Biology subjects

Batz, Z.

Publications and source records attributed to Batz, Z..

4 recordsLinked to original sources

bioRxiv2026

Multiomic analysis of non-glaucomatous human trabecular meshwork cells.

Glaucoma is an irreversible blinding disease that affects millions of individuals worldwide. Elevated intraocular pressure (IOP), regulated by the trabecular meshwork (TM) in the anterior eye, is the only modifiable risk factor. Human TM cells can be cultured from donor eyes, providing a precious resource for studying factors that induce or prevent glaucoma. The goal of this study was to produce datasets that define the molecular profile of human non-glaucomatous TM cells. Using 18 human TM cell strains cultured from non-glaucomatous individuals deposited from seven laboratories in the USA and UK, this study used transcriptomic, proteomic, lipidomic, and metabolomic analyses to characterize the molecular content of TM cells. The data herein provides the most comprehensive multiomic analyses of human TM cells to date and will be a useful resource for researchers and clinicians in the TM and glaucoma fields.

cell biology↗

bioRxiv2026

Chromatin dynamics identifies 78 genes at loci associated with elevated intraocular pressure and primary open-angle glaucoma

Primary open-angle glaucoma (POAG) is a chronic neurodegenerative disorder, and elevated intraocular pressure (IOP) represents the major, and only modifiable, risk factor for the disease. We modeled increased IOP by treating three primary human trabecular meshwork (TM) cell strains with dexamethasone, then generated a high-resolution map of promoter-centered chromatin contacts and regulatory modules to decipher how the genomic architecture and epigenetic state of disease-associated loci contribute to pathogenesis. We identify dynamic changes in chromatin compartments and looping, cis-regulatory elements and transcription factor hubs corresponding to altered transcriptional profile. By integrating GWAS-associated variants with dexamethasone-induced 3D chromatin landscape, we discovered 26 IOP- and 52 POAG- candidate causal genes, which belong to vesicle transport, TLR, MAPK and hippo-YAP signaling pathways. We also uncovered transcriptional regulatory role of 103 non-coding lead variants. Our studies provide a mechanistic framework of genetic complexity associated with ocular hypertension and POAG pathogenesis in addition to targets for therapies.

genomics↗

bioRxiv2025

Simple 3D-Printed Stirred Bioreactor Enhances Retinal Organoid Production Via Improved Oxygenation

Retinal organoids (ROs), derived from human pluripotent stem cells (hPSCs), simulate in vivo development and retinal morphology, providing a platform to study retinal development and diseases. However, current differentiation protocols often yield inconsistent results with substantial cell line and batch variability. These protocols utilize static culture methods that rely on passive oxygen diffusion to reach the vessel bottom, where adherent hPSCs initially differentiate. Static culture is standard for adherent monolayer cells and is presumed suitable for RO differentiation. We questioned this assumption given that, during differentiation, the monolayer hPSCs become highly structured and multi-layered, first as neural rosettes and then as optic vesicles (OVs). We hypothesized that the cellular oxygen consumption rate would exceed the rate of delivery via passive diffusion, particularly to inner regions of emerging OVs. To test this hypothesis, we measured dissolved oxygen concentrations at the vessel bottom and found that within hours of media change, oxygen dropped to < 1 %, a level considered non-physiologically hypoxic, which imperils cell viability. This non-physiological hypoxia caused OV degeneration, hypoxic marker expression, and necrosis. To address this problem, we developed a novel 3D-printed stirred bioreactor (SBR) that maintains physiological oxygen levels between [~]4-6%. This approach significantly improved organoid yield, quality, and reproducibility while being easily adaptable to typical laboratory cell culture workflows. We conclude that non-physiological hypoxia, a previously unappreciated condition, is a limiting factor underlying inconsistent yield and quality in RO production. Physiological oxygenation levels can be restored by the SBR platform, resulting in greater consistency and improved production outcomes.

bioengineering↗

bioRxiv2022

PLAE web app enables powerful searching and multiple visualizations across one million unified single-cell ocular transcriptomes

PURPOSETo create a high performance reactive web application to query single cell gene expression data across cell type, species, study, and other factors. METHODSWe updated the content and structure of the underlying data (single cell Eye in a Disk, scEiaD) and wrote the web application PLAE (https://plae.nei.nih.gov) to visualize and explore it. RESULTSThe new portal provides quick visualization of over a million individual cells from vertebrate eye-and body transcriptomes encomopassing four species, 60 cell types, six ocular tissues, and 23 body tissues across 37 publications. To demonstrate the value of this unified pan-eye dataset, we replicate known neurogenic and cone macula markers as well as propose six new cone human region markers. CONCLUSIONThe PLAE web application provides the eye community a powerful and quick means to test hypotheses related to gene expression across a highly diverse, community-derived database.

genomics↗