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Torres-Velarde JM, Allen KN, Salvador-Pascual A, Leija RG, Luong D, Moreno-Santillán DD, Ensminger DC, Vázquez-Medina JP. Peroxiredoxin 6 suppresses ferroptosis in lung endothelial cells. Free Radic Biol Med 2024; 218:82-93. [PMID: 38579937 PMCID: PMC11177496 DOI: 10.1016/j.freeradbiomed.2024.04.208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Peroxiredoxin 6 (Prdx6) repairs peroxidized membranes by reducing oxidized phospholipids, and by replacing oxidized sn-2 fatty acyl groups through hydrolysis/reacylation by its phospholipase A2 (aiPLA2) and lysophosphatidylcholine acyltransferase activities. Prdx6 is highly expressed in the lung, and intact lungs and cells null for Prdx6 or with single-point mutations that inactivate either Prdx6-peroxidase or aiPLA2 activity alone exhibit decreased viability, increased lipid peroxidation, and incomplete repair when exposed to paraquat, hyperoxia, or organic peroxides. Ferroptosis is form of cell death driven by the accumulation of phospholipid hydroperoxides. We studied the role of Prdx6 as a ferroptosis suppressor in the lung. We first compared the expression Prdx6 and glutathione peroxidase 4 (GPx4) and visualized Prdx6 and GPx4 within the lung. Lung Prdx6 mRNA levels were five times higher than GPx4 levels. Both Prdx6 and GPx4 localized to epithelial and endothelial cells. Prdx6 knockout or knockdown sensitized lung endothelial cells to erastin-induced ferroptosis. Cells with genetic inactivation of either aiPLA2 or Prdx6-peroxidase were more sensitive to ferroptosis than WT cells, but less sensitive than KO cells. We then conducted RNA-seq analyses in Prdx6-depleted cells to further explore how the loss of Prdx6 sensitizes lung endothelial cells to ferroptosis. Prdx6 KD upregulated transcriptional signatures associated with selenoamino acid metabolism and mitochondrial function. Accordingly, Prdx6 deficiency blunted mitochondrial function and increased GPx4 abundance whereas GPx4 KD had the opposite effect on Prdx6. Moreover, we detected Prdx6 and GPx4 interactions in intact cells, suggesting that both enzymes cooperate to suppress lipid peroxidation. Notably, Prdx6-depleted cells remained sensitive to erastin-induced ferroptosis despite the compensatory increase in GPx4. These results show that Prdx6 suppresses ferroptosis in lung endothelial cells and that both aiPLA2 and Prdx6-peroxidase contribute to this effect. These results also show that Prdx6 supports mitochondrial function and modulates several coordinated cytoprotective pathways in the pulmonary endothelium.
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Affiliation(s)
| | - Kaitlin N Allen
- Department of Integrative Biology, University of California, Berkeley, USA
| | | | - Roberto G Leija
- Department of Integrative Biology, University of California, Berkeley, USA
| | - Diamond Luong
- Department of Integrative Biology, University of California, Berkeley, USA
| | | | - David C Ensminger
- Department of Integrative Biology, University of California, Berkeley, USA
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2
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Perycz M, Dabrowski MJ, Jardanowska-Kotuniak M, Roura AJ, Gielniewski B, Stepniak K, Dramiński M, Ciechomska IA, Kaminska B, Wojtas B. Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors. Acta Neuropathol Commun 2024; 12:72. [PMID: 38711090 PMCID: PMC11071216 DOI: 10.1186/s40478-024-01779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The RE1-silencing transcription factor (REST) acts either as a repressor or activator of transcription depending on the genomic and cellular context. REST is a key player in brain cell differentiation by inducing chromatin modifications, including DNA methylation, in a proximity of its binding sites. Its dysfunction may contribute to oncogenesis. Mutations in IDH1/2 significantly change the epigenome contributing to blockade of cell differentiation and glioma development. We aimed at defining how REST modulates gene activation and repression in the context of the IDH mutation-related phenotype in gliomas. We studied the effects of REST knockdown, genome wide occurrence of REST binding sites, and DNA methylation of REST motifs in IDH wild type and IDH mutant gliomas. We found that REST target genes, REST binding patterns, and TF motif occurrence proximal to REST binding sites differed in IDH wild-type and mutant gliomas. Among differentially expressed REST targets were genes involved in glial cell differentiation and extracellular matrix organization, some of which were differentially methylated at promoters or gene bodies. REST knockdown differently impacted invasion of the parental or IDH1 mutant glioma cells. The canonical REST-repressed gene targets showed significant correlation with the GBM NPC-like cellular state. Interestingly, results of REST or KAISO silencing suggested the interplay between these TFs in regulation of REST-activated and repressed targets. The identified gene regulatory networks and putative REST cooperativity with other TFs, such as KAISO, show distinct REST target regulatory networks in IDH-WT and IDH-MUT gliomas, without concomitant DNA methylation changes. We conclude that REST could be an important therapeutic target in gliomas.
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Affiliation(s)
- Malgorzata Perycz
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Michal J Dabrowski
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Marta Jardanowska-Kotuniak
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
- Doctoral School of Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adria-Jaume Roura
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Stepniak
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Dramiński
- Computational Biology Group, Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland
| | - Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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3
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Ananthapadmanabhan V, Shows KH, Dickinson AJ, Litovchick L. Insights from the protein interaction Universe of the multifunctional "Goldilocks" kinase DYRK1A. Front Cell Dev Biol 2023; 11:1277537. [PMID: 37900285 PMCID: PMC10600473 DOI: 10.3389/fcell.2023.1277537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Human Dual specificity tyrosine (Y)-Regulated Kinase 1A (DYRK1A) is encoded by a dosage-dependent gene located in the Down syndrome critical region of human chromosome 21. The known substrates of DYRK1A include proteins involved in transcription, cell cycle control, DNA repair and other processes. However, the function and regulation of this kinase is not fully understood, and the current knowledge does not fully explain the dosage-dependent function of this kinase. Several recent proteomic studies identified DYRK1A interacting proteins in several human cell lines. Interestingly, several of known protein substrates of DYRK1A were undetectable in these studies, likely due to a transient nature of the kinase-substrate interaction. It is possible that the stronger-binding DYRK1A interacting proteins, many of which are poorly characterized, are involved in regulatory functions by recruiting DYRK1A to the specific subcellular compartments or distinct signaling pathways. Better understanding of these DYRK1A-interacting proteins could help to decode the cellular processes regulated by this important protein kinase during embryonic development and in the adult organism. Here, we review the current knowledge of the biochemical and functional characterization of the DYRK1A protein-protein interaction network and discuss its involvement in human disease.
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Affiliation(s)
- Varsha Ananthapadmanabhan
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States
| | - Kathryn H. Shows
- Department of Biology, Virginia State University, Petersburg, VA, United States
| | - Amanda J. Dickinson
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - Larisa Litovchick
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States
- Massey Cancer Center, Richmond, VA, United States
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4
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Messingschlager M, Bartel-Steinbach M, Mackowiak SD, Denkena J, Bieg M, Klös M, Seegebarth A, Straff W, Süring K, Ishaque N, Eils R, Lehmann I, Lermen D, Trump S. Genome-wide DNA methylation sequencing identifies epigenetic perturbations in the upper airways under long-term exposure to moderate levels of ambient air pollution. ENVIRONMENTAL RESEARCH 2023; 233:116413. [PMID: 37343754 DOI: 10.1016/j.envres.2023.116413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/30/2023] [Accepted: 06/11/2023] [Indexed: 06/23/2023]
Abstract
While the link between exposure to high levels of ambient particulate matter (PM) and increased incidences of respiratory and cardiovascular diseases is widely recognized, recent epidemiological studies have shown that low PM concentrations are equally associated with adverse health effects. As DNA methylation is one of the main mechanisms by which cells regulate and stabilize gene expression, changes in the methylome could constitute early indicators of dysregulated signaling pathways. So far, little is known about PM-associated DNA methylation changes in the upper airways, the first point of contact between airborne pollutants and the human body. Here, we focused on cells of the upper respiratory tract and assessed their genome-wide DNA methylation pattern to explore exposure-associated early regulatory changes. Using a mobile epidemiological laboratory, nasal lavage samples were collected from a cohort of 60 adults that lived in districts with records of low (Simmerath) or moderate (Stuttgart) PM10 levels in Germany. PM10 concentrations were verified by particle measurements on the days of the sample collection and genome-wide DNA methylation was determined by enzymatic methyl sequencing at single-base resolution. We identified 231 differentially methylated regions (DMRs) between moderately and lowly PM10 exposed individuals. A high proportion of DMRs overlapped with regulatory elements, and DMR target genes were involved in pathways regulating cellular redox homeostasis and immune response. In addition, we found distinct changes in DNA methylation of the HOXA gene cluster whose methylation levels have previously been linked to air pollution exposure but also to carcinogenesis in several instances. The findings of this study suggest that regulatory changes in upper airway cells occur at PM10 levels below current European thresholds, some of which may be involved in the development of air pollution-related diseases.
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Affiliation(s)
- Marey Messingschlager
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Molecular Epidemiology Unit, Charitéplatz 1, 10117, Berlin, Germany; Freie Universität Berlin, Institute for Biology, Königin-Luise-Strasse 12-16, 14195, Berlin, Germany
| | - Martina Bartel-Steinbach
- Fraunhofer Institute for Biomedical Engineering IBMT, Josef-von-Fraunhofer-Weg 1, 66280, Sulzbach, Germany
| | - Sebastian D Mackowiak
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Johanna Denkena
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Matthias Bieg
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Matthias Klös
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Molecular Epidemiology Unit, Charitéplatz 1, 10117, Berlin, Germany
| | - Anke Seegebarth
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Molecular Epidemiology Unit, Charitéplatz 1, 10117, Berlin, Germany
| | - Wolfgang Straff
- Environmental Medicine and Health Effects Assessment, German Environment Agency, Corrensplatz 1, 14195, Berlin, Germany
| | - Katrin Süring
- Environmental Medicine and Health Effects Assessment, German Environment Agency, Corrensplatz 1, 14195, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Roland Eils
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Charitéplatz 1, 10117, Berlin, Germany; German Center for Lung Research (DZL), Germany; Health Data Science Unit, Heidelberg University Hospital and BioQuant, University of Heidelberg, Germany; Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 14, 14195, Berlin, Germany
| | - Irina Lehmann
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Molecular Epidemiology Unit, Charitéplatz 1, 10117, Berlin, Germany; German Center for Lung Research (DZL), Germany.
| | - Dominik Lermen
- Fraunhofer Institute for Biomedical Engineering IBMT, Josef-von-Fraunhofer-Weg 1, 66280, Sulzbach, Germany
| | - Saskia Trump
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Digital Health, Molecular Epidemiology Unit, Charitéplatz 1, 10117, Berlin, Germany
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5
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Thapa B, Adhikari NP, Tiwari PB, Chapagain PP. A 5'-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA. J Chem Inf Model 2022; 63:2095-2103. [PMID: 36563044 DOI: 10.1021/acs.jcim.2c01294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methyl CpG binding proteins (MBPs) are transcription factors that recognize the methylated CpG sites in DNA and mediate the DNA methylation signal into various downstream cellular processes. The C2H2 zinc finger (ZF) protein, Kaiso, also an MBP, preferentially binds to two symmetrically methylated CpG sites in DNA sequences via C-terminal C2H2 ZF domains and mediates the transcription regulation process. Investigation of the molecular mechanism of the recognition of methylated DNA (meDNA) by Kaiso is important to understand how this protein reads and translates this methylation signal into downstream transcription outcomes. Despite previous studies in Kaiso-meDNA interactions, detailed structural investigations on the sequence-specific interaction of Kaiso with the meDNA sequence are still lacking. In this work, we used molecular modeling and molecular dynamics (MD) simulation-based computational approaches to investigate the recognition of various methylated DNA sequences by Kaiso. Our MD simulation results show that the Kaiso-meDNA interaction is sequence specific. The recognition of meDNA by Kaiso is enhanced in the MeECad sequence compared to the MeCG2 sequence. Compared to the 5'-flanking T/A pair in MeCG2, both MeCG2_mutCG and MeECad sequences show that a C/G base pair allows GLU535 of Kaiso to preferably recognize and bind the core mCpG site. The core mCGmCG site is crucial for the recognition process and formation of a stable complex. Our results reveal that the 5'-flanking nucleotides are also important for the enhanced binding and recognition of methylated sites.
