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A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies

View ORCID ProfileCarmen Martin-Alonso, View ORCID ProfileShervin Tabrizi, View ORCID ProfileKan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, View ORCID ProfileJ. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
doi: https://doi.org/10.1101/2023.01.13.524003
Carmen Martin-Alonso
1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA, USA
2Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Cambridge, MA, USA
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  • ORCID record for Carmen Martin-Alonso
Shervin Tabrizi
1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA, USA
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
4Department of Radiation Oncology, Massachusetts General Hospital; Boston, MA, USA
5Harvard Medical School; Boston, MA, USA
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  • ORCID record for Shervin Tabrizi
Kan Xiong
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
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Timothy Blewett
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
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Sahil Patel
1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA, USA
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
6Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital; Boston, MA, USA
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Zhenyi An
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
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Sainetra Sridhar
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
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Ahmet Bekdemir
1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA, USA
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Douglas Shea
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
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Ava P. Amini
7Microsoft Research New England; Cambridge, MA, USA
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Shih-Ting Wang
1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA, USA
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Jesse Kirkpatrick
1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA, USA
2Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Cambridge, MA, USA
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Justin Rhoades
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
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Todd R. Golub
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
5Harvard Medical School; Boston, MA, USA
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J. Christopher Love
1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA, USA
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
8Department of Chemical Engineering, Massachusetts Institute of Technology; Cambridge, MA, USA
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  • For correspondence: clove@mit.edu viktor@broadinstitute.org sbhatia@mit.edu
Viktor A. Adalsteinsson
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
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  • For correspondence: clove@mit.edu viktor@broadinstitute.org sbhatia@mit.edu
Sangeeta N. Bhatia
1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA, USA
2Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology; Cambridge, MA, USA
3Broad Institute of MIT and Harvard; Cambridge, MA, USA
9Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Cambridge, MA, USA
10Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
11Wyss Institute at Harvard University; Boston, USA
12Howard Hughes Medical Institute; Cambridge, MA, USA
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  • For correspondence: clove@mit.edu viktor@broadinstitute.org sbhatia@mit.edu
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Abstract

Liquid biopsies are enabling minimally invasive monitoring and molecular profiling of diseases across medicine, but their sensitivity remains limited by the scarcity of cell-free DNA (cfDNA) in blood. Here, we report an intravenous priming agent that is given prior to a blood draw to increase the abundance of cfDNA in circulation. Our priming agent consists of nanoparticles that act on the cells responsible for cfDNA clearance to slow down cfDNA uptake. In tumor-bearing mice, this agent increases the recovery of circulating tumor DNA (ctDNA) by up to 60-fold and improves the sensitivity of a ctDNA diagnostic assay from 0% to 75% at low tumor burden. We envision that this priming approach will significantly improve the performance of liquid biopsies across a wide range of clinical applications in oncology and beyond.

Competing Interest Statement

A provisional patent has been filed on this work: PCT/US2022/013769 (ST, CMA, KX, SNB, VAA, JCL). T.R. Golub has advisor roles (paid) at Foundation Medicine, GlaxoSmithKline and Sherlock Biosciences. J.C.L. has interests in Sunflower Therapeutics PBC, Pfizer, Honeycomb Biotechnologies, OneCyte Biotechnologies, QuantumCyte, Amgen, and Repligen. J.C.L.'s interests are reviewed and managed under MIT's policies for potential conflicts of interest. V.A. Adalsteinsson is a member of the scientific advisory boards of AGCT GmbH and Bertis Inc., which were not involved in this study. S.N.B. reports compensation for cofounding, consulting for, and/or board member-ship in Glympse Bio, Satellite Bio, CEND Therapeutics, Catalio Capital, Intergalactic Therapeutics, Port Therapeutics, Vertex Pharmaceuticals, and Moderna, and receives sponsored research funding from Johnson & Johnson, Revitope, and Owlstone. The remaining authors report no conflicts of interest.

Footnotes

  • ↵§ These authors jointly supervised this work.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 14, 2023.
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A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, J. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
bioRxiv 2023.01.13.524003; doi: https://doi.org/10.1101/2023.01.13.524003
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A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, J. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
bioRxiv 2023.01.13.524003; doi: https://doi.org/10.1101/2023.01.13.524003

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