Different Stimuli for Inference of Gene Regulatory Network in Rheumatoid Arthritis

Peter Kupfer, Sebastian Vlaic, René Huber, Raimund W. Kinne, Reinhard Guthke

2013

Abstract

Since genetic and epigenetic factors are known to be involved in the pathogenesis of rheumatoid arthritis the search for key players in this disease is one of the most important challenges. For this purpose gene regulatory networks are one possibility to reveal underlying interactions for different stimuli. In this study we analyzed the cellular response of synovial fibroblasts to 4 different stimuli. We infered a gene regulatory network that is able to explain the observed data for stimulation by TNF-a, TGF-b1, IL-1 and PDGF-D simultaneously.

References

  1. Amizuka, N., Henderson, J. E., White, J. H., Karaplis, A. C., Goltzman, D., Sasaki, T., and Ozawa, H. (2000). Recent studies on the biological action of parathyroid hormone (pth)-related peptide (pthrp) and pth/pthrp receptor in cartilage and bone. Histol Histopathol, 15(3):957-70.
  2. Aomatsu, K., Arao, T., Sugioka, K., Matsumoto, K., Tamura, D., Kudo, K., Kaneda, H., Tanaka, K., Fujita, Y., Shimomura, Y., and Nishio, K. (2011). Tgfinduces sustained upregulation of snai1 and snai2 through smad and non-smad pathways in a human corneal epithelial cell line. Invest Ophthalmol Vis Sci, 52(5):2437-43.
  3. Bascom, C. C., Wolfshohl, J. R., Coffey, Jr, R. J., Madisen, L., Webb, N. R., Purchio, A. R., Derynck, R., and Moses, H. L. (1989). Complex regulation of transforming growth factor beta 1, beta 2, and beta 3 mrna expression in mouse fibroblasts and keratinocytes by transforming growth factors beta 1 and beta 2. Mol Cell Biol, 9(12):5508-15.
  4. Braddock, M. (2001). The transcription factor egr-1: a potential drug in wound healing and tissue repair. Ann Med, 33(5):313-8.
  5. Bramlage, C. P., Häupl, T., Kaps, C., Ungethüm, U., Krenn, V., Pruss, A., Müller, G. A., Strutz, F., and Burmester, G.-R. (2006). Decrease in expression of bone morphogenetic proteins 4 and 5 in synovial tissue of patients with osteoarthritis and rheumatoid arthritis. Arthritis Res Ther, 8(3):R58.
  6. Falcon, S. and Gentleman, R. (2007). Using GOstats to test gene lists for GO term association. Bioinformatics, 23(2):257-8.
  7. Ferrari, F., Bortoluzzi, S., Coppe, A., Sirota, A., Safran, M., Shmoish, M., Ferrari, S., Lancet, D., Danieli, G. A., and Bicciato, S. (2007). Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics, 8:446.
  8. Funk, J. L., Cordaro, L. A., Wei, H., Benjamin, J. B., and Yocum, D. E. (1998). Synovium as a source of increased amino-terminal parathyroid hormone-related protein expression in rheumatoid arthritis. a possible role for locally produced parathyroid hormone-related protein in the pathogenesis of rheumatoid arthritis. J Clin Invest, 101(7):1362-71.
  9. Goodman, F. R. (2002). Limb malformations and the human hox genes. Am J Med Genet, 112(3):256-65.
  10. Guo, X., Day, T. F., Jiang, X., Garrett-Beal, L., Topol, L., and Yang, Y. (2004). Wnt/beta-catenin signaling is sufficient and necessary for synovial joint formation. Genes Dev, 18(19):2404-17.
  11. Hartmann, C. and Tabin, C. J. (2001). Wnt-14 plays a pivotal role in inducing synovial joint formation in the developing appendicular skeleton. Cell, 104(3):341- 51.
  12. Hecker, M., Goertsches, R. H., Engelmann, R., Thiesen, H.-J., and Guthke, R. (2009). Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics, 10:262.
  13. Horiguchi, M., Akiyama, H., Ito, H., Shigeno, C., and Nakamura, T. (2000). Tumour necrosis factor-alpha up-regulates the expression of bmp-4 mrna but inhibits chondrogenesis in mouse clonal chondrogenic ec cells, atdc5. Cytokine, 12(5):526-30.
  14. Huber, L. C., Distler, O., Tarner, I., Gay, R. E., Gay, S., and Pap, T. (2006). Synovial fibroblasts: key players in rheumatoid arthritis. Rheumatology (Oxford), 45(6):669-75.
  15. Ikegame, M., Ishibashi, O., Yoshizawa, T., Shimomura, J., Komori, T., Ozawa, H., and Kawashima, H. (2001). Tensile stress induces bone morphogenetic protein 4 in preosteoblastic and fibroblastic cells, which later differentiate into osteoblasts leading to osteogenesis in the mouse calvariae in organ culture. J Bone Miner Res, 16(1):24-32.
  16. Irizarry, R. A., Hobbs, B., Collin, F., Beazer-Barclay, Y. D., Antonellis, K. J., Scherf, U., and Speed, T. P. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4(2):249-64.
  17. Johnson, R. L. and Tabin, C. J. (1997). Molecular models for vertebrate limb development. Cell, 90(6):979-90.