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Affiliation(s)
- Bidhya Thapa
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.,Padma Kanya Multiple Campus, Tribhuvan University, Bagbazar, Kathmandu 44613, Nepal
| | - Narayan P Adhikari
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal
| | - Purushottam B Tiwari
- Department of Oncology, Georgetown University, Washington, DC 20057, United States
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida 33199, United States.,Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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6
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The remodeling of Z-DNA in the mammalian germ line. Biochem Soc Trans 2022; 50:1875-1884. [PMID: 36454621 PMCID: PMC9788570 DOI: 10.1042/bst20221015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022]
Abstract
We recently discovered a novel biological process, the scheduled remodeling of Z-DNA structures in the developing fetal mouse male germ cells [Nat. Cell Biol. 24, 1141-1153]. This process affects purine/pyrimidine dinucleotide repeat (PPR) rich sequences, which can form stable left-handed Z-DNA structures. The protein that carries out this function is identified as ZBTB43, member of a large family of ZBTB proteins. Z-DNA remodeling by ZBTB43 not only coincides with global remodeling of DNA methylation and chromatin events in the male germ line, but it also is a prerequisite for de novo DNA methylation. When ZBTB43 changes DNA structure from the left-handed zigzag shaped Z-DNA to the regular smooth right-handed B-DNA, it also generates a suitable substrate for the de novo DNA methyltransferase, DNMT3A. By instructing de novo DNA methylation at PPRs in prospermatogonia, ZBTB43 safeguards epigenomic integrity of the male gamete. PPRs are fragile sequences, sites of large deletions and rearrangements in mammalian cells, and this fragility is thought to be due to Z-DNA structure formation rather than the sequence itself. This idea is now supported by the in vivo finding that DNA double strand breaks accumulate in mutant prospermatogonia which lack ZBTB43-dependent Z-DNA remodeling. If unrepaired, double stranded DNA breaks can lead to germ line mutations. Therefore, by preventing such breaks ZBTB43 is critical for guarding genome stability between generations. Here, we discuss the significance and implications of these findings in more detail.
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7
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Marchal C, Defossez PA, Miotto B. Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38. Epigenetics 2022; 17:2122-2143. [PMID: 36000449 DOI: 10.1080/15592294.2022.2111135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation on CpGs regulates transcription in mammals, both by decreasing the binding of methylation-repelled factors and by increasing the binding of methylation-attracted factors. Among the latter, zinc finger proteins have the potential to bind methylated CpGs in a sequence-specific context. The protein ZBTB38 is unique in that it has two independent sets of zinc fingers, which recognize two different methylated consensus sequences in vitro. Here, we identify the binding sites of ZBTB38 in a human cell line, and show that they contain the two methylated consensus sequences identified in vitro. In addition, we show that the distribution of ZBTB38 sites is highly unusual: while 10% of the ZBTB38 sites are also bound by CTCF, the other 90% of sites reside in closed chromatin and are not bound by any of the other factors mapped in our model cell line. Finally, a third of ZBTB38 sites are found upstream of long and active CpG islands. Our work therefore validates ZBTB38 as a methyl-DNA binder in vivo and identifies its unique distribution in the genome.
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Affiliation(s)
- Claire Marchal
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | | | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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8
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Tian W, Yuan H, Qin S, Liu W, Zhang B, Gu L, Zhou J, Deng D. Kaiso phosphorylation at threonine 606 leads to its accumulation in the cytoplasm, reducing its transcriptional repression of the tumor suppressor
CDH1
. Mol Oncol 2022; 16:3192-3209. [PMID: 35851744 PMCID: PMC9441001 DOI: 10.1002/1878-0261.13292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/09/2022] [Accepted: 07/18/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Wei Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Hongfan Yuan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Sisi Qin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Wensu Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Cancer Etiology Peking University Cancer Hospital and Institute China
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9
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Cao X, Cheng J, Huang Y, Lan X, Lei C, Chen H. Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq. Front Vet Sci 2022; 8:782409. [PMID: 34977215 PMCID: PMC8715921 DOI: 10.3389/fvets.2021.782409] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Annotating regulatory elements could benefit the interpretation of the molecular mechanism of genome-wide association study (GWAS) hits. In this work, we performed transposase-accessible chromatin with sequencing (ATAC-seq) to annotate the cattle muscle genome's functional elements. A total of 10,023 and 11,360 peaks were revealed in muscle genomes of adult and embryo cattle, respectively. The two peak sets produced 8,850 differentially accessible regions (DARs), including 2,515 promoters and 4,319 putative enhancers. These functional elements were associated with the cell cycle, muscle development, and lipid metabolism. A total of 15 putative enhancers were selected for a dual-luciferase reporter assay, and 12 of them showed enhancer activity in cattle myoblasts. Interestingly, the GeneHancer database has annotated the interactions of eight active enhancers with gene promoters, such as embryo-specific peak1053 (log2FC = 1.81, embryo/adult, E/A) with ligand-dependent nuclear receptor corepressor-like protein (LCORL) and embryo-specific peak4218 (log2FC = 1.81) with FERM domain-containing 8 (FRMD8). A total of 295 GWAS loci from the animal QTL database were mapped to 183 putative enhancers, including rs109554838 (associated with cattle body weight and average daily gain) to peak1053 and rs110294629 (associated with beef shear force and tenderness score) to peak4218. Notably, peak4218 has been found to be involved in mouse embryo development. Deleting peak4218 clearly reduced luciferase activity (P = 3.30E-04). Our comparative enhancer map is expected to benefit the area of beef cattle breeding.
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Affiliation(s)
- Xiukai Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Jie Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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10
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Cao M, Wang L, Xu D, Bi X, Guo S, Xu Z, Chen L, Zheng D, Li P, Xu J, Zheng S, Wang H, Wang B, Lu J, Li K. The synergistic interaction landscape of chromatin regulators reveals their epigenetic regulation mechanisms across five cancer cell lines. Comput Struct Biotechnol J 2022; 20:5028-5039. [PMID: 36187922 PMCID: PMC9483781 DOI: 10.1016/j.csbj.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/28/2022] [Accepted: 09/06/2022] [Indexed: 11/03/2022] Open
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11
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Singhal SK, Byun JS, Park S, Yan T, Yancey R, Caban A, Hernandez SG, Hewitt SM, Boisvert H, Hennek S, Bobrow M, Ahmed MSU, White J, Yates C, Aukerman A, Vanguri R, Bareja R, Lenci R, Farré PL, De Siervi A, Nápoles AM, Vohra N, Gardner K. Kaiso (ZBTB33) subcellular partitioning functionally links LC3A/B, the tumor microenvironment, and breast cancer survival. Commun Biol 2021; 4:150. [PMID: 33526872 PMCID: PMC7851134 DOI: 10.1038/s42003-021-01651-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 12/29/2020] [Indexed: 12/30/2022] Open
Abstract
The use of digital pathology for the histomorphologic profiling of pathological specimens is expanding the precision and specificity of quantitative tissue analysis at an unprecedented scale; thus, enabling the discovery of new and functionally relevant histological features of both predictive and prognostic significance. In this study, we apply quantitative automated image processing and computational methods to profile the subcellular distribution of the multi-functional transcriptional regulator, Kaiso (ZBTB33), in the tumors of a large racially diverse breast cancer cohort from a designated health disparities region in the United States. Multiplex multivariate analysis of the association of Kaiso’s subcellular distribution with other breast cancer biomarkers reveals novel functional and predictive linkages between Kaiso and the autophagy-related proteins, LC3A/B, that are associated with features of the tumor immune microenvironment, survival, and race. These findings identify effective modalities of Kaiso biomarker assessment and uncover unanticipated insights into Kaiso’s role in breast cancer progression. Through automated image analysis, Singhal et al quantify nuclear versus cytoplasmic distribution of the Kaiso transcription factor in breast cancer patient tissue. They find that Kaiso distribution correlates with breast cancer subtype and overall survival, and discover a link between cytoplasmic Kaiso and autophagy marker LC3.
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Affiliation(s)
- Sandeep K Singhal
- Department of Pathology, School of Medicine and Health Sciences, Department of Computer Science, School of Electrical Engineering and Computer Science, University of North Dakota, Grand Forks, ND, USA
| | - Jung S Byun
- Division of Intramural Research, National Institutes of Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Samson Park
- Division of Intramural Research, National Institutes of Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Tingfen Yan
- Division of Intramural Research, National Institutes of Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA.,National Institutes of Genome Research, National Institutes of Health, Bethesda, MD, USA
| | - Ryan Yancey
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, NY, USA
| | - Ambar Caban
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, NY, USA
| | - Sara Gil Hernandez
- Division of Intramural Research, National Institutes of Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Centers for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | - Md Shakir Uddin Ahmed
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Al, USA
| | - Jason White
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Al, USA
| | - Clayton Yates
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, Al, USA
| | - Andrew Aukerman
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, NY, USA
| | - Rami Vanguri
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, NY, USA
| | - Rohan Bareja
- Department Computer Science Department, Columbia University, New York, NY, USA
| | - Romina Lenci
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, NY, USA
| | - Paula Lucia Farré
- Laboratorio de Oncologıa Molecular y Nuevos Blancos Terapeuticos, Instituto de Biologıa y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Adriana De Siervi
- Laboratorio de Oncologıa Molecular y Nuevos Blancos Terapeuticos, Instituto de Biologıa y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Anna María Nápoles
- Division of Intramural Research, National Institutes of Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Nasreen Vohra
- Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Kevin Gardner
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, NY, USA.
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12
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Sensitivity of transcription factors to DNA methylation. Essays Biochem 2020; 63:727-741. [PMID: 31755929 PMCID: PMC6923324 DOI: 10.1042/ebc20190033] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022]
Abstract
Dynamic binding of transcription factors (TFs) to regulatory elements controls transcriptional states throughout organism development. Epigenetics modifications, such as DNA methylation mostly within cytosine-guanine dinucleotides (CpGs), have the potential to modulate TF binding to DNA. Although DNA methylation has long been thought to repress TF binding, a more recent model proposes that TF binding can also inhibit DNA methylation. Here, we review the possible scenarios by which DNA methylation and TF binding affect each other. Further in vivo experiments will be required to generalize these models.
