Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing

Priyank Shukla, Claus Vogl, Barbara Wallner, Doris Rigler, Mathias Mueller, Sabine Macho-Maschler

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    BACKGROUND: EMT is an important process in embryonic development, especially during gastrulation and organ formation. Furthermore it has been implicated in physiological processes like wound healing, and pathological conditions e.g. organ fibrosis and cancer. In late stage tumorigenesis, cells that underwent EMT are motile and may invade other parts of the body to form distant metastases. Madin-Darby Canine Kidney (MDCK) cells are widely used as a model to study epithelial polarity and EMT.OBSERVATIONS: We performed deep sequencing to build the transcriptome and miRNAome of epithelial and mesenchymal states in MDCK cells. With RNA-Seq, half of the genes known in the dog genome were detected, of which one third were differentially expressed during the process of EMT. Novel differentially regulated genes include interferon-stimulated genes and those involved in slit and netrin signaling. Gene set enrichment analysis of differentially expressed genes revealed TGFß1 as a central signaling factor. With miRNA-Seq, miRNAs that are known to be important regulators of EMT were detected and new candidates were predicted. miRNA target prediction combined with pathway analysis allowed us to identify additional pathways: Jak-Stat signaling and Pancreatic cancer. We also identified clusters (based on genomic coordinates) and families (based on sequence similarity) of significantly differentially expressed miRNAs, of which some were regulated by TGFß. Additionally we identified 25 completely novel miRNAs with a stable hairpin structure. One of the mesenchymal specific novel miRNAs was predicted to target genes involved in cell division, growth factor activity, and cellular adhesion complexes.CONCLUSIONS: We present the transcriptome and miRNAome of EMT in MDCK cells. We also investigated gene signatures and the interplay between miRNA and mRNA expression levels. Thereby, we increase the knowledge on the transcriptional landscape of mRNAs and miRNAs during the process of EMT.
    LanguageEnglish
    Title of host publicationUnknown Host Publication
    Number of pages1
    Publication statusPublished - 25 Aug 2015
    EventThe 6th EMBO Meeting - Birmingham, UK
    Duration: 25 Aug 2015 → …

    Conference

    ConferenceThe 6th EMBO Meeting
    Period25/08/15 → …

    Fingerprint

    High-Throughput Nucleotide Sequencing
    Madin Darby Canine Kidney Cells
    Epithelial-Mesenchymal Transition
    MicroRNAs
    Transcriptome
    Genes
    Physiological Phenomena
    Gastrulation
    Messenger RNA
    Pancreatic Neoplasms
    Human Body
    Cell Division
    Wound Healing
    Interferons
    Embryonic Development
    Intercellular Signaling Peptides and Proteins
    Carcinogenesis
    Fibrosis
    Genome
    Dogs

    Keywords

    • MDCK Epithelial-mesenchymal transition
    • Ras
    • Next Generation Sequencing (NGS)
    • Transcriptome
    • miRNAome

    Cite this

    Shukla, P., Vogl, C., Wallner, B., Rigler, D., Mueller, M., & Macho-Maschler, S. (2015). Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing. In Unknown Host Publication
    Shukla, Priyank ; Vogl, Claus ; Wallner, Barbara ; Rigler, Doris ; Mueller, Mathias ; Macho-Maschler, Sabine. / Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing. Unknown Host Publication. 2015.
    @inproceedings{c0d8b0be98a54609a694222688d72b4e,
    title = "Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing",
    abstract = "BACKGROUND: EMT is an important process in embryonic development, especially during gastrulation and organ formation. Furthermore it has been implicated in physiological processes like wound healing, and pathological conditions e.g. organ fibrosis and cancer. In late stage tumorigenesis, cells that underwent EMT are motile and may invade other parts of the body to form distant metastases. Madin-Darby Canine Kidney (MDCK) cells are widely used as a model to study epithelial polarity and EMT.OBSERVATIONS: We performed deep sequencing to build the transcriptome and miRNAome of epithelial and mesenchymal states in MDCK cells. With RNA-Seq, half of the genes known in the dog genome were detected, of which one third were differentially expressed during the process of EMT. Novel differentially regulated genes include interferon-stimulated genes and those involved in slit and netrin signaling. Gene set enrichment analysis of differentially expressed genes revealed TGF{\ss}1 as a central signaling factor. With miRNA-Seq, miRNAs that are known to be important regulators of EMT were detected and new candidates were predicted. miRNA target prediction combined with pathway analysis allowed us to identify additional pathways: Jak-Stat signaling and Pancreatic cancer. We also identified clusters (based on genomic coordinates) and families (based on sequence similarity) of significantly differentially expressed miRNAs, of which some were regulated by TGF{\ss}. Additionally we identified 25 completely novel miRNAs with a stable hairpin structure. One of the mesenchymal specific novel miRNAs was predicted to target genes involved in cell division, growth factor activity, and cellular adhesion complexes.CONCLUSIONS: We present the transcriptome and miRNAome of EMT in MDCK cells. We also investigated gene signatures and the interplay between miRNA and mRNA expression levels. Thereby, we increase the knowledge on the transcriptional landscape of mRNAs and miRNAs during the process of EMT.",
    keywords = "MDCK Epithelial-mesenchymal transition, Ras, Next Generation Sequencing (NGS), Transcriptome, miRNAome",
    author = "Priyank Shukla and Claus Vogl and Barbara Wallner and Doris Rigler and Mathias Mueller and Sabine Macho-Maschler",
    year = "2015",
    month = "8",
    day = "25",
    language = "English",
    booktitle = "Unknown Host Publication",

    }

    Shukla, P, Vogl, C, Wallner, B, Rigler, D, Mueller, M & Macho-Maschler, S 2015, Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing. in Unknown Host Publication. The 6th EMBO Meeting, 25/08/15.

    Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing. / Shukla, Priyank; Vogl, Claus; Wallner, Barbara; Rigler, Doris; Mueller, Mathias; Macho-Maschler, Sabine.

    Unknown Host Publication. 2015.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    TY - GEN

    T1 - Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing

    AU - Shukla, Priyank

    AU - Vogl, Claus

    AU - Wallner, Barbara

    AU - Rigler, Doris

    AU - Mueller, Mathias

    AU - Macho-Maschler, Sabine

    PY - 2015/8/25

    Y1 - 2015/8/25

    N2 - BACKGROUND: EMT is an important process in embryonic development, especially during gastrulation and organ formation. Furthermore it has been implicated in physiological processes like wound healing, and pathological conditions e.g. organ fibrosis and cancer. In late stage tumorigenesis, cells that underwent EMT are motile and may invade other parts of the body to form distant metastases. Madin-Darby Canine Kidney (MDCK) cells are widely used as a model to study epithelial polarity and EMT.OBSERVATIONS: We performed deep sequencing to build the transcriptome and miRNAome of epithelial and mesenchymal states in MDCK cells. With RNA-Seq, half of the genes known in the dog genome were detected, of which one third were differentially expressed during the process of EMT. Novel differentially regulated genes include interferon-stimulated genes and those involved in slit and netrin signaling. Gene set enrichment analysis of differentially expressed genes revealed TGFß1 as a central signaling factor. With miRNA-Seq, miRNAs that are known to be important regulators of EMT were detected and new candidates were predicted. miRNA target prediction combined with pathway analysis allowed us to identify additional pathways: Jak-Stat signaling and Pancreatic cancer. We also identified clusters (based on genomic coordinates) and families (based on sequence similarity) of significantly differentially expressed miRNAs, of which some were regulated by TGFß. Additionally we identified 25 completely novel miRNAs with a stable hairpin structure. One of the mesenchymal specific novel miRNAs was predicted to target genes involved in cell division, growth factor activity, and cellular adhesion complexes.CONCLUSIONS: We present the transcriptome and miRNAome of EMT in MDCK cells. We also investigated gene signatures and the interplay between miRNA and mRNA expression levels. Thereby, we increase the knowledge on the transcriptional landscape of mRNAs and miRNAs during the process of EMT.

    AB - BACKGROUND: EMT is an important process in embryonic development, especially during gastrulation and organ formation. Furthermore it has been implicated in physiological processes like wound healing, and pathological conditions e.g. organ fibrosis and cancer. In late stage tumorigenesis, cells that underwent EMT are motile and may invade other parts of the body to form distant metastases. Madin-Darby Canine Kidney (MDCK) cells are widely used as a model to study epithelial polarity and EMT.OBSERVATIONS: We performed deep sequencing to build the transcriptome and miRNAome of epithelial and mesenchymal states in MDCK cells. With RNA-Seq, half of the genes known in the dog genome were detected, of which one third were differentially expressed during the process of EMT. Novel differentially regulated genes include interferon-stimulated genes and those involved in slit and netrin signaling. Gene set enrichment analysis of differentially expressed genes revealed TGFß1 as a central signaling factor. With miRNA-Seq, miRNAs that are known to be important regulators of EMT were detected and new candidates were predicted. miRNA target prediction combined with pathway analysis allowed us to identify additional pathways: Jak-Stat signaling and Pancreatic cancer. We also identified clusters (based on genomic coordinates) and families (based on sequence similarity) of significantly differentially expressed miRNAs, of which some were regulated by TGFß. Additionally we identified 25 completely novel miRNAs with a stable hairpin structure. One of the mesenchymal specific novel miRNAs was predicted to target genes involved in cell division, growth factor activity, and cellular adhesion complexes.CONCLUSIONS: We present the transcriptome and miRNAome of EMT in MDCK cells. We also investigated gene signatures and the interplay between miRNA and mRNA expression levels. Thereby, we increase the knowledge on the transcriptional landscape of mRNAs and miRNAs during the process of EMT.

    KW - MDCK Epithelial-mesenchymal transition

    KW - Ras

    KW - Next Generation Sequencing (NGS)

    KW - Transcriptome

    KW - miRNAome

    M3 - Conference contribution

    BT - Unknown Host Publication

    ER -

    Shukla P, Vogl C, Wallner B, Rigler D, Mueller M, Macho-Maschler S. Exploring transcriptome and miRNAome of Epithelial to Mesenchymal Transition (EMT) in MDCK cells by deep sequencing. In Unknown Host Publication. 2015