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Ko J, Hemphill M, Yang Z, Sewell E, Na YJ, Sandsmark DK, Haber M, Fisher SA, Torre EA, Svane KC, Omelchenko A, Firestein BL, Diaz-Arrastia R, Kim J, Meaney DF, Issadore D. Diagnosis of traumatic brain injury using miRNA signatures in nanomagnetically isolated brain-derived extracellular vesicles. LAB ON A CHIP 2018; 18:3617-3630. [PMID: 30357245 PMCID: PMC6334845 DOI: 10.1039/c8lc00672e] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The accurate diagnosis and clinical management of traumatic brain injury (TBI) is currently limited by the lack of accessible molecular biomarkers that reflect the pathophysiology of this heterogeneous disease. To address this challenge, we developed a microchip diagnostic that can characterize TBI more comprehensively using the RNA found in brain-derived extracellular vesicles (EVs). Our approach measures a panel of EV miRNAs, processed with machine learning algorithms to capture the state of the injured and recovering brain. Our diagnostic combines surface marker-specific nanomagnetic isolation of brain-derived EVs, biomarker discovery using RNA sequencing, and machine learning processing of the EV miRNA cargo to minimally invasively measure the state of TBI. We achieved an accuracy of 99% identifying the signature of injured vs. sham control mice using an independent blinded test set (N = 77), where the injured group consists of heterogeneous populations (injury intensity, elapsed time since injury) to model the variability present in clinical samples. Moreover, we successfully predicted the intensity of the injury, the elapsed time since injury, and the presence of a prior injury using independent blinded test sets (N = 82). We demonstrated the translatability in a blinded test set by identifying TBI patients from healthy controls (AUC = 0.9, N = 60). This approach, which can detect signatures of injury that persist across a variety of injury types and individual responses to injury, more accurately reflects the heterogeneity of human TBI injury and recovery than conventional diagnostics, opening new opportunities to improve treatment of traumatic brain injuries.
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Affiliation(s)
- J Ko
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - M Hemphill
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Z Yang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - E Sewell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Y J Na
- Department of Medicine, Division of Nephrology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - D K Sandsmark
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - M Haber
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - S A Fisher
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E A Torre
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - K C Svane
- Department of Cell Biology and Neuroscience, Rutgers, the State University of New Jersey, NJ 08854, USA
| | - A Omelchenko
- Department of Cell Biology and Neuroscience, Rutgers, the State University of New Jersey, NJ 08854, USA
| | - B L Firestein
- Department of Cell Biology and Neuroscience, Rutgers, the State University of New Jersey, NJ 08854, USA
| | - R Diaz-Arrastia
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - J Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA and Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - D F Meaney
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA. and Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - D Issadore
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA. and Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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