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13
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Hidalgo-Sastre A, Desztics J, Dantes Z, Schulte K, Ensarioglu HK, Bassey-Archibong B, Öllinger R, Engleiter T, Rayner L, Einwächter H, Daniel JM, Altaee ASA, Steiger K, Lesina M, Rad R, Reichert M, von Figura G, Siveke JT, Schmid RM, Lubeseder-Martellato C. Loss of Wasl improves pancreatic cancer outcome. JCI Insight 2020; 5:127275. [PMID: 32434991 DOI: 10.1172/jci.insight.127275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/22/2020] [Indexed: 12/20/2022] Open
Abstract
Several studies have suggested an oncogenic role for the neural Wiskott-Aldrich syndrome protein (N-WASP, encoded by the Wasl gene), but thus far, little is known about its function in pancreatic ductal adenocarcinoma (PDAC). In this study, we performed in silico analysis of WASL expression in PDAC patients and found a correlation between low WASL expression and prolonged survival. To clarify the role of Wasl in pancreatic carcinogenesis, we used 2 oncogenic Kras-based PDAC mouse models with pancreas-specific Wasl deletion. In line with human data, both mouse models had an increased survival benefit due to either impaired tumor development in the presence of the tumor suppressor Trp53 or the delayed tumor progression and senescent phenotype upon genetic ablation of Trp53. Mechanistically, loss of Wasl resulted in cell-autonomous senescence through displacement of the N-WASP binding partners WASP-interacting protein (WIP) and p120ctn; vesicular accumulation of GSK3β, as well as YAP1 and phosphorylated β-catenin, which are components of the destruction complex; and upregulation of Cdkn1a(p21), a master regulator of senescence. Our findings, thus, indicate that Wasl functions in an oncogenic manner in PDAC by promoting the deregulation of the p120-catenin/β-catenin/p21 pathway. Therefore, strategies to reduce N-WASP activity might improve the survival outcomes of PDAC patients.
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Affiliation(s)
- Ana Hidalgo-Sastre
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany
| | - Judit Desztics
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany
| | - Zahra Dantes
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany
| | - Katharina Schulte
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany
| | - Hilal Kabadayi Ensarioglu
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany.,Department of Histology and Embryology, Manisa Celal Bayar University, Turkey
| | | | - Rupert Öllinger
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany.,Institute of Molecular Oncology and Functional Genomics and
| | - Thomas Engleiter
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany.,Institute of Molecular Oncology and Functional Genomics and
| | - Lyndsay Rayner
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Henrik Einwächter
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany
| | - Juliet M Daniel
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | | | - Katia Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Marina Lesina
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany
| | - Roland Rad
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany.,Institute of Molecular Oncology and Functional Genomics and
| | - Maximilian Reichert
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany
| | - Guido von Figura
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany
| | - Jens T Siveke
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) partner site Essen, Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland M Schmid
- Klinik und Poliklinik für Innere Medizin II, Technical University of Munich, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK) partner site Essen, Essen, Germany
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14
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Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ. Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. J Mol Biol 2019:S0022-2836(19)30617-5. [PMID: 31689433 DOI: 10.1016/j.jmb.2019.10.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 01/09/2023]
Abstract
Epigenetic DNA modification impacts gene expression, but the underlying molecular mechanisms are only partly understood. Adding a methyl group to a cytosine base locally modifies the structural features of DNA in multiple ways, which may change the interaction with DNA-binding transcription factors (TFs) and trigger a cascade of downstream molecular events. Cells can be probed using various functional genomics assays, but it is difficult to disentangle the confounded effects of DNA modification on TF binding, chromatin accessibility, intranuclear variation in local TF concentration, and rate of transcription. Here we discuss how high-throughput in vitro profiling of protein-DNA interactions has enabled comprehensive characterization and quantification of the methylation sensitivity of TFs. Despite the limited structural data for DNA containing methylated cytosine, automated analysis of structural information in the Protein Data Bank (PDB) shows how 5-methylcytosine (5mC) can be recognized in various ways by amino acid side chains. We discuss how a context-dependent effect of methylation on DNA groove geometry can affect DNA binding by homeodomain proteins and how principled modeling of ChIP-seq data can overcome the confounding that makes the interpretation of in vivo data challenging. The emerging picture is that epigenetic modifications affect TF binding in a highly context-specific manner, with a direction and effect size that depend critically on their position within the TF binding site and the amino acid sequence of the TF. With this improved mechanistic knowledge, we have come closer to understanding how cells use DNA modification to acquire, retain, and change their identity.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Remo Rohs
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA; Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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15
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Janiszewski A, Talon I, Chappell J, Collombet S, Song J, De Geest N, To SK, Bervoets G, Marin-Bejar O, Provenzano C, Vanheer L, Marine JC, Rambow F, Pasque V. Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming. Genome Res 2019; 29:1659-1672. [PMID: 31515287 PMCID: PMC6771397 DOI: 10.1101/gr.249706.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022]
Abstract
Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis, and the derivation of induced pluripotent stem cells (iPSCs). X-Chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. Although XCI has long been studied, providing important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. Here, we use allele-specific transcriptomics to study XCR during mouse iPSC reprogramming in order to elucidate the timing and mechanisms of chromosome-wide reversal of gene silencing. We show that XCR is hierarchical, with subsets of genes reactivating early, late, and very late during reprogramming. Early genes are activated before the onset of late pluripotency genes activation. Early genes are located genomically closer to genes that escape XCI, unlike genes reactivating late. Early genes also show increased pluripotency transcription factor (TF) binding. We also reveal that histone deacetylases (HDACs) restrict XCR in reprogramming intermediates and that the severe hypoacetylation state of the inactive X Chromosome (Xi) persists until late reprogramming stages. Altogether, these results reveal the timing of transcriptional activation of monoallelically repressed genes during iPSC reprogramming, and suggest that allelic activation involves the combined action of chromatin topology, pluripotency TFs, and chromatin regulators. These findings are important for our understanding of gene silencing, maintenance of cell identity, reprogramming, and disease.
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Affiliation(s)
- Adrian Janiszewski
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Irene Talon
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Joel Chappell
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Samuel Collombet
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Juan Song
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Natalie De Geest
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - San Kit To
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Oskar Marin-Bejar
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Caterina Provenzano
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Lotte Vanheer
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium.,Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, B-3000 Leuven, Belgium
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16
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Movva R, Greenside P, Marinov GK, Nair S, Shrikumar A, Kundaje A. Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays. PLoS One 2019; 14:e0218073. [PMID: 31206543 PMCID: PMC6576758 DOI: 10.1371/journal.pone.0218073] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 05/24/2019] [Indexed: 11/19/2022] Open
Abstract
The relationship between noncoding DNA sequence and gene expression is not well-understood. Massively parallel reporter assays (MPRAs), which quantify the regulatory activity of large libraries of DNA sequences in parallel, are a powerful approach to characterize this relationship. We present MPRA-DragoNN, a convolutional neural network (CNN)-based framework to predict and interpret the regulatory activity of DNA sequences as measured by MPRAs. While our method is generally applicable to a variety of MPRA designs, here we trained our model on the Sharpr-MPRA dataset that measures the activity of ∼500,000 constructs tiling 15,720 regulatory regions in human K562 and HepG2 cell lines. MPRA-DragoNN predictions were moderately correlated (Spearman ρ = 0.28) with measured activity and were within range of replicate concordance of the assay. State-of-the-art model interpretation methods revealed high-resolution predictive regulatory sequence features that overlapped transcription factor (TF) binding motifs. We used the model to investigate the cell type and chromatin state preferences of predictive TF motifs. We explored the ability of our model to predict the allelic effects of regulatory variants in an independent MPRA experiment and fine map putative functional SNPs in loci associated with lipid traits. Our results suggest that interpretable deep learning models trained on MPRA data have the potential to reveal meaningful patterns in regulatory DNA sequences and prioritize regulatory genetic variants, especially as larger, higher-quality datasets are produced.
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Affiliation(s)
- Rajiv Movva
- The Harker School, San Jose, CA, United States of America
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Peyton Greenside
- Biomedical Informatics Training Program, Stanford University, Stanford, CA, United States of America
| | - Georgi K. Marinov
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, United States of America
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA, United States of America
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, United States of America
- Department of Computer Science, Stanford University, Stanford, CA, United States of America
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17
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Mahmood N, Rabbani SA. DNA Methylation Readers and Cancer: Mechanistic and Therapeutic Applications. Front Oncol 2019; 9:489. [PMID: 31245293 PMCID: PMC6579900 DOI: 10.3389/fonc.2019.00489] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is a major epigenetic process that regulates chromatin structure which causes transcriptional activation or repression of genes in a context-dependent manner. In general, DNA methylation takes place when methyl groups are added to the appropriate bases on the genome by the action of "writer" molecules known as DNA methyltransferases. How these methylation marks are read and interpreted into different functionalities represents one of the main mechanisms through which the genes are switched "ON" or "OFF" and typically involves different types of "reader" proteins that can recognize and bind to the methylated regions. A tightly balanced regulation exists between the "writers" and "readers" in order to mediate normal cellular functions. However, alterations in normal methylation pattern is a typical hallmark of cancer which alters the way methylation marks are written, read and interpreted in different disease states. This unique characteristic of DNA methylation "readers" has identified them as attractive therapeutic targets. In this review, we describe the current state of knowledge on the different classes of DNA methylation "readers" identified thus far along with their normal biological functions, describe how they are dysregulated in cancer, and discuss the various anti-cancer therapies that are currently being developed and evaluated for targeting these proteins.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
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18
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Short SP, Barrett CW, Stengel KR, Revetta FL, Choksi YA, Coburn LA, Lintel MK, McDonough EM, Washington MK, Wilson KT, Prokhortchouk E, Chen X, Hiebert SW, Reynolds AB, Williams CS. Kaiso is required for MTG16-dependent effects on colitis-associated carcinoma. Oncogene 2019; 38:5091-5106. [PMID: 30858547 PMCID: PMC6586520 DOI: 10.1038/s41388-019-0777-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/27/2018] [Accepted: 02/12/2019] [Indexed: 01/26/2023]
Abstract
The myeloid translocation gene family member MTG16 is a transcriptional corepressor that relies on the DNA-binding ability of other proteins to determine specificity. One such protein is the ZBTB family member Kaiso, and the MTG16:Kaiso interaction is necessary for repression of Kaiso target genes such as matrix metalloproteinase-7. Using the azoxymethane and dextran sodium sulfate (AOM/DSS) murine model of colitis-associated carcinoma, we previously determined that MTG16 loss accelerates tumorigenesis and inflammation. However, it was unknown whether this effect was modified by Kaiso-dependent transcriptional repression. To test for a genetic interaction between MTG16 and Kaiso in inflammatory carcinogenesis, we subjected single and double knockout (DKO) mice to the AOM/DSS protocol. Mtg16−/− mice demonstrated increased colitis and tumor burden; in contrast, disease severity in Kaiso−/− mice was equivalent to wild type controls. Surprisingly, Kaiso deficiency in the context of MTG16 loss reversed injury and pro-tumorigenic responses in the intestinal epithelium following AOM/DSS treatment, and tumor numbers were returned to near to wild type levels. Transcriptomic analysis of non-tumor colon tissue demonstrated that changes induced by MTG16 loss were widely mitigated by concurrent Kaiso loss, and DKO mice demonstrated downregulation of metabolism and cytokine-associated gene sets with concurrent activation of DNA damage checkpoint pathways as compared with Mtg16−/−. Further, Kaiso knockdown in intestinal enteroids reduced stem- and WNT-associated phenotypes, thus abrogating the induction of these pathways observed in Mtg16−/− samples. Together, these data suggest that Kaiso modifies MTG16-driven inflammation and tumorigenesis and suggests that Kaiso deregulation contributes to MTG16-dependent colitis and CAC phenotypes.
