Computational design and application of endogenous promoters for transcriptionally targeted gene therapy for rheumatoid arthritis.

The promoter regions of genes that are differentially regulated in the synovial membrane during the course of rheumatoid arthritis (RA) represent attractive candidates for application in transcriptionally targeted gene therapy. In this study, we applied an unbiased computational approach to define proximal-promoters from a gene expression profiling study of murine experimental arthritis. Synovium expression profiles from progressing stages of collagen-induced arthritis (CIA) were classified into six distinct groups using k-means clustering. Using an algorithm based on local over-representation and comparative genomics, we identified putatively functional transcription factor-binding sites (TFBS) in TATA-dependent proximal-promoters. Applying a filter based on spacing between TATA box and transcription start site (TSS) combined with the presence of over-represented nuclear factor kappaB (NFkappaB), AP-1, or CCAAT/enhancer-binding protein beta (C/EBPbeta) sites, 382 candidate murine and human promoters were reduced to 66, corresponding to 45 genes. In vitro, 9 out of 10 computationally defined promoter regions conferred cytokine-inducible expression in murine cells and human synovial fibroblasts. Under these conditions, the serum amyloid A3 (Saa3) promoter showed the strongest transcriptional induction and strength. We applied this promoter for driving therapeutically efficacious levels of the interleukin-1 receptor antagonist (Il1rn) in a disease-regulated fashion. These results demonstrate the value of bioinformatics for guiding the selection of endogenous promoters for transcriptionally targeted gene therapy.

• Publication year

  2009

• Venue

  Molecular Therapy

• Publication date

  2009-11-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1038/mt.2009.182PMID 19690516PMCID PMC2835043
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Uncovering cis Regulatory Codes Using Synthetic Promoter Shuffling

  2008cited by this paper
• Dynamic Protein Associations Define Two Phases of IL-1β Transcriptional Activation1

  2008cited by this paper
• Treatment of arthritis with a selective inhibitor of c-Fos/activator protein-1

  2008cited by this paper
• Transgene persistence and cell turnover in the diarthrodial joint: implications for gene therapy of chronic joint diseases.

  2007cited by this paper
• Computational identification and functional validation of regulatory motifs in cartilage-expressed genes.

  2007cited by this paper
• C/EBPα induces PU.1 and interacts with AP-1 and NF-κB to regulate myeloid development

  2007cited by this paper
• The Mouse Genome Database (MGD): mouse biology and model systems

  2007cited by this paper
• C/EBPalpha induces PU.1 and interacts with AP-1 and NF-kappaB to regulate myeloid development.

  2007cited by this paper
• Reduction of arthritis following intra-articular administration of an adeno-associated virus serotype 5 expressing a disease-inducible TNF-blocking agent

  2007cited by this paper
• Application of a disease-regulated promoter is a safer mode of local IL-4 gene therapy for arthritis

  2007cited by this paper
• Identification of muscle-specific regulatory modules in Caenorhabditis elegans.

  2007cited by this paper
• BMC Bioinformatics BioMed Central Review Computational analyses of eukaryotic promoters

  2007cited by this paper
• Programming gene expression with combinatorial promoters

  2007cited by this paper
• Predicting transcription factor binding sites using local over-representation and comparative genomics

  2006cited by this paper
• Genome-wide analysis of mammalian promoter architecture and evolution

  2006cited by this paper
• DNA motifs in human and mouse proximal promoters predict tissue-specific expression.

  2006cited by this paper
• Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters

  2006cited by this paper
• Quantification of mRNA levels in joint capsule and articular cartilage of the murine knee joint by RT-PCR: Kinetics of stromelysin and IL-1 mRNA levels during arthritis

  2005cited by this paper
• Genome-wide promoter extraction and analysis in human, mouse, and rat

  2005cited by this paper
• Gene transfer to human joints: progress toward a gene therapy of arthritis.

  2005cited by this paper
• Soluble interleukin-1 receptor accessory protein ameliorates collagen-induced arthritis by a different mode of action from that of interleukin-1 receptor antagonist.

  2005cited by this paper
• Microarray Analysis Supports a Role for CCAAT/Enhancer-binding Protein-β in Brain Injury*[boxs]

  2004cited by this paper
• JASPAR: an open-access database for eukaryotic transcription factor binding profiles

  2004cited by this paper
• An inflammation-inducible adenoviral expression system for local treatment of the arthritic joint

  2004cited by this paper
• Local activation of STAT-1 and STAT-3 in the inflamed synovium during zymosan-induced arthritis: exacerbation of joint inflammation in STAT-1 gene-knockout mice.

  2004cited by this paper
• CLICK and EXPANDER: a system for clustering and visualizing gene expression data

  2003cited by this paper
• Regulation of matrix metalloproteinases: An overview

  2003cited by this paper
• Lentiviral-mediated gene delivery to synovium: potent intra-articular expression with amplification by inflammation.

  2003cited by this paper
• Regulatory Sequence Analysis Tools

  2003cited by this paper
• Transcriptional Targeting in Cancer Gene Therapy

  2003cited by this paper
• Endogenous regulation of a therapeutic transgene restores homeostasis in arthritic joints.

  2002cited by this paper
• C3-Tat/HIV-regulated intraarticular human interleukin-1 receptor antagonist gene therapy results in efficient inhibition of collagen-induced arthritis superior to cytomegalovirus-regulated expression of the same transgene.

  2002cited by this paper
• The RNA polymerase II core promoter: a key component in the regulation of gene expression.

