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Herlofsen SR, Høiby T, Cacchiarelli D, Zhang X, Mikkelsen TS, Brinchmann JE. Brief report: importance of SOX8 for in vitro chondrogenic differentiation of human mesenchymal stromal cells. Stem Cells 2015; 32:1629-35. [PMID: 24449344 DOI: 10.1002/stem.1642] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 10/16/2013] [Accepted: 12/11/2013] [Indexed: 01/05/2023]
Abstract
The transcription factor SOX9 is believed to be the master regulator of chondrogenesis. SOX8 is another SOX group E transcription factor with a high degree of homology to SOX9. Here, we demonstrate that SOX8 mRNA levels decrease during in vitro dedifferentiation of human articular chondrocytes and increase during chondrogenic differentiation of mesenchymal stromal cells. Knockdown of SOX9 reduced the expression of SOX8, COL2A1, and a range of other chondrogenic molecules. SOX8 knockdown reduced the expression of a large number of overlapping chondrogenic molecules, but not SOX9. Neither siSOX9 nor siSOX8 altered expression of the hypertrophic marker gene COL10A1. siSOX9, but not siSOX8 led to upregulation of hypertrophy associated genes MMP13 and ALPL. Transfection of synthetic SOX5, 6, and 9 mRNA trio upregulated SOX8, COL2A1, and ACAN, but not COL10A1 mRNA. Replacement of synthetic SOX9 by SOX8 in the SOX trio showed similar but lower chondrogenic effect. We conclude that SOX8 expression is regulated by SOX9, and that both together with SOX5 and SOX6 are required as a SOX quartet for transcription of COL2A1 and a large number of other chondrogenic molecules. Neither SOX8 nor SOX9 affect COL10A1 expression, but SOX9 inhibits chondrocyte hypertrophy through inhibition of MMP13 and ALPL expression.
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Affiliation(s)
- Sarah R Herlofsen
- Norwegian Center for Stem Cell Research and Institute of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
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Micklem DR, Blø M, Bergström P, Hodneland E, Tiron C, Høiby T, Gjerdrum C, Hammarsten O, Lorens JB. Flow cytometry-based functional selection of RNA interference triggers for efficient epi-allelic analysis of therapeutic targets. BMC Biotechnol 2014; 14:57. [PMID: 24952598 PMCID: PMC4074332 DOI: 10.1186/1472-6750-14-57] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/18/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The dose-response relationship is a fundamental pharmacological parameter necessary to determine therapeutic thresholds. Epi-allelic hypomorphic analysis using RNA interference (RNAi) can similarly correlate target gene dosage with cellular phenotypes. This however requires a set of RNAi triggers empirically determined to attenuate target gene expression to different levels. RESULTS In order to improve our ability to incorporate epi-allelic analysis into target validation studies, we developed a novel flow cytometry-based functional screening approach (CellSelectRNAi) to achieve unbiased selection of shRNAs from high-coverage libraries that knockdown target gene expression to predetermined levels. Employing a Gaussian probability model we calculated that knockdown efficiency is inferred from shRNA sequence frequency profiles derived from sorted hypomorphic cell populations. We used this approach to generate a hypomorphic epi-allelic cell series of shRNAs to reveal a functional threshold for the tumor suppressor p53 in normal and transformed cells. CONCLUSION The unbiased CellSelectRNAi flow cytometry-based functional screening approach readily provides an epi-allelic series of shRNAs for graded reduction of target gene expression and improved phenotypic validation.