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Affiliation(s)
- Sarah P Short
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Program in Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Caitlyn W Barrett
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Program in Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Frank L Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Yash A Choksi
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Program in Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA.,Veterans Affairs Tennessee Valley Health Care System, Nashville, TN, 37232, USA
| | - Lori A Coburn
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Veterans Affairs Tennessee Valley Health Care System, Nashville, TN, 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Mary K Lintel
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Elizabeth M McDonough
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Department of Pediatrics, Division of Gastroenterology, Our Lady of the Lake Children's Hospital, Baton Rouge, TN, 70808, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Keith T Wilson
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Program in Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Veterans Affairs Tennessee Valley Health Care System, Nashville, TN, 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
| | - Egor Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Xi Chen
- Department of Public Health Sciences and the Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.,Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
| | - Albert B Reynolds
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA.,Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
| | - Christopher S Williams
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. .,Program in Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA. .,Veterans Affairs Tennessee Valley Health Care System, Nashville, TN, 37232, USA. .,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. .,Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA.
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19
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Hiramatsu S, Watanabe KS, Zeggar S, Asano Y, Miyawaki Y, Yamamura Y, Katsuyama E, Katsuyama T, Watanabe H, Takano-Narazaki M, Matsumoto Y, Kawabata T, Sada KE, Wada J. Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells. Sci Rep 2019; 9:3054. [PMID: 30816218 PMCID: PMC6395770 DOI: 10.1038/s41598-019-38809-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/20/2018] [Indexed: 01/18/2023] Open
Abstract
Global DNA hypomethylation in CD4+ cells in systemic lupus erythematosus (SLE) was suggested to play a key role in the pathogenesis. To identify new methylation-sensitive genes, we integrated genome-wide DNA methylation and mRNA profiling data in CD4+ cells of MRL/lpr (MRL) and C57BL6/J (B6) mice. We identified Cathepsin E (Ctse), in which 13 methyl-CpGs within 583 bp region of intron 1 were hypomethylated, and Ctse mRNA upregulated in MRL compared with B6 mice. One of methyl-CpGs, mCGCG was 93.3 ± 2.05% methylated in B6 mice, while 80.0 ± 6.2% methylated and mutated to CGGG in MRL mice. Kaiso is known to bind to mCGCG and we hypothesized that it represses expression of Ctse in B6 mice. The binding of Kaiso to mCGCG site in B6 mice was reduced in MRL mice revealed by ChIP-PCR. EL4 cells treated with 5-azaC and/or Trichostatin A showed the suppression of binding of Kaiso to mCGCG motif by ChIP-PCR and the overexpression of Ctse was demonstrated by qPCR. Ctse gene silencing by siRNA in EL4 cells resulted in reduction of IL-10 secretion. The hypomethylation of mCGCG motif, reduced recruitment of Kaiso, and increased expression of Ctse and Il-10 in CD4+ cells may be involved in the pathogenesis of SLE.
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Affiliation(s)
- Sumie Hiramatsu
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Katsue S Watanabe
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Sonia Zeggar
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Yosuke Asano
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Yoshia Miyawaki
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Yuriko Yamamura
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Eri Katsuyama
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Takayuki Katsuyama
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Haruki Watanabe
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Mariko Takano-Narazaki
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Yoshinori Matsumoto
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Tomoko Kawabata
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Ken-Ei Sada
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Jun Wada
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan.
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20
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Pierre CC, Hercules SM, Yates C, Daniel JM. Dancing from bottoms up - Roles of the POZ-ZF transcription factor Kaiso in Cancer. Biochim Biophys Acta Rev Cancer 2018; 1871:64-74. [PMID: 30419310 DOI: 10.1016/j.bbcan.2018.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/05/2018] [Accepted: 10/07/2018] [Indexed: 12/11/2022]
Abstract
The POZ-ZF transcription factor Kaiso was discovered two decades ago as a binding partner for p120ctn. Since its discovery, roles for Kaiso in diverse biological processes (epithelial-to-mesenchymal transition, apoptosis, inflammation) and several signalling pathways (Wnt/β-catenin, TGFβ, EGFR, Notch) have emerged. While Kaiso's biological role in normal tissues has yet to be fully elucidated, Kaiso has been increasingly implicated in multiple human cancers including colon, prostate, ovarian, lung, breast and chronic myeloid leukemia. In the majority of human cancers investigated to date, high Kaiso expression correlates with aggressive tumor characteristics including proliferation and metastasis, and/or poor prognosis. More recently, interest in Kaiso stems from its apparent correlation with racial disparities in breast and prostate cancer incidence and survival outcomes in people of African Ancestry. This review discusses Kaiso's role in various cancers, and Kaiso's potential for driving racial disparities in incidence and/or outcomes in people of African ancestry.
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Affiliation(s)
- Christina C Pierre
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Shawn M Hercules
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Clayton Yates
- Department of Biology, Center for Cancer Research, Tuskegee University, Tuskegee, AL, USA
| | - Juliet M Daniel
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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21
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Wu X, Xie S, Wang L, Fan P, Ge S, Xie XQ, Wu W. A computational strategy for finding novel targets and therapeutic compounds for opioid dependence. PLoS One 2018; 13:e0207027. [PMID: 30403753 PMCID: PMC6221321 DOI: 10.1371/journal.pone.0207027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/22/2018] [Indexed: 12/13/2022] Open
Abstract
Opioids are widely used for treating different types of pains, but overuse and abuse of prescription opioids have led to opioid epidemic in the United States. Besides analgesic effects, chronic use of opioid can also cause tolerance, dependence, and even addiction. Effective treatment of opioid addiction remains a big challenge today. Studies on addictive effects of opioids focus on striatum, a main component in the brain responsible for drug dependence and addiction. Some transcription regulators have been associated with opioid addiction, but relationship between analgesic effects of opioids and dependence behaviors mediated by them at the molecular level has not been thoroughly investigated. In this paper, we developed a new computational strategy that identifies novel targets and potential therapeutic molecular compounds for opioid dependence and addiction. We employed several statistical and machine learning techniques and identified differentially expressed genes over time which were associated with dependence-related behaviors after exposure to either morphine or heroin, as well as potential transcription regulators that regulate these genes, using time course gene expression data from mouse striatum. Moreover, our findings revealed that some of these dependence-associated genes and transcription regulators are known to play key roles in opioid-mediated analgesia and tolerance, suggesting that an intricate relationship between opioid-induce pain-related pathways and dependence may develop at an early stage during opioid exposure. Finally, we determined small compounds that can potentially target the dependence-associated genes and transcription regulators. These compounds may facilitate development of effective therapy for opioid dependence and addiction. We also built a database (http://daportals.org) for all opioid-induced dependence-associated genes and transcription regulators that we discovered, as well as the small compounds that target those genes and transcription regulators.
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Affiliation(s)
- Xiaojun Wu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Siwei Xie
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Peihao Fan
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Songwei Ge
- School of Information, Renmin University of China, Beijing, China
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Wei Wu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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22
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Bormann F, Stinzing S, Tierling S, Morkel M, Markelova MR, Walter J, Weichert W, Roßner F, Kuhn N, Perner J, Dietz J, Ispasanie S, Dietel M, Schäfer R, Heinemann V, Sers C. Epigenetic regulation of Amphiregulin and Epiregulin in colorectal cancer. Int J Cancer 2018; 144:569-581. [PMID: 30252132 DOI: 10.1002/ijc.31892] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/05/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022]
Abstract
Expression of the epidermal growth factor ligands amphiregulin (AREG) and epiregulin (EREG) is positively correlated with a response to EGFR-targeted therapies in colorectal cancer. Gene-body methylation sites, which show a strong inverse correlation with AREG and EREG gene expression, were identified in cell lines using targeted 454 FLX-bisulfite sequencing and SIRPH analyses for AREG/EREG promoters and intragenic CpGs. Upon treatment of colorectal cancer cells with 5-aza-2'-desoxycytidine, methylation decreases at specific intragenic CpGs accompanied by upregulation of AREG and EREG gene expression. The same AREG gene-body methylation was also found in human colorectal cancer samples and is independent of KRAS and NRAS mutations. Methylation is specifically decreased in the tumor epithelial compartment as compared to stromal tissue and normal epithelium. Investigation of a promoter/enhancer function of the AREG exon 2 region revealed a potential promoter function in reverse orientation. Retrospective comparison of the predictive power of AREG gene-body methylation versus AREG gene expression using samples from colorectal cancer patients treated with anti-EGFR inhibitors with complete clinical follow-up revealed that AREG expression is superior to AREG gene methylation. AREG and EREG genes undergo a complex regulation involving both intragenic methylation and promoter-dependent control.
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Affiliation(s)
- Felix Bormann
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Sebastian Stinzing
- Department of Hematology and Medical Oncology, Klinikum der Universität München (LMU); German Cancer Consortium site Munich (DKTK); German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken
| | - Markus Morkel
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | | | - Jörn Walter
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken
| | - Wilko Weichert
- DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany.,Institute of Pathology, Technical University Munich, Germany and Munich German Cancer Consortium (DKTK), German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Florian Roßner
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Natalia Kuhn
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Juliane Perner
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Johanna Dietz
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Sylvia Ispasanie
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin, Germany
| | - Manfred Dietel
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | - Reinhold Schäfer
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | - Volker Heinemann
- Department of Hematology and Medical Oncology, Klinikum der Universität München (LMU); German Cancer Consortium site Munich (DKTK); German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Christine Sers
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
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23
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Hudson NO, Buck-Koehntop BA. Zinc Finger Readers of Methylated DNA. Molecules 2018; 23:E2555. [PMID: 30301273 PMCID: PMC6222495 DOI: 10.3390/molecules23102555] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is a prevalent epigenetic modification involved in regulating a number of essential cellular processes, including genomic accessibility and transcriptional outcomes. As such, aberrant alterations in global DNA methylation patterns have been associated with a growing number of disease conditions. Nevertheless, the full mechanisms by which DNA methylation information is interpreted and translated into genomic responses is not yet fully understood. Methyl-CpG binding proteins (MBPs) function as important mediators of this essential process by selectively reading DNA methylation signals and translating this information into down-stream cellular outcomes. The Cys₂His₂ zinc finger scaffold is one of the most abundant DNA binding motifs found within human transcription factors, yet only a few zinc finger containing proteins capable of conferring selectivity for mCpG over CpG sites have been characterized. This review summarizes our current structural understanding for the mechanisms by which the zinc finger MBPs evaluated to date read this essential epigenetic mark. Further, some of the biological implications for mCpG readout elicited by this family of MBPs are discussed.
