Letter pubs.acs.org/jpr
Pharmaceutical Relevant Cytokine Receptors: Lessons from the First Drafts of the Human Proteome Christoph Garbers* and Stefan Rose-John* Institute of Biochemistry, Kiel University, Olshausenstrasse 40, 24098 Kiel, Germany ABSTRACT: Although a plethora of human proteins are ubiquitously expressed, several proteins with high pharmaceutical relevance show a tissue- or cell-type specific expression pattern. Science across all disciplines, ranging from developmental biology to personalized medicine, would benefit from detailed knowledge about this so-called human proteome. Two recent publications in Nature use large-scale proteomics to create first drafts of the human proteome, which are freely accessible online. In this Letter, we analyze the proteomic data with regard to the expression of three different cytokine receptors, the Tumor Necrosis Factor (TNF)α Receptor I (TNFRSF1A) and II (TNFRSF1B) and the Interleukin-6 Receptor (IL-6R). Therapeutic inhibition of these proteins is highly effective in a high number of inflammatory diseases, and TNFα blocking agents alone were sold for almost $30 billion in 2013. We find that the known expression pattern of the three receptors is not reflected in the current drafts of the human proteome, as the proteomics data fail to detect protein expression in several cell types and tissues which are known to express these cytokine receptors. Thus, our results suggest that the current drafts of the human proteome are far from complete, and that the data have to be used with caution especially in terms of personalized medicine. KEYWORDS: human proteome, proteome map, interleukin-6, tumor necrosis factor
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psoriasis. Their combined sales in 2013 were close to $30 billion.4 The great therapeutic benefit by targeting TNFα can be explained through the high expression of TNFRSF1A and B in several types of immune cells, which can be seen on the level of the mRNA, for example in BioGPS5 (Figure 1a). Although mRNA expression does not always correlate with protein expression (for example, due to epigenetic regulation, stability of the mRNA or the protein), several publications have shown a correlation between mRNA and protein levels of both proteins.6−8 Whereas expression of TNFRSF1B appears to be restricted to immune cells, the TNFRSF1A is expressed more ubiquitously. Unfortunately, this is not reflected in the current draft of the human proteome. Kim et al.1 found TNFRSF1A expression only in fetal heart, and TNFRSF1B just in B and CD8+ T cells (Figure 1b). Wilhelm et al.2 detected TNFRSF1A in platelets and heart, whereas TNFRSF1B appears to only be expressed in cytotoxic T cells (Figure 1c). In contrast, TNFRSF1A expression is annotated in a variety of tissues in The Human Protein Atlas (http://www.proteinatlas.org/), which matches the known expression pattern. The expression of TNFRSF1B, however, was also by this approach not detected in immune cells. Next, we checked for the expression of the receptor of interleukin-6 (IL-6). The monoclonal antibody tocilizumab,
wo new large-scale proteomics resources termed Human Proteome Map1 and ProteomicsDB,2 which present expression data of nearly all human proteins obtained via mass-spectrometry, were presented in a recent issue of Nature. These large data sets, which can be freely accessed online (http://www.humanproteomemap.org/ and https://www. proteomicsdb.org/), provide a catalogue illustrating which proteins are expressed in 60 human tissues and more than 100 different cell lines. Detailed knowledge about the human proteome is useful in many ways, and mass spectrometry is a promising method to address this issue. An accompanying comment by Lawrence and Villén in Nature Biotechnology especially highlighted the importance of these works for further development of personalized medicine to anticipate which organs might be treated by certain therapeutics.3 Despite the fact that we largely agree with this optimistic view, we would like to point out a potential problem in the usage of the data sets for the evaluation in terms of personalized medicine and other applications. Tumour Necrosis Factor-α (TNFα) is a prototypically pro-inflammatory cytokine that activates its target cells through binding to either TNF Receptor I (TNFRSF1A) or TNFRII (TNFRSF1B). Therapeutic inhibition of TNFα is long known to be beneficial, and consequently the three biologics adalimumab (Humira, Abbot Laboratories), infliximab (Remicade, Johnson & Johnson), and etanercept (Enbrel, Amgen), which prevent binding of TNFα to its receptors, are approved by the FDA to treat a variety of inflammatory diseases, including rheumatoid arthritis (RA) and © XXXX American Chemical Society
Received: August 20, 2014
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Figure 1. (a) Quantitative expression data for IL6R (green), TNFRSF1A (blue), and TNFRSF1B (red) in different tissues were obtained from BioGPS.5 (b) Qualitative expression data for IL6R (green), TNFRSF1A (blue), and TNFRSF1B (red) according to the Human Proteome Map.1 Unfilled squares denote no expression. (c) Qualitative expression data for IL6R (green), TNFRSF1A (blue), and TNFRSF1B (red) according to ProteomicsDB.2 Unfilled squares denote no expression. For some of the tissues like fetal tissues, B cells or platelets, no quantitative data could be retrieved from BioGPS.
