Biology subjects

Eden, A.

Publications and source records attributed to Eden, A..

6 recordsLinked to original sources

bioRxiv2026

Improved deconvolution of circulating tumor DNA from ultra-low-pass whole-genome methylation sequencing using CelFiE-ISH

Liquid biopsy using ultra-low-pass whole-genome sequencing (ULP-WGS, [~]0.25x coverage) is a promising tool to detect circulating tumor DNA (ctDNA) for cancer management, and the use of the native Oxford Nanopore (ONT) sequencing platform adds DNA methylation to the set of detectable features. Here, we test the performance of methylation-based cell-type deconvolution in ULP-WGS samples from diverse epithelial malignancies and investigate several new computational strategies using our CelFiE-ISH deconvolution framework. We find that incorporating larger numbers of markers restricted to the epithelial cell lineage can reduce the cancer fraction limit of detection down to 1.7-3.1%, matching or exceeding the 3% floor of established copy-number alteration (CNA) benchmarks. Our study provides a useful strategy for analysis of ULP-WGS ONT data and indicates that marker selection remains a key challenge for analyzing methylation-based cancer datasets.

genomics↗

bioRxiv2026

Systematic errors in enzymatic conversion limit cell-free DNA methylation specificity

Enzymatic methylation sequencing (EM-seq) converts unmethylated cytosines to uracils while preserving DNA integrity, making it attractive for liquid biopsies. Here we report a reproducible fragment-level over-conversion error in EM-seq, which is not observed in bisulfite-based conversion or in Oxford Nanopore sequencing. While bisulfite and nanopore errors occur at sporadic CpGs, EM-seq generates molecules that appear fully unmethylated, introducing a false-positive background signal that severely limits deconvolution specificity in cfDNA analysis.

genomics↗

bioRxiv2025

Methylation-Based Deconvolution Unveils Glioblastoma Heterogeneity and Cell-Type Composition Linked to Patient Survival

BackgroundIDH-wildtype glioblastoma (GBM) is an aggressive, heterogeneous brain tumor with limited treatment options. DNA methylation profiling allows detailed tumor characterization. This study applies methylation-based deconvolution to define GBMs cellular composition and its association with patient outcomes. MethodsWe generated oligodendroglial precursor cells at various developmental stages from enriched human neural progenitor cultures and used their DNA methylation signatures, along with published signatures of brain tumor and tumor microenvironment-relevant cell types, to deconvolve 263 adult GBMs (Heidelberg-cohort). Tumor purity was estimated using RF_Purify. An independent cohort of 199 GBMs from TCGA and GEO, all treated with standard-of-care therapy, was similarly deconvolved, followed by Kaplan-Meier survival analysis to assess the prognostic value of neoplastic component proportions. ResultsDeconvolution uncovered distinct cellular compositions, consistent with single-cell RNA sequencing findings. Tumor purity analysis showed neoplastic fractions averaged 70% of tumor bulk, predominantly oligodendrocyte-like (43%), oligodendrocyte precursor-like (27%), astrocyte-like (19%), and mesenchymal stem cell-like (11%) populations. Non-neoplastic fractions were enriched for macrophages, vascular cells, and immune populations. A higher oligodendrocyte-like signature was linked to poorer survival (median survival 14.3 vs. 15.3 months; p = 0.017), while a higher astrocyte-like signature correlated with improved outcomes (15.3 vs. 13.4 months; p = 0.044). The astrocyte-to-oligodendrocyte ratio emerged as a strong prognostic marker, with a higher ratio predicting significantly longer survival (15.8 vs. 11.9 months; p < 0.00011). ConclusionsMethylation-based deconvolution provides insight into GBM heterogeneity, highlighting the prognostic relevance of the astrocyte-to-oligodendrocyte ratio, which may guide personalized treatment strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/640603v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@942af0org.highwire.dtl.DTLVardef@18f2626org.highwire.dtl.DTLVardef@111a756org.highwire.dtl.DTLVardef@1194b_HPS_FORMAT_FIGEXP M_FIG A. We generated oligodendroglial precursor cells (OPs) at various developmental stages from enriched human neural progenitor cultures. A reference atlas of methylation signatures from 14 normal cell types, including the in vitro-generated cells, combined with published profiles of brain tumor and tumor microenvironment-relevant cell types, was applied to deconvolve 263 GBM samples based on their methylation profiles (Heidelberg cohort). Cell type proportions were analyzed with RF_Purify to estimate tumor purity and distinguish neoplastic from non-neoplastic components. B. An independent cohort of 199 GBMs from TCGA and GEO, with available clinical data and all treated with standard-of-care therapy, was similarly deconvolved based on methylation profiles. Kaplan-Meier survival analysis assessed the prognostic impact of cell type proportions, identifying the astrocyte-to-oligodendrocyte ratio as the most significant marker. (Created with BioRender.com) C_FIG Key pointsO_LIMethylation-based deconvolution incorporating in-vitro-derived oligodendrocyte precursor differentiation data reveals GBM heterogeneity C_LIO_LIGBMs neoplastic fraction is dominated by oligodendrocyte-lineage cells C_LIO_LIAstrocyte/oligodendrocyte ratio is a strong prognostic marker for patient survival C_LI Importance of the studyThis study advances neuro-oncology research by using methylation-based deconvolution to uncover the cellular heterogeneity of glioblastoma. By constructing a comprehensive reference atlas and identifying cell-type-specific methylation signatures, it provides prognostic insights into the distinct cellular compositions of glioblastoma. Combining deconvolution results with purity analysis enables the differentiation between neoplastic and non-neoplastic tumor components. This approach complements single-cell RNA sequencing while offering greater clinical applicability, as DNA methylation profiling can be performed on FFPE or fresh frozen samples, unlike the more costly and tissue-sensitive single-cell methods. Importantly, the identification of the astrocyte-to-oligodendrocyte ratio as a strong prognostic marker highlights key cellular determinants of glioblastoma survival. These findings deepen our understanding of glioblastoma biology and offer a practical tool for patient stratification.