  2002cited by this paper
• Inhibitor of nuclear factor kappaB kinase beta is a key regulator of synovial inflammation.

  2001cited by this paper
• Inhibitor of nuclear factor κB kinase β is a key regulator of synovial inflammation

  2001cited by this paper
• Enhanced expression and DNA binding activity of two CCAAT/enhancer‐binding protein isoforms, C/EBPβ and C/EBPδ, in rheumatoid synovium

  2000cited by this paper
• TRANSFAC: an integrated system for gene expression regulation

  2000cited by this paper
• DNA binding sites: representation and discovery

  2000cited by this paper
• Efficient Transformation of Primary Human Amniocytes by E1 Functions of Ad5: Generation of New Cell Lines for Adenoviral Vector Production

  2000cited by this paper
• Enhanced expression and DNA binding activity of two CCAAT/enhancer-binding protein isoforms, C/EBPbeta and C/EBPdelta, in rheumatoid synovium.

  2000cited by this paper
• C/EBP beta in rheumatoid arthritis: correlation with inflammation, not disease specificity.

  1999cited by this paper
• Synthetic muscle promoters: activities exceeding naturally occurring regulatory sequences

  1999cited by this paper
• AP-1 and NF-kappaB regulation in rheumatoid arthritis and murine collagen-induced arthritis.

  1998cited by this paper
• Role of PU.1 in Hematopoiesis

  1998cited by this paper
• A two-component expression system that responds to inflammatory stimuli in vivo

  1997cited by this paper
• The role of IFN regulatory factor-1 in synovitis and nitric oxide production.

  1997cited by this paper
• Prevention of murine collagen-induced arthritis in the knee and ipsilateral paw by local expression of human interleukin-1 receptor antagonist protein in the knee.

  1997cited by this paper
• Inflammation-induced recombinant protein expression in vivo using promoters from acute-phase protein genes.

  1995cited by this paper
• Induction of the mouse serum amyloid A3 gene by cytokines requires both C/EBP family proteins and a novel constitutive nuclear factor

  1994cited by this paper
• Biological properties of recombinant human monocyte-derived interleukin 1 receptor antagonist.

  1990cited by this paper
• Methods for discovering novel motifs in nucleic acid sequences

  1989cited by this paper
• Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.

  1982cited by this paper

• Recent Advances in Studies of Serum Amyloid A: Implications in Inflammation, Immunity and Tumor Metastasis

  2025cites this paper
• Anti-arthritis Effect of Anti-chitinase-3-like 1 Antibody Through Inhibition of MMP3

  2025cites this paper
• Bub1 suppresses inflammatory arthritis–associated bone loss in mice through inhibition of TNFα–mediated osteoclastogenesis

  2024cites this paper
• Serum amyloid A and metabolic disease: evidence for a critical role in chronic inflammatory conditions

  2023cites this paper
• Injection site vaccinology of a recombinant vaccinia-based vector reveals diverse innate immune signatures

  2021cites this paper
• Systems vaccinology analysis of a recombinant vaccinia-based vector reveals diverse innate immune signatures at the injection site

  2020cites this paper
• The serum amyloid A3 promoter-driven luciferase reporter mice is a valuable tool to image early renal fibrosis development and shows the therapeutic effect of glucosyl-hesperidin treatment

  2019cites this paper
• Imaging, myeloid precursor immortalization, and genome editing for defining mechanisms of leukocyte recruitment in vivo

  2018cites this paper
• 10 Gene Therapy Challenges in Arthritis

  2017cites this paper
• Suppression of the inflammatory response by disease-inducible interleukin-10 gene therapy in a three-dimensional micromass model of the human synovial membrane

  2016cites this paper
• Serum Amyloid A3 Gene Expression in Adipocytes is an Indicator of the Interaction with Macrophages

  2016cites this paper
• Disease-Regulated Gene Therapy with Anti-Inflammatory Interleukin-10 Under the Control of the CXCL10 Promoter for the Treatment of Rheumatoid Arthritis

  2016cites this paper
• Transcriptional and post-transcriptional control of therapeutic gene expression during disease activity

  2015cites this paper
• Disease-regulated local IL-10 gene therapy diminishes synovitis and cartilage proteoglycan depletion in experimental arthritis

  2014cites this paper
• Systems biology approach for new target and biomarker identification.

  2013cites this paper
• Rho Kinase Inhibitor Y-27632 Prolongs the Life Span of Adult Human Keratinocytes, Enhances Skin Equivalent Development, and Facilitates Lentiviral Transduction

  2012cites this paper
• Gene profiling of Chikungunya virus arthritis in a mouse model reveals significant overlap with rheumatoid arthritis.

  2012cites this paper
• ADENO-ASSOCIATED VIRUS (AAV)-MEDIATED JOINT RESTORATION APPROACHES: CHARACTERIZATION AND APPLICATION

  2012cites this paper
• A novel hybrid promoter responsive to pathophysiological and pharmacological regulation

  2011cites this paper
• A novel Saa3-promoter reporter distinguishes inflammatory subtypes in experimental arthritis and human synovial fibroblasts

  2011cites this paper
• Toll-like receptor 4 signalling is specifically TGF-beta-activated kinase 1 independent in synovial fibroblasts.

  2011cites this paper
• A pivotal role for antigen-presenting cells overexpressing SOCS3 in controlling invariant NKT cell responses during collagen-induced arthritis

  2011cites this paper
• Gene Therapy Challenges in Arthritis

  2011cites this paper