type of immune cells (Figure 1b). Wilhelm et al.2 did not detect IL-6R expression at all (Figure 1c). TNFα and IL-6, two proteins with enormous therapeutic potential, illustrate that the current drafts of the human proteome are far from complete. Wilhelm et al.2 offer as an explanation for missing proteins among others that they might be no longer expressed for evolutionary reasons or might be expressed with extreme spatiotemporal specificity. As highlighted above, both explanations cannot be correct for TNFα and IL-6 receptors. Furthermore, expression of the receptor for IL-11, the closest homologue of IL-6, was not detected in the two data sets, although IL-11 signaling is critical for gastrointestinal tumor development14 and recombinant IL-11 (under the trade name “Oprelvekin”) is approved by the FDA
which blocks binding of IL-6 to its receptor (IL-6R), is approved for several inflammatory diseases, including RA, systemic lupus erythematosus and Castleman’s Disease.9 Consequently, IL6R expression is found on neutrophils and T cells as well as hepatocytes5 (Figure 1a), as IL-6 is the most important mediator of the liver acute phase response.10 IL6R mRNA expression has been shown to correlate with protein expression.11−13 IL-6 signaling in the epidermis, which is suggested by the mRNA data (Figure 1a), is not known to be functionally related to the biological activity of IL-6R blockade. Like for TNF receptors, the current drafts of the human proteome do not reflect this. Kim et al.1 detected IL-6R in adult ovary and adult gallbladder, two tissues not well-known as targets for IL-6. They did not detect IL-6R in the liver or any B
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(6) Brennan, F. M.; Gibbons, D. L.; Mitchell, T.; Cope, A. P.; Maini, R. N.; Feldmann, M. Eur. J. Immunol. 1992, 22 (7), 1907−1912. (7) Smolnikar, K.; Löffek, S.; Schulz, T.; Michna, H.; Diel, P. Breast Cancer Res. Treat. 2000, 63 (3), 249−259. (8) Wen, W.; Sanelli, T.; Ge, W.; Strong, W.; Strong, M. J. Neurosci. Res. 2006, 55 (1), 87−95. (9) Tanaka, T.; Narazaki, M.; Kishimoto, T. Annu. Rev. Pharmacol. Toxicol. 2012, 52, 199−219. (10) Scheller, J.; Garbers, C.; Rose-John, S. Semin. Immunol. 2014, 26 (1), 2−12. (11) Liao, W.; Lin, J.-X.; Wang, L.; Li, P.; Leonard, W. Nat. Immunol. 2011, 12 (6), 551−559. (12) Ladenburger, A.; Seehase, M.; Kramer, B.; Thomas, W.; Wirbelauer, J.; Speer, C.; Kunzmann, S. Am. J. Physiol.: Lung Cell. Mol. Physiol. 2010, 299 (4), 84. (13) Garbers, C.; Kuck, F.; Aparicio-Siegmund, S.; Konzak, K.; Kessenbrock, M.; Sommerfeld, A.; Haussinger, D.; Lang, P. A.; Brenner, D.; Mak, T. W.; Rose-John, S.; Essmann, F.; Schulze-Osthoff, K.; Piekorz, R. P.; Scheller, J. Cell Cycle 2013, 12 (21), 3421−32. (14) Putoczki, T.; Thiem, S.; Loving, A.; Busuttil, R.; Wilson, N.; Ziegler, P.; Nguyen, P.; Preaudet, A.; Farid, R.; Edwards, K.; Boglev, Y.; Luwor, R.; Jarnicki, A.; Horst, D.; Boussioutas, A.; Heath, J.; Sieber, O.; Pleines, I.; Kile, B.; Nash, A.; Greten, F.; McKenzie, B.; Ernst, M. Cancer Cell 2013, 24 (2), 257−271. (15) Garbers, C.; Scheller, J. Biol. Chem. 2013, 394 (9), 1145−61. (16) Ezkurdia, I.; Vázquez, J.; Valencia, A.; Tress, M. J. Proteome Res. 2014, 13 (8), 3854−3855.
to treat severe thrombocytopenia associated with chemotherapy.15 Thus, we think that important proteins are currently missing in the human proteome drafts. The reason for this is unclear. Although it is common knowledge that some peptides are more difficult to detect via MS techniques, it would be very surprising if this affects all receptors of a given cytokine family. Interestingly, Ezkurdia et al.16 could show the exact opposite for the expression pattern of olfactory receptors. Both proteomic studies reported expression of these proteins in a variety of cell types and tissues, although they are thought to only be expressed in nasal tissue, which was not analyzed.16 We therefore agree with Ezkurdia et al. and propose to execute great caution when using the current human proteome data with respect to the therapeutic evaluation and personalized medicine. Researchers should furthermore consult other available projects that annotate cell- and tissue-specific protein expression pattern, for example, the Human Protein Atlas. We feel that more data are clearly needed to reflect all proteins encompassing the human proteome.
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AUTHOR INFORMATION
Corresponding Authors
*E-mail:
[email protected]. Phone: +49 431 880 3336. Fax: +49 431 880 5007. *E-mail:
[email protected]. Phone: +49 431 880 1676. Fax: +49 431 880 5007. Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS The work of C.G. and S.R.-J. is supported by grants from the Deutsche Forschungsgemeinschaft (Bonn, Germany) via the SFB877 (projects A1 and A10) and the Cluster of Excellence “Inflammation at Interfaces”.
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REFERENCES
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