cancer biology↗

bioRxiv2022

A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer

Global loss of DNA methylation in mammalian genomes occurs during aging and cancer, primarily in heterochromatin-associated Partially Methylated Domains (PMDs). It has previously been shown that local sequence context (100bp) has a strong influence on the rate of demethylation of individual CpG dinucleotides within PMDs. Here, we train a deep learning model to capture this sequence dependence, finding that methylation loss in healthy tissues and cancer can be predicted with high accuracy based on the 150bp surrounding a CpG. We use a published whole-genome map of the re-methylation rate of newly synthesized DNA during mitosis to show that CpGs with a "slow-loss" sequence context are efficiently re-methylated, while CpGs with a "fast-loss" sequence context are inefficiently re-methylated. Intriguingly, we find that the 10% most slow-loss CpGs lose almost no DNA methylation in healthy cell types, but lose significant DNA methylation in many cancer types. This finding suggests that loss of DNA methylation at slow-loss CpGs could underlie some cancer-specific transcriptional deregulation that has been linked to DNA hypomethylation, including the derepression of cancer antigens and transposable elements.

genomics↗

bioRxiv2021

Detecting cell-of-origin and cancer-specific features of cell-free DNA with Nanopore sequencing

The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for clinical sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy number alterations (CNA) from the circulating tumor DNA (ctDNA) of cancer patients. Here, we show that cell-type and cancer-specific methylation changes can also be detected, as well as cancer-associated fragmentation signatures. This feasibility study suggests that ONT shallow WGS could be a powerful tool for liquid biopsy, especially real-time medical applications.

genomics↗

bioRxiv2021

Infection of brain pericytes underlying neuropathology of COVID-19 patients

A wide range of neurological manifestations have been associated with the development of COVID-19 following SARS-CoV-2 infection. However, the etiology of the neurological symptomatology is still largely unexplored. Here, we used state-of-the-art multiplexed immunostaining of human brains (n = 6 COVID-19, median age = 69,5 years; and n = 7 control, median age = 68 years), and demonstrated that expression of the SARS-CoV-2 receptor ACE2 is restricted to a subset of neurovascular pericytes. Strikingly, neurological symptoms were exclusive to, and ubiquitous in, patients that exhibited moderate to high ACE2 expression in peri-vascular cells. Viral particles were identified in the vascular wall and paralleled by peri-vascular inflammation, as signified by T cell and macrophage infiltration. Furthermore, fibrinogen leakage indicated compromised integrity of the blood-brain barrier. Notably, cerebrospinal fluid from an additional 16 individuals (n = 8 COVID-19, median age = 67 years; and n = 8 control, median age = 69,5 years) exhibited significantly lower levels of the pericyte marker PDGFR{beta} in SARS-CoV-2-infected cases, indicative of disrupted pericyte homeostasis. We conclude that pericyte infection by SARS-CoV-2 underlies virus entry into the privileged central nervous system space, as well as neurological symptomatology due to peri-vascular inflammation and a locally compromised blood-brain barrier.

pathology↗