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Mass-encoded synthetic biomarkers for multiplexed urinary monitoring of disease

Abstract

Biomarkers are becoming increasingly important in the clinical management of complex diseases, yet our ability to discover new biomarkers remains limited by our dependence on endogenous molecules. Here we describe the development of exogenously administered 'synthetic biomarkers' composed of mass-encoded peptides conjugated to nanoparticles that leverage intrinsic features of human disease and physiology for noninvasive urinary monitoring. These protease-sensitive agents perform three functions in vivo: they target sites of disease, sample dysregulated protease activities and emit mass-encoded reporters into host urine for multiplexed detection by mass spectrometry. Using mouse models of liver fibrosis and cancer, we show that these agents can noninvasively monitor liver fibrosis and resolution without the need for invasive core biopsies and substantially improve early detection of cancer compared with current clinically used blood biomarkers. This approach of engineering synthetic biomarkers for multiplexed urinary monitoring should be broadly amenable to additional pathophysiological processes and point-of-care diagnostics.

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Figure 1: Schematic of the approach.
Figure 2: Urinary detection of in vivo protease activity with peptide-nanoworms.
Figure 3: Photocaged iCORE libraries for multiplexed profiling of protease activities by LC-MS/MS.
Figure 4: Urinary biomarkers of hepatic fibrosis and resolution in DDC-treated mice.
Figure 5: Synthetic urinary biomarkers outperform serum CEA in early cancer detection.

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Acknowledgements

We thank R. Cook, N. Schiller and M. Brown (Swanson Biotechnology Center (SBC), Massachusetts Institute of Technology (MIT)) for peptide synthesis and tissue sectioning, C. Whittaker (SBC, MIT) for bioinformatic insight, R. Tomaino (Harvard Taplin mass spectrometry facility) for mass spectrometry analysis, F. Giammo and D. Kim (MIT) for initial probe work and urine purification, S. Carr (Broad Institute of MIT/Harvard) for mass spectrometry expertise and M. Sailor (University of California San Diego (UCSD)), J. Park (UCSD) and S. Friedman (Mount Sinai School of Medicine) for insightful discussions. This work was funded by the US National Institutes of Health (Bioengineering Research Partnership: R01 CA124427 to S.N.B.), the Kathy and Curt Marble Cancer Research Fund to S.N.B. and US National Institutes of Health grants U19 AI066313 and 1R21 DK075857 to D.S. G.A.K. is supported by the Ruth L. Kirschstein National Research Service Award (F32CA159496-01). S.N.B. is a Howard Hughes Institute Investigator.

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G.A.K., G.v.M. and S.N.B. conceived the study and designed the experiments. G.v.M. and S.M. performed the in vitro substrate screen and initial pharmacokinetic studies. G.A.K. developed the mass-encoding scheme. G.A.K., G.M. and O.A. performed the fibrosis experiments. Y.P., D.Y.S., S.B.L. and D.S. developed and provided expertise for the fibrosis progression and reversal protocols, and performed fibrosis quantification assays. G.A.K. and A.D.W. performed cancer experiments. G.A.K. and I.A.P. collected in vivo mass spectrometry data. G.A.K., G.v.M. and S.N.B. wrote the manuscript.

Corresponding author

Correspondence to Sangeeta N Bhatia.

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The authors declare no competing financial interests.

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Kwong, G., von Maltzahn, G., Murugappan, G. et al. Mass-encoded synthetic biomarkers for multiplexed urinary monitoring of disease. Nat Biotechnol 31, 63–70 (2013). https://doi.org/10.1038/nbt.2464

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