Transcriptome comparison between human and mouse

in arthritisMarc Bonin1, Till Sörensen1, Bijana Smiljanovic1, Andreas Grützkau2, Christoforos Nikolaou3, Ioannis Pandis4 , George Kollias3, Anthony Rowe5, Thomas Häupl1

1 Department of Rheumatology and Clinical Immunology, Charité University Hospital, Berlin, Germany, 2 German Arthritis Research Center, Berlin, Germany, 3Biomedical Sciences Research Centre „Alexander Fleming“, Institute of Immunology, Vari, 4 Imperial College London, London, United Kingdom, 5 Janssen Research and Development, High Wycombe Buckinghamshire, United Kindom

Thomas HäuplDepartment of Rheumatology and Clinical ImmunologyCharité University HospitalCharitéplatz 1D-10117 Berlin Germany

Tel: +49(0) 30 450 513 291Fax: +49(0) 30 450 513 968E-Mail: thomas.haeupl@charite.deWeb: www.charite-bioinformatik.de

Contacts:

In order to characterize such differences and to find models matching with disease subgroups, we started a pilot investigation based on published transcriptomes to develop bioinformatic strategies of interspecies gene expression comparison.

Background:

Objective:

Methods:

Results:

Conclusion:

www.charite-bioinformatik.de

From GEO repository Affymetrix based transcriptomes of synovial fibroblasts from rheumatoid arthritis (RA) and osteoarthritis (OA) patients (GEO-accession: GSE13837) and mouse BALBc wt (GSE17160) with similar stimulation (TNF-alpha) and time point after stimulation (12 hours) were selected. MAS5 algorithms of signal extraction and pairwise comparison were performed. The BioRetis database was used for group comparisons, candidate gene selection and data sharing. Differentially expressed genes were exported for interspecies comparison in a filemaker database. Affymetrix annotation files were used for mapping of orthologous genes.

The number of differentially expressed genes induced by TNF in synovial fibroblasts from RA, OA and BALBc were 1584, 1476 and 503 respectively. Comparison of genes overexpressed in RA and OA revealed up to 70% overlap. Murine and human response was similar for 197 genes in all three groups, 45 only between BALBc and RA and 24 only between BALBc and OA. Ranking the genes by dominance, 7 genes were overlapping between the top 10 of both human cells, OA and RA, and 13 out of the top 20. All overlapping genes in human revealed a high correlation (R=0.795). In contrast, overlap between RA and BALBc SFbl responses revealed only 4 genes out of the top 10 and 5 out of the top 20 in each and a weaker correlation (0.392). Pathway tools including IPA identify TNF as a potential upstream regulator amongst others. However, the reference list of genes for scoring in IPA seemed to be longer in human and to overlap by less than 60% of the murine reference candidates.

Interspecies comparison in this defined experiment revealed first insight in common responses but also demonstrates substantial differences. This suggest that systematic investigations are needed to provide a reliable basis for interspecies comparison and the improvement of drug target selection and preclinical testing.

Animal models are essential for development of new therapeutics but targeted therapies with biologics reveal differences in responsiveness suggesting substantial differences in the molecular pathomechanisms of human and murine arthritis. To characterize such differences, we investigated transcriptomes to develop bioinformatic strategies of interspecies gene expression comparison.

