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Liu W, Kurkewich JL, Stoddart A, Khan S, Anandan D, Gaubil AN, Wolfgeher DJ, Jueng L, Kron SJ, McNerney ME. CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex. Cell Rep 2024; 43:114227. [PMID: 38735044 DOI: 10.1016/j.celrep.2024.114227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 03/16/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor-suppressive functions of CUX1. Here, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 regulates hematopoietic lineage commitment and homeostasis via pioneer factor activity, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.
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Affiliation(s)
- Weihan Liu
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Angela Stoddart
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Saira Khan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Dhivyaa Anandan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Alexandre N Gaubil
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Donald J Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Lia Jueng
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen J Kron
- The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Megan E McNerney
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL 60637, USA.
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2
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Roy L, Bobbs A, Sattler R, Kurkewich JL, Dausinas PB, Nallathamby P, Cowden Dahl KD. CD133 Promotes Adhesion to the Ovarian Cancer Metastatic Niche. Cancer Growth Metastasis 2018; 11:1179064418767882. [PMID: 29662326 PMCID: PMC5894897 DOI: 10.1177/1179064418767882] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/09/2018] [Indexed: 12/25/2022]
Abstract
Cancer stem cells (CSCs) are an attractive therapeutic target due to their predicted role in both metastasis and chemoresistance. One of the most commonly agreed on markers for ovarian CSCs is the cell surface protein CD133. CD133+ ovarian CSCs have increased tumorigenicity, resistance to chemotherapy, and increased metastasis. Therefore, we were interested in defining how CD133 is regulated and whether it has a role in tumor metastasis. Previously we found that overexpression of the transcription factor, ARID3B, increased the expression of PROM1 (CD133 gene) in ovarian cancer cells in vitro and in xenograft tumors. We report that ARID3B directly regulates PROM1 expression. Importantly, in a xenograft mouse model of ovarian cancer, knockdown of PROM1 in cells expressing exogenous ARID3B resulted in increased survival time compared with cells expressing ARID3B and a control short hairpin RNA. This indicated that ARID3B regulation of PROM1 is critical for tumor growth. Moreover, we hypothesized that CD133 may affect metastatic spread. Given that the peritoneal mesothelium is a major site of ovarian cancer metastasis, we explored the role of PROM1 in mesothelial attachment. PROM1 expression increased adhesion to mesothelium in vitro and ex vivo. Collectively, our work demonstrates that ARID3B regulates PROM1 adhesion to the ovarian cancer metastatic niche.
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Affiliation(s)
- Lynn Roy
- Harper Cancer Research Institute, South Bend, IN, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN, USA
| | - Alexander Bobbs
- Harper Cancer Research Institute, South Bend, IN, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN, USA
| | - Rachel Sattler
- Harper Cancer Research Institute, South Bend, IN, USA.,Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Jeffrey L Kurkewich
- Harper Cancer Research Institute, South Bend, IN, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Paige B Dausinas
- Harper Cancer Research Institute, South Bend, IN, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN, USA
| | - Prakash Nallathamby
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Karen D Cowden Dahl
- Harper Cancer Research Institute, South Bend, IN, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN, USA.,Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
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3
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Kurkewich JL, Boucher A, Klopfenstein N, Baskar R, Kapur R, Dahl R. The mirn23a and mirn23b microrna clusters are necessary for proper hematopoietic progenitor cell production and differentiation. Exp Hematol 2017; 59:14-29. [PMID: 29288704 DOI: 10.1016/j.exphem.2017.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 12/17/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022]
Abstract
Mice deficient for microRNA (miRNA) cluster mirn23a exhibit increased B lymphopoiesis at the expense of myelopoiesis, whereas hematopoietic stem and progenitor cell (HSPC) populations are unchanged. Mammals possess a paralogous mirn23b gene that can give rise to three mature miRNAs (miR-23b, miR-24-1, and miR-27b) that have identical seed/mRNA-targeting sequences to their mirn23a counterparts. To assess whether compound deletion of mirn23a and mirn23b exacerbates the hematopoietic phenotype observed in mirn23a-/- mice, we generated a compound mirn23a-/-mirn23bfl/fl:Mx1-Cre conditional knockout mouse and assayed hematopoietic development after excision of mirn23b. Loss of both genes in adult bone marrow further skewed HSPC differentiation toward B cells at the expense of myeloid cells, demonstrating a dosage-dependent effect on regulating cell differentiation. Strikingly, double-knockout (DKO) mice had decreased bone marrow cellularity with significantly decreased hematopoietic stem cell and HSPC populations, a phenotype not observed in mice deficient for mirn23a alone. Competitive transplantation assays showed decreased contribution of mirn23a-/-mirn23b-/- HSPCs to hematopoietic lineages at 6 and 12 weeks after transplantation. Defects in the proliferation of mirn23a-/-b-/- HSPCs was not observed; however, DKO cells were more apoptotic compared with both wild-type and mirn23a-/- cells. Together, our data show that complete loss of mirn23a/mirn23b miRNAs results in decreased blood production and affects lineage output in a concentration-dependent manner.
