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Than BLN, Linnekamp JF, Starr TK, Largaespada DA, Rod A, Zhang Y, Bruner V, Abrahante J, Schumann A, Luczak T, Walter J, Niemczyk A, O'Sullivan MG, Medema JP, Fijneman RJA, Meijer GA, Van den Broek E, Hodges CA, Scott PM, Vermeulen L, Cormier RT. CFTR is a tumor suppressor gene in murine and human intestinal cancer. Oncogene 2016; 35:4179-87. [PMID: 26751771 DOI: 10.1038/onc.2015.483] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 10/22/2015] [Accepted: 11/14/2015] [Indexed: 12/27/2022]
Abstract
CFTR, the cystic fibrosis (CF) gene, encodes for the CFTR protein that plays an essential role in anion regulation and tissue homeostasis of various epithelia. In the gastrointestinal (GI) tract CFTR promotes chloride and bicarbonate secretion, playing an essential role in ion and acid-base homeostasis. Cftr has been identified as a candidate driver gene for colorectal cancer (CRC) in several Sleeping Beauty DNA transposon-based forward genetic screens in mice. Further, recent epidemiological and clinical studies indicate that CF patients are at high risk for developing tumors in the colon. To investigate the effects of CFTR dysregulation on GI cancer, we generated Apc(Min) mice that carried an intestinal-specific knockout of Cftr. Our results indicate that Cftr is a tumor suppressor gene in the intestinal tract as Cftr mutant mice developed significantly more tumors in the colon and the entire small intestine. In Apc(+/+) mice aged to ~1 year, Cftr deficiency alone caused the development of intestinal tumors in >60% of mice. Colon organoid formation was significantly increased in organoids created from Cftr mutant mice compared with wild-type controls, suggesting a potential role of Cftr in regulating the intestinal stem cell compartment. Microarray data from the Cftr-deficient colon and the small intestine identified dysregulated genes that belong to groups of immune response, ion channel, intestinal stem cell and other growth signaling regulators. These associated clusters of genes were confirmed by pathway analysis using Ingenuity Pathway Analysis and gene set enrichment analysis (GSEA). We also conducted RNA Seq analysis of tumors from Apc(+/+) Cftr knockout mice and identified sets of genes dysregulated in tumors including altered Wnt β-catenin target genes. Finally we analyzed expression of CFTR in early stage human CRC patients stratified by risk of recurrence and found that loss of expression of CFTR was significantly associated with poor disease-free survival.
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Affiliation(s)
- B L N Than
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - J F Linnekamp
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - T K Starr
- Department of Genetics, Cell Biology and Development, Center for Genome Engineering, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA.,Department of Obstetrics, Gynecology and Women's Health, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA
| | - D A Largaespada
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - A Rod
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - Y Zhang
- University of Minnesota Supercomputing Institute, Minneapolis, MN, USA
| | - V Bruner
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - J Abrahante
- Department of Genetics, Cell Biology and Development, Center for Genome Engineering, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA
| | - A Schumann
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - T Luczak
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - J Walter
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - A Niemczyk
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - M G O'Sullivan
- College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA
| | - J P Medema
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - R J A Fijneman
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - G A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - E Van den Broek
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - C A Hodges
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - P M Scott
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - L Vermeulen
- Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, the Netherlands
| | - R T Cormier
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
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Ouadid-Ahidouch H, Rodat-Despoix L, Matifat F, Morin G, Ahidouch A. DNA methylation of channel-related genes in cancers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2621-8. [PMID: 25703813 DOI: 10.1016/j.bbamem.2015.02.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 02/04/2015] [Accepted: 02/12/2015] [Indexed: 12/31/2022]
Abstract
DNA methylation at CpG sites is an epigenetic mechanism that regulates cellular gene expression. In cancer cells, aberrant methylation is correlated with the abnormalities in expression of genes that are known to be involved in the particular characteristics of cancer cells such as proliferation, apoptosis, migration or invasion. During the past 30 years, accumulating data have definitely convinced the scientific community that ion channels are involved in cancerogenesis and cancer properties. As they are situated at the cell surface, they might be prime targets in the development of new therapeutic strategies besides their potential use as prognostic factors. Despite the progress in our understanding of the remodeling of ion channels in cancer cells, the molecular mechanisms underlying their over- or down-expression remained enigmatic. In this review, we aimed to summarize the available data on gene promoter methylation of ion channels and to investigate their clinical significance as novel biomarkers in cancer. This article is part of a Special Issue entitled: Membrane channels and transporters in cancers.