  18. Karaplis, A. C., Luz, A., Glowacki, J., Bronson, R. T., Tybulewicz, V. L., Kronenberg, H. M., and Mulligan, R. C. (1994). Lethal skeletal dysplasia from targeted disruption of the parathyroid hormone-related peptide gene. Genes Dev, 8(3):277-89.
  19. Karouzakis, E., Neidhart, M., Gay, R. E., and Gay, S. (2006). Molecular and cellular basis of rheumatoid joint destruction. Immunol Lett, 106(1):8-13.
  20. Kiriyama, T., Gillespie, M. T., Glatz, J. A., Fukumoto, S., Moseley, J. M., and Martin, T. J. (1993). Transforming growth factor beta stimulation of parathyroid hormone-related protein (pthrp): a paracrine regulator? Mol Cell Endocrinol, 92(1):55-62.
  21. Kupfer, P., Guthke, R., Pohlers, D., Huber, R., Koczan, D., and Kinne, R. W. (2012). Batch correction of microarray data substantially improves the identification of genes differentially expressed in rheumatoid arthritis and osteoarthritis. BMC Med Genomics, 5(1):23.
  22. Liu, C., Rangnekar, V. M., Adamson, E., and Mercola, D. (1998). Suppression of growth and transformation and induction of apoptosis by egr-1. Cancer Gene Ther, 5(1):3-28.
  23. Maioli, E., Fortino, V., Torricelli, C., Arezzini, B., and Gardi, C. (2002). Effect of parathyroid hormonerelated protein on fibroblast proliferation and collagen metabolism in human skin. Exp Dermatol, 11(4):302- 10.
  24. Matys, V. (2006). TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes. Nucleic Acids Research, 34(90001):D108-D110.
  25. Nieto, M. A., Sargent, M. G., Wilkinson, D. G., and Cooke, J. (1994). Control of cell behavior during vertebrate development by slug, a zinc finger gene. Science, 264(5160):835-9.
  26. Nikitin, A., Egorov, S., Daraselia, N., and Mazo, I. (2003). Pathway studio-the analysis and navigation of molecular networks. Bioinformatics (Oxford, England), 19(16):2155-2157. PMID: 14594725.
  27. Saito, A., Hino, S.-i., Murakami, T., Kanemoto, S., Kondo, S., Saitoh, M., Nishimura, R., Yoneda, T., Furuichi, T., Ikegawa, S., Ikawa, M., Okabe, M., and Imaizumi, K. (2009). Regulation of endoplasmic reticulum stress response by a bbf2h7-mediated sec23a pathway is essential for chondrogenesis. Nat Cell Biol, 11(10):1197-204.
  28. Sheng, Z., Li, L., Zhu, L. J., Smith, T. W., Demers, A., Ross, A. H., Moser, R. P., and Green, M. R. (2010). A genome-wide rna interference screen reveals an essential creb3l2-atf5-mcl1 survival pathway in malignant glioma with therapeutic implications. Nat Med, 16(6):671-7.
  29. Shi, L., Jones, W. D., Jensen, R. V., Harris, S. C., and Perkins, e. a. (2008). The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics, 9(Suppl 9):S10. PMID: 18793455 PMCID: 2537561.
  30. Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., and Ideker, T. (2011). Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (Oxford, England), 27(3):431-432. PMID: 21149340.
  31. Smyth, G. K. (2005). Limma: linear models for microarray data. In Gentleman, R., Carey, V., Dudoit, S., Irizarry, R., and Huber, W., editors, Bioinformatics and Computational Biology Solutions using R and Bioconductor, pages 397-420. Springer, New York.
  32. Spagnoli, A., O'Rear, L., Chandler, R. L., Granero-Molto, F., Mortlock, D. P., Gorska, A. E., Weis, J. A., Longobardi, L., Chytil, A., Shimer, K., and Moses, H. L. (2007). Tgf-beta signaling is essential for joint morphogenesis. J Cell Biol, 177(6):1105-17.
  33. Tsumaki, N., Nakase, T., Miyaji, T., Kakiuchi, M., Kimura, T., Ochi, T., and Yoshikawa, H. (2002). Bone morphogenetic protein signals are required for cartilage formation and differently regulate joint development during skeletogenesis. J Bone Miner Res, 17(5):898- 906.
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Paper Citation


in Harvard Style

Kupfer P., Vlaic S., Huber R., W. Kinne R. and Guthke R. (2013). Different Stimuli for Inference of Gene Regulatory Network in Rheumatoid Arthritis . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 282-287. DOI: 10.5220/0004196402820287


in Bibtex Style

@conference{bioinformatics13,
author={Peter Kupfer and Sebastian Vlaic and René Huber and Raimund W. Kinne and Reinhard Guthke},
title={Different Stimuli for Inference of Gene Regulatory Network in Rheumatoid Arthritis},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={282-287},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004196402820287},
isbn={978-989-8565-35-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - Different Stimuli for Inference of Gene Regulatory Network in Rheumatoid Arthritis
SN - 978-989-8565-35-8
AU - Kupfer P.
AU - Vlaic S.
AU - Huber R.
AU - W. Kinne R.
AU - Guthke R.
PY - 2013
SP - 282
EP - 287
DO - 10.5220/0004196402820287