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Affiliation(s)
- Jeffrey L Kurkewich
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA; Harper Cancer Research Institute, South Bend, IN, USA
| | - Austin Boucher
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA; Harper Cancer Research Institute, South Bend, IN, USA
| | - Nathan Klopfenstein
- Harper Cancer Research Institute, South Bend, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA
| | - Ramdas Baskar
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Reuben Kapur
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard Dahl
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA; Harper Cancer Research Institute, South Bend, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA.
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4
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Kurkewich JL, Hansen J, Klopfenstein N, Zhang H, Wood C, Boucher A, Hickman J, Muench DE, Grimes HL, Dahl R. The miR-23a~27a~24-2 microRNA cluster buffers transcription and signaling pathways during hematopoiesis. PLoS Genet 2017; 13:e1006887. [PMID: 28704388 PMCID: PMC5531666 DOI: 10.1371/journal.pgen.1006887] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 07/27/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023] Open
Abstract
MicroRNA cluster mirn23a has previously been shown to promote myeloid development at the expense of lymphoid development in overexpression and knockout mouse models. This polarization is observed early in hematopoietic development, with an increase in common lymphoid progenitors (CLPs) and a decrease in all myeloid progenitor subsets in adult bone marrow. The pool size of multipotential progenitors (MPPs) is unchanged; however, in this report we observe by flow cytometry that polarized subsets of MPPs are changed in the absence of mirn23a. Additionally, in vitro culture of MPPs and sorted MPP transplants showed that these cells have decreased myeloid and increased lymphoid potential in vitro and in vivo. We investigated the mechanism by which mirn23a regulates hematopoietic differentiation and observed that mirn23a promotes myeloid development of hematopoietic progenitors through regulation of hematopoietic transcription factors and signaling pathways. Early transcription factors that direct the commitment of MPPs to CLPs (Ikzf1, Runx1, Satb1, Bach1 and Bach2) are increased in the absence of mirn23a miRNAs as well as factors that commit the CLP to the B cell lineage (FoxO1, Ebf1, and Pax5). Mirn23a appears to buffer transcription factor levels so that they do not stochastically reach a threshold level to direct differentiation. Intriguingly, mirn23a also inversely regulates the PI3 kinase (PI3K)/Akt and BMP/Smad signaling pathways. Pharmacological inhibitor studies, coupled with dominant active/dominant negative biochemical experiments, show that both signaling pathways are critical to mirn23a’s regulation of hematopoietic differentiation. Lastly, consistent with mirn23a being a physiological inhibitor of B cell development, we observed that the essential B cell transcription factor EBF1 represses expression of mirn23a. In summary, our data demonstrates that mirn23a regulates a complex array of transcription and signaling pathways to modulate adult hematopoiesis. MicroRNAs (miRNAs) are small ~22 nucleotide long RNA molecules that are involved in regulating multiple cellular processes through inhibiting the expression of target proteins. We previously identified a gene (mirn23a) that codes for 3 miRNAs that control the development of immune cells in the bone marrow. The miRNAs promote the development of innate immune cells, macrophages and granulocytes, while repressing the development of B cells. Here we show that mirn23a miRNAs negatively affect the expression of multiple proteins that are involved in directing blood progenitor cells to become B cells. Additionally, we observed that modulation of FoxO1 and Smad proteins, downstream effectors of two signaling pathways (PI3 kinase/ Akt and BMP/ Smad), is critical to direct immune cell development. This is the first observation that these pathways are potentially coregulated during the commitment of blood progenitors to mature cells of the immune system. Consistent with mirn23a being a critical gene for committing progenitors to innate immune cells at the expense of B cells, we observed that a critical B cell protein represses the expression of mirn23a. In conclusion, we demonstrate the mirn23a regulation of blood development is due to a complex regulation of both transcription factors and signaling pathways.