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Affiliation(s)
- Nicholas O Hudson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
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24
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Ocskó T, Tóth DM, Hoffmann G, Tubak V, Glant TT, Rauch TA. Transcription factor Zbtb38 downregulates the expression of anti-inflammatory IL1r2 in mouse model of rheumatoid arthritis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:1040-1047. [PMID: 30343694 DOI: 10.1016/j.bbagrm.2018.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 09/09/2018] [Accepted: 09/13/2018] [Indexed: 11/29/2022]
Abstract
DNA methylation is a decisive regulator of gene expression. Differentially methylated promoters were described in rheumatoid arthritis (RA), but we do not know how these epimutations can trigger a proinflammatory cytokine milieu. B cell-focused DNA methylome studies identified a group of genes that had undergone disease-associated changes in a murine model of RA. An arthritis-specific epimutation (hypomethylation) was detected in the promoter region of the Zbtb38 gene, which encodes a transcriptional repressor. Gene expression studies revealed that hypomethylation of the Zbtb38 promoter was accompanied by disease-specific repressor expression, and two anti-inflammatory factors interleukin 1 receptor 2 gene (IL1r2) and interleukin-1 receptor antagonist (IL1rn) were among the downregulated genes. We hypothesized that Zbtb38 repressor could induce downregulated expression of these anti-inflammatory genes and that this could significantly contribute to arthritis pathogenesis. Our studies demonstrate that Zbtb38 forms a molecular bridge between an arthritis-associated epimutation (DNA hypomethylation in Zbtb38 promoter) and transcriptional silencing of the IL1r2 gene in B cells. In this way, disease-associated DNA hypomethylation can support autoimmune arthritis by interfering with an anti-inflammatory pathway.
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Affiliation(s)
- Tímea Ocskó
- Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, 1735 W. Harrison Street, Chicago, IL 60612, United States of America
| | - Dániel M Tóth
- Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, 1735 W. Harrison Street, Chicago, IL 60612, United States of America
| | - Gyula Hoffmann
- Department of Genetics, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Vilmos Tubak
- Hungarian Academy of Sciences, Biological Research Centre, Institute of Biochemistry, Szeged, Hungary
| | - Tibor T Glant
- Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, 1735 W. Harrison Street, Chicago, IL 60612, United States of America
| | - Tibor A Rauch
- Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, 1735 W. Harrison Street, Chicago, IL 60612, United States of America; Institute of Medical Biology, University of Pécs, Pécs, Hungary; Section of Bioinformatics and Computational Medicine, János Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
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25
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Biswas S, Rao CM. Epigenetic tools (The Writers, The Readers and The Erasers) and their implications in cancer therapy. Eur J Pharmacol 2018; 837:8-24. [PMID: 30125562 DOI: 10.1016/j.ejphar.2018.08.021] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 02/08/2023]
Abstract
Addition of chemical tags on the DNA and modification of histone proteins impart a distinct feature on chromatin architecture. With the advancement in scientific research, the key players underlying these changes have been identified as epigenetic modifiers of the chromatin. Indeed, the plethora of enzymes catalyzing these modifications, portray the diversity of epigenetic space and the intricacy in regulating gene expression. These epigenetic players are categorized as writers: that introduce various chemical modifications on DNA and histones, readers: the specialized domain containing proteins that identify and interpret those modifications and erasers: the dedicated group of enzymes proficient in removing these chemical tags. Research over the past few decades has established that these epigenetic tools are associated with numerous disease conditions especially cancer. Besides, with the involvement of epigenetics in cancer, these enzymes and protein domains provide new targets for cancer drug development. This is certain from the volume of epigenetic research conducted in universities and R&D sector of pharmaceutical industry. Here we have highlighted the different types of epigenetic enzymes and protein domains with an emphasis on methylation and acetylation. This review also deals with the recent developments in small molecule inhibitors as potential anti-cancer drugs targeting the epigenetic space.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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26
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Ding Y, Herman JA, Toledo CM, Lang JM, Corrin P, Girard EJ, Basom R, Delrow JJ, Olson JM, Paddison PJ. ZNF131 suppresses centrosome fragmentation in glioblastoma stem-like cells through regulation of HAUS5. Oncotarget 2018; 8:48545-48562. [PMID: 28596487 PMCID: PMC5564707 DOI: 10.18632/oncotarget.18153] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022] Open
Abstract
Zinc finger domain genes comprise ∼3% of the human genome, yet many of their functions remain unknown. Here we investigated roles for the vertebrate-specific BTB domain zinc finger gene ZNF131 in the context of human brain tumors. We report that ZNF131 is broadly required for Glioblastoma stem-like cell (GSC) viability, but dispensable for neural progenitor cell (NPC) viability. Examination of gene expression changes after ZNF131 knockdown (kd) revealed that ZNF131 activity notably promotes expression of Joubert Syndrome ciliopathy genes, including KIF7, NPHP1, and TMEM237, as well as HAUS5, a component of Augmin/HAUS complex that facilitates microtubule nucleation along the mitotic spindle. Of these genes only kd of HAUS5 displayed GSC-specific viability loss. Critically, HAUS5 ectopic expression was sufficient to suppress viability defects of ZNF131 kd cells. Moreover, ZNF131 and HAUS5 kd phenocopied each other in GSCs, each causing: mitotic arrest, centrosome fragmentation, loss of Augmin/HAUS complex on the mitotic spindle, and loss of GSC self-renewal and tumor formation capacity. In control NPCs, we observed centrosome fragmentation and lethality only when HAUS5 kd was combined with kd of HAUS2 or HAUS4, demonstrating that the complex is essential in NPCs, but that GSCs have heightened requirement. Our results suggest that GSCs differentially rely on ZNF131-dependent expression of HAUS5 as well as the Augmin/HAUS complex activity to maintain the integrity of centrosome function and viability.
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Affiliation(s)
- Yu Ding
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Novartis Institute for Biomedical Research, Shanghai, China
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.,Nurix Inc., San Francisco, CA, USA
| | - Jackie M Lang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Philip Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ryan Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
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27
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Rhie SK, Yao L, Luo Z, Witt H, Schreiner S, Guo Y, Perez AA, Farnham PJ. ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters. Genome Res 2018; 28:310-320. [PMID: 29429977 PMCID: PMC5848610 DOI: 10.1101/gr.228809.117] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/26/2018] [Indexed: 12/29/2022]
Abstract
High expression of the transcription factor ZFX is correlated with proliferation, tumorigenesis, and patient survival in multiple types of human cancers. However, the mechanism by which ZFX influences transcriptional regulation has not been determined. We performed ChIP-seq in four cancer cell lines (representing kidney, colon, prostate, and breast cancers) to identify ZFX binding sites throughout the human genome. We identified roughly 9000 ZFX binding sites and found that most of the sites are in CpG island promoters. Moreover, genes with promoters bound by ZFX are expressed at higher levels than genes with promoters not bound by ZFX. To determine if ZFX contributes to regulation of the promoters to which it is bound, we performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Many genes with promoters bound by ZFX were down-regulated upon ZFX knockdown, supporting the hypothesis that ZFX acts as a transcriptional activator. Surprisingly, ZFX binds at +240 bp downstream from the TSS of the responsive promoters. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucleosome, suggesting that ZFX may play a critical role in promoter architecture. We have also shown that a closely related zinc finger protein ZNF711 has a similar binding pattern at CpG island promoters, but ZNF711 may play a subordinate role to ZFX. This functional characterization of ZFX provides important new insights into transcription, chromatin structure, and the regulation of the cancer transcriptome.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Lijun Yao
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Zhifei Luo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Heather Witt
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Yu Guo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Andrew A Perez
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
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28
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DeSUMOylation switches Kaiso from activator to repressor upon hyperosmotic stress. Cell Death Differ 2018; 25:1938-1951. [PMID: 29472715 DOI: 10.1038/s41418-018-0078-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 01/16/2018] [Accepted: 01/26/2018] [Indexed: 12/31/2022] Open
Abstract
Kaiso is a member of the BTB/POZ zinc finger family, which is involved in cancer progression, cell cycle control, apoptosis, and WNT signaling. Depending on promoter context, it may function as either a transcriptional repressor or activator. Previous studies found that Kaiso might be SUMOylated due to heat shock, but the biological significance of Kaiso SUMOylation is unclear. Here, we find that K42 is the only amino acid within Kaiso that is modified with SUMO. Kaiso is monoSUMOylated at lysine 42 in cell lines of kidney origin under normal physiological conditions. SUMOylated Kaiso can activate transcription from exogenous methylated promoters, wherein the deSUMOylated form of the protein kept the ability to be a repressor. Rapid Kaiso deSUMOylation occurs in response to hyperosmotic stress and is reversible upon return to an isotonic environment. DeSUMOylation occurs within minutes in HEK293 cells treated with 100 mM NaCl and relaxes in 3 h even in a salt-containing medium. Genomic editing of Kaiso by conversion of K42 into R42 (K42R) in HEK293 cells that resulted in fully deSUMOylated endogenous protein led to misregulation of genes associated with ion transport, blood pressure, and the immune response. TRIM25 was significantly repressed in two K42R HEK293 clones. By a series of rescue experiments with K42R and KO HEK293 cells, we show that TRIM25 is a direct transcriptional target for Kaiso. In the absence of Kaiso, the level of TRIM25 is insensitive to hyperosmotic stress. Extending our observations to animal models, we show that in response to a high salt diet, Kaiso knockout mice are characterized by significantly higher blood pressure increases when compared to wild-type animals. Thus, we propose a novel biological role for Kaiso in the regulation of homeostasis.
