Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood Plasma

Zac Chatterton; Natalia Mendelev; Sean Chen; Walter Carr; Gary H Kamimori; Yongchao Ge; Andrew J Dwork; Fatemeh Haghighi

doi:10.3389/fnmol.2021.672614

Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood Plasma

Front Mol Neurosci. 2021 Jul 2:14:672614. doi: 10.3389/fnmol.2021.672614. eCollection 2021.

Authors

Zac Chatterton^{1

2

3

4

5}, Natalia Mendelev^{1

2

3

4}, Sean Chen^{1

2

3

4}, Walter Carr^{6

7}, Gary H Kamimori⁶, Yongchao Ge³, Andrew J Dwork^{8

9

10}, Fatemeh Haghighi^{1

2

3

4}

Affiliations

¹ Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
² Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
³ Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
⁴ Medical Epigenetics, James J. Peters VA Medical Center, New York, NY, United States.
⁵ Brain and Mind Centre, School of Medical Science, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
⁶ Walter Reed Army Institute of Research, Silver Spring, MD, United States.
⁷ Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States.
⁸ Department of Pathology and Cell Biology, Columbia University, New York, NY, United States.
⁹ Department of Psychiatry, Columbia University, New York, NY, United States.
¹⁰ Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY, United States.

Abstract

Sampling the live brain is difficult and dangerous, and withdrawing cerebrospinal fluid is uncomfortable and frightening to the subject, so new sources of real-time analysis are constantly sought. Cell-free DNA (cfDNA) derived from glia and neurons offers the potential for wide-ranging neurological disease diagnosis and monitoring. However, new laboratory and bioinformatic strategies are needed. DNA methylation patterns on individual cfDNA fragments can be used to ascribe their cell-of-origin. Here we describe bisulfite sequencing assays and bioinformatic processing methods to identify cfDNA derived from glia and neurons. In proof-of-concept experiments, we describe the presence of both glia- and neuron-cfDNA in the blood plasma of human subjects following mild trauma. This detection of glia- and neuron-cfDNA represents a significant step forward in the translation of liquid biopsies for neurological diseases.

Keywords: cfDNA; diagnostic; epigenetic; glia; neuron; neurotrauma.

Abstract

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