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DIP2C regulates expression of the tumor suppressor gene CDKN2A
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized candidate

breast and lung cancer gene. The gene contains a DMAP1 binding domain, pointing to

potential involvement in DNMT1-dependent methylation. To study the role of DIP2C in

tumor development, we engineered human DIP2C knockout cell systems by rAAV-mediated

gene targeting. Homo- and heterozygous RKO DIP2C knockout cells displayed enlarged cells

and growth retardation. This phenotype was most pronounced in DIP2C-/- knockouts, and

these cells also displayed a significant decrease in DIP2C mRNA levels. RNA sequencing

revealed 780 genes affected by the loss of DIP2C, including the cellular senescence marker

P16INK4a. Functional annotation of the regulated genes shows enrichment of genes involved

with cell death processes, cell structure and motility. Furthermore, KEGG pathway analysis

shows association of 19 genes with pathways in cancer. In conclusion, the phenotypic data

and expression changes induced by loss of DIP2C indicate that the gene function may be

important for several biological processes implicated in cancer, and that loss of gene function

may be a trigger of cellular senescence.

National Category
Medical Genetics
Identifiers
URN: urn:nbn:se:uu:diva-235565OAI: oai:DiVA.org:uu-235565DiVA: diva2:761234
Available from: 2014-11-05 Created: 2014-11-05 Last updated: 2018-01-11
In thesis
1. Understanding Cancer Mutations by Genome Editing
Open this publication in new window or tab >>Understanding Cancer Mutations by Genome Editing
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Mutational analyses of cancer genomes have identified novel candidate cancer genes with hitherto unknown function in cancer. To enable phenotyping of mutations in such genes, we have developed a scalable technology for gene knock-in and knock-out in human somatic cells based on recombination-mediated construct generation and a computational tool to design gene targeting constructs. Using this technology, we have generated somatic cell knock-outs of the putative cancer genes ZBED6 and DIP2C in human colorectal cancer cells. In ZBED6-/- cells complete loss of functional ZBED6 was validated and loss of ZBED6 induced the expression of IGF2. Whole transcriptome and ChIP-seq analyses revealed relative enrichment of ZBED6 binding sites at upregulated genes as compared to downregulated genes. The functional annotation of differentially expressed genes revealed enrichment of genes related to cell cycle and cell proliferation and the transcriptional modulator ZBED6 affected the cell growth and cell cycle of human colorectal cancer cells. In DIP2C-/-cells, transcriptome sequencing revealed 780 differentially expressed genes as compared to their parental cells including the tumour suppressor gene CDKN2A. The DIP2C regulated genes belonged to several cancer related processes such as angiogenesis, cell structure and motility. The DIP2C-/-cells were enlarged and grew slower than their parental cells. To be able to directly compare the phenotypes of mutant KRAS and BRAF in colorectal cancers, we have introduced a KRASG13D allele in RKO BRAFV600E/-/-/ cells. The expression of the mutant KRAS allele was confirmed and anchorage independent growth was restored in KRASG13D cells. The differentially expressed genes both in BRAF and KRAS mutant cells included ERBB, TGFB and histone modification pathways. Together, the isogenic model systems presented here can provide insights to known and novel cancer pathways and can be used for drug discovery.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. 37 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1054
Keyword
Genome editing, rAAV, ZBED6, DIP2C, KRAS, BRAF, colorectal cancer, tumor driver genes, cancer pathways
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-235680 (URN)978-91-554-9106-2 (ISBN)
Public defence
2014-12-19, Rudbeck Salen, Uppsala University, Rudbeck Laboratory SE-751 85, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2014-11-27 Created: 2014-11-07 Last updated: 2018-01-11

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