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29
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Bassey-Archibong BI, Hercules SM, Rayner LGA, Skeete DHA, Smith Connell SP, Brain I, Daramola A, Banjo AAF, Byun JS, Gardner K, Dushoff J, Daniel JM. Kaiso is highly expressed in TNBC tissues of women of African ancestry compared to Caucasian women. Cancer Causes Control 2017; 28:1295-1304. [PMID: 28887687 PMCID: PMC5681979 DOI: 10.1007/s10552-017-0955-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 08/31/2017] [Indexed: 12/22/2022]
Abstract
Purpose Triple-negative breast cancer (TNBC) is most prevalent in young women of African ancestry (WAA) compared to women of other ethnicities. Recent studies found a correlation between high expression of the transcription factor Kaiso, TNBC aggressiveness, and ethnicity. However, little is known about Kaiso expression and localization patterns in TNBC tissues of WAA. Herein, we analyze Kaiso expression patterns in TNBC tissues of African (Nigerian), Caribbean (Barbados), African American (AA), and Caucasian American (CA) women. Methods Formalin-fixed and paraffin embedded (FFPE) TNBC tissue blocks from Nigeria and Barbados were utilized to construct a Nigerian/Barbadian tissue microarray (NB-TMA). This NB-TMA and a commercially available TMA comprising AA and CA TNBC tissues (AA-CA-YTMA) were subjected to immunohistochemistry to assess Kaiso expression and subcellular localization patterns, and correlate Kaiso expression with TNBC clinical features. Results Nigerian and Barbadian women in our study were diagnosed with TNBC at a younger age than AA and CA women. Nuclear and cytoplasmic Kaiso expression was observed in all tissues analyzed. Analysis of Kaiso expression in the NB-TMA and AA-CA-YTMA revealed that nuclear Kaiso H scores were significantly higher in Nigerian, Barbadian, and AA women compared with CA women. However, there was no statistically significant difference in nuclear Kaiso expression between Nigerian versus Barbadian women, or Barbadian versus AA women. Conclusions High levels of nuclear Kaiso expression were detected in patients with a higher degree of African heritage compared to their Caucasian counterparts, suggesting a role for Kaiso in TNBC racial disparity. Electronic supplementary material The online version of this article (doi:10.1007/s10552-017-0955-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Shawn M Hercules
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | | - Desiree H A Skeete
- Department of Pathology, Queen Elizabeth Hospital (QEH), Bridgetown, Barbados.,Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Suzanne P Smith Connell
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados.,Department of Radiation Oncology, Queen Elizabeth Hospital (QEH), Bridgetown, Barbados
| | - Ian Brain
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Adetola Daramola
- Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital (LUTH), Lagos, Nigeria
| | - Adekunbiola A F Banjo
- Department of Anatomic and Molecular Pathology, Lagos University Teaching Hospital (LUTH), Lagos, Nigeria
| | - Jung S Byun
- Genetics Branch, National Institute of Health, Bethesda, MD, USA
| | - Kevin Gardner
- Genetics Branch, National Institute of Health, Bethesda, MD, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Juliet M Daniel
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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Xue X, Zhang J, Lan H, Xu Y, Wang H. Kaiso protects human umbilical vein endothelial cells against apoptosis by differentially regulating the expression of B-cell CLL/lymphoma 2 family members. Sci Rep 2017; 7:7116. [PMID: 28769046 PMCID: PMC5540925 DOI: 10.1038/s41598-017-07559-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/29/2017] [Indexed: 12/15/2022] Open
Abstract
Endothelial cell injury can promote the development of various cardiovascular diseases, thus, fully understanding the mechanisms underlying the maintenance of vascular endothelial cell homoeostasis may help prevent and treat cardiovascular disease. Kaiso, a zinc finger and BTB domain containing transcription factor, is key to embryonic development and cancer, but how Kaiso interacts with vascular endothelium is not fully understood. We report that Kaiso has an anti-apoptotic function in human umbilical vein endothelial cells (HUVECs) and human microvascular endothelial cells (HMEC-1s). Overexpression of Kaiso significantly increased cell viability and inhibited hydrogen peroxide-induced apoptosis. Furthermore, Kaiso increased expression of B-cell CLL/lymphoma 2 (BCL2) and reduced expression of BCL2-associated X protein (BAX) and BCL2-interacting killer (BIK) by differentially regulating gene promoter activity. Methylated DNA and specific Kaiso binding site (KBS) contributed to gene regulatory activity of Kaiso. In addition, p120ctn functioned cooperatively in Kaiso-mediated transcriptional regulation.
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Affiliation(s)
- Xiaodong Xue
- Department of Cardiovascular Surgery, General Hospital of Shenyang Military Area Command, No.83, Wenhua Road, Shenhe District, Shenyang City, Liaoning, 110016, China
| | - Jian Zhang
- Department of Cardiovascular Surgery, General Hospital of Shenyang Military Area Command, No.83, Wenhua Road, Shenhe District, Shenyang City, Liaoning, 110016, China
| | - Huai Lan
- Department of Cardiovascular Surgery, General Hospital of Shenyang Military Area Command, No.83, Wenhua Road, Shenhe District, Shenyang City, Liaoning, 110016, China
| | - Yinli Xu
- Department of Cardiovascular Surgery, General Hospital of Shenyang Military Area Command, No.83, Wenhua Road, Shenhe District, Shenyang City, Liaoning, 110016, China
| | - Huishan Wang
- Department of Cardiovascular Surgery, General Hospital of Shenyang Military Area Command, No.83, Wenhua Road, Shenhe District, Shenyang City, Liaoning, 110016, China.
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Abstract
Recent technological advances have made it possible to decode DNA methylomes at single-base-pair resolution under various physiological conditions. Many aberrant or differentially methylated sites have been discovered, but the mechanisms by which changes in DNA methylation lead to observed phenotypes, such as cancer, remain elusive. The classical view of methylation-mediated protein-DNA interactions is that only proteins with a methyl-CpG binding domain (MBD) can interact with methylated DNA. However, evidence is emerging to suggest that transcription factors lacking a MBD can also interact with methylated DNA. The identification of these proteins and the elucidation of their characteristics and the biological consequences of methylation-dependent transcription factor-DNA interactions are important stepping stones towards a mechanistic understanding of methylation-mediated biological processes, which have crucial implications for human development and disease.
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Guo Y, Gifford DK. Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding. BMC Genomics 2017; 18:45. [PMID: 28061806 PMCID: PMC5219757 DOI: 10.1186/s12864-016-3434-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 12/19/2016] [Indexed: 11/25/2022] Open
Abstract
Background The combinatorial binding of trans-acting factors (TFs) to the DNA is critical to the spatial and temporal specificity of gene regulation. For certain regulatory regions, more than one regulatory module (set of TFs that bind together) are combined to achieve context-specific gene regulation. However, previous approaches are limited to either pairwise TF co-association analysis or assuming that only one module is used in each regulatory region. Results We present a new computational approach that models the modular organization of TF combinatorial binding. Our method learns compact and coherent regulatory modules from in vivo binding data using a topic model. We found that the binding of 115 TFs in K562 cells can be organized into 49 interpretable modules. Furthermore, we found that tens of thousands of regulatory regions use multiple modules, a structure that cannot be observed with previous hard clustering based methods. The modules discovered recapitulate many published protein-protein physical interactions, have consistent functional annotations of chromatin states, and uncover context specific co-binding such as gene proximal binding of NFY + FOS + SP and distal binding of NFY + FOS + USF. For certain TFs, the co-binding partners of direct binding (motif present) differs from those of indirect binding (motif absent); the distinct set of co-binding partners can predict whether the TF binds directly or indirectly with up to 95% accuracy. Joint analysis across two cell types reveals both cell-type-specific and shared regulatory modules. Conclusions Our results provide comprehensive cell-type-specific combinatorial binding maps and suggest a modular organization of combinatorial binding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3434-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuchun Guo
- MIT, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA
| | - David K Gifford
- MIT, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
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Misregulation of DNA Methylation Regulators in Cancer. DNA AND HISTONE METHYLATION AS CANCER TARGETS 2017. [DOI: 10.1007/978-3-319-59786-7_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Nat Biotechnol 2016; 34:1180-1190. [PMID: 27701403 PMCID: PMC5125825 DOI: 10.1038/nbt.3678] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 08/16/2016] [Indexed: 02/07/2023]
Abstract
Massively parallel reporter assays (MPRAs) enable nucleotide-resolution dissection of transcriptional regulatory regions, such as enhancers, but only few regions at a time. Here we present a combined experimental and computational approach, Systematic high-resolution activation and repression profiling with reporter tiling using MPRA (Sharpr-MPRA), that allows high-resolution analysis of thousands of regions simultaneously. Sharpr-MPRA combines dense tiling of overlapping MPRA constructs with a probabilistic graphical model to recognize functional regulatory nucleotides, and to distinguish activating and repressive nucleotides, using their inferred contribution to reporter gene expression. We used Sharpr-MPRA to test 4.6 million nucleotides spanning 15,000 putative regulatory regions tiled at 5-nucleotide resolution in two human cell types. Our results recovered known cell-type-specific regulatory motifs and evolutionarily conserved nucleotides, and distinguished known activating and repressive motifs. Our results also showed that endogenous chromatin state and DNA accessibility are both predictive of regulatory function in reporter assays, identified retroviral elements with activating roles, and uncovered 'attenuator' motifs with repressive roles in active chromatin.
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Affiliation(s)
- Jason Ernst
- Department of Biological Chemistry, University of California, Los Angeles, California, USA
- Computer Science Department, University of California, Los Angeles, California, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California Los Angeles, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Alexandre Melnikov
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Xiaolan Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Li Wang
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Peter Rogov
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Tarjei S. Mikkelsen
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Manolis Kellis
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Bohne F, Langer D, Martiné U, Eider CS, Cencic R, Begemann M, Elbracht M, Bülow L, Eggermann T, Zechner U, Pelletier J, Zabel BU, Enklaar T, Prawitt D. Kaiso mediates human ICR1 methylation maintenance and H19 transcriptional fine regulation. Clin Epigenetics 2016; 8:47. [PMID: 27152123 PMCID: PMC4857248 DOI: 10.1186/s13148-016-0215-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/26/2016] [Indexed: 11/21/2022] Open
Abstract
Background Genomic imprinting evolved in a common ancestor to marsupials and eutherian mammals and ensured the transcription of developmentally important genes from defined parental alleles. The regulation of imprinted genes is often mediated by differentially methylated imprinting control regions (ICRs) that are bound by different proteins in an allele-specific manner, thus forming unique chromatin loops regulating enhancer-promoter interactions. Factors that maintain the allele-specific methylation therefore are essential for the proper transcriptional regulation of imprinted genes. Binding of CCCTC-binding factor (CTCF) to the IGF2/H19-ICR1 is thought to be the key regulator of maternal ICR1 function. Disturbances of the allele-specific CTCF binding are causative for imprinting disorders like the Silver-Russell syndrome (SRS) or the Beckwith-Wiedemann syndrome (BWS), the latter one being associated with a dramatically increased risk to develop nephroblastomas. Methods Kaiso binding to the human ICR1 was detected and analyzed by chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays (EMSA). The role of Kaiso-ICR1 binding on DNA methylation was tested by lentiviral Kaiso knockdown and CRISPR/Cas9 mediated editing of a Kaiso binding site. Results We find that another protein, Kaiso (ZBTB33), characterized as binding to methylated CpG repeats as well as to unmethylated consensus sequences, specifically binds to the human ICR1 and its unmethylated Kaiso binding site (KBS) within the ICR1. Depletion of Kaiso transcription as well as deletion of the ICR1-KBS by CRISPR/Cas9 genome editing results in reduced methylation of the paternal ICR1. Additionally, Kaiso affects transcription of the lncRNA H19 and specifies a role for ICR1 in the transcriptional regulation of this imprinted gene. Conclusions Kaiso binding to unmethylated KBS in the human ICR1 is necessary for ICR1 methylation maintenance and affects transcription rates of the lncRNA H19. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0215-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florian Bohne
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - David Langer
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Ursula Martiné
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Claudia S Eider
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Regina Cencic
- Department of Biochemistry and the Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
| | - Matthias Begemann
- Institute of Human Genetics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Luzie Bülow
- Institute of Human Genetics, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Ulrich Zechner
- Institute of Human Genetics, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Jerry Pelletier
- Department of Biochemistry and the Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
| | - Bernhard Ulrich Zabel
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Mathildenstr. 1, 79106 Freiburg, Germany
| | - Thorsten Enklaar
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Dirk Prawitt
- Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Langenbeckstr. 1, 55101 Mainz, Germany.,Centre for Paediatrics and Adolescent Medicine, University Medical Centre, Obere Zahlbacher Str. 63, 55131 Mainz, Germany
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Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation. Sci Rep 2015; 5:17328. [PMID: 26612583 PMCID: PMC4661471 DOI: 10.1038/srep17328] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/29/2015] [Indexed: 11/13/2022] Open
Abstract
The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript.