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Affiliation(s)
- Jeffrey L. Kurkewich
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Justin Hansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Nathan Klopfenstein
- Harper Cancer Research Institute, South Bend, IN, United States of America
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, United States of America
| | - Helen Zhang
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Christian Wood
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Austin Boucher
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Joseph Hickman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - David E. Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States of America
| | - H. Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States of America
| | - Richard Dahl
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, United States of America
- * E-mail:
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5
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Kurkewich JL, Klopfenstein N, Hallas WM, Wood C, Sattler RA, Das C, Tucker H, Dahl R, Cowden Dahl KD. Arid3b Is Critical for B Lymphocyte Development. PLoS One 2016; 11:e0161468. [PMID: 27537840 PMCID: PMC4990195 DOI: 10.1371/journal.pone.0161468] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/06/2016] [Indexed: 11/18/2022] Open
Abstract
Arid3a and Arid3b belong to a subfamily of ARID (AT-rich interaction domain) transcription factors. The Arid family is involved in regulating chromatin accessibility, proliferation, and differentiation. Arid3a and Arid3b are closely related and share a unique REKLES domain that mediates their homo- and hetero-multimerization. Arid3a was originally isolated as a B cell transcription factor binding to the AT rich matrix attachment regions (MARS) of the immunoglobulin heavy chain intronic enhancer. Deletion of Arid3a results in a highly penetrant embryonic lethality with severe defects in erythropoiesis and hematopoietic stem cells (HSCs). The few surviving Arid3a-/- (<1%) animals have decreased HSCs and early progenitors in the bone marrow, but all mature lineages are normally represented in the bone marrow and periphery except for B cells. Arid3b-/- animals die around E7.5 precluding examination of hematopoietic development. So it is unclear whether the phenotype of Arid3a loss on hematopoiesis is dependent or independent of Arid3b. In this study we circumvented this limitation by also examining hematopoiesis in mice with a conditional allele of Arid3b. Bone marrow lacking Arid3b shows decreased common lymphoid progenitors (CLPs) and downstream B cell populations while the T cell and myeloid lineages are unchanged, reminiscent of the adult hematopoietic defect in Arid3a mice. Unlike Arid3a-/- mice, HSC populations are unperturbed in Arid3b-/- mice. This study demonstrates that HSC development is independent of Arid3b, whereas B cell development requires both Arid3a and Arid3b transcription factors.