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Affiliation(s)
- David R Micklem
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
- BerGenBio A/S, N-5009, Bergen, Norway
| | - Magnus Blø
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
- BerGenBio A/S, N-5009, Bergen, Norway
| | - Petra Bergström
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, S-413 45 Göteborg, Sweden
| | - Erlend Hodneland
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Crina Tiron
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Torill Høiby
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | | | - Ola Hammarsten
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, S-413 45 Göteborg, Sweden
| | - James B Lorens
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
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Herlofsen SR, Bryne JC, Høiby T, Wang L, Issner R, Zhang X, Coyne MJ, Boyle P, Gu H, Meza-Zepeda LA, Collas P, Mikkelsen TS, Brinchmann JE. Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells. BMC Genomics 2013; 14:105. [PMID: 23414147 PMCID: PMC3620534 DOI: 10.1186/1471-2164-14-105] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [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: 12/03/2012] [Accepted: 02/12/2013] [Indexed: 01/01/2023] Open
Abstract
Background For safe clinical application of engineered cartilage made from mesenchymal stem cells (MSCs), molecular mechanisms for chondrogenic differentiation must be known in detail. Changes in gene expression and extracellular matrix synthesis have been extensively studied, but the epigenomic modifications underlying these changes have not been described. To this end we performed whole-genome chromatin immunoprecipitation and deep sequencing to quantify six histone modifications, reduced representation bisulphite sequencing to quantify DNA methylation and mRNA microarrays to quantify gene expression before and after 7 days of chondrogenic differentiation of MSCs in an alginate scaffold. To add to the clinical relevance of our observations, the study is based on primary bone marrow-derived MSCs from four donors, allowing us to investigate inter-individual variations. Results We see two levels of relationship between epigenetic marking and gene expression. First, a large number of genes ontogenetically linked to MSC properties and the musculoskeletal system are epigenetically prepatterned by moderate changes in H3K4me3 and H3K9ac near transcription start sites. Most of these genes remain transcriptionally unaltered. Second, transcriptionally upregulated genes, more closely associated with chondrogenesis, are marked by H3K36me3 in gene bodies, highly increased H3K4me3 and H3K9ac on promoters and 5' end of genes, and increased H3K27ac and H3K4me1 marking in at least one enhancer region per upregulated gene. Within the 7-day time frame, changes in promoter DNA methylation do not correlate significantly with changes in gene expression. Inter-donor variability analysis shows high level of similarity between the donors for this data set. Conclusions Histone modifications, rather than DNA methylation, provide the primary epigenetic control of early differentiation of MSCs towards the chondrogenic lineage.
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Affiliation(s)
- Sarah R Herlofsen
- Institute of Immunology and Norwegian Center for Stem Cell Research, Oslo University Hospital Rikshospitalet, Oslo 0424, Norway.
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Gjerdrum C, Tiron C, Høiby T, Stefansson I, Haugen H, Sandal T, Collet K, Li S, McCormack E, Gjertsen BT, Micklem D, Akslen L, Glackin C, Lorens J. Abstract B105: Axl is an essential epithelial-to-mesenchymal transition-induced regulator of breast cancer metastasis and patient survival. Mol Cancer Ther 2009. [DOI: 10.1158/1535-7163.targ-09-b105] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Metastasis underlies the majority of cancer-related deaths. Hence, furthering our understanding of the molecular mechanisms that enable tumor cell dissemination is a vital health issue. Epithelial-to-mesenchymal transitions (EMT) endow carcinoma cells with enhanced migratory and survival attributes that facilitate malignant progression. Characterization of EMT effectors is likely to yield new insights into metastasis and novel avenues for treatment. We show that the presence of the receptor tyrosine kinase Axl in mammography-detected primary breast cancers independently predicts strongly reduced overall patient survival, and matched patient metastatic lesions show enhanced Axl expression. We demonstrate that Axl is strongly induced by epithelial-to-mesenchymal transition in pre-malignant mammary epithelial cells that establishes an autocrine signaling loop with its ligand, Gas6. Using epi-allelic RNA interference analysis in metastatic breast cancer cells we delineated a distinct threshold of Axl expression for mesenchymal-like in vitro cell invasiveness, and to form tumors in foreign and tissue engineered microenvironments in vivo. Importantly, Axl knockdown completely prevented the spread of highly metastatic breast carcinoma cells from the mammary gland to lymph nodes and several major organs, and increased overall survival, in two different optical imaging-based experimental breast cancer models. Thus, Axl represents a novel downstream effector of tumor cell EMT that is required for breast cancer metastasis. The detection and targeted treatment of Axl-expressing tumors represents an important new therapeutic strategy for breast cancer.
Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B105.
