<p>1 Supplementary data </p><p>2 Table S1 Pre-clinical overview Sample BIPED Biomarker Results (short description) Ref ID type classification Age-related decrease in healthy dogs >12mth (n=8) compared to Active MMP- Investigative Canine SF ≤12mth (n=6). Increased in dogs 94 2 (Diagnostic) with FMCP (n=159) compared to healthy controls (n=32). Increased in dogs with FMCP (n=159) compared to healthy controls (n=32). Correlates with the Investigative degree of cartilage lesions of the Active MMP- (Diagnostic, Canine SF medial coronoid process and medial 94 9 Burden of aspects of the humerus condyle, Disease) classified by the modified Outerbridge cartilage scores, in dogs with FMCP. Increased in dogs with FMCP Investigative Active MPO Canine SF (n=159) compared to healthy 94 (Diagnostic) controls (n=32). Decreased in idealized ACL reconstructed knee joints compared to sham-surgical controls (p < 0.05) Asparagine Ovine SF 95 Investigative and associated with metabolic pathways in early degenerative joint disease. Age-related decrease in healthy CTX-II Canine SF dogs >12mth (n=13) compared to 94 Investigative ≤12mth (n=15). Decreased in idealized ACL reconstructed knee joints compared Hydroxyproli to sham-surgical controls (p < 0.05) Ovine SF 95 Investigative ne and associated with metabolic pathways in early degenerative joint disease. Increased SF-level in FCA- and Murine MIA-induced OA rats compared Investigative IL-1β serum and 62 with control rats. Serum-level (Diagnostic) SF unchanged. Increased in ACLT-induced OA rats Murine Investigative compared to sham-surgery and non- 96 SF (Diagnostic) surgery controls. IL-6 Murine Decreased in fat-1 transgenic mice, 97 Investigative serum characterized by a reduced systemic ratio of n-6:n-3 polyunsaturated</p><p>Page 1 of 3 fatty acids, compared to WT mice. However not associated with idiopathic development of early- stage knee OA in these mice. Increased SF-level in FCA- and Murine MIA-induced OA rats compared Investigative serum and 62 with control rats. Serum-level only (Diagnostic) SF increased in the MIA model. Increased in idealized ACL reconstructed knee joints compared to sham-surgical controls (p < 0.05) Isobutyrate Ovine SF 95 Investigative and associated with metabolic pathways in early degenerative joint disease. Increased SF-level in FCA- and Murine MIA-induced OA rats compared Investigative KC/GRO serum and 62 with control rats. Serum-level only (Diagnostic) SF increased in the FCA model. Increased SF-level in FCA- and Murine MIA-induced OA rats compared Investigative MCP-1 serum and 62 with control rats. Serum-level (Diagnostic) SF unchanged. Increased SF-level in FCA- and Murine MIA-induced OA rats compared Investigative MIP-3α serum and 62 with control rats. Serum-level only (Diagnostic) SF increased in the FCA model. Decreased in ACLT-induced OA Murine Investigative PACAP rats compared to sham-surgery and 96 SF (Diagnostic) non-surgery controls. Increased SF-level and decreased serum-level in racehorses with osteochondral injury (n=22) Equine compared with control racehorses serum, Investigative SDF-1 (n=37) both before and after race 98 plasma (Diagnostic) training. No difference in plasma- and SF levels. Serum SDF-1 correlated with inflammation scores, but not cartilage scores. Decreased in idealized ACL reconstructed knee joints compared to sham-surgical controls (p < 0.05) Serine Ovine SF 95 Investigative and associated with metabolic pathways in early degenerative joint disease. TNF-α Murine Decreased in fat-1 transgenic mice, 97 Investigative serum characterized by a reduced systemic ratio of n-6:n-3 polyunsaturated fatty acids, compared to WT mice.</p><p>Page 2 of 3 However not associated with idiopathic development of early- stage knee OA in these mice. Increased SF-level in FCA- and Murine MIA-induced OA rats compared Investigative serum and 62 with control rats. Serum-level (Diagnostic) SF unchanged. 3 Abbreviations: ACL, Anterior cruciate ligament; ACLT, Anterior cruciate ligament transection; CTX-II, Carboxy-terminal cross- 4 linked fragment of type II collagen; FCA, Freund’s complete adjuvant; FMCP, Fragmented medial coronoid process; Ihh, Indian 5 Hedgehog; IL-1β, Interleukin-1β; IL-6, Interleukin-6; KC/GRO; Keratinocyte chemoattractant/ human growth-regulated oncogene; 6 MCP-1, monocyte chemoattractant protein 1; MIP-3α, macrophage inflammatory protein 3α; MMP, Matrix metalloproteinase; MPO, 7 Myeloperoxidase; OA, Osteoarthritis; PACAP, Pituitary adenylate cyclase-activating polypeptide; SDF-1, Stromal cell-derived 8 factor-1; SF, Synovial fluid; TNF-α, Tumor necrosis factor- α, WT; Wild-type</p><p>Page 3 of 3</p>