer, mRNAs were enriched by poly-A pull-down. Then, sequencing libraries constructed with Illumina TruSeq RNA prep kit were sequenced using Illumina HiSeq2000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). We multiplexed samples in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. Sequence reads were mapped back to the Drosophila genome (flybase genome annotation version r5.51) using Tophat. With the uniquely mapped reads, we quantified gene expression levels using Cufflinks (FPKM values). Next, we performed data normalization on the read counts and applied a negative binomial statistical framework using the Bioconductor package DESeq to quantify differential expression between experimental and control data. Results: Gene list enrichment analysis of the downregulated muscle transcriptome by ISCs Yki overexpressioin revealed a striking enrichment of multiple metabolic processes impinging on carbohydrate metabolism, amino acid metabolism, metabolism of vitamins and cofactors, and metabolism of xenobiotics by cytochrome P450. Interestingly, target genes of Foxo, a transcription factor inhibited by insulin/IGF signaling, are enriched in the upregulated muscle transcriptome of ISCs Yki overepxression flies. In particular, induction of InR and Thor, well-characterized targets of Foxo, are validated with qPCR. Conclusions: Our study represents ISCs overproliferation induced by Yki overepxression remotedly regulates muscle function and gene expression probally via modulation of insulin signaling in muscle. Our results show that RNA-seq offers a comprehensive evaluation of signaling network and biological process in organ communication.
2015-02-01 | GSE65325 | GEO
Project description:In this study, we demonstrated that tumor-bearing flies exhibit enhanced avoidance of bitter substances, and it is correlated with the severity of the tumor in our genetic models. To identify tumor-secreted cytokines uniquely upregulated in the malignant tumor model (GMR>ykiSA) compared to the mild tumor model (GMR>ykiWT), we performed RNA-sequencing analysis on both types of yki-induced tumor tissues.
2025-11-19 | GSE310403 | GEO