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Affiliation(s)
- Halima Ouadid-Ahidouch
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France.
| | - Lise Rodat-Despoix
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France
| | - Fabrice Matifat
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France
| | - Gilles Morin
- EA 4666 and Department of Molecular and Clinical Genetics, Amiens University Hospital, University of Picardie Jules Verne, Amiens, France
| | - Ahmed Ahidouch
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France; Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir Morocco
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3
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The CpG island in the murine foxl2 proximal promoter is differentially methylated in primary and immortalized cells. PLoS One 2013; 8:e76642. [PMID: 24098544 PMCID: PMC3788739 DOI: 10.1371/journal.pone.0076642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 08/30/2013] [Indexed: 11/23/2022] Open
Abstract
Forkhead box L2 (Foxl2), a member of the forkhead transcription factor family, plays important roles in pituitary follicle-stimulating hormone synthesis and in ovarian maintenance and function. Mutations in the human FOXL2 gene cause eyelid malformations and premature ovarian failure. FOXL2/Foxl2 is expressed in pituitary gonadotrope and thyrotrope cells, the perioptic mesenchyme of the developing eyelid, and ovarian granulosa cells. The mechanisms governing this cell-restricted expression have not been described. We mapped the Foxl2 transcriptional start site in immortalized murine gonadotrope-like cells, LβT2, by 5’ rapid amplification of cDNA ends and then PCR amplified approximately 1 kb of 5’ flanking sequence from murine genomic DNA. When ligated into a reporter plasmid, the proximal promoter conferred luciferase activity in both homologous (LβT2) and, unexpectedly, heterologous (NIH3T3) cells. In silico analyses identified a CpG island in the proximal promoter and 5’ untranslated region, suggesting that Foxl2 transcription might be regulated epigenetically. Indeed, pyrosequencing and quantitative analysis of DNA methylation using real-time PCR revealed Foxl2 proximal promoter hypomethylation in homologous compared to some, though not all, heterologous cell lines. The promoter was also hypomethylated in purified murine gonadotropes. In vitro promoter methylation completely silenced reporter activity in heterologous and homologous cells. Collectively, the data suggest that differential proximal promoter DNA methylation may contribute to cell-specific Foxl2 expression in some cellular contexts. However, gonadotrope-specific expression of the gene cannot be explained by promoter hypomethylation alone.
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von Kanel T, Gerber D, Schaller A, Baumer A, Wey E, Jackson CB, Gisler FM, Heinimann K, Gallati S. Quantitative 1-Step DNA Methylation Analysis with Native Genomic DNA as Template. Clin Chem 2010; 56:1098-106. [PMID: 20472822 DOI: 10.1373/clinchem.2009.142828] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: DNA methylation analysis currently requires complex multistep procedures based on bisulfite conversion of unmethylated cytosines or on methylation-sensitive endonucleases. To facilitate DNA methylation analysis, we have developed a quantitative 1-step assay for DNA methylation analysis.
Methods: The assay is based on combining methylation-sensitive FastDigest® endonuclease digestion and quantitative real-time PCR (qPCR) in a single reaction. The first step consists of DNA digestion, followed by endonuclease inactivation and qPCR. The degree of DNA methylation is evaluated by comparing the quantification cycles of a reaction containing a methylation-sensitive endonuclease with the reaction of a sham mixture containing no endonuclease. Control reactions interrogating an unmethylated locus allow the detection and correction of artifacts caused by endonuclease inhibitors, while simultaneously permitting copy number assessment of the locus of interest.
Results: With our novel approach, we correctly diagnosed the imprinting disorders Prader–Willi syndrome and Angelman syndrome in 35 individuals by measuring methylation levels and copy numbers for the SNRPN (small nuclear ribonucleoprotein polypeptide N) promoter. We also demonstrated that the proposed correction model significantly (P < 0.05) increases the assay’s accuracy with low-quality DNA, allowing analysis of DNA samples with decreased digestibility, as is often the case in retrospective studies.