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Abstract
β-catenin is widely regarded as the primary transducer of canonical WNT signals to the nucleus. In most vertebrates, there are eight additional catenins that are structurally related to β-catenin, and three α-catenin genes encoding actin-binding proteins that are structurally related to vinculin. Although these catenins were initially identified in association with cadherins at cell-cell junctions, more recent evidence suggests that the majority of catenins also localize to the nucleus and regulate gene expression. Moreover, the number of catenins reported to be responsive to canonical WNT signals is increasing. Here, we posit that multiple catenins form a functional network in the nucleus, possibly engaging in conserved protein-protein interactions that are currently better characterized in the context of actin-based cell junctions.
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38
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Pierre CC, Longo J, Bassey-Archibong BI, Hallett RM, Milosavljevic S, Beatty L, Hassell JA, Daniel JM. Methylation-dependent regulation of hypoxia inducible factor-1 alpha gene expression by the transcription factor Kaiso. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1432-41. [PMID: 26514431 DOI: 10.1016/j.bbagrm.2015.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/01/2015] [Accepted: 10/23/2015] [Indexed: 01/19/2023]
Abstract
Low oxygen tension (hypoxia) is a common characteristic of solid tumors and strongly correlates with poor prognosis and resistance to treatment. In response to hypoxia, cells initiate a cascade of transcriptional events regulated by the hypoxia inducible factor-1 (HIF-1) heterodimer. Since the oxygen-sensitive HIF-1α subunit is stabilized during hypoxia, it functions as the regulatory subunit of the protein. To date, while the mechanisms governing HIF-1α protein stabilization and function have been well studied, those governing HIF1A gene expression are not fully understood. However, recent studies have suggested that methylation of a HIF-1 binding site in the HIF1A promoter prevents its autoregulation. Here we report that the POZ-ZF transcription factor Kaiso modulates HIF1A gene expression by binding to the methylated HIF1A promoter in a region proximal to the autoregulatory HIF-1 binding site. Interestingly, Kaiso's regulation of HIF1A occurs primarily during hypoxia, which is consistent with the finding that Kaiso protein levels peak after 4 h of hypoxic incubation and return to normoxic levels after 24 h. Our data thus support a role for Kaiso in fine-tuning HIF1A gene expression after extended periods of hypoxia.
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Affiliation(s)
- Christina C Pierre
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Joseph Longo
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Robin M Hallett
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Laura Beatty
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John A Hassell
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Juliet M Daniel
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
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Hong JY, Oh IH, McCrea PD. Phosphorylation and isoform use in p120-catenin during development and tumorigenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:102-14. [PMID: 26477567 DOI: 10.1016/j.bbamcr.2015.10.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 12/12/2022]
Abstract
P120-catenin is essential to vertebrate development, modulating cadherin and small-GTPase functions, and growing evidence points also to roles in the nucleus. A complexity in addressing p120-catenin's functions is its many isoforms, including optional splicing events, alternative points of translational initiation, and secondary modifications. In this review, we focus upon how choices in the initiation of protein translation, or the earlier splicing of the RNA transcript, relates to primary sequences that harbor established or putative regulatory phosphorylation sites. While certain p120 phosphorylation events arise via known kinases/phosphatases and have defined outcomes, in most cases the functional consequences are still to be established. In this review, we provide examples of p120-isoforms as they relate to phosphorylation events, and thereby to isoform dependent protein-protein associations and downstream functions. We also provide a view of upstream pathways that determine p120's phosphorylation state, and that have an impact upon development and disease. Because other members of the p120 subfamily undergo similar processing and phosphorylation, as well as related catenins of the plakophilin subfamily, what is learned regarding p120 will by extension have wide relevance in vertebrates.
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Affiliation(s)
- Ji Yeon Hong
- Division of Cardiology, Department of Medicine, Severance Biomedical Science Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, Republic of Korea.
| | - Il-Hoan Oh
- The Catholic University of Korea, Catholic High Performance Cell Therapy Center, 505 Banpo-dong, Seocho-Ku, Seoul 137-701, Republic of Korea
| | - Pierre D McCrea
- Department of Genetics, University of Texas MD Anderson Cancer Center, University of Texas Graduate School of Biomedical Science, Houston, TX 77030, USA.
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Hamidi T, Singh AK, Chen T. Genetic alterations of DNA methylation machinery in human diseases. Epigenomics 2015; 7:247-65. [PMID: 25942534 DOI: 10.2217/epi.14.80] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA methylation plays a critical role in the regulation of chromatin structure and gene expression and is involved in a variety of biological processes. The levels and patterns of DNA methylation are regulated by both DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) and 'demethylating' proteins, including the ten-eleven translocation (TET) family of dioxygenases (TET1, TET2 and TET3). The effects of DNA methylation on chromatin and gene expression are largely mediated by methylated DNA 'reader' proteins, including MeCP2. Numerous mutations in DNMTs, TETs and MeCP2 have been identified in cancer and developmental disorders, highlighting the importance of the DNA methylation machinery in human development and physiology. In this review, we describe these mutations and discuss how they may lead to disease phenotypes.
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Affiliation(s)
- Tewfik Hamidi
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park - Research Division, 1808 Park Road 1C, P. O. Box 389, Smithville, TX 78957, USA
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Long MD, van den Berg PR, Russell JL, Singh PK, Battaglia S, Campbell MJ. Integrative genomic analysis in K562 chronic myelogenous leukemia cells reveals that proximal NCOR1 binding positively regulates genes that govern erythroid differentiation and Imatinib sensitivity. Nucleic Acids Res 2015; 43:7330-48. [PMID: 26117541 PMCID: PMC4551916 DOI: 10.1093/nar/gkv642] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/10/2015] [Indexed: 01/05/2023] Open
Abstract
To define the functions of NCOR1 we developed an integrative analysis that combined ENCODE and NCI-60 data, followed by in vitro validation. NCOR1 and H3K9me3 ChIP-Seq, FAIRE-seq and DNA CpG methylation interactions were related to gene expression using bootstrapping approaches. Most NCOR1 combinations (24/44) were associated with significantly elevated level expression of protein coding genes and only very few combinations related to gene repression. DAVID's biological process annotation revealed that elevated gene expression was uniquely associated with acetylation and ETS binding. A matrix of gene and drug interactions built on NCI-60 data identified that Imatinib significantly targeted the NCOR1 governed transcriptome. Stable knockdown of NCOR1 in K562 cells slowed growth and significantly repressed genes associated with NCOR1 cistrome, again, with the GO terms acetylation and ETS binding, and significantly dampened sensitivity to Imatinib-induced erythroid differentiation. Mining public microarray data revealed that NCOR1-targeted genes were significantly enriched in Imatinib response gene signatures in cell lines and chronic myelogenous leukemia (CML) patients. These approaches integrated cistrome, transcriptome and drug sensitivity relationships to reveal that NCOR1 function is surprisingly most associated with elevated gene expression, and that these targets, both in CML cell lines and patients, associate with sensitivity to Imatinib.
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Affiliation(s)
- Mark D Long
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Patrick R van den Berg
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - James L Russell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Prashant K Singh
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Sebastiano Battaglia
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Moray J Campbell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
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Qin S, Zhang B, Tian W, Gu L, Lu Z, Deng D. Kaiso mainly locates in the nucleus in vivo and binds to methylated, but not hydroxymethylated DNA. Chin J Cancer Res 2015; 27:148-55. [PMID: 25937776 DOI: 10.3978/j.issn.1000-9604.2015.04.03] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/23/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE Kaiso is upregulated in many cancers and proposed to bind with both methylated- and unmethylated-DNA in the nucleus as a transcriptional repressor. The objective is to define its subcellular localization in vivo and exact binding DNA sequences in cells. METHODS Compartmentalization of exogenous Kaiso in cells was tracked with enhanced green fluorescence protein (EGFP) tag. The endogenous Kaiso expression in gastric carcinoma tissue was examined with immunohistochemical staining. Kaiso-DNA binding was tested using electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation assay (ChIP). RESULTS Kaiso mainly localized in the nucleus of cancer and stromal cells in vivo, but remained in the cytoplasm of cultured cells. Most importantly, nuclear Kaiso can bind with the methylated-CGCG-containing sequence in the CDKN2A promoter, but not with the hydroxymethylated-CGCG sequence in HCT116 cells. CONCLUSIONS Kaiso locates mainly in the nucleus in vivo where it binds with the methylated-CGCG sequences, but does not bind with the hydroxymethylated-CGCG sequences.
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Affiliation(s)
- Sisi Qin
- Beijing Key Laboratory of Carcinogenesis and Translational Research, Division of Cancer Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Baozhen Zhang
- Beijing Key Laboratory of Carcinogenesis and Translational Research, Division of Cancer Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Wei Tian
- Beijing Key Laboratory of Carcinogenesis and Translational Research, Division of Cancer Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Liankun Gu
- Beijing Key Laboratory of Carcinogenesis and Translational Research, Division of Cancer Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zheming Lu
- Beijing Key Laboratory of Carcinogenesis and Translational Research, Division of Cancer Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Dajun Deng
- Beijing Key Laboratory of Carcinogenesis and Translational Research, Division of Cancer Etiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
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van de Ven RAH, Tenhagen M, Meuleman W, van Riel JJG, Schackmann RCJ, Derksen PWB. Nuclear p120-catenin regulates the anoikis resistance of mouse lobular breast cancer cells through Kaiso-dependent Wnt11 expression. Dis Model Mech 2015; 8:373-84. [PMID: 25713299 PMCID: PMC4381336 DOI: 10.1242/dmm.018648] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/12/2015] [Indexed: 01/02/2023] Open
Abstract
E-cadherin inactivation underpins the progression of invasive lobular breast carcinoma (ILC). In ILC, p120-catenin (p120) translocates to the cytosol where it controls anchorage independence through the Rho-Rock signaling pathway, a key mechanism driving tumor growth and metastasis. We now demonstrate that anchorage-independent ILC cells show an increase in nuclear p120, which results in relief of transcriptional repression by Kaiso. To identify the Kaiso target genes that control anchorage independence we performed genome-wide mRNA profiling on anoikis-resistant mouse ILC cells, and identified 29 candidate target genes, including the established Kaiso target Wnt11. Our data indicate that anchorage-independent upregulation of Wnt11 in ILC cells is controlled by nuclear p120 through inhibition of Kaiso-mediated transcriptional repression. Finally, we show that Wnt11 promotes activation of RhoA, which causes ILC anoikis resistance. Our findings thereby establish a mechanistic link between E-cadherin loss and subsequent control of Rho-driven anoikis resistance through p120- and Kaiso-dependent expression of Wnt11.
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Affiliation(s)
| | - Milou Tenhagen
- Department of Pathology, UMC Utrecht, 3584 CX Utrecht, The Netherlands
| | - Wouter Meuleman
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands. Division of Molecular Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands. Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg, 2628 CD Delft, The Netherlands
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Abstract
The arrival of multicellularity in evolution facilitated cell-cell signaling in conjunction with adhesion. As the ectodomains of cadherins interact with each other directly in trans (as well as in cis), spanning the plasma membrane and associating with multiple other entities, cadherins enable the transduction of "outside-in" or "inside-out" signals. We focus this review on signals that originate from the larger family of cadherins that are inwardly directed to the nucleus, and thus have roles in gene control or nuclear structure-function. The nature of cadherin complexes varies considerably depending on the type of cadherin and its context, and we will address some of these variables for classical cadherins versus other family members. Substantial but still fragmentary progress has been made in understanding the signaling mediators used by varied cadherin complexes to coordinate the state of cell-cell adhesion with gene expression. Evidence that cadherin intracellular binding partners also localize to the nucleus is a major point of interest. In some models, catenins show reduced binding to cadherin cytoplasmic tails favoring their engagement in gene control. When bound, cadherins may serve as stoichiometric competitors of nuclear signals. Cadherins also directly or indirectly affect numerous signaling pathways (e.g., Wnt, receptor tyrosine kinase, Hippo, NFκB, and JAK/STAT), enabling cell-cell contacts to touch upon multiple biological outcomes in embryonic development and tissue homeostasis.