Acknowledgement: BTCure IMI grant agreement no. 115142

BALBc

197

2445

237

837505 418

503

RA OA14761584

65% / 70%

15%44%

15%48%

R2 = 0,633R = 0,795

RA vs OA gene symbolRA

rank change call

RArank SLR

RA TNF 12h

signal

OA rank

change call

OArank SLR

OA TNF 12h

signal

GABBR1 /// UBD 1 1 2480,43 10 10 204,95CCL5 2 2 6240,07 3 3 1522,4CXCL11 3 3 2499,43 4 4 321,4CXCL10 4 4 7595,07 5 5 1306,2TRPA1 5 5 2617,83 2 2 764,75ELOVL7 6 6 993,733 1 1 899,2IBSP 7 7 226,633 9 9 46,2IDO1 8 8 3307,53 14 15 1653,35IL8 9 9 2857,3 11 11 1634,55CXCL9 10 10 1180,8 49 55 226,4CCL20 11 11 296,4 8 8 150,8RSAD2 12 12 5617,83 15 16 2214,7IL32 13 13 697,867 6 6 328,1TNFSF15 14 14 547 85 96 626,2IFI44L 15 15 1569,17 27 29 625,35CX3CL1 16 16 171,9 763 72 69,4TFPI2 17 17 4417,9 28 30 1609,5MEOX1 18 18 582,4 18 19 116,05CR1 /// CR1L 19 19 76,9667NOD2 20 20 368,9 24 25 93,8

Figure 1

Genes identified as induced in synovial fibroblasts after 12h of stimulation with TNFa.

R2 = 0,153R = 0,392

RA vs BALBc

Figure 2 A

Figure 2 B gene symbol

RA rank

change call

RArank SLR

RA TNF 12h

signal

BALBc rank

change call

BALBcrank SLR

BALBc TNF 12h

signal

GABBR1 /// UBD 1 1 2480,43 29 27 110,05CCL5 2 2 6240,07 5 5 1779,9CXCL11 3 3 2499,43 8 8 352,1CXCL10 4 4 7595,07 6 6 1256,1TRPA1 5 5 2617,83 ELOVL7 6 6 993,733 IBSP 7 7 226,633 IDO1 8 8 3307,53 IL8 9 9 2857,3 CXCL9 10 10 1180,8 2 2 660,25CCL20 11 11 296,4 3 3 643,35RSAD2 12 12 5617,83 389 414 404,3IL32 13 13 697,867 TNFSF15 14 14 547 IFI44L 15 15 1569,17 154 104 140,25CX3CL1 16 16 171,9 194 368 293TFPI2 17 17 4417,9 MEOX1 18 18 582,4 CR1 /// CR1L 19 19 76,9667 NOD2 20 20 368,9 C15orf48 21 21 866,7 OASL 22 22 920,467 SSTR2 23 536 96,6667 TLR2 24 23 1469,73 44 37 924,25BIRC3 25 24 1186,5 62 48 1385,55GBP4 26 25 781,2 89 67 1287,65CD274 27 26 721,967 NEURL3 28 27 245,3 FAM26F 29 28 879,7 CFB 30 29 214,6 CXCL6 31 30 183,067 SERPINB2 32 921 2861,57 19 19 146,45ISG20 33 31 1424,93 CXCL3 34 32 243,8 7 7 1683,25PPP4R4 35 33 39,1 TNFSF13B 36 34 4453,1 OAS1 37 35 3022,93 317 223 1329,2RCSD1 38 922 41,1667 TNFAIP6 39 36 12500,5 132 360 51,55MMP1 40 37 8597,27 HCK 41 38 307,6 C8orf4 42 39 208,5 MX1 43 40 7086,53 TNFAIP3 44 41 2591,47 25 23 1113,15HSD11B1 45 42 3980,63 IL4I1 46 43 499,033 GBP5 47 44 114,967 BST2 48 537 425,8 447 451 2721,8IFIT2 49 45 1803,83 200 171 437,75CMPK2 50 46 5332,07 206 205 246,95

Upstream regulators suggested by Ingenuity Pathway Analysis (IPA): 1584 genes induced in RA synovial fibroblasts by TNF alpha were uploaded into IPA and upstream regulators were ranked by the likelyhood to overlap with regulator specific reference genes in IPA.

regulator ranking

candidate ranking

Figure 3

Table 1:

genes uploaded to IPA search in species related to TNF as upstream regulatorhuman: 1584 human 151mouse: 1584 mouse 65overlap: 1584 human AND mouse 37

ArthroMark grant no 01EC1009A