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Kosela Paterczyk H, Paziewska A, Kulecka M, Karczmarski J, Dabrowska M, Kluska A, Balabas A, Piatkowska M, Mikula M, Rutkowski P, Ostrowski J. Serum miRNA abundances discriminate imatinib-naive patients with advanced gastrointestinal stromal tumors (GIST) from those in remission on Imatinib therapy. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx387.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Mikula M, Skrzypczak M, Goryca K, Paczkowska K, Ledwon JK, Statkiewicz M, Kulecka M, Grzelak M, Dabrowska M, Kuklinska U, Karczmarski J, Rumienczyk I, Jastrzebski K, Miaczynska M, Ginalski K, Bomsztyk K, Ostrowski J. Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy. Nucleic Acids Res 2016; 44:10150-10164. [PMID: 27587583 PMCID: PMC5137434 DOI: 10.1093/nar/gkw763] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 01/20/2023] Open
Abstract
Genome-wide mechanisms that coordinate expression of subsets of functionally related genes are largely unknown. Recent studies show that receptor tyrosine kinases and components of signal transduction cascades including the extracellular signal-regulated protein kinase (ERK), once thought to act predominantly in the vicinity of plasma membrane and in the cytoplasm, can be recruited to chromatin encompassing transcribed genes. Genome-wide distribution of these transducers and their relationship to transcribing RNA polymerase II (Pol2) could provide new insights about co-regulation of functionally related gene subsets. Chromatin immunoprecipitations (ChIP) followed by deep sequencing, ChIP-Seq, revealed that genome-wide binding of epidermal growth factor receptor, EGFR and ERK pathway components at EGF-responsive genes was highly correlated with characteristic mitogen-induced Pol2-profile. Endosomes play a role in intracellular trafficking of proteins including their nuclear import. Immunofluorescence revealed that EGF-activated EGFR, MEK1/2 and ERK1/2 co-localize on endosomes. Perturbation of endosome internalization process, through the depletion of AP2M1 protein, resulted in decreased number of the EGFR containing endosomes and inhibition of Pol2, EGFR/ERK recruitment to EGR1 gene. Thus, mitogen-induced co-recruitment of EGFR/ERK components to subsets of genes, a kinase module possibly pre-assembled on endosome to synchronize their nuclear import, could coordinate genome-wide transcriptional events to ensure effective cell proliferation.
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Affiliation(s)
- M Mikula
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - M Skrzypczak
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089, Poland
| | - K Goryca
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - K Paczkowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - J K Ledwon
- Medical Center for Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - M Statkiewicz
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - M Kulecka
- Medical Center for Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - M Grzelak
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089, Poland
| | - M Dabrowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - U Kuklinska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - J Karczmarski
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - I Rumienczyk
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland
| | - K Jastrzebski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - M Miaczynska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - K Ginalski
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089, Poland
| | - K Bomsztyk
- University of Washington, Department of Medicine, 850 Republican Street, Seattle, WA, USA
| | - J Ostrowski
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Genetics, Roentgena 5, 02-781 Warsaw, Poland.,Medical Center for Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Roentgena 5, 02-781 Warsaw, Poland
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Klimek-Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Brągoszewski P, Denisenko O, Bomsztyk K, Ostrowski J. Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa. Br J Cancer 2006; 94:586-92. [PMID: 16404425 PMCID: PMC2361188 DOI: 10.1038/sj.bjc.6602938] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The heterogeneous nuclear ribonucleoprotein K (hnRNP K) protein is an RNA-binding protein involved in many processes that compose gene expression. K protein is upregulated in the malignant processes and has been shown to modulate the expression of genes involved in mitogenic responses and tumorigenesis. To explore the possibility that there are alternative isoforms of K protein expressed in colon cancer, we amplified and sequenced K protein mRNA that was isolated from colorectal cancers as well as from normal tissues surrounding the tumours. Sequencing revealed a single G-to-A base substitution at position 274 that was found in tumours and surrounding mucosa, but not in individuals that had no colorectal tumour. This substitution most likely reflects an RNA editing event because it was not found in the corresponding genomic DNAs. Sequencing of RNA from normal colonic mucosa of patients with prior resection of colorectal cancer revealed only the wild-type K protein transcript, indicating that G274A isoform is tumour related. To our knowledge, this is the first example of an RNA editing event in cancer and its surrounding tissue, a finding that may offer a new diagnostic and treatment marker.
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Affiliation(s)
- K Klimek-Tomczak
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - M Mikula
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - A Dzwonek
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - A Paziewska
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - J Karczmarski
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - E Hennig
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - J M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland
| | - P Brągoszewski
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
| | - O Denisenko
- Department of Medicine, UW Medicine Lake Union, University of Washington, Seattle, WA 98109, USA
| | - K Bomsztyk
- Department of Medicine, UW Medicine Lake Union, University of Washington, Seattle, WA 98109, USA
| | - J Ostrowski
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland
- Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Roentgena 5, Warsaw 02-781, Poland. E-mail:
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