Conclusions: Our novel DNA methylation assay reduces both the hands-on time and errors caused by handling and pipetting and allows methylation analyses to be completed within 90 min after DNA extraction. Combined with its precision and reliability, these features make the assay well suited for diagnostic procedures as well as high-throughput analyses.
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Affiliation(s)
- Thomas von Kanel
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Dominik Gerber
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - André Schaller
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Alessandra Baumer
- Institute for Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Eva Wey
- Institute for Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Christopher B Jackson
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Franziska M Gisler
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Karl Heinimann
- Division of Medical Genetics, University Children’s Hospital and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sabina Gallati
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
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Lewandowska MA, Costa FF, Bischof JM, Williams SH, Soares MB, Harris A. Multiple mechanisms influence regulation of the cystic fibrosis transmembrane conductance regulator gene promoter. Am J Respir Cell Mol Biol 2009; 43:334-41. [PMID: 19855085 DOI: 10.1165/rcmb.2009-0149oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene is driven by a promoter that cannot alone account for the temporal and tissue-specific regulation of the gene. This has led to the search for additional regulatory elements that cooperate with the basal promoter to achieve coordinated expression. We previously identified two alternative upstream exons of the gene that were mutually exclusive of the first exon, and one of which showed temporal regulation in the human and sheep lung. We now demonstrate that this alternative splice product generates a stable protein, which initiates translation at an ATG in exon 4, and thus lacks the N terminus of CFTR. The other splice variant inhibits translation of the protein. In a search for the promoter used by the upstream exons, we identified a novel element that contributes to the activity of the basal CFTR promoter in airway epithelial cells, but does not function independently. Finally, we demonstrate that, in primary airway cells, skin fibroblasts, and both airway and intestinal cell lines, the CFTR promoter is unmethylated, irrespective of CFTR expression status. Thus, methylation is not the main cause of inactivation of CFTR transcription.
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Affiliation(s)
- Marzena A Lewandowska
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614, USA
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Ellsworth RE, Jamison DC, Touchman JW, Chissoe SL, Braden Maduro VV, Bouffard GG, Dietrich NL, Beckstrom-Sternberg SM, Iyer LM, Weintraub LA, Cotton M, Courtney L, Edwards J, Maupin R, Ozersky P, Rohlfing T, Wohldmann P, Miner T, Kemp K, Kramer J, Korf I, Pepin K, Antonacci-Fulton L, Fulton RS, Minx P, Hillier LW, Wilson RK, Waterston RH, Miller W, Green ED. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Proc Natl Acad Sci U S A 2000; 97:1172-7. [PMID: 10655503 PMCID: PMC15558 DOI: 10.1073/pnas.97.3.1172] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous advances in elucidating the function of the encoded protein and the physiological basis of cystic fibrosis. However, numerous areas of cystic fibrosis biology require additional investigation, some of which would be facilitated by information about the long-range sequence context of the CFTR gene. For example, the latter might provide clues about the sequence elements responsible for the temporal and spatial regulation of CFTR expression. We thus sought to establish the sequence of the chromosomal segments encompassing the human CFTR and mouse Cftr genes, with the hope of identifying conserved regions of biologic interest by sequence comparison. Bacterial clone-based physical maps of the relevant human and mouse genomic regions were constructed, and minimally overlapping sets of clones were selected and sequenced, eventually yielding approximately 1.6 Mb and approximately 358 kb of contiguous human and mouse sequence, respectively. These efforts have produced the complete sequence of the approximately 189-kb and approximately 152-kb segments containing the human CFTR and mouse Cftr genes, respectively, as well as significant amounts of flanking DNA. Analyses of the resulting data provide insights about the organization of the CFTR/Cftr genes and potential sequence elements regulating their expression. Furthermore, the generated sequence reveals the precise architecture of genes residing near CFTR/Cftr, including one known gene (WNT2/Wnt2) and two previously unknown genes that immediately flank CFTR/Cftr.
