Ultrasensitive detection of neuronal DNA using genome-wide non-CG methylation patterns
- 1The Hebrew University of Jerusalem
Abstract
Methylation-based liquid biopsies can identify the tissue origins of circulating cell-free DNA (cfDNA). A major constraint on the sensitivity of these assays is the limited number of cell-type-specific CpG markers. Here we exploit the high abundance of non-CpG (CpH) methylation in neurons to enable ultrasensitive detection of neuronal DNA. We show that neurons carry 100-fold higher CpH methylation than other tissues, in which apparent CpH methylation largely reflects experimental artifacts. Using a computational criterion to identify cfDNA molecules carrying clusters of methylated CpA sites, we detect neuronal DNA at proportions as low as 20 parts per million. Analysis of 231 samples from 163 individuals revealed minimal neuronal cfDNA in the plasma of healthy subjects; elevated levels in patients with measles or acute neurological conditions; strikingly high levels in brain-dead donors, indicating extensive ongoing neuronal death; and the highest levels in the cerebrospinal fluid of patients in a neurological intensive care unit. These findings establish genome-wide, fragment-level analysis of non-CpG methylation as an ultrasensitive approach for blood-based monitoring of brain injury and disease.
Related
- Characterization of lysine methylation during neuronal differentiation of LUHMES cells
- DNA Methylation Patterns Between Serous Uterine and Ovarian Carcinomas Indicate Shared Markers with Fallopian Tube Epithelium and Distinctions Consistent with Histopathology
- DNA polymerase kappa supports repair-associated DNA synthesis and neuronal genome resilience
- Cortex-wide neuronal dynamics underpin quasi-periodic patterns in resting-state fMRI
- Early Prenatal Cell-Free DNA Methylation Landscape Informs Epigenetic Purification of the Circulating Fetal Genome
BibTeX
@misc{loyfer2026ultrasensitive,
title = {{Ultrasensitive detection of neuronal DNA using genome-wide non-CG methylation patterns}},
author = {N. Loyfer and A. Horn and S. Hart and J. Rosenski and S. Piyanzin and J. Magenheim and O. Sabag and A. Avniel Aran and Y. Langer and N. Barsoum and G. Rosenthal and M. Gat and K. Olthoff and A. Shaked and R. Shemer and B. Glaser and T. Kaplan and Y. Dor},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.29.761818},
url = {https://www.biorxiv.org/content/10.64898/2026.10.29.761818v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Ultrasensitive detection of neuronal DNA using genome-wide non-CG methylation patterns
AU - N. Loyfer
AU - A. Horn
AU - S. Hart
AU - J. Rosenski
AU - S. Piyanzin
AU - J. Magenheim
AU - O. Sabag
AU - A. Avniel Aran
AU - Y. Langer
AU - N. Barsoum
AU - G. Rosenthal
AU - M. Gat
AU - K. Olthoff
AU - A. Shaked
AU - R. Shemer
AU - B. Glaser
AU - T. Kaplan
AU - Y. Dor
PY - 2026
DA - 2026/10/29
PB - bioRxiv
DO - 10.64898/2026.10.29.761818
UR - https://www.biorxiv.org/content/10.64898/2026.10.29.761818v1
AB - Methylation-based liquid biopsies can identify the tissue origins of circulating cell-free DNA (cfDNA). A major constraint on the sensitivity of these assays is the limited number of cell-type-specific CpG markers. Here we exploit the high abundance of non-CpG (CpH) methylation in neurons to enable ultrasensitive detection of neuronal DNA. We show that neurons carry 100-fold higher CpH methylation than other tissues, in which apparent CpH methylation largely reflects experimental artifacts. Using a computational criterion to identify cfDNA molecules carrying clusters of methylated CpA sites, we detect neuronal DNA at proportions as low as 20 parts per million. Analysis of 231 samples from 163 individuals revealed minimal neuronal cfDNA in the plasma of healthy subjects; elevated levels in patients with measles or acute neurological conditions; strikingly high levels in brain-dead donors, indicating extensive ongoing neuronal death; and the highest levels in the cerebrospinal fluid of patients in a neurological intensive care unit. These findings establish genome-wide, fragment-level analysis of non-CpG methylation as an ultrasensitive approach for blood-based monitoring of brain injury and disease.
ER -