Biology subjects

Werner, J. M.

Publications and source records attributed to Werner, J. M..

7 recordsLinked to original sources

bioRxiv2026

Multi-omic spatial mapping of the human habenula defines the molecular and anatomical organization of medial and lateral subregions

The habenula (Hb) is a small epithalamic midline structure critical for reward processing and mood regulation that is implicated in many complex brain disorders, including depression and addiction. The molecular anatomy of the Hb has been well-characterized in model organisms, but little is known about its organization in the human brain, including the transcriptomic and epigenetic signatures of spatially-organized lateral (LHb) and medial (MHb) cell types. Here, we generated a high resolution spatiomolecular map of the human Hb using both multiomic single nucleus sequencing (snMultiome) and spatially-resolved transcriptomics. We measured gene expression and chromatin accessibility across 4 MHb and 5 LHb neuronal cell types as defined by transcriptomic conservation with rodents and zebrafish. We identified cell type-specific molecular specializations related to GABAergic and glutamatergic signaling as well as regulatory relationships between open chromatin regions, transcription factors, and target genes associated with depression and addiction. High resolution spatial transcriptomics identified the anatomical location of heterogeneous LHb subpopulations, including two putative inhibitory populations in the LHb. We further characterized cell-type relationships between Hb neurons and glial subtypes and predicted ligand-receptor interactions between LHb and MHb neurons. Finally, we delineated Hb cell types and spatial domains enriched in genes associated with genetic risk for psychiatric disorders, identifying the strongest enrichment in the MHb. Collectively, the generated data and analyses resolve the spatiomolecular organization of the human Hb and identify molecular-genetic associations with neuropsychiatric disease.

neuroscience↗

bioRxiv2026

DESI-MS-Based Analysis of Drug Distribution in Human Renal Cystic Tissue Using the Chorioallantoic Membrane (CAM) as a 3D In Vivo Model

The chorioallantoic membrane (CAM) model represents a promising three-dimensional in vivo platform for preclinical drug testing in human tissues. In this study, we investigated whether the tissue penetration and distribution of benzbromarone, a known inhibitor of the Ca2+ activated chloride channel TMEM16A and potential therapeutic agent for autosomal dominant polycystic kidney disease (ADPKD), can be successfully visualized in human renal cyst tissue cultured on the CAM. To this end, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) combined with an ultrahigh-resolution time-of-flight mass spectrometer was employed. We achieved spatially resolved molecular mapping of endogenous metabolites and lipids as well as the applied compound. MSI enabled clear differentiation between CAM and cystic tissue based on their distinct lipid profiles. Benzbromarone was reproducibly detected in the cyst specimens and exhibited selective accumulation along the cyst epithelium, which is considered the principal site of action. These observations were complemented by multivariate analyses including Uniform Manifold Approximation and Projection (UMAP), and sparse multinomial logistic zero-sum classification. The data-driven approach confirmed molecular differences between tissue types and allowed accurate classification of drug-treated and untreated regions. This study demonstrates that topically applied benzbromarone penetrates human renal cyst tissue in the CAM model and localizes to pharmacologically relevant tissue regions, notably the location of the Ca2+ activated chloride channel TMEM16A in the epithelial lining. The integration of high-resolution DESI-MSI with advanced statistical analysis provides a robust and label-free method to study drug distribution in human tissue grafts. Our findings contribute to the advancement of translational research in analytical chemistry and pharmacology.

biochemistry↗

bioRxiv2025

The misplaced mouse Pax6 interneuron subclass: A cross-species transcriptomic reassignment

Subclass cell-types are strongly conserved across mammalian brains, making the systemic absence of a caudal ganglionic eminence (CGE) Pax6 interneuron subclass in mouse transcriptional atlases unexpected. Through cross-species transcriptomic analysis, we identify a Pax6 subclass homolog in mouse and uncover primate-specific divergence in the Sncg subclass. Our results highlight the pitfalls of relying on single marker genes and provide evolution-aware annotations and marker sets to support robust cross-mammal interneuron comparisons.

neuroscience↗

bioRxiv2025

Cell Type-Agnostic Transcriptomic Signatures Enable Uniform Comparisons of Neurodevelopment

Single-cell transcriptomics has revolutionized our understanding of neurodevelopmental cell identities, yet, predicting a cell types developmental state from its transcriptome remains a challenge. We perform a meta-analysis of developing human brain datasets comprising over 2.8 million cells, identifying both tissue-level and cell-autonomous predictors of developmental age. While tissue composition predicts age within individual studies, it fails to generalize, whereas specific cell type proportions reliably track developmental time across datasets. Training regularized regression models to infer cell-autonomous maturation, we find that a cell type-agnostic model achieves the highest accuracy (error = 2.6 weeks), robustly capturing developmental dynamics across diverse cell types and datasets. This model generalizes to human neural organoids, accurately predicting normal developmental trajectories (R = 0.91) and disease-induced shifts in vitro. Furthermore, it extends to the developing mouse brain, revealing an accelerated developmental tempo relative to humans. Our work provides a unified framework for comparing neurodevelopment across contexts, model systems, and species.

neuroscience↗

bioRxiv2022

Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating T cells.

Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying the heterogeneous functional and dysfunctional states of human tumor-infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify tissue-specific and general gene-regulatory landscapes in the wide breadth of CD8+ TIL functional states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor entity-matching samples, and prioritize key elements by super-enhancer analysis. Our results reveal a human core chromatin trajectory to TIL dysfunction and identify involved key enhancers, transcriptional regulators, and deregulated target genes in this process. Finally, we validate enhancer regulation at immunotherapeutically relevant loci by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study provides a framework for understanding and manipulating cell-state-specific gene-regulatory cues from human tumor infiltrating lymphocytes.

immunology↗

bioRxiv2021

Cross-tissue analysis of allelic X-chromosome inactivation ratios resolves features of human development

X-chromosome inactivation (XCI) is a random, permanent, and developmentally early epigenetic event that occurs during mammalian embryogenesis. We harness these features of XCI to investigate characteristics of early lineage specification events during human development. We initially assess the consistency of X-inactivation and establish a robust set of XCI-escape genes. By analyzing variance in XCI ratios across tissues and individuals, we find that XCI is completed prior to tissue specification and at a time when 6-16 cells are fated for all tissue lineages. Additionally, we exploit tissue specific variability to characterize the number of cells present at the time of each tissues lineage commitment, ranging from approximately 20 cells in liver and whole blood tissues to 80 cells in brain tissues. By investigating variance of XCI ratios using adult tissue, we resolve key features of human development otherwise difficult to ascertain experimentally and develop scalable methods easily applicable to future data.

developmental biology↗

bioRxiv2019

Hingepoints and neural folds reveal conserved features of primary neurulation in the zebrafish forebrain

ABSTRACTPrimary neurulation is the process by which the neural tube, the central nervous system precursor, is formed from the neural plate. Incomplete neural tube closure occurs frequently, yet underlying causes remain poorly understood. Developmental studies in amniotes and amphibians have identified hingepoint and neural fold formation as key morphogenetic events and hallmarks of primary neurulation, the disruption of which causes neural tube defects. In contrast, the mode of neurulation in teleosts such as zebrafish has remained highly debated. Teleosts are thought to have evolved a unique pattern of neurulation, whereby the neural plate infolds in absence of hingepoints and neural folds (NFs), at least in the hindbrain/trunk where it has been studied. We report here on zebrafish forebrain morphogenesis where we identify these morphological landmarks. Our findings reveal a deeper level of conservation of neurulation than previously recognized and establish the zebrafish as a model to understand human neural tube development.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