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A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection

Nature Biomedical Engineering volume 4, pages 601–609 (2020)Cite this article

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Abstract

In organ transplantation, infection and rejection are major causes of graft loss. They are linked by the net state of immunosuppression. To diagnose and treat these conditions earlier, and to improve long-term patient outcomes, refined strategies for the monitoring of patients after graft transplantation are needed. Here, we show that a fast and inexpensive assay based on CRISPR–Cas13 accurately detects BK polyomavirus DNA and cytomegalovirus DNA from patient-derived blood and urine samples, as well as CXCL9 messenger RNA (a marker of graft rejection) at elevated levels in urine samples from patients experiencing acute kidney transplant rejection. The assay, which we adapted for lateral-flow readout, enables—via simple visualization—the post-transplantation monitoring of common opportunistic viral infections and of graft rejection, and should facilitate point-of-care post-transplantation monitoring.

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Fig. 1: CRISPR diagnostics enable single-molecule detection of BKV and CMV DNA.
Fig. 2: CRISPR detects BKV and CMV from human urine and blood samples over a wide range of viral loads.
Fig. 3: CRISPR-based diagnostics can detect CXCL9 mRNA as an indicator for acute cellular rejection.
Fig. 4: Lateral flow enables detection of viral DNA (BKV, CMV) for point-of-care testing.
Fig. 5: Monitoring of CXCL9 mRNA levels with lateral flow.

Data availability

The authors declare that the data supporting the findings of this study are available within the paper and its Supplementary information files. The raw and analysed datasets generated during the study are available for research purposes from the corresponding authors on reasonable request, and the availability of raw patient data is subject to approval from the Institutional Review Board.

Code availability

The lateral-flow quantification app code is available at https://github.com/jackievaleri/lateral_flow_quantification_app.

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Acknowledgements

We thank R. Zaffini from viral microbiology (BWH) for helpful discussion about BKV testing and qPCR; the Crimson Core at BWH for providing samples from patients with CMV and BKV; and H. de Puig, N. Angenent-Mari, A. Dy and X. Tan for helpful discussions. M.M.K. was supported by the German Academy of Sciences, Leopoldina (LPDS 2018-01), the Clinician Scientist Program Berta–Ottenstein of the Faculty of Medicine, University of Freiburg, Germany and the Emmy Noether Programme (KA5060/1-1). M.A.A. was supported by a National Science Foundation graduate research fellowship (award no. 1122374). V.K. was supported by the DFG (grant no. 403877094). J.J.C. was supported by MIT’s Center for Microbiome Informatics and Therapeutics, the Paul G. Allen Frontiers Group and the Wyss Institute.

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Authors and Affiliations

  1. Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Michael M. Kaminski, Miguel A. Alcantar, Allison C. Huske, Jacqueline A. Valeri & James J. Collins

  2. Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany

    Michael M. Kaminski & Robert Greensmith

  3. Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Berlin, Germany

    Michael M. Kaminski & Robert Greensmith

  4. Schuster Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    Isadora T. Lape, Jamil Azzi & Leonardo V. Riella

  5. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA

    Jacqueline A. Valeri & James J. Collins

  6. Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA, USA

    Francisco M. Marty

  7. Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA

    Verena Klämbt

  8. Montefiore Einstein Center for Transplantation, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA

    Enver Akalin

  9. Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    James J. Collins

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  1. Michael M. Kaminski
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Contributions

M.M.K., L.V.R. and J.J.C. designed the study. M.M.K., M.A.A., A.C.H., I.L. and R.G. performed experiments. J.A.V. and M.A.A. programmed the smartphone app, and V.K. contributed to the design and analysis of experiments. L.V.R. and E.A. provided clinical samples. F.M.M. and J.A. advised on the collection and testing of clinical specimens. All authors contributed to the writing of the manuscript and interpretation of data.

Corresponding authors

Correspondence to Leonardo V. Riella or James J. Collins.

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Competing interests

A patent application related to this work is pending. J.J.C. is co-founder and director of Sherlock Biosciences.

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Supplementary information

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Supplementary Video 1

A smartphone-based software application for the quantification of band intensities.

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Kaminski, M.M., Alcantar, M.A., Lape, I.T. et al. A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection. Nat Biomed Eng 4, 601–609 (2020). https://doi.org/10.1038/s41551-020-0546-5

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