Plasma Kidney Injury Molecule-1 in Systemic Lupus Erythematosus: Discordance Between ELISA and Proximity Extension Assay

Oligonucleotide-labeled antibodies (Olink, Olink Proteomics) and aptamers (SomaScan, SomaLogic) are increasingly used in biomarker discovery and research. However, few studies have compared the protein levels measured on proteomics platforms with those measured using conventional immunoaffinity assays.1Hayek SS, Raffield LM, Gao Y, et al. Assay-related differences in SuPAR levels: implications for measurement and data interpretation. medRxiv. Preprint posted online June 28, 2021. https://doi.org/10.1101/2021.06.23.21259148Google Scholar, 2Raffield L.M. Dang H. Pratte K.A. et al.Comparison of proteomic assessment methods in multiple cohort studies.Proteomics. 2020; 20e1900278Crossref PubMed Scopus (39) Google Scholar, 3Katz D.H. Abstract 9892: proteomic profiling of cardiometabolic phenotypes: a comparison of aptamer-based and antibody-based affinity platforms.Circulation. 2021; 144: A9892https://www.ahajournals.org/doi/abs/10.1161/circ.144.suppl_1.9892Date accessed: March 10, 2022Google Scholar, 4Liu R.X. Thiessen-Philbrook H.R. Vasan R.S. et al.Comparison of proteomic methods in evaluating biomarker-AKI associations in cardiac surgery patients.Transl Res. 2021; 238: 49-62Abstract Full Text Full Text PDF PubMed Scopus (10) Google Scholar, 5Tin A. Yu B. Ma J. et al.Reproducibility and variability of protein analytes measured using a multiplexed modified aptamer assay.J Appl Lab Med. 2019; 4: 30-39Crossref PubMed Scopus (33) Google Scholar This may be especially relevant in the setting of autoimmune diseases, such as systemic lupus erythematosus (SLE), where anti–double-stranded DNA (anti-dsDNA) antibodies could interfere with immunoassay technologies that use oligonucleotide-based antibodies (Olink) or aptamers (SomaScan). In this study, we compared measurements of plasma kidney injury molecule-1 (KIM-1), a sensitive marker of tubular injury with prognostic value,6Bonventre J.V. Kidney injury molecule-1 (KIM-1): a specific and sensitive biomarker of kidney injury.Scand J Clin Lab Invest Suppl. 2008; 241: 78-83Crossref PubMed Scopus (120) Google Scholar,7Schmidt I.M. Srivastava A. Sabbisetti V. et al.Plasma kidney injury molecule 1 in CKD: findings from the Boston Kidney Biopsy Cohort and CRIC studies.Am J Kidney Dis. 2022; 79: 231-243.e1https://doi.org/10.1053/j.ajkd.2021.05.013Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar across 2 different immunoassay technologies in patients with and without SLE. We measured plasma KIM-1 levels in 446 individuals enrolled in the Boston Kidney Biopsy Cohort, a prospective, observational cohort study of patients with chronic kidney disease (Item S1), using the microbead-based sandwich enzyme-linked immunosorbent assay (ELISA) and a proximity extension assay (Olink). The proximity extension assay uses oligonucleotide-labeled antibodies that bind to the target protein. The measurements and assay performance of both ELISA and the Olink platform in the Boston Kidney Biopsy Cohort were described previously in detail.7Schmidt I.M. Srivastava A. Sabbisetti V. et al.Plasma kidney injury molecule 1 in CKD: findings from the Boston Kidney Biopsy Cohort and CRIC studies.Am J Kidney Dis. 2022; 79: 231-243.e1https://doi.org/10.1053/j.ajkd.2021.05.013Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar,8Schmidt I.M. Mothi S.S. Wilson P.C. et al.Circulating plasma biomarkers in biopsy-confirmed kidney disease.Clin J Am Soc Nephrol. 2022; 17: 27-37Crossref PubMed Scopus (4) Google Scholar Using Spearman correlation coefficients, we investigated differences in plasma KIM-1 measurements between the 2 assays in individuals with and without SLE and in individuals with negative versus positive anti-dsDNA levels (assay reference range, ≤25 vs >25 IU/mL). The corresponding 95% confidence intervals (CIs) were reported as bias-corrected and accelerated bootstrap estimates.9Chan W. Chan D.W. Bootstrap standard error and confidence intervals for the correlation corrected for range restriction: a simulation study.Psychol Methods. 