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.
Geurts
Jeroen
J
Rheumatology Research and Advanced Therapeutics, Department of Rheumatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
Joosten
Leo A B
LA
Takahashi
Nozomi
N
Arntz
Onno J
OJ
Glück
Anton
A
Bennink
Miranda B
MB
van den Berg
Wim B
WB
van de Loo
Fons A J
FA
D000256:Adenoviridae / Q000235:genetics; D000465:Algorithms; D000818:Animals; D001172:Arthritis, Rheumatoid / Q000628:therapy*; D002417:Cattle; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D004797:Enzyme-Linked Immunosorbent Assay; D015316:Genetic Therapy / Q000379:methods*; D006367:HeLa Cells; D006801:Humans; D053590:Interleukin 1 Receptor Antagonist Protein / Q000235:genetics / Q000502:physiology; D016086:Lentivirus / Q000235:genetics; D008297:Male; D051379:Mice; D008957:Models, Genetic; D041681:NIH 3T3 Cells; D011401:Promoter Regions, Genetic / Q000235:genetics*; D000685:Serum Amyloid A Protein / Q000235:genetics
D053590:Interleukin 1 Receptor Antagonist Protein; C489625:SAA3P protein, human; D000685:Serum Amyloid A Protein
Nat Biotechnol. 1999 Mar;17(3):241-5
10096290
Nucleic Acids Res. 2008 Jan;36(Database issue):D724-8
18158299
Arthritis Rheum. 2002 Jun;46(6):1661-70
12115199
Nucleic Acids Res. 2000 Jan 1;28(1):316-9
10592259
Genome Biol. 2005;6(8):R72
16086854
Mol Ther. 2007 Jun;15(6):1114-20
17440444
Ann Rheum Dis. 2007 Sep;66(9):1143-50
17363402
J Clin Invest. 1990 May;85(5):1694-7
2139669
BMC Bioinformatics. 2006 Aug 31;7:396
16945132
Gene Ther. 2007 Dec;14(23):1632-8
17851546
Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8698-703
15939878
Nat Biotechnol. 1997 Oct;15(10):1002-6
9335054
PLoS One. 2008 Apr 30;3(4):e2030
18446205
Genome Res. 2007 Mar;17(3):348-57
17284674
Bioinformatics. 2000 Jan;16(1):16-23
10812473
Genome Res. 2007 Oct;17(10):1438-47
17785538
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D91-4
14681366
Autoimmunity. 1998;28(4):197-208
9892501
Nucleic Acids Res. 1982 May 11;10(9):2997-3011
7048259
Gene Ther. 2004 Apr;11(7):581-90
14973543
Rheumatol Int. 1997;16(5):197-205
9032819
Genes Dev. 2002 Oct 15;16(20):2583-92
12381658
J Immunol. 1997 Oct 1;159(7):3549-54
9317154
Comput Appl Biosci. 1989 Oct;5(4):293-8
2684350
Nucleic Acids Res. 2003 Jul 1;31(13):3593-6
12824373
Clin Immunol. 1999 Jun;91(3):271-82
10370372
Nat Biotechnol. 2008 Jul;26(7):817-23
18587386
Mol Ther. 2003 Apr;7(4):460-6
12727108
Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6275-80
16606849
BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S3
17903284
J Biomed Biotechnol. 2003;2003(2):110-137
12721516
Arthritis Rheum. 2005 Jul;52(7):2202-11
15986350
Nat Genet. 2006 Jun;38(6):626-35
16645617
Blood Cells Mol Dis. 2007 Nov-Dec;39(3):340-3
17669672
J Biol Chem. 2004 Apr 2;279(14):14409-17
14736879
Arthritis Rheum. 2000 Jul;43(7):1591-6
10902764
Bioinformatics. 2003 Sep 22;19(14):1787-99
14512350
Hum Gene Ther. 2000 Oct 10;11(15):2105-16
11044912
Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5346-50
7539915
J Clin Invest. 2002 May;109(9):1223-9
11994411
Arthritis Rheum. 2001 Aug;44(8):1897-907
11508443
Arthritis Rheum. 1997 May;40(5):893-900
9153551
Genome Biol. 2006;7(8):R78
16916456
Mol Cell Biol. 1994 Jul;14(7):4475-84
8007954
J Immunol. 2008 Jul 1;181(1):503-12
18566416
Mol Syst Biol. 2007;3:145
18004278
Stem Cells. 1998;16(1):25-37
9474745
Arthritis Rheum. 2004 Jun;50(6):2014-23
15188379
Mol Cell Biochem. 2003 Nov;253(1-2):269-85
14619979