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Affiliation(s)
- Pierre D McCrea
- Department of Genetics, University of Texas MD Anderson Cancer Center; Program in Genes & Development, Graduate School in Biomedical Sciences, Houston, Texas, USA.
| | - Meghan T Maher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Cara J Gottardi
- Cellular and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA; Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
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Pemov A, Sung H, Hyland PL, Sloan JL, Ruppert SL, Baldwin AM, Boland JF, Bass SE, Lee HJ, Jones KM, Zhang X, Mullikin JC, Widemann BC, Wilson AF, Stewart DR. Genetic modifiers of neurofibromatosis type 1-associated café-au-lait macule count identified using multi-platform analysis. PLoS Genet 2014; 10:e1004575. [PMID: 25329635 PMCID: PMC4199479 DOI: 10.1371/journal.pgen.1004575] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 07/08/2014] [Indexed: 01/27/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant, monogenic disorder of dysregulated neurocutaneous tissue growth. Pleiotropy, variable expressivity and few NF1 genotype-phenotype correlates limit clinical prognostication in NF1. Phenotype complexity in NF1 is hypothesized to derive in part from genetic modifiers unlinked to the NF1 locus. In this study, we hypothesized that normal variation in germline gene expression confers risk for certain phenotypes in NF1. In a set of 79 individuals with NF1, we examined the association between gene expression in lymphoblastoid cell lines with NF1-associated phenotypes and sequenced select genes with significant phenotype/expression correlations. In a discovery cohort of 89 self-reported European-Americans with NF1 we examined the association between germline sequence variants of these genes with café-au-lait macule (CALM) count, a tractable, tumor-like phenotype in NF1. Two correlated, common SNPs (rs4660761 and rs7161) between DPH2 and ATP6V0B were significantly associated with the CALM count. Analysis with tiled regression also identified SNP rs4660761 as significantly associated with CALM count. SNP rs1800934 and 12 rare variants in the mismatch repair gene MSH6 were also associated with CALM count. Both SNPs rs7161 and rs4660761 (DPH2 and ATP6V0B) were highly significant in a mega-analysis in a combined cohort of 180 self-reported European-Americans; SNP rs1800934 (MSH6) was near-significant in a meta-analysis assuming dominant effect of the minor allele. SNP rs4660761 is predicted to regulate ATP6V0B, a gene associated with melanosome biology. Individuals with homozygous mutations in MSH6 can develop an NF1-like phenotype, including multiple CALMs. Through a multi-platform approach, we identified variants that influence NF1 CALM count. Neurofibromatosis type 1 (NF1) is a relatively common genetic disease that increases the chance to develop a variety of benign and malignant tumors. People with NF1 also typically feature a large number of birthmarks called café-au-lait macules. It is difficult to predict severity or specific problems in NF1. We sought to identify genes (other than NF1, the gene that causes the disease) that influence severity in NF1. We determined the number of café-au-lait macules in two groups of people with NF1. We measured the gene expression of about 10,000 genes in the cultured white blood cells from one group of people. We then sequenced a group of genes whose expression level was increased in people with higher numbers of café-au-lait macules. In the first group, we found common variants in genes MSH6 and near DPH2 and ATP6V0B that were significantly associated with the number of café-au-lait macules. Some of these variants were close to significant in the second group of people. The two variants near DPH2 and ATP6V0B were very significant when analysed in both groups combined. Our work is among the first to identify genetic variants that influence the severity of NF1.
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Affiliation(s)
- Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
| | - Heejong Sung
- Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Paula L. Hyland
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
| | - Jennifer L. Sloan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sarah L. Ruppert
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Andrea M. Baldwin
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joseph F. Boland
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
| | - Sara E. Bass
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
| | - Hyo Jung Lee
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kristine M. Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
| | - Xijun Zhang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
| | | | - James C. Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Rockville, Maryland, United States of America
| | - Brigitte C. Widemann
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexander F. Wilson
- Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail:
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Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol 2014; 15:469. [PMID: 25239471 PMCID: PMC4203885 DOI: 10.1186/s13059-014-0469-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 09/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene expression is epigenetically regulated by a combination of histone modifications and methylation of CpG dinucleotides in promoters. In normal cells, CpG-rich promoters are typically unmethylated, marked with histone modifications such as H3K4me3, and are highly active. During neoplastic transformation, CpG dinucleotides of CG-rich promoters become aberrantly methylated, corresponding with the removal of active histone modifications and transcriptional silencing. Outside of promoter regions, distal enhancers play a major role in the cell type-specific regulation of gene expression. Enhancers, which function by bringing activating complexes to promoters through chromosomal looping, are also modulated by a combination of DNA methylation and histone modifications. RESULTS Here we use HCT116 colorectal cancer cells with and without mutations in DNA methyltransferases, the latter of which results in a 95% reduction in global DNA methylation levels. These cells are used to study the relationship between DNA methylation, histone modifications, and gene expression. We find that the loss of DNA methylation is not sufficient to reactivate most of the silenced promoters. In contrast, the removal of DNA methylation results in the activation of a large number of enhancer regions as determined by the acquisition of active histone marks. CONCLUSIONS Although the transcriptome is largely unaffected by the loss of DNA methylation, we identify two distinct mechanisms resulting in the upregulation of distinct sets of genes. One is a direct result of DNA methylation loss at a set of promoter regions and the other is due to the presence of new intragenic enhancers.
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Londin ER, Adijanto J, Philp N, Novelli A, Vitale E, Perria C, Serra G, Alesi V, Surrey S, Fortina P. Donor splice-site mutation in CUL4B is likely cause of X-linked intellectual disability. Am J Med Genet A 2014; 164A:2294-9. [PMID: 24898194 DOI: 10.1002/ajmg.a.36629] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 05/14/2014] [Indexed: 12/21/2022]
Abstract
X-linked intellectual disability is the most common form of cognitive disability in males. Syndromic intellectual disability encompasses cognitive deficits with other medical and behavioral manifestations. Recently, a large family with a novel form of syndromic X-linked intellectual disability was characterized. Eight of 24 members of the family are male and had cognitive dysfunction, short stature, aphasia, skeletal abnormalities, and minor anomalies. To identify the causative gene(s), we performed exome sequencing in three affected boys, both parents, and an unaffected sister. We identified a haplotype consisting of eight variants located in cis within the linkage region that segregated with affected members in the family. Of these variants, two were novel. The first was at the splice-donor site of intron 7 (c.974+1G>T) in the cullin-RING ubiquitin ligase (E3) gene, CUL4B. This variant is predicted to result in failure to splice and remove intron 7 from the primary transcript. The second variant mapped to the 3'-UTR region of the KAISO gene (c.1127T>G). Sanger sequencing validated the variants in these relatives as well as in three affected males and five carriers. The KAISO gene variant was predicted to create a binding site for the microRNAs miR-4999 and miR-4774; however, luciferase expression assays failed to validate increased targeting of these miRNAs to the variant 3'-UTR. This SNP may affect 3'-UTR structure leading to decreased mRNA stability. Our results suggest that the intellectual disability phenotype in this family is caused by aberrant splicing and removal of intron 7 from CUL4B gene primary transcript.
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Affiliation(s)
- Eric R Londin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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48
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Baubec T, Schübeler D. Genomic patterns and context specific interpretation of DNA methylation. Curr Opin Genet Dev 2014; 25:85-92. [PMID: 24614011 DOI: 10.1016/j.gde.2013.11.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/29/2013] [Indexed: 12/21/2022]
Abstract
Methylation of CpG dinucleotides is a reversible modification of DNA that is highly prevalent throughout mammalian genomes. Recent advances generated genomic DNA methylation maps during cellular differentiation at unprecedented resolution. Combined with functional assays this revealed that dynamics in DNA methylation coincide with changes in regulatory activity and that transcription factors play an important role in shaping methylation patterns. This tightly links DNA methylation with underlying DNA sequence features and suggests that a substantial fraction of methylation changes occur downstream of gene regulation. Here we discuss our current understanding of the context-dependent readout of DNA methylation and criteria that need to be fulfilled for this modification to be instructive for gene regulation.
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Affiliation(s)
- Tuncay Baubec
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland.
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland; University of Basel, Faculty of Science, Petersplatz 1, Basel 4003, Switzerland.
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49
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Blattler A, Farnham PJ. Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem 2013; 288:34287-94. [PMID: 24151070 DOI: 10.1074/jbc.r113.512517] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA methylation, which occurs predominantly at CpG dinucleotides, is a potent epigenetic repressor of transcription. Because DNA methylation is reversible, there is much interest in understanding the mechanisms by which it can be regulated by DNA-binding transcription factors. We discuss several models that, by incorporating sequence motifs, CpG density, and methylation levels, attempt to link the binding of a transcription factor with the acquisition or loss of DNA methylation at promoters and distal regulatory elements. Additional in vivo genome-wide characterization of transcription factor binding patterns and high-resolution DNA methylation analyses are clearly required for stronger support of each model.
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Affiliation(s)
- Adam Blattler
- From the Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 and
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50
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The POZ-ZF transcription factor Kaiso (ZBTB33) induces inflammation and progenitor cell differentiation in the murine intestine. PLoS One 2013; 8:e74160. [PMID: 24040197 PMCID: PMC3764064 DOI: 10.1371/journal.pone.0074160] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/26/2013] [Indexed: 01/08/2023] Open
Abstract
Since its discovery, several studies have implicated the POZ-ZF protein Kaiso in both developmental and tumorigenic processes. However, most of the information regarding Kaiso’s function to date has been gleaned from studies in Xenopus laevis embryos and mammalian cultured cells. To examine Kaiso’s role in a relevant, mammalian organ-specific context, we generated and characterized a Kaiso transgenic mouse expressing a murine Kaiso transgene under the control of the intestine-specific villin promoter. Kaiso transgenic mice were viable and fertile but pathological examination of the small intestine revealed distinct morphological changes. Kaiso transgenics (KaisoTg/+) exhibited a crypt expansion phenotype that was accompanied by increased differentiation of epithelial progenitor cells into secretory cell lineages; this was evidenced by increased cell populations expressing Goblet, Paneth and enteroendocrine markers. Paradoxically however, enhanced differentiation in KaisoTg/+ was accompanied by reduced proliferation, a phenotype reminiscent of Notch inhibition. Indeed, expression of the Notch signalling target HES-1 was decreased in KaisoTg/+ animals. Finally, our Kaiso transgenics exhibited several hallmarks of inflammation, including increased neutrophil infiltration and activation, villi fusion and crypt hyperplasia. Interestingly, the Kaiso binding partner and emerging anti-inflammatory mediator p120ctn is recruited to the nucleus in KaisoTg/+ mice intestinal cells suggesting that Kaiso may elicit inflammation by antagonizing p120ctn function.
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