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Affiliation(s)
- R E Ellsworth
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Dixméras I, Lapouméroulie C, Tallec LP, Bens M, Elion J, Vandewalle A, Denamur E. CFTR regions containing duodenum specific DNase I hypersensitive sites drive expression in intestinal crypt cells but not in fibroblasts. Biochem Biophys Res Commun 1998; 250:328-34. [PMID: 9753629 DOI: 10.1006/bbrc.1998.9292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have investigated CFTR specific intestinal expression by transfection assays in mouse cultured fibroblasts and transimmortalized intestinal crypt m-ICc12 cells using the beta-galactosidase gene linked to rat CFTR non-coding regions. Two constructs were studied, one encompassing a 5.3 kb region 5' to the gene where numerous duodenum-specific DNase I hypersensitive sites (DHSs) were previously mapped and the other including a 1.3 kb 3' region in which novel DHSs had been identified. In transient transfection assays, transgenes were expressed in m-ICc12 cells but not in fibroblasts. In m-ICc12 cells, the pattern of expression of the chromosomally integrated transgenes paralleled the endogenous expression of CFTR and beta-galactosidase activity was detected in cells containing villin and forming domes. Thus, a 6.6 kb region encompassing 5' and 3' non-coding parts of rat CFTR is able to drive specific expression of a reporter gene in cultured mouse intestinal cells having kept a crypt phenotype.
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Affiliation(s)
- I Dixméras
- Institut National de la Santé et de la Recherche Médicale (INSERM) unité 458, Hôpital Robert Debré, Paris, France
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Vuillaumier S, Dixmeras I, Messaï H, Lapouméroulie C, Lallemand D, Gekas J, Chehab FF, Perret C, Elion J, Denamur E. Cross-species characterization of the promoter region of the cystic fibrosis transmembrane conductance regulator gene reveals multiple levels of regulation. Biochem J 1997; 327 ( Pt 3):651-62. [PMID: 9581539 PMCID: PMC1218840 DOI: 10.1042/bj3270651] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene is highly conserved within vertebrate species. Its pattern of expression in vivo seems to be tightly regulated both developmentally and in a tissue-specific manner, but shows differences with species. To identify transcriptional regulatory elements in the CFTR promoter region, we have used a combined approach based both on the analysis of the chromatin structure in vivo in rat tissues and on evolutionary clues (i.e. phylogenetic footprinting). In CFTR-expressing tissues, 15 DNase I-hypersensitive sites were identified within a 36 kb region encompassing exon 1. Eleven of them are clustered in a 3.5 kb region that exhibits eleven phylogenetic footprints observed when comparing sequences from eight mammalian species representing four orders (Primates, Artiodactylia, Lagomorpha and Rodentia). Comparison of the two sets of data allows the identification of two types of regulatory elements. Some are conserved between species, such as a non-consensus cAMP response element (CRE) and a PMA-responsive element (TRE) located respectively at positions -0.1 and -1.3 kb relative to ATG. Some are species-specific elements such as a 300 bp purine.pyrimidine (Pu.Py) stretch that is present only in rodents. Analysis of protein/DNA interactions in vitro with rat tissue protein extracts on the conserved elements revealed that the TRE site binds a specific heterodimeric complex composed of Fra-2, Jun D and a protein immunologically related to Jun/CRE-binding protein in the duodenum, whereas the CRE-like site binds ATF-1 ubiquitously. Functional analysis in Caco-2 cells showed that the CRE-like site supports a high basal transcriptional activity but is not able by itself to induce a response to cAMP, whereas the TRE site acts as a weak transactivator stimulated by PMA. Lastly, we found that the rodent-specific Pu.Py stretch confers nuclease S1 hypersensitivity under conditions of acidic pH and supercoiling. This indicates a non-B DNA conformation and thus reinforces the biological significance of non-random Pu.Py strand asymmetry in the regulation of transcription. Thus the tight transcriptional regulation of CFTR expression involves the combination of multiple regulatory elements that act in the chromatin environment in vivo. Some of them are conserved throughout evolution, such as the CRE-like element, which is clearly involved in the basal level of transcription; others are species-specific.
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Affiliation(s)
- S Vuillaumier
- INSERM U 458, Hôpital Robert Debré, 48 boulevard Sérurier, 75019 Paris, France
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