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Affiliation(s)
| | | | | | | | | | | | | | - Shan Li
- 2 Beckman Center, City of Hope, Duarte, CA
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Høiby T, Zhou H, Mitsiou DJ, Stunnenberg HG. A facelift for the general transcription factor TFIIA. ACTA ACUST UNITED AC 2007; 1769:429-36. [PMID: 17560669 DOI: 10.1016/j.bbaexp.2007.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 04/20/2007] [Accepted: 04/24/2007] [Indexed: 10/23/2022]
Abstract
TFIIA was classified as a general transcription factor when it was first identified. Since then it has been debated to what extent it can actually be regarded as "general". The most notable feature of TFIIA is the proteolytical cleavage of the TFIIAalphabeta into a TFIIAalpha and TFIIAbeta moiety which has long remained a mystery. Recent studies have showed that TFIIA is cleaved by Taspase1 which was initially identified as the protease for the proto-oncogene MLL. Cleavage of TFIIA does not appear to serve as a step required for its activation as the uncleaved TFIIA in the Taspase1 knock-outs adequately support bulk transcription. Instead, cleavage of TFIIA seems to affect its turn-over and may be a part of an intricate degradation mechanism that allows fine-tuning of cellular levels of TFIIA. Cleavage might also be responsible for switching transcription program as the uncleaved and cleaved TFIIA might have distinct promoter specificity during development and differentiation. This review will focus on functional characteristics of TFIIA and discuss novel insights in the role of this elusive transcription factor.
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Affiliation(s)
- Torill Høiby
- NCMLS, Department of Molecular Biology, 191, Radboud University of Nijmegen, PO Box 91001, 6500 HB Nijmegen, The Netherlands
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Zhou H, Spicuglia S, Hsieh JJD, Mitsiou DJ, Høiby T, Veenstra GJC, Korsmeyer SJ, Stunnenberg HG. Uncleaved TFIIA is a substrate for taspase 1 and active in transcription. Mol Cell Biol 2006; 26:2728-35. [PMID: 16537915 PMCID: PMC1430320 DOI: 10.1128/mcb.26.7.2728-2735.2006] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In higher eukaryotes, the large subunit of the general transcription factor TFIIA is encoded by the single TFIIAalphabeta gene and posttranslationally cleaved into alpha and beta subunits. The molecular mechanisms and biological significance of this proteolytic process have remained obscure. Here, we show that TFIIA is a substrate of taspase 1 as reported for the trithorax group mixed-lineage leukemia protein. We demonstrate that recombinant taspase 1 cleaves TFIIA in vitro. Transfected taspase 1 enhances cleavage of TFIIA, and RNA interference knockdown of endogenous taspase 1 diminishes cleavage of TFIIA in vivo. In taspase 1-/- MEF cells, only uncleaved TFIIA is detected. In Xenopus laevis embryos, knockdown of TFIIA results in phenotype and expression defects. Both defects can be rescued by expression of an uncleavable TFIIA mutant. Our study shows that uncleaved TFIIA is transcriptionally active and that cleavage of TFIIA does not serve to render TFIIA competent for transcription. We propose that cleavage fine tunes the transcription regulation of a subset of genes during differentiation and development.
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Affiliation(s)
- Huiqing Zhou
- NCMLS, Department of Molecular Biology, 191, Radboud University of Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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Høiby T, Mitsiou DJ, Zhou H, Erdjument-Bromage H, Tempst P, Stunnenberg HG. Cleavage and proteasome-mediated degradation of the basal transcription factor TFIIA. EMBO J 2004; 23:3083-91. [PMID: 15257296 PMCID: PMC514921 DOI: 10.1038/sj.emboj.7600304] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Accepted: 06/07/2004] [Indexed: 11/09/2022] Open
Abstract
The transcription factor TFIIA is encoded by two genes, TFIIAalphabeta and TFIIAgamma. In higher eukaryotes, the TFIIAalphabeta is translated as a precursor and undergoes proteolytic cleavage; the regulation and biological implications of the cleavage have remained elusive. We determined by Edman degradation that the TFIIAbeta subunit starts at Asp 278. We found that a cleavage recognition site (CRS), a string of amino acids QVDG at positions -6 to -3 from Asp 278, is essential for cleavage. Mutations in the CRS that prevent cleavage significantly prolong the half-life of TFIIA. Consistently, the cleaved TFIIA is a substrate for the ubiquitin pathway and proteasome-mediated degradation. We show that mutations in the putative phosphorylation sites of TFIIAbeta greatly affect degradation of the beta-subunit. We propose that cleavage and subsequent degradation fine-tune the amount of TFIIA in the cell and consequently the level of transcription.
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Affiliation(s)
- Torill Høiby
- NCMLS, Department of Molecular Biology, HB Nijmegen, The Netherlands
| | - Dimitra J Mitsiou
- NCMLS, Department of Molecular Biology, HB Nijmegen, The Netherlands
| | - Huiqing Zhou
- NCMLS, Department of Molecular Biology, HB Nijmegen, The Netherlands
| | | | - Paul Tempst
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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