2004; 9: 369-385Crossref PubMed Scopus (32) Google Scholar Sixty-eight Boston Kidney Biopsy Cohort participants had SLE and were compared with 378 individuals with diseases other than SLE (Table S1). The mean ages were 39 ± 15 and 55 ± 16 years, the mean estimated glomerular filtration rates were 85 ± 37 and 52 ± 33 mL/min/1.73 m2, and the median proteinurias (interquartile range) were 1.5 (0.7-3.2) and 1.7 (0.4-4.2) g/g creatinine in individuals with and without SLE, respectively. Eighty-seven percent of individuals with SLE were women and 46% of those without SLE were women. Among those with SLE, 62% had proliferative and 27% had nonproliferative histopathologic lesions in the kidneys. Spearman’s ρ between plasma KIM-1 measurements from both assays in the entire cohort was 0.89 (95% CI, 0.85-0.92; P < 0.001). Spearman’s ρ was 0.69 (95% CI, 0.47-0.82; P < 0.001) in individuals with SLE, and Spearman’s ρ was 0.90 (95% CI, 0.85-0.93; P < 0.001) in individuals with diseases other than SLE (Fig 1). Forty-three individuals with SLE had available anti-dsDNA levels measured using the chemiluminescent QUANTA Flash dsDNA assay (Werfen). The correlation between the 2 assays was lower in 34 individuals with anti-dsDNA antibody levels >25 IU/mL (ρ = 0.70; 95% CI, 0.37-0.88; P < 0.001) than in 9 individuals with anti-dsDNA levels ≤25 IU/mL (ρ = 0.92; 95% CI, 0.68-1.0; P = 0.001). In this study, we found differences in the concordance of plasma KIM-1 measurements by proximity extension assay versus ELISA according to SLE status. Few studies have compared assay specificity and correlation between different assay technologies.1Hayek SS, Raffield LM, Gao Y, et al. Assay-related differences in SuPAR levels: implications for measurement and data interpretation. medRxiv. Preprint posted online June 28, 2021. https://doi.org/10.1101/2021.06.23.21259148Google Scholar, 2Raffield L.M. Dang H. Pratte K.A. et al.Comparison of proteomic assessment methods in multiple cohort studies.Proteomics. 2020; 20e1900278Crossref PubMed Scopus (39) Google Scholar, 3Katz D.H. Abstract 9892: proteomic profiling of cardiometabolic phenotypes: a comparison of aptamer-based and antibody-based affinity platforms.Circulation. 2021; 144: A9892https://www.ahajournals.org/doi/abs/10.1161/circ.144.suppl_1.9892Date accessed: March 10, 2022Google Scholar, 4Liu R.X. Thiessen-Philbrook H.R. Vasan R.S. et al.Comparison of proteomic methods in evaluating biomarker-AKI associations in cardiac surgery patients.Transl Res. 2021; 238: 49-62Abstract Full Text Full Text PDF PubMed Scopus (10) Google Scholar, 5Tin A. Yu B. Ma J. et al.Reproducibility and variability of protein analytes measured using a multiplexed modified aptamer assay.J Appl Lab Med. 2019; 4: 30-39Crossref PubMed Scopus (33) Google Scholar In a prior study, correlations between ELISA and SomaScan aptamer–based assays for multiple proteins ranged from high for some proteins (eg, C-reactive protein) to none (eg, platelet endothelial cell adhesion molecule-1).2 In a recent study that compared soluble urokinase plasminogen activator receptor levels measured by conventional ELISA with the Olink and SomaScan platforms in 3 different cohorts, assay correlations varied widely across the cohorts (Spearman’s ρ = 0.3-0.8). Soluble urokinase plasminogen activator receptor had a weaker magnitude of association with adverse clinical outcomes when measured on the proteomics platforms compared with ELISA.1Hayek SS, Raffield LM, Gao Y, et al. Assay-related differences in SuPAR levels: implications for measurement and data interpretation. medRxiv. Preprint posted online June 28, 2021. https://doi.org/10.1101/2021.06.23.21259148Google Scholar Although cross-reactivity, epitope availability, and negative cooperative binding could all influence the concordance between assay technologies,2Raffield L.M. Dang H. Pratte K.A. et al.Comparison of proteomic assessment methods in multiple cohort studies.Proteomics. 