Biology subjects

Schulze-Hentrich, J.

Publications and source records attributed to Schulze-Hentrich, J..

4 recordsLinked to original sources

bioRxiv2026

Dynamic transcriptional remodeling in alcohol use disorder reveals immune dysregulation and adaptive shifts in coagulation during therapy

BackgroundChronic alcohol use disorder (AUD) is associated with profound dysregulation of immune function, neuroinflammation, and systemic stress responses, which contribute to both the maintenance of addiction and alcohol-related organ damage. While brain transcriptomic studies have established neuroimmune signaling and synaptic remodeling as central features of AUD, peripheral blood signatures during early withdrawal and recovery remain underexplored. Understanding the dynamic transcriptional changes in peripheral blood accompanying supervised withdrawal therapy is critical for identifying reversible molecular processes versus persistent trait-like alterations. MethodsRNA sequencing (RNA-seq) was performed on peripheral blood from individuals with alcohol use disorder (AUD, n = 100) and healthy controls (n = 74) at baseline and after three weeks of supervised withdrawal therapy. Differentially expressed genes (DEGs) were identified using linear mixed models assessing main effects of group, time, and their interaction. Functional enrichment and co-expression network analyses were performed to identify coordinated biological processes. ResultsAt baseline, more than 1,000 genes were differentially expressed between AUD and control participants, showing robust dysregulation of immune-related pathways. After three weeks of withdrawal, the number of DEGs decreased markedly to 141, indicating partial transcriptomic normalization. Nevertheless, immune dysregulation persisted despite treatment, particularly linked to B cell activation and cell-cell junctions. Interaction analyses (group x time) identified 16 genes whose expression dynamically changed with therapy, highlighting strong enrichment for fatty acid pathways. Co-expression network analysis revealed that baseline modules were enriched for genes associated with secretory granules and immune signaling, while therapy-related co-expression shifts involved coagulation and platelet activation processes. ConclusionsAUD is associated with widespread but partly reversible transcriptomic dysregulation in peripheral blood. These findings support a system-level view of AUD as a disorder of intertwined immune, metabolic, and coagulation biology and suggest that longitudinal blood transcriptomics may help identify both rapidly therapy-responsive and more stable molecular targets for relapse prevention.

molecular biology↗

bioRxiv2026

MethylBench: A comprehensive benchmark of DNA methylation profiling methods across diverse sequencing platforms

BackgroundDNA methylation can be profiled using multiple technologies that vary in resolution, coverage and cost. Prior benchmarking efforts have laid important groundwork, yet critical gaps remain. The SEQC2 EpiQC study[14] provided a multi-platform QC framework across whole-genome bisulfite sequencing (WGBS), oxidative bisulfite sequencing, enzymatic deamination, ONT and Illumina 850k arrays, showing high overall concordance but limited replication and no coverage of current enzymatic conversion, hybridization-based panels or modern long-read chemistries. More recently, Sigurpalsdottir et al.[40] systematically compared methylation detection tools within the long-read domain, demonstrating high ONT accuracy relative to oxidative bisulfite sequencing, but restricted their analysis to ONT and PacBio, excluding short-read, targeted-panel and array-based platforms as well as the biological interpretability of differential methylation across platform classes. A comprehensive cross-platform benchmark addressing coverage heterogeneity and annotation redundancy in the interpretation of differentially methylated cytosines thus remains absent. MethodsWe compared six widely used technologies - Illumina EPIC array, TWIST, Whole-Genome Enzymatic Conversion (WGEC), Reduced Representation Bisulfite Sequencing (RRBS), Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) - using GIAB reference samples and ten blood/fibroblast samples from 5 individuals. We assessed CpG coverage, consistency of differentially methylated cytosine (DMC) detection, and genomic annotation, with particular attention to overlapping signals across assays. ResultsDespite major assay differences, all technologies consistently identified DMCs enriched in promoter and intronic regions, marking these as robust hotspots of epigenetic variability. Annotation redundancy strongly shaped initial interpretations, with CpG island-related categories largely disappearing once annotations were collapsed to unique features. Sequencing-based methods (WGEC, TWIST, ONT) achieved the most comprehensive coverage, while EPIC arrays reliably captured promoter-associated differences despite limited scope. ONT showed strong concordance with short-read methods after coverage filtering, but required higher, more uniform coverage for reproducible CpG-level agreement. PacBio showed a coverage-independent discrepancy, with concordance plateauing regardless of mean coverage - pointing to residual technology-specific bias rather than a simple coverage effect. ConclusionsCross-platform benchmarking yields coherent biological insights once coverage and annotation redundancies are addressed. EPIC arrays remain valuable for promoter-focused cohort studies, WGEC and TWIST enable genome-wide discovery and ONT offers unique phasing and multimodal potential - together guiding method selection and more robust interpretation of DNA methylation data.

genomics↗

bioRxiv2025

Transcriptional Dysregulation in the Hippocampus of a murine model for Parkinson's Disease Cognition Impairment is Driven by Sex, Age, and Alpha-synuclein overexpression

Cognitive impairment is the most common and detrimental, but understudied non-motor symptom of Parkinsons disease (PD). Neuropathologically, it is associated with alpha-synuclein (Syn) misfolding and synapse loss in hippocampus and prefrontal cortex, leading to cognition loss and ultimately dementia. The molecular underpinnings of PD-associated cognitive dysfunction are unknown. In the present study, longitudinal gene expression profiling was performed to characterise molecular hippocampal alterations in a transgenic mouse overexpressing E46K mutated Syn, a model of early PD with loss of synaptophysin, a proxy marker of cognition, in hippocampus and cortex. Comparing 4 different ages of mice from both sexes showed that hippocampal gene expression changes were sexually dimorphic and strongly modulated by age and Syn overexpression. Pathways that emerged across different comparisons were connected to a variety of neuronal functions, collagen synthesis/remodelling, cellular stress, and inflammatory responses. The findings indicate that sex and age are essential covariates to consider when studying PD-associated cognitive decline. The uncovering of early events leading to disease in an animal model is an essential step toward prognostic biomarker identification and early interventions, which may have implications for monitoring, and for timing of therapeutic approaches.

neuroscience↗

bioRxiv2024

Self-assembly of hybrid 3D cultures by integrating living and synthetic cells

Self-assembly, a fundamental property of living matter, drives the interconnected cellular organization of tissues. Synthetic cell models have been developed as bionic materials to mimic inherent cellular features such as self-assembly. Here, we leverage co-assembly of synthetic and natural cells to create hybrid living 3D cancer cultures. We screened synthetic cell models, including giant unilamellar vesicles, coacervates, microdroplet emulsions, proteinosomes, and colloidosomes, for their ability to form hybrid tumoroids. Our results identify the balance of inter- and extracellular adhesion and synthetic cell surface tension as key material properties driving successful co-assembly of hybrids. We further demonstrate that these synthetic cells can establish artificial tumor immune microenvironments (ART-TIMEs), mimicking immunogenic signals within tumoroids. Using the ART-TIME approach, we identify co-signaling mechanisms between PD-1 and CD2 as a driver in immune evasion of pancreatic ductal adenocarcinoma. Our findings demonstrate the 3D bottom-up self-assembly of hybrid cancer microenvironments to replace immune components with defined bionic materials, pushing the boundaries to functionally integrating living and non-living matter.

synthetic biology↗