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Affiliation(s)
- Jeffrey L Kurkewich
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America.,Harper Cancer Research Institute, South Bend, Indiana, United States of America
| | - Nathan Klopfenstein
- Harper Cancer Research Institute, South Bend, Indiana, United States of America.,Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, Indiana, United States of America
| | - William M Hallas
- Harper Cancer Research Institute, South Bend, Indiana, United States of America.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, South Bend, Indiana, United States of America
| | - Christian Wood
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America.,Harper Cancer Research Institute, South Bend, Indiana, United States of America
| | - Rachel A Sattler
- Harper Cancer Research Institute, South Bend, Indiana, United States of America.,Deparment of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Chhaya Das
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Haley Tucker
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Richard Dahl
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America.,Harper Cancer Research Institute, South Bend, Indiana, United States of America.,Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, Indiana, United States of America
| | - Karen D Cowden Dahl
- Harper Cancer Research Institute, South Bend, Indiana, United States of America.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, South Bend, Indiana, United States of America.,Deparment of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
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6
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Kurkewich JL, Bikorimana E, Nguyen T, Klopfenstein N, Zhang H, Hallas WM, Stayback G, McDowell MA, Dahl R. The mirn23a microRNA cluster antagonizes B cell development. J Leukoc Biol 2016; 100:665-677. [PMID: 27084569 DOI: 10.1189/jlb.1hi0915-398rr] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 03/21/2016] [Indexed: 12/20/2022] Open
Abstract
Ablation of microRNA synthesis by deletion of the microRNA-processing enzyme Dicer has demonstrated that microRNAs are necessary for normal hematopoietic differentiation and function. However, it is still unclear which specific microRNAs are required for hematopoiesis and at what developmental stages they are necessary. This is especially true for immune cell development. We previously observed that overexpression of the products of the mirn23a gene (microRNA-23a, -24-2, and 27a) in hematopoietic progenitors increased myelopoiesis with a reciprocal decrease in B lymphopoiesis, both in vivo and in vitro. In this study, we generated a microRNA-23a, -24-2, and 27a germline knockout mouse to determine whether microRNA-23a, -24-2, and 27a expression was essential for immune cell development. Characterization of hematopoiesis in microRNA-23a, -24-2, and 27a-/- mice revealed a significant increase in B lymphocytes in both the bone marrow and the spleen, with a concomitant decrease in myeloid cells (monocytes/granulocytes). Analysis of the bone marrow progenitor populations revealed a significant increase in common lymphoid progenitors and a significant decrease in both bone marrow common myeloid progenitors and granulocyte monocyte progenitors. Gene-expression analysis of primary hematopoietic progenitors and multipotent erythroid myeloid lymphoid cells showed that microRNA-23a, -24-2, and 27a regulates essential B cell gene-expression networks. Overexpression of microRNA-24-2 target Tribbles homolog 3 can recapitulate the microRNA-23a, -24-2, and 27a-/- phenotype in vitro, suggesting that increased B cell development in microRNA-23a, -24-2, and 27a null mice can be partially explained by a Tribbles homolog 3-dependent mechanism. Data from microRNA-23a, -24-2, and 27a-/- mice support a critical role for this microRNA cluster in regulating immune cell populations through repression of B lymphopoiesis.
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Affiliation(s)
- Jeffrey L Kurkewich
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Emmanuel Bikorimana
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, Indiana, USA
| | - Tan Nguyen
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, Indiana, USA
| | - Nathan Klopfenstein
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, Indiana, USA
| | - Helen Zhang
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - William M Hallas
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, Indiana, USA
| | - Gwen Stayback
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA; and
| | - Mary Ann McDowell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA; and
| | - Richard Dahl
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, Indiana, USA
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7
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Bulla GA, Aylmer CM, Dust AL, Kurkewich JL, Mire LK, Estanda AB. Genome-wide analysis of hepatic gene silencing in hepatoma cell variants. Genomics 2012; 100:176-83. [PMID: 22659237 DOI: 10.1016/j.ygeno.2012.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/18/2012] [Accepted: 05/22/2012] [Indexed: 10/28/2022]
Abstract
Genome-wide gene expression profiling was carried out on rat hepatoma cells and compared to profiles of hepatoma "variant" cell lines derived via a stringent selection protocol that enriches for rare cells (<1 in 100,000 cells) that fail to drive liver function. Results show 132 genes that are strongly (>5-fold) repressed in each of the four variant cell lines tested. An additional 68 genes were repressed in 3 of 4 variant cell lines. Importantly, several of the repressed genes are members of transcriptional activation pathways, suggesting that they may contribute to maintaining the hepatic phenotype. Ectopic expression of the HNF1A gene in a variant cell line resulted in activation of 56 genes, 37 of which were included in the repressed data set. These data suggest that a high level of reprogramming occurs when hepatoma cells convert to a non-differentiated phenotype, a process that can be partially reversed by the introduction of transcription factors.
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Affiliation(s)
- Gary A Bulla
- Department of Biological Sciences, Eastern Illinois University, 600 Lincoln Avenue, Charleston, IL 61920, USA.
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