2020; 20e1900278Crossref PubMed Scopus (39) Google Scholar it is possible that autoantibodies (eg, anti-dsDNA antibodies, which can bind to diverse DNA structures and nucleoprotein complexes, and may have DNA-related catalytic activity)10Wang X. Xia Y. Anti-double stranded DNA antibodies: origin, pathogenicity, and targeted therapies.Front Immunol. 2019; 10: 1667Crossref PubMed Scopus (47) Google Scholar interfere with measurements dependent on proximity-based oligonucleotide amplicons used in the Olink platform. Although our sample size of individuals with available anti-dsDNA levels was small, our results showing lower correlation with higher anti-dsDNA levels highlight a potential limitation to the use of oligonucleotide-based assay technologies in patients with diseases characterized by the presence of autoantibodies. More broadly, our results emphasize the possibility of disease-specific interference phenomena for biomarker assays and the importance of cross-platform validation studies. Research idea and study design: IMS, SSW; data acquisition: MRC, VS, AS, SSW; data analysis/interpretation: IMS, AS, GY, JVB, SSW; statistical analysis: IMS; supervision or mentorship: SSW, JVB. Each author contributed important intellectual content during manuscript drafting or revision and accepts accountability for the overall work by ensuring that questions pertaining to the accuracy or integrity of any portion of the work are appropriately investigated and resolved. Funding for the Boston Kidney Biopsy Cohort was provided by the National Institutes of Health (NIH) grant R01DK093574 (Dr Waikar). Dr Schmidt is supported by the American Philosophical Society Daland Fellowship in Clinical Investigation. Dr Srivastava is supported by NIH grant K23DK120811, National Institute of Diabetes and Digestive and Kidney Diseases. Kidney Precision Medicine Project Opportunity Pool grant under U2CDK114886, and core resources from the George M. O’Brien Kidney Research Center at Northwestern University (NU-GoKIDNEY) P30DK114857. Dr Waikar is also supported by NIH grants UH3DK114915, U01DK085660, U01DK104308, R01DK103784, R01DK093574, and R21DK119751. Dr Bonventre is supported by grants U01DK085660, R01DK072381, and R37DK39773. None of the funders of this study had any role in the study design; collection, analysis, and interpretation of data; writing the report; and the decision to submit the report for publication. Dr Srivastava reports personal fees from Horizon Therapeutics, PLC, AstraZeneca, CVS Caremark, and Tate & Latham (medicolegal consulting). Dr Bonventre is a cofounder of and holds equity in Goldfinch Bio and Autonomous Medical Devices, is a coinventor on KIM-1 patents assigned to Mass General Brigham, has received consulting income related to biomarkers from Biomarin, Aldeyra, PTC, Praxis, and Sarepta, and has received laboratory support from Kantum Pharma. Dr Bonventre’s interests were reviewed and are managed by Brigham and Women’s Hospital and Mass General Brigham in accordance with their conflict-of-interest policies. Dr Waikar reports personal fees from Public Health Advocacy Institute, CVS, Roth Capital Partners, Kantum Pharma, Mallinckrodt, Wolters Kluewer, GE Health Care, GSK, Mass Medical International, Barron and Budd (vs Fresenius), JNJ, Venbio, Strataca, Takeda, Cerus, Pfizer, Bunch and James, Harvard Clinical Research Institute (aka Baim) and grants and personal fees from Allena Pharmaceuticals. The remaining authors declare that they have no relevant financial interests. The authors thank the staff and participants of the Boston Kidney Biopsy Cohort study for their important contributions and invaluable assistance. Received March 18, 2022 as a submission to the expedited consideration track with 2 external peer reviews. Direct editorial input from the Statistical Editor, an Associate Editor, and the Editor-in-Chief. Accepted in revised form April 24, 2022. Download .pdf (.11 MB) Help with pdf files Supplementary File (PDF)Item S1; Table S1.

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